1
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Walson PD. Personalized Minimal Effective Concentration Therapy. Clin Ther 2023; 45:1289-1292. [PMID: 37838561 DOI: 10.1016/j.clinthera.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/22/2023] [Accepted: 09/17/2023] [Indexed: 10/16/2023]
Abstract
It has been recognized for literally centuries that patients should be given only the amount of medication necessary to treat disease(s) or relieve symptoms. It is also well known that this amount can vary greatly between patients or even over time in the same patient. The ability to identify this amount, that is, to "personalize" dosing, requires a reliable measure of a patient's response to treatment. The development of analytical methods for the accurate measurement of pharmacologically meaningful drug concentrations in physiologic fluids, combined with mathematical methods for reliable prediction of how dosing changes affect these concentrations, has led to the development of therapeutic drug management (TDM) for more effective individualization of dosing. Using TDM, clinicians modify dosing to achieve concentrations or exposures (ie, AUC) found to be effective in patients with similar clinical attributes and conditions. These concentrations, called therapeutic (or target) concentrations or exposure ranges (TRs), are specific to both disease/condition and patient population. TDM is routinely used by many clinicians to adjust dosing of a wide range of medications for maximal efficacy and limited toxicity, thereby improving clinical outcomes. Failure to properly perform TDM or to appreciate the limitations of TDM have, however, contributed to the delayed acceptance of TDM by clinicians. This Commentary briefly discusses the limitations and the benefits of TR-guided TDM, and then discusses immunosuppressant drugs and anticancer medications as examples of drugs that require clinicians to change their prescribing practices from giving all patients the same or maximal tolerated doses, to instead adjusting individual doses to achieve minimal effective concentrations identified using circulating tumor- or graft-derived DNA or copy number instability rather than published TRs.
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Affiliation(s)
- Philip D Walson
- Department of Clinical Pharmacology, University Medical School Goettingen, Hannover, Germany.
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2
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Ren S, Zeng G, Yi Y, Liu L, Tu H, Chai T, Hu L. Combinations of plasma cfDNA concentration, integrity and tumor markers are promising biomarkers for early diagnosis of non-small cell lung cancer. Heliyon 2023; 9:e20851. [PMID: 37860559 PMCID: PMC10582504 DOI: 10.1016/j.heliyon.2023.e20851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023] Open
Abstract
Background Circulating cell-free DNA (cfDNA) concentration and integrity as noninvasive biomarkers play an important role in cancer diagnosis, prognosis and therapy monitoring. However, few studies have been conducted on the combination of plasma cfDNA concentration, integrity and tumor markers (CEA, CA125, NSE and CYFRA21-1) for cancer detection. Thus, the purpose of this study was to investigate the diagnostic value of combining plasma cfDNA concentration, integrity and tumor markers in early detection of non-small cell lung cancer (NSCLC). Methods Plasma cfDNA concentration from 50 healthy controls and 84 NSCLC patients were assessed by quantitative real-time PCR of ALU repeated sequence. Plasma cfDNA integrity was calculated as the ratio of long to short fragments (ALU115/60). Results Plasma cfDNA concentration (ALU60 and ALU115) and integrity ALU115/60 were significantly higher in NSCLC patients with stage III/IV than in healthy controls (p = 0.0002, p < 0.0001, and p = 0.0093, respectively). The receiver operating characteristic (ROC) curve for discriminating NSCLC patients from healthy controls had an area under the curve (AUC) of 0.936 (95 % CI, 0.939-0.996). Moreover, the combination of plasma cfDNA concentration, integrity and tumor markers (CEA, CA125, NSE and CYFRA21-1) had higher diagnostic performance than either plasma cfDNA concentration alone, integrity alone or tumor markers alone, with sensitivity, specificity and AUC value of 94.05%, 90.00% and 0.968, respectively. These results demonstrated that the combination of plasma cfDNA concentration, integrity and tumor markers could significantly improve the diagnostic accuracy of NSCLC. Conclusion Combination of plasma cfDNA concentration, integrity and tumor markers is a promising biomarker for early diagnosis of NSCLC.
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Affiliation(s)
- Sai Ren
- Department of Laboratory Medicine, The People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Guichuan Zeng
- Department of Ultrasound, Jian She Hospital, Chongqing, China
| | - Yuling Yi
- Department of Laboratory Medicine, The People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Ling Liu
- Department of Laboratory Medicine, The People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Hongmei Tu
- Department of Laboratory Medicine, The People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Tingjia Chai
- Endocrine Laboratory, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China
| | - Liyi Hu
- Department of Laboratory Medicine, The People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
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3
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Eikenboom EL, Wilting SM, Deger T, Srebniak MI, Van Veghel-Plandsoen M, Boers RG, Boers JB, van IJcken WFJ, Gribnau JH, Atmodimedjo P, Dubbink HJ, Martens JWM, Spaander MCW, Wagner A. Liquid Biopsies for Colorectal Cancer and Advanced Adenoma Screening and Surveillance: What to Measure? Cancers (Basel) 2023; 15:4607. [PMID: 37760576 PMCID: PMC10526371 DOI: 10.3390/cancers15184607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Colorectal cancer (CRC) colonoscopic surveillance is effective but burdensome. Circulating tumor DNA (ctDNA) analysis has emerged as a promising, minimally invasive tool for disease detection and management. Here, we assessed which ctDNA assay might be most suitable for a ctDNA-based CRC screening/surveillance blood test. In this prospective, proof-of-concept study, patients with colonoscopies for Lynch surveillance or the National Colorectal Cancer screening program were included between 7 July 2019 and 3 June 2022. Blood was drawn, and if advanced neoplasia (adenoma with villous component, high-grade dysplasia, ≥10 mm, or CRC) was detected, it was analyzed for chromosomal copy number variations, single nucleotide variants, and genome-wide methylation (MeD-seq). Outcomes were compared with corresponding patients' tissues and the MeD-seq results of healthy blood donors. Two Lynch carriers and eight screening program patients were included: five with CRC and five with advanced adenomas. cfDNA showed copy number variations and single nucleotide variants in one patient with CRC and liver metastases. Eight patients analyzed with MeD-seq showed clustering of Lynch-associated and sporadic microsatellite instable lesions separate from microsatellite stable lesions, as did healthy blood donors. In conclusion, whereas copy number changes and single nucleotide variants were only detected in one patient, cfDNA methylation profiles could discriminate all microsatellite instable advanced neoplasia, rendering this tool particularly promising for LS surveillance. Larger studies are warranted to validate these findings.
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Affiliation(s)
- Ellis L. Eikenboom
- Department of Clinical Genetics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (E.L.E.); (M.I.S.); (M.V.V.-P.)
- Department of Gastroenterology & Hepatology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Saskia M. Wilting
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (S.M.W.); (T.D.); (J.W.M.M.)
| | - Teoman Deger
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (S.M.W.); (T.D.); (J.W.M.M.)
| | - Malgorzata I. Srebniak
- Department of Clinical Genetics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (E.L.E.); (M.I.S.); (M.V.V.-P.)
| | - Monique Van Veghel-Plandsoen
- Department of Clinical Genetics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (E.L.E.); (M.I.S.); (M.V.V.-P.)
| | - Ruben G. Boers
- Department of Developmental Biology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (R.G.B.); (J.B.B.); (J.H.G.)
| | - Joachim B. Boers
- Department of Developmental Biology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (R.G.B.); (J.B.B.); (J.H.G.)
| | | | - Joost H. Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (R.G.B.); (J.B.B.); (J.H.G.)
| | - Peggy Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (P.A.); (H.J.D.)
| | - Hendrikus J. Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (P.A.); (H.J.D.)
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (S.M.W.); (T.D.); (J.W.M.M.)
| | - Manon C. W. Spaander
- Department of Gastroenterology & Hepatology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus MC Cancer Institute, University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (E.L.E.); (M.I.S.); (M.V.V.-P.)
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Matsas A, Stefanoudakis D, Troupis T, Kontzoglou K, Eleftheriades M, Christopoulos P, Panoskaltsis T, Stamoula E, Iliopoulos DC. Tumor Markers and Their Diagnostic Significance in Ovarian Cancer. Life (Basel) 2023; 13:1689. [PMID: 37629546 PMCID: PMC10455076 DOI: 10.3390/life13081689] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/27/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Ovarian cancer (OC) is characterized by silent progression and late-stage diagnosis. It is critical to detect and accurately diagnose the disease early to improve survival rates. Tumor markers have emerged as valuable tools in the diagnosis and management of OC, offering non-invasive and cost-effective options for screening, monitoring, and prognosis. PURPOSE This paper explores the diagnostic importance of various tumor markers including CA-125, CA15-3, CA 19-9, HE4,hCG, inhibin, AFP, and LDH, and their impact on disease monitoring and treatment response assessment. METHODS Article searches were performed on PubMed, Scopus, and Google Scholar. Keywords used for the searching process were "Ovarian cancer", "Cancer biomarkers", "Early detection", "Cancer diagnosis", "CA-125","CA 15-3","CA 19-9", "HE4","hCG", "inhibin", "AFP", "LDH", and others. RESULTS HE4, when combined with CA-125, shows improved sensitivity and specificity, particularly in early-stage detection. Additionally, hCG holds promise as a prognostic marker, aiding treatment response prediction and outcome assessment. Novel markers like microRNAs, DNA methylation patterns, and circulating tumor cells offer potential for enhanced diagnostic accuracy and personalized management. Integrating these markers into a comprehensive panel may improve sensitivity and specificity in ovarian cancer diagnosis. However, careful interpretation of tumor marker results is necessary, considering factors such as age, menopausal status, and comorbidities. Further research is needed to validate and refine diagnostic algorithms, optimizing the clinical significance of tumor markers in ovarian cancer management. In conclusion, tumor markers such as CA-125, CA15-3, CA 19-9, HE4, and hCG provide valuable insights into ovarian cancer diagnosis, monitoring, and prognosis, with the potential to enhance early detection.
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Affiliation(s)
- Alkis Matsas
- Laboratory of Experimental Surgery and Surgical Research ‘N.S. Christeas’, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Dimitrios Stefanoudakis
- Second Department of Obstetrics and Gynecology, Medical School, “Aretaieion” University Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Theodore Troupis
- Department of Anatomy, Faculty of Health Sciences, Medical School, National and Kapodistrian University of Athens, MikrasAsias Str. 75, 11627 Athens, Greece
| | - Konstantinos Kontzoglou
- Laboratory of Experimental Surgery and Surgical Research ‘N.S. Christeas’, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Makarios Eleftheriades
- Second Department of Obstetrics and Gynecology, Medical School, “Aretaieion” University Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Panagiotis Christopoulos
- Second Department of Obstetrics and Gynecology, Medical School, “Aretaieion” University Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Theodoros Panoskaltsis
- Second Department of Obstetrics and Gynecology, Medical School, “Aretaieion” University Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Eleni Stamoula
- Department of Clinical Pharmacology, School of Medicine, Aristotle University of Thessaloniki, University Campus Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dimitrios C. Iliopoulos
- Laboratory of Experimental Surgery and Surgical Research ‘N.S. Christeas’, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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Kabzinski J, Kucharska-Lusina A, Majsterek I. RNA-Based Liquid Biopsy in Head and Neck Cancer. Cells 2023; 12:1916. [PMID: 37508579 PMCID: PMC10377854 DOI: 10.3390/cells12141916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Head and neck cancer (HNC) is a prevalent and diverse group of malignancies with substantial morbidity and mortality rates. Early detection and monitoring of HNC are crucial for improving patient outcomes. Liquid biopsy, a non-invasive diagnostic approach, has emerged as a promising tool for cancer detection and monitoring. In this article, we review the application of RNA-based liquid biopsy in HNC. Various types of RNA, including messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), circular RNA (circRNA) and PIWI-interacting RNA (piRNA), are explored as potential biomarkers in HNC liquid-based diagnostics. The roles of RNAs in HNC diagnosis, metastasis, tumor resistance to radio and chemotherapy, and overall prognosis are discussed. RNA-based liquid biopsy holds great promise for the early detection, prognosis, and personalized treatment of HNC. Further research and validation are necessary to translate these findings into clinical practice and improve patient outcomes.
