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Zhao Y, Fu W, Wang L. Biomarkers in aortic dissection: Diagnostic and prognostic value from clinical research. Chin Med J (Engl) 2024; 137:257-269. [PMID: 37620283 PMCID: PMC10836883 DOI: 10.1097/cm9.0000000000002719] [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: 02/11/2023] [Indexed: 08/26/2023] Open
Abstract
ABSTRACT Aortic dissection is a life-threatening condition for which diagnosis mainly relies on imaging examinations, while reliable biomarkers to detect or monitor are still under investigation. Recent advances in technologies provide an unprecedented opportunity to yield the identification of clinically valuable biomarkers, including proteins, ribonucleic acids (RNAs), and deoxyribonucleic acids (DNAs), for early detection of pathological changes in susceptible patients, rapid diagnosis at the bedside after onset, and a superior therapeutic regimen primarily within the concept of personalized and tailored endovascular therapy for aortic dissection.
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Affiliation(s)
- Yufei Zhao
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Vascular Surgery Institute,Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Weiguo Fu
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Vascular Surgery Institute,Zhongshan Hospital, Fudan University, Shanghai 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Department of Vascular Surgery, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, Fujian 361015, China
| | - Lixin Wang
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Vascular Surgery Institute,Zhongshan Hospital, Fudan University, Shanghai 200032, China
- National Clinical Research Center for Interventional Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Department of Vascular Surgery, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, Fujian 361015, China
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Daniels TE, Zitkovsky EK, Laumann LE, Kunicki ZJ, Price DJ, Peterson AL, Dennery PA, Kao HT, Parade SH, Price LH, Abrantes AM, Tyrka AR. Circulating Cell-Free Mitochondrial DNA and Depressive Symptoms Among Low-Active Adults Who Smoke. Psychosom Med 2024; 86:37-43. [PMID: 37769227 PMCID: PMC10843087 DOI: 10.1097/psy.0000000000001254] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
OBJECTIVES Mitochondrial dysfunction is implicated in the pathophysiology of psychiatric disorders. Levels of circulating cell-free mitochondrial DNA (cf-mtDNA) are observed to be altered in depression. However, the few studies that have measured cf-mtDNA in depression have reported conflicting findings. This study examined cf-mtDNA and depressive symptoms in low-active adults who smoke. METHODS Participants were adults 18 to 65 years old ( N = 109; 76% female) with low baseline physical activity and depressive symptoms recruited for a smoking cessation study. Self-report measures assessed depression severity, positive and negative affect, and behavioral activation. Blood was collected and analyzed for cf-mtDNA. Relationships between depressive symptoms and cf-mtDNA were examined with correlations and linear regression. RESULTS Levels of cf-mtDNA were associated with categorically defined depression (Center for Epidemiologic Studies Depression Scale score >15), lower positive affect, and decreased behavioral activation ( p < .05). Relationships remained significant after adjustment for age, sex, and nicotine dependence. In a linear regression model including all depressive symptom measures as predictors, Center for Epidemiologic Studies Depression Scale group and lower positive affect remained significant. CONCLUSIONS This work suggests that mitochondrial changes are associated with depressive symptoms in low-active adults who smoke. Higher levels of cf-mtDNA in association with depression and with lower positive affect and decreased behavioral activation are consistent with a possible role for mitochondrial function in depressive symptoms.
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Affiliation(s)
- Teresa E. Daniels
- Mood Disorders Research Program and Laboratory for Clinical and Translational Neuroscience, Butler Hospital, 345 Blackstone Boulevard, Providence, RI, 02906, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, 345 Blackstone Boulevard, Providence, RI, 02906, USA
- Initiative on Stress, Trauma, and Resilience (STAR), Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Emily K. Zitkovsky
- Mood Disorders Research Program and Laboratory for Clinical and Translational Neuroscience, Butler Hospital, 345 Blackstone Boulevard, Providence, RI, 02906, USA
- Warren Alpert Medical School of Brown University, 222 Richmond St, Providence, RI, 02903, USA
| | - Laura E. Laumann
- Department of Psychological Sciences, University of Connecticut, 406 Babbidge Road, Unit 1020, Storrs, CT, 06269, USA
| | - Zachary J. Kunicki
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, 345 Blackstone Boulevard, Providence, RI, 02906, USA
| | - Destiny J. Price
- Department of Psychiatry, New York State Psychiatric Institute and Columbia University Irving Medical Center, 1051 Riverside Dr, New York, NY 10032, USA
| | - Abigail L. Peterson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
| | - Phyllis A. Dennery
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
- Department of Pediatrics, Warren Alpert Medical School of Brown University, 593 Eddy St, Providence, RI, 02903, USA
| | - Hung-Teh Kao
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, 345 Blackstone Boulevard, Providence, RI, 02906, USA
| | - Stephanie H. Parade
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, 345 Blackstone Boulevard, Providence, RI, 02906, USA
- Initiative on Stress, Trauma, and Resilience (STAR), Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
- Bradley/Hasbro Children’s Research Center, E.P. Bradley Hospital, East Providence, RI, USA
| | - Lawrence H. Price
- Mood Disorders Research Program and Laboratory for Clinical and Translational Neuroscience, Butler Hospital, 345 Blackstone Boulevard, Providence, RI, 02906, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, 345 Blackstone Boulevard, Providence, RI, 02906, USA
| | - Ana M. Abrantes
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, 345 Blackstone Boulevard, Providence, RI, 02906, USA
- Behavioral Medicine and Addictions Research Department, Butler Hospital, 345 Blackstone Boulevard, Providence, RI, 02906, USA
| | - Audrey R. Tyrka
- Mood Disorders Research Program and Laboratory for Clinical and Translational Neuroscience, Butler Hospital, 345 Blackstone Boulevard, Providence, RI, 02906, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, 345 Blackstone Boulevard, Providence, RI, 02906, USA
- Initiative on Stress, Trauma, and Resilience (STAR), Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
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Adhit KK, Wanjari A, Menon S, K S. Liquid Biopsy: An Evolving Paradigm for Non-invasive Disease Diagnosis and Monitoring in Medicine. Cureus 2023; 15:e50176. [PMID: 38192931 PMCID: PMC10772356 DOI: 10.7759/cureus.50176] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/08/2023] [Indexed: 01/10/2024] Open
Abstract
Liquid biopsy stands as an innovative instrument in the realm of precision medicine, enabling non-invasive disease diagnosis and the early detection of cancer. Liquid biopsy helps in the extraction of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), and cell-free DNA (cfDNA) from blood samples and other body fluids, thereby facilitating disease diagnosis and prediction of high-risk patients. Various techniques such as advanced sequencing methods and biomarker-based cell capture have led to the isolation and study of the different biomarkers such as ctDNA, cfDNA, and CTCs. These biopsies also have immense potential in the early detection and diagnosis of various diseases across all medical specialties, prediction and screening of high-risk cases, and detection of different immune response patterns in response to infectious diseases, and also help in predicting treatment outcomes. Although liquid biopsy has the potential to disrupt the field of medical diagnosis, it is met by various challenges such as limited tumor-derived components, less specificity, and inadequate advancement in methods to isolate biomarkers. Despite all these challenges, liquid biopsies provide the potential to become a minimally invasive method of diagnosis that would facilitate real-time monitoring of patients, which differentiates them from traditional tissue biopsies. This article aims to provide a complete overview of the current technologies, different biomarkers, and body fluids that can be used in liquid biopsy and its clinical applications and the potential impact that liquid biopsy holds in the field of precision medicine, facilitating early diagnosis and prompt management of various diseases and cancers.
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Affiliation(s)
- Kanishk K Adhit
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Anil Wanjari
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Sharanya Menon
- Pathology, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Siddhaarth K
- Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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Schrag D, Beer TM, McDonnell CH, Nadauld L, Dilaveri CA, Reid R, Marinac CR, Chung KC, Lopatin M, Fung ET, Klein EA. Blood-based tests for multicancer early detection (PATHFINDER): a prospective cohort study. Lancet 2023; 402:1251-1260. [PMID: 37805216 PMCID: PMC11027492 DOI: 10.1016/s0140-6736(23)01700-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/29/2023] [Accepted: 08/11/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND Multicancer early detection (MCED) blood tests can detect a cancer signal from circulating cell-free DNA (cfDNA). PATHFINDER was a prospective cohort study investigating the feasibility of MCED testing for cancer screening. METHODS In this prospective cohort study done in oncology and primary care outpatient clinics at seven US health networks, a convenience sample of adults aged 50 years or older without signs or symptoms of cancer consented to MCED testing. We collected blood, analysed cfDNA, and returned results to participants' doctors. If a methylation signature indicative of cancer was detected, predicted cancer signal origin(s) informed diagnostic assessment. The primary outcome was time to, and extent of, diagnostic testing required to confirm the presence or absence of cancer. This trial is registered at ClinicalTrials.gov, NCT04241796, and is completed. FINDINGS Between Dec 12, 2019, and Dec 4, 2020, we recruited 6662 participants. 4204 (63·5%) of 6621 participants with analysable results were women, 2417 (36·5%) were men, and 6071 (91·7%) were White. A cancer signal was detected in 92 (1·4%) of 6621 participants with analysable results. 35 (38%) participants were diagnosed with cancer (true positives) and 57 (62%) had no cancer diagnosis (false positives). Excluding two participants whose diagnostic assessments began before MCED test results were reported, median time to diagnostic resolution was 79 days (IQR 37-219): 57 days (33-143) in true-positive and 162 days (44-248) in false-positive participants. Most participants had both laboratory tests (26 [79%] of 33 with true-positive results and 50 [88%] of 57 with false-positive results) and imaging (30 [91%] of 33 with true-positive results and 53 [93%] of 57 with false-positive results). Fewer procedures were done in participants with false-positive results (17 [30%] of 57) than true-positive results (27 [82%] of 33) and few had surgery (one with a false-positive result and three with a true-positive result). INTERPRETATION This study supports the feasibility of MCED screening for cancer and underscores the need for further research investigating the test's clinical utility. FUNDING GRAIL.
