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Zarkavelis G, Amylidi AL, Torounidou N, Yerolatsite M, Keravasili A, Keramisanou V, Mauri D. Exploring RAS mutation incidence and temporal heterogeneity in metastatic colorectal cancer patients - a single-institution experience utilising circulating tumour DNA. Contemp Oncol (Pozn) 2024; 28:45-50. [PMID: 38800532 PMCID: PMC11117156 DOI: 10.5114/wo.2024.138899] [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: 02/14/2024] [Accepted: 03/25/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Colorectal cancer (CRC) remains a significant global health challenge, ranking among the leading causes of neoplastic mortality. Despite transformative therapeutic advances, a considerable proportion of patients are diagnosed with metastatic disease, and 15-30% of those initially presenting with early-stage CRC eventually experience recurrence. Comprehensive molecular testing, especially the evaluation of microsatellite instability and mutations in KRAS/NRAS or BRAF genes, is essential upon diagnosis of stage IV disease, guiding treatment decisions. Material and methods This manuscript explores the mutational landscape of KRAS and NRAS in patients with CRC, employing digital polymerase chain reaction (PCR) BEAMing for the detection of mutations in liquid biopsy. Our study enrolled patients with histologically confirmed CRC and stage IV disease, focusing on identifying mutations in KRAS and NRAS genes during various stages of therapy. Results Evaluating baseline, midline, and progression samples, we found that 66.6% maintained consistent mutational status post-disease progression, while 33.3% exhibited a shift in mutational status. The application of techniques with high sensitivity, such as BEAMing Digital PCR, is pivotal for accurate circulating tumour DNA (ctDNA) mutation detection. The study underscores the significance of continuous molecular monitoring in guiding therapeutic decisions for patients with metastatic CRC. Conclusions Our findings contribute to our understanding of the evolving mutational landscape and the potential clinical implications of ctDNA ana- lysis in the era of personalised cancer medicine.
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Affiliation(s)
- George Zarkavelis
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
| | - Anna Lea Amylidi
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
| | - Nanteznta Torounidou
- Department of Medical Oncology, University Hospital of Ioannina, Ioannina, Greece
| | - Melina Yerolatsite
- Department of Medical Oncology, University Hospital of Ioannina, Ioannina, Greece
| | - Athanasia Keravasili
- Department of Medical Oncology, University Hospital of Ioannina, Ioannina, Greece
| | - Varvara Keramisanou
- Department of Medical Oncology, University Hospital of Ioannina, Ioannina, Greece
| | - Davide Mauri
- Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
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Long Y, Zhao J, Ma W, He C, Pei W, Hou J, Hou C, Huo D. Fe Single-Atom Carbon Dots Nanozyme Collaborated with Nucleic Acid Exonuclease III-Driven DNA Walker Cascade Amplification Strategy for Circulating Tumor DNA Detection. Anal Chem 2024; 96:4774-4782. [PMID: 38477105 DOI: 10.1021/acs.analchem.3c04202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Circulating tumor DNA (ctDNA), as a next-generation tumor marker, enables early screening and monitoring of cancer through noninvasive testing. Exploring the development of new methods for ctDNA detection is an intriguing study. In this work, a unique electrochemical biosensor for the ctDNA detector was constructed in the first utilizing Fe single-atom nanozymes-carbon dots (SA Fe-CDs) as a signaling carrier in collaboration with a DNA walker cascade amplification strategy triggered by nucleic acid exonuclease III (Exo III). The electrochemical active surface area of AuNPs/rGO modified onto a glassy carbon electrode (AuNPs/rGO/GCE) was about 1.43 times that of a bare electrode (bare GCE), with good electrical conductivity alongside a high heterogeneous electron transfer rate (5.81 × 10-3 cm s-1), that is, as well as the ability to load more molecules. Sequentially, the DNA walker cascade amplification strategy driven by Exo III effectively converted the target ctDNA into an amplified biosignal, ensuring the sensitivity and specificity of ctDNA. Ultimately, the electrochemical signal was further amplified by introducing SA Fe-CDs nanozymes, which could serve as catalysts for 3,3',5,5'-tetramethylbenzidine (TMB) oxidation with facile responding (Vmax = 0.854 × 10-6 M s-1) and robust annexation (Km = 0.0069 mM). The integration of the triple signal amplification approach achieved detection limits as low as 1.26 aM (S/N = 3) for a linearity spanning from 5 aM to 50 nM. In this regard, our proposal for a biosensor with exceptional assay properties in complicated serum environments had great potential for early and timely diagnosis of cancer.
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Affiliation(s)
- Yanyi Long
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Jiaying Zhao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Wanting Ma
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Congjuan He
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Wen Pei
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Jingzhou Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing 401331, P. R. China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing 401331, P. R. China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, P. R. China
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Shang X, Zhang C, Kong R, Zhao C, Wang H. Construction of a Diagnostic Model for Small Cell Lung Cancer Combining Metabolomics and Integrated Machine Learning. Oncologist 2024; 29:e392-e401. [PMID: 37706531 PMCID: PMC10911920 DOI: 10.1093/oncolo/oyad261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 08/09/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND To date, no study has systematically explored the potential role of serum metabolites and lipids in the diagnosis of small cell lung cancer (SCLC). Therefore, we aimed to conduct a case-cohort study that included 191 cases of SCLC, 91 patients with lung adenocarcinoma, 82 patients with squamous cell carcinoma, and 97 healthy controls. METHODS Metabolomics and lipidomics were applied to analyze different metabolites and lipids in the serum of these patients. The SCLC diagnosis model (d-model) was constructed using an integrated machine learning technology and a training cohort (n = 323) and was validated in a testing cohort (n=138). RESULTS Eight metabolites, including 1-mristoyl-sn-glycero-3-phosphocholine, 16b-hydroxyestradiol, 3-phosphoserine, cholesteryl sulfate, D-lyxose, dioctyl phthalate, DL-lactate and Leu-Phe, were successfully selected to distinguish SCLC from controls. The d-model was constructed based on these 8 metabolites and showed improved diagnostic performance for SCLC, with the area under curve (AUC) of 0.933 in the training cohort and 0.922 in the testing cohort. Importantly, the d-model still had an excellent diagnostic performance after adjusting the stage and related clinical variables and, combined with the progastrin-releasing peptide (ProGRP), showed the best diagnostic performance with 0.975 of AUC for limited-stage patients. CONCLUSION This study is the first to analyze the difference between metabolomics and lipidomics and to construct a d-model to detect SCLC using integrated machine learning. This study may be of great significance for the screening and early diagnosis of SCLC patients.
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Affiliation(s)
- Xiaoling Shang
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong University, Jinan, People’s Republic of China
| | - Chenyue Zhang
- Department of Integrated Therapy, Fudan University Shanghai Cancer Center, Shanghai Medical College, Shanghai, People’s Republic of China
| | - Ronghua Kong
- Department of Breast Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
| | - Chenglong Zhao
- Department of Pathology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, Shandong, People’s Republic of China
| | - Haiyong Wang
- Department of Internal Medicine-Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, People’s Republic of China
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Witz A, Dardare J, Betz M, Gilson P, Merlin JL, Harlé A. Tumor-derived cell-free DNA and circulating tumor cells: partners or rivals in metastasis formation? Clin Exp Med 2024; 24:2. [PMID: 38231464 PMCID: PMC10794481 DOI: 10.1007/s10238-023-01278-9] [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: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 01/18/2024]
Abstract
The origin of metastases is a topic that has sparked controversy. Despite recent advancements, metastatic disease continues to pose challenges. The first admitted model of how metastases develop revolves around cells breaking away from the primary tumor, known as circulating tumor cells (CTCs). These cells survive while circulating through the bloodstream and subsequently establish themselves in secondary organs, a process often referred to as the "metastatic cascade". This intricate and dynamic process involves various steps, but all the mechanisms behind metastatic dissemination are not yet comprehensively elucidated. The "seed and soil" theory has shed light on the phenomenon of metastatic organotropism and the existence of pre-metastatic niches. It is now established that these niches can be primed by factors secreted by the primary tumor before the arrival of CTCs. In particular, exosomes have been identified as important contributors to this priming. Another concept then emerged, i.e. the "genometastasis" theory, which challenged all other postulates. It emphasizes the intriguing but promising role of cell-free DNA (cfDNA) in metastasis formation through oncogenic formation of recipient cells. However, it cannot be ruled out that all these theories are intertwined. This review outlines the primary theories regarding the metastases formation that involve CTCs, and depicts cfDNA, a potential second player in the metastasis formation. We discuss the potential interrelationships between CTCs and cfDNA, and propose both in vitro and in vivo experimental strategies to explore all plausible theories.
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Affiliation(s)
- Andréa Witz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France.
| | - Julie Dardare
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Margaux Betz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Pauline Gilson
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Jean-Louis Merlin
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Alexandre Harlé
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
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Li S, Gu Y, Geng Z, Li K, Hu Y, Liu Q, Fu R, Liu P. Tweezer PCR: A Highly Specific Method for Accurate Identification of Low-Abundance Mutations. Anal Chem 2023; 95:17679-17690. [PMID: 37971891 DOI: 10.1021/acs.analchem.3c03467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Somatic mutation is a valuable biomarker for tracking tumor progression and migration due to its distinctive feature in various tumors and its wide distribution throughout body fluids. However, accurately detecting somatic mutations from the abundant DNA of noncancerous origins remains a practical challenge in the clinic. Herein, we developed an ultraspecific method, called tweezer PCR, for detecting low-abundance mutations inspired by the design of DNA origami. The high specificity of tweezer PCR relies on a tweezer-shaped primer containing six basic functional units: a primer, a hairpin, a linker, a blocker, a spacer, and a toehold. After optimizing the structure of the tweezer-shaped primer and enhancing its specificity by adding additional Mg2+ and Na+, tweezer PCR distinguished as low as 20 copies of mutations from 2 million copies of wild-type templates per test. By testing synthesized plasmids and plasma samples gathered from nonsmall-cell lung cancer patients, tweezer PCR showed higher specificity and robustness for detecting low-copy-number mutations in contrast with digital droplet PCR. Additionally, the need for conventional instruments makes tweezer PCR a practically accessible method for testing low-abundance mutations. Because of its numerous advantages, we believe that tweezer PCR offers a precise, robust, and pragmatic tool for cancer screening, prognosis, and genotyping in the clinic.
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Affiliation(s)
- Shanglin Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- Changping Laboratory, Beijing 102206, China
| | - Yin Gu
- State Key Laboratory of Space Medicine, China Astronaut Research and Training Center, Beijing 100094, China
| | - Zhi Geng
- Shimadzu Research Laboratory (Shanghai) Co. Ltd, Shanghai 201206, China
| | - Kaiyi Li
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yawei Hu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- Changping Laboratory, Beijing 102206, China
| | - Qiang Liu
- Beijing Haidian Hospital, Beijing 100080, China
| | - Rongxin Fu
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing 100084, China
- Changping Laboratory, Beijing 102206, China
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Liu Z, Li X, Zhang R, Ji L, Gong L, Ji Y, Zhou F, Yin Y, Li K, Sun P, Pu Z, Wang Q, Zou J. Identification of DNA variants at ultra-low variant allele frequencies via Taq polymerase cleavage of wild-specific blockers. Anal Bioanal Chem 2023; 415:6537-6549. [PMID: 37702773 DOI: 10.1007/s00216-023-04931-0] [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: 07/11/2023] [Revised: 08/27/2023] [Accepted: 08/29/2023] [Indexed: 09/14/2023]
Abstract
Detecting mutations related to tumors holds immense clinical significance for cancer diagnosis and treatment. However, the presence of highly redundant wild DNA poses a challenge for the advancement of low-copy mutant ctDNA genotyping in cancer cases. To address this, a Taqman qPCR strategy to identify rare mutations at low variant allele fractions (VAFs) has been developed. This strategy combines mutant-specific primers with wild-specific blockers. Diverging from other blocker-mediated PCRs, which rely on primer-induced strand displacement or the use of modified oligos resistant to Taq polymerase, our innovation is built upon the cleavage of specific blockers by Taq polymerase. Given its unique design, which does not hinge on strand displacement or base modification, we refer to this novel method as unmodified-blocker cleavage PCR (UBC-PCR). Multiple experiments consistently confirmed that variant distinction was improved significantly by introduction of 5' unmatched blockers into the reaction. Moreover, UBC-PCR successfully detected mutant DNA at VAFs as low as 0.01% across six different variant contexts. Multiplex UBC-PCR was also performed to identify a reference target and three mutations with a sensitivity of 0.01% VAFs in one single tube. In profiling the gene status from 12 lung cancer ctDNA samples and 22 thyroid cancer FNA DNA samples, UBC-PCR exhibited a 100% concordance rate with ddPCR and a commercial ARMS kit, respectively. Our work demonstrates that UBC-PCR can identify low-abundance variants with high sensitivity in multiplex reactions, independent of strand displacement and base modification. This strategy holds the potential to significantly impact clinical practice and precision medicine.
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Affiliation(s)
- Zhaocheng Liu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Xiushuai Li
- Department of Neurosurgery, The Affiliated Wuxi Second Hospital of Nanjing Medical University, 68 Zhongshan Road, Wuxi, 214122, Jiangsu Province, China
| | - Rui Zhang
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Li Ji
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Lingli Gong
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Yong Ji
- Department of Thoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Fengsheng Zhou
- Department of Ultrasound, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Ying Yin
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Koukou Li
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Ping Sun
- Department of Pathology, Jiangnan University Medical Center, Wuxi, 214023, Jiangsu, China
| | - Zhening Pu
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Qing Wang
- Department of Neurosurgery, The Affiliated Wuxi Second Hospital of Nanjing Medical University, 68 Zhongshan Road, Wuxi, 214122, Jiangsu Province, China.
| | - Jian Zou
- Department of Laboratory Medicine, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, 299 Qingyang Road, Wuxi, 214023, Jiangsu, China.
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China.