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Affiliation(s)
- Jacek Kabzinski
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Aleksandra Kucharska-Lusina
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
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Filatova AA, Alekseeva LA, Savin IA, Sen'kova AV, Zenkova MA, Mironova NL. The Effect of Cell-Free DNA from Blood Serum of Mice with Metastatic Melanoma on Enhancement of Oncogenic Properties of Melanoma Cells. Biochemistry (Mosc) 2023; 88:995-1007. [PMID: 37751869 DOI: 10.1134/s0006297923070118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 09/28/2023]
Abstract
Currently, a significant increase in the levels of circulating cell-free DNA (cfDNA) in the blood of patients is considered as a generally recognized marker of the development of oncological diseases. Although the tumor-associated cfDNA has been well studied, its biological functions remain unclear. In this work, we investigated the effect of cfDNA isolated from the blood serum of the mice with B16-F10 metastatic melanoma on the properties of the B16-F10 melanoma cells in vitro. It was found that the profile of cfDNA isolated from the blood serum of mice with melanoma differs significantly from the cfDNA isolated from the blood serum of healthy mice, and is similar to the genomic DNA of B16 cells with regards to abundance of oncogenes and mobile genetic elements (MGE). It was shown that the cfDNA of mice with melanoma penetrated into B16 cells, resulting in the increase in abundance of oncogenes and MGE fragments, and caused 5-fold increase of the mRNA level of the secreted DNase Dnase1l3 and a slight increase of the mRNA level of the Jun, Fos, Ras, and Myc oncogenes. cfDNA of the healthy mice caused increase of the mRNA level of intracellular regulatory DNase EndoG and 4-fold increase of the mRNA level of Fos and Ras oncogenes, which are well-known triggers of a large number of signal cascades, from apoptosis inhibition to increased tumor cell proliferation. Thus, it is obvious that the circulating cfDNA of tumor origin is able to penetrate into the cells and, despite the fact that no changes were found in the level of viability and migration activity of the tumor cells, cfDNA, even with a single exposure, can cause changes at the cellular level that increase oncogenicity of the recipient cells.
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Affiliation(s)
- Alina A Filatova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Ludmila A Alekseeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Innokenty A Savin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Aleksandra V Sen'kova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Nadezhda L Mironova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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Gajda-Walczak A, Potęga A, Kowalczyk A, Sek S, Zięba S, Kowalik A, Kudelski A, Nowicka AM. New, fast and cheap prediction tests for BRCA1 gene mutations identification in clinical samples. Sci Rep 2023; 13:7316. [PMID: 37147448 PMCID: PMC10163215 DOI: 10.1038/s41598-023-34588-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/03/2023] [Indexed: 05/07/2023] Open
Abstract
Despite significant progress in cancer therapy, cancer is still the second cause of mortality in the world. The necessity to make quick therapeutic decisions forces the development of procedures allowing to obtain a reliable result in a quick and unambiguous manner. Currently, detecting predictive mutations, including BRCA1, is the basis for effectively treating advanced breast cancer. Here, we present new insight on gene mutation detection. We propose a cheap BRCA1 mutation detection tests based on the surface plasmon resonance (SPR) or quartz crystal microbalance with energy dissipation (QCM-D) response changes recorded during a hybridization process of an oligonucleotide molecular probe with DNA fragments, with and without the BRCA1 mutation. The changes in the morphology of the formed DNA layer caused by the presence of the mutation were confirmed by atomic force microscopy. The unique property of the developed SPR and QCM tests is really short time of analysis: ca. 6 min for SPR and ca. 25 min for QCM. The proposed tests have been verified on 22 different DNA extracted from blood leukocytes collected from cancer patients: 17 samples from patients with various BRCA1 gene mutation variants including deletion, insertion and missense single-nucleotide and 5 samples from patients without any BRCA1 mutation. Our test is a response to the need of medical diagnostics for a quick, unambiguous test to identify mutations of the BRCA1 gene, including missense single-nucleotide (SNPs).
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Affiliation(s)
| | - Agnieszka Potęga
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Narutowicza 11/12 Str., 80-233, Gdańsk, Poland
| | - Agata Kowalczyk
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Str., 02-093, Warsaw, Poland
| | - Slawomir Sek
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101 Str., 02-089, Warsaw, Poland
| | - Sebastian Zięba
- Molecular Diagnostics, Holy Cross Cancer Center, Stefana Artwińskiego 3 Str., 25-734, Kielce, Poland
| | - Artur Kowalik
- Molecular Diagnostics, Holy Cross Cancer Center, Stefana Artwińskiego 3 Str., 25-734, Kielce, Poland
- Division of Medical Biology, Institute of Biology, Jan Kochanowski University, Uniwersytecka 7 Str., 25-406, Kielce, Poland
| | - Andrzej Kudelski
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Str., 02-093, Warsaw, Poland
| | - Anna M Nowicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1 Str., 02-093, Warsaw, Poland.
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Sestokaite A, Gedvilaite V, Cicenas S, Sabaliauskaite R, Jarmalaite S. Surveillance of cfDNA Hot Spot Mutations in NSCLC Patients during Disease Progression. Int J Mol Sci 2023; 24:ijms24086958. [PMID: 37108122 PMCID: PMC10138687 DOI: 10.3390/ijms24086958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Non-small cell cancer (NSCLC) has been identified with a great variation of mutations that can be surveyed during disease progression. The aim of the study was to identify and monitor lung cancer-specific mutations incidence in cell-free DNA as well as overall plasma cell-free DNA load by means of targeted next-generation sequencing. Sequencing libraries were prepared from cell-free DNA (cfDNA) isolated from 72 plasma samples of 41 patients using the Oncomine Lung cfDNA panel covering hot spot regions of 11 genes. Sequencing was performed with the Ion Torrent™ Ion S5™ system. Four genes were detected with highest mutation incidence: KRAS (43.9% of all cases), followed by ALK (36.6%), TP53 (31.7%), and PIK3CA (29.3%). Seven patients had co-occurring KRAS + TP53 (6/41, 14.6%) or KRAS + PIK3CA (7/41, 17.1%) mutations. Moreover, the mutational status of TP53 as well an overall cell-free DNA load were confirmed to be predictors of poor progression-free survival (HR = 2.5 [0.8-7.7]; p = 0.029 and HR = 2.3 [0.9-5.5]; p = 0.029, respectively) in NSCLC patients. In addition, TP53 mutation status significantly predicts shorter overall survival (HR = 3.4 [1.2-9.7]; p < 0.001). We demonstrated that TP53 mutation incidence as well as a cell-free DNA load can be used as biomarkers for NSCLC monitoring and can help to detect the disease progression prior to radiological confirmation of the status.
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Affiliation(s)
- Agne Sestokaite
- National Cancer Institute, Santariskiu 1, 08406 Vilnius, Lithuania
- Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, 10257 Vilnius, Lithuania
| | - Vaida Gedvilaite
- National Cancer Institute, Santariskiu 1, 08406 Vilnius, Lithuania
| | - Saulius Cicenas
- National Cancer Institute, Santariskiu 1, 08406 Vilnius, Lithuania
| | | | - Sonata Jarmalaite
- National Cancer Institute, Santariskiu 1, 08406 Vilnius, Lithuania
- Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio Ave. 7, 10257 Vilnius, Lithuania
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Yannick Ouedraogo S, Zhou X, Chen H, Chen F, Ma C. Recent advances in biosensors and sequencing technologies for the detection of mutations. Microchem J 2023; 185:108306. [DOI: 10.1016/j.microc.2022.108306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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10
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El Hejjioui B, Bouguenouch L, Melhouf MA, El Mouhi H, Bennis S. Clinical Evidence of Circulating Tumor DNA Application in Aggressive Breast Cancer. Diagnostics (Basel) 2023; 13:470. [PMID: 36766575 PMCID: PMC9914403 DOI: 10.3390/diagnostics13030470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/28/2022] [Accepted: 01/01/2023] [Indexed: 01/31/2023] Open
Abstract
Breast cancer is clinically and biologically heterogeneous and is classified into different subtypes according to the molecular landscape of the tumor. Triple-negative breast cancer is a subtype associated with higher tumor aggressiveness, poor prognosis, and poor response to treatment. In metastatic breast cancer, approximately 6% to 10% of new breast cancer cases are initially staged IV (de novo metastatic disease). The number of metastatic recurrences is estimated to be 20-30% of all existing breast tumor cases, whereby the need to develop specific genetic markers to improve the prognosis of patients suffering from these deadly forms of breast cancer. As an alternative, liquid biopsy methods can minutely identify the molecular architecture of breast cancer, including aggressive forms, which provides new perspectives for more precise diagnosis and more effective therapeutics. This review aimed to summarize the current clinical evidence for the application of circulating tumor DNA in managing breast cancer by detailing the increased usefulness of this biomarker as a diagnostic, prognostic, monitoring, and surveillance marker for breast cancer.
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Affiliation(s)
- Brahim El Hejjioui
- Biomedical and Translational Research Laboratory, Faculty of Medicine and Pharmacy, Sidi Mohamed Ben Abdellah University, Fez 30050, Morocco
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | - Laila Bouguenouch
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | | | - Hind El Mouhi
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | - Sanae Bennis
- Biomedical and Translational Research Laboratory, Faculty of Medicine and Pharmacy, Sidi Mohamed Ben Abdellah University, Fez 30050, Morocco
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Kong W, Chen T, Li Y. Diagnosis, Monitoring, and Prognosis of Liquid Biopsy in Cancer Immunotherapy. Methods Mol Biol 2023; 2695:127-143. [PMID: 37450116 DOI: 10.1007/978-1-0716-3346-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Liquid biopsy (LB), as a minimally invasive method of gleaning insight into the dynamics of diseases through a patient fluid sample, represents an interesting tool that can advise in disease monitoring, treatment selection, early diagnosis, evaluation of the response, and prognosis. Cancer immunotherapy is a breakthrough in cancer treatment, which is now recognized as the "fourth pillar" of cancer treatment, after surgery, chemotherapy, and radiotherapy. Liquid biopsy offers a different befalling for beneath invasive diagnosis, real-time accommodating monitoring, and analysis options, involving the isolation of circulating biomarkers, such as cell-free DNA (cfDNA), circulating tumor cells (CTCs), exosomes, and microRNAs (miRNAs). The biomarkers herein have great potential to allow the realization of liquid biopsy for predicting the immunotherapy response and precision medicine. Liquid biopsy offers an alternative, less invasive approach to select cancer patients who would benefit from immunotherapy and to monitor patients during their disease course. This review focuses on the use of liquid biopsy in the immunotherapy treatment of patients with cancer. In this review, we addressed the different promising liquid biopsy-based biomarkers in cancer patients that enable the selection of patients who benefit from immunotherapy and the monitoring of patients during this therapy.
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Affiliation(s)
- Weiying Kong
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, China
| | - Tengxiang Chen
- Guizhou Provincial Key Laboratory of Pathogenesis & Drug Research on Common Chronic Diseases, Department of Physiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China.
| | - Yixin Li
- The Department of Histology and Embryology, Guizhou Medical University, Guiyang, Guizhou, China
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Balla A, Bhak J, Biró O. The application of circulating tumor cell and cell-free DNA liquid biopsies in ovarian cancer. Mol Cell Probes 2022; 66:101871. [PMID: 36283501 DOI: 10.1016/j.mcp.2022.101871] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Ovarian cancer is the deadliest gynecological cancer. 70% of the cases are diagnosed at late stages with already developed metastases due to the absence of easily noticeable symptoms. Early-stage ovarian cancer has a good prognosis with a 5-year survival rate reaching 95%, hence the identification of effective biomarkers for early diagnosis is important. Advances in liquid biopsy-based methods can have a significant impact not just on the development of an efficient screening strategy, but also in clinical decision-making with additional molecular profiling and genetic alterations linked to therapy resistance. Despite the well-known advantages of liquid biopsy, there are still challenges that need to be addressed before its routine use in clinical practice. Various liquid biopsy-based biomarkers have been investigated in ovarian cancer; however, in this review, we are concentrating on the current use of cell-free DNA (cfDNA) and circulating tumor cells (CTCs) in disease management, focusing on their emerging importance in clinical practice. We also discuss the technical aspects of these workflows. The analysis of cfDNA is often chosen for the detection of mutations, copy number aberrations, and DNA methylation changes, whereas CTC analysis provides a unique opportunity to study whole cells, thus allowing DNA, RNA, and protein-based molecular profiling as well as in vivo studies. Combined solutions which merge the strengths of cfDNA and CTC approaches should be developed to maximize the potential of liquid biopsy technology.