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Affiliation(s)
- Deb Schrag
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | | | | | | | | | - Robert Reid
- US Oncology Research, VA Cancer Specialists, Fairfax, VA, USA
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Maktabi MA, Vossaert L, Van den Veyver IB. Cell-based Noninvasive Prenatal Testing (cbNIPT)-A Review on the Current Developments and Future Prospects. Clin Obstet Gynecol 2023; 66:636-648. [PMID: 37650673 PMCID: PMC10491429 DOI: 10.1097/grf.0000000000000798] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Considering the diagnostic limitations of cfDNA-based noninvasive prenatal testing (NIPT), scientists have long been interested in isolating and analyzing rare intact fetal and trophoblast cells from maternal blood or endocervical samples to diagnose fetal genetic conditions. These cells may be scarce and difficult to isolate, but they are a direct source of pure fetal genetic material. In this review, we summarize the history of cell-based NIPT, present an updated review on its current developments, evaluate its genetic diagnostic potential, and discuss its future prospects for clinical use.
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Affiliation(s)
| | - Liesbeth Vossaert
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ignatia B Van den Veyver
- Department of Obstetrics and Gynecology
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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Hou F, Sun XD, Deng ZY. Diagnostic value of cell-free DNA in thyroid cancer: A systematic review and meta-analysis. Medicine (Baltimore) 2023; 102:e32928. [PMID: 36800605 PMCID: PMC9935987 DOI: 10.1097/md.0000000000032928] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
OBJECTIVE An increasing number of studies have shown the potential diagnostic value of cell-free DNA (cfDNA) as a new biomarker in the management of thyroid cancer (TC); however, the accuracy of research results is inconsistent. This meta-analysis is the first to synthesize published results and evaluate the application value of circulating cfDNA in the diagnosis of TC. METHODS A search strategy was developed according to PICO (P: Patient; I: Intervention; C: Comparison; O: Outcome) principles. We searched 5 databases until October 2022. Original studies that examined cfDNA for the diagnosis of TC and used pathology as the gold standard were included in this meta-analysis. A random-effects model was used to pool the data extracted from individual studies, including the number of patients and the numbers of true positives, false positives, true negatives, and false negatives. RESULTS A total of 622 patients with TC, 547 patients with benign thyroid nodules, and 98 healthy individuals were included in 20 studies reported in 14 articles. The types of cfDNA included in the research include specific mutations of cfDNA, methylation of cfDNA, the content of cfDNA, and cfDNA index. After rigorous statistical analysis, the pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the summary receiver operating characteristic curve were 0.76 (95% confidence interval [CI] 0.62-0.85), 0.87 (95% CI 0.78-0.93), 5.08 (95% CI 3.3-10.3), 0.28 (95% CI 0.17-0.46), 21 (95% CI 9-49), and 0.89 (95% CI 0.86-0.91), respectively. The meta-regression results showed that the number of cfDNAs, cfDNA methylation status, and sample size were the sources of heterogeneity in the specificity of the study. A subgroup analysis showed that the quantitative analysis group (cfDNA level) had a higher diagnostic accuracy than that of the qualitative analysis group (cfDNA methylation, mutation, or integrity index), with a sensitivity of 0.84, specificity of 0.89, and area under the curve of 0.91. CONCLUSIONS The results of this meta-analysis suggest that cfDNA has value as an adjunct for the diagnosis of TC. Quantitative detection of cfDNA can achieve relatively high diagnostic accuracy. However, due to heterogeneity, the test results based on cfDNA for TC should be interpreted with caution.
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Affiliation(s)
- Fei Hou
- Department of Nuclear Medicine, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming, China
| | - Xiao-Dan Sun
- Publicity Department, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming, China
| | - Zhi-Yong Deng
- Department of Nuclear Medicine, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming, China
- * Correspondence: Zhi-Yong Deng, Department of Nuclear Medicine, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming 650118, China (e-mail: )
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Michelson J, Rausser S, Peng A, Yu T, Sturm G, Trumpff C, Kaufman BA, Rai AJ, Picard M. MitoQuicLy: a high-throughput method for quantifying cell-free DNA from human plasma, serum, and saliva. bioRxiv 2023:2023.01.04.522744. [PMID: 36711938 PMCID: PMC9882007 DOI: 10.1101/2023.01.04.522744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Circulating cell-free mitochondrial DNA (cf-mtDNA) is an emerging biomarker of psychobiological stress and disease which predicts mortality and is associated with various disease states. To evaluate the contribution of cf-mtDNA to health and disease states, standardized high-throughput procedures are needed to quantify cf-mtDNA in relevant biofluids. Here, we describe MitoQuicLy: Mito chondrial DNA Qu antification in c ell-free samples by Ly sis. We demonstrate high agreement between MitoQuicLy and the commonly used column-based method, although MitoQuicLy is faster, cheaper, and requires a smaller input sample volume. Using 10 µL of input volume with MitoQuicLy, we quantify cf-mtDNA levels from three commonly used plasma tube types, two serum tube types, and saliva. We detect, as expected, significant inter-individual differences in cf-mtDNA across different biofluids. However, cf-mtDNA levels between concurrently collected plasma, serum, and saliva from the same individual differ on average by up to two orders of magnitude and are poorly correlated with one another, pointing to different cf-mtDNA biology or regulation between commonly used biofluids in clinical and research settings. Moreover, in a small sample of healthy women and men (n=34), we show that blood and saliva cf-mtDNAs correlate with clinical biomarkers differently depending on the sample used. The biological divergences revealed between biofluids, together with the lysis-based, cost-effective, and scalable MitoQuicLy protocol for biofluid cf-mtDNA quantification, provide a foundation to examine the biological origin and significance of cf-mtDNA to human health.
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Affiliation(s)
- Jeremy Michelson
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Shannon Rausser
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Amanda Peng
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Temmie Yu
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Gabriel Sturm
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, USA
| | - Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Brett A. Kaufman
- Center for Metabolism and Mitochondrial Medicine and the Vascular Medicine Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine
| | - Alex J. Rai
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA,Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, USA,New York State Psychiatric Institute, New York, NY, USA,Corresponding author: 1051 Riverside Drive, Kolb 4, New York, NY 10032, United States; (646) 774-5026;
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Yang A, Liu S, Yang X, Guo Z, Li J, Li X, Li Q. Uncovering Novel Prognostic Factors of Sudden Sensorineural Hearing Loss by Whole-Genome Sequencing of Cell-Free DNA. J Int Adv Otol 2022; 18:459-464. [PMID: 36349665 PMCID: PMC9682783 DOI: 10.5152/iao.2022.21493] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 05/04/2022] [Indexed: 09/17/2023] Open
Abstract
BACKGROUND Sudden sensorineural hearing loss is a common disease with several etiologic hypotheses, such as infection, vascular occlusion, inflammation, oxidative stress, etc. Studies have reported that the concentration of cell-free DNA in plasma will elevate in these situations. Former studies have reported that the whole-genome sequencing of cell-free DNA has high accuracy and sensitivity in inferring gene expressions. In this study, we plan to use the whole-genome sequencing of cell-free DNA to uncover novel prognostic factors of sudden sensorineural hearing loss and provide new insight into the clinical application of cell-free DNA. METHODS In this study, 84 sudden sensorineural hearing loss patients (47 in recovery group and 37 in no-recovery group) were enrolled. After whole-genome sequencing of the cell-free DNA, the protein-protein interaction network was constructed using the differentially expressed genes. Multinomial logistics regression analysis was used to analyze the prognostic factors of hearing improvement. RESULTS In this study, we found distinct patterns of expressed and unexpressed genes in cell-free DNA sequence read depth coverage in sudden sensorineural hearing loss patients. The top centrality hub genes IGF1, NOTCH1, APOE, FAM3C, RPS6KB1, and RELB were identified from the protein-protein interaction network. Multinomial logistics regression analysis demonstrated that the coverage patterns of 3 key differentially expressed genes (NOTCH1, APOE, and RELB) are significantly different in sudden sensorineural hearing loss with and without hearing recovery. CONCLUSION The cell-free DNA could have more applications in diverse diseases, and the coverage patterns of 3 differentially expressed genes (NOTCH1, APOE, and RELB) are independent prognostic factors of sudden sensorineural hearing loss. Their expression levels may play a critical role in the hearing improvement of sudden sensorineural hearing loss patients.
