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Wang D, Zhang Z, Shen H, Jin F, Liang J, Shen D, Song H, Zhang J, Xu W, Tang Y, Xu X. Comparison of plasma and blood cell samples in metagenomic next-generation sequencing for identification of the causative pathogens of fever. Heliyon 2024; 10:e31677. [PMID: 38841453 PMCID: PMC11152940 DOI: 10.1016/j.heliyon.2024.e31677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) of plasma DNA has become an attractive diagnostic method for infectious diseases; however, the rate of false-positive results is high. This study aims to evaluate the diagnostic accuracy of mNGS in plasma versus blood cell samples for immunocompromised children with febrile diseases. Methods The results of conventional microbiological test (CMT) and mNGS using plasma and blood cells in 106 patients with 128 episodes of febrile diseases from the Department of Hematology/Oncology were analyzed and described. Results The positivity rates for CMT and mNGS of plasma and blood cells were 35.9 %, 84.4 % and 46.9 %, respectively (P < 0.001). Notably, mNGS identified multiple pathogens in a single specimen in 68.5 % of plasma samples and 38.3 % of blood cell samples (P < 0.001). Furthermore, plasma and blood cell mNGS identified causative pathogens in 58 and 46 cases, accounting for 53.7 % and 76.7 % of the mNGS-positive cases for each sample type, respectively (P = 0.002). By integrating results from both plasma and blood cell samples, causative pathogens were identified in 77 cases (60.2 %), enhancing sensitivity to 87.5 % but reducing specificity to 15.0 %, compared to plasma (65.9 % sensitivity and 20.0 % specificity) and blood cell samples (52.3 % sensitivity and 80.0 % specificity). Conclusions mNGS of plasma is sensitive but has a high false-positive rate, while mNGS of blood cells has low sensitivity but higher specificity.
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Affiliation(s)
- Di Wang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Zihan Zhang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
| | - Heping Shen
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Fenfen Jin
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Juan Liang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Diying Shen
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Hua Song
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Jingying Zhang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Weiqun Xu
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Yongmin Tang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Xiaojun Xu
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
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David D, Das M, Mani Chandra H. A comparative study on the detection of Mycobacterium leprae DNA in urine samples of leprosy patients using Rlep-PCR with other conventional samples. Mol Biol Rep 2024; 51:504. [PMID: 38616219 DOI: 10.1007/s11033-024-09470-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 03/22/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND Mycobacterium leprae causes leprosy that is highly stigmatized and chronic infectious skin disease. Only some diagnostic tools are being used for the identification M. leprae in clinical samples, such as bacillary detection, and histopathological tests. These methods are invasive and often have low sensitivity. Currently, the PCR technique has been used as an effective tool fordetecting M. leprae DNA across different clinical samples. The current study aims to detect M. leprae DNA in urine samples of untreated and treated leprosy patients using the Rlep gene (129 bp) and compared the detection among Ridley-Jopling Classification. METHODS Clinical samples (Blood, Urine, and Slit Skin Smears (SSS)) were collected from leprosy and Non-leprosy patients. DNA extraction was performed using standard laboratory protocol and Conventional PCR was carried out for all samples using Rlep gene target and the amplicons of urine samples were sequenced by Sanger sequencing to confirm the Rlep gene target. RESULTS The M. leprae DNA was successfully detected in all clinical samples across all types of leprosy among all the study groups using RLEP-PCR. Rlep gene target was able to detect the presence of M. leprae DNA in 79.17% of urine, 58.33% of blood, and 50% of SSS samples of untreated Smear-Negative leprosy patients. The statistical significant difference (p = 0.004) was observed between BI Negative (Slit Skin Smear test) and RLEP PCR positivity in urine samples of untreated leprosy group. CONCLUSION The PCR positivity using Rlep gene target (129 bp) was highest in all clinical samples among the study groups, across all types of leprosy. Untreated tuberculoid and PNL leprosy patients showed the highest PCR positivity in urine samples, indicating its potential as a non-invasive diagnostic tool for leprosy and even for contact screening.
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Affiliation(s)
- Diana David
- Molecular Biology and Immunology, Schieffelin Institute of Health Research and Leprosy Centre, Karigiri, Vellore, Tamil Nadu, 632106, India
- Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamil Nadu, 632115, India
| | - Madhusmita Das
- Molecular Biology and Immunology, Schieffelin Institute of Health Research and Leprosy Centre, Karigiri, Vellore, Tamil Nadu, 632106, India
| | - Harish Mani Chandra
- Department of Biotechnology, Thiruvalluvar University, Serkkadu, Vellore, Tamil Nadu, 632115, India.
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Gonzalez T, Nie Q, Chaudhary LN, Basel D, Reddi HV. Methylation signatures as biomarkers for non-invasive early detection of breast cancer: A systematic review of the literature. Cancer Genet 2024; 282-283:1-8. [PMID: 38134587 DOI: 10.1016/j.cancergen.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
BACKGROUND Early detection of breast cancer would help alleviate the burden of treatment for early-stage breast cancer and help patient prognosis. There is currently no established gene panel that utilizes the potential of DNA methylation as a molecular signature for the early detection of breast cancer. This systematic review aims to identify the optimal methylation biomarkers for a non-invasive liquid biopsy assay and the gaps in knowledge regarding biomarkers for early detection of breast cancer. METHODS Following the PRISMA-ScR method, Pubmed and Google Scholar was searched for publications related to methylation biomarkers in breast cancer over a five-year period. Eligible publications were mined for key data fields such as study aims, cohort demographics, types of breast cancer studied, technologies used, and outcomes. Data was analyzed to address the objectives of the review. RESULTS Literature search identified 112 studies of which based on eligibility criteria, 13 studies were included. 28 potential methylation gene targets were identified, of which 23 were methylated at the promoter region, 1 was methylated in the body of the gene and 4 were methylated at yet to be identified locations. CONCLUSIONS Our evaluation shows that at minimum APC, RASSFI, and FOXA1 genes would be a promising set of genes to start with for the early detection of breast cancer, based on the sensitivity and specificity outlined in the studies. Prospective studies are needed to optimize biomarkers for broader impact in early detection of breast cancer.
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Affiliation(s)
- Tessa Gonzalez
- Division of Precision Medicine and Cytogenetics, Department of Pathology, Medical College of Wisconsin, CT, USA
| | - Qian Nie
- Division of Precision Medicine and Cytogenetics, Department of Pathology, Medical College of Wisconsin, CT, USA
| | - Lubna N Chaudhary
- Division of Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, CT, USA
| | - Donald Basel
- Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, CT, USA
| | - Honey V Reddi
- Division of Precision Medicine and Cytogenetics, Department of Pathology, Medical College of Wisconsin, CT, USA.
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Wang H, Wang Y, Zhang D, Li P. Circulating nucleosomes as potential biomarkers for cancer diagnosis and treatment monitoring. Int J Biol Macromol 2024; 262:130005. [PMID: 38331061 DOI: 10.1016/j.ijbiomac.2024.130005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/03/2024] [Accepted: 02/04/2024] [Indexed: 02/10/2024]
Abstract
Nucleosomes play a crucial role in regulating gene expression through their composition and post-translational modifications. When cells die, intracellular endonucleases are activated and cleave chromatin into oligo- and mono-nucleosomes, which are then released into the body fluids. Studies have shown that the levels of nucleosomes are increased in serum and plasma in various cancer types, suggesting that analysis of circulating nucleosomes can provide an initial assessment of carcinogenesis. However, it should be noted that elevated serum nucleosome levels may not accurately diagnose certain tumor types, as increased cell death may occur in different pathological conditions. Nevertheless, detection of circulating nucleosomes and their histone modifications, along with specific tumor markers, can help diagnose certain types of cancer. Furthermore, monitoring changes in circulating nucleosome levels during chemotherapy or radiotherapy in patients with malignancies can provide valuable insights into clinical outcomes and therapeutic efficacy. The utilization of circulating nucleosomes as biomarkers is an exciting and emerging area of research, with the potential for early detection of various diseases and monitoring of treatment response. Integrating nucleosome-based biomarkers with existing ones may improve the specificity and sensitivity of current assays, offering the possibility of personalized precision medical treatment for patients.
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Affiliation(s)
- Huawei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, 1 Ningde Road, Qingdao 266073, China.
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Igder S, Zamani M, Fakher S, Siri M, Ashktorab H, Azarpira N, Mokarram P. Circulating Nucleic Acids in Colorectal Cancer: Diagnostic and Prognostic Value. DISEASE MARKERS 2024; 2024:9943412. [PMID: 38380073 PMCID: PMC10878755 DOI: 10.1155/2024/9943412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/07/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer in the world and the fourth leading cause of cancer-related mortality. DNA (cfDNA/ctDNA) and RNA (cfRNA/ctRNA) in the blood are promising noninvasive biomarkers for molecular profiling, screening, diagnosis, treatment management, and prognosis of CRC. Technological advancements that enable precise detection of both genetic and epigenetic abnormalities, even in minute quantities in circulation, can overcome some of these challenges. This review focuses on testing for circulating nucleic acids in the circulation as a noninvasive method for CRC detection, monitoring, detection of minimal residual disease, and patient management. In addition, the benefits and drawbacks of various diagnostic techniques and associated bioinformatics tools have been detailed.
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Affiliation(s)
- Somayeh Igder
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Fakher
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division and Cancer Center, Howard University College of Medicine, Washington, DC, USA
| | - Negar Azarpira
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokarram
- Autophagy Research Center, Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
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Chen H, Zheng Y, Zhang X, Liu S, Yin Y, Guo Y, Wang X, Zhang Y, Zhao C, Gai W, Wang H. Clinical evaluation of cell-free and cellular metagenomic next-generation sequencing of infected body fluids. J Adv Res 2024; 55:119-129. [PMID: 36889461 PMCID: PMC10770109 DOI: 10.1016/j.jare.2023.02.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/14/2023] [Accepted: 02/26/2023] [Indexed: 03/08/2023] Open
Abstract
INTRODUCTION Previous studies have evaluated metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) for pathogen detection in blood and body fluid samples. However, no study has assessed the diagnostic efficacy of mNGS using cellular DNA. OBJECTIVES This is the first study to systematically evaluate the efficacy of cfDNA and cellular DNA mNGS for pathogen detection. METHODS A panel of seven microorganisms was used to compare cfDNA and cellular DNA mNGS assays concerning limits of detection (LoD), linearity, robustness to interference, and precision. In total, 248 specimens were collected between December 2020 and December 2021. The medical records of all the patients were reviewed. These specimens were analysed using cfDNA and cellular DNA mNGS assays, and the mNGS results were confirmed using viral qPCR, 16S rRNA, and internal transcribed spacer (ITS) amplicon next-generation sequencing. RESULTS The LoD of cfDNA and cellular DNA mNGS was 9.3 to 149 genome equivalents (GE)/mL and 27 to 466 colony-forming units (CFU)/mL, respectively. The intra- and inter-assay reproducibility of cfDNA and cellular DNA mNGS was 100%. Clinical evaluation revealed that cfDNA mNGS was good at detecting the virus in blood samples (receiver operating characteristic (ROC) area under the curve (AUC), 0.9814). In contrast, the performance of cellular DNA mNGS was better than that of cfDNA mNGS in high host background samples. Overall, the diagnostic efficacy of cfDNA combined with cellular DNA mNGS (ROC AUC, 0.8583) was higher than that of cfDNA (ROC AUC, 0.8041) or cellular DNA alone (ROC AUC, 0.7545). CONCLUSION Overall, cfDNA mNGS is good for detecting viruses, and cellular DNA mNGS is suitable for high host background samples. The diagnostic efficacy was higher when cfDNA and cellular DNA mNGS were combined.
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Affiliation(s)
- Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yafeng Zheng
- WillingMed Technology (Beijing) Co., Ltd, Beijing, China
| | - Xiaoyang Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Si Liu
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yifan Guo
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Xiaojuan Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Yawei Zhang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Chunjiang Zhao
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China
| | - Wei Gai
- WillingMed Technology (Beijing) Co., Ltd, Beijing, China.
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, China.