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Affiliation(s)
- Abigél Balla
- Clinomics Europe Ltd., Budapest, Hungary; Semmelweis University, Károly Rácz Doctoral School of Clinical Medicine, Budapest, Hungary
| | - Jong Bhak
- Clinomics Inc. UNIST, Ulsan, 44916, Republic of Korea
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Ahmed F, Mehdi Dar G, Mohan Singh A, Apurva, Kumar A, Athar A, Parveen F, Mahajan B, Singh Saluja S. Molecular approaches in cancer. Clin Chim Acta 2022; 537:60-73. [DOI: https:/doi.org/10.1016/j.cca.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Ahmed F, Mehdi Dar G, Mohan Singh A, Apurva, Kumar A, Athar A, Parveen F, Mahajan B, Singh Saluja S. Molecular approaches in cancer. Clin Chim Acta 2022; 537:60-73. [DOI: 10.1016/j.cca.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]
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Ding J, Zhao W. The Application of Liquid Biopsy Techniques in High-Risk Population for Hepatocellular Carcinoma. Cancer Manag Res 2022; 14:2735-2748. [PMID: 36133739 PMCID: PMC9484767 DOI: 10.2147/cmar.s373165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/27/2022] [Indexed: 12/01/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignant tumors of the digestive system and has a 5-year overall survival rate of 14.1%. Many HCC patients are diagnosed at an advanced stage, and thus early screening is essential for reducing the mortality of HCC. In addition to commonly used detection indicators such as serum alpha-fetoprotein (AFP), lens culinaris agglutinin-reactive fraction of alpha-fetoprotein (AFP-L3) and abnormal prothrombin (protein induced by vitamin K absence II, PIVKA-II), liquid biopsy techniques have been demonstrated to have diagnostic value in HCC detection. Compared with invasive procedures, liquid biopsy can detect circulatory metabolites of malignant neoplasms. Liquid biopsy techniques can detect circulating tumor cells, circulating tumor DNA, circulating RNA and exosomes and have been used in the early screening, diagnosis and prognostic evaluation of HCC. This paper reviews the molecular biological characteristics and application of different liquid biopsy techniques, and aim to highlight promising biomarkers that may be feasible options for early-stage HCC evaluation to improve early screening in populations at high risk for HCC.
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Affiliation(s)
- Jingnuo Ding
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, JiangSu Province, 215000, People's Republic of China
| | - Weifeng Zhao
- Department of Infectious Diseases, The First Affiliated Hospital of Soochow University, Suzhou, JiangSu Province, 215000, People's Republic of China
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Gattuso G, Crimi S, Lavoro A, Rizzo R, Musumarra G, Gallo S, Facciponte F, Paratore S, Russo A, Bordonaro R, Isola G, Bianchi A, Libra M, Falzone L. Liquid Biopsy and Circulating Biomarkers for the Diagnosis of Precancerous and Cancerous Oral Lesions. Noncoding RNA 2022; 8:60. [PMID: 36005828 PMCID: PMC9414906 DOI: 10.3390/ncrna8040060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 12/19/2022] Open
Abstract
Oral cancer is one of the most common malignancies worldwide, accounting for 2% of all cases annually and 1.8% of all cancer deaths. To date, tissue biopsy and histopathological analyses are the gold standard methods for the diagnosis of oral cancers. However, oral cancer is generally diagnosed at advanced stages with a consequent poor 5-year survival (~50%) due to limited screening programs and inefficient physical examination strategies. To address these limitations, liquid biopsy is recently emerging as a novel minimally invasive tool for the early identification of tumors as well as for the evaluation of tumor heterogeneity and prognosis of patients. Several studies have demonstrated that liquid biopsy in oral cancer could be useful for the detection of circulating biomarkers including circulating tumor DNA (ctDNA), microRNAs (miRNAs), proteins, and exosomes, thus improving diagnostic strategies and paving the way to personalized medicine. However, the application of liquid biopsy in oral cancer is still limited and further studies are needed to better clarify its clinical impact. The present manuscript aims to provide an updated overview of the potential use of liquid biopsy as an additional tool for the management of oral lesions by describing the available methodologies and the most promising biomarkers.
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Simarro J, Pérez-Simó G, Mancheño N, Ansotegui E, Muñoz-Núñez CF, Gómez-Codina J, Juan Ó, Palanca S. Technical Validation and Clinical Implications of Ultrasensitive PCR Approaches for EGFR-Thr790Met Mutation Detection in Pretreatment FFPE Samples and in Liquid Biopsies from Non-Small Cell Lung Cancer Patients. Int J Mol Sci 2022; 23:ijms23158526. [PMID: 35955661 PMCID: PMC9369170 DOI: 10.3390/ijms23158526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 02/04/2023] Open
Abstract
In pretreatment tumor samples of EGFR-mutated non-small cell lung cancer (NSCLC) patients, EGFR-Thr790Met mutation has been detected in a variable prevalence by different ultrasensitive assays with controversial prognostic value. Furthermore, its detection in liquid biopsy (LB) samples remains challenging, being hampered by the shortage of circulating tumor DNA (ctDNA). Here, we describe the technical validation and clinical implications of a real-time PCR with peptide nucleic acid (PNA-Clamp) and digital droplet PCR (ddPCR) for EGFR-Thr790Met detection in diagnosis FFPE samples and in LB. Limit of blank (LOB) and limit of detection (LOD) were established by analyzing negative and low variant allele frequency (VAF) FFPE and LB specimens. In a cohort of 78 FFPE samples, both techniques showed an overall agreement (OA) of 94.20%. EGFR-Thr790Met was detected in 26.47% of cases and was associated with better progression-free survival (PFS) (16.83 ± 7.76 vs. 11.47 ± 1.83 months; p = 0.047). In LB, ddPCR was implemented in routine diagnostics under UNE-EN ISO 15189:2013 accreditation, increasing the detection rate of 32.43% by conventional methods up to 45.95%. During follow-up, ddPCR detected EGFR-Thr790Met up to 7 months before radiological progression. Extensively validated ultrasensitive assays might decipher the utility of pretreatment EGFR-Thr790Met and improve its detection rate in LB studies, even anticipating radiological progression.
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Affiliation(s)
- Javier Simarro
- Molecular Biology Unit, Service of Clinical Analysis, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (J.S.); (G.P.-S.)
- Clinical and Translational Cancer Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
| | - Gema Pérez-Simó
- Molecular Biology Unit, Service of Clinical Analysis, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (J.S.); (G.P.-S.)
- Clinical and Translational Cancer Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
| | - Nuria Mancheño
- Pathology Department, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
| | - Emilio Ansotegui
- Pulmonology Department, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain;
| | | | - José Gómez-Codina
- Medical Oncology Department, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (J.G.-C.); (Ó.J.)
| | - Óscar Juan
- Medical Oncology Department, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (J.G.-C.); (Ó.J.)
| | - Sarai Palanca
- Molecular Biology Unit, Service of Clinical Analysis, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (J.S.); (G.P.-S.)
- Clinical and Translational Cancer Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), 46026 Valencia, Spain
- Biochemistry and Molecular Biology Department, Universidad de Valencia, 46010 Valencia, Spain
- Correspondence: ; Tel.: +34-961-244586
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Yi XF, Song J, Gao RL, Sun L, Wu ZX, Zhang SL, Huang LT, Ma JT, Han CB. Efficacy of Osimertinib in EGFR-Mutated Advanced Non-small-Cell Lung Cancer With Different T790M Status Following Resistance to Prior EGFR-TKIs: A Systematic Review and Meta-analysis. Front Oncol 2022; 12:863666. [PMID: 35785185 PMCID: PMC9242653 DOI: 10.3389/fonc.2022.863666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose Epidermal growth factor receptor (EGFR) T790M-negative/unknown advanced non-small cell lung cancer (NSCLC) patients lack subsequent approved targeted therapies. This meta-analysis aimed to assess the efficacy of osimertinib in advanced NSCLC patients with different T790M status after resistance to prior first- or second-generation EGFR-tyrosine kinase inhibitors (EGFR-TKIs) and to predict the subgroups that may benefit beside T790M-positive disease. Methods PubMed, Embase, Web of Science, and Cochrane Library databases were searched for relevant trials. Meeting abstracts were also reviewed to identify appropriate studies. Studies evaluating the efficacy and/or survival outcomes of osimertinib in patients with different T790M status (positive, negative, or unknown) after resistance to prior first- or second-generation EGFR-TKIs were enrolled, and data were pooled to assess hazard ratios (HRs) or relative risk ratios (RRs) in terms of overall survival (OS), progression-free survival (PFS), and objective response rate (ORR). Results A total of 1,313 EGFR-mutated NSCLC patients from 10 retrospective and one prospective studies treated with osimertinib after resistance to first- or second-generation EGFR-TKIs were included. In overall groups, T790M-positive patients showed an improved OS (HR=0.574, p=0.015), PFS (HR = 0.476, p = 0.017), and ORR (RR = 2.025, p = 0.000) compared with T790M-negative patients. In the brain metastases subgroup, no significant difference in OS was observed between T790M-positive and T790M-negative patients (HR = 0.75, p = 0.449) or between T790M-positive and T790M-unknown patients (HR = 0.90, p = 0.673). In the plasma genotyping subgroup, PFS was similar between T790M-positive and T790M-negative patients (HR = 1.033, p = 0.959). Conclusion Patients with progressive brain metastases on first- or second-generation EGFR-TKIs can benefit from subsequent osimertinib therapy regardless of T790M status. Patients with plasma T790M-negative status and lack of tissue genotyping should be allowed to receive osimertinib treatment.
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Pietri E, Balsano R, Coriano M, Gelsomino F, Leonardi F, Bui S, Gnetti L, Valle RD, Garajová I. The implication of liquid biopsies to predict chemoresistance in pancreatic cancer. Cancer Drug Resist 2022; 4:559-572. [PMID: 35582309 PMCID: PMC9094078 DOI: 10.20517/cdr.2021.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 03/08/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022]
Abstract
Pancreatic cancer is one of the most aggressive diseases among solid tumors. Most patients are diagnosed with advanced or metastatic disease and are characterized by poor chemosensitivity. Therefore, earlier diagnosis and novel therapeutic possibilities for pancreatic cancer patients are urgently needed. Liquid biopsy is an emerging technology that allows the noninvasive sampling of tumor material. Nowadays, liquid biopsy has shown promising results as diagnostic, prognostic and predictive biomarkers, but it has not yet been universally adopted into regular use by clinicians. In this review, we describe different components of liquid biopsy, especially circulating tumor cells, circulating tumor DNA and exosomes and their potential clinical utility for pancreatic cancer patients.