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Affiliation(s)
- Anni Yang
- Department of Otolaryngology—Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- Allergy Center, Department of Otolaryngology Head and Neck Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Siyuan Liu
- Department of Otolaryngology—Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xuexi Yang
- Institute of Antibody Engineering School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Zhiwei Guo
- Institute of Antibody Engineering School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
| | - Jingjing Li
- Department of Otolaryngology—Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiangping Li
- Department of Otolaryngology—Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Qi Li
- Department of Otolaryngology—Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
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Taner T, Bruner J, Emaumaullee J, Bonaccorsi-Riani E, Zarrinpar A. New Approaches to the Diagnosis of Rejection and Prediction of Tolerance in Liver Transplantation. Transplantation 2022; 106:1952-1962. [PMID: 35594482 PMCID: PMC9529763 DOI: 10.1097/tp.0000000000004160] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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] [Indexed: 02/04/2023]
Abstract
Immunosuppression after liver transplantation is essential for preventing allograft rejection. However, long-term drug toxicity and associated complications necessitate investigation of immunosuppression minimization and withdrawal protocols. Development of such protocols is hindered by reliance on current paradigms for monitoring allograft function and rejection status. The current standard of care for diagnosis of rejection is histopathologic assessment and grading of liver biopsies in accordance with the Banff Rejection Activity Index. However, this method is limited by cost, sampling variability, and interobserver variation. Moreover, the invasive nature of biopsy increases the risk of patient complications. Incorporating noninvasive techniques may supplement existing methods through improved understanding of rejection causes, hepatic spatial architecture, and the role of idiopathic fibroinflammatory regions. These techniques may also aid in quantification and help integrate emerging -omics analyses with current assessments. Alternatively, emerging noninvasive methods show potential to detect and distinguish between different types of rejection while minimizing risk of adverse advents. Although biomarkers have yet to replace biopsy, preliminary studies suggest that several classes of analytes may be used to detect rejection with greater sensitivity and in earlier stages than traditional methods, possibly when coupled with artificial intelligence. Here, we provide an overview of the latest efforts in optimizing the diagnosis of rejection in liver transplantation.
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Affiliation(s)
- Timucin Taner
- Departments of Surgery & Immunology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Julia Bruner
- Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Juliet Emaumaullee
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eliano Bonaccorsi-Riani
- Abdominal Transplant Unit, Cliniques Universitaires Saint Luc, Université Catholique de Louvain, Brussels, Belgium
| | - Ali Zarrinpar
- Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA
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Briggs GD, Gelzinnis S, Meakes S, King KL, Balogh ZJ. NOT ALL CELL-FREE MITOCHONDRIAL DNA IS EQUAL IN TRAUMA PATIENTS. Shock 2022; 58:231-235. [PMID: 36125357 PMCID: PMC9512242 DOI: 10.1097/shk.0000000000001969] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/20/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]
Abstract
ABSTRACT Mitochondrial DNA (mtDNA) acts as a proinflammatory damage-associated molecular pattern that stimulates innate immune activation via Toll-like receptor 9, similarly to bacterial DNA. A number of clinical studies have measured elevated cell-free mtDNA in the plasma of trauma patients, thought to originate from tissue injury and inflammatory processes; however, the magnitude of this increase, the absolute concentration, and the association with poor outcomes varies considerably across studies. Measurements of cell-free mtDNA in healthy individuals have shown that the majority of "cell-free" mtDNA (>95%) can be centrifuged/filtered from plasma in the size range of 0.45 to 5 μm, suggesting that there are larger forms of mtDNA-containing complexes in the plasma that could be considered cell-free. Whether this is true for trauma patients (and other relevant disease states) and the clinical relevance of the larger forms of mtDNA is unknown. These findings from healthy individuals also suggest that the centrifugation speeds used to generate cell-free plasma (which are rarely consistent among studies) could result in mixed populations of cell-free mtDNA that could confound associations with outcomes. We demonstrate in this study of 25 major trauma patients that the majority of the cell-free mtDNA in trauma patient plasma (>95%) is removed after centrifugation at 16,000g. Despite the larger forms of mtDNA being predominant, they do not correlate with outcomes or expected parameters such as injury/shock severity, multiple organ failure, and markers of inflammation, whereas low-molecular-weight cell-free mtDNA correlates strongly with these variables.
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Affiliation(s)
- Gabrielle D. Briggs
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Scott Gelzinnis
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Department of Traumatology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Simone Meakes
- Department of Traumatology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Kate L. King
- Department of Traumatology, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Zsolt J. Balogh
- School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
- Department of Traumatology, John Hunter Hospital, Newcastle, New South Wales, Australia
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Waldschmidt JM, Yee AJ, Vijaykumar T, Pinto Rengifo RA, Frede J, Anand P, Bianchi G, Guo G, Potdar S, Seifer C, Nair MS, Kokkalis A, Kloeber JA, Shapiro S, Budano L, Mann M, Friedman R, Lipe B, Campagnaro E, O’Donnell EK, Zhang CZ, Laubach JP, Munshi NC, Richardson PG, Anderson KC, Raje NS, Knoechel B, Lohr JG. Cell-free DNA for the detection of emerging treatment failure in relapsed/ refractory multiple myeloma. Leukemia 2022; 36:1078-1087. [PMID: 35027656 PMCID: PMC8983453 DOI: 10.1038/s41375-021-01492-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 09/20/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022]
Abstract
Interrogation of cell-free DNA (cfDNA) represents an emerging approach to non-invasively estimate disease burden in multiple myeloma (MM). Here, we examined low-pass whole genome sequencing (LPWGS) of cfDNA for its predictive value in relapsed/ refractory MM (RRMM). We observed that cfDNA positivity, defined as ≥10% tumor fraction by LPWGS, was associated with significantly shorter progression-free survival (PFS) in an exploratory test cohort of 16 patients who were actively treated on diverse regimens. We prospectively determined the predictive value of cfDNA in 86 samples from 45 RRMM patients treated with elotuzumab, pomalidomide, bortezomib, and dexamethasone in a phase II clinical trial (NCT02718833). PFS in patients with tumor-positive and -negative cfDNA after two cycles of treatment was 1.6 and 17.6 months, respectively (HR 7.6, P < 0.0001). Multivariate hazard modelling confirmed cfDNA as independent risk factor (HR 96.6, P = 6.92e-05). While correlating with serum-free light chains and bone marrow, cfDNA additionally discriminated patients with poor PFS among those with the same response by IMWG criteria. In summary, detectability of MM-derived cfDNA, as a measure of substantial tumor burden with therapy, independently predicts poor PFS and may provide refinement for standard-of-care response parameters to identify patients with poor response to treatment earlier than is currently feasible.
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Affiliation(s)
- Johannes M. Waldschmidt
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew J. Yee
- Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital, Boston, MA, USA
| | - Tushara Vijaykumar
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ricardo A. Pinto Rengifo
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Julia Frede
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Praveen Anand
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Giada Bianchi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Guangwu Guo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sayalee Potdar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles Seifer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Monica S. Nair
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Antonis Kokkalis
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jake A. Kloeber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | | | - Mason Mann
- Massachusetts General Hospital, Boston, MA, USA
| | | | - Brea Lipe
- University of Rochester, Rochester, NY, USA
| | | | - Elizabeth K. O’Donnell
- Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital, Boston, MA, USA
| | - Cheng-Zhong Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jacob P. Laubach
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Nikhil C. Munshi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Paul G. Richardson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Kenneth C. Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Noopur S. Raje
- Harvard Medical School, Boston, MA, USA,Massachusetts General Hospital, Boston, MA, USA
| | - Birgit Knoechel
- Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jens G. Lohr
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
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12
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Sundby RT, Pan A, Shern JF. Liquid biopsies in pediatric oncology: opportunities and obstacles. Curr Opin Pediatr 2022; 34:39-47. [PMID: 34840249 PMCID: PMC8727502 DOI: 10.1097/mop.0000000000001088] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Liquid biopsies have emerged as a noninvasive alternative to tissue biopsy with potential applications during all stages of pediatric oncology care. The purpose of this review is to provide a survey of pediatric cell-free DNA (cfDNA) studies, illustrate their potential applications in pediatric oncology, and to discuss technological challenges and approaches to overcome these hurdles. RECENT FINDINGS Recent literature has demonstrated liquid biopsies' ability to inform treatment selection at diagnosis, monitor clonal evolution during treatment, sensitively detect minimum residual disease following local control, and provide sensitive posttherapy surveillance. Advantages include reduced procedural anesthesia, molecular profiling unbiased by tissue heterogeneity, and ability to track clonal evolution. Challenges to wider implementation in pediatric oncology, however, include blood volume restrictions and relatively low mutational burden in childhood cancers. Multiomic approaches address challenges presented by low-mutational burden, and novel bioinformatic analyses allow a single assay to yield increasing amounts of information, reducing blood volume requirements. SUMMARY Liquid biopsies hold tremendous promise in pediatric oncology, enabling noninvasive serial surveillance with adaptive care. Already integrated into adult care, recent advances in technologies and bioinformatics have improved applicability to the pediatric cancer landscape.
