1
|
Chen L, Yang G, Qu F. Aptamer-based sensors for fluid biopsies of protein disease markers. Talanta 2024; 276:126246. [PMID: 38796994 DOI: 10.1016/j.talanta.2024.126246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/29/2024]
Abstract
Fluid biopsy technology, characterized by its minimally invasive nature, speed, and continuity, has become a rapidly advancing and widely applied real-time diagnostic technique. Among various biomarkers, proteins represent the most abundant class of disease indicators. The sensitive and accurate detection of protein markers in bodily fluids is significantly influenced by the control exerted by recognition ligands. Aptamers, which are structurally dynamic functional oligonucleotides, exhibit high affinity, specific recognition of targets, and notable characteristics of high editability and modularity. These features make aptamer universal "recognition-capture" components, contribute to a significant leap in their applications within the biosensor domain. In this context, we provide a comprehensive review of the extensive application of aptamer-based biosensors in fluid biopsy. We systematically compile the characteristics and construction strategies of aptamer-based biosensors tailored for fluid biopsy, including aptamer sequences, affinity (KD), fluid background, sensing technologies, sensor construction strategies, incubation time, detection performance, and influencing factors. Furthermore, a comparative analysis of their advantages and disadvantages was conducted. In conclusion, we delineate and deliberate on prospective research trajectories and challenges that lie ahead in the realm of aptamer-based biosensors for fluid biopsy.
Collapse
Affiliation(s)
- Li Chen
- School of Life Science, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Ge Yang
- CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China.
| | - Feng Qu
- School of Life Science, Key Laboratory of Molecular Medicine and Biotherapy, Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Beijing Institute of Technology, Beijing, 100081, China.
| |
Collapse
|
2
|
Peng H, Pan M, Zhou Z, Chen C, Xing X, Cheng S, Zhang S, Zheng H, Qian K. The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples. Front Cell Dev Biol 2024; 12:1385041. [PMID: 38784382 PMCID: PMC11111958 DOI: 10.3389/fcell.2024.1385041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.
Collapse
Affiliation(s)
- Hongwei Peng
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Pan
- Taihe Skills Training Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zongning Zhou
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Congbo Chen
- Department of Urology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xing Xing
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shaoping Cheng
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shanshan Zhang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Zheng
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| |
Collapse
|
3
|
Bhambhani C, Kang Q, Hovelson DH, Sandford E, Olesnavich M, Dermody SM, Wolfgang J, Tuck KL, Brummel C, Bhangale AD, He K, Gutierrez MG, Lindstrom RH, Liu CJ, Tuck M, Kandarpa M, Mierzwa M, Casper K, Prince ME, Krauss JC, Talpaz M, Henry NL, Giraldez MD, Ramnath N, Tomlins SA, Swiecicki PL, Brenner JC, Tewari M. ctDNA transiting into urine is ultrashort and facilitates noninvasive liquid biopsy of HPV+ oropharyngeal cancer. JCI Insight 2024; 9:e177759. [PMID: 38516891 PMCID: PMC11018327 DOI: 10.1172/jci.insight.177759] [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: 11/20/2023] [Accepted: 02/02/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUNDTransrenal cell-free tumor DNA (TR-ctDNA), which transits from the bloodstream into urine, has the potential to enable noninvasive cancer detection for a wide variety of nonurologic cancer types.MethodsUsing whole-genome sequencing, we discovered that urine TR-ctDNA fragments across multiple cancer types are predominantly ultrashort (<50 bp) and, therefore, likely to be missed by conventional ctDNA assays. We developed an ultrashort droplet digital PCR assay to detect TR-ctDNA originating from HPV-associated oropharyngeal squamous cell carcinoma (HPV+ OPSCC) and confirmed that assaying ultrashort DNA is critical for sensitive cancer detection from urine samples.ResultsTR-ctDNA was concordant with plasma ctDNA for cancer detection in patients with HPV+ OPSCC. As proof of concept for using urine TR-ctDNA for posttreatment surveillance, in a small longitudinal case series, TR-ctDNA showed promise for noninvasive detection of recurrence of HPV+ OPSCC.ConclusionOur data indicate that focusing on ultrashort fragments of TR-ctDNA will be important for realizing the full potential of urine-based cancer diagnostics. This has implications for urine-based detection of a wide variety of cancer types and for facilitating access to care through at-home specimen collections.FundingNIH grants R33 CA229023, R21 CA225493; NIH/National Cancer Institute grants U01 CA183848, R01 CA184153, and P30CA046592; American Cancer Society RSG-18-062-01-TBG; American Cancer Society Mission Boost grant MBGI-22-056-01-MBG; and the A. Alfred Taubman Medical Research Institute.
Collapse
Affiliation(s)
| | - Qing Kang
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Daniel H. Hovelson
- Michigan Center for Translational Pathology
- Department of Computational Medicine & Bioinformatics
| | - Erin Sandford
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Mary Olesnavich
- Department of Internal Medicine, Division of Hematology/Oncology
| | | | - Jenny Wolfgang
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Kirsten L. Tuck
- Department of Internal Medicine, Division of Hematology/Oncology
| | | | | | - Kuang He
- Department of Internal Medicine, Division of Hematology/Oncology
| | | | | | - Chia-Jen Liu
- Michigan Center for Translational Pathology
- Department of Pathology
| | - Melissa Tuck
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Malathi Kandarpa
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Michelle Mierzwa
- Department of Radiation Oncology, and
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Keith Casper
- Department of Otolaryngology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Mark E. Prince
- Department of Otolaryngology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - John C. Krauss
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Moshe Talpaz
- Department of Internal Medicine, Division of Hematology/Oncology
| | - N. Lynn Henry
- Department of Internal Medicine, Division of Hematology/Oncology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Maria D. Giraldez
- Department of Internal Medicine, Division of Hematology/Oncology
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío, Consejo Superior de Investigaciones Científicas, University of Seville, Seville, Spain
| | - Nithya Ramnath
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Scott A. Tomlins
- Michigan Center for Translational Pathology
- Department of Pathology
- Department of Urology
| | - Paul L. Swiecicki
- Department of Internal Medicine, Division of Hematology/Oncology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - J. Chad Brenner
- Department of Otolaryngology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
- Department of Pharmacology
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, and
- Center for Computational Biology and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
4
|
Najafi S, Asemani Y, Majidpoor J, Mahmoudi R, Aghaei-Zarch SM, Mortezaee K. Tumor-educated platelets. Clin Chim Acta 2024; 552:117690. [PMID: 38056548 DOI: 10.1016/j.cca.2023.117690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 12/08/2023]
Abstract
Beyond traditional roles in homeostasis and coagulation, growing evidence suggests that platelets also reflect malignant transformation in cancer. Platelets are present in the tumor microenvironment where they interact with cancer cells. This interaction results in direct and indirect "education" as evident by platelet alterations in adhesion molecules, glycoproteins, nucleic acids, proteins and various receptors. Subsequently, these tumor-educated platelets (TEPs) circulate throughout the body and play pivotal roles in promotion of tumor growth and dissemination. Accordingly, platelet status can be considered a unique blood-based biomarker that can potentially predict prognosis and therapeutic success. Recently, liquid biopsies including TEPs have received much attention as safe, minimally invasive and sensitive alternatives for patient management. Herein, we provide an overview of TEPs and explore their benefits and limitations in cancer.
Collapse
Affiliation(s)
- Sajad Najafi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yahya Asemani
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jamal Majidpoor
- Department of Anatomy, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Reza Mahmoudi
- Department of Toxicology and Pharmacology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohsen Aghaei-Zarch
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Keywan Mortezaee
- Department of Anatomy, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran.
| |
Collapse
|
5
|
Liu W, Lee LP. Toward Rapid and Accurate Molecular Diagnostics at Home. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206525. [PMID: 36416278 DOI: 10.1002/adma.202206525] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/14/2022] [Indexed: 05/26/2023]
Abstract
The global outbreaks of infectious diseases have significantly driven an imperative demand for rapid and accurate molecular diagnostics. Nucleic acid amplification tests (NAATs) feature high sensitivity and high specificity; however, the labor-intensive sample preparation and nucleic acid amplification steps remain challenging in order to carry out rapid and precision molecular diagnostics at home. This review discusses the advances and challenges of automatic solutions of sample preparation integrated with on-chip nucleic acid amplification for effective and accurate molecular diagnostics at home. The sample preparation methods of whole blood, urine, saliva/nasal swab, and stool on chip are examined. Then, the repurposable integrated sample preparation on a chip using various biological samples is investigated. Finally, the on-chip NAATs that can be integrated with automated sample preparation are evaluated. The user-friendly approaches with combined sample preparation and NAATs can be the game changers for next-generation rapid and precision home diagnostics.