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Buckley DN, Lewinger JP, Gooden G, Spillman M, Neuman M, Guo XM, Tew BY, Miller H, Khetan VU, Shulman LP, Roman L, Salhia B. OvaPrint-A Cell-free DNA Methylation Liquid Biopsy for the Risk Assessment of High-grade Serous Ovarian Cancer. Clin Cancer Res 2023; 29:5196-5206. [PMID: 37812492 PMCID: PMC10722131 DOI: 10.1158/1078-0432.ccr-23-1197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/08/2023] [Accepted: 10/05/2023] [Indexed: 10/10/2023]
Abstract
PURPOSE High-grade serous ovarian carcinoma (HGSOC) is the most lethal epithelial ovarian cancer (EOC) and is often diagnosed at late stage. In women with a known pelvic mass, surgery followed by pathologic assessment is the most reliable way to diagnose EOC and there are still no effective screening tools in asymptomatic women. In the current study, we developed a cell-free DNA (cfDNA) methylation liquid biopsy for the risk assessment of early-stage HGSOC. EXPERIMENTAL DESIGN We performed reduced representation bisulfite sequencing to identify differentially methylated regions (DMR) between HGSOC and normal ovarian and fallopian tube tissue. Next, we performed hybridization probe capture for 1,677 DMRs and constructed a classifier (OvaPrint) on an independent set of cfDNA samples to discriminate HGSOC from benign masses. We also analyzed a series of non-HGSOC EOC, including low-grade and borderline samples to assess the generalizability of OvaPrint. A total of 372 samples (tissue n = 59, plasma n = 313) were analyzed in this study. RESULTS OvaPrint achieved a positive predictive value of 95% and a negative predictive value of 88% for discriminating HGSOC from benign masses, surpassing other commercial tests. OvaPrint was less sensitive for non-HGSOC EOC, albeit it may have potential utility for identifying low-grade and borderline tumors with higher malignant potential. CONCLUSIONS OvaPrint is a highly sensitive and specific test that can be used for the risk assessment of HGSOC in symptomatic women. Prospective studies are warranted to validate OvaPrint for HGSOC and further develop it for non-HGSOC EOC histotypes in both symptomatic and asymptomatic women with adnexal masses.
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Affiliation(s)
- David N. Buckley
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Juan Pablo Lewinger
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California
| | - Gerald Gooden
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Monique Spillman
- Division of Gynecologic Oncology, Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Monica Neuman
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - X. Mona Guo
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Ben Yi Tew
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Heather Miller
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Varun U. Khetan
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Lee P. Shulman
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Lynda Roman
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Keck School of Medicine of University of Southern California, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Los Angeles, California
| | - Bodour Salhia
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, California
- USC Norris Comprehensive Cancer Center, Los Angeles, California
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Wu C, Yu X, Gai W, Liu Y, Qi Y, Zheng Y, Zhang N, Cai X, Li G, Chen B. Diagnostic value of plasma and blood cells metagenomic next-generation sequencing in patients with sepsis. Biochem Biophys Res Commun 2023; 683:149079. [PMID: 37871447 DOI: 10.1016/j.bbrc.2023.10.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/25/2023] [Accepted: 10/02/2023] [Indexed: 10/25/2023]
Abstract
BACKGROUND Several studies have investigated the detection of plasma cell-free DNA (cfDNA) using metagenomic next-generation sequencing (mNGS). However, to our knowledge, no study has evaluated the diagnostic value of mNGS detection using blood cells. In this study, we aimed to evaluate the performance of a whole blood mNGS assay which includes the results of plasma and blood cells mNGS detection. METHODS We selected a panel of seven microorganisms to validate both the plasma and blood cells assay for their limits of detection (LoD), linearity, precision, and robustness to interference. In a multicentered prospective study conducted from January 2021 to April 2022, we tested 253 septic patients with plasma and blood cells mNGS and compared it with blood cultures (BCs). The performance of pathogen detection was compared between mNGS and BCs. RESULTS The LoD for plasma and blood cells mNGS was 8.3-140 genome equivalents (GE)/mL and 26 to 534 colony-forming units (CFU) or copies/mL, respectively. The inter- and intra-assay reproducibility of both plasma and blood cells mNGS was 100%. Compared to plasma mNGS alone, the sensitivity of whole blood mNGS was increased by 18.04% when using BCs as the standard (67.21% vs 85.25%). Furthermore, the sensitivity of whole blood mNGS in diagnosing bloodstream infections (BSIs) was 85.21%, which was significantly higher than that of BCs (36.09%, P<0.0001) and plasma mNGS (69.82%; P = 0.0007). Additional analysis showed that blood cells mNGS was able to detect bacteria missed by plasma mNGS, while plasma mNGS was effective at detecting viruses. CONCLUSIONS Our findings indicate that whole blood mNGS shows great potential as a promising diagnostic technique for BSIs owing to its ability to identify pathogens with higher sensitivity.
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Affiliation(s)
- Chen Wu
- Department of Emergency Medicine, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Xin Yu
- Department of Respiratory and Critical Care Medicine, Characteristic Medical Center of Chinese People's Armed Police Forces, Tianjin 300162, China
| | - Wei Gai
- WillingMed Technology (Beijing) Co., Ltd, Beijing, China
| | - Yanxia Liu
- Intensive Care Unit, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Ying Qi
- Intensive Care Unit, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Yafeng Zheng
- WillingMed Technology (Beijing) Co., Ltd, Beijing, China
| | - Na Zhang
- Department of Respiratory and Critical Care Medicine, Characteristic Medical Center of Chinese People's Armed Police Forces, Tianjin 300162, China
| | - Xianglong Cai
- Department of Respiratory and Critical Care Medicine, Characteristic Medical Center of Chinese People's Armed Police Forces, Tianjin 300162, China
| | - Guoqiang Li
- Department of Respiratory and Critical Care Medicine, Characteristic Medical Center of Chinese People's Armed Police Forces, Tianjin 300162, China.
| | - Bing Chen
- Department of Emergency Medicine, The Second Hospital of Tianjin Medical University, Tianjin 300211, China; Intensive Care Unit, The Second Hospital of Tianjin Medical University, Tianjin 300211, China.
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Keup C, Kimmig R, Kasimir-Bauer S. The Diversity of Liquid Biopsies and Their Potential in Breast Cancer Management. Cancers (Basel) 2023; 15:5463. [PMID: 38001722 PMCID: PMC10670968 DOI: 10.3390/cancers15225463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Analyzing blood as a so-called liquid biopsy in breast cancer (BC) patients has the potential to adapt therapy management. Circulating tumor cells (CTCs), extracellular vesicles (EVs), cell-free DNA (cfDNA) and other blood components mirror the tumoral heterogeneity and could support a range of clinical decisions. Multi-cancer early detection tests utilizing blood are advancing but are not part of any clinical routine yet. Liquid biopsy analysis in the course of neoadjuvant therapy has potential for therapy (de)escalation.Minimal residual disease detection via serial cfDNA analysis is currently on its way. The prognostic value of blood analytes in early and metastatic BC is undisputable, but the value of these prognostic biomarkers for clinical management is controversial. An interventional trial confirmed a significant outcome benefit when therapy was changed in case of newly emerging cfDNA mutations under treatment and thus showed the clinical utility of cfDNA analysis for therapy monitoring. The analysis of PIK3CA or ESR1 variants in plasma of metastatic BC patients to prescribe targeted therapy with alpesilib or elacestrant has already arrived in clinical practice with FDA-approved tests available and is recommended by ASCO. The translation of more liquid biopsy applications into clinical practice is still pending due to a lack of knowledge of the analytes' biology, lack of standards and difficulties in proving clinical utility.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45147 Essen, Germany
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Kanaujia R, Sharma V, Biswal M, Singh S, Ray P, Angrup A. Microbial cell-free DNA detection: Minimally invasive diagnosis of infectious diseases. Indian J Med Microbiol 2023; 46:100433. [PMID: 37945127 DOI: 10.1016/j.ijmmb.2023.100433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 07/07/2023] [Accepted: 07/19/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Detection of infectious diseases, especially among immunocompromised and patients on prolonged anti-microbial treatment, remains challenging, limited by conventional techniques with low sensitivity and long-turnaround time. Molecular detection by polymerase chain reaction (PCR) also has limited utility as it requires a targeted approach with prior suspicion of the infecting organism. Advancements in sequencing methodologies, specifically next-generation sequencing (NGS), have presented a promising opportunity to identify pathogens in cases where conventional techniques may be inadequate. However, the direct application of these techniques for diagnosing invasive infections is still limited by the need for invasive sampling, highlighting the pressing need to develop and implement non-invasive or minimally invasive approaches to improve the diagnosis of invasive infections. OBJECTIVES The objectives of this article are to explore the notable features, clinical utility, and constraints associated with the detection of microbial circulating cell-free DNA (mcfDNA) as a minimally invasive diagnostic tool for infectious diseases. CONTENT The mcfDNA detection provides an opportunity to identify micro-organisms in the blood of a patient. It is especially beneficial in immunocompromised patients where invasive sampling is not possible or where repeated cultures are negative. This review will discuss the applications and constraints of detecting mcfDNA for diagnosing infections and the various platforms available for its detection.
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Affiliation(s)
| | - Vikas Sharma
- Department of Medical Microbiology, PGIMER, Chandigarh, India
| | - Manisha Biswal
- Department of Medical Microbiology, PGIMER, Chandigarh, India
| | - Shreya Singh
- Department of Medical Microbiology, AIMS, Mohali, India
| | - Pallab Ray
- Department of Medical Microbiology, PGIMER, Chandigarh, India
| | - Archana Angrup
- Department of Medical Microbiology, PGIMER, Chandigarh, India.
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Sharma P, Gupta RK, Anthwal D, Dass M, Yadav R, Behera A, Sethi S, Singhal R, Dhooria S, Aggarwal AN, Haldar S. Evaluation of Mycobacterium tuberculosis derived cell-free DNA using pleural fluid and paired plasma samples for the diagnosis of pleural tuberculosis. Tuberculosis (Edinb) 2023; 142:102369. [PMID: 37536090 DOI: 10.1016/j.tube.2023.102369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/13/2023] [Accepted: 06/25/2023] [Indexed: 08/05/2023]
Abstract
Pleural tuberculosis (pTB) is a grave clinical challenge. A novel cell-free M. tuberculosis DNA (cfM.tb-DNA) probe-based-qPCR assay was developed for the diagnosis of pTB. Total cell-free DNA was extracted from pleural fluid (PF) and paired plasma samples and cfM.tb-DNA was quantified by probe-based qPCR targeting devR (109-bp) gene of M. tuberculosis in patients with pleural effusion. Patient categorization was done using 'Composite-Reference-Standard' formulated for the study. Assay cut-offs were determined from samples in the 'Development set' (n = 17; 'Definite & Probable' pTB; n = 9 and 'Non-TB'; n = 8) by ROC-curve analysis and applied to 'Validation set' (n = 112; 'Definite' pTB; n = 8, 'Probable' pTB; n = 34, 'Possible' pTB; n = 28 and 'Non-TB'; n = 42). cfM.tb-DNA qPCR had a sensitivity of 62.5% (95%CI; 24.4,91.4) in 'Definite' pTB category and 59.5% (95%CI; 43.2,74.3) in 'Definite & Probable' pTB category with 95.2% (95%CI; 83.8,99.4) specificity using PF. In plasma (n = 85), the assay had a sub-optimal sensitivity of 7.6% (95%CI; 0.95,25.1) with 88.2% (95%CI; 72.5,96.7) specificity in 'Definite & Probable' pTB group. Xpert MTB/RIF assay detected only six-samples in the 'Validation set'. Logistic regression analysis indicated that PF-cfM.tb-DNA qPCR provided incremental advantage over existing pTB diagnostic algorithms. To the best of our knowledge, this is the first report describing the utility of cfM.tb-DNA for pTB diagnosis in India.
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Affiliation(s)
- Pratibha Sharma
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Kumar Gupta
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Divya Anthwal
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Manisha Dass
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Yadav
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ashish Behera
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sunil Sethi
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ritu Singhal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Sahajal Dhooria
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ashutosh Nath Aggarwal
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sagarika Haldar
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
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Tagawa M, Aoki M. Clinical utility of liquid biopsy in canine oral malignant melanoma using cell-free DNA. Front Vet Sci 2023; 10:1182093. [PMID: 37408834 PMCID: PMC10319414 DOI: 10.3389/fvets.2023.1182093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/05/2023] [Indexed: 07/07/2023] Open
Abstract
Introduction Cell-free DNA (cfDNA), an extracellular free DNA released into the bloodstream by cells, is a potentially useful noninvasive marker to detect human malignancies and monitor response to treatment. In the present study, we evaluated the utility of circulating cfDNA in canine patients with oral malignant melanoma (OMM) in assessing therapeutic response and clinical outcomes. Methods Plasma samples were collected from 12 dogs with OMM and 9 healthy controls. cfDNA concentration was quantified by real-time PCR resulting in short (99bp) and long (218bp) fragments of long interspersed nuclear element-1 (LINE-1), and the DNA integrity index (DII) was then calculated (218/99). A follow-up study was conducted on 6 dogs with OMM, and the plasma cfDNA and DII were quantified throughout disease progression. Results Although cfDNA levels obtained from dogs with OMM were not significantly different compared to those obtained from healthy controls, the DII was significantly lower in dogs with OMM than in healthy controls. The DII tended to decrease as the disease stage progressed. Moreover, changes in cfDNA concentration and DII along the clinical course were observed when major changes, such as metastasis or apparent tumor progression, were observed. Discussion The results of our study suggest that measurements of serum cfDNA and DII using LINE-1 might be valuable new biomarkers for monitoring OMM progression in dogs. This preliminary study demonstrated the potential clinical utility of monitoring plasma cfDNA in canine patients with OMM.