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Britze TE, Jakobsen KK, Grønhøj C, von Buchwald C. A systematic review on the role of biomarkers in liquid biopsies and saliva samples in the monitoring of salivary gland cancer. Acta Otolaryngol 2023; 143:709-713. [PMID: 37534452 DOI: 10.1080/00016489.2023.2238757] [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: 05/25/2023] [Accepted: 07/16/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND Salivary gland cancer is a rare disease, and approximately 20% of tumors in the salivary glands are malignant. Reliable biomarkers may have a role in monitoring salivary gland cancer. AIM To review the current literature on the role of biomarkers in liquid biopsies and saliva samples in the monitoring of salivary gland cancer. MATERIALS AND METHOD This study systematically reviewed the literature on studies detecting salivary gland cancer by biomarkers in liquid biopsies and saliva samples by systematically searching PubMed and Embase between 1 January 2013 and 7 March 2023. RESULTS Five studies covering 64 malignant cases of salivary gland cancer were included, which considered inflammatory biomarkers or markers of genetic material in either blood or saliva. In saliva, there were demonstrated elevations of CA-19-9 in malignant cases, and elevations of miRNA in malignant and benign cases. In blood, there were demonstrated elevations of IL-33 in malignant and benign cases, elevations of ctDNA in malignant cases, and elevations of CTC in malignant cases. CONCLUSION AND SIGNIFICANCE The studies indicate that there is potential in the detection method. The studies detecting genetic material by liquid biopsies showed the most promising results. At present, there is still progression to be made before the method can be implemented for diagnostic use.
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Affiliation(s)
- Theresa Emilia Britze
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kathrine Kronberg Jakobsen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Christian Grønhøj
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, Copenhagen, Denmark
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Anoop TM, Basu PK, Chandramohan K, Thomas A, Manoj S. Evolving utility of exosomes in pancreatic cancer management. World J Methodol 2023; 13:46-58. [PMID: 37456979 PMCID: PMC10348087 DOI: 10.5662/wjm.v13.i3.46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/02/2023] [Accepted: 05/31/2023] [Indexed: 06/20/2023] Open
Abstract
Despite the development of newer oncological treatment, the survival of patients with pancreatic cancer (PC) remains poor. Recent studies have identified exosomes as essential mediators of intercellular communications and play a vital role in tumor initiation, metastasis and chemoresistance. Thus, the utility of liquid biopsies using exosomes in PC management can be used for early detection, diagnosis, monitoring as well as drug delivery vehicles for cancer therapy. This review summarizes the function, and clinical applications of exosomes in cancers as minimally invasive liquid biomarker in diagnostic, prognostic and therapeutic roles.
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Affiliation(s)
- Thattungal Manoharan Anoop
- Department of Medical Oncology, Regional Cancer Center, Medical College Campus, Thiruvananthapuram 695011, Kerala, India
| | - Palash Kumar Basu
- Department of Avionics, Indian Institute of Space Science & Technology (IIST), Thiruvananthapuram 695547, Kerala, India
| | - K Chandramohan
- Surgical Oncology, Regional Cancer Center, Thiruvananthapuram 695011, Kerala, India
| | - Ajai Thomas
- Department of Medical Oncology, Regional Cancer Center, Medical College Campus, Thiruvananthapuram 695011, Kerala, India
| | - S Manoj
- Department of Medical Oncology, Regional Cancer Center, Medical College Campus, Thiruvananthapuram 695011, Kerala, India
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Kumar RR, Kumar A, Chuang CH, Shaikh MO. Recent Advances and Emerging Trends in Cancer Biomarker Detection Technologies. Ind Eng Chem Res 2023. [DOI: 10.1021/acs.iecr.2c04097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Rajkumar Rakesh Kumar
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Amit Kumar
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Cheng-Hsin Chuang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Muhammad Omar Shaikh
- Sustainability Science and Management, Tunghai University, Taichung 407224, Taiwan
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Lee SH, Cha B, Ko J, Afzal M, Park J. Acoustofluidic separation of proteins from platelets in human blood plasma using aptamer-functionalized microparticles. BIOMICROFLUIDICS 2023; 17:024105. [PMID: 37153865 PMCID: PMC10162022 DOI: 10.1063/5.0140096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/20/2023] [Indexed: 05/10/2023]
Abstract
Microfluidic liquid biopsy has emerged as a promising clinical assay for early diagnosis. Herein, we propose acoustofluidic separation of biomarker proteins from platelets in plasma using aptamer-functionalized microparticles. As model proteins, C-reactive protein and thrombin were spiked in human platelet-rich plasma. The target proteins were selectively conjugated with their corresponding aptamer-functionalized microparticles of different sizes, and the particle complexes served as a mobile carrier for the conjugated proteins. The proposed acoustofluidic device was composed of an interdigital transducer (IDT) patterned on a piezoelectric substrate and a disposable polydimethylsiloxane (PDMS) microfluidic chip. The PDMS chip was placed in a tilted arrangement with the IDT to utilize both vertical and horizontal components of surface acoustic wave-induced acoustic radiation force (ARF) for multiplexed assay at high-throughput. The two different-sized particles experienced the ARF at different magnitudes and were separated from platelets in plasma. The IDT on the piezoelectric substrate could be reusable, while the microfluidic chip can be replaceable for repeated assays. The sample processing throughput with the separation efficiency >95% has been improved such that the volumetric flow rate and flow velocity were 1.6 ml/h and 37 mm/s, respectively. For the prevention of platelet activation and protein adsorption to the microchannel, polyethylene oxide solution was introduced as sheath flows and coating on to the walls. We conducted scanning electron microscopy, x-ray photoemission spectroscopy , and sodium dodecyl sulfate- analysis before and after the separation to confirm the protein capture and separation. We expect that the proposed approach will provide new prospects for particle-based liquid biopsy using blood.
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Affiliation(s)
- Song Ha Lee
- Department of Mechanical Engineering, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Beomseok Cha
- Department of Mechanical Engineering, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Jeongu Ko
- Department of Mechanical Engineering, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
| | - Muhammad Afzal
- Center of Immunology Marseille-Luminy, Aix-Marseille University, 171 Av, De Luminy, 13009 Marseille, France
| | - Jinsoo Park
- Department of Mechanical Engineering, Chonnam National University, 77 Yongbong-ro, Buk-gu, Gwangju 61186, Republic of Korea
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11
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Gong C, Mao X, Wang Z, Luo Z, Liu Z, Ben Y, Zhang W, Guo Z. Near-Infrared Light Regulation of Capture and Release of ctDNA Platforms Based on the DNA Assembly System. Front Bioeng Biotechnol 2022; 10:891727. [PMID: 35832403 PMCID: PMC9272789 DOI: 10.3389/fbioe.2022.891727] [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: 03/08/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Despite recent progress, a challenge remains on how to gently release and recover viable ctDNA captured on DNA probe-based devices. Here, a reusable detector was successfully manufactured for the capture and release of ctDNA by means of an UCNPs@SiO2-Azo/CD-probe. Biocompatible NIR light is used to excite UCNPs and convert into local UV light. Continuous irradiation induces a rapid release of the entire ctDNA-probe–CD complex from the functionalized surface via the trans−cis isomerization of azo units without disrupting the ctDNA-structure receptor. Specifically, these composite chips allow reloading DNA probes for reusable ctDNA detection with no obvious influence on their efficiency. The results of our study demonstrated the potential application of this platform for the quantitative detection of ctDNA and the individualized analysis of cancer patients.
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Affiliation(s)
- Chaihong Gong
- School of Life Science, Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Jianghan University, Wuhan, China
| | - Xiaowei Mao
- School of Environment and Health, Jianghan University, Wuhan, China
| | - Zhe Wang
- School of Medicine, Jianghan University, Wuhan, China
| | - Zhang Luo
- School of Life Science, Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Jianghan University, Wuhan, China
| | - Zhifan Liu
- School of Life Science, Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Jianghan University, Wuhan, China
| | - Yali Ben
- School of Medicine, Jianghan University, Wuhan, China
- *Correspondence: Yali Ben, ; Weiying Zhang,
| | - Weiying Zhang
- School of Life Science, Key Laboratory of Optoelectronic Chemical Materials and Devices of Ministry of Education, Jianghan University, Wuhan, China
- *Correspondence: Yali Ben, ; Weiying Zhang,
| | - Zhenzhong Guo
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan, China
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12
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Dhiman A, Vining CC, Witmer HDD, Sood D, Shergill A, Kindler H, Roggin KK, Posner MC, Ahmed OS, Liauw S, Pitroda S, Liao CY, Karrison T, Weichselbaum R, Polite B, Eng OS, Catenacci DVT, Turaga KK. Phase II Prospective, Open-Label Randomized Controlled Trial Comparing Standard of Care Chemotherapy With and Without Sequential Cytoreductive Interventions for Patients with Oligometastatic Foregut Adenocarcinoma and Undetectable Circulating Tumor Deoxyribose Nucleic Acid (ctDNA) Levels. Ann Surg Oncol 2022; 29:10.1245/s10434-021-11249-7. [PMID: 34988836 PMCID: PMC8730296 DOI: 10.1245/s10434-021-11249-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/07/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Metastatic adenocarcinomas of foregut origin are aggressive and have limited treatment options, poor quality of life, and a dismal prognosis. A subset of such patients with limited metastatic disease might have favorable outcomes with locoregional metastasis-directed therapies. This study investigates the role of sequential cytoreductive interventions in addition to the standard of care chemotherapy in patients with oligometastatic foregut adenocarcinoma. METHODS This is a single-center, phase II, open-label randomized clinical trial. Eligible patients include adults with synchronous or metachronous oligometastatic (metastasis limited to two sites and amenable for curative/ablative treatment) adenocarcinoma of the foregut without progression after induction chemotherapy and having undetectable ctDNA. These patients will undergo induction chemotherapy and will then be randomized (1:1) to either sequential curative intervention followed by maintenance chemotherapy versus routine continued chemotherapy. The primary endpoint is progression-free survival (PFS), and a total of 48 patients will be enrolled to detect an improvement in the median PFS in the intervention arm with a hazard ratio (HR) of 0.5 with 80% power and a one-sided alpha of 0.1. Secondary endpoints include disease-free survival (DFS) in the intervention arm, overall survival (OS), ctDNA conversion rate pre/post-induction chemotherapy, ctDNA PFS, PFS2, adverse events, quality of life, and financial toxicity. DISCUSSION This is the first randomized study that aims to prospectively evaluate the efficacy and safety of surgical/ablative interventions in patients with ctDNA-negative oligometastatic adenocarcinoma of foregut origin post-induction chemotherapy. The results from this study will likely develop pertinent, timely, and relevant knowledge in oncology.
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Affiliation(s)
- Ankit Dhiman
- Section of General Surgery and Surgical Oncology, Department of Surgery, University of Chicago Medicine, Chicago, IL, USA
| | - Charles C Vining
- Section of General Surgery and Surgical Oncology, Department of Surgery, University of Chicago Medicine, Chicago, IL, USA
| | - Hunter D D Witmer
- Section of General Surgery and Surgical Oncology, Department of Surgery, University of Chicago Medicine, Chicago, IL, USA
| | - Divya Sood
- Section of General Surgery and Surgical Oncology, Department of Surgery, University of Chicago Medicine, Chicago, IL, USA
| | - Ardaman Shergill
- Section of Hematology/Oncology, Department of Medicine, University of Chicago Medicine, Chicago, IL, USA
| | - Hedy Kindler
- Section of Hematology/Oncology, Department of Medicine, University of Chicago Medicine, Chicago, IL, USA
| | - Kevin K Roggin
- Section of General Surgery and Surgical Oncology, Department of Surgery, University of Chicago Medicine, Chicago, IL, USA
| | - Mitchell C Posner
- Section of General Surgery and Surgical Oncology, Department of Surgery, University of Chicago Medicine, Chicago, IL, USA
| | | | - Stanley Liauw
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, USA
- The Ludwig Center for Metastasis Research, University of Chicago, Chicago, IL, USA
| | - Sean Pitroda
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, USA
- The Ludwig Center for Metastasis Research, University of Chicago, Chicago, IL, USA
| | - Chih-Yi Liao
- Section of Hematology/Oncology, Department of Medicine, University of Chicago Medicine, Chicago, IL, USA
| | - Theodore Karrison
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Ralph Weichselbaum
- Department of Radiation and Cellular Oncology, University of Chicago, Chicago, IL, USA
- The Ludwig Center for Metastasis Research, University of Chicago, Chicago, IL, USA
| | - Blase Polite
- Section of Hematology/Oncology, Department of Medicine, University of Chicago Medicine, Chicago, IL, USA
| | - Oliver S Eng
- Section of General Surgery and Surgical Oncology, Department of Surgery, University of Chicago Medicine, Chicago, IL, USA
| | - Daniel V T Catenacci
- Section of Hematology/Oncology, Department of Medicine, University of Chicago Medicine, Chicago, IL, USA
| | - Kiran K Turaga
- Section of General Surgery and Surgical Oncology, Department of Surgery, University of Chicago Medicine, Chicago, IL, USA.