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Affiliation(s)
- R Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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13
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Janovičová Ľ, Gromová B, Drobná D, Konečná B, Renczés E, Borbélyová V, Hodosy J, Celec P. Sex Difference in Plasma Deoxyribonuclease Activity in Rats. Physiol Res 2021; 70:913-920. [PMID: 34717068 PMCID: PMC8815475 DOI: 10.33549/physiolres.934766] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/14/2021] [Indexed: 11/25/2022] Open
Abstract
Extracellular DNA (ecDNA) activates immune cells and is involved in the pathogenesis of diseases associated with inflammation such as sepsis, rheumatoid arthritis or metabolic syndrome. DNA can be cleaved by deoxyribonucleases (DNases), some of which are secreted out of cells. The aim of this experiment was to describe plasma DNase activity in relation to extracellular DNA in adult rats, to analyse potential sex differences and to prove whether they are related to endogenous testosterone. Adult Lewis rats (n=28) of both sexes were included in the experiment. Male rats were gonadectomized or sham-operated and compared to intact female rats. Plasma ecDNA and DNase activity were measured using fluorometry and single radial enzyme diffusion assay, respectively. Concentrations of nuclear ecDNA and mitochondrial ecDNA were determined using real-time PCR. Females had 60% higher plasma DNase activity than males ( p=0.03). Gonadectomy did not affect plasma DNase in males. Neither the concentration of total ecDNA, nor nuclear or mitochondrial DNA in plasma differed between the groups. No significant correlations between DNase and ecDNA were found. From previous studies on mice, it was expected, that male rats will have higher DNase activity. In contrast, our study in rats showed the opposite sex difference. This sex difference seems not to be caused by endogenous testosterone. Interestingly, no sex differences were observed in plasma ecDNA suggesting a complex or missing association between plasma ecDNA and DNase. The observed sex difference in plasma DNase should be taken into account in animal models of ecDNA-associated diseases.
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Affiliation(s)
- Ľ Janovičová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia.
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14
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Dai R, Yu Y, Zhang H, Li L, Jiang Y, Liu R, Zhang H. Analysis of 17,428 pregnant women undergoing non-invasive prenatal testing for fetal chromosome in Northeast China. Medicine (Baltimore) 2021; 100:e24740. [PMID: 33578623 PMCID: PMC10545248 DOI: 10.1097/md.0000000000024740] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 11/13/2020] [Accepted: 01/16/2021] [Indexed: 11/26/2022] Open
Abstract
ABSTRACT Non-invasive prenatal testing (NIPT) is an incomparable prenatal screening technology, but we should undergo amniocentesis to confirm fetal chromosome when pregnancies receive a positive result via NIPT. We aimed to investigate the detection rate and positive predictive value of NIPT results in pregnancies from Northeast China, and to determine the reasons for false positive and false negative NIPT results.This study evaluates 17,428 singleton pregnancies had undergone NIPT detection. 202 samples were NIPT positive with the detection rate was 1.16% (202/17,428). Among all the positive samples, 160 samples (79.21%) were referred for an amniocentesis procedure to investigate the fetal chromosome. The positive predictive value of T21, T18, and T13 was found to be 75% with a 0.07% false positive rate. Positive predictive value from high to low was as follows: trisomy 21 (84.38%), followed by trisomy 18 (61.54%), autosomal abnormalities (52.94%), sex chromosomal abnormalities (38.46%), and trisomy 13 (33.33%). The positive predictive values for sex chromosome abnormalities turned out to be mosaic sex chromosome aneuploidies (83.33%), followed by XYY (57.14%), XXY (37.50%), XXX (36.36%), and Monosomy X (28.95%). Out of the 160 samples had amniocentesis, the true positive cases in trisomy 21 had a higher percentage of Z-scores compared with the false positive cases in trisomy 21 (P < .05). And the true positive cases in trisomy 18 had a significantly higher percentage of Z-scores compared with the false positive cases in trisomy 18 (P < .01).These findings indicate that the positive predictive value of T21, T18, and T13 was found to be 75% with a 0.07% false positive rate. It is worth noting that the positive predictive value of NIPT for autosomes and sex chromosomes. Moreover, if women receive a positive result via NIPT, they should pay attention to the results with undergoing further prenatal diagnosis.
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Ye P, Cai P, Xie J, Wei Y. The diagnostic accuracy of digital PCR, ARMS and NGS for detecting KRAS mutation in cell-free DNA of patients with colorectal cancer: A protocol for systematic review and meta-analysis. Medicine (Baltimore) 2020; 99:e20708. [PMID: 32590745 PMCID: PMC7328928 DOI: 10.1097/md.0000000000020708] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
INTRODUCTION Cetuximab and panitumumab have been used clinically to treat metastatic colorectal cancer for more than 15 years. Before the treatment is given, it is required to determine the KRAS mutation status since it would lead to drug resistance. Tumor tissue sample is traditionally used for cancer genotyping. In recent years, liquid biopsy sample has been intensively investigated as a surrogate for tumor tissue sample due to its non-invasiveness and better presentation of tumor heterogeneity. The aim of this study is to systematically summarize the accuracy of KRAS mutation measurement in colorectal cancer using cell-free DNA in liquid biopsy samples, with tumor tissue sample as reference (gold standard). METHODS AND ANALYSIS We will search literatures in the following databases: Pubmed, Embase, and Cochrane Library. Systemic review and meta-analysis will be performed to summarize the accuracy of KRAS mutation measurement in colorectal cancer using liquid biopsy sample, and subgroup analysis will be performed on different testing platforms, and on metastatic and non-metastatic colorectal cancer. TIMELINE This study will start on June 1, 2020, and is expected to be finished by November 1, 2020. ETHICS AND DISSEMINATION Ethical approval will not be required since the data obtained and analyzed in this study will not be on individual patients. Study results will be disseminated as an official publication in a peer-reviewed journal.Registration: PROSPERO CRD42020176682.
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Affiliation(s)
- Peng Ye
- Department of Anatomy and Histology, College of Medicine, Chengdu University
| | - Peiling Cai
- Department of Anatomy and Histology, College of Medicine, Chengdu University
| | - Jing Xie
- Department of Pathology and Clinical Laboratory, Sichuan Provincial Fourth People's Hospital
| | - Yuanyuan Wei
- Department of Physiology, College of Medicine, Chengdu University, Chengdu, China
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16
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Pairawan S, Hess KR, Janku F, Sanchez NS, Mills Shaw KR, Eng C, Damodaran S, Javle M, Kaseb AO, Hong DS, Subbiah V, Fu S, Fogelman DR, Raymond VM, Lanman RB, Meric-Bernstam F. Cell-free Circulating Tumor DNA Variant Allele Frequency Associates with Survival in Metastatic Cancer. Clin Cancer Res 2020; 26:1924-1931. [PMID: 31852833 PMCID: PMC7771658 DOI: 10.1158/1078-0432.ccr-19-0306] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 02/09/2019] [Revised: 06/13/2019] [Accepted: 12/12/2019] [Indexed: 01/05/2023]
Abstract
PURPOSE Physicians are expected to assess prognosis both for patient counseling and for determining suitability for clinical trials. Increasingly, cell-free circulating tumor DNA (cfDNA) sequencing is being performed for clinical decision making. We sought to determine whether variant allele frequency (VAF) in cfDNA is associated with prognosis. EXPERIMENTAL DESIGN We performed a retrospective analysis of 298 patients with metastatic disease who underwent clinical comprehensive cfDNA analysis and assessed association between VAF and overall survival. RESULTS cfDNA mutations were detected in 240 patients (80.5%). Median overall survival (OS) was 11.5 months. cfDNA mutation detection and number of nonsynonymous mutations (NSM) significantly differed between tumor types, being lowest in appendiceal cancer and highest in colon cancer. Having more than one NSM detected was associated with significantly worse OS (HR = 2.3; P < 0.0001). VAF was classified by quartiles, Q1 lowest, Q4 highest VAF. Higher VAF levels were associated with a significantly worse overall survival (VAF Q3 HR 2.3, P = 0.0069; VAF Q4 HR = 3.8, P < 0.0001) on univariate analysis. On multivariate analysis, VAF Q4, male sex, albumin level <3.5 g/dL, number of nonvisceral metastatic sites >0 and number of prior therapies >4 were independent predictors of worse OS. CONCLUSIONS Higher levels of cfDNA VAF and a higher number of NSMs were associated with worse OS in patients with metastatic disease. Further study is needed to determine optimal VAF thresholds for clinical decision making and the utility of cfDNA VAF as a prognostic marker in different tumor types.
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Affiliation(s)
- Seyed Pairawan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kenneth R Hess
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Filip Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nora S Sanchez
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kenna R Mills Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cathy Eng
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Senthilkumar Damodaran
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Milind Javle
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ahmed O Kaseb
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David S Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Siqing Fu
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David R Fogelman
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Abstract
INTRODUCTION Primary Central Nervous System Lymphoma (PCNSL) remains a diagnostic challenge due to the variable clinical manifestations. Liquid biopsies, particularly those involving cell-free DNA (cfDNA) from plasma, are rapidly emerging as important and minimally invasive adjuncts to traditional biopsies. However, conventional pathology may be still essential to obtain a diagnosis. PATIENT CONCERNS A 56-year-old woman presented with a progressive headache, dizziness, blurred vision, and lower limbs weakness with dysesthesia. Atypical clinical and radiological presentations, previous empirical treatment in another hospital, together with the patient's refusal to stereotactic brain biopsy made it challenging to diagnose. Her status deteriorated continuously during hospitalization. DIAGNOSIS Lumber punctual was performed, and CSF cytological analysis revealed malignancy cells with a high nuclear-cytoplasmic ratio. However, these cells were too loose to perform immunohistochemical stains. Genetic aberrations detections with CSF and peripheral blood sample were also inconclusive. We made a "cell-block" using the sedimentary cells collected from CSF collected through multiple aspirations via an Omaya reservoir. We further performed cytopathological and immunohistochemical analysis using this "cell-block," which finally confirmed the diagnosis of diffuse large-B cell PCNSL. INTERVENTIONS Intracranial chemotherapy began afterwards (MTX 15 mg and dexamethasone 5 mg, twice per weeks). OUTCOMES Unfortunately, this patient was dead 2 weeks later due to severe myelosuppression and secondary septic shock. CONCLUSION We provided "cell-block" method, which collects cell components from large amount of CSF for cytology and immunohistochemical analysis. "Cell-block" cytology can be an alternative diagnostic method in diagnosis of PCNSL.