Collapse
Affiliation(s)
- Wenpeng Liu
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - Luke P Lee
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| |
Collapse
|
6
|
Kim T, Kim J, Kim T, Oak CH, Ryoo S. Transrenal DNA detection of Mycobacterium tuberculosis in patients with pulmonary tuberculosis. Int J Mycobacteriol 2023; 12:66-72. [PMID: 36926765 DOI: 10.4103/ijmy.ijmy_12_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
Background Multiple attempts have been made to use biological samples other than sputum to diagnose tuberculosis (TB). Sputum acid-fast bacillus (AFB) microscopy is the fastest, most straightforward, and most inexpensive method for diagnosing pulmonary TB. However, urine can be used in place of sputum owing to its various advantages, such as a noninvasive method of collection, convenient handling and storage, and minimal risk of infection in health-care workers involved in sample collection. In this study, we aimed to assess the suitability of urine as a sample to obtain transrenal DNA (trDNA) to diagnose TB. This study involved several patients with TB undergoing inpatient treatment, whose AFB microscopy showed negative inversion. Methods Here, 51 urine samples were collected from 40 patients with TB and examined to confirm the presence of trDNA. First, we compared the efficiency of two trDNA extraction methods. An automated magnetic bead-based method and a more efficient anchoring extraction method. Statistical analyses were performed using Excel software (Microsoft Office Professional Plus 2019). Results Although molecular diagnosis using GeneXpert yielded negative results, a peculiarity was observed. There was no significant difference between GeneXpert findings and our results nor was there any difference in the sequential trDNA samples obtained. However, even when GeneXpert results were negative, trDNA was detected in seven out of ten samples using the anchor extraction method. Conclusions Further studies are needed to establish biomarkers for the progression of TB treatment.
Collapse
Affiliation(s)
- Taeyoon Kim
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon, Republic of Korea
| | - Jehun Kim
- Department of Internal Medicine, Division of Pulmonology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Republic of Korea
| | - Taeyun Kim
- Department of Internal Medicine, Division of Pulmonology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Republic of Korea
| | - Chul-Ho Oak
- Department of Internal Medicine, Division of Pulmonology, Kosin University Gospel Hospital, Kosin University College of Medicine, Busan, Republic of Korea
| | - Sungweon Ryoo
- Clinical Research Center, Masan National Tuberculosis Hospital, Changwon, Republic of Korea
| |
Collapse
|
7
|
Chang A, Mzava O, Djomnang LAK, Lenz JS, Burnham P, Kaplinsky P, Andama A, Connelly J, Bachman CM, Cattamanchi A, Steadman A, De Vlaminck I. Metagenomic DNA sequencing to quantify Mycobacterium tuberculosis DNA and diagnose tuberculosis. Sci Rep 2022; 12:16972. [PMID: 36216964 PMCID: PMC9551046 DOI: 10.1038/s41598-022-21244-x] [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: 06/03/2022] [Accepted: 09/26/2022] [Indexed: 12/29/2022] Open
Abstract
Tuberculosis (TB) remains a significant cause of mortality worldwide. Metagenomic next-generation sequencing has the potential to reveal biomarkers of active disease, identify coinfection, and improve detection for sputum-scarce or culture-negative cases. We conducted a large-scale comparative study of 428 plasma, urine, and oral swab samples from 334 individuals from TB endemic and non-endemic regions to evaluate the utility of a shotgun metagenomic DNA sequencing assay for tuberculosis diagnosis. We found that the composition of the control population had a strong impact on the measured performance of the diagnostic test: the use of a control population composed of individuals from a TB non-endemic region led to a test with nearly 100% specificity and sensitivity, whereas a control group composed of individuals from TB endemic regions exhibited a high background of nontuberculous mycobacterial DNA, limiting the diagnostic performance of the test. Using mathematical modeling and quantitative comparisons to matched qPCR data, we found that the burden of Mycobacterium tuberculosis DNA constitutes a very small fraction (0.04 or less) of the total abundance of DNA originating from mycobacteria in samples from TB endemic regions. Our findings suggest that the utility of a minimally invasive metagenomic sequencing assay for pulmonary tuberculosis diagnostics is limited by the low burden of M. tuberculosis and an overwhelming biological background of nontuberculous mycobacterial DNA.
Collapse
Affiliation(s)
- Adrienne Chang
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| | - Omary Mzava
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| | - Liz-Audrey Kounatse Djomnang
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| | - Joan Sesing Lenz
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| | - Philip Burnham
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| | - Peter Kaplinsky
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| | - Alfred Andama
- grid.11194.3c0000 0004 0620 0548Department of Internal Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | | | | | - Adithya Cattamanchi
- grid.266102.10000 0001 2297 6811Center for Tuberculosis and Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA USA
| | | | - Iwijn De Vlaminck
- grid.5386.8000000041936877XNancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY USA
| |
Collapse
|
8
|
Tivey A, Church M, Rothwell D, Dive C, Cook N. Circulating tumour DNA - looking beyond the blood. Nat Rev Clin Oncol 2022; 19:600-612. [PMID: 35915225 PMCID: PMC9341152 DOI: 10.1038/s41571-022-00660-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2022] [Indexed: 02/06/2023]
Abstract
Over the past decade, various liquid biopsy techniques have emerged as viable alternatives to the analysis of traditional tissue biopsy samples. Such surrogate 'biopsies' offer numerous advantages, including the relative ease of obtaining serial samples and overcoming the issues of interpreting one or more small tissue samples that might not reflect the entire tumour burden. To date, the majority of research in the area of liquid biopsies has focused on blood-based biomarkers, predominantly using plasma-derived circulating tumour DNA (ctDNA). However, ctDNA can also be obtained from various non-blood sources and these might offer unique advantages over plasma ctDNA. In this Review, we discuss advances in the analysis of ctDNA from non-blood sources, focusing on urine, cerebrospinal fluid, and pleural or peritoneal fluid, but also consider other sources of ctDNA. We discuss how these alternative sources can have a distinct yet complementary role to that of blood ctDNA analysis and consider various technical aspects of non-blood ctDNA assay development. We also reflect on the settings in which non-blood ctDNA can offer distinct advantages over plasma ctDNA and explore some of the challenges associated with translating these alternative assays from academia into clinical use.
Collapse
Affiliation(s)
- Ann Tivey
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
- The Christie NHS Foundation Trust, Manchester, UK
| | - Matt Church
- The Christie NHS Foundation Trust, Manchester, UK
| | - Dominic Rothwell
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, The University of Manchester, Manchester, UK
| | - Caroline Dive
- Division of Cancer Sciences, The University of Manchester, Manchester, UK
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, The University of Manchester, Manchester, UK
| | - Natalie Cook
- Division of Cancer Sciences, The University of Manchester, Manchester, UK.
- The Christie NHS Foundation Trust, Manchester, UK.
| |
Collapse
|
9
|
Ranches G, Zeidler M, Kessler R, Hoelzl M, Hess MW, Vosper J, Perco P, Schramek H, Kummer KK, Kress M, Krogsdam A, Rudnicki M, Mayer G, Huettenhofer A. Exosomal mitochondrial tRNAs and miRNAs as potential predictors of inflammation in renal proximal tubular epithelial cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:794-813. [PMID: 35664695 PMCID: PMC9136061 DOI: 10.1016/j.omtn.2022.04.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/28/2022] [Indexed: 12/02/2022]
Abstract
Exosomes have emerged as a valuable repository of novel biomarkers for human diseases such as chronic kidney disease (CKD). From a healthy control group, we performed microRNA (miRNA) profiling of urinary exosomes and compared it with a cell culture model of renal proximal tubular epithelial cells (RPTECs). Thereby, a large fraction of abundant urinary exosomal miRNAs could also be detected in exosomes derived from RPTECs, indicating them as a suitable model system for investigation of CKD. We subsequently analyzed exosomes from RPTECs in pro-inflammatory and pro-fibrotic states, mimicking some aspects of CKD. Following cytokine treatment, we observed a significant increase in exosome release and identified 30 dysregulated exosomal miRNAs, predominantly associated with the regulation of pro-inflammatory and pro-fibrotic-related pathways. In addition to miRNAs, we also identified 16 dysregulated exosomal mitochondrial RNAs, highlighting a pivotal role of mitochondria in sensing renal inflammation. Inhibitors of exosome biogenesis and release significantly altered the abundance of selected candidate miRNAs and mitochondrial RNAs, thus suggesting distinct sorting mechanisms of different non-coding RNA (ncRNA) species into exosomes. Hence, these two exosomal ncRNA species might be employed as potential indicators for predicting the pathogenesis of CKD and also might enable effective monitoring of the efficacy of CKD treatment.