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13
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Xue C, Wang L, Huang H, Wang R, Yuan P, Wu ZS. Stimuli-Induced Upgrade of Nuclease-Resistant DNA Nanostructure Composed of a Single Molecular Beacon for Detecting Mutant Genes. ACS Sens 2021; 6:4029-4037. [PMID: 34731570 DOI: 10.1021/acssensors.1c01423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As a kind of cell-free DNA in the bloodstream liberated from tumor cells, circulating tumor DNAs (ctDNAs) have been recognized as promising biomarkers in the field of early cancer diagnosis. However, robust, sensitive, and accurate detection of ctDNA in serum remains extremely challenging, especially toward the mutant KRAS gene, one of the most frequently mutated genes. Although DNA oligonucleotides as emerging practical signaling materials have been developed as sensitive and accurate tools, some intrinsic defects need to be overcome, such as fragility in complex biological environments. In this work, on the basis of the hydrophilicity-promoted assembly, a core/shell DNA nanostructure (DNS-MB) probe is constructed from only one hairpin-shaped probe (cholesterol-modified palindromic molecular beacon, Chol-PMB) for the amplification detection of KRAS mutation in serum without the need for any auxiliary probe. Chol-PMB is designed to recognize target DNA and serve as a polymerization primer and template, and thus target species can initiate polymerization-based strand displacement amplification (SDA). Moreover, target DNA is able to induce further aggregation of DNS-MB particles due to the enzymatic cross-linking effect, leading to a structural upgrade. The DNS-MB probe exhibits a detection limit of 50 fM and a wide quantitative range (from 50 fM to 160 nM). In addition, single nucleotide polymorphisms can be discriminated, such as mutant KRAS G12D (KRAS-M), providing a desirable platform for screening ctDNAs. More excitingly, because the termini of DNA components are hidden inward from nuclease attack, DNS-MB circumvents a false-positive signal even in freshly sampled serum and is suitable for application in the complex biological milieu. As a proof of concept, the DNS-MB probe is expected to provide useful insight into the development of simple and degradation-resistant DNA probes for substantially amplified detection of ctDNAs in complex serum, showing potential applications in the field of early tumor diagnosis.
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Affiliation(s)
- Chang Xue
- College of Chemical Engineering, Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Lei Wang
- College of Chemical Engineering, Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Hong Huang
- College of Chemical Engineering, Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Ruozhong Wang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Pei Yuan
- College of Chemical Engineering, Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zai-Sheng Wu
- College of Chemical Engineering, Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
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14
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Personalization of medical treatments in oncology: time for rethinking the disease concept to improve individual outcomes. EPMA J 2021; 12:545-558. [PMID: 34642594 PMCID: PMC8495186 DOI: 10.1007/s13167-021-00254-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/01/2021] [Indexed: 12/12/2022]
Abstract
The agenda of pharmacology discovery in the field of personalized oncology was dictated by the search of molecular targets assumed to deterministically drive tumor development. In this perspective, genes play a fundamental "causal" role while cells simply act as causal proxies, i.e., an intermediate between the molecular input and the organismal output. However, the ceaseless genomic change occurring across time within the same primary and metastatic tumor has broken the hope of a personalized treatment based only upon genomic fingerprint. Indeed, current models are unable in capturing the unfathomable complexity behind the outbreak of a disease, as they discard the contribution of non-genetic factors, environment constraints, and the interplay among different tiers of organization. Herein, we posit that a comprehensive personalized model should view at the disease as a "historical" process, in which different spatially and timely distributed factors interact with each other across multiple levels of organization, which collectively interact with a dynamic gene-expression pattern. Given that a disease is a dynamic, non-linear process - and not a static-stable condition - treatments should be tailored according to the "timing-frame" of each condition. This approach can help in detecting those critical transitions through which the system can access different attractors leading ultimately to diverse outcomes - from a pre-disease state to an overt illness or, alternatively, to recovery. Identification of such tipping points can substantiate the predictive and the preventive ambition of the Predictive, Preventive and Personalized Medicine (PPPM/3PM). However, an unusual effort is required to conjugate multi-omics approaches, data collection, and network analysis reconstruction (eventually involving innovative Artificial Intelligent tools) to recognize the critical phases and the relevant targets, which could help in patient stratification and therapy personalization.
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15
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Morcuende-Ventura V, Hermoso-Durán S, Abian-Franco N, Pazo-Cid R, Ojeda JL, Vega S, Sanchez-Gracia O, Velazquez-Campoy A, Sierra T, Abian O. Fluorescence Liquid Biopsy for Cancer Detection Is Improved by Using Cationic Dendronized Hyperbranched Polymer. Int J Mol Sci 2021; 22:6501. [PMID: 34204408 PMCID: PMC8234380 DOI: 10.3390/ijms22126501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/19/2022] Open
Abstract
(1) Background: Biophysical techniques applied to serum samples characterization could promote the development of new diagnostic tools. Fluorescence spectroscopy has been previously applied to biological samples from cancer patients and differences from healthy individuals were observed. Dendronized hyperbranched polymers (DHP) based on bis(hydroxymethyl)propionic acid (bis-MPA) were developed in our group and their potential biomedical applications explored. (2) Methods: A total of 94 serum samples from diagnosed cancer patients and healthy individuals were studied (20 pancreatic ductal adenocarcinoma, 25 blood donor, 24 ovarian cancer, and 25 benign ovarian cyst samples). (3) Results: Fluorescence spectra of serum samples (fluorescence liquid biopsy, FLB) in the presence and the absence of DHP-bMPA were recorded and two parameters from the signal curves obtained. A secondary parameter, the fluorescence spectrum score (FSscore), was calculated, and the diagnostic model assessed. For pancreatic ductal adenocarcinoma (PDAC) and ovarian cancer, the classification performance was improved when including DHP-bMPA, achieving high values of statistical sensitivity and specificity (over 85% for both pathologies). (4) Conclusions: We have applied FLB as a quick, simple, and minimally invasive promising technique in cancer diagnosis. The classification performance of the diagnostic method was further improved by using DHP-bMPA, which interacted differentially with serum samples from healthy and diseased subjects. These preliminary results set the basis for a larger study and move FLB closer to its clinical application, providing useful information for the oncologist during patient diagnosis.
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Affiliation(s)
- Violeta Morcuende-Ventura
- Instituto de Nanociencia y Materiales de Aragón (INMA), Química Orgánica, Facultad de Ciencias, CSIC-Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain;
- Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (S.H.-D.), (S.V.), (A.V.-C.)
| | - Sonia Hermoso-Durán
- Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (S.H.-D.), (S.V.), (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
| | | | - Roberto Pazo-Cid
- Hospital Universitario Miguel Servet (HUMS), Paseo Isabel la Católica, 1-3, 50009 Zaragoza, Spain;
| | - Jorge L. Ojeda
- Department of Statistical Methods, Universidad de Zaragoza, 50009 Zaragoza, Spain;
| | - Sonia Vega
- Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (S.H.-D.), (S.V.), (A.V.-C.)
| | | | - Adrian Velazquez-Campoy
- Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (S.H.-D.), (S.V.), (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Fundación ARAID, Gobierno de Aragón, 50018 Zaragoza, Spain
| | - Teresa Sierra
- Instituto de Nanociencia y Materiales de Aragón (INMA), Química Orgánica, Facultad de Ciencias, CSIC-Universidad de Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain;
| | - Olga Abian
- Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, 50018 Zaragoza, Spain; (S.H.-D.), (S.V.), (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
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16
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Chatfield-Reed K, Roche VP, Pan Q. cfDNA detection for HPV+ squamous cell carcinomas. Oral Oncol 2021; 115:104958. [PMID: 33582486 PMCID: PMC8331111 DOI: 10.1016/j.oraloncology.2020.104958] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022]
Abstract
High-risk human papillomavirus (HPV) is an etiologic factor in a spectrum of squamous cell carcinomas including anal, cervical, and oropharyngeal. HPV cell free DNA (cfDNA) is shed from the primary tumor into systemic circulation and can be detected using several platforms including quantitative PCR, digital droplet PCR, or next generation sequencing. Levels of HPV cfDNA at time of initial presentation is associated with known poor prognostic clinicopathologic variables, such as advanced stage and, locoregional and distant metastases. Moreover, longitudinal sampling revealed that persistent or increasing HPV cfDNA levels are indicative of treatment relapse and, in some studies, HPV cfDNA detection predicted treatment failures prior to routine post-treatment clinical imaging. A liquid biopsy platform using HPV cfDNA offers unique advantages over traditional approaches and may have clinical utility for detection of minimum residual disease, treatment response, and disease progression in patients with HPV+ cancers.
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Affiliation(s)
- Kate Chatfield-Reed
- University Hospitals Seidman Cancer Center, Cleveland, OH 44106, United States; Department of Otolaryngology-Head and Neck Surgery, University Hospitals Cleveland Medical Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States
| | - Veronique P Roche
- Department of Otolaryngology-Head and Neck Surgery, University Hospitals Cleveland Medical Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States; Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States
| | - Quintin Pan
- University Hospitals Seidman Cancer Center, Cleveland, OH 44106, United States; Department of Otolaryngology-Head and Neck Surgery, University Hospitals Cleveland Medical Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States; Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, United States.
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17
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Cai YX, Yang X, Lin S, Xu YW, Zhu SW, Fan DM, Zhao M, Zhang YB, Yang XX, Li X. Low-Coverage Sequencing of Urine Sediment DNA for Detection of Copy Number Aberrations in Bladder Cancer. Cancer Manag Res 2021; 13:1943-1953. [PMID: 33664588 PMCID: PMC7924115 DOI: 10.2147/cmar.s295675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/15/2021] [Indexed: 01/08/2023] Open
Abstract
Purpose Chromosomal copy number aberrations (CNAs) are a hallmark of bladder cancer and a useful target for diagnostic explorations. Here we constructed a low-coverage whole-genome sequencing method for the detection of CNAs in urine sediment DNA from patients with bladder cancer. Patients and Methods We conducted a prospective study using urine sediment samples from 65 patients with bladder tumors, including 54 patients with bladder cancer and 11 patients with benign bladder tumors. Forty-three healthy individuals were included as normal controls. DNA was extracted from urine sediments and analyzed by low-coverage whole-genome sequencing to compare differences in CNAs among these three groups. CNAs are defined by arbitrary R values (normal range ± 2). When these values exceed ± 0.2 of normal range, gain/duplication or loss/deletion are suspected. Results With this method, CNAs were detected in 39 of 51 patients with bladder cancer, 2 of 10 patients with benign bladder tumors, and 8 of 39 normal controls. The lengths of DNA deletion and duplication were significantly larger in patients with bladder cancer than in patients with benign tumors or normal controls (P < 0.05). Bladder cancer duplicate CNAs mainly occurred on chromosomes 1q, 5p, 6p, 7p, 8q, and 13q, while deletions mainly occurred on 2q, 8p, 9q, 9p, and 11p. Those regions contained bladder cancer tumor-related genes, such as STK3, COX6C, SPAG1, CDKAL1, C9orf53, CDKN2A, CDKN2B, MIR31, and IFNA1. The number of CNAs detected in urine sediment DNA during the follow-up period was significantly reduced. Conclusion Our sequencing method is highly sensitive and can detect a minimal chromosome repeat/microdeletion change of 0.15 Mb. The use of 0.1~0.3× low-coverage whole-genome sequencing can be used to detect bladder cancer CNAs in urine sediment DNA. This method provides a promising method for noninvasive diagnosis of bladder cancer, but still needs further verification in a larger sample size.
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Affiliation(s)
- Yun-Xi Cai
- Shenzhen Key Laboratory of Viral Oncology, The Clinical Innovation & Research Center (CIRC), Shenzhen Hospital, Southern Medical University, Shenzhen, 518110, People's Republic of China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, 510500, People's Republic of China
| | - Xu Yang
- Shenzhen Key Laboratory of Viral Oncology, The Clinical Innovation & Research Center (CIRC), Shenzhen Hospital, Southern Medical University, Shenzhen, 518110, People's Republic of China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, 510500, People's Republic of China
| | - Sheng Lin
- Laboratory of Molecular Medicine, Shenzhen Health Development Research Center, Shenzhen, 518040, People's Republic of China
| | - Ya-Wen Xu
- Department of Urology, Zhujiang Hospital, Southern Medical University, Guangzhou, 510000, People's Republic of China
| | - Shan-Wen Zhu
- Reproductive Medicine Center, Huizhou Central People's Hospital, Huizhou, 516000, People's Republic of China
| | - Dong-Mei Fan
- Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Min Zhao
- PANACRO (Hefei) Pharmaceutical Technology Co., Ltd., Hefei, People's Republic of China
| | - Yuan-Bin Zhang
- Shenzhen Key Laboratory of Viral Oncology, The Clinical Innovation & Research Center (CIRC), Shenzhen Hospital, Southern Medical University, Shenzhen, 518110, People's Republic of China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, 510500, People's Republic of China
| | - Xue-Xi Yang
- Institute of Antibody Engineering, School of Laboratory Medical and Biotechnology, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Xin Li
- Shenzhen Key Laboratory of Viral Oncology, The Clinical Innovation & Research Center (CIRC), Shenzhen Hospital, Southern Medical University, Shenzhen, 518110, People's Republic of China.,The Third School of Clinical Medicine, Southern Medical University, Guangzhou, 510500, People's Republic of China
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18
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Murillo Carrasco A, Acosta O, Ponce J, Cotrina J, Aguilar A, Araujo J, Rebaza P, Pinto JA, Fujita R, Buleje J. PUM1 and RNase P genes as potential cell-free DNA markers in breast cancer. J Clin Lab Anal 2021; 35:e23720. [PMID: 33522650 PMCID: PMC8059717 DOI: 10.1002/jcla.23720] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Cell-free DNA (cfDNA) is used in clinical research to identify biomarkers for diagnosis of and follow-up on cancer. Here, we propose a fast and innovative approach using traditional housekeeping genes as cfDNA targets in a copy number analysis. We focus on the application of highly sensitive technology such as digital PCR (dPCR) to differentiate breast cancer (BC) patients and controls by quantifying regions of PUM1 and RPPH1 (RNase P) in plasma samples. METHODS We conducted a case-control study with 82 BC patients and 82 healthy women. cfDNA was isolated from plasma using magnetic beads and quantified by spectrophotometry to estimate total cfDNA. Then, both PUM1 and RPPH1 genes were specifically quantified by dPCR. Data analysis was calibrated using a reference genomic DNA in different concentrations. RESULTS We found RNase P and PUM1 values were correlated in the patient group (intraclass correlation coefficient [ICC] = 0.842), but they did not have any correlation in healthy women (ICC = 0.519). In dPCR quantification, PUM1 showed the capacity to distinguish early-stage patients and controls with good specificity (98.67%) and sensitivity (100%). Conversely, RNase P had lower cfDNA levels in triple-negative BC patients than luminal subtypes (p < 0.025 for both), confirming their utility for patient classification. CONCLUSION We propose the PUM1 gene as a cfDNA marker for early diagnosis of BC and RNase P as a cfDNA marker related to hormonal status and subtype classification in BC. Further studies with larger sample sizes are warranted.