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18
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Kaseb AO, Sánchez NS, Sen S, Kelley RK, Tan B, Bocobo AG, Lim KH, Abdel-Wahab R, Uemura M, Pestana RC, Qiao W, Xiao L, Morris J, Amin HM, Hassan MM, Rashid A, Banks KC, Lanman RB, Talasaz A, Mills-Shaw KR, George B, Haque A, Raghav KPS, Wolff RA, Yao JC, Meric-Bernstam F, Ikeda S, Kurzrock R. Molecular Profiling of Hepatocellular Carcinoma Using Circulating Cell-Free DNA. Clin Cancer Res 2019; 25:6107-6118. [PMID: 31363003 PMCID: PMC9292132 DOI: 10.1158/1078-0432.ccr-18-3341] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [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: 10/12/2018] [Revised: 02/15/2019] [Accepted: 07/25/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Molecular profiling has been used to select patients for targeted therapy and determine prognosis. Noninvasive strategies are critical to hepatocellular carcinoma (HCC) given the challenge of obtaining liver tissue biopsies. EXPERIMENTAL DESIGN We analyzed blood samples from 206 patients with HCC using comprehensive genomic testing (Guardant Health) of circulating tumor DNA (ctDNA). RESULTS A total of 153/206 (74.3%) were men; median age, 62 years (range, 18-91 years). A total of 181/206 patients had ≥1 alteration. The total number of alterations was 680 (nonunique); median number of alterations/patient was three (range, 1-13); median mutant allele frequency (% cfDNA), 0.49% (range, 0.06%-55.03%). TP53 was the common altered gene [>120 alterations (non-unique)] followed by EGFR, MET, ARID1A, MYC, NF1, BRAF, and ERBB2 [20-38 alterations (nonunique)/gene]. Of the patients with alterations, 56.9% (103/181) had ≥1 actionable alterations, most commonly in MYC, EGFR, ERBB2, BRAF, CCNE1, MET, PIK3CA, ARID1A, CDK6, and KRAS. In these genes, amplifications occurred more frequently than mutations. Hepatitis B (HBV)-positive patients were more likely to have ERBB2 alterations, 35.7% (5/14) versus 8.8% HBV-negative (P = 0.04). CONCLUSIONS This study represents the first large-scale analysis of blood-derived ctDNA in HCC in United States. The genomic distinction based on HCC risk factors and the high percentage of potentially actionable genomic alterations suggests potential clinical utility for this technology.
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Affiliation(s)
- Ahmed O Kaseb
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Nora S Sánchez
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shiraj Sen
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robin K Kelley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Benjamin Tan
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Andrea G Bocobo
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Kian H Lim
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Reham Abdel-Wahab
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Arizona Clinical Oncology Department, Assiut University Hospital, Assiut, Egypt
| | - Marc Uemura
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Wei Qiao
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lianchun Xiao
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey Morris
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hesham M Amin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Manal M Hassan
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Asif Rashid
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | - Kenna R Mills-Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bhawana George
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Abedul Haque
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kanwal P S Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert A Wolff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - James C Yao
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Funda Meric-Bernstam
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sadakatsu Ikeda
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of California San Diego, Moores Cancer Center, La Jolla, California.
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19
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Liebs S, Nonnenmacher A, Klauschen F, Keilholz U, Vecchione L. Liquid biopsy assessment of synchronous malignancies: a case report and review of the literature. ESMO Open 2019; 4:e000528. [PMID: 31555482 PMCID: PMC6735668 DOI: 10.1136/esmoopen-2019-000528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 04/28/2019] [Indexed: 12/31/2022] Open
Abstract
Assessment of patients with synchronous primary cancers and metastases is challenging, as it can be difficult to assign the metastases to the correct primary due to low differentiation, high similarity on histology or inaccessibility of tumour tissue. Systemic treatment for metastatic disease, however, needs to be directed at the leading histology or cover multiple tumour types with the same regimen. Considering the additional obstacles in cancer management, including tumour heterogeneity and clonal evolution, blood-based genomic profiling (‘liquid biopsy’) is suggested to be a useful tool to provide accessible tumour-derived biomarkers. We herein report a case of a patient with independent primary tumours of the colon and pancreas, as well as liver metastases. All lesions were resected and genotyped revealing KRAS mutations G12C and G12D in the primary tumours, respectively. The G12D mutation detected in the pancreatic tumour was retrieved in the metastasis, thus confirming the pancreatic cancer to be the origin of the liver lesions. The prevalence of the pancreatic tumour was additionally verified by the detection of the G12D variant in circulating cell-free DNA (cfDNA). This case demonstrates the utility of liquid biopsy to identify the predominant tumour burden in patients with multiple primary cancers, based on the detection of the tumour-associated gene mutation in the plasma. Serial monitoring through liquid biopsies might allow disease surveillance to guide cancer management. The review of the literature highlights the importance of liquid biopsies in personalised oncology, even though only one case report refers to the benefit of cfDNA analysis in a patient affected by synchronous primary tumours.
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Affiliation(s)
- Sandra Liebs
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany.,Charite Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Anika Nonnenmacher
- Charite Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frederick Klauschen
- German Cancer Consortium, German Cancer Research Center, Heidelberg, Germany.,Institute of Pathology, Charite University Hospital Berlin, Berlin, Germany
| | - Ulrich Keilholz
- Charite Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Loredana Vecchione
- Charite Comprehensive Cancer Center, Charité - Universitätsmedizin Berlin, Berlin, Germany
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González-Billalabeitia E, Conteduca V, Wetterskog D, Jayaram A, Attard G. Circulating tumor DNA in advanced prostate cancer: transitioning from discovery to a clinically implemented test. Prostate Cancer Prostatic Dis 2019; 22:195-205. [PMID: 30413805 PMCID: PMC6398580 DOI: 10.1038/s41391-018-0098-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [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: 06/10/2018] [Revised: 08/21/2018] [Accepted: 09/08/2018] [Indexed: 12/13/2022]
Abstract
The genomic landscape of metastatic castration-resistant prostate cancer (mCRPC) differs from that of the primary tumor and is dynamic during tumor progression. The real-time and repeated characterization of this process via conventional solid tumor biopsies is challenging. Alternatively, circulating cell-free DNA (cfDNA) containing circulating tumor DNA (ctDNA) can be obtained from patient plasma using minimally disruptive blood draws and is amenable to sequential analysis. ctDNA has high overlap with the genomic sequences of biopsies from metastases and has the advantage of being representative of multiple metastases. The availability of techniques with high sensitivity and specificity, such as next-generation sequencing (NGS) and digital PCR, has greatly contributed to the development of the cfDNA field and enabled the detection of genomic alterations at low ctDNA fractions. In mCRPC, a number of clinically relevant genomic alterations have been tracked in ctDNA, including androgen receptor (AR) aberrations, which have been shown to be associated with an adverse outcome to novel antiandrogen therapies, and alterations in homologous recombination repair (HRR) genes, which have been associated with a response to PARP inhibitors. Several clinical applications have been proposed for cfDNA analysis, including its use as a prognostic tool, as a predictive biomarker, to monitor tumor response and to identify novel mechanisms of resistance. To date, the cfDNA analysis has provided interesting results, but there is an urgent need for these findings to be confirmed in prospective clinical trials.
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Affiliation(s)
- Enrique González-Billalabeitia
- Servicio de Hematología y Oncología Médica, Hospital Universitario Morales Meseguer, IMIB-Universidad de Murcia, Murcia, 30008, Spain.
- Universidad Católica San Antonio de Murcia (UCAM), Murcia, 30107, Spain.
| | - Vincenza Conteduca
- Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST), IRCCS, Meldola, 47014, Italy
- Research Department of Oncology, University College London Cancer Institute, London, UK
| | - Daniel Wetterskog
- Research Department of Oncology, University College London Cancer Institute, London, UK
| | - Anuradha Jayaram
- Research Department of Oncology, University College London Cancer Institute, London, UK
| | - Gerhardt Attard
- Research Department of Oncology, University College London Cancer Institute, London, UK.