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Affiliation(s)
- Michihito Tagawa
- Veterinary Medical Center, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
- Department of Veterinary Associated Science, Okayama University of Science, Imabari, Japan
| | - Minori Aoki
- Veterinary Medical Center, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido, Japan
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Ning W, Zhang C, Tian Z, Wu M, Luo Z, Hu S, Pan H, Li Y. Ω-shaped fiber optic LSPR biosensor based on mismatched hybridization chain reaction and gold nanoparticles for detection of circulating cell-free DNA. Biosens Bioelectron 2023; 228:115175. [PMID: 36871422 DOI: 10.1016/j.bios.2023.115175] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/10/2023] [Accepted: 02/20/2023] [Indexed: 02/23/2023]
Abstract
Circulating cell-free DNA (cfDNA) is a promising biomarker of liquid biopsy, but it still faces some difficulties in achieving sensitive and convenient detection. Herein, an Ω-shaped fiber optic localized surface plasmon resonance (FO-LSPR) biosensor based on hybridization chain reaction (HCR) coupled with gold nanoparticles (AuNPs) was developed, and applied in simple and sensitive detection of cfDNA. Specifically, one-base mismatch was designed in HCR hairpins (H1 and H2) to obtain high reaction efficiency, and AuNPs was introduced onto H1 through poly-adenine to construct HCR coupled with AuNPs strategy. Meanwhile, target cfDNA was designed into two domains: one could trigger HCR to generate dsDNA concatemer carrying numerous AuNPs, and the other could hybridize with capture DNA on the surface of Ω-shaped fiber optic (FO) probes. Thus, the presence of target cfDNA would initiate HCR, and bring the formed dsDNA concatemer and AuNPs to approach the probe surface, resulting in dramatically amplified LSPR signal. Besides, HCR required simple isothermal and enzyme-free condition, and Ω-shaped FO probe with high refractive index sensitivity just needed to be immersed into HCR solution directly for signal monitoring. Benefiting from the synergetic amplification of mismatched HCR and AuNPs, the proposed biosensor exhibited high sensitivity with a limit of detection of 14.0 pM, and therefore could provide a potential strategy for biomedical analysis and disease diagnosis.
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Affiliation(s)
- Wei Ning
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Chuyan Zhang
- Medical Equipment Innovation Research Center, Precision Medicine Center, Med+X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Mengfan Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Zewei Luo
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, 610065, China
| | - Shunming Hu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongzhi Pan
- The Affiliated Zhoupu Hospital, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China.
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610041, China.
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Bányász B, Antal J, Dénes B. False Positives in Brucellosis Serology: Wrong Bait and Wrong Pond? Trop Med Infect Dis 2023; 8:tropicalmed8050274. [PMID: 37235322 DOI: 10.3390/tropicalmed8050274] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
This review summarizes the status of resolving the problem of false positive serologic results (FPSR) in Brucella serology, compiles our knowledge on the molecular background of the problem, and highlights some prospects for its resolution. The molecular basis of the FPSRs is reviewed through analyzing the components of the cell wall of Gram-negative bacteria, especially the surface lipopolysaccharide (LPS) with details related to brucellae. After evaluating the efforts that have been made to solve target specificity problems of serologic tests, the following conclusions can be drawn: (i) resolving the FPSR problem requires a deeper understanding than we currently possess, both of Brucella immunology and of the current serology tests; (ii) the practical solutions will be as expensive as the related research; and (iii) the root cause of FPSRs is the application of the same type of antigen (S-type LPS) in the currently approved tests. Thus, new approaches are necessary to resolve the problems stemming from FPSR. Such approaches suggested by this paper are: (i) the application of antigens from R-type bacteria; or (ii) the further development of specific brucellin-based skin tests; or (iii) the application of microbial cell-free DNA as analyte, whose approach is detailed in this paper.
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Affiliation(s)
- Borbála Bányász
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, 1143 Budapest, Hungary
- Laboratory of Immunology, Veterinary Diagnostic Directorate, National Food Chain Safety Office, 1143 Budapest, Hungary
| | - József Antal
- Omixon Biocomputing Ltd., 1117 Budapest, Hungary
| | - Béla Dénes
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, 1143 Budapest, Hungary
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Cao Y, Jiang T, Lin Y, Fang X, Ding P, Song H, Li P, Li Y. Time-series prediction and detection of potential pathogens in bloodstream infection using mcfDNA sequencing. Front Cell Infect Microbiol 2023; 13:1144625. [PMID: 37249984 PMCID: PMC10213887 DOI: 10.3389/fcimb.2023.1144625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 04/18/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction Next-generation sequencing of microbial cell free DNA (mcfDNA-seq) has emerged as a promising diagnostic method for blood stream infection (BSI) and offers the potential to detect pathogens before blood culture. However, its application is limited by a lack of clinical validation. Methods We conducted sequential mcfDNA-seq on blood samples from ICU participants at high risk of BSI due to pneumonia, or intravascular catheterization; and explored whether mcfDNA-seq could diagnose and detect pathogens in advance of blood culture positivity. Blood culture results were used as evaluation criteria. Results A total of 111 blood samples were collected during the seven days preceding and on the day of onset of 16 BSI episodes from 13 participants. The diagnostic and total predictive sensitivity of mcfDNA-seq were 90% and 87.5%, respectively. The proportion of pathogenic bacteria was relatively high in terms of both diagnosis and prediction. The reads per million of etiologic agents trended upwards in the days approaching the onset of BSI. Discussion Our work found that mcfDNA-seq has high diagnostic sensitivity and could be used to identify pathogens before the onset of BSI, which could help expand the clinical application of mcfDNA-seq.
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Affiliation(s)
- Yinghao Cao
- Department of Clinical Laboratory Medicine, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Clinical Laboratory Medicine, The Sixth Medical Center of People's Liberation Army (PLA) General Hospital of Beijing, Beijing, China
| | - Tingting Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, An Hui Medical University, Hefei, China
- Biosecurity Department, Chinese People's Liberation Army (PLA) Center for Disease Control and Prevention, Beijing, China
| | - Yanfeng Lin
- Biosecurity Department, Chinese People's Liberation Army (PLA) Center for Disease Control and Prevention, Beijing, China
| | - Xiaofeng Fang
- Department of Clinical Laboratory Medicine, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Clinical Laboratory Medicine, The Sixth Medical Center of People's Liberation Army (PLA) General Hospital of Beijing, Beijing, China
| | - Peipei Ding
- Department of Clinical Laboratory Medicine, The Sixth Medical Center of People's Liberation Army (PLA) General Hospital of Beijing, Beijing, China
| | - Hongbin Song
- Department of Epidemiology and Biostatistics, School of Public Health, An Hui Medical University, Hefei, China
- Biosecurity Department, Chinese People's Liberation Army (PLA) Center for Disease Control and Prevention, Beijing, China
| | - Peng Li
- Biosecurity Department, Chinese People's Liberation Army (PLA) Center for Disease Control and Prevention, Beijing, China
| | - Yanjun Li
- Department of Clinical Laboratory Medicine, School of Medicine, South China University of Technology, Guangzhou, China
- Department of Clinical Laboratory Medicine, The Sixth Medical Center of People's Liberation Army (PLA) General Hospital of Beijing, Beijing, China
- School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, China
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Xu Y, Cai J, Zhong K, Wen Y, Cai L, He G, Liao H, Zhang C, Fu S, Chen T, Cai J, Zhong X, Chen C, Huang M, Cheng Y, Pan M. Plasma-only circulating tumor DNA analysis detects minimal residual disease and predicts early relapse in hepatocellular carcinoma patients undergoing curative resection. Front Oncol 2023; 13:1119744. [PMID: 36959801 PMCID: PMC10028131 DOI: 10.3389/fonc.2023.1119744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Background Minimal residual disease (MRD) is considered an essential factor leading to relapse within 2 years (early relapse) after radical surgery, which is challenging to be detected by conventional imaging. Circulating tumor DNA (ctDNA) provides a novel approach for detecting MRD and predicting clinical outcomes. Here, we tried to construct a fixed panel for plasma-only ctDNA NGS to enable tumor-uninformed MRD detection in hepatocellular carcinoma (HCC). Methods Here, we performed the followings: (i) profiling genomic alteration spectrum of ctDNA from the Chinese HCC cohort consisting of 493 individuals by NGS; (ii) screening of MRD monitoring genes; and (iii) performance evaluation of MRD monitoring genes in predicting early relapse in the ZJZS2020 cohort comprising 20 HCC patients who underwent curative resection. Results A total of 493 plasma samples from the Chinese HCC cohort were detected using a 381/733-gene NGS panel to characterize the mutational spectrum of ctDNA. Most patients (94.1%, 464/493) had at least one mutation in ctDNA. The variants fell most frequently in TP53 (45.1%), LRP1B (20.2%), TERT (20.2%), FAT1 (16.2%), and CTNNB1 (13.4%). By customized filtering strategy, 13 MRD monitoring genes were identified, and any plasma sample with one or more MRD monitoring gene mutations was considered MRD-positive. In the ZJZS2020 cohort, MRD positivity presented a sensitivity of 75% (6/8) and a specificity of 100% (6/6) in identifying early postoperative relapse. The Kaplan-Meier analysis revealed a significantly short relapse-free survival (RFS; median RFS, 4.2 months vs. NR, P=0.002) in the MRD-positive patients versus those with MRD negativity. Cox regression analyses revealed MRD positivity as an independent predictor of poor RFS (HR 13.00, 95% CI 2.60-69.00, P=0.002). Conclusions We successfully developed a 13-gene panel for plasma-only MRD detection, which was effective and convenient for predicting the risk of early postoperative relapse in HCC.
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Affiliation(s)
- Yuyan Xu
- Department of Hepatobiliary Surgery II, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jianpeng Cai
- Department of Pancreatobiliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Kaihang Zhong
- Department of Hepatobiliary Surgery II, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yaohong Wen
- Department of Hepatobiliary Surgery II, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lei Cai
- Department of Hepatobiliary Surgery II, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Guolin He
- Department of Hepatobiliary Surgery II, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Hangyu Liao
- Department of Hepatobiliary Surgery II, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Cheng Zhang
- Department of Hepatobiliary Surgery II, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Shunjun Fu
- Department of Hepatobiliary Surgery II, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Tingting Chen
- Medical Affairs, 3D Medicines, Inc., Shanghai, China
| | - Jinping Cai
- Medical Affairs, 3D Medicines, Inc., Shanghai, China
| | - Xuefeng Zhong
- Medical Affairs, 3D Medicines, Inc., Shanghai, China
| | - Chunzhu Chen
- Medical Affairs, 3D Medicines, Inc., Shanghai, China
| | - Mengli Huang
- Medical Affairs, 3D Medicines, Inc., Shanghai, China
| | - Yuan Cheng
- Department of Hepatobiliary Surgery II, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Mingxin Pan
- Department of Hepatobiliary Surgery II, General Surgery Center, Zhujiang Hospital, Southern Medical University, Guangzhou, China
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Hadipour M, Fasihi Harandi M, Mirhendi H, Yousofi Darani H. Diagnosis of echinococcosis by detecting circulating cell-free DNA and miRNA. Expert Rev Mol Diagn 2023; 23:133-142. [PMID: 36756744 DOI: 10.1080/14737159.2023.2178903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
INTRODUCTION Diagnosis of echinococcosis is difficult and usually performed based on clinical findings, imaging, and serological test. However, all of them have limitations, especially in follow-up approaches. AREAS COVERED Detection of cell-free DNA (cfDNA) and micro-RNA (miRNA) is currently a hot topic for diagnosis of echinococcosis diseases. For detecting cell-free DNA in echinococcosis patient's samples such as sera, some techniques are based on next-generation sequencing (NGS), DNA-deep sequencing, some are based on PCR-based methods, and a few works related to the detection of miRNA for the diagnosis of human echinococcosis. EXPERT OPINION In the detection of cell-free DNA in echinococcosis patient' samples, NGS and DNA-deep sequencing have shown high level of sensitivity, but are not suitable for routine clinical examination as they are expensive and inaccessible in the majority of endemic areas. However, PCR-based methods have shown a sensitivity of about 20-25%. To improve the sensitivity of these tests, improving the DNA extraction method, designing appropriate primers for detecting short-length fragments of circulating DNA, using a higher volume of a serum sample, and application of more sensitive PCR methods are recommended. In the field of miRNA detection, further works are recommended.
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Affiliation(s)
- Mahboubeh Hadipour
- Department of parasitology and mycology, Faculty of medicine, Isfahan University of Medical sciences, Isfahan, Iran
| | - Majid Fasihi Harandi
- Research center for Hydatid disease in Iran, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Hossein Mirhendi
- Department of parasitology and mycology, Faculty of medicine, Isfahan University of Medical sciences, Isfahan, Iran
| | - Hossein Yousofi Darani
- Department of parasitology and mycology, Faculty of medicine, Isfahan University of Medical sciences, Isfahan, Iran
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El Hejjioui B, Bouguenouch L, Melhouf MA, El Mouhi H, Bennis S. Clinical Evidence of Circulating Tumor DNA Application in Aggressive Breast Cancer. Diagnostics (Basel) 2023; 13:470. [PMID: 36766575 PMCID: PMC9914403 DOI: 10.3390/diagnostics13030470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/28/2022] [Accepted: 01/01/2023] [Indexed: 01/31/2023] Open
Abstract
Breast cancer is clinically and biologically heterogeneous and is classified into different subtypes according to the molecular landscape of the tumor. Triple-negative breast cancer is a subtype associated with higher tumor aggressiveness, poor prognosis, and poor response to treatment. In metastatic breast cancer, approximately 6% to 10% of new breast cancer cases are initially staged IV (de novo metastatic disease). The number of metastatic recurrences is estimated to be 20-30% of all existing breast tumor cases, whereby the need to develop specific genetic markers to improve the prognosis of patients suffering from these deadly forms of breast cancer. As an alternative, liquid biopsy methods can minutely identify the molecular architecture of breast cancer, including aggressive forms, which provides new perspectives for more precise diagnosis and more effective therapeutics. This review aimed to summarize the current clinical evidence for the application of circulating tumor DNA in managing breast cancer by detailing the increased usefulness of this biomarker as a diagnostic, prognostic, monitoring, and surveillance marker for breast cancer.