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Affiliation(s)
- Elisabetta Pietri
- Medical Oncology Unit, University Hospital of Parma, Parma 43126, Italy.,Authors contributed equally
| | - Rita Balsano
- Medical Oncology Unit, University Hospital of Parma, Parma 43126, Italy.,Authors contributed equally
| | - Matilde Coriano
- Medical Oncology Unit, University Hospital of Parma, Parma 43126, Italy
| | - Fabio Gelsomino
- Department of Oncology and Hematology, University Hospital of Modena, Modena 41124, Italy
| | | | - Simona Bui
- Medical Oncology Unit, University Hospital of Parma, Parma 43126, Italy
| | - Letizia Gnetti
- Unit of Pathological Anatomy, University Hospital of Parma, Parma 43126, Italy
| | | | - Ingrid Garajová
- Medical Oncology Unit, University Hospital of Parma, Parma 43126, Italy
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Nakamura Y, Olsen S, Zhang N, Liao J, Yoshino T. Comprehensive Genomic Profiling of Circulating Tumor DNA in Patients with Previously Treated Metastatic Colorectal Cancer: Analysis of a Real-World Healthcare Claims Database. Curr Oncol 2022; 29:3433-3448. [PMID: 35621667 PMCID: PMC9139639 DOI: 10.3390/curroncol29050277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 11/27/2022] Open
Abstract
We used a real-world database (GuardantINFORMTM) to analyze the treatment choices for patients with mCRC who underwent next-generation sequencing of circulating tumor DNA (ctDNA) using a commercially available test (Guardant360®) after first- or second-line therapy. From 18,875 patients with claims for CRC, 1064 had confirmed metastatic disease and sufficient histories for analysis (median age 59 years, 44.8% female, 44.5% left-sided). ctDNA was detectable for 997/1064 (93.7%) patients. Clinically actionable molecular profiles were present for 507/1064 (47.7%) patients, including those who had not received targeted therapy in the previous line (410/926, 44.3%). Second- or third-line targeted therapies were administered to 338/1064 patients (31.8%) and were considered matched for 193/338 (57.1%) patients. Therapies administered after testing were informed by the ctDNA results in 56.7% of patients overall (603/1064). Time to treatment discontinuation was most favorable for patients with a clinically actionable ctDNA profile who received matched therapy. This analysis demonstrates the real-world clinical value of plasma-based comprehensive genomic profiling for selecting appropriate molecular-targeted therapies in mCRC patients with disease progression after first- or second-line therapy.
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Affiliation(s)
- Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (Y.N.); (T.Y.)
- Translational Research Support Section, National Cancer Center Hospital East, Kashiwa 277-8577, Japan
| | - Steven Olsen
- Department of Medical Affairs, Guardant Health Asia, Middle East, Africa, Inc., Tokyo Port City Takeshiba Office Tower 9th Floor, 1-7-1 Kaigan, Minato-ku, Tokyo 105-7590, Japan
- Correspondence: ; Tel.: +81-3-6778-5160
| | - Nicole Zhang
- Department of Outcomes and Evidence, Guardant Health, Inc., Redwood City, CA 94063, USA; (N.Z.); (J.L.)
| | - Jiemin Liao
- Department of Outcomes and Evidence, Guardant Health, Inc., Redwood City, CA 94063, USA; (N.Z.); (J.L.)
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (Y.N.); (T.Y.)
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Yang X, Xu X, Zhang C, Ji T, Wan T, Liu W. The diagnostic value and prospects of gene mutations in circulating tumor DNA for head and neck cancer monitoring. Oral Oncol 2022; 128:105846. [DOI: 10.1016/j.oraloncology.2022.105846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
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Abstract
Cell-free DNA applications for screening, diagnosis and treatment monitoring are increasingly being developed for a range of different cancers. While most of these applications investigate circulating tumor DNA (ctDNA) or methylation profiles of ctDNA, circulating bacterial DNA (cbDNA) has also been detected in plasma and serum samples from cancer patients. Recent publications have the detection of cbDNA in studies of breast, gastric, colorectal, hepatocellular and ovarian cancers. In several cases, distinction between patients and healthy controls was possible, based on cbDNA profiles, in addition to potential prognostic value. A large pan-cancer study demonstrated the feasibility of cbDNA to distinguish between four types of cancer and healthy controls, even in patients with early-stage disease. While improvements in, and standardization of laboratory and bioinformatics analyses are needed, and the clinical relevance of cbDNA yet to be ascertained for each cancer type, cbDNA analysis presents an exciting prospect for future liquid biopsy screening and diagnostics in cancer.
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Affiliation(s)
- Tamara Glyn
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Rachel Purcell
- Department of Surgery, University of Otago, Christchurch, New Zealand
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Liu Y, Xia H, Li M, Chen Y, Zhou W, Chen Y, Wu Y, Ali L. Overexpressed RING Finger 44 Correlates with Poor Prognosis in Hepatocellular Carcinoma. Journal of Healthcare Engineering 2022; 2022:1-18. [PMID: 35494516 PMCID: PMC9042607 DOI: 10.1155/2022/3522866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022]
Abstract
Introduction Liver carcinoma is one of the most common cancers in the world and remains one of the most difficult cancers to treat. Hepatocellular cancer is the most important type of liver cancer (90%). RING Finger 44 (RNF44) is one of the E3 ligases, which play an important role in substrate recognition. It was also reported that RING Finger 44 was connected with resistant melanoma. But the relationship between RNF44 and HCC remained unknown. Materials and Methods To analyze the role of RING Finger 44 gene in hepatocellular carcinoma, we used bioinformatics to analyze the expression level, genetic changes, immunohistochemistry, immune infiltration, diagnostic value, survival, and functional enrichment of RING Finger 44. Results Through analyzing The Genotype-Tissue Expression and The Cancer Genome Atlas databases, we found that the expression level of RING Finger 44 was significantly increased in hepatocellular carcinoma tissues. Meanwhile, the expression of RING Finger 44 was connected with immune cell infiltration and survival time, and the expression level of RING Finger 44 could perform as a useful diagnostic and prognostic index. The functional enrichment analysis of RING Finger 44 provided some possible pathways of RING Finger 44 in hepatocellular carcinoma, which provided an important direction for the further experiments in vitro or in vivo. Conclusions RING Finger 44, the high expression level of which predicts poor prognosis, is a potential oncogene in hepatocellular carcinoma.
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Behel V, Choughule A, Noronha V, Patil V, Menon N, Singh A, Kumar S, Kumar R, Shah S, More S, Banavali S, Chandrani P, Prabhash K. Clinical utility of liquid biopsy (cell-free DNA) based EGFR mutation detection post treatment initiation as a disease monitoring tool in patients with advanced EGFR-mutant NSCLC. Clin Lung Cancer 2022; 23:410-418. [DOI: 10.1016/j.cllc.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/07/2022] [Accepted: 04/10/2022] [Indexed: 12/15/2022]
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Solanky D, Ahmed AA, Fierer J, Golts E, Jones M, Mehta SR. Utility of Plasma Microbial Cell-Free DNA Decay Kinetics After Aortic Valve Replacement for Bartonella Endocarditis: Case Report. Front Trop Dis 2022. [DOI: 10.3389/fitd.2022.842100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BackgroundDetection and sequencing of circulating microbial cell-free DNA (mcfDNA) in plasma is an increasingly popular tool for diagnosing many infectious diseases, but could also be used to monitor the progress of infection. However, the decay of this microbial cell-free DNA in blood following treatment has not been previously characterized.Case PresentationA 53 year-old male was diagnosed with Bartonella quintana bioprosthetic aortic valve endocarditis by sequencing of the mcfDNA in the blood (Karius, Redwood City, CA). We then monitored the kinetics of decay of mcfDNA after parenteral antibiotics and valve resection in this individual. We measured plasma mcfDNA (Karius) in serial samples obtained in the operating room to calculate mcfDNA half-life after valve resection. After four weeks of parenteral antibiotics, Bartonella mcfDNA signal decreased by 78%. The signal subsequently rose during operative manipulation of the infected valve but dropped 81-fold over four hours following valve resection. The half-life of mcfDNA between the time shortly following resection of the infected valve and 24 to 48 hours post-operatively was between 35 and 115 minutes. The trend in mcfDNA signal was characterized by rapid and then slower phases of decay within 24 hours, and little change between 24 and 48 hours.ConclusionsThis study is one of the first to characterize decay kinetics of mcfDNA and highlights the potential of monitoring mcfDNA in addressing major challenges in infective endocarditis management, including monitoring the response to therapy, and as an early screen for recurrence.
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Audetat A, Tschida C, Kreston S, Stephen A, D’alessio B, Bondy M, Jackson L, Mellert H, Givens N, Sathyanarayana UG, Pestano GA. Analytic and Clinical Validation of a Pan-Cancer NGS Liquid Biopsy Test for the Detection of Copy Number Amplifications, Fusions and Exon Skipping Variants. Diagnostics (Basel) 2022; 12:729. [PMID: 35328282 PMCID: PMC8947661 DOI: 10.3390/diagnostics12030729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/08/2022] [Accepted: 03/15/2022] [Indexed: 02/01/2023] Open
Abstract
Liquid biopsies are an integral part of the diagnosis of cancer. Here, we have extended previous validation studies of a new targeted NGS panel to include the detection of copy number amplifications (CNAs), fusions, and exon skipping variants. Detection of these gene classes included specimens from clinical and healthy donors and cell lines (fusions: ROS1, EML4-ALK, NTRK1; exon skipping: MET exon 14; CNAs: HER2, CDK6, EGFR, MYC, and MET). The limit of detection (LOD) for fusion/skipping was 42 copies (QC threshold was three copies) and was verified using three additional fusion/skipping variants. LOD for CNAs was 1.40-fold-change (QC threshold = 1.15-fold change) and was verified with three additional CNAs. In repeatability and intermediate precision (within lab) studies, all fusion/skipping variants were detected in all runs and all days of testing (n = 18/18; 100%); average CV for repeatability was 20.5% (range 8.7–34.8%), and for intermediate precision it was 20.8% (range 15.7–30.5%). For CNAs, 28/29 (96.6%) copy gains were detected. For CNAs, the average CV was 1.85% (range 0% to 5.49%) for repeatability and 6.59% (range 1.65% to 9.22%) for intermediate precision. The test panel meets the criteria for being highly sensitive and specific and extends its utility for the serial detection of clinically relevant variants in cancer.
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Mohamadzaheri M, Cheraghi H, Shirani D, Hatamkhani A. Relationship between plasma cell-free DNA changes and lysyl oxidase during the treatment and prognosis of canine transmissible venereal tumors. BMC Vet Res 2022; 18:76. [PMID: 35189882 PMCID: PMC8862336 DOI: 10.1186/s12917-022-03173-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/09/2022] [Indexed: 11/22/2022] Open
Abstract
Background Transmissible venereal tumors (TVT) are a wide range of canine tumors for which there are no effective markers to monitor the therapeutic response in real-time. Circulating biomarkers can be valuable in early cancer diagnosis and prognosis. Accordingly, this study aimed to investigate the significance of the cell-free DNA (cfDNA) and cfDNA integrity index to monitor the response of TVTs to vincristine and compare them with lysyl oxidase activity. Plasma and sera were collected from fifteen male dogs within four weeks before drug administration. The analytical method was mainly based on the quantitative polymerase chain reaction (qPCR) technique for short and long cfDNAs and lysyl oxidase activity was measured in serum. Results The results of the cfDNA integrity index showed a significant (p < 0.05) difference in the baseline concentration compared to the second and third weeks (with cut-off values of 1.118 and 93.33% specificity). The cfDNA integrity index increased over time due to the reduction of short cfDNAs in the first week after treatment. Lysyl oxidase activity increased during the fourth week (p < 0.001), but there were no significant differences in the other weeks compared to the baseline. The ROC analysis of lysyl oxidase revealed high sensitivity (100%) and specificity (90%) on the second and third weeks compared to the baseline. Multivariate analysis between cfDNA integrity index and lysyl oxidase showed significant correlation (p < 0.05) only in baseline results. Conclusions Overall, short cfDNA, the cfDNA integrity index, and lysyl oxidase activity can be proposed as diagnostic biomarkers and putative prognostic candidates in TVT patients. These biomarkers can be combined with cytology to quickly diagnose TVT. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03173-z.