Collapse
Affiliation(s)
- Glory Ranches
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Maximilian Zeidler
- Institute of Physiology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Roman Kessler
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Martina Hoelzl
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Michael W. Hess
- Institute of Histology and Embryology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Jonathan Vosper
- Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Paul Perco
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Herbert Schramek
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Kai K. Kummer
- Institute of Physiology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Michaela Kress
- Institute of Physiology, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Anne Krogsdam
- Division of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Michael Rudnicki
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Gert Mayer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Alexander Huettenhofer
- Division of Genomics and RNomics, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| |
Collapse
|
10
|
Hirahata T, ul Quraish R, Quraish AU, ul Quraish S, Naz M, Razzaq MA. Liquid Biopsy: A Distinctive Approach to the Diagnosis and Prognosis of Cancer. Cancer Inform 2022; 21:11769351221076062. [PMID: 35153470 PMCID: PMC8832574 DOI: 10.1177/11769351221076062] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer is a leading cause of morbidity and mortality worldwide. Over the past decades, the concept of precision cancer medicine has emerged as a novel approach in the field of oncology that aims to tailor the most effective treatment options to each individual cancer patient based on the genetic profile of the tumor of each individual patient. Recently, tissue biopsy has become an essential part of cancer care and is widely used to characterize the tumor. However, tissue biopsy techniques face different challenges due to their invasiveness, cost, time, and adversity in potential sampling due to tissue heterogeneity. To overcome these issues, a non-invasive approach has developed, which is known as liquid biopsy. It is a simple, fast, and worthwhile technique based on the analysis of circulating tumor DNA (which is a fraction of cfDNA), circulating tumor cells (CTCs), and other tumor-derived material in blood plasma. This review provides an overview of the concept of liquid biopsy and briefly discusses the role of ctDNA and CTC analysis as tools for early diagnosis and prognosis of cancer. In this review, we also speculate on the advantages of liquid biopsy as opposed to tissue biopsy and postulate that liquid biopsy may be a comprehensive approach to overcome the current limitations associated with costly, invasive, and time-consuming tissue biopsy.
Collapse
Affiliation(s)
| | | | | | | | - Munazzah Naz
- Hirahata Gene Therapy Laboratory, HIC Clinic, Tokyo, Japan
| | | |
Collapse
|
11
|
Kondratskaya VA, Pokrovskaya MS, Doludin YV, Borisova AL, Limonova AS, Meshkov АN, Drapkina OM. Influence of preanalytical variables on the quality of cell-free DNA. Biobanking of cell-free DNA material. КАРДИОВАСКУЛЯРНАЯ ТЕРАПИЯ И ПРОФИЛАКТИКА 2022. [DOI: 10.15829/1728-8800-2021-3114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The search for early disease markers and the development of diagnostic systems has recently been expanding within genomics. Genomic deoxyribonucleic acid (DNA), cell-free DNA (cfDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. It has been shown that cfDNA that enters the bloodstream, in particular, as a result of apoptosis, necrosis, active tumor secretion and metastasis, is of great importance for studying molecular mechanisms of the pathological process and application in clinical practice. Circulating nucleic acid analysis can be used to monitor response to treatment, assess drug resistance, and quantify minimal residual disease. The review article reflects the following information about the biomaterial: source of cfDNA, methods of cfDNA isolation, storage and use for the diagnosis of certain diseases. Cell-free DNA can be present in biological fluids such as blood, urine, saliva, synovial and cerebrospinal fluid. In most cases, cfDNA is isolated from blood derivatives (serum and plasma), while it is most correct to use blood plasma for cfDNA isolation. Optimal and economically justifiable is the use of ethylenediaminetetra-acetic acid tubes for taking blood and obtaining plasma with subsequent cfDNA isolation. There is evidence that the optimal shelf life in an ethylenediaminetetra-acetic acid tube from the moment of blood sampling to subsequent isolation is a 2-hour interval. After centrifugation, cfDNA in plasma (or serum) can be stored for a long time at a temperature of -80O C. Storage at -20O C is undesirable, since DNA fragmentation increases.
Collapse
Affiliation(s)
| | - M. S. Pokrovskaya
- National Medical Research Center for Therapy and Preventive Medicine
| | - Yu. V. Doludin
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. L. Borisova
- National Medical Research Center for Therapy and Preventive Medicine
| | - A. S. Limonova
- National Medical Research Center for Therapy and Preventive Medicine
| | - А. N. Meshkov
- National Medical Research Center for Therapy and Preventive Medicine
| | - O. M. Drapkina
- National Medical Research Center for Therapy and Preventive Medicine
| |
Collapse
|
12
|
de Godoy Torso N, Pereira JKN, Visacri MB, Vasconcelos PENS, Loren P, Saavedra K, Saavedra N, Salazar LA, Moriel P. Dysregulated MicroRNAs as Biomarkers or Therapeutic Targets in Cisplatin-Induced Nephrotoxicity: A Systematic Review. Int J Mol Sci 2021; 22:12765. [PMID: 34884570 PMCID: PMC8657822 DOI: 10.3390/ijms222312765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/07/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022] Open
Abstract
The purpose of this systematic review was to map out and summarize scientific evidence on dysregulated microRNAs (miRNAs) that can be possible biomarkers or therapeutic targets for cisplatin nephrotoxicity and have already been tested in humans, animals, or cells. In addition, an in silico analysis of the two miRNAs found to be dysregulated in the majority of studies was performed. A literature search was performed using eight databases for studies published up to 4 July 2021. Two independent reviewers selected the studies and extracted the data; disagreements were resolved by a third and fourth reviewers. A total of 1002 records were identified, of which 30 met the eligibility criteria. All studies were published in English and reported between 2010 and 2021. The main findings were as follows: (a) miR-34a and miR-21 were the main miRNAs identified by the studies as possible biomarkers and therapeutic targets of cisplatin nephrotoxicity; (b) the in silico analysis revealed 124 and 131 different strongly validated targets for miR-34a and miR-21, respectively; and (c) studies in humans remain scarce.
Collapse
Affiliation(s)
- Nadine de Godoy Torso
- School of Medical Sciences, University of Campinas, Campinas 13083894, Brazil; (N.d.G.T.); (J.K.N.P.); (M.B.V.); (P.E.N.S.V.)
| | - João Kleber Novais Pereira
- School of Medical Sciences, University of Campinas, Campinas 13083894, Brazil; (N.d.G.T.); (J.K.N.P.); (M.B.V.); (P.E.N.S.V.)
| | - Marília Berlofa Visacri
- School of Medical Sciences, University of Campinas, Campinas 13083894, Brazil; (N.d.G.T.); (J.K.N.P.); (M.B.V.); (P.E.N.S.V.)
| | | | - Pía Loren
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile; (P.L.); (K.S.); (N.S.); (L.A.S.)
| | - Kathleen Saavedra
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile; (P.L.); (K.S.); (N.S.); (L.A.S.)
| | - Nicolás Saavedra
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile; (P.L.); (K.S.); (N.S.); (L.A.S.)
| | - Luis A. Salazar
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile; (P.L.); (K.S.); (N.S.); (L.A.S.)