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Affiliation(s)
- Brahim El Hejjioui
- Biomedical and Translational Research Laboratory, Faculty of Medicine and Pharmacy, Sidi Mohamed Ben Abdellah University, Fez 30050, Morocco
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | - Laila Bouguenouch
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | | | - Hind El Mouhi
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | - Sanae Bennis
- Biomedical and Translational Research Laboratory, Faculty of Medicine and Pharmacy, Sidi Mohamed Ben Abdellah University, Fez 30050, Morocco
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Guo P, Zheng H, Li Y, Li Y, Xiao Y, Zheng J, Zhu X, Xu H, He Z, Zhang Q, Chen J, Qiu M, Jiang M, Liu P, Chen H. Hepatocellular carcinoma detection via targeted enzymatic methyl sequencing of plasma cell-free DNA. Clin Epigenetics 2023; 15:2. [PMID: 36600275 DOI: 10.1186/s13148-022-01420-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Epigenetic variants carried by circulating tumor DNA can be used as biomarkers for early detection of hepatocellular carcinoma (HCC) by noninvasive liquid biopsy. However, traditional methylation analysis method, bisulfite sequencing, with disadvantages of severe DNA damage, is limited in application of low-amount cfDNA analysis. RESULTS Through mild enzyme-mediated conversion, enzymatic methyl sequencing (EM-seq) is ideal for precise determination of cell-free DNA methylation and provides an opportunity for HCC early detection. EM-seq of methylation control DNA showed that enzymatic conversion of unmethylated C to U was more efficient than bisulfite conversion. Moreover, a relatively large proportion of incomplete converted EM-seq reads contains more than 3 unconverted CH site (CH = CC, CT or CA), which can be removed by filtering to improve accuracy of methylation detection by EM-seq. A cohort of 241 HCC, 76 liver disease, and 279 normal plasma samples were analyzed for methylation value on 1595 CpGs using EM-seq and targeted capture. Model training identified 283 CpGs with significant differences in methylation levels between HCC and non-HCC samples. A HCC screening model based on these markers can efficiently distinguish HCC sample from non-HCC samples, with area under the curve of 0.957 (sensitivity = 90%, specificity = 97%) in the test set, performing well in different stages as well as in serum α-fetoprotein/protein induced by vitamin K absence-II negative samples. CONCLUSION Filtering of reads with ≥ 3 CHs derived from incomplete conversion can significantly reduce the noise of EM-seq detection. Based on targeted EM-seq analysis of plasma cell-free DNA, our HCC screening model can efficiently distinguish HCC patients from non-HCC individuals with high sensitivity and specificity.
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Affiliation(s)
- Ping Guo
- School of Medicine, Huaqiao University, Xiamen, 361021, Fujian, People's Republic of China.,Xiamen Vangenes Biotechnology CO., LTD, Xiamen, 361015, Fujian, People's Republic of China
| | - Hailing Zheng
- Xiamen Vangenes Biotechnology CO., LTD, Xiamen, 361015, Fujian, People's Republic of China
| | - Yihan Li
- Xiamen Hospital of Beijing University of Chinese Medicine, Xiamen, 361001, Fujian, People's Republic of China
| | - Yuntong Li
- Zhongshan Hospital, Xiamen University, Xiamen, 361004, Fujian, People's Republic of China
| | - Yue Xiao
- Xiamen Vangenes Biotechnology CO., LTD, Xiamen, 361015, Fujian, People's Republic of China
| | - Jin Zheng
- Xiamen Vangenes Biotechnology CO., LTD, Xiamen, 361015, Fujian, People's Republic of China
| | - Xingqiang Zhu
- Xiamen Vangenes Biotechnology CO., LTD, Xiamen, 361015, Fujian, People's Republic of China
| | - Huan Xu
- Xiamen Vangenes Biotechnology CO., LTD, Xiamen, 361015, Fujian, People's Republic of China
| | - Zhi He
- Xiamen Vangenes Biotechnology CO., LTD, Xiamen, 361015, Fujian, People's Republic of China
| | - Qian Zhang
- Xiamen Hospital of Beijing University of Chinese Medicine, Xiamen, 361001, Fujian, People's Republic of China
| | - Jinchun Chen
- Xiamen Hospital of Beijing University of Chinese Medicine, Xiamen, 361001, Fujian, People's Republic of China
| | - Mingshan Qiu
- Xiamen Hospital of Beijing University of Chinese Medicine, Xiamen, 361001, Fujian, People's Republic of China
| | - Min Jiang
- The Second Affiliated Hospital of Fujian University of Traditional Chinese Medicine, Fuzhou, 350003, Fujian, People's Republic of China
| | - Pingguo Liu
- Zhongshan Hospital, Xiamen University, Xiamen, 361004, Fujian, People's Republic of China.
| | - Hongliang Chen
- Xiamen Vangenes Biotechnology CO., LTD, Xiamen, 361015, Fujian, People's Republic of China. .,School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China.
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Wilson-Robles H, Warry E, Miller T, Jarvis J, Matsushita M, Miller P, Herzog M, Turatsinze JV, Kelly TK, Butera ST, Michel G. Monitoring plasma nucleosome concentrations to measure disease response and progression in dogs with hematopoietic malignancies. PLoS One 2023; 18:e0281796. [PMID: 37163491 PMCID: PMC10171669 DOI: 10.1371/journal.pone.0281796] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/12/2023] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Hematopoietic malignancies are extremely common in pet dogs and represent nearly 30% of the malignancies diagnosed in this population each year. Clinicians commonly use existing tools such as physical exam findings, radiographs, ultrasound and baseline blood work to monitor these patients for treatment response and remission. Circulating biomarkers, such as prostate specific antigen or carcinoembryonic antigen, can be useful tools for monitoring treatment response and remission status in human cancer patients. To date, there has a been a lack of useful circulating biomarkers available to veterinary oncology patients. METHODS Circulating plasma nucleosome concentrations were evaluated at diagnosis, throughout treatment and during remission monitoring for 40 dogs with lymphoma, acute myelogenous leukemia and multiple myeloma. Additionally, C-reactive protein and thymidine kinase-1 levels were recorded. RESULTS Plasma nucleosome concentrations were significantly higher at diagnosis and progressive disease than they were when dogs were in remission. All but two dogs had plasma nucleosome concentrations that returned to the low range during treatment. These two dogs had the shortest progression free and overall survival times. Dogs with the highest plasma nucleosome concentrations had a significantly shorter first progression free survival than dogs with lower plasma nucleosome concentrations at diagnosis. Plasma nucleosome concentrations correlated better with disease response and progression than either thymidine kinase or C reactive protein. CONCLUSIONS Plasma nucleosome concentrations can be a useful tool for treatment monitoring and disease progression in dogs with hematopoietic malignancies.
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Affiliation(s)
- Heather Wilson-Robles
- Small Animal Clinical Sciences Department, Texas A&M University, College Station, Texas, United States of America
- Volition Veterinary Diagnostics Development, Henderson, Nevada, United States of America
| | - Emma Warry
- Small Animal Clinical Sciences Department, Texas A&M University, College Station, Texas, United States of America
| | - Tasha Miller
- Small Animal Clinical Sciences Department, Texas A&M University, College Station, Texas, United States of America
| | - Jill Jarvis
- Small Animal Clinical Sciences Department, Texas A&M University, College Station, Texas, United States of America
| | - Matthew Matsushita
- Small Animal Clinical Sciences Department, Texas A&M University, College Station, Texas, United States of America
| | - Pamela Miller
- Small Animal Clinical Sciences Department, Texas A&M University, College Station, Texas, United States of America
| | - Marielle Herzog
- Belgian Volition SRL, Parc Scientifique Crealys, Isnes, Belgium
| | | | - Theresa K Kelly
- Volition America LLC, Henderson, Nevada, United States of America
| | - S Thomas Butera
- Volition Veterinary Diagnostics Development, Henderson, Nevada, United States of America
| | - Gaetan Michel
- Belgian Volition SRL, Parc Scientifique Crealys, Isnes, Belgium
- Volition America LLC, Henderson, Nevada, United States of America
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21
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Shah UJ, Alsulimani A, Ahmad F, Mathkor DM, Alsaieedi A, Harakeh S, Nasiruddin M, Haque S. Bioplatforms in liquid biopsy: advances in the techniques for isolation, characterization and clinical applications. Biotechnol Genet Eng Rev 2022; 38:339-383. [PMID: 35968863 DOI: 10.1080/02648725.2022.2108994] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Tissue biopsy analysis has conventionally been the gold standard for cancer prognosis, diagnosis and prediction of responses/resistances to treatments. The existing biopsy procedures used in clinical practice are, however, invasive, painful and often associated with pitfalls like poor recovery of tumor cells and infeasibility for repetition in single patients. To circumvent these limitations, alternative non-invasive, rapid and economical, yet sturdy, consistent and dependable, biopsy techniques are required. Liquid biopsy is an emerging technology that fulfills these criteria and potentially much more in terms of subject-specific real-time monitoring of cancer progression, determination of tumor heterogeneity and treatment responses, and specific identification of the type and stages of cancers. The present review first briefly revisits the state-of-the-art technique of liquid biopsy and then proceeds to address in detail, the advances in the potential clinical applications of four major biological agencies present in liquid biopsy samples (circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), exosomes and tumor-educated platelets (TEPs)). Finally, the authors conclude with the limitations that need to be addressed in order for liquid biopsy to effectively replace the conventional invasive biopsy methods in the clinical settings.
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Affiliation(s)
- Ushma Jaykamal Shah
- MedGenome Labs Ltd, Kailash Cancer Hospital and Research Center, Vadodara, India
| | - Ahmad Alsulimani
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | - Faraz Ahmad
- Department of Biotechnology, School of Bio Sciences and Technology (SBST), Vellore Institute of Technology, Vellore, India
| | - Darin Mansor Mathkor
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Ahdab Alsaieedi
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, and Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mohammad Nasiruddin
- MedGenome Labs Ltd, Narayana Health City, Bangalore, India.,Genomics Lab, Orbito Asia Diagnostics, Coimbatore, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
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22
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Liquid Biopsies in Colorectal Liver Metastases: Towards the Era of Precision Oncologic Surgery. Cancers (Basel) 2022; 14:cancers14174237. [PMID: 36077774 PMCID: PMC9455047 DOI: 10.3390/cancers14174237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/26/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Tumor mutational analysis has been incorporated into the management of patients with CRLM since it can provide valuable prognostic information as well as guide peri-operative systemic treatment. Unlike tumor biopsy, liquid biopsy has emerged as a promising, non-invasive alternative that can detect cell-derived markers from a variety of body fluids and might better characterize all subclones present at a specific time point and allow sequential monitoring of disease evolution. Although not currently considered standard of care, an increasing number of cancer centers are nowadays routinely using liquid biopsies in the treatment of CRLM patients with promising results. The current review provides an overview of liquid biopsies in cancer therapeutics and focuses on the application of this relatively new approach on patients with CRLM.
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23
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Sánchez-Herrero E, Serna-Blasco R, Robado de Lope L, González-Rumayor V, Romero A, Provencio M. Circulating Tumor DNA as a Cancer Biomarker: An Overview of Biological Features and Factors That may Impact on ctDNA Analysis. Front Oncol 2022; 12:943253. [PMID: 35936733 PMCID: PMC9350013 DOI: 10.3389/fonc.2022.943253] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer cells release nucleic acids, freely or associated with other structures such as vesicles into body fluids, including blood. Among these nucleic acids, circulating tumor DNA (ctDNA) has emerged as a minimally invasive biomarker for tumor molecular profiling. However, certain biological characteristics of ctDNA are still unknown. Here, we provide an overview of the current knowledge about ctDNA biological features, including size and structure as well as the mechanisms of ctDNA shedding and clearance, and the physio-pathological factors that determine ctDNA levels. A better understanding of ctDNA biology is essential for the development of new methods that enable the analysis of ctDNA.