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Affiliation(s)
- Alexis Murillo Carrasco
- Facultad de Medicina Humana, Centro de Investigación de Genética y Biología Molecular, Instituto de Investigación, Universidad de San Martín de Porres, Lima, Perú
| | - Oscar Acosta
- Facultad de Medicina Humana, Centro de Investigación de Genética y Biología Molecular, Instituto de Investigación, Universidad de San Martín de Porres, Lima, Perú.,Facultad de Farmacia y Bioquímica, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Jaime Ponce
- Oncosalud-AUNA, Unidad de la Mama, Lima, Perú
| | - José Cotrina
- Departamento de Cirugía de Mamas, Instituto Nacional de Enfermedades Neoplásicas-INEN, Lima, Perú
| | - Alfredo Aguilar
- Oncosalud-AUNA, Unidad de Investigación Básica y Traslacional, Lima, Perú
| | - Jhajaira Araujo
- Oncosalud-AUNA, Unidad de Investigación Básica y Traslacional, Lima, Perú
| | | | - Joseph A Pinto
- Oncosalud-AUNA, Unidad de Investigación Básica y Traslacional, Lima, Perú
| | - Ricardo Fujita
- Facultad de Medicina Humana, Centro de Investigación de Genética y Biología Molecular, Instituto de Investigación, Universidad de San Martín de Porres, Lima, Perú
| | - José Buleje
- Facultad de Medicina Humana, Centro de Investigación de Genética y Biología Molecular, Instituto de Investigación, Universidad de San Martín de Porres, Lima, Perú
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Utility of Circulating Tumor DNA in Different Clinical Scenarios of Breast Cancer. Cancers (Basel) 2020; 12:cancers12123797. [PMID: 33339259 PMCID: PMC7766337 DOI: 10.3390/cancers12123797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 12/22/2022] Open
Abstract
Simple Summary This review is focused on the concept of a specific type of “liquid biopsy”, circulating cell-free tumor DNA (ctDNA). It explores the advantages and limitations of using this technique and the latest advances of using it in different clinical scenarios of breast cancer: early, metastatic, and locally advanced disease. It provides the latest advances in this area applied to clinical research and clinical practice, as well as the importance of the collaboration between clinicians and laboratory teams to fully grasp the potential of ctDNA in a precision medicine era. Abstract Breast cancer is a complex disease whose molecular mechanisms are not completely understood. Developing target therapies is a promising approach. Therefore, understanding the biological behavior of the tumor is a challenge. Tissue biopsy in the metastatic setting remains the standard method for diagnosis. Nevertheless, it has been associated with some disadvantages: It is an invasive procedure, it may not represent tumor heterogeneity, and it does not allow for treatment efficacy to be assessed or early recurrences to be detected. Analysis of circulating tumor DNA (ctDNA) may help to overcome this as it is a non-invasive method of monitoring the disease. In early-stage disease, it can detect early recurrences and monitor tumors’ genomic profiles, identifying the emergence of new genetic alterations which can be related to tumor-acquired resistance. In the metastatic setting, the analysis of ctDNA may also allow for the anticipation of clinical and radiological progression of the disease, selection of targeted therapies, and for a photogram of tumor heterogeneity to be provided. It may also detect disease progression earlier in locally advanced tumors submitted to neoadjuvant treatment, and identify minimal residual disease. ctDNA analysis may guide clinical decision-making in different scenarios, in a precision medicine era, once it acts as a repository of genetic tumor material, allowing for a comprehensive mutation profiling analysis. In this review, we focused on recent advances towards the implementation of ctDNA in a clinical routine for breast cancer.
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Lastraioli E, Antonuzzo L, Fantechi B, Di Cerbo L, Di Costanzo A, Lavacchi D, Armenio M, Arcangeli A, Castiglione F, Messerini L, Di Costanzo F. KRAS and NRAS mutation detection in circulating DNA from patients with metastatic colorectal cancer using BEAMing assay: Concordance with standard biopsy and clinical evaluation. Oncol Lett 2020; 21:15. [PMID: 33240421 PMCID: PMC7681220 DOI: 10.3892/ol.2020.12276] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
Patients with metastatic colorectal cancer (mCRC) are routinely screened for either K- and N-RAS to select the appropriate treatment. The present study aimed to evaluate the concordance between K- and NRAS status in the tissue (either primary tumor or metastasis) and the plasma of patients with mCRC and to identify the associations between K- and NRAS mutations in ctDNA and the clinicopathological parameters. Samples from a total of 31 patients with mCRC with measurable disease according to the Response Evaluation Criteria in Solid Tumors were analyzed. For all patients, K- and NRAS status was determined in the tissue by matrix-assisted laser desorption/ionization time of flight mass spectrometry. For the detection of RAS mutations in cell-free tumor DNA also defined as circulating tumor DNA (ctDNA), the OncoBEAM® RAS CRC kit (Sysmex Inostics) was used. A total of 6/31 tissue samples expressed wild-type KRAS, whereas 25/31 presented mutations. In addition, 7/31 plasma samples expressed wild-type KRAS, mutations were detected in 22/31 patients, and for 2/31 patients, the test did not provide a conclusive result. A total of 24/31 patients expressed wild-type NRAS, 6/31 had mutations and 1/21 was not informative. For the KRAS mutational status, a moderate concordance (agreement, 85.18%; Cohen's k, 0.513) between the tissue and plasma analysis was observed; for NRAS, a fair agreement (agreement, 83.33%; Cohen's k, 0.242) was obtained. In conclusion, both tissue and plasma analyses should be performed for the management of patients with mCRC. To better exploit the beads, emulsions, amplification, magnetics (BEAMing) technique in the clinical setting, studies aimed at determining the RAS status to monitor therapy and during follow-up are warranted.
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Affiliation(s)
- Elena Lastraioli
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Lorenzo Antonuzzo
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
| | - Beatrice Fantechi
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
| | - Luisa Di Cerbo
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
| | - Alessandro Di Costanzo
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
| | - Daniele Lavacchi
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
| | - Miriam Armenio
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Annarosa Arcangeli
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Francesca Castiglione
- Section of Pathological Anatomy, Department of Health Sciences, University of Florence, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
| | - Luca Messerini
- Department of Experimental and Clinical Medicine, University of Florence, I-50134 Florence, Italy
| | - Francesco Di Costanzo
- Medical Oncology Unit, Azienda Ospedaliero-Universitaria Careggi, I-50134 Florence, Italy
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21
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Marczynski GT, Laus AC, Dos Reis MB, Reis RM, Vazquez VDL. Circulating tumor DNA (ctDNA) detection is associated with shorter progression-free survival in advanced melanoma patients. Sci Rep 2020; 10:18682. [PMID: 33122747 PMCID: PMC7596487 DOI: 10.1038/s41598-020-75792-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023] Open
Abstract
BRAF, NRAS and TERT mutations occur in more than 2/3 of melanomas. Its detection in patient's blood, as circulating tumor DNA (ctDNA), represents a possibility for identification and monitoring of metastatic disease. We proposed to standardize a liquid biopsy platform to identify hotspot mutations in BRAF, NRAS and TERT in plasma samples from advanced melanoma patients and investigate whether it was associated to clinical outcome. Firstly, we performed digital polymerase chain reaction using tumor cell lines for validation and determination of limit of detection (LOD) of each assay and screened plasma samples from healthy individuals to determine the limit of blank (LOB). Then, we selected 19 stage III and IV patients and determined the somatic mutations status in tumor tissue and track them in patients' plasma. We established a specific and sensitive methodology with a LOD ranging from 0.13 to 0.37%, and LOB ranging from of 0 to 5.201 copies/reaction. Somatic mutations occurred in 17/19 (89%) patients, of whom seven (41%) had ctDNA detectable their paired plasma. ctDNA detection was associated with shorter progression free survival (p = 0.01). In conclusion, our data support the use of ctDNA as prognosis biomarker, suggesting that patients with detectable levels have an unfavorable outcome.
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Affiliation(s)
- Gabriella Taques Marczynski
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela St, Barretos, SP, 14784-400, Brazil
| | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela St, Barretos, SP, 14784-400, Brazil
| | - Mariana Bisarro Dos Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela St, Barretos, SP, 14784-400, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela St, Barretos, SP, 14784-400, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Vinicius de Lima Vazquez
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331, Antenor Duarte Villela St, Barretos, SP, 14784-400, Brazil.
- Surgery Department of Melanoma, Sarcoma and Mesenchymal Tumors, Barretos Cancer Hospital, Barretos, Brazil.
- Barretos School of Health Sciences Dr. Paulo Prata - FACISB, Barretos, Brazil.
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22
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Morris AH, Orbach SM, Bushnell GG, Oakes RS, Jeruss JS, Shea LD. Engineered Niches to Analyze Mechanisms of Metastasis and Guide Precision Medicine. Cancer Res 2020; 80:3786-3794. [PMID: 32409307 PMCID: PMC7501202 DOI: 10.1158/0008-5472.can-20-0079] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 03/04/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022]
Abstract
Cancer metastasis poses a challenging problem both clinically and scientifically, as the stochastic nature of metastatic lesion formation introduces complexity for both early detection and the study of metastasis in preclinical models. Engineered metastatic niches represent an emerging approach to address this stochasticity by creating bioengineered sites where cancer can preferentially metastasize. As the engineered niche captures the earliest metastatic cells at a nonvital location, both noninvasive and biopsy-based monitoring of these sites can be performed routinely to detect metastasis early and monitor alterations in the forming metastatic niche. The engineered metastatic niche also provides a new platform technology that serves as a tunable site to molecularly dissect metastatic disease mechanisms. Ultimately, linking the engineered niches with advances in sensor development and synthetic biology can provide enabling tools for preclinical cancer models and fosters the potential to impact the future of clinical cancer care.
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Affiliation(s)
- Aaron H Morris
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Sophia M Orbach
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
| | - Grace G Bushnell
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan
- Department of Internal Medicine, Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Robert S Oakes
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland
| | - Jacqueline S Jeruss
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan.
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Lonnie D Shea
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan
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Jiang J, Adams HP, Lange M, Siemann S, Feldkamp M, McNamara S, Froehler S, Yaung SJ, Yao L, Balasubramanyam A, Tikoo N, Ju C, Achenbach HJ, Krügel R, Palma JF. Plasma-based longitudinal mutation monitoring as a potential predictor of disease progression in subjects with adenocarcinoma in advanced non-small cell lung cancer. BMC Cancer 2020; 20:885. [PMID: 32933495 PMCID: PMC7493404 DOI: 10.1186/s12885-020-07340-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 08/25/2020] [Indexed: 12/18/2022] Open
Abstract
Background Identifying and tracking somatic mutations in cell-free DNA (cfDNA) by next-generation sequencing (NGS) has the potential to transform the clinical management of subjects with advanced non-small cell lung cancer (NSCLC). Methods Baseline tumor tissue (n = 47) and longitudinal plasma (n = 445) were collected from 71 NSCLC subjects treated with chemotherapy. cfDNA was enriched using a targeted-capture NGS kit containing 197 genes. Clinical responses to treatment were determined using RECIST v1.1 and correlations between changes in plasma somatic variant allele frequencies and disease progression were assessed. Results Somatic variants were detected in 89.4% (42/47) of tissue and 91.5% (407/445) of plasma samples. The most commonly mutated genes in tissue were TP53 (42.6%), KRAS (25.5%), and KEAP1 (19.1%). In some subjects, the allele frequencies of mutations detected in plasma increased 3–5 months prior to disease progression. In other cases, the allele frequencies of detected mutations declined or decreased to undetectable levels, indicating clinical response. Subjects with circulating tumor DNA (ctDNA) levels above background had significantly shorter progression-free survival (median: 5.6 vs 8.9 months, respectively; log-rank p = 0.0183). Conclusion Longitudinal monitoring of mutational changes in plasma has the potential to predict disease progression early. The presence of ctDNA mutations during first-line treatment is a risk factor for earlier disease progression in advanced NSCLC.
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Affiliation(s)
- John Jiang
- Roche Sequencing Solutions, 4300 Hacienda Dr, Pleasanton & Potsdam, California, 94588, USA
| | - Hans-Peter Adams
- Signature Diagnostics GmbH, Hermannswerder 20A, 14473, Potsdam, Germany
| | - Maria Lange
- Signature Diagnostics GmbH, Hermannswerder 20A, 14473, Potsdam, Germany
| | - Sandra Siemann
- Signature Diagnostics GmbH, Hermannswerder 20A, 14473, Potsdam, Germany
| | - Mirjam Feldkamp
- Signature Diagnostics GmbH, Hermannswerder 20A, 14473, Potsdam, Germany
| | - Sylvie McNamara
- Signature Diagnostics GmbH, Hermannswerder 20A, 14473, Potsdam, Germany
| | | | - Stephanie J Yaung
- Roche Sequencing Solutions, 4300 Hacienda Dr, Pleasanton & Potsdam, California, 94588, USA
| | - Lijing Yao
- Roche Sequencing Solutions, 4300 Hacienda Dr, Pleasanton & Potsdam, California, 94588, USA
| | | | - Nalin Tikoo
- Roche Molecular Systems, 4300 Hacienda Dr., Pleasanton, CA, 94588, USA
| | - Christine Ju
- Roche Molecular Systems, 4300 Hacienda Dr., Pleasanton, CA, 94588, USA
| | | | - Rainer Krügel
- Johanniter Krankenhaus im Fläming, Johanniterstraße 1, 14929, Treuenbrietzen, Germany
| | - John F Palma
- Roche Sequencing Solutions, 4300 Hacienda Dr, Pleasanton & Potsdam, California, 94588, USA.