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Affiliation(s)
- Mona Mohamadzaheri
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Razi University, Kermanshah, Iran
| | - Hadi Cheraghi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Razi University, Kermanshah, Iran.
| | - Darioush Shirani
- Department of Small Animal Internal Medicine, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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Liu C, Xiang X, Han S, Lim HY, Li L, Zhang X, Ma Z, Yang L, Guo S, Soo R, Ren B, Wang L, Goh BC. Blood-based liquid biopsy: Insights into early detection and clinical management of lung cancer. Cancer Lett 2022; 524:91-102. [PMID: 34656690 DOI: 10.1016/j.canlet.2021.10.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/22/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022]
Abstract
Currently, early detection of lung cancer relies on the characterisation of images generated from computed tomography (CT). However, lung tissue biopsy, a highly invasive surgical procedure, is required to confirm CT-derived diagnostic results with very high false-positive rates. Hence, a non-invasive or minimally invasive biomarkers is essential to complement the existing low-dose CT (LDCT) for early detection, improve responses to a certain treatment, predict cancer recurrence, and to evaluate prognosis. In the past decade, liquid biopsies (e.g., blood) have been demonstrated to be highly effective for lung cancer biomarker discovery. In this review, the roles of emerging liquid biopsy-derived biomarkers such as circulating nucleic acids, circulating tumour cells (CTCs), long non-coding RNA (lncRNA), and microRNA (miRNA), as well as exosomes, have been highlighted. The advantages and limitations of these blood-based minimally invasive biomarkers have been discussed. Furthermore, the current progress of the identified biomarkers for clinical management of lung cancer has been summarised. Finally, a potential strategy for the early detection of lung cancer, using a combination of LDCT scans and well-validated biomarkers, has been discussed.
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Affiliation(s)
- Cuiliu Liu
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Xiaoqiang Xiang
- Department of Clinical Pharmacy and Pharmacy Administration, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Shuangqing Han
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Hannah Ying Lim
- Department of Pharmacy, Faculty of Science, National University of Singapore, 117543, Singapore
| | - Lingrui Li
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Xing Zhang
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Zhaowu Ma
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China
| | - Li Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shuliang Guo
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ross Soo
- Department of Haematology-Oncology, National University Cancer Institute, 119228, Singapore
| | - Boxu Ren
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, 434023, China.
| | - Lingzhi Wang
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore.
| | - Boon Cher Goh
- Department of Haematology-Oncology, National University Cancer Institute, 119228, Singapore; Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117600, Singapore
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Chen S, Yang M, Zhong N, Yu D, Jian J, Jiang D, Xiao Y, Wei W, Wang T, Lou Y, Zhou Z, Xu W, Wan W, Wu Z, Wei H, Liu T, Zhao J, Yang X, Xiao J. Quantified CIN Score From Cell-free DNA as a Novel Noninvasive Predictor of Survival in Patients With Spinal Metastasis. Front Cell Dev Biol 2021; 9:767340. [PMID: 34957099 PMCID: PMC8696126 DOI: 10.3389/fcell.2021.767340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Purpose: Most currently available scores for survival prediction of patients with bone metastasis lack accuracy. In this study, we present a novel quantified CIN (Chromosome Instability) score modeled from cfDNA copy number variation (CNV) for survival prediction. Experimental Design: Plasma samples collected from 67 patients with bone metastases from 11 different cancer types between November 2015 and May 2016 were sent through low-coverage whole genome sequencing followed by CIN computation to make a correlation analysis between the CIN score and survival prognosis. The results were validated in an independent cohort of 213 patients. Results: During the median follow-up period of 598 (95% CI 364-832) days until December 25, 2018, 124 (44.3%) of the total 280 patients died. Analysis of the discovery dataset showed that CIN score = 12 was the optimal CIN cutoff. Validation dataset showed that CIN was elevated (score ≥12) in 87 (40.8%) patients, including 5 (5.75%) with head and neck cancer, 11 (12.6%) with liver and gallbladder cancer, 11 (12.6%) with cancer from unidentified sites, 21 (24.1%) with lung cancer, 7 (8.05%) with breast cancer, 4 (4.60%) with thyroid cancer, 6 (6.90%) with colorectal cancer, 4 (4.60%) with kidney cancer, 2 (2.30%) with prostate cancer, and 16 (18.4%) with other types of cancer. Further analysis showed that patients with elevated CIN were associated with worse survival (p < 0.001). For patients with low Tokuhashi score (≤8) who had predictive survival of less than 6 months, the CIN score was able to distinguish patients with a median overall survival (OS) of 443 days (95% CI 301-585) from those with a median OS of 258 days (95% CI 184-332). Conclusion: CNV examination in bone metastatic cancer from cfDNA is superior to the traditional predictive model in that it provides a noninvasive and objective method of monitoring the survival of patients with spine metastasis.
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Affiliation(s)
- Su Chen
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Minglei Yang
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Nanzhe Zhong
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Dong Yu
- Center of Translational Medicine, Naval Medical University, Shanghai, China
| | - Jiao Jian
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Dongjie Jiang
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Yasong Xiao
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Wei Wei
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | | | - Yan Lou
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Zhenhua Zhou
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Wei Xu
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Wan Wan
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Zhipeng Wu
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Haifeng Wei
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Tielong Liu
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jian Zhao
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xinghai Yang
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Jianru Xiao
- Department of Orthopedic Oncology, Changzheng Hospital, Naval Medical University, Shanghai, China
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Abstract
Many studies have reported an increase in the level of circulating cell-free DNA (cfDNA) in the blood of patients with cancer. cfDNA mainly comes from tumor cells and, therefore, carries features of its genomic profile. Moreover, tumor-derived cfDNA can act like oncoviruses, entering the cells of vulnerable organs, transforming them and forming metastatic nodes. Another source of cfDNA is immune cells, including neutrophils that generate neutrophil extracellular traps (NETs). Despite the potential eliminative effect of NETs on tumors, in some cases, their excessive generation provokes tumor growth as well as invasion. Considering both possible pathological contributions of cfDNA, as an agent of oncotransformation and the main component of NETs, the study of deoxyribonucleases (DNases) as anticancer and antimetastatic agents is important and promising. This review considers the pathological role of cfDNA in cancer development and the role of DNases as agents to prevent and/or prohibit tumor progression and the development of metastases.
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Affiliation(s)
| | - Nadezhda Mironova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia;
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31
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Park H, Kim I, Kim HJ, Shin DY, Lee SY, Kwon OH, Kim DY, Lee KH, Ahn JS, Park J, Sohn SK, Lee JO, Cheong JW, Kim KH, Kim HG, Kim H, Lee YJ, Nam SH, Do YR, Park SG, Park SK, Bae SH, Song HH, Oh D, Jung CW, Park S. Ultra-deep sequencing mutation analysis of the BCR/ABL1 kinase domain in newly diagnosed chronic myeloid leukemia patients. Leuk Res 2021; 111:106728. [PMID: 34673444 DOI: 10.1016/j.leukres.2021.106728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/28/2022]
Abstract
Ultra-deep sequencing detects low-frequency genetic mutations with high sensitivity. We used this approach to prospectively examine mutations in the BCR/ABL1 tyrosine kinase from patients with newly diagnosed, chronic-phase chronic myeloid leukemia (CML) treated with the tyrosine kinase inhibitor nilotinib. Between May 2013 and November 2014, 50 patients from 18 institutions were enrolled in the study. We screened 103 somatic mutations and found that mutations in the P-loop domain were the most frequent (173/454 mutations in the P-loop) and noted the presence of the V299 L mutation (dasatinib-resistant/nilotinib-sensitive) in 98 % of patients (49/50). No patients had Y253H, E255 V, or F359 V/C/I mutations, which would recommend dasatinib rather than nilotinib treatment. The S417Y mutation was associated with lower achievement of a major molecular response (MMR) at 6 months, and the V371A mutation was associated with reduced MMR and MR4.5 durations (MMR for 2 years: 100 % for no mutation vs. 75 % for mutation, P=0.039; MR4.5 for 15 months: 94.1 % vs. 25 %, P=0.002). Patients with known nilotinib-resistant mutations had lower rates of MR4.5 achievement. In conclusion, ultra-deep sequencing is a sensitive method for genetic-based treatment decisions. Based on the results of these mutational analyses, nilotinib treatment is a promising option for Korean patients with CML.
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Affiliation(s)
- Hyunkyung Park
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea; Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, South Korea
| | - Inho Kim
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea.
| | - Hyeong-Joon Kim
- Department of Internal Medicine, Chonnam National University, Hwasun Hospital, Hwasun, South Korea.
| | - Dong-Yeop Shin
- Department of Internal Medicine, Seoul National University Hospital, Biomedical Research Institute, Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | | | | | - Dae-Young Kim
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Kyoo-Hyung Lee
- Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jae-Sook Ahn
- Department of Internal Medicine, Chonnam National University, Hwasun Hospital, Hwasun, South Korea
| | - Jinny Park
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, South Korea
| | - Sang-Kyun Sohn
- Department of Internal Medicine, Kyungpook National University Hospital, Daegu, South Korea
| | - Jeong-Ok Lee
- Department of Internal Medicine, Seoul National University, Bundang Hospital, Seongnam, South Korea
| | - June-Won Cheong
- Department of Internal Medicine, Yonsei University, Severance Hospital, Seoul, South Korea
| | - Kyoung Ha Kim
- Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, South Korea
| | - Hoon-Gu Kim
- Department of Internal Medicine, Gyeongsang Institute of Health Sciences, Gyeongsang National University College of Medicine and Gyeongsang National University Changwon Hospital, Changwon, South Korea
| | - Hawk Kim
- Department of Internal Medicine, Ulsan University Hospital, Ulsan, South Korea
| | - Yoo Jin Lee
- Department of Internal Medicine, Ulsan University Hospital, Ulsan, South Korea
| | - Seung-Hyun Nam
- Department of Internal Medicine, VHS Medical Center, Seoul, South Korea
| | - Young Rok Do
- Department of Internal Medicine, Keimyung University Dongsan Medical Center, Daegu, South Korea
| | - Sang-Gon Park
- Department of Internal Medicine, Chosun University Hospital, Gwangju, South Korea
| | - Seong Kyu Park
- Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, South Korea
| | - Sung Hwa Bae
- Department of Internal Medicine, Daegu Catholic University Medical Center, Daegu, South Korea
| | - Hun Ho Song
- Department of Internal Medicine, Kangdong Sacred Heart Hospital, Seoul, South Korea
| | - Doyeun Oh
- Department of Internal Medicine, CHA Bundang Medical Center, Seongnam, South Korea
| | - Chul Won Jung
- Department of Internal Medicine, Samsung Medical Center, Seoul, South Korea
| | - Seonyang Park
- Department of Internal Medicine, Inje University, Haeundae Paik Hospital, Busan, South Korea
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López-Carrasco A, Berbegall AP, Martín-Vañó S, Blanquer-Maceiras M, Castel V, Navarro S, Noguera R. Intra-Tumour Genetic Heterogeneity and Prognosis in High-Risk Neuroblastoma. Cancers (Basel) 2021; 13:5173. [PMID: 34680323 PMCID: PMC8534138 DOI: 10.3390/cancers13205173] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/15/2022] Open
Abstract
Spatial ITH is defined by genomic and biological variations within a tumour acquired by tumour cell evolution under diverse microenvironments, and its role in NB patient prognosis is understudied. In this work, we applied pangenomic techniques to detect chromosomal aberrations in at least two different areas of each tumour and/or in simultaneously obtained solid and liquid biopsies, detecting ITH in the genomic profile of almost 40% of HR-NB. ITH was better detected when comparing one or more tumour pieces and liquid biopsy (50%) than between different tumour pieces (21%). Interestingly, we found that patients with ITH analysed by pangenomic techniques had a significantly better survival rate that those with non-heterogeneous tumours, especially in cases without MYCN amplification. Moreover, all patients in the studied cohort with high ITH (defined as 50% or more genomic aberration differences between areas of a tumour or simultaneously obtained samples) survived after 48 months. These results clearly support analysing at least two solid tumour areas (separately or mixed) and liquid samples to provide more accurate genomic diagnosis, prognosis and therapy options in HR-NB.
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Affiliation(s)
- Amparo López-Carrasco
- Department of Pathology, Medical School, University of Valencia-INCLIVA, 46010 Valencia, Spain; (A.L.-C.); (A.P.B.); (S.M.-V.); (M.B.-M.); (S.N.)
- CIBER of Cancer (CIBERONC), 28029 Madrid, Spain
| | - Ana P. Berbegall
- Department of Pathology, Medical School, University of Valencia-INCLIVA, 46010 Valencia, Spain; (A.L.-C.); (A.P.B.); (S.M.-V.); (M.B.-M.); (S.N.)