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21
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Labgaa I, Villacorta-Martin C, D’Avola D, Craig A, von Felden J, Martins-Filho SN, Sia D, Stueck A, Ward SC, Fiel MI, Mahajan M, Tabrizian P, Thung SN, Ang C, Friedman SL, Llovet JM, Schwartz M, Villanueva A. A pilot study of ultra-deep targeted sequencing of plasma DNA identifies driver mutations in hepatocellular carcinoma. Oncogene 2018; 37:3740-3752. [PMID: 29628508 PMCID: PMC6035113 DOI: 10.1038/s41388-018-0206-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [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: 07/04/2017] [Revised: 01/12/2018] [Accepted: 02/16/2018] [Indexed: 01/28/2023]
Abstract
Cellular components of solid tumors including DNA are released into the bloodstream, but data on circulating-free DNA (cfDNA) in hepatocellular carcinoma (HCC) are still scarce. This study aimed at analyzing mutations in cfDNA and their correlation with tissue mutations in patients with HCC. We included 8 HCC patients treated with surgical resection for whom we collected paired tissue and plasma/serum samples. We analyzed 45 specimens, including multiregional tumor tissue sampling (n = 24), peripheral blood mononuclear cells (PMBC, n = 8), plasma (n = 8) and serum (n = 5). Ultra-deep sequencing (5500× coverage) of all exons was performed in a targeted panel of 58 genes, including frequent HCC driver genes and druggable mutations. Mutations detected in plasma included known HCC oncogenes and tumor suppressors (e.g., TERT promoter, TP53, and NTRK3) as well as a candidate druggable mutation (JAK1). This approach increased the detection rates previously reported for mutations in plasma of HCC patients. A thorough characterization of cis mutations found in plasma confirmed their tumoral origin, which provides definitive evidence of the release of HCC-derived DNA fragments into the bloodstream. This study demonstrates that ultra-deep sequencing of cfDNA is feasible and can confidently detect somatic mutations found in tissue; these data reinforce the role of plasma DNA as a promising minimally invasive tool to interrogate HCC genetics.
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Affiliation(s)
- Ismail Labgaa
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Department of Visceral Surgery, Lausanne University Hospital CHUV, Switzerland
| | - Carlos Villacorta-Martin
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Delia D’Avola
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Liver Unit and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Clinica Universidad de Navarra, Pamplona, Spain
| | - Amanda Craig
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Johann von Felden
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sebastiao N. Martins-Filho
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Department of Pathology, University of Sao Paulo School of Medicine. Sao Paulo, Brazil,Department of Pathology and Laboratory Medicine, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Daniela Sia
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Ashley Stueck
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York (US),Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Stephen C. Ward
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York (US)
| | - M. Isabel Fiel
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Milind Mahajan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Parissa Tabrizian
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Department of Surgery, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Swan N. Thung
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Celina Ang
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Scott L. Friedman
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Josep M. Llovet
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Liver Cancer Translational Research Laboratory, BCLC Group, IDIBAPS, CIBEREHD, Hospital Clinic, Universitat de Barcelona, Catalonia (Spain),Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Myron Schwartz
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Department of Surgery, Icahn School of Medicine at Mount Sinai, New York (US)
| | - Augusto Villanueva
- Division of Liver Diseases, Department of Medicine, Liver Cancer Program, Tisch Cancer Institute, Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York (US),Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York (US),Correspondence should be addressed to: Augusto Villanueva, MD, PhD, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, 1425 Madison Ave, Box 1123, Room 11-70E, New York, NY 10029,
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22
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Liu L, Toung JM, Jassowicz AF, Vijayaraghavan R, Kang H, Zhang R, Kruglyak KM, Huang HJ, Hinoue T, Shen H, Salathia NS, Hong DS, Naing A, Subbiah V, Piha-Paul SA, Bibikova M, Granger G, Barnes B, Shen R, Gutekunst K, Fu S, Tsimberidou AM, Lu C, Eng C, Moulder SL, Kopetz ES, Amaria RN, Meric-Bernstam F, Laird PW, Fan JB, Janku F. Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification. Ann Oncol 2018; 29:1445-1453. [PMID: 29635542 PMCID: PMC6005020 DOI: 10.1093/annonc/mdy119] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [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] [Indexed: 12/18/2022] Open
Abstract
Background Targeted methylation sequencing of plasma cell-free DNA (cfDNA) has a potential to expand liquid biopsies to patients with tumors without detectable oncogenic alterations, which can be potentially useful in early diagnosis. Patients and methods We developed a comprehensive methylation sequencing assay targeting 9223 CpG sites consistently hypermethylated according to The Cancer Genome Atlas. Next, we carried out a clinical validation of our method using plasma cfDNA samples from 78 patients with advanced colorectal cancer, non-small-cell lung cancer (NSCLC), breast cancer or melanoma and compared results with patients' outcomes. Results Median methylation scores in plasma cfDNA samples from patients on therapy were lower than from patients off therapy (4.74 versus 85.29; P = 0.001). Of 68 plasma samples from patients off therapy, methylation scores detected the presence of cancer in 57 (83.8%), and methylation-based signatures accurately classified the underlying cancer type in 45 (78.9%) of these. Methylation scores were most accurate in detecting colorectal cancer (96.3%), followed by breast cancer (91.7%), melanoma (81.8%) and NSCLC (61.1%), and most accurate in classifying the underlying cancer type in colorectal cancer (88.5%), followed by NSCLC (81.8%), breast cancer (72.7%) and melanoma (55.6%). Low methylation scores versus high were associated with longer survival (10.4 versus 4.4 months, P < 0.001) and longer time-to-treatment failure (2.8 versus 1.6 months, P = 0.016). Conclusions Comprehensive targeted methylation sequencing of 9223 CpG sites in plasma cfDNA from patients with common advanced cancers detects the presence of cancer and underlying cancer type with high accuracy. Methylation scores in plasma cfDNA correspond with treatment outcomes.
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Affiliation(s)
- L Liu
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
| | - J M Toung
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A F Jassowicz
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Vijayaraghavan
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H Kang
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Zhang
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - K M Kruglyak
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H J Huang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T Hinoue
- Van Andel Research Institute, Grand Rapids, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H Shen
- Van Andel Research Institute, Grand Rapids, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - N S Salathia
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D S Hong
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Naing
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - V Subbiah
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S A Piha-Paul
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M Bibikova
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - G Granger
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - B Barnes
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Shen
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - K Gutekunst
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Fu
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A M Tsimberidou
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Lu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Eng
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S L Moulder
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - E S Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - F Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - P W Laird
- Van Andel Research Institute, Grand Rapids, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J-B Fan
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - F Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA.
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23
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Abstract
The diagnosis of malignant biliary strictures remains problematic, especially in the perihilar region and in primary sclerosing cholangitis (PSC). Conventional cytology obtained during endoscopic retrograde cholangiography (ERC)-guided brushings of biliary strictures is suboptimal due to limited sensitivity, albeit it remains the gold standard with a high specificity. Emerging technologies are being developed and validated to address this pressing unmet patient need. Such technologies include enhanced visualization of the biliary tree by cholangioscopy, intraductal ultrasound, and confocal laser endomicroscopy. Conventional cytology can be aided by employing complementary and advanced cytologic techniques such as fluorescent in situ hybridization (FISH), and this technique should be widely adapted. Interrogation of bile and serum by examining extracellular vesicle number and cargo, and exploiting next-generation sequencing and proteomic technologies, is also being explored. Examination of circulating cell-free deoxyribonucleic acid (cfDNA) for differentially methylated regions is a promising test which is being rigorously validated. The special expertise required for these analyses has to date hampered their validation and adaptation. Herein, we will review these emerging technologies to inform the reader of the progress made and encourage further studies, as well as adaptation of validated approaches.
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Affiliation(s)
- Sumera Rizvi
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - John Eaton
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Ju Dong Yang
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | | | - Gregory J. Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
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24
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Strickler JH, Loree JM, Ahronian LG, Parikh AR, Niedzwiecki D, Pereira AAL, McKinney M, Korn WM, Atreya CE, Banks KC, Nagy RJ, Meric-Bernstam F, Lanman RB, Talasaz A, Tsigelny IF, Corcoran RB, Kopetz S. Genomic Landscape of Cell-Free DNA in Patients with Colorectal Cancer. Cancer Discov 2018; 8:164-173. [PMID: 29196463 PMCID: PMC5809260 DOI: 10.1158/2159-8290.cd-17-1009] [Citation(s) in RCA: 195] [Impact Index Per Article: 32.5] [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: 09/08/2017] [Revised: 11/14/2017] [Accepted: 11/29/2017] [Indexed: 01/10/2023]
Abstract
"Liquid biopsy" approaches analyzing cell-free DNA (cfDNA) from the blood of patients with cancer are increasingly utilized in clinical practice. However, it is not yet known whether cfDNA sequencing from large cohorts of patients with cancer can detect genomic alterations at frequencies similar to those observed by direct tumor sequencing, and whether this approach can generate novel insights. Here, we report next-generation sequencing data from cfDNA of 1,397 patients with colorectal cancer. Overall, frequencies of genomic alterations detected in cfDNA were comparable to those observed in three independent tissue-based colorectal cancer sequencing compendia. Our analysis also identified a novel cluster of extracellular domain (ECD) mutations in EGFR, mediating resistance by blocking binding of anti-EGFR antibodies. Patients with EGFR ECD mutations displayed striking tumor heterogeneity, with 91% harboring multiple distinct resistance alterations (range, 1-13; median, 4). These results suggest that cfDNA profiling can effectively define the genomic landscape of cancer and yield important biological insights.Significance: This study provides one of the first examples of how large-scale genomic profiling of cfDNA from patients with colorectal cancer can detect genomic alterations at frequencies comparable to those observed by direct tumor sequencing. Sequencing of cfDNA also generated insights into tumor heterogeneity and therapeutic resistance and identified novel EGFR ectodomain mutations. Cancer Discov; 8(2); 164-73. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 127.