| | - Patricia Moriel
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083970, Brazil
| |
Collapse
|
13
|
Liu W, Yue F, Lee LP. Integrated Point-of-Care Molecular Diagnostic Devices for Infectious Diseases. Acc Chem Res 2021; 54:4107-4119. [PMID: 34699183 DOI: 10.1021/acs.accounts.1c00385] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The global outbreaks of deadly infectious diseases caused by pathogenic microorganisms have threatened public health worldwide and significantly motivated scientists to satisfy an urgent need for a rapid and accurate detection of pathogens. Traditionally, the culture-based technique is considered as the gold standard for pathogen detection, yet it has a long turnaround time due to the overnight culturing and pathogen isolation. Alternatively, nucleic acid amplification tests provide a relatively shorter turnaround time to identify whether pathogens exist in individuals with high sensitivity and high specificity. In most cases, nucleic acid amplification tests undergo three steps: sample preparation, nucleic acid amplification, and signal transduction. Despite the explosive advancement in nucleic acid amplification and signal transduction technologies, the complex and labor-intensive sample preparation steps remain a bottleneck to create a transformative integrated point-of-care (POC) molecular diagnostic device. Researchers have attempted to simplify and integrate the sample preparations for nucleic acid-based molecular diagnostic devices with innovative progress in integration strategies, engineered materials, reagent storages, and fluid actuation. Therefore, understanding the know-how and obtaining truthful knowledge of existing integrated POC molecular diagnostic devices comprising sample preparations, nucleic acid amplification, and signal transduction can generate innovative solutions to achieve personalized precision medicine and improve global health.In this Account, we discuss the challenges of automated sample preparation solutions integrated with nucleic acid amplification and signal transduction for rapid and precise home diagnostics. Blood, nasal swab, saliva, urine, and stool are emphasized as the most commonly used clinical samples for integrated POC molecular diagnostics of infectious diseases. Even though these five types of samples possess relatively correlated biomarkers due to the human body's circulatory system, each shows unique properties and exclusive advantages for molecular diagnostics in specific situations, which are included in this Account. We examine different integrated POC devices for sample preparation, which includes pathogen isolation and enrichment from the crude sample and nucleic acid purification from isolated pathogens. We present the promising on-chip integration approaches for nucleic acid amplification. We also investigate the on-chip integration methods for reagent storage, which is crucial to simplify the manual operation for end-users. Finally, we present several integrated POC molecular diagnostic devices for infectious diseases. The integrated sample preparation and nucleic acid amplification approach reviewed here can potentially impact the next generation of POC molecular home diagnostic chips, which will significantly impact public health, emergency medicine, and global biosecurity.
Collapse
Affiliation(s)
- Wenpeng Liu
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston 02115, Massachusetts, United States
| | - Fei Yue
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston 02115, Massachusetts, United States
| | - Luke P Lee
- Renal Division and Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston 02115, Massachusetts, United States
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley 94720, California, United States
- Institute of Quantum Biophysics, Department of Biophysics, Sungkyunkwan University, Suwon 16419, Korea
| |
Collapse
|
14
|
Oreskovic A, Waalkes A, Holmes EA, Rosenthal CA, Wilson DPK, Shapiro AE, Drain PK, Lutz BR, Salipante SJ. Characterizing the molecular composition and diagnostic potential of Mycobacterium tuberculosis urinary cell-free DNA using next-generation sequencing. Int J Infect Dis 2021; 112:330-337. [PMID: 34562627 PMCID: PMC8627387 DOI: 10.1016/j.ijid.2021.09.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Urine cell-free DNA (cfDNA) is an attractive target for diagnosing pulmonary Mycobacterium tuberculosis (MTB) infection, but has not been thoroughly characterized as a biomarker. METHODS This study was performed to investigate the size and composition of urine cfDNA from tuberculosis (TB) patients with minimal bias using next-generation sequencing (NGS). A combination of DNA extraction and single-stranded sequence library preparation methods demonstrated to recover short, highly degraded cfDNA fragments was employed. Urine cfDNA from 10 HIV-positive patients with pulmonary TB and two MTB-negative controls was examined. RESULTS MTB-derived cfDNA was identifiable by NGS from all MTB-positive patients and was absent from negative controls. MTB cfDNA was significantly shorter than human cfDNA, with median fragment lengths of ≤19-52 bp and 42-92 bp, respectively. MTB cfDNA abundance increased exponentially with decreased fragment length, having a peak fragment length of ≤19 bp in most samples. In addition, we identified a larger fraction of short human genomic cfDNA, ranging from 29 to 53 bp, than previously reported. Urine cfDNA fragments spanned the MTB genome with relative uniformity, but nucleic acids derived from multicopy elements were proportionately over-represented. CONCLUSIONS TB urine cfDNA is a potentially powerful biomarker but is highly fragmented, necessitating special procedures to maximize its recovery and detection.
Collapse
Affiliation(s)
- Amy Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Elizabeth A Holmes
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Christopher A Rosenthal
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Douglas P K Wilson
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa; Edendale Hospital, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Adrienne E Shapiro
- Department of Medicine, University of Washington, Seattle, Washington, USA; Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Paul K Drain
- Department of Medicine, University of Washington, Seattle, Washington, USA; Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA; Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA.
| |
Collapse
|
15
|
Zhou X, Kurywchak P, Wolf-Dennen K, Che SP, Sulakhe D, D’Souza M, Xie B, Maltsev N, Gilliam TC, Wu CC, McAndrews KM, LeBleu VS, McConkey DJ, Volpert OV, Pretzsch SM, Czerniak BA, Dinney CP, Kalluri R. Unique somatic variants in DNA from urine exosomes of individuals with bladder cancer. Mol Ther Methods Clin Dev 2021; 22:360-376. [PMID: 34514028 PMCID: PMC8408559 DOI: 10.1016/j.omtm.2021.05.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/21/2021] [Indexed: 01/03/2023]
Abstract
Bladder cancer (BC), a heterogeneous disease characterized by high recurrence rates, is diagnosed and monitored by cystoscopy. Accurate clinical staging based on biopsy remains a challenge, and additional, objective diagnostic tools are needed urgently. We used exosomal DNA (exoDNA) as an analyte to examine cancer-associated mutations and compared the diagnostic utility of exoDNA from urine and serum of individuals with BC. In contrast to urine exosomes from healthy individuals, urine exosomes from individuals with BC contained significant amounts of DNA. Whole-exome sequencing of DNA from matched urine and serum exosomes, bladder tumors, and normal tissue (peripheral blood mononuclear cells) identified exonic and 3' UTR variants in frequently mutated genes in BC, detectable in urine exoDNA and matched tumor samples. Further analyses identified somatic variants in driver genes, unique to urine exoDNA, possibly because of the inherent intra-tumoral heterogeneity of BC, which is not fully represented in random small biopsies. Multiple variants were also found in untranslated portions of the genome, such as microRNA (miRNA)-binding regions of the KRAS gene. Gene network analyses revealed that exoDNA is associated with cancer, inflammation, and immunity in BC exosomes. Our findings show utility of exoDNA as an objective, non-invasive strategy to identify novel biomarkers and targets for BC.
Collapse
Affiliation(s)
- Xunian Zhou
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paul Kurywchak
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kerri Wolf-Dennen
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sara P.Y. Che
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dinanath Sulakhe
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Mark D’Souza
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Bingqing Xie
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Natalia Maltsev
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - T. Conrad Gilliam
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Chia-Chin Wu
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathleen M. McAndrews
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Valerie S. LeBleu
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David J. McConkey
- Johns Hopkins Greenberg Bladder Cancer Institute, Baltimore, MD, USA
| | - Olga V. Volpert
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shanna M. Pretzsch
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bogdan A. Czerniak
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Colin P. Dinney
- Department of Urology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Raghu Kalluri
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- School of Bioengineering, Rice University, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
16
|
Oreskovic A, Panpradist N, Marangu D, Ngwane MW, Magcaba ZP, Ngcobo S, Ngcobo Z, Horne DJ, Wilson DPK, Shapiro AE, Drain PK, Lutz BR. Diagnosing Pulmonary Tuberculosis by Using Sequence-Specific Purification of Urine Cell-Free DNA. J Clin Microbiol 2021; 59:e0007421. [PMID: 33789959 PMCID: PMC8373247 DOI: 10.1128/jcm.00074-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/19/2021] [Indexed: 01/17/2023] Open
Abstract
Transrenal urine cell-free DNA (cfDNA) is a promising tuberculosis (TB) biomarker, but is challenging to detect because of the short length (<100 bp) and low concentration of TB-specific fragments. We aimed to improve the diagnostic sensitivity of TB urine cfDNA by increasing recovery of short fragments during sample preparation. We developed a highly sensitive sequence-specific purification method that uses hybridization probes immobilized on magnetic beads to capture short TB cfDNA (50 bp) with 91.8% average efficiency. Combined with short-target PCR, the assay limit of detection was ≤5 copies of cfDNA in 10 ml urine. In a clinical cohort study in South Africa, our urine cfDNA assay had 83.7% sensitivity (95% CI: 71.0 to 91.5%) and 100% specificity (95% CI: 86.2 to 100%) for diagnosis of active pulmonary TB when using sputum Xpert MTB/RIF as the reference standard. The detected cfDNA concentration was 0.14 to 2,804 copies/ml (median 14.6 copies/ml) and was inversely correlated with CD4 count and days to culture positivity. Sensitivity was nonsignificantly higher in HIV-positive (88.2%) compared to HIV-negative patients (73.3%), and was not dependent on CD4 count. Sensitivity remained high in sputum smear-negative (76.0%) and urine lipoarabinomannan (LAM)-negative (76.5%) patients. With improved sample preparation, urine cfDNA is a viable biomarker for TB diagnosis. Our assay has the highest reported accuracy of any TB urine cfDNA test to date and has the potential to enable rapid non-sputum-based TB diagnosis across key underserved patient populations.