- CIBER of Cancer (CIBERONC), 28029 Madrid, Spain
| | - Susana Martín-Vañó
- Department of Pathology, Medical School, University of Valencia-INCLIVA, 46010 Valencia, Spain; (A.L.-C.); (A.P.B.); (S.M.-V.); (M.B.-M.); (S.N.)
- CIBER of Cancer (CIBERONC), 28029 Madrid, Spain
| | - Maite Blanquer-Maceiras
- Department of Pathology, Medical School, University of Valencia-INCLIVA, 46010 Valencia, Spain; (A.L.-C.); (A.P.B.); (S.M.-V.); (M.B.-M.); (S.N.)
- CIBER of Cancer (CIBERONC), 28029 Madrid, Spain
| | - Victoria Castel
- Clinical and Translational Oncology Research Group, Investigation Institute La Fe, 46026 Valencia, Spain;
| | - Samuel Navarro
- Department of Pathology, Medical School, University of Valencia-INCLIVA, 46010 Valencia, Spain; (A.L.-C.); (A.P.B.); (S.M.-V.); (M.B.-M.); (S.N.)
- CIBER of Cancer (CIBERONC), 28029 Madrid, Spain
| | - Rosa Noguera
- Department of Pathology, Medical School, University of Valencia-INCLIVA, 46010 Valencia, Spain; (A.L.-C.); (A.P.B.); (S.M.-V.); (M.B.-M.); (S.N.)
- CIBER of Cancer (CIBERONC), 28029 Madrid, Spain
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Abstract
Brain cancers are among the top causes of death worldwide. Although, the survival rates vary widely depending on the type of the tumor, early diagnosis could generally benefit in better prognosis outcomes of the brain cancer patients. Conventionally, neuroimaging and biopsy are the most widely used approaches in diagnosis, subtyping, and prognosis monitoring of brain cancers, while emerging liquid biopsy assays using peripheral blood or cerebrospinal fluid have demonstrated many favorable characteristics in this task, especially due to their minimally invasive and easiness in sampling nature. Here, we review the recent studies in the liquid biopsy of brain cancers. We discuss the methodologies and performances of various assays on diagnosis, tumor subtyping, relapse prediction as well as prognosis monitoring in brain cancers, which approaches have made a big step toward clinical benefits of brain cancer patients.
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Affiliation(s)
- Yunyun An
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Fei Fan
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaobing Jiang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Sun
- Shenzhen Bay Laboratory, Shenzhen, China
- BGI-Shenzhen, Shenzhen, China
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Jianfeng W, Yutao W, Jianbin B. Long non-coding RNAs correlate with genomic stability in prostate cancer: A clinical outcome and survival analysis. Genomics 2021; 113:3141-3151. [PMID: 34174340 DOI: 10.1016/j.ygeno.2021.06.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/30/2021] [Accepted: 06/21/2021] [Indexed: 01/03/2023]
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) participate in the regulation of genomic stability. Understanding their biological functions can help us identify the mechanisms of the occurrence and progression of cancers and can provide theoretical guidance and the basis for treatment. RESULTS Based on the mutation hypothesis, we proposed a computational framework to identify genomic instability-related lncRNAs. Based on the differentially-expressed lncRNAs (DElncRNAs), we constructed a genomic instability-derived lncRNA signature (GILncSig) to calculate and stratify outcomes in patients with prostate cancer. It is an independent predictor of overall survival. The area under the curve = 0.805. This value may be more significant than the classic prognostic markers TP53 and Speckle-type POZ protein (SPOP) in terms of outcome prediction. CONCLUSIONS In summary, we conducted a computation approach and resource for mining genome instability-related lncRNAs. It may turn out to be highly significant for genomic instability and customized decision-making for patients with prostate cancer. It also may lead to effective methods and resources to study the molecular mechanism of genomic instability-related lncRNAs.
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Affiliation(s)
- Wang Jianfeng
- Department of Urology, The First Hospital of China Medical University, Shenyang, Liaoning, PR China
| | - Wang Yutao
- Department of Urology, The First Hospital of China Medical University, Shenyang, Liaoning, PR China
| | - Bi Jianbin
- Department of Urology, The First Hospital of China Medical University, Shenyang, Liaoning, PR China.
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Chen ZG, Wang Y, Fong WP, Hu MT, Liang JY, Wang L, Li YH. A quantitative score of immune cell infiltration predicts the prognosis in pancreatic ductal adenocarcinoma. Int Immunopharmacol 2021; 98:107890. [PMID: 34174701 DOI: 10.1016/j.intimp.2021.107890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 06/06/2021] [Accepted: 06/11/2021] [Indexed: 12/20/2022]
Abstract
Pancreatic Ductal Adenocarcinoma (PDAC) is characterized by an extensive and dense fibrous stroma, which plays an active role in tumor growth and metastasis. Despite the growing importance of the tumor microenvironment in PDAC prognosis, the immune cell infiltration landscape of PDAC has not been elucidated. In this study, we applied a credible computational algorithm to comprehensively estimate the immune cell infiltration (ICI) patterns of 876 PDAC patients. Two ICI phenotypes were identified, and a ICIscore was constructed using ssGSEA algorithm. The ICIscore could significantly predict the prognosis and chemotherapy benefit of PDAC patients in both the discovery and the five validation cohorts. Multivariate cox analysis also identified the independent predictive role of the ICIscore in PDAC prognosis. A high ICIscore subtype was characterized by immune-active signaling pathways and anti-tumor immunity while a low ICIscore subtype was associated with tumor progressive signaling pathways. Four immunotherapy cohorts further supported the use of the ICIscore as a prognostic biomarker for patients receiving immune checkpoint inhibitors in other cancer types. The ICIscore reveals a close relationship between the ICI environment and prognosis and may provide new treatment strategies for PDAC patients.
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Affiliation(s)
- Zhi-Gang Chen
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Yun Wang
- Department of Hematologic Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - William Pat Fong
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ming-Tao Hu
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jie-Ying Liang
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Lingyun Wang
- Department of Gastroenterology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, PR China.
| | - Yu-Hong Li
- Department of Medical Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
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Koval AP, Blagodatskikh KA, Kushlinskii NE, Shcherbo DS. The Detection of Cancer Epigenetic Traces in Cell-Free DNA. Front Oncol 2021; 11:662094. [PMID: 33996585 PMCID: PMC8118693 DOI: 10.3389/fonc.2021.662094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
Nucleic acid fragments found in blood circulation originate mostly from dying cells and carry signs pointing to specific features of the parental cell types. Deciphering these clues may be transformative for numerous research and clinical applications but strongly depends on the development and implementation of robust analytical methods. Remarkable progress has been achieved in the reliable detection of sequence alterations in cell-free DNA while decoding epigenetic information from methylation and fragmentation patterns requires more sophisticated approaches. This review discusses the currently available strategies for detecting and analyzing the epigenetic marks in the liquid biopsies.
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Affiliation(s)
- Anastasia P Koval
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Konstantin A Blagodatskikh
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nikolay E Kushlinskii
- Laboratory of Clinical Biochemistry, N.N. Blokhin Cancer Research Medical Center of Oncology, Moscow, Russia
| | - Dmitry S Shcherbo
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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Lorusso L, Cappagli V, Valerio L, Giani C, Viola D, Puleo L, Gambale C, Minaldi E, Campopiano MC, Matrone A, Bottici V, Agate L, Molinaro E, Elisei R. Thyroid Cancers: From Surgery to Current and Future Systemic Therapies through Their Molecular Identities. Int J Mol Sci 2021; 22:3117. [PMID: 33803747 PMCID: PMC8003273 DOI: 10.3390/ijms22063117] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/16/2022] Open
Abstract
Differentiated thyroid cancers (DTC) are commonly and successfully treated with total thyroidectomy plus/minus radioiodine therapy (RAI). Medullary thyroid cancer (MTC) is only treated with surgery but only intrathyroidal tumors are cured. The worst prognosis is for anaplastic (ATC) and poorly differentiated thyroid cancer (PDTC). Whenever a local or metastatic advanced disease is present, other treatments are required, varying from local to systemic therapies. In the last decade, the efficacy of the targeted therapies and, in particular, tyrosine kinase inhibitors (TKIs) has been demonstrated. They can prolong the disease progression-free survival and represent the most important therapeutic option for the treatment of advanced and progressive thyroid cancer. Currently, lenvatinib and sorafenib are the approved drugs for the treatment of RAI-refractory DTC and PDTC while advanced MTC can be treated with either cabozantinib or vandetanib. Dabrafenib plus trametinib is the only approved treatment by FDA for BRAFV600E mutated ATC. A new generation of TKIs, specifically for single altered oncogenes, is under evaluation in phase 2 and 3 clinical trials. The aim of this review was to provide an overview of the current and future treatments of thyroid cancer with regards to the advanced and progressive cases that require systemic therapies that are becoming more and more targeted on the molecular identity of the tumor.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Rossella Elisei
- Endocrine Unit, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (L.L.); (V.C.); (L.V.); (C.G.); (D.V.); (L.P.); (C.G.); (E.M.); (M.C.C.); (A.M.); (V.B.); (L.A.); (E.M.)
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Panagopoulou M, Esteller M, Chatzaki E. Circulating Cell-Free DNA in Breast Cancer: Searching for Hidden Information towards Precision Medicine. Cancers (Basel) 2021; 13:728. [PMID: 33578793 DOI: 10.3390/cancers13040728] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Our research focuses in the elucidation of the nature of circulating cell-free DNA (ccfDNA) as a biological entity and its exploitation as a liquid biopsy biomaterial. Working on breast cancer, it became clear that although a promising biosource, its clinical exploitation is burdened mainly by gaps in knowledge about its biology and specific characteristics. The current review covers multiple aspects of ccfDNA in breast cancer. We cover key issues such as quantity, integrity, releasing structures, methylation specific changes, release mechanisms, biological role. Machine learning approaches for analyzing ccfDNA-generated data to produce classifiers for clinical use are also discussed. Abstract Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.
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Mellert H, Reese J, Jackson L, Maxwell V, Tschida C, Pestano GA. Targeted Next-Generation Sequencing of Liquid Biopsy Samples from Patients with NSCLC. Diagnostics (Basel) 2021; 11:155. [PMID: 33494470 PMCID: PMC7912015 DOI: 10.3390/diagnostics11020155] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/02/2023] Open
Abstract
Liquid biopsy tests have become an integral part of the molecular diagnosis of patients with non-small cell lung cancer (NSCLC). We describe a new test panel that uses very low input (20 ng) of cell-free nucleic acids extracted from human plasma, which is designed to yield results in less than 72 h. In this study, we performed novel amplicon-based targeted next-generation sequencing with a semiconductor-based system, the Ion GeneStudio S5 Prime. The analytic performance of the assay was evaluated using contrived and retrospectively collected clinical specimens. The cumulative percent coefficient of variation for the new test process was very precise at 8.4% for inter-day, 4.0% for inter-operator and 3.4% for inter-instrument. We also observed significant agreement (95.7-100%) with an orthogonal, high-sensitivity droplet digital™ Polymerase Chain Reaction (ddPCR) test. This method offers a valuable supplement to assessing targeted mutations from blood while conserving specimens and maintaining sensitivity, with rapid turn-around times to actionable results.
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Affiliation(s)
- Hestia Mellert
- Biodesix Inc., 2970 Wilderness Place Suite 100, Boulder, CO 80301, USA; (J.R.); (L.J.); (V.M.); (C.T.); (G.A.P.)