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Affiliation(s)
- Estela Sánchez-Herrero
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- +D Department, Atrys Health, Barcelona, Spain
| | - Roberto Serna-Blasco
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
| | - Lucia Robado de Lope
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
| | | | - Atocha Romero
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Majadahonda, Spain
- *Correspondence: Atocha Romero, ; orcid.org/0000-0002-1634-7397
| | - Mariano Provencio
- Liquid Biopsy Laboratory. Biomedical Sciences Research Institute Puerta de Hierro-Majadahonda, Majadahonda, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro-Majadahonda, Majadahonda, Spain
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24
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Janovičová Ľ, Čonka J, Lauková L, Celec P. Variability of endogenous deoxyribonuclease activity and its pathophysiological consequences. Mol Cell Probes 2022; 65:101844. [DOI: 10.1016/j.mcp.2022.101844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/01/2022] [Accepted: 07/01/2022] [Indexed: 10/17/2022]
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25
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Tutanov O, Tamkovich S. The Influence of Proteins on Fate and Biological Role of Circulating DNA. Int J Mol Sci 2022; 23:7224. [PMID: 35806228 PMCID: PMC9266439 DOI: 10.3390/ijms23137224] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Circulating DNA has already proven itself as a valuable tool in translational medicine. However, one of the overlooked areas of circulating DNA research is its association with different proteins, despite considerable evidence that this association might impact DNA's fate in circulation and its biological role. In this review, we attempt to shed light on current ideas about circulating DNA origins and forms of circulation, known biological effects, and the clinical potential of circulating tumor deoxyribonucleoprotein complexes.
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Affiliation(s)
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
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26
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Kılınç N, Onbaşılar M, Çayır A. Evaluation of circulating cell-free nucleic acids in health workers occupationally exposed to ionizing radiation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:40543-40549. [PMID: 35083692 DOI: 10.1007/s11356-022-18828-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Radiology workers might constantly be exposed to low-dose ionizing radiation due to their profession. Low doses of radiation in a short exposure time have the potential to alter the genome, which might potentially lead to diseases. The main objective of this study was to determine whether the amount of cell-free nucleic acids in plasma samples of radiation-exposed workers was different from the general public, in other words, non-exposed individuals. In this context, we investigated the association between radiation exposure and cell-free nucleic acids concentration by using radiation exposure parameters. The study consisted of 40 radiology workers and 40 individuals who were not exposed to ionizing radiation. The plasma concentrations of cell-free DNA, RNA, and miRNA were measured fluorometrically. We found that the ccfRNA concentration of the radiation-exposed group was significantly different from that of the non-exposed group (p = 0.0001). However, there are no differences between both groups in terms of ccfDNA and ccfmiRNA concentration. The concentration of ccfDNA is significantly correlated with working time in the fluoroscopy field (p < 0.05). We found that the concentration of ccfmiRNA was significantly correlated with working time in plain radiography (p < 0.01) and computed tomography (p < 0.05) and with total working time (p < 0.01). Similarly, the concentrations of ccfRNA were significantly correlated with working time in computed tomography (p < 0.01) and with the total working time (p < 0.05) of the workers. We found that imaging number in computed tomography significantly altered the level of ccfRNA (p = 0.006) and that working time in the computed tomography field significantly affected the ccfRNA concentration (p = 0.03, R2 = 0.36 for model). Finally, we determined that total working time was significantly associated with total ccfRNA concentration (p < 0.05, R2 = 0.25 for model). In conclusion, total RNA measured in radiation-exposed workers has the potential to predict the radiation exposure risk. Furthermore, total working time and working time in the tomography field significantly alter the level of free nucleic acids.
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Affiliation(s)
- Nihal Kılınç
- Medical Pathology, Faculty of Medicine, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Mehmet Onbaşılar
- School of Graduate Studies, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | - Akın Çayır
- Vocational School of Health Services, Canakkale Onsekiz Mart University, Canakkale, Turkey.
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27
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Nicu AT, Medar C, Chifiriuc MC, Gradisteanu Pircalabioru G, Burlibasa L. Epigenetics and Testicular Cancer: Bridging the Gap Between Fundamental Biology and Patient Care. Front Cell Dev Biol 2022; 10:861995. [PMID: 35465311 PMCID: PMC9023878 DOI: 10.3389/fcell.2022.861995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/22/2022] [Indexed: 11/15/2022] Open
Abstract
Testicular cancer is the most common solid tumor affecting young males. Most testicular cancers are testicular germ cell tumors (TGCTs), which are divided into seminomas (SGCTs) and non-seminomatous testicular germ cell tumors (NSGCTs). During their development, primordial germ cells (PGCs) undergo epigenetic modifications and any disturbances in their pattern might lead to cancer development. The present study provides a comprehensive review of the epigenetic mechanisms–DNA methylation, histone post-translational modifications, bivalent marks, non-coding RNA–associated with TGCT susceptibility, initiation, progression and response to chemotherapy. Another important purpose of this review is to highlight the recent investigations regarding the identification and development of epigenetic biomarkers as powerful tools for the diagnostic, prognostic and especially for epigenetic-based therapy.
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Affiliation(s)
- Alina-Teodora Nicu
- Faculty of Biology, University of Bucharest, Bucharest, Romania
- Department of Genetics, University of Bucharest, Bucharest, Romania
| | - Cosmin Medar
- University of Medicine and Pharmacy “Carol Davila”, Clinical Hospital “Prof. dr Theodor Burghele”, Bucharest, Romania
| | - Mariana Carmen Chifiriuc
- Faculty of Biology, University of Bucharest, Bucharest, Romania
- Research Institute of University of Bucharest (ICUB), Bucharest, Romania
- Academy of Romanian Scientists, Bucharest, Romania
- Romanian Academy, Bucharest, Romania
| | | | - Liliana Burlibasa
- Faculty of Biology, University of Bucharest, Bucharest, Romania
- Department of Genetics, University of Bucharest, Bucharest, Romania
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28
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Hirahata T, ul Quraish R, Quraish AU, ul Quraish S, Naz M, Razzaq MA. Liquid Biopsy: A Distinctive Approach to the Diagnosis and Prognosis of Cancer. Cancer Inform 2022; 21:11769351221076062. [PMID: 35153470 PMCID: PMC8832574 DOI: 10.1177/11769351221076062] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer is a leading cause of morbidity and mortality worldwide. Over the past decades, the concept of precision cancer medicine has emerged as a novel approach in the field of oncology that aims to tailor the most effective treatment options to each individual cancer patient based on the genetic profile of the tumor of each individual patient. Recently, tissue biopsy has become an essential part of cancer care and is widely used to characterize the tumor. However, tissue biopsy techniques face different challenges due to their invasiveness, cost, time, and adversity in potential sampling due to tissue heterogeneity. To overcome these issues, a non-invasive approach has developed, which is known as liquid biopsy. It is a simple, fast, and worthwhile technique based on the analysis of circulating tumor DNA (which is a fraction of cfDNA), circulating tumor cells (CTCs), and other tumor-derived material in blood plasma. This review provides an overview of the concept of liquid biopsy and briefly discusses the role of ctDNA and CTC analysis as tools for early diagnosis and prognosis of cancer. In this review, we also speculate on the advantages of liquid biopsy as opposed to tissue biopsy and postulate that liquid biopsy may be a comprehensive approach to overcome the current limitations associated with costly, invasive, and time-consuming tissue biopsy.
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Affiliation(s)
| | | | | | | | - Munazzah Naz
- Hirahata Gene Therapy Laboratory, HIC Clinic, Tokyo, Japan
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29
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Camus V, Viennot M, Lévêque E, Viailly PJ, Tonnelet D, Veresezan EL, Drieux F, Etancelin P, Dubois S, Stamatoullas A, Tilly H, Bohers E, Jardin F. Circulating tumor DNA in primary mediastinal large B-cell lymphoma versus classical Hodgkin lymphoma: a retrospective study. Leuk Lymphoma 2022; 63:834-844. [PMID: 35075971 DOI: 10.1080/10428194.2021.2010060] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Few data exist concerning circulating tumor DNA (ctDNA) relevance in primary mediastinal B-cell lymphoma (PMBL). To explore this topic, we applied a 9-gene next-generation sequencing pipeline to samples from forty-four PMBL patients (median age 36.5 years). The primary endpoint was a similarity between paired biopsy/plasma mutational profiles. We detected at least one variant in 32 plasma samples (80%). The similarity between the biopsy and ctDNA genetic profiles for the 30 patients with paired mutated biopsy/plasma samples was greater than or equal to 80% in 19 patients (63.3%). We then compared PMBL ctDNA features with those of a cohort of Hodgkin lymphoma patients (n = 60). The top three mutated genes were SOCS1, TNFAIP3, and B2M in both lymphoma types. PMBL displayed more alterations in TNFAIP3 (71.9% vs. 46.3%, p = 0.029) and GNA13 (46.9% vs. 17.1%, p = 0.013) than cHL. Our 9-gene set may delineate tumor genotypes using ctDNA samples from both lymphoma types.
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Affiliation(s)
- Vincent Camus
- Department of Hematology, Centre Henri Becquerel, Rouen, France.,INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Mathieu Viennot
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Emilie Lévêque
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | | | - David Tonnelet
- Department of Nuclear Medicine and Radiology, Centre Henri Becquerel and QuantIF (Litis EA4108 - FR CNRS 3638), Rouen, France
| | | | - Fanny Drieux
- Department of Pathology, Centre Henri Becquerel, Rouen, France
| | | | - Sydney Dubois
- Department of Hematology, Centre Henri Becquerel, Rouen, France.,INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Aspasia Stamatoullas
- Department of Hematology, Centre Henri Becquerel, Rouen, France.,INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Hervé Tilly
- Department of Hematology, Centre Henri Becquerel, Rouen, France.,INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Elodie Bohers
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Fabrice Jardin
- Department of Hematology, Centre Henri Becquerel, Rouen, France.,INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
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30
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Jin Y, Allen EG, Jin P. Cell-free DNA methylation as a potential biomarker in brain disorders. Epigenomics 2022; 14:369-374. [PMID: 35034473 PMCID: PMC9066291 DOI: 10.2217/epi-2021-0416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Yulin Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Emily G Allen
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Peng Jin
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
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31
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Marvaso G, Volpe S, Pepa M, Zaffaroni M, Corrao G, Augugliaro M, Nolè F, De Cobelli O, Jereczek-Fossa BA. Recent Advances in the Management of Hormone-Sensitive Oligometastatic Prostate Cancer. Cancer Manag Res 2022; 14:89-101. [PMID: 35023972 PMCID: PMC8747627 DOI: 10.2147/cmar.s321136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/08/2021] [Indexed: 12/11/2022] Open
Abstract
After primary treatment for prostate cancer with either radical prostatectomy or radiotherapy, a significant proportion of patients are at risk of developing metastases. In recent years, a deeper understanding of the underlying biology together with improved imaging techniques and the advent of new therapeutic options including metastases-directed therapies and new drugs have revolutionized the management of low-burden metastatic disease, also known as oligometastatic state. The purpose of this narrative review is to report the recent developments in the management of hormone-sensitive oligometastatic prostate cancer patients.
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Affiliation(s)
- Giulia Marvaso
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Stefania Volpe
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Matteo Pepa
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Mattia Zaffaroni
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Giulia Corrao
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Matteo Augugliaro
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Franco Nolè
- Medical Oncology Division of Urogenital & Head & Neck Tumors, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Ottavio De Cobelli
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Department of Urology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Barbara Alicja Jereczek-Fossa
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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32
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Jackson AM, Amato-Menker C, Bettinotti M. Cell-free DNA diagnostics in transplantation utilizing next generation sequencing. Hum Immunol 2021; 82:850-858. [PMID: 34600770 DOI: 10.1016/j.humimm.2021.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/29/2021] [Accepted: 07/12/2021] [Indexed: 12/25/2022]
Abstract
The use of Next Generation Sequencing (NGS) to interrogate cell-free DNA (cfDNA) as a transplant diagnostic provides a crucial step in improving the accuracy of post-transplant monitoring of allograft health. cfDNA interrogation provides a powerful, yet minimally invasive, biomarker for disease and tissue injury. cfDNA can be isolated from a variety of body fluids and analyzed using bioinformatics to unlock its origins. Furthermore, cfDNA characteristics can reveal the mechanisms and conditions under which it was generated and released. In transplantation, donor-derived cfDNA monitoring provides a tool for identifying active allograft injury at the time of transplant, infection, and rejection. Multiple detection and interrogation methods for cfDNA detection are now being evaluated for clinical validity and hold the promise to provide minimally invasive, quantitative, and reproducible measures of allograft injury across organ types.