Collapse
Affiliation(s)
- Amy Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Diana Marangu
- Department of Paediatrics and Child Health, University of Nairobi, Nairobi, Kenya
| | - M. William Ngwane
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa
| | - Zanele P. Magcaba
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa
| | - Sindiswa Ngcobo
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa
| | - Zinhle Ngcobo
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa
| | - David J. Horne
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Douglas P. K. Wilson
- Umkhuseli Innovation and Research Management, Pietermaritzburg, South Africa
- Edendale Hospital, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Adrienne E. Shapiro
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Paul K. Drain
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| |
Collapse
|
17
|
Gillardie ML, Babba O, Mahinc C, Duthel M, de Bengy C, Morineaud C, Rivollier E, Flori P. Molecular approach to the epidemiology of urinary schistosomiasis in France. PLoS Negl Trop Dis 2021; 15:e0009515. [PMID: 34228747 PMCID: PMC8284649 DOI: 10.1371/journal.pntd.0009515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 07/16/2021] [Accepted: 05/28/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The diagnosis of urogenital schistosomiasis is based on the complementarity of serological technique and microscopic examination (ME). Between 2015 and 2019, the number of urinary schistosomiasis tests received in our laboratory increased sharply from 300 to 900 per year. Therefore, we wanted to evaluate the reliability of urine microscopic examination (ME, reference and routine technique) from urine sample by comparing it to other techniques (antigenic technique and PCR). To this end, we optimized two real-time PCRs targeting respectively Schistosoma haematobium (Sh) and Schistosoma mansoni (Sm). METHODOLOGY/PRINCIPAL FINDINGS 914 urine samples from 846 patients suspected of urogenital schistosomiasis were prescribed and analyzed by PCR and also by antigenic technique for the first 143 samples. The antigenic technique evaluated was Schisto POC-CCA, Rapid Medical Diagnostics. These results (antigenic technique and PCR) were compared to ME which was performed from all urines. The percentage of 14% (128/914) positive cases with the PCR technique and the percentage of 6.0% (54/914) positive cases with ME is significantly different (Chi 2 test, p<0.001). These 128 positive PCRs correspond to 120 different patients, 88.3% (106/120) of them were young migrants and 11.7% (14/120) were French patients returning from travel. Among these migrants, more than 75% (80/106) came from French-speaking West Africa. In addition, the Schisto POC-CCA showed a specificity of 39% (46/117), too poor to be used as a screening tool in low or non-endemic areas. CONCLUSION/SIGNIFICANCE Targeted Sh and Sm PCRs in urine are reliable techniques compared to ME (reference technique). In view of our results, we decided to screen urinary schistosomiasis by direct ME always coupled by the PCR technique, which has shown better reliability criteria.
Collapse
Affiliation(s)
- Marie-Laure Gillardie
- University of Saint-Etienne, GIMAP-EA-3064, Saint Etienne, France
- Parasitology and Mycology, department of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Oussama Babba
- University of Saint-Etienne, GIMAP-EA-3064, Saint Etienne, France
- Parasitology and Mycology, department of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Caroline Mahinc
- Parasitology and Mycology, department of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Maureen Duthel
- University of Saint-Etienne, GIMAP-EA-3064, Saint Etienne, France
- Parasitology and Mycology, department of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Claire de Bengy
- University of Saint-Etienne, GIMAP-EA-3064, Saint Etienne, France
- Parasitology and Mycology, department of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Clotilde Morineaud
- Department of Public Health, University Hospital of Poitiers, Poitiers, France
| | - Elisabeth Rivollier
- Department PASS, University Hospital of Saint-Etienne, Saint Etienne, France
| | - Pierre Flori
- University of Saint-Etienne, GIMAP-EA-3064, Saint Etienne, France
- Parasitology and Mycology, department of Infectious Agents and Hygiene, University Hospital of Saint-Etienne, Saint-Etienne, France
| |
Collapse
|
18
|
Ferreira D, Miranda J, Martins-Lopes P, Adega F, Chaves R. Future Perspectives in Detecting EGFR and ALK Gene Alterations in Liquid Biopsies of Patients with NSCLC. Int J Mol Sci 2021; 22:ijms22083815. [PMID: 33916986 PMCID: PMC8067613 DOI: 10.3390/ijms22083815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/28/2021] [Accepted: 04/03/2021] [Indexed: 02/07/2023] Open
Abstract
Non-small-cell lung cancer (NSCLC) is a major cause of death worldwide. Alterations in such genes as EGFR and ALK are considered important biomarkers in NSCLC due to the existence of targeted therapies with specific tyrosine kinase inhibitors (TKIs). However, specific resistance-related mutations can occur during TKI treatment, which often result in therapy inefficacy. Liquid biopsies arise as a reliable tool for the early detection of these types of alterations, allowing a non-invasive follow-up of the patients. Furthermore, they can be essential for cancer screening, initial diagnosis and to check surgery success. Despite the great advantages of liquid biopsies in NSCLC and the high input that next-generation sequencing (NGS) approaches can provide in this field, its use in oncology is still limited. With improvement of assay sensitivity and the establishment of clinical guidelines for liquid biopsy analysis, it is expected that they will be used in routine procedures. This review focuses on the usefulness of liquid biopsies of NSCLC patients as a means to detect alterations in EGFR and ALK genes and in disease management, highlighting the impact of NGS methods.
Collapse
Affiliation(s)
- Daniela Ferreira
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
| | - Juliana Miranda
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
| | - Paula Martins-Lopes
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
- Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Filomena Adega
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
| | - Raquel Chaves
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
- Correspondence: ; Tel.: +351-259-350936
| |
Collapse
|
19
|
Oreskovic A, Lutz BR. Ultrasensitive hybridization capture: Reliable detection of <1 copy/mL short cell-free DNA from large-volume urine samples. PLoS One 2021; 16:e0247851. [PMID: 33635932 PMCID: PMC7909704 DOI: 10.1371/journal.pone.0247851] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/12/2021] [Indexed: 12/19/2022] Open
Abstract
Urine cell-free DNA (cfDNA) is a valuable non-invasive biomarker with broad potential clinical applications, but there is no consensus on its optimal pre-analytical methodology, including the DNA extraction step. Due to its short length (majority of fragments <100 bp) and low concentration (ng/mL), urine cfDNA is not efficiently recovered by conventional silica-based extraction methods. To maximize sensitivity of urine cfDNA assays, we developed an ultrasensitive hybridization method that uses sequence-specific oligonucleotide capture probes immobilized on magnetic beads to improve extraction of short cfDNA from large-volume urine samples. Our hybridization method recovers near 100% (95% CI: 82.6-117.6%) of target-specific DNA from 10 mL urine, independent of fragment length (25-150 bp), and has a limit of detection of ≤5 copies of double-stranded DNA (0.5 copies/mL). Pairing hybridization with an ultrashort qPCR design, we can efficiently capture and amplify fragments as short as 25 bp. Our method enables amplification of cfDNA from 10 mL urine in a single qPCR well, tolerates variation in sample composition, and effectively removes non-target DNA. Our hybridization protocol improves upon both existing silica-based urine cfDNA extraction methods and previous hybridization-based sample preparation protocols. Two key innovations contribute to the strong performance of our method: a two-probe system enabling recovery of both strands of double-stranded DNA and dual biotinylated capture probes, which ensure consistent, high recovery by facilitating optimal probe density on the bead surface, improving thermostability of the probe-bead linkage, and eliminating interference by endogenous biotin. We originally designed the hybridization method for tuberculosis diagnosis from urine cfDNA, but expect that it will be versatile across urine cfDNA targets, and may be useful for other cfDNA sample types and applications beyond cfDNA. To make our hybridization method accessible to new users, we present a detailed protocol and straightforward guidelines for designing new capture probes.