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Koçana CÇ, Toprak SF, Sözer S. Extracellular genetic materials and their application in clinical practice. Cancer Genet 2020; 252-253:48-63. [PMID: 33387935 DOI: 10.1016/j.cancergen.2020.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/12/2020] [Accepted: 12/20/2020] [Indexed: 11/20/2022]
Abstract
This study reviews the possible origins, functional roles, and diagnostic applications of 'extracellular genetic material' (EGM), a novel term introduced to cover DNA, RNA, and DNA/RNA-related molecules released from all types of cells into the extracellular region. The literature on EGMs shows them to play a dual role in diverse, fine-tuning mechanisms involved in both homeostasis and pathological events, including cancerogenesis and genometastasis. Recent developments in the next-generation technology have provided successful applications of low quantities of genomic materials into the diagnostic field, yielding high sensitivity and specificity in test results. Also, the successful application of EGMs into diagnostics has afforded promising outcomes for researchers and clinicians. This study of EGM provides a deeper understanding of the subject as an area of interest, especially cell-free DNA, aiming toward the eventual development of new therapeutic applications and diagnostic strategies.
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Affiliation(s)
- Cemal Çağıl Koçana
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selin Fulya Toprak
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selçuk Sözer
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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Konečná B, Gaál Kovalčíková A, Pančíková A, Novák B, Kovaľová E, Celec P, Tóthová Ľ. Salivary Extracellular DNA and DNase Activity in Periodontitis. Applied Sciences 2020; 10:7490. [DOI: 10.3390/app10217490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Extracellular DNA (ecDNA) is a potential marker and predictor in several inflammatory diseases. Periodontitis, a chronic inflammatory disease, is associated with epithelial cell death and could lead to release of DNA. Our aim was to analyze salivary DNA concentration and deoxyribonuclease (DNase) activity in periodontitis patients. We hypothesized that salivary ecDNA will be higher than in controls and could serve as a marker of periodontitis severity. Samples of saliva were collected from 25 patients with chronic periodontitis and 29 age-matched controls. DNA was quantified fluorometrically in whole saliva, as well as in supernatants after centrifugation (depletion of cells at 1600× g) and in double-centrifuged supernatants (depletion of cell debris at 1600× g and 16,000× g). The subcellular origin of ecDNA was assessed using real-time PCR. In comparison to controls, patients with periodontitis had twofold higher salivary DNA (p < 0.01), higher mitochondrial DNA in centrifuged supernatants (p < 0.05) and lower nuclear ecDNA in double-centrifuged samples (p < 0.05). No correlations were found between salivary DNA and oral health status, but mitochondrial DNA positively correlated with papillary bleeding index in centrifuged samples. Salivary DNase activity was comparable between the groups. In conclusion, we proved that salivary DNA is higher in periodontitis. The source of the higher mitochondrial DNA in cell-free saliva and the causes of lower nuclear ecDNA remain to be elucidated. Further studies should focus on the role of mitochondrial DNA as a potential driver of inflammation in periodontitis.
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Gašperšič J, Videtič Paska A. Potential of modern circulating cell-free DNA diagnostic tools for detection of specific tumour cells in clinical practice. Biochem Med (Zagreb) 2020; 30:030504. [PMID: 32774122 PMCID: PMC7394254 DOI: 10.11613/bm.2020.030504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/20/2020] [Indexed: 12/11/2022] Open
Abstract
Personalized medicine is a developing field of medicine that has gained in importance in recent decades. New diagnostic tests based on the analysis of circulating cell-free DNA (cfDNA) were developed as a tool of diagnosing different cancer types. By detecting the subpopulation of mutated DNA from cancer cells, it is possible to detect the presence of a specific tumour in early stages of the disease. Mutation analysis is performed by quantitative polymerase chain reaction (qPCR) or the next generation sequencing (NGS), however, cfDNA protocols need to be modified carefully in preanalytical, analytical, and postanalytical stages. To further improve treatment of cancer the Food and Drug Administration approved more than 20 companion diagnostic tests that combine cancer drugs with highly efficient genetic diagnostic tools. Tools detect mutations in the DNA originating from cancer cells directly through the subpopulation of cfDNA, the circular tumour DNA (ctDNA) analysis or with visualization of cells through intracellular DNA probes. A large number of ctDNA tests in clinical studies demonstrate the importance of new findings in the field of cancer diagnosis. We describe the innovations in personalized medicine: techniques for detecting ctDNA and genomic DNA (gDNA) mutations approved Food and Drug Administration companion genetic diagnostics, candidate genes for assembling the cancer NGS panels, and a brief mention of the multitude of cfDNA currently in clinical trials. Additionally, an overview of the development steps of the diagnostic tools will refresh and expand the knowledge of clinics and geneticists for research opportunities beyond the development phases.
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Affiliation(s)
- Jernej Gašperšič
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Alja Videtič Paska
- Medical Centre for Molecular Biology, Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Abstract
Background Lung adenocarcinoma (ACA) is the most common subtype of non-small-cell lung cancer. About 70%–80% patients are diagnosed at an advanced stage; therefore, the survival rate is poor. It is urgent to discover accurate markers that can differentiate the late stages of lung ACA from the early stages. With the development of biochips, researchers are able to efficiently screen large amounts of biological analytes for multiple purposes. Methods Our team downloaded GSE75037 and GSE32863 from the Gene Expression Omnibus (GEO) database. Next, we utilized GEO’s online tool, GEO2R, to analyze the differentially expressed genes (DEGs) between stage I and stage II–IV lung ACA. The using the Cytoscape software was used to analyze the DEGs and the protein-protein interaction (PPI) network was further constructed. The function of the DEGs were further analyzed by cBioPortal and Gene Expression Profiling Interactive Analysis (GEPIA) online tools. We validated these results in 72 pairs human samples. Results We identified 109 co-DEGs, most of which were involved in either proliferation, S phase of mitotic cell cycle, regulation of exit from mitosis, DNA replication initiation, DNA replication, and chromosome segregation. Utilizing cBioPortal and University of California Santa Cruz databases, we further confirmed 35 hub genes. Two of these genes, encoding CDC28 protein kinase regulatory subunit 2 (CKS2) and RecQ-mediated genome instability 2 (RMI2), were upregulated in lung ACA compared with adjacent normal tissues. The Kaplan–Meier curves revealed upregulation of CKS2 and RMI2 are associated with worse survival. Using CMap analysis, we discovered 10 small molecular compounds that reversed the altered DEGs, the top five are phenoxybenzamine, adiphenine, resveratrol, and trifluoperazine. We also evaluated 72 pairs resected samples, results revealed that upregulation of CKS2 and RMI2 in lung ACA were associated with larger tumor size. Our results allow the deeper recognizing of the mechanisms of the progression of lung ACA, and may indicate potential therapeutic strategies for the therapy of lung ACA.
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Affiliation(s)
- Dayong Xiao
- Department of Thoracic Surgery, The People's Hospital of Wanning, Wanning, Hainan, China
| | - Siyuan Dong
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Shize Yang
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhenghua Liu
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
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Polski A, Xu L, Prabakar RK, Kim JW, Shah R, Jubran R, Kuhn P, Cobrinik D, Hicks J, Berry JL. Cell-Free DNA Tumor Fraction in the Aqueous Humor Is Associated With Therapeutic Response in Retinoblastoma Patients. Transl Vis Sci Technol 2020; 9:30. [PMID: 33062393 PMCID: PMC7533735 DOI: 10.1167/tvst.9.10.30] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 08/22/2020] [Indexed: 12/17/2022] Open
Abstract
Purpose The aqueous humor (AH) liquid biopsy enables in vivo evaluation of tumor-derived cell-free DNA (cfDNA) from retinoblastoma (RB) eyes. Herein, we test our hypothesis that longitudinal dynamics of AH cfDNA—including tumor fraction (TFx) and somatic copy number alteration (SCNA) amplitude—correspond to therapeutic response. Methods Eyes with ≥3 AH extractions during intravitreal chemotherapy (IVM) or at secondary enucleation between 2015 to 2019 were included. AH cfDNA was sequenced to assess RB SCNA amplitude; ichorCNA software was used to estimate TFx. Eyes without SCNAs or with TFx < 0.10 across all samples were excluded. Therapeutic responses for each eye were determined from clinical records. Statistical analyses included Mann-Whitney U and Pearson correlation tests. Results Twenty eyes of 20 patients underwent ≥3 AH extractions; 6 eyes lacked SCNAs or had TFx < 0.10 throughout sampling and were excluded. Clinical progression was associated with significantly higher SCNA amplitudes and TFx values than regression (P ≤ 0.04). Relative increases in TFx (ΔTFx 1.86 ± 2.22) were associated with disease progression, whereas relative decreases in TFx (ΔTFx 0.53 ± 0.36) were associated with disease regression (P < 0.00001). A ≥15% increase in TFx relative to baseline during treatment was associated with an over 90-fold increased likelihood of clinical progression (odds ratio = 90.67, 95% confidence interval = 8.30–990.16, P = 0.0002). TFx and SCNA amplitude were significantly positively correlated throughout sampling (P ≤ 0.002). Conclusions Longitudinal changes in AH-derived cfDNA TFx and SCNA amplitude are concordant with clinical responses of intraocular RB during active therapy. Translational Relevance Longitudinal evaluation of AH cfDNA may provide an objective, quantitative way to monitor therapeutic response and disease burden in RB patients.
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Affiliation(s)
- Ashley Polski
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, CA, USA.,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Liya Xu
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, CA, USA.,Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Rishvanth K Prabakar
- Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Jonathan W Kim
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, CA, USA.,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Rachana Shah
- Cancer and Blood Disease Institute at Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Rima Jubran
- Cancer and Blood Disease Institute at Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Peter Kuhn
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Cobrinik
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, CA, USA.,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - James Hicks
- Department of Biological Sciences, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jesse L Berry
- The Vision Center at Children's Hospital Los Angeles, Los Angeles, CA, USA.,USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,The Saban Research Institute, Children's Hospital Los Angeles, Los Angeles, CA, USA
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Pall AH, Jakobsen KK, Grønhøj C, von Buchwald C. Circulating tumour DNA alterations as biomarkers for head and neck cancer: a systematic review. Acta Oncol 2020; 59:845-850. [PMID: 32223478 DOI: 10.1080/0284186x.2020.1742930] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) is a significant global burden. The development of a diagnostic or recurrence monitoring test could evolve from the exploitation of molecular markers such as tumour-specific DNA alterations in plasma. The aim of this study was to report specific genetic alterations of DNA in plasma from HNSCC patients, report the diagnostic accuracy, and discuss potentials for a diagnostic or recurrence monitoring test based on circulating tumour DNA (ctDNA).Methods: A systematic search was performed in PubMed, Embase, and Cochrane Library for articles published in English between 1 January 1980 and 24 October 2018. The search terms used were related to ctDNA methylations and mutations in HNSCC patients.Results: We identified 16 studies from four countries (p = 1156 patients, c = 601 controls) examining ctDNA alterations of HNSCC patients. CtDNA methylations were significantly increased in HNSCC patients compared to controls. Five studies investigated ctDNA mutations in HNSCC. The most frequent examined gene mutation was TP53. Eleven studies investigated ctDNA methylations in HNSCC. Nine studies calculated the diagnostic accuracy of ctDNA methylations in HNSCC compared to controls. The most frequent examined gene methylations were CDKN2A, DAPK1, RASSF1, and P15.Conclusion: We found that increasing the number of ctDNA genetic methylations resulted in an increase in diagnostic sensitivity accuracy. No studies investigating ctDNA mutations included a control group. A combination of multiple human ctDNA gene alterations with viral ctDNA are promising tools for developing a ctDNA biomarker for HNSCC.
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Affiliation(s)
- Amalie Hartvig Pall
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Kathrine Kronberg Jakobsen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christian Grønhøj
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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Meeks JJ, Al-Ahmadie H, Faltas BM, Taylor JA, Flaig TW, DeGraff DJ, Christensen E, Woolbright BL, McConkey DJ, Dyrskjøt L. Genomic heterogeneity in bladder cancer: challenges and possible solutions to improve outcomes. Nat Rev Urol 2020; 17:259-270. [PMID: 32235944 PMCID: PMC7968350 DOI: 10.1038/s41585-020-0304-1] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/14/2022]
Abstract
Histological and molecular analyses of urothelial carcinoma often reveal intratumoural and intertumoural heterogeneity at the genomic, transcriptional and cellular levels. Despite the clonal initiation of the tumour, progression and metastasis often arise from subclones that can develop naturally or during therapy, resulting in molecular alterations with a heterogeneous distribution. Variant histologies in tumour tissues that have developed distinct morphological characteristics divergent from urothelial carcinoma are extreme examples of tumour heterogeneity. Ultimately, heterogeneity contributes to drug resistance and relapse after therapy, resulting in poor survival outcomes. Mutation profile differences between patients with muscle-invasive and metastatic urothelial cancer (interpatient heterogeneity) probably contribute to variability in response to chemotherapy and immunotherapy as first-line treatments. Heterogeneity can occur on multiple levels and averaging or normalizing these alterations is crucial for clinical trial and drug design to enable appropriate therapeutic targeting. Identification of the extent of heterogeneity might shape the choice of monotherapy or additional combination treatments to target different drivers and genetic events. Identification of the lethal tumour cell clones is required to improve survival of patients with urothelial carcinoma.