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24
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Yap K, Cohen EN, Reuben JM, Khoury JD. Circulating Tumor Cells: State-of-the-art Update on Technologies and Clinical Applications. Curr Hematol Malig Rep 2020; 14:353-357. [PMID: 31364034 DOI: 10.1007/s11899-019-00531-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
PURPOSE OF REVIEW Circulating tumor cells represent rare events in the peripheral blood of patients with cancer that can provide insight into tumor biology. CTC enumeration, isolation, and analysis represent liquid biopsy approaches whose role in the management of patients with cancer continues to evolve in the era of precision medicine. This review presents an overview of technologies central to studying CTCs. RECENT FINDINGS Technologies for CTC isolation can be divided into two categories: label-dependent and label-independent. Label-dependent techniques utilize biological properties such as cell surface proteins, while label-independent techniques utilize distinctive physical properties such as cell size, density, and plasticity. Advances in microfluidics designs as well as hybrid combinations of label-dependent and label-independent techniques have resulted in unprecedented improvements in CTC isolation, permitting not only the detection and enumeration of these rare events but also providing the means for studying them and exploring them as a new dimension of cancer biomarkers. With advances in tools for isolating and studying CTCs in hand, questions regarding the clinical utility of CTC enumeration in peripheral blood, detection of CTC-associated biomarkers, and analysis of dynamic changes in CTCs during the course of cancer therapy represent exciting new opportunities for cancer research.
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Affiliation(s)
- Kristofor Yap
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, MS-072, Houston, TX, 77030, USA
| | - Evan N Cohen
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, MS-072, Houston, TX, 77030, USA
| | - James M Reuben
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, MS-072, Houston, TX, 77030, USA
| | - Joseph D Khoury
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, MS-072, Houston, TX, 77030, USA.
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25
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Song W, Wang H, Tian Y, Liu S, Chen X, Cui J, Zhao Y. Refractory solitary cervical lymph node metastasis after esophageal squamous cell carcinoma surgery and its successful treatment with immune checkpoint inhibitor: A case report and literature review. Medicine (Baltimore) 2020; 99:e19440. [PMID: 32150096 PMCID: PMC7478472 DOI: 10.1097/md.0000000000019440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
RATIONALE Although the early detection and treatment of non-metastatic esophageal cancer has improved, these patients' prognoses are still poor. Most patients with radical treatment for esophageal cancer will relapse in 3 years, and the best treatment strategy after recurrence has not been uniformly accepted. Multiform treatments may be beneficial to recurrent patients. PATIENT CONCERNS A 60-year-old male patient, due to routinely health examination, ulcerated lesions 30 cm away from the incisors were found by gastroscopy, pathology showed esophageal squamous cell carcinoma (ESCC). DIAGNOSIS Due to the patient's pathology, he was diagnosed with ESCC. INTERVENTIONS The patient underwent radical surgery for ESCC on June 28, 2015. The left cervical lymph node metastasis occurred after 20 months, and lymph node metastasis carcinoma resection was performed. After that, concurrent chemoradiotherapy was implemented, 40 days after the end of the 4 courses of chemotherapy, the left cervical metastatic lymph nodes relapsed, radioactive particle implantation was carried out, and progressed again after 1 month. The patient took apatinib for 1 week but could not tolerate due to hand-foot syndrome. Immune checkpoint inhibitor (ICI) was administered since October 27, 2017. OUTCOMES The therapeutic effect of immune checkpoint inhibitor was evaluated as partial response (PR) after 6 courses of treatment and complete response (CR) after 15 courses of treatment. To our knowledge, this is the first case report of successful immunotherapy for refractory esophageal squamous cell carcinoma. LESSONS The emergence of ICIs promotes the treatment of esophageal cancer to a new era. Our observations suggest that patients for whom schedule to receive anti-programmed cell death protein-1 (anti-PD-1)/programmed cell death-ligand 1 (PD-L1) immunotherapy may require genomic testing to predict whether tumors respond to ICIs. In this case, we also present the predictors for the efficacy of targeted immunotherapy. At present, no matter which predictor of PD-L1 expression, tumor mutational burden (TMB), microsatellite instability (MSI), and tumor-infiltrating lymphocyte (TIL), a single predictor may be unconvincing and cannot accurately estimate the efficacy of immunotherapy. Multiplex detecting methods and combined biomarkers may provide new strategies. Consensus need to be reached in order to be widely applied in future studies.
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Affiliation(s)
| | | | | | - Shiwei Liu
- Department of Bone and Joint Surgery, the First Hospital of Jilin University, Changchun, Jilin, China
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Zhang S, Su M, Sun Z, Lu H, Zhang Y. The signature of pharmaceutical sensitivity based on ctDNA mutation in eleven cancers. Exp Biol Med (Maywood) 2020; 245:720-732. [PMID: 32050795 DOI: 10.1177/1535370220906518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
IMPACT STATEMENT Gene mutations are closely related to cancers and drug sensitivity and noninvasive liquid biopsy was used to detect mutations of ctDNA in plasma. In this study, we performed exon sequencing of 416 cancer-related genes for cancer primary tissue and plasma samples of 20 patients in 11 cancers and obtained the comprehensive mutation landscape. We found that liquid biopsy is reliable in place of tissue biopsy. And 31 potential unique mutation prognostic markers were screened in 7 cancer types. Moreover, the drug-mutation network (DMN) was constructed and 9 gene mutations (B-Mut-9) were confirmed that can be served as drug biomarkers in blood. Our study showed that the variation in ctDNA can be used as the biomarkers for cancer prognosis and drug efficacy prediction. This can provide a reference for clinical noninvasive testing.
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Affiliation(s)
- Shumei Zhang
- College of Information and Computer Engineering, Northeast Forestry University, Harbin 150040, China
| | - Mu Su
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Zhongyi Sun
- School of Life Science and Technology, Computational Biology Research Center, Harbin Institute of Technology, Harbin 150001, China
| | - Haibo Lu
- Department of Gastrointestinal Medical Oncology, Harbin Medical University Cancer Hospital, Harbin 150081, China
| | - Yan Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou 51000, China
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27
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An Y, Guan Y, Xu Y, Han Y, Wu C, Bao C, Zhou B, Wang H, Zhang M, Liu W, Qiu L, Han Z, Chen Y, Xia X, Wang J, Liu Z, Huang W, Yi X, Huang J. The diagnostic and prognostic usage of circulating tumor DNA in operable hepatocellular carcinoma. Am J Transl Res 2019; 11:6462-6474. [PMID: 31737198 PMCID: PMC6834494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
Circulating tumor DNA (ctDNA) is a promising noninvasive biomarker for hepatocellular carcinoma (HCC). In this study, we aimed to assess the diagnostic and prognostic value of ctDNA in HCC. Twenty-six operable HCC, 10 hepatitis and 10 cirrhosis patients were enrolled in this study. Treatment-naïve blood samples were collected from all patients, nevertheless resected tissue and postoperative blood samples were only collected from HCC patients. A custom-designed sequencing panel covering 354 genes was used to identify somatic mutations. Collectively, we identified 139 somatic mutations from 25 HCC baseline plasma samples (96.2%). TP53 (50.00%) was the most common mutant gene, and R249S was the most recurrent mutation (19.2%). Twenty-three patients (88.5%) carried at least one ctDNA mutation validated in matched tissue, and the driver mutations exhibited an advanced concordance than non-driver mutations (67.6% vs. 33.8%, P = 0.0002). For HCC patients, the number of mutations in ctDNA (R2 = 0.1682, P = 0.0375), maximal variant allele frequency (VAF) in ctDNA (R2 = 0.4974, P < 0.0001) and ctDNA concentration (R2 = 0.2676, P = 0.0068) were linearly correlated with tumor size. Multiple circulating cell-free DNA (cfDNA) parameters could be used in differentiating malignant lesions from benign lesions, and the performance was no less than blood alpha-fetoprotein (AFP). HCC patients with detectable mutation in postoperative plasma had a poor DFS than those without (17.5 months vs. 6.7 months, HR = 7.655, P < 0.0001), and postoperative cfDNA status (HR = 10.293, P < 0.0001) was an independent risk factors for recurrence. In conclusion, ctDNA profiling is potentially valuable in differential diagnosis and prognostic evaluation of HCC.
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Affiliation(s)
- Yan An
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Yanfang Guan
- Geneplus-BeijingBeijing 102206, China
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University28 West Xianning Road, Xi’an 710049, China
| | - Yaping Xu
- Geneplus-BeijingBeijing 102206, China
| | - Yingxin Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Chi Wu
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
| | - Chaohui Bao
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Boping Zhou
- Shenzhen People’s Hospital, Second Clinical Medical College of Jinan UniversityShenzhen 518109, China
| | - Haiyan Wang
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
| | - Mingxia Zhang
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
| | - Weilong Liu
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
| | - Lin Qiu
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Zeguang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome at ShanghaiShanghai 201203, China
| | - Yongsheng Chen
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University28 West Xianning Road, Xi’an 710049, China
| | | | - Jiayin Wang
- Department of Computer Science and Technology, School of Electronic and Information Engineering, Xi’an Jiaotong University28 West Xianning Road, Xi’an 710049, China
| | | | - Wanqiu Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
| | - Xin Yi
- Geneplus-BeijingBeijing 102206, China
| | - Jian Huang
- Key Laboratory of Systems Biomedicine (Ministry of Education) and Collaborative Innovation Center of Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong UniversityShanghai 200240, China
- Shenzhen People’s Hospital, Second Clinical Medical College of Jinan UniversityShenzhen 518109, China
- Shenzhen Key Laboratory of Infection and Immunity, Shenzhen Third People’s Hospital, Guangdong Medical CollegeShenzhen 518112, China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome at ShanghaiShanghai 201203, China
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28
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Cytogenetics and Cytogenomics Evaluation in Cancer. Int J Mol Sci 2019; 20:ijms20194711. [PMID: 31547595 PMCID: PMC6801775 DOI: 10.3390/ijms20194711] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/07/2023] Open
Abstract
The availability of cytogenetics and cytogenomics technologies improved the detection and identification of tumor molecular signatures as well as the understanding of cancer initiation and progression. The use of large-scale and high-throughput cytogenomics technologies has led to a fast identification of several cancer candidate biomarkers associated with diagnosis, prognosis, and therapeutics. The advent of array comparative genomic hybridization and next-generation sequencing technologies has significantly improved the knowledge about cancer biology, underlining driver genes to guide targeted therapy development, drug-resistance prediction, and pharmacogenetics. However, few of these candidate biomarkers have made the transition to the clinic with a clear benefit for the patients. Technological progress helped to demonstrate that cellular heterogeneity plays a significant role in tumor progression and resistance/sensitivity to cancer therapies, representing the major challenge of precision cancer therapy. A paradigm shift has been introduced in cancer genomics with the recent advent of single-cell sequencing, since it presents a lot of applications with a clear benefit to oncological patients, namely, detection of intra-tumoral heterogeneity, mapping clonal evolution, monitoring the development of therapy resistance, and detection of rare tumor cell populations. It seems now evident that no single biomarker could provide the whole information necessary to early detect and predict the behavior and prognosis of tumors. The promise of precision medicine is based on the molecular profiling of tumors being vital the continuous progress of high-throughput technologies and the multidisciplinary efforts to catalogue chromosomal rearrangements and genomic alterations of human cancers and to do a good interpretation of the relation genotype-phenotype.
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Mallampati S, Zalles S, Duose DY, Hu PC, Medeiros LJ, Wistuba II, Kopetz S, Luthra R. Development and Application of Duplex Sequencing Strategy for Cell-Free DNA-Based Longitudinal Monitoring of Stage IV Colorectal Cancer. J Mol Diagn 2019; 21:994-1009. [PMID: 31401123 DOI: 10.1016/j.jmoldx.2019.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/08/2019] [Accepted: 06/12/2019] [Indexed: 02/09/2023] Open
Abstract
Potential applications of cell-free DNA (cfDNA)-based molecular profiling have used in patients with diverse malignant tumors. However, capturing all cfDNA that originates from tumor cells and identifying true variants present in this minute fraction remain challenges to the widespread application of cfDNA-based liquid biopsies in the clinical setting. In this study, we evaluate a systematic approach and identify key components of wet bench and bioinformatics strategies to address these challenges. We found that concentration of enrichment oligonucleotides, elements of the library preparation, and the structure of adaptors are critical for achieving high enrichment of target regions, retaining variant allele frequencies accurately throughout all involved steps of library preparation, and obtaining high variant coverage. We developed a dual molecular barcode-integrated error elimination strategy to remove sequencing artifacts and a background error correction strategy to distinguish true variants from abundant false-positive variants. We further describe a clinical application of this cfDNA-based duplex sequencing approach that can be used to monitor disease progression in patients with stage IV colorectal cancer. The findings also suggest that cfDNA-based molecular testing observations are highly concordant with observations obtained by traditional imaging methods. Overall, the findings presented in this study have potential implications for early detection of cancer, identification of minimal residual disease, and evaluation of therapeutic responses in patients with cancer.
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Affiliation(s)
- Saradhi Mallampati
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephanie Zalles
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Dzifa Y Duose
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peter C Hu
- School of Health Professions, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas; Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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30
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Ribeiro IP, de Melo JB, Carreira IM. Head and neck cancer: searching for genomic and epigenetic biomarkers in body fluids - the state of art. Mol Cytogenet 2019; 12:33. [PMID: 31333762 PMCID: PMC6621978 DOI: 10.1186/s13039-019-0447-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) affects multiple sites of the upper aerodigestive tract and exhibited high incidence and mortality worldwide, being frequently diagnosed at advanced stage. Early detection of HNSCC plays a crucial role in a successful therapy. In the last years, the survival rates of these tumors have not improved significantly due to the late diagnosis and the lack of precise disease biomarkers and targeted therapies. The introduction in the clinical practice of body fluids to detect and analyze circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) and exosomes provides a minimally or non-invasive method also called as liquid biopsy for diagnostic and prognostic biomarkers detection, representing a shift of paradigm in precision medicine through the revolution in the way to perform HNSCC diagnosis and to screen high risk population. Despite the use of body fluids being an emergent and up-to date issue to early diagnosis HNSCC and their recurrences, no strategy has yet proven to be consistently effective and able to be translated to clinical application in the routine clinical management of these patients. In this review we will discuss the recent discoveries using blood and saliva to identify biomarkers for the early detection and prognosis of HNSCC.