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Affiliation(s)
| | - Jonathan M Loree
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Leanne G Ahronian
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Aparna R Parikh
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | | | | | | | - W Michael Korn
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Caris Life Sciences, Phoenix, Arizona
| | - Chloe E Atreya
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | | | | | | | | | | | - Igor F Tsigelny
- University of California, San Diego, San Diego, California
- CureMatch Inc., San Diego, California
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts.
| | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, Texas.
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25
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Ortiz MV, Magnan H, Slotkin EK, Ambati SR, Chou AJ, Wexler LH, Meyers PA, Walsh MF, Heaton T, Girardi LN, Wolden SL, Price AP, Kennedy JA, Zehir A, Hameed M, Berger MF, Kentsis A, Shukla N. Intracardiac Low-grade Sarcoma Following Treatment for Ewing Sarcoma. J Pediatr Hematol Oncol 2017; 39:e443-5. [PMID: 28060130 DOI: 10.1097/MPH.0000000000000754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A 16-year-old male was diagnosed with Ewing sarcoma of the ribcage with pulmonary metastases. Six months after completion of scheduled therapy, he was found to have a new intracardiac mass, presumed recurrent Ewing sarcoma. EWSR1 fusion was not detected by droplet digital polymerase chain reaction from blood plasma. After no improvement with salvage chemotherapy, he underwent surgical resection that identified a low-grade spindle cell sarcoma. Despite the near-synchronous presentation of 2 unrelated sarcomas, extensive genomic analyses did not reveal any unifying somatic or germline mutations nor any apparent cancer predisposition. This case also highlights the potential role of utilizing plasma cell-free DNA for diagnosing tumors in locations where biopsy confers high morbidity.
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26
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Maas M, Hegemann M, Rausch S, Bedke J, Stenzl A, Todenhöfer T. Circulating tumor cells and their role in prostate cancer. Asian J Androl 2017; 21:213572. [PMID: 28836508 PMCID: PMC6337952 DOI: 10.4103/aja.aja_29_17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 02/08/2017] [Accepted: 06/02/2017] [Indexed: 12/28/2022] Open
Abstract
Circulating tumor cells (CTC) have become an important biomarker in patients with advanced prostate cancer. CTC count has been demonstrated to be a prognostic factor for overall survival in patients with metastatic castration-resistant prostate cancer (mCRPC). In localized prostate cancer, a clear correlation between CTC counts and clinicopathological risk parameters and outcome has not been observed. Currently, the focus of research is shifting from CTC enumeration towards molecular characterization of CTC leading to the discovery of markers predicting treatment response. The role of androgen receptor splice variants expressed by CTC as markers of resistance to abiraterone and enzalutamide has been assessed by various studies. The identification of CTC markers predicting treatment response represents a key step to guide the selection of treatment (e.g., abiraterone/enzalutamide vs taxanes), particularly in patients with mCRPC. As an alternative to CTC, the analysis of circulating tumor DNA has been shown to enable a noninvasive disease characterization having high potential to promote precision oncology.
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Affiliation(s)
- Moritz Maas
- Department of Urology, University Hospital Tuebingen, Hoppe-Seyler-Straße 3, Tuebingen 72076, Germany
| | - Miriam Hegemann
- Department of Urology, University Hospital Tuebingen, Hoppe-Seyler-Straße 3, Tuebingen 72076, Germany
| | - Steffen Rausch
- Department of Urology, University Hospital Tuebingen, Hoppe-Seyler-Straße 3, Tuebingen 72076, Germany
| | - Jens Bedke
- Department of Urology, University Hospital Tuebingen, Hoppe-Seyler-Straße 3, Tuebingen 72076, Germany
| | - Arnulf Stenzl
- Department of Urology, University Hospital Tuebingen, Hoppe-Seyler-Straße 3, Tuebingen 72076, Germany
| | - Tilman Todenhöfer
- Department of Urology, University Hospital Tuebingen, Hoppe-Seyler-Straße 3, Tuebingen 72076, Germany
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27
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Fujii T, Barzi A, Sartore-Bianchi A, Cassingena A, Siravegna G, Karp DD, Piha-Paul SA, Subbiah V, Tsimberidou AM, Huang HJ, Veronese S, Di Nicolantonio F, Pingle S, Vibat CRT, Hancock S, Berz D, Melnikova VO, Erlander MG, Luthra R, Kopetz ES, Meric-Bernstam F, Siena S, Lenz HJ, Bardelli A, Janku F. Mutation-Enrichment Next-Generation Sequencing for Quantitative Detection of KRAS Mutations in Urine Cell-Free DNA from Patients with Advanced Cancers. Clin Cancer Res 2017; 23:3657-3666. [PMID: 28096270 PMCID: PMC5511562 DOI: 10.1158/1078-0432.ccr-16-2592] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [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: 10/14/2016] [Revised: 12/17/2016] [Accepted: 12/19/2016] [Indexed: 02/05/2023]
Abstract
Purpose: Tumor-derived cell-free DNA (cfDNA) from urine of patients with cancer offers noninvasive biological material for detection of cancer-related molecular abnormalities such as mutations in Exon 2 of KRASExperimental Design: A quantitative, mutation-enrichment next-generation sequencing test for detecting KRASG12/G13 mutations in urine cfDNA was developed, and results were compared with clinical testing of archival tumor tissue and plasma cfDNA from patients with advanced cancer.Results: With 90 to 110 mL of urine, the KRASG12/G13 cfDNA test had an analytical sensitivity of 0.002% to 0.006% mutant copies in wild-type background. In 71 patients, the concordance between urine cfDNA and tumor was 73% (sensitivity, 63%; specificity, 96%) for all patients and 89% (sensitivity, 80%; specificity, 100%) for patients with urine samples of 90 to 110 mL. Patients had significantly fewer KRASG12/G13 copies in urine cfDNA during systemic therapy than at baseline or disease progression (P = 0.002). Compared with no changes or increases in urine cfDNA KRASG12/G13 copies during therapy, decreases in these measures were associated with longer median time to treatment failure (P = 0.03).Conclusions: A quantitative, mutation-enrichment next-generation sequencing test for detecting KRASG12/G13 mutations in urine cfDNA had good concordance with testing of archival tumor tissue. Changes in mutated urine cfDNA were associated with time to treatment failure. Clin Cancer Res; 23(14); 3657-66. ©2017 AACR.
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Affiliation(s)
- Takeo Fujii
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Afsaneh Barzi
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda and Università degli Studi di Milano, Milano, Italy
| | - Andrea Cassingena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda and Università degli Studi di Milano, Milano, Italy
| | - Giulia Siravegna
- Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Daniel D Karp
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarina A Piha-Paul
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Apostolia M Tsimberidou
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Helen J Huang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Silvio Veronese
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda and Università degli Studi di Milano, Milano, Italy
| | - Federica Di Nicolantonio
- Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | | | | | | | - David Berz
- Beverly Hills Cancer Center, Beverly Hills, California
- City of Hope, Duarte, California
| | | | | | - Rajyalakshmi Luthra
- Department of Hematopathology, Molecular Diagnostic Laboratory, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - E Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda and Università degli Studi di Milano, Milano, Italy
| | - Heinz-Josef Lenz
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | - Alberto Bardelli
- Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Torino, Italy
- Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Filip Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Myatt L, Hauth J, Leveno K, Peaceman A, Ramin S, Samuels P, Saade G, Sorokin Y, Clifton R, Reddy U, Silver R. Cell-Free Total and Fetal DNA in First Trimester Maternal Serum and Subsequent Development of Preeclampsia. Am J Perinatol 2017; 34:191-198. [PMID: 27398706 PMCID: PMC5358543 DOI: 10.1055/s-0035-1570383] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Objective The objective of this study was to assess the relationship between first trimester cell-free total and fetal DNA in maternal plasma and the subsequent development of preeclampsia. Study Design Nested case-control study of patients enrolled in the Combined Antioxidant and Preeclampsia Prediction Studies prediction study of 175 women who did and 175 women who did not develop preeclampsia. The predictive values of cell-free total and fetal DNA and the subsequent development of preeclampsia were measured using receiver operating characteristic curves. Results Cell-free total DNA was higher in African American (median; 25-75%; 6.15; 0.14-28.73; p = 0.02) and Hispanic (4.95; 0.20-26.82; p = 0.037) compared with white women (2.33; 0.03-13.10). Levels of cell-free total DNA were also associated with maternal body mass index (BMI) (p = 0.02). Cell-free total DNA levels were similar between women who later developed preeclampsia (3.52; 0.11-25.3) and controls (3.74; 0.12-21.14, p = 0.96). Conclusion There is no significant difference in levels of cell-free total DNA in the first trimester in women who subsequently develop preeclampsia. Levels of cell-free total DNA in the first trimester are increased in African American and Hispanic compared with white women, and levels increase with increasing BMI.