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Affiliation(s)
- Joshua J Meeks
- Departments of Urology and Biochemistry, Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
| | - Hikmat Al-Ahmadie
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Bishoy M Faltas
- Department of Medicine and Department of Cell and Developmental biology, Weill-Cornell Medicine, New York, NY, USA
| | - John A Taylor
- Department of Urology, University of Kansas Medical Center, Kansas City, KS, USA
| | | | - David J DeGraff
- Departments of Pathology, Biochemistry & Molecular Biology and Surgery, Division of Urology, Pennsylvania State University, College of Medicine, Hershey, PA, USA
| | - Emil Christensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
| | | | - David J McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Brady Urological Institute, Johns Hopkins University, Baltimore, MD, USA
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus N, Denmark
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Wouters Y, Dalloyaux D, Christenhusz A, Roelofs HMJ, Wertheim HF, Bleeker‐Rovers CP, te Morsche RH, Wanten GJA. Droplet digital polymerase chain reaction for rapid broad-spectrum detection of bloodstream infections. Microb Biotechnol 2020; 13:657-668. [PMID: 31605465 PMCID: PMC7111091 DOI: 10.1111/1751-7915.13491] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/21/2019] [Accepted: 09/17/2019] [Indexed: 11/30/2022] Open
Abstract
The droplet digital polymerase chain reaction (ddPCR) is a novel molecular technique that allows rapid quantification of rare target DNA sequences. Aim of this study was to explore the feasibility of the ddPCR technique to detect pathogen DNA in whole blood and to assess the diagnostic accuracy of ddPCR to detect bloodstream infections (BSIs), benchmarked against blood cultures. Broad-range primers and probes were designed to detect bacterial 16S rRNA (and Gram stain for differentiation) and fungal 28S rRNA. To determine the detection limit of ddPCR, 10-fold serial dilutions of E. coli and C. albicans were spiked in both PBS and whole blood. The diagnostic accuracy of ddPCR was tested in historically collected frozen blood samples from adult patients suspected of a BSI and compared with blood cultures. Analyses were independently performed by two research analysts. Outcomes included sensitivity and specificity of ddPCR. Within 4 h, blood samples were drawn, and DNA was isolated and analysed. The ddPCR detection limit was approximately 1-2 bacteria or fungi per ddPCR reaction. In total, 45 blood samples were collected from patients, of which 15 (33%) presented with positive blood cultures. The overall sensitivity of ddPCR was 80% (95% CI 52-96) and specificity 87% (95% CI 69-96). In conclusion, the ddPCR technique has considerable potential and is able to detect very low amounts of pathogen DNA in whole blood within 4 h. Currently, ddPCR has a reasonable sensitivity and specificity, but requires further optimization to make it more useful for clinical practice.
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Affiliation(s)
- Yannick Wouters
- Intestinal Failure UnitDepartment of Gastroenterology and HepatologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Daisy Dalloyaux
- Intestinal Failure UnitDepartment of Gastroenterology and HepatologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Anke Christenhusz
- Intestinal Failure UnitDepartment of Gastroenterology and HepatologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Hennie M. J. Roelofs
- Intestinal Failure UnitDepartment of Gastroenterology and HepatologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Heiman F. Wertheim
- Department of Medical MicrobiologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Chantal P. Bleeker‐Rovers
- Department of Internal Medicine and Infectious DiseasesRadboud University Medical CentreNijmegenThe Netherlands
| | - René H. te Morsche
- Intestinal Failure UnitDepartment of Gastroenterology and HepatologyRadboud University Medical CentreNijmegenThe Netherlands
| | - Geert J. A. Wanten
- Intestinal Failure UnitDepartment of Gastroenterology and HepatologyRadboud University Medical CentreNijmegenThe Netherlands
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Peng R, Zhang R, Zhang J, Tan P, Han Y, Zhang K, Lin G, Xie J, Li J. Continual Improvement of the Reliability of EML4-ALK Rearrangement Detection in Non-Small-Cell Lung Cancer: A Long-Term Comparison of ALK Detection in China. J Mol Diagn 2020; 22:876-884. [PMID: 32302779 DOI: 10.1016/j.jmoldx.2020.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/24/2019] [Accepted: 03/30/2020] [Indexed: 12/01/2022] Open
Abstract
The results of EML4-ALK testing are critical to manage ALK tyrosine kinase receptor inhibitor treatment. Thus, the accurate detection of ALK rearrangement is increasingly becoming a matter of serious concern. To address this issue, a long-term EML4-ALK proficiency testing (PT) scheme was launched in China in 2015, serving as an educational tool for assessing and improving the testing quality of EML4-ALK fusion detection. Responses across 20 different PT samples interrogating three different variants and wild-type samples were collected between 2015 and 2019. Performance was analyzed by evaluating the detection methods, kits, and pre-analytic practices used to further display the landscape of changing conditions of the reliability of EML4-ALK testing. During the 5 years, 3224 results reported from 988 laboratories were evaluated, with an overall error rate of 5.36%. Along with an increasing number of participating laboratories, the error rate within each of the different methods showed a significantly downward trend over the years. No obvious differences in the error rates were found regarding the testing methods or kit manufacturers. Moreover, the individual performance of the laboratories improved when they participated in more PT scheme rounds. The data demonstrated that the performance of individual Chinese laboratories for EML4-ALK testing continuously improved over time by participating PT schemes, regardless of their method. However, care must be taken in standardized operations and validations.
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Affiliation(s)
- Rongxue Peng
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiawei Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
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Baghban R, Roshangar L, Jahanban-Esfahlan R, Seidi K, Ebrahimi-Kalan A, Jaymand M, Kolahian S, Javaheri T, Zare P. Tumor microenvironment complexity and therapeutic implications at a glance. Cell Commun Signal 2020; 18:59. [PMID: 32264958 PMCID: PMC7140346 DOI: 10.1186/s12964-020-0530-4] [Citation(s) in RCA: 768] [Impact Index Per Article: 192.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 02/05/2020] [Indexed: 02/07/2023] Open
Abstract
The dynamic interactions of cancer cells with their microenvironment consisting of stromal cells (cellular part) and extracellular matrix (ECM) components (non-cellular) is essential to stimulate the heterogeneity of cancer cell, clonal evolution and to increase the multidrug resistance ending in cancer cell progression and metastasis. The reciprocal cell-cell/ECM interaction and tumor cell hijacking of non-malignant cells force stromal cells to lose their function and acquire new phenotypes that promote development and invasion of tumor cells. Understanding the underlying cellular and molecular mechanisms governing these interactions can be used as a novel strategy to indirectly disrupt cancer cell interplay and contribute to the development of efficient and safe therapeutic strategies to fight cancer. Furthermore, the tumor-derived circulating materials can also be used as cancer diagnostic tools to precisely predict and monitor the outcome of therapy. This review evaluates such potentials in various advanced cancer models, with a focus on 3D systems as well as lab-on-chip devices. Video abstract.
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Affiliation(s)
- Roghayyeh Baghban
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Roshangar
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Rana Jahanban-Esfahlan
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khaled Seidi
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Student Research Committees, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abbas Ebrahimi-Kalan
- Department of Neurosciences and Cognitive, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Saeed Kolahian
- Department of Experimental and Clinical Pharmacology and Pharmacogenomics, University Hospital Tuebingen, Tuebingen, Germany
| | - Tahereh Javaheri
- Health Informatics Lab, Metropolitan College, Boston University, Boston, USA
| | - Peyman Zare
- Dioscuri Center of Chromatin Biology and Epigenomics, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
- Faculty of Medicine, Cardinal Stefan Wyszyński University in Warsaw, 01-938 Warsaw, Poland
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50
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Peng R, Zhang R, Horan MP, Zhou L, Chai SY, Pillay N, Tay KH, Badrick T, Li J. From Somatic Variants Toward Precision Oncology: An Investigation of Reporting Practice for Next-Generation Sequencing-Based Circulating Tumor DNA Analysis. Oncologist 2020; 25:218-228. [PMID: 32162803 PMCID: PMC7066684 DOI: 10.1634/theoncologist.2019-0239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/18/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND With the accelerated development of next-generation sequencing (NGS), identified variants, and targeted therapies, clinicians who confront the complicated and multifarious genetic information may not effectively incorporate NGS-based circulating tumor DNA (ctDNA) analysis into routine patient care. Consequently, standardized ctDNA testing reports are of vital importance. In an effort to guarantee high-quality reporting performance, we conducted an investigation of the current detection and reporting practices for NGS-based ctDNA analysis. MATERIALS AND METHODS A set of simulated ctDNA samples with known variants at known allelic frequencies and a corresponding case scenario were distributed to 66 genetic testing laboratories for ctDNA analysis. Written reports were collected to evaluate the detection accuracy, reporting integrity, and information sufficiency using 21 predefined criteria. RESULTS Current reporting practices for NGS-based ctDNA analysis were found to be far from satisfactory, especially regarding testing interpretation and methodological details. Only 42.4% of laboratories reported the results in complete concordance with the expected results. Moreover, 74.2% of reports only listed aberrations with direct and well-known treatment consequences for the tumor type in question. Genetic aberrations for which experimental agents and/or drug access programs are available may thus be overlooked. Furthermore, methodological details for the interpretation of results were missing from the majority of reports (87.9%). CONCLUSION This proof-of-principle study suggests that the capacity for accurate identification of variants, rational interpretation of genotypes, comprehensive recommendation of potential medications, and detailed description of methodologies need to be further improved before ctDNA analysis can be formally implemented in the clinic. IMPLICATIONS FOR PRACTICE Accurate, comprehensive, and standardized clinical sequencing reports can help to translate complex genetic information into patient-centered clinical decisions, thereby shepherding precision oncology into daily practice. However, standards, guidelines, and quality requirements for clinical reports of next-generation sequencing (NGS)-based circulating tumor DNA (ctDNA) analysis are currently absent. By using a set of simulated clinical ctDNA samples and a corresponding case scenario, current practices were evaluated to identify deficiencies in clinical sequencing reports of ctDNA analysis. The recommendations provided here may serve as a roadmap for the improved implementation of NGS-based ctDNA analysis in the clinic.
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Affiliation(s)
- Rongxue Peng
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyBeijingPeople's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing HospitalBeijingPeople's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyBeijingPeople's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing HospitalBeijingPeople's Republic of China
| | - Martin P. Horan
- Royal College of Pathologists of Australasia Quality Assurance ProgramsSt LeonardsNew South WalesAustralia
| | - Li Zhou
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyBeijingPeople's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing HospitalBeijingPeople's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijingPeople's Republic of China
| | - Sze Yee Chai
- Royal College of Pathologists of Australasia Quality Assurance ProgramsSt LeonardsNew South WalesAustralia
| | - Nalishia Pillay
- Royal College of Pathologists of Australasia Quality Assurance ProgramsSt LeonardsNew South WalesAustralia
| | - Kwang Hong Tay
- Royal College of Pathologists of Australasia Quality Assurance ProgramsSt LeonardsNew South WalesAustralia
| | - Tony Badrick
- Royal College of Pathologists of Australasia Quality Assurance ProgramsSt LeonardsNew South WalesAustralia
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyBeijingPeople's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing HospitalBeijingPeople's Republic of China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical SciencesBeijingPeople's Republic of China
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