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Affiliation(s)
- Ilda Patrícia Ribeiro
- 1Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Pólo Ciências da Saúde, Coimbra, Portugal.,2iCBR-CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Joana Barbosa de Melo
- 1Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Pólo Ciências da Saúde, Coimbra, Portugal.,2iCBR-CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Isabel Marques Carreira
- 1Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, Pólo Ciências da Saúde, Coimbra, Portugal.,2iCBR-CIMAGO - Center of Investigation on Environment Genetics and Oncobiology - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
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31
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Kunnath AP, Priyashini T. Potential Applications of Circulating Tumor DNA Technology as a Cancer Diagnostic Tool. Cureus 2019; 11:e4907. [PMID: 31423385 PMCID: PMC6689482 DOI: 10.7759/cureus.4907] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Cancer is one of the greatest threats posed to society, necessitating appropriate diagnosis methods. Modern targeted therapies have greatly advanced the treatment of several solid tumors. The rational use of these agents requires optimal strategies for the rapid and accurate detection of targetable genomic alterations at the time of initial diagnosis and when acquired resistance to targeted therapies develops. Currently used techniques, such as tissue genotyping, have limitations such as difficulty in categorizing tumors, needing frequent sampling, and difficulty in obtaining samples. To overcome these issues, cost-effective and non-invasive methods are an urgent requisite, which would provide an insight into the real-time dynamics of cancers via circulating biomarkers. Circulating tumor DNA (ctDNA), commonly termed “liquid biopsy,” has emerged as a new, promising non-invasive tool to detect biomarkers in several cancers. The present review aimed to understand the biological concept of ctDNA and its potential as a biomarker in cancer studies and the clinical utility of this evolutionary diagnostic technique.
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Affiliation(s)
- Anil P Kunnath
- Department of Applied Biomedical Science and Biotechnology, International Medical University, Kuala Lumpur, MYS
| | - Thirujothi Priyashini
- Department of Applied Biomedical Science and Biotechnology, International Medical University, Kuala Lumpur, MYS
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32
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Stenzinger A, Allen JD, Maas J, Stewart MD, Merino DM, Wempe MM, Dietel M. Tumor mutational burden standardization initiatives: Recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions. Genes Chromosomes Cancer 2019; 58:578-588. [PMID: 30664300 PMCID: PMC6618007 DOI: 10.1002/gcc.22733] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/14/2019] [Accepted: 01/14/2019] [Indexed: 01/10/2023] Open
Abstract
Characterization of tumors utilizing next‐generation sequencing methods, including assessment of the number of somatic mutations (tumor mutational burden [TMB]), is currently at the forefront of the field of personalized medicine. Recent clinical studies have associated high TMB with improved patient response rates and survival benefit from immune checkpoint inhibitors; hence, TMB is emerging as a biomarker of response for these immunotherapy agents. However, variability in current methods for TMB estimation and reporting is evident, demonstrating a need for standardization and harmonization of TMB assessment methodology across assays and centers. Two uniquely placed organizations, Friends of Cancer Research (Friends) and the Quality Assurance Initiative Pathology (QuIP), have collaborated to coordinate efforts for international multistakeholder initiatives to address this need. Friends and QuIP, who have partnered with several academic centers, pharmaceutical organizations, and diagnostic companies, have adopted complementary, multidisciplinary approaches toward the goal of proposing evidence‐based recommendations for achieving consistent TMB estimation and reporting in clinical samples across assays and centers. Many factors influence TMB assessment, including preanalytical factors, choice of assay, and methods of reporting. Preliminary analyses highlight the importance of targeted gene panel size and composition, and bioinformatic parameters for reliable TMB estimation. Herein, Friends and QuIP propose recommendations toward consistent TMB estimation and reporting methods in clinical samples across assays and centers. These recommendations should be followed to minimize variability in TMB estimation and reporting, which will ensure reliable and reproducible identification of patients who are likely to benefit from immune checkpoint inhibitors.
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Affiliation(s)
- Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg (on behalf of QuIP® GmbH, Berlin, Germany), Heidelberg, Germany
| | - Jeffrey D Allen
- Science Policy, Friends of Cancer Research, Washington, District of Columbia
| | - Jörg Maas
- Management Department, QuIP® GmbH, Berlin, Germany
| | - Mark D Stewart
- Science Policy, Friends of Cancer Research, Washington, District of Columbia
| | - Diana M Merino
- Science Policy, Friends of Cancer Research, Washington, District of Columbia
| | - Madison M Wempe
- Science Policy, Friends of Cancer Research, Washington, District of Columbia
| | - Manfred Dietel
- Institute of Pathology, Charité Berlin (on behalf of QuIP® GmbH, Berlin, Germany), Berlin, Germany
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33
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Lai J, Du B, Wang Y, Wu R, Yu Z. Next-generation sequencing of circulating tumor DNA for detection of gene mutations in lung cancer: implications for precision treatment. Onco Targets Ther 2018; 11:9111-9116. [PMID: 30588023 PMCID: PMC6299472 DOI: 10.2147/ott.s174877] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Lung cancer remains a major global health problem, which causes millions of deaths annually. Because the prognosis is mainly determined by the stage of lung cancer, precise early diagnosis is of great significance to improve the survival and prognosis. Circulating tumor DNA (ctDNA) has been recognized as a sensitive and specific biomarker for the detection of early- and late-stage lung cancer, and next-generation sequencing (NGS) of ctDNA has been accepted as a noninvasive tool for early identification and monitoring of cancer mutations. This study aimed to assess the value of NGS-based ctDNA analysis in detecting gene mutations in lung cancer patients. Methods A total of 101 subjects with pathological diagnosis of lung cancer were enrolled, and blood samples were collected. ctDNA samples were prepared and subjected to NGS assays. Results There were 31 cases harboring 40 gene mutations, and EGFR was the most frequently mutated gene (27.72%). In addition, there were seven cases with double mutations and one case with triple mutations, with EGFR p.T790M mutation exhibiting the highest frequency. Conclusion Our findings demonstrate that NGS of ctDNA is effective in detecting gene mutations in lung cancer patients, and may be used as a liquid biopsy for lung cancer, which facilitates the development of precision treatment regimens for lung cancer.
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Affiliation(s)
- Jinhuo Lai
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian Province, People's Republic of China,
| | - Bin Du
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian Province, People's Republic of China,
| | - Yao Wang
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian Province, People's Republic of China,
| | - Riping Wu
- Department of Oncology, Fujian Medical University Union Hospital, Fuzhou 350001, Fujian Province, People's Republic of China,
| | - Zongyang Yu
- Department of Medical Oncology, Fuzhou General Hospital of PLA, Fuzhou 350025, Fujian Province, People's Republic of China
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34
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Kosovec JE, Zaidi AH, Pounardjian TS, Jobe BA. The Potential Clinical Utility of Circulating Tumor DNA in Esophageal Adenocarcinoma: From Early Detection to Therapy. Front Oncol 2018; 8:610. [PMID: 30619750 PMCID: PMC6297385 DOI: 10.3389/fonc.2018.00610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/28/2018] [Indexed: 12/11/2022] Open
Abstract
Esophageal adenocarcinoma (EAC) is a lethal cancer requiring improved screening strategies and treatment options due to poor detection methods, aggressive progression, and therapeutic resistance. Emerging circulating tumor DNA (ctDNA) technologies may offer a unique non-invasive strategy to better characterize the highly heterogeneous cancer and more clearly establish the genetic modulations leading to disease progression. The presented review describes the potential advantages of ctDNA methodologies as compared to current clinical strategies to improve clinical detection, enhance disease surveillance, evaluate prognosis, and personalize treatment. Specifically, we describe the ctDNA-targetable genetic markers of prognostic significance to stratify patients into risk of progression from benign to malignant disease and potentially offer cost-effective screening of established cancer. We also describe the application of ctDNA to more effectively characterize the heterogeneity and particular mutagenic resistance mechanisms in real-time to improve prognosis and therapeutic monitoring strategies. Lastly, we discuss the inconsistent clinical responses to currently approved therapies for EAC and the role of ctDNA to explore the dynamic regulation of novel targeted and immunotherapies to personalize therapy and improve patient outcomes. Although there are clear limitations of ctDNA technologies for immediate clinical deployment, this review presents the prospective role of such applications to potentially overcome many of the notable hurdles to treating EAC patients. A deeper understanding of complex EAC tumor biology may result in the progress toward improved clinical outcomes.
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Affiliation(s)
- Juliann E Kosovec
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, United States
| | - Ali H Zaidi
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, United States
| | - Tamar S Pounardjian
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, United States
| | - Blair A Jobe
- Esophageal and Lung Institute, Allegheny Health Network, Pittsburgh, PA, United States
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35
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Zhang Y, Zheng H, Zhan Y, Long M, Liu S, Lu J, Zang H, Fan S. Detection and application of circulating tumor cell and circulating tumor DNA in the non-small cell lung cancer. Am J Cancer Res 2018; 8:2377-2386. [PMID: 30662798 PMCID: PMC6325475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023] Open
Abstract
Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death in both men and women. The ability of cancer cells to break-off from the primary tumor and spread to distant organs is the main cause of death of cancer patients. The detection of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) is a considerable part of liquid biopsy, which contributes to the diagnosis, treatment and prognosis, and especially to identify the targetable mutations of NSCLC. This review is to discuss the detection and application of CTC and ctDNA in the diagnosis, prognostic evaluation and guiding targeted therapy of NSCLC.
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Affiliation(s)
- Yuting Zhang
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Hongmei Zheng
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Yuting Zhan
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Mengping Long
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Sile Liu
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Junmi Lu
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Hongjing Zang
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
| | - Songqing Fan
- Department of Pathology, The Second Xiangya Hospital, Central South University Changsha, Hunan, China
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36
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Gasparello J, Allegretti M, Tremante E, Fabbri E, Amoreo CA, Romania P, Melucci E, Messana K, Borgatti M, Giacomini P, Gambari R, Finotti A. Liquid biopsy in mice bearing colorectal carcinoma xenografts: gateways regulating the levels of circulating tumor DNA (ctDNA) and miRNA (ctmiRNA). JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:124. [PMID: 29941002 PMCID: PMC6020232 DOI: 10.1186/s13046-018-0788-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 06/05/2018] [Indexed: 12/22/2022]
Abstract
Background Circulating tumor DNA (ctDNA) and miRNA (ctmiRNA) are promising biomarkers for early tumor diagnosis, prognosis and monitoring, and to predict therapeutic response. However, a clear understanding of the fine control on their circulating levels is still lacking. Methods Three human colorectal carcinoma cell lines were grown in culture and as tumor xenograft models in nude mice. Chip-based and droplet digital PCR platforms were used to systematically and quantitatively assess the levels of DNAs and miRNAs released into the culture supernatants and mouse blood plasma. Results Strikingly, mutated DNAs from the same (KRAS) and different (PIK3CA and FBWX7) genomic loci were differentially detected in culture supernatants and blood, with LS174T releasing 25 to 60 times less DNA in culture, but giving rise to 7 to 8 times more DNA in blood than LoVo cells. Greater LS174T ctDNA accumulation occurred in spite of similar CD31 immunostaining (micro-vascularization) and lesser proliferation and tissue necrosis as compared to LoVo. As to the three selected miRNAs (miR-221, miR-222 and miR-141), all of them were constitutively present in the plasma of tumor-free mice. Micro-RNA miR-141 was released into HT-29 cell supernatants 10 and 6.5 times less abundantly with respect to LoVo and LS174T, respectively; on the contrary, release of miR-141 in blood of HT-29 xenografted mice was found similar to that observed in LoVo and LS174T mice. Conclusions Taken together, our results support the existence of multiple, finely tuned (non-housekeeping) control gateways that selectively regulate the release/accumulation of distinct ctDNA and miRNA species in culture and tumor xenograft models. Different xenografts (proxies of different patients) considerably differ in gateway usage, adding several layers of complexity to the well-known idea of molecular heterogeneity. We predict that even high tissue representation of mutated DNA and miRNA may result in insufficient diagnostic analyte representation in blood. In this respect, our data show that careful modeling in mice may considerably help to alleviate complexity, for instance by pre-screening for the most abundant circulating analytes in enlarged sets of tumor xenografts. Electronic supplementary material The online version of this article (10.1186/s13046-018-0788-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica Gasparello
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, Ferrara University, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Matteo Allegretti
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Elisa Tremante
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Enrica Fabbri
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, Ferrara University, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | | | - Paolo Romania
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Elisa Melucci
- Pathology, IRCSS Regina Elena National Cancer Institute, Rome, Italy
| | - Katia Messana
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy
| | - Monica Borgatti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, Ferrara University, Via Fossato di Mortara 74, 44121, Ferrara, Italy
| | - Patrizio Giacomini
- Oncogenomics and Epigenetics, IRCSS Regina Elena National Cancer Institute, Via E. Chianesi 53, 00144, Rome, Italy.
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, Ferrara University, Via Fossato di Mortara 74, 44121, Ferrara, Italy.
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, Biochemistry and Molecular Biology Section, Ferrara University, Via Fossato di Mortara 74, 44121, Ferrara, Italy
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37
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Denis JA, Guillerm E, Coulet F, Larsen AK, Lacorte JM. The Role of BEAMing and Digital PCR for Multiplexed Analysis in Molecular Oncology in the Era of Next-Generation Sequencing. Mol Diagn Ther 2018; 21:587-600. [PMID: 28667577 DOI: 10.1007/s40291-017-0287-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BEAMing polymerase chain reaction (PCR) and digital PCR (dPCR) are used for robust and accurate quantification of nucleic acids. These methods are particularly well suited for the identification of very small fractions (<1%) of variant copies such as the presence of mutant genes in a predominantly wild-type background. BEAMing and dPCR are increasingly used in diverse fields including bacteriology, virology, non-invasive prenatal testing, and oncology, in particular for the molecular analysis of liquid biopsies. In this review, we present the principles of BEAMing and dPCR as well as the trends of future technical development, focusing on the possibility of developing multiplexed mutation analysis. Finally, we will discuss why such techniques will remain useful despite the ever-decreasing costs and increased automatization of next-generation sequencing (NGS), using molecular characterization of cancer cells as an example.