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Affiliation(s)
- Annette M Jackson
- Duke University, Department of Surgery, DUMC Box 2645, Durham, NC 27710, USA.
| | - Carly Amato-Menker
- West Virginia University, Microbiology, Immunology, and Cell Biology, Morgantown, WV, USA
| | - Maria Bettinotti
- Johns Hopkins University, Department of Pathology, 2041 E. Monument Street, Baltimore, MD 21205, USA
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33
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Bredno J, Lipson J, Venn O, Aravanis AM, Jamshidi A. Clinical correlates of circulating cell-free DNA tumor fraction. PLoS One 2021; 16:e0256436. [PMID: 34432811 PMCID: PMC8386888 DOI: 10.1371/journal.pone.0256436] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/08/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Oncology applications of cell-free DNA analysis are often limited by the amount of circulating tumor DNA and the fraction of cell-free DNA derived from tumor cells in a blood sample. This circulating tumor fraction varies widely between individuals and cancer types. Clinical factors that influence tumor fraction have not been completely elucidated. METHODS AND FINDINGS Circulating tumor fraction was determined for breast, lung, and colorectal cancer participant samples in the first substudy of the Circulating Cell-free Genome Atlas study (CCGA; NCT02889978; multi-cancer early detection test development) and was related to tumor and patient characteristics. Linear models were created to determine the influence of tumor size combined with mitotic or metabolic activity (as tumor mitotic volume or excessive lesion glycolysis, respectively), histologic type, histologic grade, and lymph node status on tumor fraction. For breast and lung cancer, tumor mitotic volume and excessive lesion glycolysis (primary lesion volume scaled by percentage positive for Ki-67 or PET standardized uptake value minus 1.0, respectively) were the only statistically significant covariates. For colorectal cancer, the surface area of tumors invading beyond the subserosa was the only significant covariate. The models were validated with cases from the second CCGA substudy and show that these clinical correlates of circulating tumor fraction can predict and explain the performance of a multi-cancer early detection test. CONCLUSIONS Prognostic clinical variables, including mitotic or metabolic activity and depth of invasion, were identified as correlates of circulating tumor DNA by linear models that relate clinical covariates to tumor fraction. The identified correlates indicate that faster growing tumors have higher tumor fractions. Early cancer detection from assays that analyze cell-free DNA is determined by circulating tumor fraction. Results support that early detection is particularly sensitive for faster growing, aggressive tumors with high mortality, many of which have no available screening today.
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Affiliation(s)
- Joerg Bredno
- GRAIL, Inc., Menlo Park, California, United States of America
| | - Jafi Lipson
- GRAIL, Inc., Menlo Park, California, United States of America
| | - Oliver Venn
- GRAIL, Inc., Menlo Park, California, United States of America
| | | | - Arash Jamshidi
- GRAIL, Inc., Menlo Park, California, United States of America
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Corrao G, Zaffaroni M, Bergamaschi L, Augugliaro M, Volpe S, Pepa M, Bonizzi G, Pece S, Amodio N, Mistretta FA, Luzzago S, Musi G, Alessi S, La Fauci FM, Tordonato C, Tosoni D, Cattani F, Gandini S, Petralia G, Pravettoni G, De Cobelli O, Viale G, Orecchia R, Marvaso G, Jereczek-Fossa BA. Exploring miRNA Signature and Other Potential Biomarkers for Oligometastatic Prostate Cancer Characterization: The Biological Challenge behind Clinical Practice. A Narrative Review. Cancers (Basel) 2021; 13:cancers13133278. [PMID: 34208918 PMCID: PMC8267686 DOI: 10.3390/cancers13133278] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/16/2021] [Accepted: 06/24/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary The oligometastatic prostate cancer state is defined as the presence of a number of lesions ≤ 5 and has been significantly correlated with better survival if compared to a number of metastases > 5. In particular, patients in an oligometastatic setting could benefit from a metastates directed therapy, which could control the disease delaying the start of systemic therapies. For this reason, the selection of true-oligometastatic patients who could benefit from such approach is particularly important in this setting. The aim of the present narrative review is to report the current state of the art on the liquid biopsy-derived analytes and their reliability as biomarkers in the clinics for the identification of true-oligometastatic patients. This kind of molecular profiling could refine current developments in the era of precision oncology allowing patients’ stratification and leading to more refined therapeutic strategies. Abstract In recent years, a growing interest has been directed towards oligometastatic prostate cancer (OMPC), as patients with three to five metastatic lesions have shown a significantly better survival as compared with those harboring a higher number of lesions. The efficacy of local ablative treatments directed on metastatic lesions (metastases-directed treatments) was extensively investigated, with the aim of preventing further disease progression and delaying the start of systemic androgen deprivation therapies. Definitive diagnosis of prostate cancer is traditionally based on histopathological analysis. Nevertheless, a bioptic sample—static in nature—inevitably fails to reflect the dynamics of the tumor and its biological response due to the dynamic selective pressure of cancer therapies, which can profoundly influence spatio-temporal heterogeneity. Furthermore, even with new imaging technologies allowing an increasingly early detection, the diagnosis of oligometastasis is currently based exclusively on radiological investigations. Given these premises, the development of minimally-invasive liquid biopsies was recently promoted and implemented as predictive biomarkers both for clinical decision-making at pre-treatment (baseline assessment) and for monitoring treatment response during the clinical course of the disease. Through liquid biopsy, different biomarkers, commonly extracted from blood, urine or saliva, can be characterized and implemented in clinical routine to select targeted therapies and assess treatment response. Moreover, this approach has the potential to act as a tissue substitute and to accelerate the identification of novel and consistent predictive analytes cost-efficiently. However, the utility of tumor profiling is currently limited in OMPC due to the lack of clinically validated predictive biomarkers. In this scenario, different ongoing trials, such as the RADIOSA trial, might provide additional insights into the biology of the oligometastatic state and on the identification of novel biomarkers for the outlining of true oligometastatic patients, paving the way towards a wider ideal approach of personalized medicine. The aim of the present narrative review is to report the current state of the art on the solidity of liquid biopsy-related analytes such as CTCs, cfDNA, miRNA and epi-miRNA, and to provide a benchmark for their further clinical implementation. Arguably, this kind of molecular profiling could refine current developments in the era of precision oncology and lead to more refined therapeutic strategies in this subset of oligometastatic patients.
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Affiliation(s)
- Giulia Corrao
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
| | - Mattia Zaffaroni
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
| | - Luca Bergamaschi
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
| | - Matteo Augugliaro
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
- Correspondence:
| | - Stefania Volpe
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
| | - Matteo Pepa
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
| | - Giuseppina Bonizzi
- Department of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Salvatore Pece
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Novel Diagnostics Program, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, 88100 Catanzaro, Italy;
| | | | - Stefano Luzzago
- Department of Urology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (F.A.M.); (S.L.)
| | - Gennaro Musi
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Department of Urology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (F.A.M.); (S.L.)
| | - Sarah Alessi
- Division of Radiology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Francesco Maria La Fauci
- Unit of Medical Physics IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (F.M.L.F.); (F.C.)
| | - Chiara Tordonato
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Daniela Tosoni
- Novel Diagnostics Program, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Federica Cattani
- Unit of Medical Physics IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (F.M.L.F.); (F.C.)
| | - Sara Gandini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Giuseppe Petralia
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Division of Radiology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Gabriella Pravettoni
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Applied Research Division for Cognitive and Psychological Science, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Ottavio De Cobelli
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Department of Urology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy; (F.A.M.); (S.L.)
| | - Giuseppe Viale
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
- Department of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Roberto Orecchia
- Scientific Direction, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy;
| | - Giulia Marvaso
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
| | - Barbara Alicja Jereczek-Fossa
- Division of Radiation Oncology, IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141 Milan, Italy; (G.C.); (M.Z.); (L.B.); (S.V.); (M.P.); (G.M.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy; (S.P.); (G.M.); (C.T.); (G.P.); (G.P.); (O.D.C.); (G.V.)
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Jensen SG, Epistolio S, Madsen CL, Kyneb MH, Riva A, Paganotti A, Barizzi J, Petersen RK, Børgesen M, Molinari F, Boldorini R, Lorenzen J, Sørensen E, Christensen UB, Høgdall E, Frattini M. A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies. PLoS One 2021; 16:e0253687. [PMID: 34166445 PMCID: PMC8224962 DOI: 10.1371/journal.pone.0253687] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/10/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND A major perspective for the use of circulating tumor DNA (ctDNA) in the clinical setting of non-small cell lung cancer (NSCLC) is expected as predictive factor for resistance and response to EGFR TKI therapy and, especially, as a non-invasive alternative to tissue biopsy. However, ctDNA is both highly fragmented and mostly low concentrated in plasma and serum. On this basis, it is important to use a platform characterized by high sensitivity and linear performance in the low concentration range. This motivated us to evaluate the newly developed and commercially available SensiScreen® EGFR Liquid assay platform (PentaBase) with regard to sensitivity, linearity, repeatability and accuracy and finally to compare it to our already implemented methods. The validation was made in three independent European laboratories using two cohorts on a total of 68 unique liquid biopsies. RESULTS Using artificial samples containing 1600 copies of WT DNA spiked with 50% - 0.1% of mutant copies across a seven-log dilution scale, we assessed the sensitivity, linearity, repeatability and accuracy for the p.T790M, p.L858R and exon 19 deletion assays of the SensiScreen® EGFR Liquid assay platform. The lowest value detectable ranged from 0.5% to 0.1% with R2≥0,97 indicating good linearity. High PCR efficiency was shown for all three assays. In 102 single PCRs each containing theoretical one copy of the mutant at initiating, assays showed repeatable positivity in 75.5% - 80.4% of reactions. At low ctDNA levels, as in plasma, the SensiScreen® EGFR Liquid assay platform showed better sensitivity than the Therascreen® EGFR platform (Qiagen) and equal performance to the ctEGFR Mutation Detection Kit (EntroGen) and the IOT® Oncomine cell-free nucleic acids assay (Thermo Fisher Scientific) with 100% concordance at the sequence level. CONCLUSION For profiling clinical plasma samples, characterized by low ctDNA abundance, the SensiScreen® EGFR Liquid assay is able to identify down to 1 copy of mutant alleles and with its high sensitivity, linearity and accuracy it may be a competitive platform of choice.
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Affiliation(s)
| | | | | | | | - Alice Riva
- Institute of Pathology, Locarno, Switzerland
| | - Alessia Paganotti
- Department of Pathology, ’Maggiore della Carità’ Hospital, Novara, Italy
| | | | | | | | | | - Renzo Boldorini
- Department of Pathology, ’Maggiore della Carità’ Hospital, Novara, Italy
- Department of Health Sciences, Universitá degli Studi del Piemonte Orientale "A. Avogadro", Novara, Italy
| | - Jan Lorenzen
- Life Science Division, Danish Technological Institute, Aarhus, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | | | - Estrid Høgdall
- Department of Pathology, Herlev—Gentofte University Hospital, Herlev, Denmark
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Stance of MRD in Non-Hodgkin's Lymphoma and its upsurge in the novel era of cell-free DNA. Clin Transl Oncol 2021; 23:2206-2219. [PMID: 33991328 DOI: 10.1007/s12094-021-02635-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/02/2021] [Indexed: 10/21/2022]
Abstract
Cancer genomics has evolved over the years from understanding the pathogenesis of cancer to screening the future possibilities of cancer occurrence. Understanding the genetic profile of tumors holds a prognostic as well as a predictive value in this era of therapeutic surveillance, molecular remission, and precision medicine. Identifying molecular markers in tumors is the current standard of approach, and requires an efficient combination of an accessible sample type and a profoundly sensitive technique. Liquid biopsy or cell-free DNA has evolved as a novel sample type with promising results in recent years. Although cell-free DNA has significant role in various cancer types, this review focuses on its application in Non-Hodgkin's Lymphoma. Beginning with the current concept and clinical relevance of minimal residual disease in Non-Hodgkin's lymphoma, we discuss the literature on circulating DNA and its evolving application in the realm of cutting-edge technology.
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Lang SA, Bednarsch J, Joechle K, Amygdalos I, Czigany Z, Heij L, Ulmer TF, Neumann UP. Prognostic biomarkers for cholangiocarcinoma (CCA): state of the art. Expert Rev Gastroenterol Hepatol 2021; 15:497-510. [PMID: 33970740 DOI: 10.1080/17474124.2021.1912591] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction:Although advances in understanding the molecular basis of cholangiocarcinoma (CCA) have been made, surgery is the only curative therapy option and the overall prognosis of patients suffering from the disease remains poor. Therefore, estimation of prognosis based on known and novel biomarkers is essential for therapy guidance of CCA in both, curative and palliative settings.Areas covered:An extensive literature search on biomarkers for CCA with special emphasis on prognosis was performed. Based on this, prognostic biomarkers from serum, tumor tissue and other compartments that are currently in use or under evaluation for CCA were summarized in this review. Furthermore, an overview of new biomarkers was provided including those determined from extracellular vesicles (EVs), metabolites and nucleic acids. Finally, prognostic markers associated with potential new therapy options for the treatment of CCA were summed up.Expert opinion:So far, an optimal prognostic biomarker for CCA has not been described. However, based on the increasing knowledge about the molecular basis of CCA but also due to novel, innovative technologies, a plethora of novel prognostic biomarkers is currently under evaluation and will be available for CCA in future.