Collapse
Affiliation(s)
- Amy Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| | - Barry R. Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington, United States of America
| |
Collapse
|
20
|
Bach S, Paulis I, Sluiter NR, Tibbesma M, Martin I, van de Wiel MA, Tuynman JB, Bahce I, Kazemier G, Steenbergen RDM. Detection of colorectal cancer in urine using DNA methylation analysis. Sci Rep 2021; 11:2363. [PMID: 33504902 PMCID: PMC7840909 DOI: 10.1038/s41598-021-81900-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/11/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the second leading cause for cancer-related death globally. Clinically, there is an urgent need for non-invasive CRC detection. This study assessed the feasibility of CRC detection by analysis of tumor-derived methylated DNA fragments in urine. Urine samples, including both unfractioned and supernatant urine fractions, of 92 CRC patients and 63 healthy volunteers were analyzed for DNA methylation levels of 6 CRC-associated markers (SEPT9, TMEFF2, SDC2, NDRG4, VIM and ALX4). Optimal marker panels were determined by two statistical approaches. Methylation levels of SEPT9 were significantly increased in urine supernatant of CRC patients compared to controls (p < 0.0001). Methylation analysis in unfractioned urine appeared inaccurate. Following multivariate logistic regression and classification and regression tree analysis, a marker panel consisting of SEPT9 and SDC2 was able to detect up to 70% of CRC cases in urine supernatant at 86% specificity. First evidence is provided for CRC detection in urine by SEPT9 methylation analysis, which combined with SDC2 allows for an optimal differentiation between CRC patients and controls. Urine therefore provides a promising liquid biopsy for non-invasive CRC detection.
Collapse
Affiliation(s)
- S Bach
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - I Paulis
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - N R Sluiter
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - M Tibbesma
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - I Martin
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1089a, Amsterdam, The Netherlands
| | - M A van de Wiel
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1089a, Amsterdam, The Netherlands
| | - J B Tuynman
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - I Bahce
- Department of Pulmonary Diseases, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - G Kazemier
- Department of Surgery, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands
| | - R D M Steenbergen
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, Amsterdam, The Netherlands.
| |
Collapse
|
21
|
A facile, rapid, high-throughput extracellular vesicles analytical platform for cancer detection. Anal Chim Acta 2020; 1138:132-140. [PMID: 33161974 DOI: 10.1016/j.aca.2020.08.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/05/2020] [Accepted: 08/25/2020] [Indexed: 01/24/2023]
Abstract
Cell-derived nanoparticles, so called Extracellular Vesicles (EVs), can reflect the physiological or pathological conditions of donor cells and can provide promising biomarkers for the non-invasive diagnosis of cancers. Size-based purification method is one of the common strategies for rapid extracting EVs from biosamples, but the downstream clinical studies still remain challenges in EV enrichment with high purity and high yield. Here, such challenges could be fulfilled through the development of an arrayed Exosome Purification and Operation System (Exo-POS) for efficiently isolating EVs from complex biofluids. Human urinary EVs with mean size of approximately 170 nm were isolated successfully from donors within 30 min, and the purification of individual samples were performable in parallel. Samples purified by Exo-POS showed detectable EV-specific biomarkers and less protein impurities than that by ultrafiltration method. The results also demonstrate the great purification ability of Exo-POS to discriminate between the EV-derived proteomic and genomic expressions of cancer patients and healthy controls. The developed platform can easily be adapted to retrieve EVs from biological samples for the downstream analysis, demonstrating its potential for both rapid clinical diagnosis and biomarker discovery.
Collapse
|
22
|
Ponti G, Maccaferri M, Percesepe A, Tomasi A, Ozben T. Liquid biopsy with cell free DNA: new horizons for prostate cancer. Crit Rev Clin Lab Sci 2020; 58:60-76. [PMID: 32805148 DOI: 10.1080/10408363.2020.1803789] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Although prostate cancer (PCa) is one of the most common tumors in European males, the only minimally invasive diagnostic tool in PCa setup is the determination of PSA in serum. Cell-free DNA (cfDNA) has been demonstrated to be helpful for PCa diagnosis but has not yet been integrated into the clinical setting. This review aims to provide a systematic update of cfDNA and its fragmentation patterns in PCa reported in literature published over the last twenty years. Due to the high variability of the scientific methods adopted and a lack of standardized median cfDNA levels, results fluctuate across different studies. These differences may be due to the cfDNA source, the quantification method, or the fragmentation pattern. Blood plasma is the most frequently analyzed biological fluid, but seminal plasma has been reported to contain higher cfDNA concentration due to its vicinity to the tumor origin. CfDNA has been shown to be composed of single-stranded (ssDNA) and double-stranded DNA (dsDNA), so the total cfDNA concentration should be preferred as it corresponds best to the tumor mass. Fluorometry and capillary electrophoresis (CE) may be quick and cost-effective tools for cfDNA assessment in a clinical setting. The greatest future challenge is the elaboration of common guidelines and standardized procedures for diagnostic laboratories performing cfDNA analysis. A multiparametric approach combining the analysis of total cfDNA (both ssDNA and dsDNA), cfDNA fragment length, and specific genetic mutations (ctDNA assessment) is required for optimal future applications of liquid biopsy.
Collapse
Affiliation(s)
- Giovanni Ponti
- Division of Clinical Pathology, Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Monia Maccaferri
- Dermatology Unit, Azienda Ospedaliero-Universitaria of Modena, Modena, Italy
| | - Antonio Percesepe
- Medical Genetics Unit, Azienda Ospedaliero-Universitaria of Parma, Parma, Italy
| | - Aldo Tomasi
- Division of Clinical Pathology, Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Tomris Ozben
- Faculty of Medicine, Department of Clinical Biochemistry, Akdeniz University, Antalya, Turkey
| |
Collapse
|
23
|
Crisafulli G, Mussolin B, Cassingena A, Montone M, Bartolini A, Barault L, Martinetti A, Morano F, Pietrantonio F, Sartore-Bianchi A, Siena S, Di Nicolantonio F, Marsoni S, Bardelli A, Siravegna G. Whole exome sequencing analysis of urine trans-renal tumour DNA in metastatic colorectal cancer patients. ESMO Open 2020; 4:S2059-7029(20)30089-2. [PMID: 32149725 PMCID: PMC7001107 DOI: 10.1136/esmoopen-2019-000572] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/19/2019] [Accepted: 09/21/2019] [Indexed: 12/22/2022] Open
Abstract
Background The analysis of circulating free tumour DNA (ctDNA) in blood, commonly referred as liquid biopsy, is being used to characterise patients with solid cancers. Tumour-specific genetic variants can also be present in DNA isolated from other body fluids, such as urine. Unlike blood, urine sampling is non-invasive, can be self-performed, and allows recurrent longitudinal monitoring. The features of tumour DNA that clears from the glomerular filtration barrier, named trans-renal tumour DNA (trtDNA), are largely unexplored. Patients and methods Specimens were collected from 24 patients with KRAS or BRAF mutant metastatic colorectal cancer (mCRC). Driver mutations were assessed by droplet digital PCR (ddPCR) in ctDNA from plasma and trtDNA from urine. Whole exome sequencing (WES) was performed in DNA isolated from tissue, plasma and urine. Results Out of the 24 CRC cases, only four had sufficient DNA to allow WES analyses in urine and plasma. We found that tumour alterations primarily reside in low molecular weight fragments (less than 112 bp). In patients whose trtDNA was more than 2.69% of the urine derived DNA, cancer-specific molecular alterations, mutational signatures and copy number profiles identified in urine DNA are comparable with those detected in plasma ctDNA. Conclusions With current technologies, WES analysis of trtDNA is feasible in a small fraction of mCRC patients. Tumour-related genetic information is mainly present in low molecular weight DNA fragments. Although the limited amounts of trtDNA poses analytical challenges, enrichment of low molecular weight DNAs and optimised computational tools can improve the detection of tumour-specific genetic information in urine.