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Affiliation(s)
- Jérôme Alexandre Denis
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France. .,Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine, INSERM, UMRS 938, 75571, Paris Cedex 12, France. .,Department of Endocrine and Oncological Biochemistry, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris, France.
| | - Erell Guillerm
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,INSERM, UMRS 938 Centre de Recherche Saint-Antoine, "Instability of Microsatellites and Cancers", Team approved by the National League Against Cancer, 75571, Paris Cedex 12, France.,Departement of Genetics, Unit of Molecular Oncogenetics and Angiogenetics, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris Cedex, France
| | - Florence Coulet
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,INSERM, UMRS 938 Centre de Recherche Saint-Antoine, "Instability of Microsatellites and Cancers", Team approved by the National League Against Cancer, 75571, Paris Cedex 12, France.,Departement of Genetics, Unit of Molecular Oncogenetics and Angiogenetics, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris Cedex, France
| | - Annette K Larsen
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,Cancer Biology and Therapeutics, Centre de Recherche Saint-Antoine, INSERM, UMRS 938, 75571, Paris Cedex 12, France
| | - Jean-Marc Lacorte
- UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,INSERM, UMR_S 1166, Research Institute of Cardiovascular Disease, Metabolism and Nutrition, 75013, Paris, France.,Department of Endocrine and Oncological Biochemistry, AP-HP, University Hospitals of Pitié-Salpétrière - Charles Foix, 75651, Paris, France
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38
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Extracellular vesicles and ctDNA in lung cancer: biomarker sources and therapeutic applications. Cancer Chemother Pharmacol 2018; 82:171-183. [PMID: 29948020 DOI: 10.1007/s00280-018-3586-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/20/2018] [Indexed: 02/05/2023]
Abstract
Lung cancer is the leading cause of cancer death in the world. Recently, targeted therapy and anti-programmed cell death receptor 1 (PD-1) and anti-programmed cell death ligand 1 (PD-L1) immunotherapy have made great progress in treatment of lung cancer. However, responses to these therapies are variable, influenced by genetic alterations, high microsatellite instability and mismatch repair deficiency. Liquid biopsy of extracellular vesicles and circulating tumor DNA (ctDNA) emerges as a new promising non-invasive means that enables not only biomarker determination, but also continuous monitoring of cancer treatment. Notably, tumor extracellular vesicles play important roles in tumor formation and progression, and also serve as natural carriers for anti-tumor drugs and short-interfering RNA. In this review, we summarize the latest progress in understanding the relationships of extracellular vesicles and ctDNA in cancer biology, diagnosis and drug delivery. In particular, the application of extracellular vesicles and ctDNA in anti-PD-1/PD-L1 immunotherapy is discussed.
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39
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Lousada-Fernandez F, Rapado-Gonzalez O, Lopez-Cedrun JL, Lopez-Lopez R, Muinelo-Romay L, Suarez-Cunqueiro MM. Liquid Biopsy in Oral Cancer. Int J Mol Sci 2018; 19:ijms19061704. [PMID: 29890622 PMCID: PMC6032225 DOI: 10.3390/ijms19061704] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/25/2018] [Accepted: 06/05/2018] [Indexed: 12/17/2022] Open
Abstract
Oral cancer is one of the most prevalent forms of cancer worldwide. Carcinogenesis is a complex process, in which heterogeneity plays an important role in the development and progression of the disease. This review provides an overview of the current biological and clinical significance of circulating tumour cells (CTCs), circulating tumour DNA (ctDNA), and exosomes for diagnosis and prognosis of oral cancer. We highlight the importance of liquid biopsy—using blood and saliva—which represents a potential alternative to solid biopsy for diagnosis and prognosis. Moreover, liquid biomarkers allow for the real-time monitoring of tumour evolution and therapeutic responses, initiating the era of personalized medicine. However, in oral cancer, the impact of liquid biopsies in clinical settings is still limited, requiring further studies to discover the best scenario for its clinical use.
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Affiliation(s)
- Fatima Lousada-Fernandez
- Department of Surgery and Medical Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela, 15782 Spain.
| | - Oscar Rapado-Gonzalez
- Department of Surgery and Medical Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela, 15782 Spain.
- Liquid Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), CIBERONC, 15706 Santiago de Compostela, Spain.
| | - Jose-Luis Lopez-Cedrun
- Department of Oral and Maxillofacial Surgery, Complexo Hospitalario Universitario de A Coruña (SERGAS), 15006 La Coruña, Spain.
| | - Rafael Lopez-Lopez
- Translational Medical Oncology, Health Research Institute of Santiago de Compostela (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), ONCOMET, 15706 Santiago de Compostela, Spain.
| | - Laura Muinelo-Romay
- Liquid Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago de Compostela (IDIS), CIBERONC, 15706 Santiago de Compostela, Spain.
| | - Maria Mercedes Suarez-Cunqueiro
- Department of Surgery and Medical Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela, 15782 Spain.
- Oral Sciences, Health Research Institute of Santiago de Compostela (IDIS), 15706 Santiago de Compostela, Spain.
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40
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Yadav DK, Bai X, Yadav RK, Singh A, Li G, Ma T, Chen W, Liang T. Liquid biopsy in pancreatic cancer: the beginning of a new era. Oncotarget 2018; 9:26900-26933. [PMID: 29928492 PMCID: PMC6003564 DOI: 10.18632/oncotarget.24809] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/25/2018] [Indexed: 12/21/2022] Open
Abstract
With dismal survival rate pancreatic cancer remains one of the most aggressive and devastating malignancy. Predominantly, due to the absence of a dependable methodology for early identification and limited therapeutic options for advanced disease. However, it takes over 17 years to develop pancreatic cancer from initiation of mutation to metastatic cancer; therefore, if diagnosed early; it may increase overall survival dramatically, thus, providing a window of opportunity for early detection. Recently, genomic expression analysis defined 4 subtypes of pancreatic cancer based on mutated genes. Hence, we need simple and standard, minimally invasive test that can monitor those altered genes or their associated pathways in time for the success of precision medicine, and liquid biopsy seems to be one answer to all these questions. Again, liquid biopsy has an ability to pair with genomic tests. Additionally, liquid biopsy based development of circulating tumor cells derived xenografts, 3D organoids system, real-time monitoring of genetic mutations by circulating tumor DNA and exosome as the targeted drug delivery vehicle holds lots of potential for the treatment and cure of pancreatic cancer. At present, diagnosis of pancreatic cancer is frantically done on the premise of CA19-9 and radiological features only, which doesn't give a picture of genetic mutations and epigenetic alteration involved. In this manner, the current diagnostic paradigm for pancreatic cancer diagnosis experiences low diagnostic accuracy. This review article discusses the current state of liquid biopsy in pancreatic cancer as diagnostic and therapeutic tools and future perspectives of research in the light of circulating tumor cells, circulating tumor DNA and exosomes.
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Affiliation(s)
- Dipesh Kumar Yadav
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Xueli Bai
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Rajesh Kumar Yadav
- Department of Pharmacology, Gandaki Medical College, Tribhuwan University, Institute of Medicine, Pokhara 33700, Nepal
| | - Alina Singh
- Department of Surgery, Bir Hospital, National Academy of Medical Science, Kanti Path, Kathmandu 44600, Nepal
| | - Guogang Li
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Tao Ma
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Wei Chen
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
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Tadimety A, Closson A, Li C, Yi S, Shen T, Zhang JXJ. Advances in liquid biopsy on-chip for cancer management: Technologies, biomarkers, and clinical analysis. Crit Rev Clin Lab Sci 2018; 55:140-162. [PMID: 29388456 PMCID: PMC6101655 DOI: 10.1080/10408363.2018.1425976] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Liquid biopsy, as a minimally invasive method of gleaning insight into the dynamics of diseases through a patient fluid sample, has been growing in popularity for cancer diagnosis, prognosis, and monitoring. While many technologies have been developed and validated in research laboratories, there has also been a push to expand these technologies into other clinical settings and as point of care devices. In this article, we discuss and evaluate microchip-based technologies for circulating tumor cell (CTC), exosome, and circulating tumor nucleic acid (ctNA) capture, detection, and analysis. Such integrated systems streamline otherwise multiple-step, manual operations to get a sample-to-answer quantitation. In addition, analysis of disease biomarkers is suited to point of care settings because of ease of use, low consumption of sample and reagents, and high throughput. We also cover the basics of biomarkers and their detection in biological fluid samples suitable for liquid biopsy on-chip. We focus on emerging technologies that process a small patient sample with high spatial-temporal resolution and derive clinically meaningful results through on-chip biomarker sensing and downstream molecular analysis in a simple workflow. This critical review is meant as a resource for those interested in developing technologies for capture, detection, and analysis platforms for liquid biopsy in a variety of settings.
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Affiliation(s)
- Amogha Tadimety
- a Thayer School of Engineering , Dartmouth College , Hanover , NH , USA
| | - Andrew Closson
- a Thayer School of Engineering , Dartmouth College , Hanover , NH , USA
| | - Cathy Li
- a Thayer School of Engineering , Dartmouth College , Hanover , NH , USA
| | - Song Yi
- b Nanolite Systems , Austin , TX , USA
| | - Ting Shen
- b Nanolite Systems , Austin , TX , USA
| | - John X J Zhang
- a Thayer School of Engineering , Dartmouth College , Hanover , NH , USA
- c Dartmouth-Hitchcock Medical Center , Lebanon , NH , USA
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Cazacu IM, Luzuriaga Chavez AA, Saftoiu A, Vilmann P, Bhutani MS. A quarter century of EUS-FNA: Progress, milestones, and future directions. Endosc Ultrasound 2018; 7:141-160. [PMID: 29941723 PMCID: PMC6032705 DOI: 10.4103/eus.eus_19_18] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 03/21/2018] [Indexed: 12/11/2022] Open
Abstract
Tissue acquisition using EUS has considerably evolved since the first EUS-FNA was reported 25 years ago. Its introduction was an important breakthrough in the endoscopic field. EUS-FNA has now become a part of the diagnostic and staging algorithm for the evaluation of benign and malignant diseases of the gastrointestinal tract and of the organs in its proximity, including lung diseases. This review aims to present the history of EUS-FNA development and to provide a perspective on the recent developments in procedural techniques and needle technologies that have significantly extended the role of EUS and its clinical applications. There is a bright future ahead for EUS-FNA in the years to come as extensive research is conducted in this field and various technologies are continuously implemented into clinical practice.
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Affiliation(s)
- Irina Mihaela Cazacu
- Department of Gastroenterology, Research Center of Gastroenterology and Hepatology, University of Medicine and Pharmacy, Craiova, Romania
- Department of Gastroenterology, Hepatology, and Nutrition, University of Texas – MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Adrian Saftoiu
- Department of Gastroenterology, Research Center of Gastroenterology and Hepatology, University of Medicine and Pharmacy, Craiova, Romania
| | - Peter Vilmann
- Gastrounit, Division of Surgery, Copenhagen University Hospital Herlev, Copenhagen, Denmark
| | - Manoop S. Bhutani
- Department of Gastroenterology, Hepatology, and Nutrition, University of Texas – MD Anderson Cancer Center, Houston, Texas, USA
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43
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Pannuti A, Filipovic A, Hicks C, Lefkowitz E, Ptacek T, Stebbing J, Miele L. Novel putative drivers revealed by targeted exome sequencing of advanced solid tumors. PLoS One 2018; 13:e0194790. [PMID: 29570743 PMCID: PMC5865730 DOI: 10.1371/journal.pone.0194790] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 03/10/2018] [Indexed: 12/12/2022] Open
Abstract
Next generation sequencing (NGS) is becoming increasingly integrated into oncological practice and clinical research. NGS methods have also provided evidence for clonal evolution of cancers during disease progression and treatment. The number of variants associated with response to specific therapeutic agents keeps increasing. However, the identification of novel driver mutations as opposed to passenger (phenotypically silent or clinically irrelevant) mutations remains a major challenge. We conducted targeted exome sequencing of advanced solid tumors from 44 pre-treated patients with solid tumors including breast, colorectal and lung carcinomas, neuroendocrine tumors, sarcomas and others. We catalogued established driver mutations and putative new drivers as predicted by two distinct algorithms. The established drivers we detected were consistent with published observations. However, we also detected a significant number of mutations with driver potential never described before in each tumor type we studied. These putative drivers belong to key cell fate regulatory networks, including potentially druggable pathways. Should our observations be confirmed, they would support the hypothesis that new driver mutations are selected by treatment in clinically aggressive tumors, and indicate a need for longitudinal genomic testing of solid tumors to inform second line cancer treatment.
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Affiliation(s)
- Antonio Pannuti
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | | | - Chindo Hicks
- Department of Genetics, Louisiana State University School of Medicine, New Orleans, Louisiana, United States of America
- Biomedical Informatics Key Component, Louisiana Clinical and Translational Sciences Center, Baton Rouge, Louisiana, United States of America
| | - Elliot Lefkowitz
- Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, United States of America
- Informatics Institute, Center for Clinical and Translational Sciences, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, United States of America
| | - Travis Ptacek
- Department of Microbiology, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, United States of America
- Informatics Institute, Center for Clinical and Translational Sciences, University of Alabama at Birmingham School of Medicine, Birmingham, Alabama, United States of America
| | - Justin Stebbing
- Department of Oncology, Imperial College of Medicine, London, United Kingdom
- * E-mail: (JS); (LM)
| | - Lucio Miele
- Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
- Department of Genetics, Louisiana State University School of Medicine, New Orleans, Louisiana, United States of America
- * E-mail: (JS); (LM)
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Wang H, Stoecklein NH, Lin PP, Gires O. Circulating and disseminated tumor cells: diagnostic tools and therapeutic targets in motion. Oncotarget 2018; 8:1884-1912. [PMID: 27683128 PMCID: PMC5352105 DOI: 10.18632/oncotarget.12242] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 09/20/2016] [Indexed: 12/16/2022] Open
Abstract
Enumeration of circulating tumor cells (CTCs) in peripheral blood with the gold standard CellSearchTM has proven prognostic value for tumor recurrence and progression of metastatic disease. Therefore, the further molecular characterization of isolated CTCs might have clinical relevance as liquid biopsy for therapeutic decision-making and to monitor disease progression. The direct analysis of systemic cancer appears particularly important in view of the known disparity in expression of therapeutic targets as well as epithelial-to-mesenchymal transition (EMT)-based heterogeneity between primary and systemic tumor cells, which all substantially complicate monitoring and therapeutic targeting at present. Since CTCs are the potential precursor cells of metastasis, their in-depth molecular profiling should also provide a useful resource for target discovery. The present review will discuss the use of systemically spread cancer cells as liquid biopsy and focus on potential target antigens.