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Affiliation(s)
- Sven A Lang
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany
| | - Jan Bednarsch
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany
| | - Katharina Joechle
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany
| | - Iakovos Amygdalos
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany
| | - Zoltan Czigany
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany
| | - Lara Heij
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany
| | - Tom F Ulmer
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany
| | - Ulf P Neumann
- Department of Surgery and Transplantation, University Hospital RWTH Aachen, Aachen, Germany
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Liu L, Chen X, Wong KC. Early Cancer Detection from Genome-wide Cell-free DNA Fragmentation via Shuffled Frog Leaping Algorithm and Support Vector Machine. Bioinformatics 2021; 37:3099-3105. [PMID: 33837381 DOI: 10.1093/bioinformatics/btab236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/19/2021] [Accepted: 04/08/2021] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION Early cancer detection is significant for the patient mortality rate reduction. Although machine learning has been widely employed in that context, there are still deficiencies. In this work, we studied different machine learning algorithms for early cancer detection and proposed an Adaptive Support Vector Machine (ASVM) method by synergizing Shuffled Frog Leaping Algorithm (SFLA) and Support Vector Machine (SVM) in this paper. RESULTS As ASVM regulates SVM for parameter adaption based on data characteristics, the experimental results demonstrated the robust generalization capability of ASVM on different datasets under different settings; for instance, ASVM can enhance the sensitivity by over 10% for early cancer detection compared with SVM. Besides, our proposed ASVM outperformed Grid Search + SVM and Random Search + SVM by significant margins in terms of the area under the ROC curve (AUC) (0.938 vs. 0.922 vs. 0.921). AVAILABILITY The proposed algorithm and dataset are available at https://github.com/ElaineLIU-920/ASVM-for-Early-Cancer-Detection. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Linjing Liu
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Xingjian Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
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A novel proteomics approach to epigenetic profiling of circulating nucleosomes. Sci Rep 2021; 11:7256. [PMID: 33790358 PMCID: PMC8012598 DOI: 10.1038/s41598-021-86630-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/18/2021] [Indexed: 12/26/2022] Open
Abstract
Alteration of epigenetic modifications plays an important role in human cancer. Notably, the dysregulation of histone post-translational modifications (PTMs) has been associated with several cancers including colorectal cancer (CRC). However, the signature of histone PTMs on circulating nucleosomes is still not well described. We have developed a fast and robust enrichment method to isolate circulating nucleosomes from plasma for further downstream proteomic analysis. This method enabled us to quantify the global alterations of histone PTMs from 9 CRC patients and 9 healthy donors. Among 54 histone proteoforms identified and quantified in plasma samples, 13 histone PTMs were distinctive in CRC. Notably, methylation of histone H3K9 and H3K27, acetylation of histone H3 and citrullination of histone H2A1R3 were upregulated in plasma of CRC patients. A comparative analysis of paired samples identified 3 common histone PTMs in plasma and tumor tissue including the methylation and acetylation state of lysine 27 of histone H3. Moreover, we highlight for the first time that histone H2A1R3 citrulline is a modification upregulated in CRC patients. This new method presented herein allows the detection and quantification of histone variants and histone PTMs from circulating nucleosomes in plasma samples and could be used for biomarker discovery of cancer.
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Mitroshina IY, Sirota NP, Prokofiev VN, Kuznetsova EA. Levels of Circulating DNA in Blood Serum and DNA Damage in Leukocytes of Healthy Donors of Different Genders and Ages. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921020147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Circulating Cell-Free DNA Methylation Profiles in the Early Detection of Ovarian Cancer: A Scoping Review of the Literature. Cancers (Basel) 2021; 13:cancers13040838. [PMID: 33671298 PMCID: PMC7923044 DOI: 10.3390/cancers13040838] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/04/2021] [Accepted: 02/11/2021] [Indexed: 12/27/2022] Open
Abstract
Simple Summary There are limited non-invasive methods for detecting epithelial ovarian cancer despite early detection and treatment dramatically increasing survival. As alterations in serum or plasma cell-free (cf)DNA methylation occur early in cancer development, they are promising biomarkers for ovarian cancer. Our literature review includes 18 studies depicting a wide array of gene targets and techniques. The data suggest a good performance of these cfDNA methylation tests, with accuracies up to 91% in detecting ovarian cancer in serum or plasma. Abstract Epithelial ovarian cancer is the most lethal gynecologic malignancy and has few reliable non-invasive tests for early detection or diagnosis. Recent advances in genomic techniques have bolstered the utility of cell-free DNA (cfDNA) evaluation from peripheral blood as a viable cancer biomarker. For multiple reasons, comparing alterations in DNA methylation is particularly advantageous over other molecular assays. We performed a literature review for studies exploring cfDNA methylation in serum and plasma for the early diagnosis of ovarian cancer. The data suggest that serum/plasma cfDNA methylation tests have strong diagnostic accuracies for ovarian cancer (median 85%, range 40–91%). Moreover, there is improved diagnostic performance if multiple genes are used and if the assays are designed to compare detection of ovarian cancer with benign pelvic masses. We further highlight the vast array of possible gene targets and techniques, and a need to include more earlier-stage ovarian cancer samples in test development. Overall, we show the promise of cfDNA methylation analysis in the development of a viable diagnostic biomarker for ovarian cancer.
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Camus V, Viennot M, Lequesne J, Viailly PJ, Bohers E, Bessi L, Marcq B, Etancelin P, Dubois S, Picquenot JM, Veresezan EL, Cornic M, Burel L, Loret J, Becker S, Decazes P, Lenain P, Lepretre S, Lemasle E, Lanic H, Ménard AL, Contentin N, Tilly H, Stamatoullas A, Jardin F. Targeted genotyping of circulating tumor DNA for classical Hodgkin lymphoma monitoring: a prospective study. Haematologica 2021; 106:154-162. [PMID: 32079702 PMCID: PMC7776248 DOI: 10.3324/haematol.2019.237719] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/12/2020] [Indexed: 11/28/2022] Open
Abstract
The relevance of circulating tumor DNA (ctDNA) analysis as a liquid biopsy and minimal residual disease tool in the management of classical Hodgkin lymphoma (cHL) patients was demonstrated in retrospective settings and remains to be confirmed in a prospective setting. We developed a targeted Next-Generation sequencing (NGS) panel for fast analysis (AmpliSeq® technology) of nine commonly mutated genes in biopies and ctDNA of cHL patients. We then conducted a prospective trial to assess ctDNA follow-up at diagnosis and after two cycles (C2) of chemotherapy. Sixty cHL patients treated by first line conventional chemotherapy (BEACOPPescalated [21.3%], ABVD/ABVD-like [73.5%] and other regimens [5.2%, for elderly patients]) were assessed in this noninterventional study. The median age of the patients was 33.5 years (range: 20-86). Variants were identified in 42 (70%) patients. Mutations of NFKBIE, TNFAIP3, STAT6, PTPN1, B2M, XPO1, ITPKB, GNA13 and SOCS1 were found in 13.3%, 31.7%, 23.3%, 5%, 33.3%, 10%, 23.3%, 13.3% and 50% of patients, respectively. ctDNA concentration and genotype were correlated with clinical characteristics and presentation. Regarding early therapeutic response, 45 patients (83%, not available [NA] =6) had a negative positron emission tomography (PET) after C2 (Deauville Score 1-3). The mean of DeltaSUVmax after C2 was -78.8%. ctDNA after C2 was analysed in 54 patients (90%). ctDNA became rapidly undetectable in all cases after C2. Variant detection in ctDNA is suitable to depict the genetic features of cHL at diagnosis and may help to assess early treatment response, in association with PET. Clinical Trial reference: NCT02815137.
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Affiliation(s)
- Vincent Camus
- Department of Hematology, Centre Henri Becquerel, University of Rouen, Rouen
| | - Mathieu Viennot
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen
| | | | | | - Elodie Bohers
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen
| | - Lucile Bessi
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Bénédicte Marcq
- Department of Hematology, Centre Henri Becquerel, University of Rouen, Rouen
| | | | - Sydney Dubois
- University of Rouen and Department of Genetic Oncology, Centre Henri Becquerel, Rouen
| | | | | | - Marie Cornic
- Clinical Research Unit, Centre Henri Becquerel, Rouen
| | - Lucie Burel
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Justine Loret
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Stéphanie Becker
- Department of Nuclear Medicine and Radiology, Centre Henri Becquerel and QuantIF, Rouen, France
| | - Pierre Decazes
- Department of Nuclear Medicine and Radiology, Centre Henri Becquerel and QuantIF, Rouen
| | - Pascal Lenain
- Department of Hematology, Centre Henri Becquerel, Rouen
| | - Stéphane Lepretre
- Department of Hematology, Centre Henri Becquerel, University of Rouen, Rouen
| | - Emilie Lemasle
- Department of Hematology, Centre Henri Becquerel, Rouen, France
| | - Hélène Lanic
- Department of Hematology, Centre Henri Becquerel, Rouen, France
| | | | | | - Hervé Tilly
- Department of Hematology, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | - Fabrice Jardin
- Department of Hematology, Centre Henri Becquerel, University of Rouen, Rouen, France
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Lam VK, Zhang J, Wu CC, Tran HT, Li L, Diao L, Wang J, Rinsurongkawong W, Raymond VM, Lanman RB, Lewis J, Roarty EB, Roth J, Swisher S, Lee JJ, Gibbons DL, Papadimitrakopoulou VA, Heymach JV. Genotype-Specific Differences in Circulating Tumor DNA Levels in Advanced NSCLC. J Thorac Oncol 2020; 16:601-609. [PMID: 33388476 DOI: 10.1016/j.jtho.2020.12.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/03/2020] [Accepted: 12/13/2020] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Plasma-based circulating tumor DNA (ctDNA) is an established biomarker for molecular profiling with emerging applications in disease monitoring in multiple tumor types, including, NSCLC. However, determinants of ctDNA shedding and correlation with tumor burden are incompletely understood, particularly in advanced-stage disease. METHODS We retrospectively analyzed ctDNA-based and tissue-based genomic data and imaging from 144 patients with NSCLC. Tumor burden was quantified with computed tomography (CT) and brain magnetic resonance imaging for the overall cohort and 18F-fludeoxyglucose positron emission tomography-CT in a subset of patients. RESULTS There was a moderate but statistically significant correlation between ctDNA variant allele frequency and multiple imaging measures of tumor burden such as CT volume (rho = 0.34, p ≤ 0.0001) and metabolic tumor volume (rho = 0.36, p = 0.003). This correlation was strongest in KRAS-mutant tumors (rho = 0.56, p ≤ 0.001), followed by TP53 mutants (rho = 0.43, p ≤ 0.0001), and weakest in EGFR-mutated (EGFR+) tumors (rho = 0.24, p = 0.077). EGFR+ tumors with EGFR copy number gain had significantly higher variant allele frequency than EGFR+ without copy number gain (p ≤ 0.00001). In multivariable analysis, TP53 and EGFR mutations, visceral metastasis, and tumor burden were independent predictors of increased ctDNA shedding. CONCLUSIONS Levels of detectable ctDNA were affected not only by tumor burden but also by tumor genotype. The genotype-specific differences observed may be due to variations in DNA shedding and cellular turnover. These findings have implications for the emerging use of ctDNA in NSCLC disease monitoring and early detection.
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Affiliation(s)
- Vincent K Lam
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carol C Wu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hai T Tran
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lerong Li
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lixia Diao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Waree Rinsurongkawong
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Jeff Lewis
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Emily B Roarty
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jack Roth
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Swisher
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Jack Lee
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Koçana CÇ, Toprak SF, Sözer S. Extracellular genetic materials and their application in clinical practice. Cancer Genet 2020; 252-253:48-63. [PMID: 33387935 DOI: 10.1016/j.cancergen.2020.12.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/12/2020] [Accepted: 12/20/2020] [Indexed: 11/20/2022]
Abstract
This study reviews the possible origins, functional roles, and diagnostic applications of 'extracellular genetic material' (EGM), a novel term introduced to cover DNA, RNA, and DNA/RNA-related molecules released from all types of cells into the extracellular region. The literature on EGMs shows them to play a dual role in diverse, fine-tuning mechanisms involved in both homeostasis and pathological events, including cancerogenesis and genometastasis. Recent developments in the next-generation technology have provided successful applications of low quantities of genomic materials into the diagnostic field, yielding high sensitivity and specificity in test results. Also, the successful application of EGMs into diagnostics has afforded promising outcomes for researchers and clinicians. This study of EGM provides a deeper understanding of the subject as an area of interest, especially cell-free DNA, aiming toward the eventual development of new therapeutic applications and diagnostic strategies.
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Affiliation(s)
- Cemal Çağıl Koçana
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selin Fulya Toprak
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selçuk Sözer
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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45
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Yuan Z, Wang X, Geng X, Li Y, Mu J, Tan F, Xue Q, Gao S, He J. Liquid biopsy for esophageal cancer: Is detection of circulating cell-free DNA as a biomarker feasible? Cancer Commun (Lond) 2020; 41:3-15. [PMID: 33264481 PMCID: PMC7819547 DOI: 10.1002/cac2.12118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 08/19/2020] [Accepted: 11/19/2020] [Indexed: 12/25/2022] Open
Abstract
Esophageal cancer (EC) is a common cancer and is histopathologically classified into esophageal squamous cell carcinoma and esophageal adenocarcinoma. EC is a worldwide public health issue because of late diagnosis and lack of effective therapy. In contrast to standard tumor biopsies, liquid biopsies are emerging as a tool which is minimally invasive that can complement or even substitute more classical approaches. Specifically, cell-free DNA (cfDNA) has shown promise in cancer-related clinical applications. Indeed, cfDNA has been shown to be an effective circulating biomarker for non-invasive cancer diagnosis and monitoring of cancer patients. Although the clinical application of cfDNA has been reported on other cancers, few studies have evaluated its use in EC. Here, we review this relevant literature and discuss limitations and advantages of its application in the diagnosis and monitoring of EC.