Collapse
Affiliation(s)
- Giovanni Crisafulli
- University of Turin, Department of Oncology, Candiolo (TO), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | | | - Andrea Cassingena
- Niguarda Cancer Center, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Monica Montone
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | | | - Ludovic Barault
- University of Turin, Department of Oncology, Candiolo (TO), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | | | - Federica Morano
- Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | | | - Salvatore Siena
- Niguarda Cancer Center, ASST Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Federica Di Nicolantonio
- University of Turin, Department of Oncology, Candiolo (TO), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | - Silvia Marsoni
- IFOM - the FIRC Institute of Molecular Oncology, Milan, Italy
| | - Alberto Bardelli
- University of Turin, Department of Oncology, Candiolo (TO), Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| | - Giulia Siravegna
- University of Turin, Department of Oncology, Candiolo (TO), Italy .,Candiolo Cancer Institute, FPO - IRCCS, Candiolo TO, Italy
| |
Collapse
|
24
|
Ramanathan K, Padmanabhan G. MiRNAs as potential biomarker of kidney diseases: A review. Cell Biochem Funct 2020; 38:990-1005. [PMID: 32500596 DOI: 10.1002/cbf.3555] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/15/2020] [Accepted: 05/03/2020] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) are 22 nucleotides short, non-coding and tissue-specific single-stranded RNA which modulates target gene expression. Presently, shreds of evidence confirmed that miRNAs play a key role in kidney pathophysiology. The objectives of the present review are to summarize new research data towards the latest developments in the potential use of miRNAs as a diagnostic biomarker for kidney diseases. This holistic information will update the existing knowledge of kidney disease biomarkers. "miRNA profile for Diabetic Kidney disease, Acute kidney injury, Renal fibrosis, hemodialysis, transplants, FSGS, IgAN, etc." are the search keywords which have been used in this review. The search outcome gave an exciting insightful perception of miRNAs competence as a biomarker. Also it is observed that various samples as plasma, urine and biopsies were used for profiling the miRNA expression. The miRNAs were not only used for diagnostic biomarkers but also for therapeutic targets. Each kidney disease showed different miRNAs expression profile and few miRNAs quite common with some kidney diseases. miRNAs are simple and efficient diagnostic biomarkers for kidney diseases.
Collapse
Affiliation(s)
- Kumaresan Ramanathan
- Department of Medical Biochemistry, Division of Biomedical Sciences, School of Medicine, College of Health Sciences, Mekelle University (Ayder Campus), Mekelle, Ethiopia
| | | |
Collapse
|
25
|
Delmonico L, Alves G, Bines J. Cell free DNA biology and its involvement in breast carcinogenesis. Adv Clin Chem 2020; 97:171-223. [PMID: 32448434 DOI: 10.1016/bs.acc.2019.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Liquid biopsy represents a procedure for minimally invasive analysis of non-solid tissue, blood and other body fluids. It comprises a set of analytes that includes circulating tumor cells (CTCs) and circulating free DNA (cfDNA), RNA, long noncoding RNA (lncRNA) and micro RNA (miRNA), as well as extracellular vesicles. These novel analytes represent an alternative tool to complement diagnosis and monitor and predict response to treatment of the tumoral process and may be used for other disease processes such viral and parasitic infection. This review focuses on the biologic and molecular characteristics of cfDNA in general and the molecular changes (mutational and epigenetic) proven useful in oncologic practice for diagnosis, monitoring and treatment of breast cancer specifically.
Collapse
Affiliation(s)
- Lucas Delmonico
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Gilda Alves
- Laboratório de Marcadores Circulantes, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
| | - José Bines
- Instituto Nacional de Câncer (INCA-HCIII), Rio de Janeiro, Brazil
| |
Collapse
|
26
|
Perspectives of the Application of Liquid Biopsy in Colorectal Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6843180. [PMID: 32258135 PMCID: PMC7085834 DOI: 10.1155/2020/6843180] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is one of the most common gastrointestinal tumors and the second leading cause of cancer death worldwide. Since traditional biopsies are invasive and do not reflect tumor heterogeneity or monitor the dynamic progression of tumors, there is an urgent need for new noninvasive methods that can supplement and improve the current management strategies of CRC. Blood-based liquid biopsies are a promising noninvasive biomarker that can detect disease early, assist in staging, monitor treatment responses, and predict relapse and metastasis. Over time, an increasing number of experiments have indicated the clinical utility of liquid biopsies in CRC. In this review, we mainly focus on the development of circulating tumor cells and circulating tumor DNA as key components of liquid biopsies in CRC and introduce the potential of exosomal microRNAs as emerging liquid biopsy markers in clinical application for CRC.
Collapse
|
27
|
Oreskovic A, Brault ND, Panpradist N, Lai JJ, Lutz BR. Analytical Comparison of Methods for Extraction of Short Cell-Free DNA from Urine. J Mol Diagn 2019; 21:1067-1078. [PMID: 31442674 DOI: 10.1016/j.jmoldx.2019.07.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 07/02/2019] [Accepted: 07/23/2019] [Indexed: 11/19/2022] Open
Abstract
Urine cell-free DNA (cfDNA) is a valuable noninvasive biomarker for cancer mutation detection, infectious disease diagnosis (eg, tuberculosis), organ transplantation monitoring, and prenatal screening. Conventional silica DNA extraction does not efficiently capture urine cfDNA, which is dilute (ng/mL) and highly fragmented [30 to 100 nucleotides (nt)]. The clinical sensitivity of urine cfDNA detection increases with decreasing target length, motivating use of sample preparation methods designed for short fragments. We compared the analytical performance of two published protocols (Wizard resin/guanidinium thiocyanate and Q Sepharose), three commercial kits (Norgen, QIAamp, and MagMAX), and an in-house sequence-specific hybridization capture technique. Dependence on fragment length (25 to 150 nt), performance at low concentrations (10 copies/mL), tolerance to variable urine conditions, and susceptibility to PCR inhibition were characterized. Hybridization capture and Q Sepharose performed best overall (60% to 90% recovery), although Q Sepharose had reduced recovery (<10%) of the shortest 25-nt fragment. Wizard resin/guanidinium thiocyanate recovery was dependent on pH and background DNA concentration and was limited to <35%, even under optimal conditions. The Norgen kit led to consistent PCR inhibition but had high recovery of short fragments. The QIAamp and MagMAX kits had minimal recovery of fragments <150 and <80 nt, respectively. Urine cfDNA extraction methods differ widely in ability to capture short, dilute cfDNA in urine; using suboptimal methods may profoundly impair clinical results.
Collapse
Affiliation(s)
- Amy Oreskovic
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Norman D Brault
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Nuttada Panpradist
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - James J Lai
- Department of Bioengineering, University of Washington, Seattle, Washington
| | - Barry R Lutz
- Department of Bioengineering, University of Washington, Seattle, Washington.
| |
Collapse
|
28
|
Abstract
The study of cell-free DNA (cfDNA) is often challenging due to genomic DNA contamination, low concentration, and high fragmentation. Therefore, it is important to optimize pre-analytical and analytical procedures in order to maximize the performance of cfDNA-based analyses.In this chapter, we report the most common methods for the correct collection, centrifugation, storage, and DNA isolation from cell-free biological sources such as plasma, urines, cerebrospinal fluid, and pleural effusion fluid.
Collapse
Affiliation(s)
- Filippo Martignano
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
| |
Collapse
|
29
|
Sun IO, Lerman LO. Urinary microRNA in kidney disease: utility and roles. Am J Physiol Renal Physiol 2019; 316:F785-F793. [PMID: 30759023 PMCID: PMC6580242 DOI: 10.1152/ajprenal.00368.2018] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 01/29/2019] [Accepted: 02/11/2019] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs) are small, noncoding single-stranded RNA oligonucleotides that modulate physiological and pathological processes by modulating target gene expression. Many miRNAs display tissue-specific expression patterns, the dysregulation of which has been associated with various disease states, including kidney disease. Mounting evidence implicates miRNAs in various biological processes, such as cell proliferation and differentiation and cancer. Because miRNAs are relatively stable in tissue and biological fluids, particularly when carried by extracellular vesicles, changes in their levels may reflect the development of human disease. Urinary miRNAs originate from primary kidney and urinary tract cells, cells infiltrating the renal tissue and shed in the urine, or the systemic circulation. Although their validity as biomarkers for kidney disease has not been fully established, studies have been applying analysis of miRNAs in the urine in an attempt to detect and monitor acute and chronic renal diseases. Because appreciation of the significance of miRNAs in the renal field is on the rise, an understanding of miRNA pathways that regulate renal physiology and pathophysiology is becoming critically important. This review aims to summarize new data obtained in this field of research. It is hoped that new developments in the use of miRNAs as biomarkers and/or therapy will help manage and contain kidney disease in affected subjects.