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Affiliation(s)
- Hongxia Wang
- Department of Oncology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, P.R. China
| | - Nikolas H Stoecklein
- Department of General, Visceral and Pediatric Surgery, Medical Faculty, University Hospital of the Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | | | - Olivier Gires
- Department of Otorhinolaryngology, Head and Neck Surgery, Grosshadern Medical Center, Ludwig-Maximilians-University of Munich, Munich, Germany.,Clinical Cooperation Group Personalized Radiotherapy of Head and Neck Tumors, Helmholtz, Germany
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45
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Alcaide M, Yu S, Davidson J, Albuquerque M, Bushell K, Fornika D, Arthur S, Grande BM, McNamara S, Tertre MCD, Batist G, Huntsman DG, Cavallone L, Aguilar A, Basik M, Johnson NA, Deyell RJ, Rassekh SR, Morin RD. Targeted error-suppressed quantification of circulating tumor DNA using semi-degenerate barcoded adapters and biotinylated baits. Sci Rep 2017; 7:10574. [PMID: 28874686 PMCID: PMC5585219 DOI: 10.1038/s41598-017-10269-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 08/02/2017] [Indexed: 12/12/2022] Open
Abstract
Ultrasensitive methods for rare allele detection are critical to leverage the full potential offered by liquid biopsies. Here, we describe a novel molecular barcoding method for the precise detection and quantification of circulating tumor DNA (ctDNA). The major benefits of our design include straightforward and cost-effective production of barcoded adapters to tag individual DNA molecules before PCR and sequencing, and better control over cross-contamination between experiments. We validated our approach in a cohort of 24 patients with a broad spectrum of cancer diagnoses by targeting and quantifying single-nucleotide variants (SNVs), indels and genomic rearrangements in plasma samples. By using personalized panels targeting a priori known mutations, we demonstrate comprehensive error-suppression capabilities for SNVs and detection thresholds for ctDNA below 0.1%. We also show that our semi-degenerate barcoded adapters hold promise for noninvasive genotyping in the absence of tumor biopsies and monitoring of minimal residual disease in longitudinal plasma samples. The benefits demonstrated here include broad applicability, flexibility, affordability and reproducibility in the research and clinical settings.
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Affiliation(s)
- Miguel Alcaide
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Stephen Yu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Jordan Davidson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Marco Albuquerque
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Kevin Bushell
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Daniel Fornika
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Sarah Arthur
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Suzan McNamara
- Quebec Clinical Research Organization in Cancer (Q-CROC), Exactis Innovation and the Segal Cancer Centre, Montreal, QC, Canada
| | - Mathilde Couetoux du Tertre
- Quebec Clinical Research Organization in Cancer (Q-CROC), Exactis Innovation and the Segal Cancer Centre, Montreal, QC, Canada
| | - Gerald Batist
- Quebec Clinical Research Organization in Cancer (Q-CROC), Exactis Innovation and the Segal Cancer Centre, Montreal, QC, Canada
| | - David G Huntsman
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine and Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Luca Cavallone
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Adriana Aguilar
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark Basik
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Nathalie A Johnson
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Rebecca J Deyell
- Division of Oncology, Hematology and Bone Marrow Transplant, British Columbia Children's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - S Rod Rassekh
- Division of Oncology, Hematology and Bone Marrow Transplant, British Columbia Children's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
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46
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Yi Z, Liu B, Guan X, Ma F. Plasma cell-free DNA and survival in non-small-cell lung cancer: A meta-analysis. Mol Clin Oncol 2017; 7:167-172. [PMID: 28781780 PMCID: PMC5532691 DOI: 10.3892/mco.2017.1301] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 04/06/2017] [Indexed: 01/06/2023] Open
Abstract
In recent years, plasma cell-free DNA (cfDNA) has been attracting increasing attention as a potential tumor marker, as this method is easily applied and minimally invasive. A series of studies have confirmed the association between the level of cfDNA and overall survival (OS) in non-small-cell lung cancer (NSCLC), but the findings remain inconclusive. We herein conducted a meta-analysis of published articles evaluating the correlation between the level of cfDNA and OS. A total of 9 studies enrolling 1,170 patients were included. For the overall population, a high level of cfDNA was found to be significantly correlated with worse OS [hazard ratio (HR) = 1.57, 95% confidence interval (CI): 1.18–2.10] in NSCLC. The subgroup analysis suggested that a high cfDNA level was associated with worse outcome in stage III–IV patients (HR=1.53, 95% CI: 1.07–2.19). However, the level of cfDNA and OS were not found to be significantly associated in the subgroup of patients with tumor stage I–II. The present meta-analysis revealed that a high level of cfDNA may be correlated with poor OS in NSCLC.
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Affiliation(s)
- Zongbi Yi
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
| | - Binliang Liu
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
| | - Xiuwen Guan
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
| | - Fei Ma
- Department of Medical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, P.R. China
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47
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Han X, Wang J, Sun Y. Circulating Tumor DNA as Biomarkers for Cancer Detection. GENOMICS, PROTEOMICS & BIOINFORMATICS 2017; 15:59-72. [PMID: 28392479 PMCID: PMC5414889 DOI: 10.1016/j.gpb.2016.12.004] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 12/13/2016] [Accepted: 12/20/2016] [Indexed: 12/23/2022]
Abstract
Detection of circulating tumor DNAs (ctDNAs) in cancer patients is an important component of cancer precision medicine ctDNAs. Compared to the traditional physical and biochemical methods, blood-based ctDNA detection offers a non-invasive and easily accessible way for cancer diagnosis, prognostic determination, and guidance for treatment. While studies on this topic are currently underway, clinical translation of ctDNA detection in various types of cancers has been attracting much attention, due to the great potential of ctDNA as blood-based biomarkers for early diagnosis and treatment of cancers. ctDNAs are detected and tracked primarily based on tumor-related genetic and epigenetic alterations. In this article, we reviewed the available studies on ctDNA detection and described the representative methods. We also discussed the current understanding of ctDNAs in cancer patients and their availability as potential biomarkers for clinical purposes. Considering the progress made and challenges involved in accurate detection of specific cell-free nucleic acids, ctDNAs hold promise to serve as biomarkers for cancer patients, and further validation is needed prior to their broad clinical use.
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Affiliation(s)
- Xiao Han
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junyun Wang
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingli Sun
- CAS Key Laboratory of Genomic and Precision Medicine, China Gastrointestinal Cancer Research Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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48
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Zafon C, Díez JJ, Galofré JC, Cooper DS. Nodular Thyroid Disease and Thyroid Cancer in the Era of Precision Medicine. Eur Thyroid J 2017; 6:65-74. [PMID: 28589087 PMCID: PMC5422742 DOI: 10.1159/000457793] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 01/19/2017] [Indexed: 12/27/2022] Open
Abstract
The management of thyroid nodules, one of the main clinical challenges in endocrine clinical practice, is usually straightforward. Although the most important concern is ruling out malignancy, there are grey areas where uncertainty is frequently present: the nodules labelled as indeterminate by cytology and the extent of therapy when thyroid cancer is diagnosed pathologically. There is evidence that the current available precision medicine tools (from all the "-omics" to molecular analysis, fine-tuning imaging or artificial intelligence) may help to fill present gaps in the future. We present here a commentary on some of the current challenges faced by endocrinologists in the field of thyroid nodules and cancer, and illustrate how precision medicine may improve their diagnostic and therapeutic capabilities in the future.
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Affiliation(s)
- Carles Zafon
- Department of Endocrinology, Hospital Vall d'Hebron, and Diabetes and Metabolism Research Unit, Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona and CIBERDEM (ISCIII), Barcelona, Spain
| | - Juan J. Díez
- Department of Endocrinology and Nutrition, Hospital Ramón y Cajal, Madrid, Spain
- Department of Medicine, University of Alcalá de Henares, Madrid, Spain
| | - Juan C. Galofré
- Department of Endocrinology and Nutrition, Clínica Universidad de Navarra, University of Navarra, Pamplona, Spain
- IdiSNA (Instituto de investigación en la salud de Navarra), Pamplona, Spain
- *Dr. Juan C. Galofré, Department of Endocrinology and Nutrition, Clínica Universidad de Navarra, University of Navarro, Avenida Pio XII, 36, ES-31080 Pamplona (Spain), E-Mail
| | - David S. Cooper
- Division of Endocrinology, Diabetes and Metabolism, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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49
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Luz MCDB, Perez MM, Azzalis LA, Sousa LVDA, Adami F, Fonseca FLA, Alves BDCA. Evaluation of MCT1, MCT4 and CD147 Genes in Peripheral Blood Cells of Breast Cancer Patients and Their Potential Use as Diagnostic and Prognostic Markers. Int J Mol Sci 2017; 18:ijms18040170. [PMID: 28333070 PMCID: PMC5412261 DOI: 10.3390/ijms18040170] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/26/2016] [Accepted: 01/08/2017] [Indexed: 12/18/2022] Open
Abstract
Background: Patients with breast cancer—the deadliest cancer among women—are at constant risk of developing metastasis. Oxidative stress and hypoxia are common feature of tumor cells that can proliferate even in a resultant metabolic acidosis. Despite the low extracellular pH, intracellular pH of tumor cells remains relatively normal, or even more alkaline due to the action of a membrane protein family known as monocarboxylate transporters (MCTs). The objective of this study was to verify the diagnostic and prognostic value of MCT1, MCT4 and CD147 in tumor and peripheral blood samples of patients with breast cancer undergoing chemotherapic treatment. Methods: Differential expression of MCT1, MCT4 and CD147 obtained by qPCR was determined by 2−ΔΔCq method between biological samples (tumor and serial samples of peripheral) of patients (n = 125) and healthy women (n = 25). Results: tumor samples with higher histological grades have shown higher expression of these markers; this higher expression was also observed in blood samples obtained at diagnosis of patients when compared to healthy women and in patients with positive progression of the disease (metastasis development). Conclusion: markers studied here could be a promising strategy in routine laboratory evaluations as breast cancer diagnosis and prognosis.
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Affiliation(s)
- Maria Cláudia de B Luz
- Clinical Laboratory, Faculdade de Medicina do ABC (FMABC), Av. Príncipe de Gales, 821, CEP 09060-650 Santo André, SP, Brazil.
| | - Matheus M Perez
- Clinical Laboratory, Faculdade de Medicina do ABC (FMABC), Av. Príncipe de Gales, 821, CEP 09060-650 Santo André, SP, Brazil.
| | - Ligia A Azzalis
- Biological Science Department, UNIFESP, Rua Prof. Artur Riedel, 275, CEP 09972-270 Diadema, SP, Brazil.
| | - Luiz Vinícius de A Sousa
- Epidemiology Laboratory and Data Analysis, FMABC, Av. Príncipe de Gales, 821, CEP 09060-650 Santo André, SP, Brazil.
| | - Fernando Adami
- Epidemiology Laboratory and Data Analysis, FMABC, Av. Príncipe de Gales, 821, CEP 09060-650 Santo André, SP, Brazil.
| | - Fernando L A Fonseca
- Clinical Laboratory, Faculdade de Medicina do ABC (FMABC), Av. Príncipe de Gales, 821, CEP 09060-650 Santo André, SP, Brazil.
- Biological Science Department, UNIFESP, Rua Prof. Artur Riedel, 275, CEP 09972-270 Diadema, SP, Brazil.
| | - Beatriz da C A Alves
- Clinical Laboratory, Faculdade de Medicina do ABC (FMABC), Av. Príncipe de Gales, 821, CEP 09060-650 Santo André, SP, Brazil.
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50
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Cell-Free DNA Provides a Good Representation of the Tumor Genome Despite Its Biased Fragmentation Patterns. PLoS One 2017; 12:e0169231. [PMID: 28046008 PMCID: PMC5207727 DOI: 10.1371/journal.pone.0169231] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/13/2016] [Indexed: 12/17/2022] Open
Abstract
Cell-free DNA (cfDNA) is short, extracellular, fragmented double-stranded DNA found in plasma. Plasma of patients with solid tumor has been found to show significantly increased quantities of cfDNA. Although currently poorly understood, the mechanism of cfDNA generation is speculated to be a product of genomic DNA fragmentation during cellular apoptosis and necrosis. Sequencing of cfDNA with tumor origin has identified tumor biomarkers, elucidating molecular pathology and assisting in accurate diagnosis. In this study, we performed whole-genome sequencing ofcfDNA samples with matching tumor and whole blood samples from five patients diagnosed with stage IV gastric or lung cancer. We analyzed the coverage spectrum of the human genome in our cfDNA samples. cfDNA exhibited no large regions with significant under-coverage, although we observed unbalanced coverage depth in cfDNA at transcription start sites and exon boundaries as a consequence of biased fragmentation due to ordered nucleosome positioning. We also analyzed the copy number variant status based on the whole-genome sequencing results and found high similarity between copy number profile constructed from tumor samples and cfDNA samples. Overall, we conclude that cfDNA comprises a good representation of the tumor genome in late stage gastric and lung cancer.
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