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Affiliation(s)
- Zuyang Yuan
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Xinfeng Wang
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Xiao Geng
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Yin Li
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Juwei Mu
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Fengwei Tan
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Qi Xue
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Shugeng Gao
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
| | - Jie He
- Department of Thoracic SurgeryNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing100021P. R. China
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46
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Safi M, Najib AR. Evaluation of circulating cell-free nuclear and mitochondrial DNA levels in Syrian patients with breast tumor. Exp Ther Med 2020; 21:65. [PMID: 33365065 PMCID: PMC7716636 DOI: 10.3892/etm.2020.9497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/03/2020] [Indexed: 01/05/2023] Open
Abstract
In the last decade, the roles of circulating cell free nuclear (ccfn) and ccf mitochondrial (ccfmt) DNA as potential noninvasive biomarkers have been demonstrated in numerous different types of disease, including cancer. However, the results remain controversial. The present study aimed to investigate the roles of ccfnDNA and ccfmtDNA levels in the plasma of patients with breast cancer. A total of 84 Syrian female subjects were included in the study, who were divided into 3 groups: i) Malignant disease group (n=33); ii) benign disease group (n=26); and iii) healthy control group (n=25). CcfnDNA and ccfmtDNA were determined using real-time quantitative PCR and the reactions were followed by melting curve analysis. The results indicated no significant differences in the plasma levels of ccfnDNA, ccfmtDNA or the ratio of ccfmtDNA/ccfnDNA between the study groups. Of note, a positive correlation was observed between the ccfmtDNA/ccfnDNA ratio and age in the control group (P=0.012; r=0.505). In addition, a positive correlation was identified between ccfnDNA levels and the estrogen receptor status (P=0.045; r=0.416), while a negative correlation between ccfmtDNA/ccfnDNA ratio and the progesterone receptor status was obtained (P=0.045; r=-0.448. Aging and the role of hormones in the cells may be responsible for these results. In the future, the present study should be followed up with mutation detection analyses and large-scale studies.
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Affiliation(s)
- Milda Safi
- Department of Biochemistry and Microbiology, Faculty of Pharmacy, Damascus University, Damascus 22743, Syria
| | - Abdul Rahman Najib
- Department of Biostatistics, Faculty of Statistics, Damascus University, Damascus 22743, Syria
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47
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Zhou F, Sun S, Sun X, Chen Y, Yang X. Rapid and sensitive identification of pleural and peritoneal infections by droplet digital PCR. Folia Microbiol (Praha) 2020; 66:213-219. [PMID: 33159654 PMCID: PMC7648221 DOI: 10.1007/s12223-020-00834-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/19/2020] [Indexed: 01/08/2023]
Abstract
Pleural and peritoneal infections cause substantial morbidity and mortality. Traditional diagnostic methods rely on the cultivation of clinical samples, which usually takes days to obtain report and holds a low detection sensitivity. In this study, we evaluated a 5-fluorescent-channel droplet digital PCR (ddPCR) system and 5 assay panels for culture-independent rapid pathogen detections directly from pleural and peritoneal fluid samples. Traditional culture of the same sample was used as reference. A total of 40 pleural fluid samples and 19 peritoneal fluid samples were tested in this study. Twenty-five positives including 4 polymicrobial infections by culture and 26 positives including 11 polymicrobial infections by ddPCR were detected for pleural fluid samples; 14 positives including 2 polymicrobial infections by culture and 15 positives including 3 polymicrobial infections by ddPCR were detected for peritoneal fluid samples. Klebsiella pneumoniae was the most common bacterium detected both in pleural and in peritoneal fluid samples. The sensitivity of the ddPCR assay for pleural and peritoneal fluid samples was 96% (95% confidence interval (CI) = 79.65 to 99.90%) and 92.86% (95% CI = 66.13 to 99.82%), respectively. The turnaround time of the ddPCR assay was approximately 3 h comparing with 38.30 ± 22.44 h for culture-based identifications. Our results demonstrated that the ddPCR assay is a rapid and sensitive method for identifying pathogens responsible for pleural and peritoneal infections and would be a promising approach for early diagnosis and optimizing treatment of infections.
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Affiliation(s)
- Fangmei Zhou
- College of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, People's Republic of China
| | - Shoudong Sun
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, 310006, Zhejiang, People's Republic of China.,The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, People's Republic of China
| | - Xiling Sun
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, 310006, Zhejiang, People's Republic of China
| | - Ye Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, 310006, Zhejiang, People's Republic of China.,The First Clinical Medical College of Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, People's Republic of China
| | - Xuejing Yang
- Department of Clinical Laboratory, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Youdian Road, Hangzhou, 310006, Zhejiang, People's Republic of China.
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48
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Gassa A, Fassunke J, Schueten S, Kuhlmann L, Scherer M, Qien J, Zhao Y, Michel M, Loeser H, Wolf J, Buettner R, Doerr F, Heldwein M, Hagmeyer L, Frank K, Merkelbach-Bruse S, Quaas A, Bruns C, Hekmat K, Weiss J, Wahlers T, Alakus H. Detection of circulating tumor DNA by digital droplet PCR in resectable lung cancer as a predictive tool for recurrence. Lung Cancer 2020; 151:91-96. [PMID: 33257044 DOI: 10.1016/j.lungcan.2020.10.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 01/05/2023]
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide due to difficulties in early detection and high postsurgical recurrence rate. Current European Guidelines recommend follow-up via computerized tomography (CT) scans on regular basis within the first 2 years after radical surgical resection. Despite these efforts, recurrence rates remain high with 30-70 %. Therefore, it is imperative to develop predictive markers for metastases and postsurgical recurrence using minimally invasive methods. This prospective study aims at defining the feasibility of detecting circulating tumor DNA (ctDNA) in presurgical plasma samples of patients with lung cancer by digital droplet PCR. Resected tumor tissue and simultaneous blood samples were collected from 24 patients with lung cancer in stage I-IIIA (12 stage I, 8 stage II, 4 stage III). Genomic DNA from the tumor tissue samples were analyzed for hotspot mutations using a 17 gene panel next-generation sequencing (NGS) assay. CtDNA from corresponding plasma samples were analyzed using digital droplet PCR (ddPCR). Additionally, DNA sequencing results were correlated with patients' outcome. At least one somatic mutation was detected by NGS (96 %) in 23 of the tested tissue samples. DdPCR detected mutations in circulating cell-free DNA (ccfDNA) of nine patients' samples (9/23, 39 %). Postsurgical outcome analysis was performed for those patients who had received complete tumor resection (n = 21). Four of them suffered from an early relapse within the first two years after surgery, including two with detectable somatic mutations in ccfDNA during primary staging. Taken together, we showed that the 17 gene panel assay revealed in 23 of 24 patients at least one somatic mutation in the primary tumor by NGS. Tumor-specific mutation was detectable in 39 % from the blood of early stage lung cancer patients by ddPCR.
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Affiliation(s)
- Asmae Gassa
- Department of Cardiothoracic Surgery, University of Cologne, Germany; Department of General, Visceral, and Cancer Surgery, University of Cologne, Germany.
| | - Jana Fassunke
- Institute of Pathology, University of Cologne, Germany
| | - Sarah Schueten
- Department of Cardiothoracic Surgery, University of Cologne, Germany; Department of General, Visceral, and Cancer Surgery, University of Cologne, Germany; School of Medicine, University of Cologne, Germany
| | - Luca Kuhlmann
- Department of Cardiothoracic Surgery, University of Cologne, Germany; Department of General, Visceral, and Cancer Surgery, University of Cologne, Germany; School of Medicine, University of Cologne, Germany
| | - Marie Scherer
- Department of General, Visceral, and Cancer Surgery, University of Cologne, Germany; School of Medicine, University of Cologne, Germany
| | - Jie Qien
- Department of General, Visceral, and Cancer Surgery, University of Cologne, Germany
| | - Yue Zhao
- Department of General, Visceral, and Cancer Surgery, University of Cologne, Germany
| | - Max Michel
- Institute of Zoology, University of Cologne, Germany
| | - Heike Loeser
- Institute of Pathology, University of Cologne, Germany
| | - Juergen Wolf
- Department of Internal Medicine I, University of Cologne, Germany
| | | | - Fabian Doerr
- Department of Cardiothoracic Surgery, University of Cologne, Germany
| | - Matthias Heldwein
- Department of Cardiothoracic Surgery, University of Cologne, Germany
| | - Lars Hagmeyer
- Hospital Bethanien Solingen, Institute of Pneumology, University of Cologne, Solingen, Germany
| | - Konrad Frank
- Department of Internal Medicine III, University of Cologne, Germany
| | | | | | - Christiane Bruns
- Department of General, Visceral, and Cancer Surgery, University of Cologne, Germany
| | - Khosro Hekmat
- Department of Cardiothoracic Surgery, University of Cologne, Germany
| | - Jonathan Weiss
- Department of Internal Medicine I, University of Cologne, Germany
| | - Thorsten Wahlers
- Department of Cardiothoracic Surgery, University of Cologne, Germany
| | - Hakan Alakus
- Department of General, Visceral, and Cancer Surgery, University of Cologne, Germany
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Abstract
BACKGROUND Clinical application of immune checkpoint inhibitors (ICI), whether as monotherapy or in combination with established methods, is revolutionizing treatment of head and neck cancer. However, this change in therapeutic concepts requires reevaluation and further development of predictive and prognostic markers, since the survival rates for advanced and particularly human papillomavirus (HPV)-negative disease remain poor. MATERIALS AND METHODS A selective literature review was performed in PubMed. Literature found with the keywords "cytodiagnostics, circulating tumor cells, liquid biopsy, cfDNA, exosomes" in combination with "head and neck cancer" and/or "immune checkpoint inhibitor therapy" published until March 2020 was included. The articles were selected for their relevance for the current study by the authors. RESULTS This work provides a review of the current literature and indicates possible applications in the field of head and neck cancers. Liquid biopsy refers to the analysis of circulating tumor cells or of tumor genetic material in body fluids. This minimally invasive analysis can support therapeutic decisions and enable a personalized approach to treating head and neck cancer. DISCUSSION Before any of these approaches can be established in clinical routine, long-term data and standardization of the methods for isolating and analyzing the markers are needed.
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50
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Sciandra M, De Feo A, Parra A, Landuzzi L, Lollini PL, Manara MC, Mattia G, Pontecorvi G, Baricordi C, Guerzoni C, Bazzocchi A, Longhi A, Scotlandi K. Circulating miR34a levels as a potential biomarker in the follow-up of Ewing sarcoma. J Cell Commun Signal 2020; 14:335-347. [PMID: 32504411 PMCID: PMC7511499 DOI: 10.1007/s12079-020-00567-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/24/2020] [Indexed: 01/06/2023] Open
Abstract
Appropriate tools for monitoring sarcoma progression are still limited. The aim of the present study was to investigate the value of miR-34a-5p (miR34a) as a circulating biomarker to follow disease progression and measure the therapeutic response. Stable forced re-expression of miR34a in Ewing sarcoma (EWS) cells significantly limited tumor growth in mice. Absolute quantification of miR34a in the plasma of mice and 31 patients showed that high levels of this miRNA inversely correlated with tumor volume. In addition, miR34a expression was higher in the blood of localized EWS patients than in the blood of metastatic EWS patients. In 12 patients, we followed miR34a expression during preoperative chemotherapy. While there was no variation in the blood miR34a levels in metastatic patients at the time of diagnosis or after the last cycle of preoperative chemotherapy, there was an increase in the circulating miR34a levels in patients with localized tumors. The three patients with the highest fold-increase in the miR levels did not show evidence of metastasis. Although this analysis should be extended to a larger cohort of patients, these findings imply that detection of the miR34a levels in the blood of EWS patients may assist with the clinical management of EWS.
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Affiliation(s)
- Marika Sciandra
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136 Bologna, Italy
| | - Alessandra De Feo
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136 Bologna, Italy
| | - Alessandro Parra
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136 Bologna, Italy
| | - Lorena Landuzzi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136 Bologna, Italy
| | - Pier-Luigi Lollini
- Department of Experimental, Diagnostic and Specialty Medicine, DIMES, University of Bologna, Bologna, Italy
| | - Maria Cristina Manara
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136 Bologna, Italy
| | - Gianfranco Mattia
- Oncology Unit, Center for Gender Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Giada Pontecorvi
- Oncology Unit, Center for Gender Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Cristina Baricordi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136 Bologna, Italy
| | - Clara Guerzoni
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136 Bologna, Italy
| | - Alberto Bazzocchi
- Diagnostic and Interventional Radiology, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Alessandra Longhi
- Department of Chemotherapy, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology, IRCCS Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136 Bologna, Italy
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