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Affiliation(s)
- Leslie Myatt
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - John Hauth
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Kenneth Leveno
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Alan Peaceman
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Susan Ramin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Philip Samuels
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - George Saade
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Yoram Sorokin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Rebecca Clifton
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Uma Reddy
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
| | - Robert Silver
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, Maternal-Fetal Medicine Units Network, Bethesda, Maryland
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Kristiansen MK, Niemann I, Lindegaard JC, Christiansen M, Joergensen MW, Vogel I, Lildballe DL, Sunde L. Cell-free DNA in pregnancy with choriocarcinoma and coexistent live fetus: A case report. Medicine (Baltimore) 2016; 95:e4721. [PMID: 27631219 PMCID: PMC5402562 DOI: 10.1097/md.0000000000004721] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND This case report describes the use of analysis of cell-free DNA in the blood of a patient with a pregnancy with one live fetus and a choriocarcinoma diagnosed at 22 weeks of gestation. RESULTS The result of the analysis of 16 microsatellite loci on 14 chromosomes in the cell-free DNA in plasma was consistent with the result of the analysis of a tumor biopsy indicating biparental diploid origin of the genome. The DNA markers were discordant with the markers of the placenta indicating two separate conceptions. CONCLUSION Our results indicate that analysis of cell-free DNA in plasma allows determination of the origin of a choriocarcinoma without tissue biopsy, even in the presence of a co-existent pregnancy.
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Affiliation(s)
- Mona Kjaerboel Kristiansen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus N
- Correspondence: Mona Kristiansen, Department of Clinical Genetics, Aarhus University Hospital, Brendstrupgaardsvej 21 C, Skejby, DK-8200 Aarhus N, Denmark (e-mail: )
| | - Isa Niemann
- Department of Gynecology and Obstetrics, Aarhus University Hospital, Aarhus N
| | | | | | - Mette Warming Joergensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus N
- Institute of Pathology, Aarhus University Hospital, Aarhus C
| | - Ida Vogel
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus N
| | | | - Lone Sunde
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus N
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
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Abstract
Papillary craniopharyngioma (PCP) is an intracranial tumor that results in high levels of morbidity. We recently demonstrated that the vast majority of these tumors harbor the oncogenic BRAF V600E mutation. The pathologic diagnosis of PCP can now be confirmed using mutation specific immunohistochemistry and targeted genetic testing. Treatment with targeted agents is now also a possibility in select situations. We recently reported a patient with a multiply recurrent PCP in whom targeting both BRAF and MEK resulted in a dramatic therapeutic response with a marked anti-tumor immune response. This work shows that activation of the MAPK pathway is the likely principal oncogenic driver of these tumors. We will now investigate the efficacy of this approach in a multicenter phase II clinical trial. Post-treatment resection samples will be monitored for the emergence of resistance mechanisms. Further advances in the non-invasive diagnosis of PCP by radiologic criteria and by cell-free DNA testing could someday allow neo-adjuvant therapy for this disease in select patient populations.
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Affiliation(s)
- Priscilla K Brastianos
- Division of Neuro-OncologyMassachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USADepartment of Cancer BiologyDana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USADepartment of PathologyBrigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USADepartment of PathologyBoston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Sandro Santagata
- Division of Neuro-OncologyMassachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USADepartment of Cancer BiologyDana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USADepartment of PathologyBrigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USADepartment of PathologyBoston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA Division of Neuro-OncologyMassachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USADepartment of Cancer BiologyDana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USADepartment of PathologyBrigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USADepartment of PathologyBoston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA Division of Neuro-OncologyMassachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USADepartment of Cancer BiologyDana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02215, USADepartment of PathologyBrigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USADepartment of PathologyBoston Children's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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Neufeld-Kaiser WA, Cheng EY, Liu YJ. Positive predictive value of non-invasive prenatal screening for fetal chromosome disorders using cell-free DNA in maternal serum: independent clinical experience of a tertiary referral center. BMC Med 2015; 13:129. [PMID: 26033224 PMCID: PMC4480508 DOI: 10.1186/s12916-015-0374-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 05/18/2015] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Non-invasive prenatal screening (NIPS) for fetal chromosome abnormalities using cell-free deoxyribonucleic acid (cfDNA) in maternal serum has significantly influenced prenatal diagnosis of fetal aneuploidies since becoming clinically available in the fall of 2011. High sensitivity and specificity have been reported in multiple publications, nearly all of which have been sponsored by the commercial performing laboratories. Once results are returned, positive and negative predictive values (PPVs, NPVs) are the performance metrics most relevant to clinical management. The purpose of this report is to present independent data on the PPVs of NIPS in actual clinical practice. METHODS Charts were retrospectively reviewed for patients who had NIPS and were seen March 2012 to December 2013 in a tertiary academic referral center. NIPS results were compared to diagnostic genetic test results, fetal ultrasound results, and clinical phenotype/outcomes. The PPV was calculated using standard epidemiological methods. Correlation between screen results and both maternal age at delivery and gestational age at time of screening was assessed using Wilcoxon's rank sum test. RESULTS Of 632 patients undergoing NIPS, 92 % of tests were performed in one of the four major commercial laboratories offering testing. However, all four laboratories are represented in both the normal and abnormal results groups. There were 55 abnormal NIPS results. Forty-one of 55 abnormal NIPS results were concordant with abnormal fetal outcomes, 12 were discordant, and 2 were undetermined. The PPV for all conditions included in the screen was 77.4 % (95 % CI, 63.4 - 87.3). Of 578 patients with normal NIPS results, normal pregnancy outcome was confirmed for 156 (27 %) patients. This incomplete follow-up of normal NIPS results does not affect PPV calculations, but it did preclude calculations of sensitivity, specificity, and NPV. Maternal age at delivery was significantly lower for patients with abnormal discordant results, compared to patients with abnormal concordant results (P = 0.034). Gestational age at time of screening was not associated with concordance of screen results (P = 0.722). CONCLUSIONS The experience of using NIPS in clinical practice confirms that abnormal results cannot be considered diagnostic. Pre-test counseling should emphasize this. Diagnostic genetic testing should always be offered following abnormal NIPS results.
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Affiliation(s)
- Whitney A Neufeld-Kaiser
- Department of Pathology, Cytogenetics and Genomics Laboratory, University of Washington School of Medicine, Box 357470, HSB H474B, 1959 NE Pacific Street, Seattle, WA, 98195-7470, USA.
| | - Edith Y Cheng
- Maternal Fetal Medicine and Medical Genetics, Departments of Obstetrics and Gyencology and Internal Medicine, University of Washington School of Medicine, Seattle, WA, USA.
| | - Yajuan J Liu
- Department of Pathology, Cytogenetics and Genomics Laboratory, University of Washington School of Medicine, Box 357470, HSB H474B, 1959 NE Pacific Street, Seattle, WA, 98195-7470, USA.
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Haghiac M, Vora NL, Basu S, Johnson KL, Presley L, Bianchi DW, Hauguel-de Mouzon S. Increased death of adipose cells, a path to release cell-free DNA into systemic circulation of obese women. Obesity (Silver Spring) 2012; 20:2213-9. [PMID: 22836687 PMCID: PMC3483388 DOI: 10.1038/oby.2012.138] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Remodeling of adipose tissue is required to support the expansion of adipose mass. In obesity, an increased death of adipocytes contributes to the accelerated cellular turnover. We have shown that obesity in pregnancy is associated with metabolic and immune alterations in the adipose tissue. In this study, we characterized the mechanisms responsible for increased death of adipose cells of pregnant obese women and its functional consequences. We postulated that a higher turnover of dead cells in white adipose tissue of obese women would translate into release of cell-free DNA (cfDNA) into their systemic circulation. Increase in adipose mass of obese compared to lean women results from a lesser number of hypertrophic adipocytes and an accumulation of macrophages in the stromal vascular fraction (SVF). The adipocytes of obese displayed enhanced necrosis with a loss of perilipin staining at the plasma membrane. Apoptosis was prominent in SVF cells with an increased expression of caspase 9 and caspase 3 and a higher rate of terminal deoxynucleotidyl transferase-mediated deoxyuridine triphosphate nick end-labeling (TUNEL) positive CD68 macrophages in obese vs. lean. Whereas circulating fetal cfDNA concentrations were not changed, there was a twofold increase in circulating glyceraldehyde-3-phosphate dehydrogenase (GAPDH) cfDNA and adipose tissue GAPDH mRNA in obese women. The maternal systemic GAPDH cfDNA was positively correlated with BMI and gestational weight gain. These data suggest that the active remodeling of adipose tissue of obese pregnant women results in an increased release of cfDNA of maternal origin into the circulation.
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Affiliation(s)
- Maricela Haghiac
- Department of Obstetrics and Gynecology, MetroHealth Medical Center Case Western Reserve University, Cleveland, Ohio, USA
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Benirschke K, Willes L. Deportation of trophoblastic emboli to maternal lung: A source of cell-free DNA in maternal blood? Chimerism 2010; 1:15-8. [PMID: 21327145 PMCID: PMC3035106 DOI: 10.4161/chim.1.1.12140] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 04/06/2010] [Accepted: 04/23/2010] [Indexed: 11/19/2022]
Abstract
During human pregnancy there is a continuous transport of numerous syncytiotrophoblastic cells from the intervillous space of the placenta into the maternal lung. There these cells undergo apoptosis and the fetal nuclear DNA is liberated within the pulmonary capillaries to become cffDNA in the maternal serum. We have examined the sections of lungs of 11 pregnant women (from 8 weeks to term gestation) who had come to the Medical Examiner's Offices after their traumatic demise. We then identified the deported, embolized trophoblastic cells in pulmonary capillaries and attempted to show them to contain hCG immunohistochemically but were unable to do this. We also determined their apoptotic profiles by TUNEL reaction.
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Affiliation(s)
- Kurt Benirschke
- Professor of Pathology and Reproductive Medicine; Resident in Pathology; UCSD; Department of Pathology; University of California Medical Center; San Diego, CA USA
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