Collapse
Affiliation(s)
- In O Sun
- Division of Nephrology and Hypertension, Mayo Clinic , Rochester, Minnesota
- Division of Nephrology, Department of Internal Medicine, Presbyterian Medical Center, Jeonju, Korea
| | - Lilach O Lerman
- Division of Nephrology and Hypertension, Mayo Clinic , Rochester, Minnesota
| |
Collapse
|
30
|
Xu Y, Kim YH, Jeong P, Piao XM, Byun YJ, Seo SP, Kang HW, Kim WT, Lee JY, Ryu DH, Choi JW, Kim IY, Moon SK, Choi YH, Yun SJ, Kim WJ. Urinary Cell-Free DNA IQGAP3/BMP4 Ratio as a Prognostic Marker for Non-Muscle-Invasive Bladder Cancer. Clin Genitourin Cancer 2019; 17:e704-e711. [PMID: 31088707 DOI: 10.1016/j.clgc.2019.04.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 01/05/2023]
Abstract
BACKGROUND Disease monitoring in non-muscle-invasive bladder cancer (NMIBC) patients is crucial for early identification of disease recurrence and progression. High IQGAP3/BMP4 and IQGAP3/FAM107A ratios in urinary cell-free DNA (ucfDNA) are a diagnostic biomarker for bladder cancer. We aimed to investigate whether the levels of these biomarkers in ucfDNA can be used to monitor disease recurrence or progression in patients with NMIBC. PATIENTS AND METHODS A total of 103 patients with NMIBC (pTa-pT1) were enrolled. The IQGAP3/BMP4 and IQGAP3/FAM107A ratios in ucfDNA were measured by real-time PCR, and the results were compared with clinical outcome by Kaplan-Meier curves and Cox regression analyses. RESULTS Overall, 55 patients (53.4%) experienced recurrence and 29 (28.2%) experienced disease progression during a median follow-up of 42.7 months (range, 6.1-172.2 months). Kaplan-Meier analysis revealed that NMIBC patients with a high IQGAP3/BMP4 ratio had worse recurrence-free survival and progression-free survival (PFS) (P = .001 and < .001, respectively), and those with a high IQGAP3/FAM107A ratio had worse PFS (P = .006). Multivariate Cox regression analysis revealed that the IQGAP3/BMP4 ratio was independently associated with recurrence-free survival (hazard ratio, 2.462; P = .003) and PFS (hazard ratio = 3.871; P = .004), whereas the IQGAP3/FAM107A ratio was not an independent factor for PFS (P = .079). CONCLUSION The IQGAP3/BMP4 ratio in ucfDNA might be a valuable novel biomarker for predicting disease recurrence and progression in patients with NMIBC.
Collapse
Affiliation(s)
- Yanjie Xu
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea; Department of Surgery, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Ye-Hwan Kim
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Pildu Jeong
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Xuan-Mei Piao
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Young Joon Byun
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Sung Pil Seo
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Ho Won Kang
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Won Tae Kim
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Jong-Young Lee
- Department of Business Data Convergence, Chungbuk National University, Cheongju, Korea; Theragen Etex Bio Institute, Suwon, Korea
| | - Dong Hee Ryu
- Department of Surgery, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Jae-Woon Choi
- Department of Surgery, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Isaac Y Kim
- Section of Urologic Oncology and Dean and Betty Gallo Prostate Cancer Center, The Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Sung-Kwon Moon
- Department of Food Science and Technology, Chung-Ang University, Ansung, Korea
| | - Yung Hyun Choi
- Department of Biochemistry, College of Oriental Medicine, Dong-Eui University, Busan, Korea
| | - Seok Joong Yun
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea
| | - Wun-Jae Kim
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, Korea.
| |
Collapse
|
31
|
Muluhngwi P, Valdes Jr R, Fernandez-Botran R, Burton E, Williams B, Linder MW. Cell-free DNA diagnostics: current and emerging applications in oncology. Pharmacogenomics 2019; 20:357-380. [DOI: 10.2217/pgs-2018-0174] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Liquid biopsy is a noninvasive dynamic approach for monitoring disease over time. It offers advantages including limited risks of blood sampling, opportunity for more frequent sampling, lower costs and theoretically non-biased sampling compared with tissue biopsy. There is a high degree of concordance between circulating tumor DNA mutations versus primary tumor mutations. Remote sampling of circulating tumor DNA can serve as viable option in clinical diagnostics. Here, we discuss the progress toward broad adoption of liquid biopsy as a diagnostic tool and discuss knowledge gaps that remain to be addressed.
Collapse
Affiliation(s)
- Penn Muluhngwi
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Roland Valdes Jr
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Rafael Fernandez-Botran
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Eric Burton
- Department of Neurology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Brian Williams
- Department of Neurosurgery, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Mark W Linder
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY 40202, USA
| |
Collapse
|
32
|
Osumi H, Shinozaki E, Yamaguchi K, Zembutsu H. Clinical utility of circulating tumor DNA for colorectal cancer. Cancer Sci 2019; 110:1148-1155. [PMID: 30742729 PMCID: PMC6447957 DOI: 10.1111/cas.13972] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 02/05/2019] [Accepted: 02/08/2019] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is currently the most common type of cancer in Japan, and its prognosis has improved because of development of diagnosis and advancement in treatments including surgery and chemotherapy. However, because of intratumor heterogeneity and clonal evolution, tumors often develop resistance to treatment. Genotyping tumor tissue in search of somatic genetic alterations for actionable information has become routine examination in clinical practice. However, the inherent molecular heterogeneity of metastatic tumors and the ability of cancer genomes to dynamically evolve are not properly captured by tissue specimens only. Circulating tumor DNA (ctDNA) carrying tumor‐specific genetic or epigenetic alterations is released into the circulation from tumor cells undergoing apoptosis or necrosis. Analysis of ctDNA has the potential to change clinical practice by exploiting blood rather than tissue, as a source of information. Here, we provide an overview of the characteristics of ctDNA and focus on detection methods for ctDNA, and the feasibility of use of ctDNA to monitor tumor dynamics for patients with colorectal cancer.
Collapse
Affiliation(s)
- Hiroki Osumi
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Eiji Shinozaki
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kensei Yamaguchi
- Department of Gastroenterology, Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hitoshi Zembutsu
- Cancer Precision Medicine Center, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| |
Collapse
|
33
|
Abstract
Urine could be a convenient source of biomarkers for different diseases and clinical applications, mostly for cancer diagnosis, prognosis, treatment monitoring, and prenatal diagnosis. The ultra-noninvasive sampling and the possibility to analyze large volume are the main undisputed advantages of urine-based protocols. Recent and comprehensive studies showed that urinary cell-free DNA (ucfDNA) is informative to identify the genomic signature of patients, resulting in a huge tool to track the tumor evolution and for personalized medicine in urological and non-urological cancer.In this chapter, we reported the main published evidences on ucfDNA, with the aim at discussing its promising and translatable role in clinical practices.
Collapse
Affiliation(s)
- Samanta Salvi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy.
| | - Valentina Casadio
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy
| |
Collapse
|
34
|
Urinary Exosomal and cell-free DNA Detects Somatic Mutation and Copy Number Alteration in Urothelial Carcinoma of Bladder. Sci Rep 2018; 8:14707. [PMID: 30279572 PMCID: PMC6168539 DOI: 10.1038/s41598-018-32900-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 09/17/2018] [Indexed: 12/22/2022] Open
Abstract
Urothelial bladder carcinoma (UBC) is characterized by a large number of genetic alterations. DNA from urine is a promising source for liquid biopsy in urological malignancies. We aimed to assess the availability of cell-free DNA (cfDNA) and exosomal DNA (exoDNA) in urine as a source for liquid biopsy in UBC. We included 9 patients who underwent surgery for UBC and performed genomic profiling of tumor samples and matched urinary cfDNA and exoDNA. For mutation analysis, deep sequencing was performed for 9 gene targets and shallow whole genome sequencing (sWGS) was used for the detection of copy number variation (CNV). We analyzed whether genetic alteration in tumor samples was reflected in urinary cfDNA or exoDNA. To measure the similarity between copy number profiles of tumor tissue and urinary DNA, the Pearson’s correlation coefficient was calculated. We found 17 somatic mutations in 6 patients. Of the 17 somatic mutations, 14 and 12 were identified by analysis of cfDNA and exoDNA with AFs of 56.2% and 65.6%, respectively. In CNV analysis using sWGS, although the mean depth was 0.6X, we found amplification of MDM2, ERBB2, CCND1 and CCNE1, and deletion of CDKN2A, PTEN and RB1, all known to be frequently altered in UBC. CNV plots of cfDNA and exoDNA showed a similar pattern with those from the tumor samples. Pearson’s correlation coefficients of tumor vs. cfDNA (0.481) and tumor vs. exoDNA (0.412) were higher than that of tumor vs. normal (0.086). We successfully identified somatic mutations and CNV in UBC using urinary cfDNA and exoDNA. Urinary exoDNA could be another source for liquid biopsy. Also, CNV analysis using sWGS is an alternative strategy for liquid biopsy, providing data from the whole genome at a low cost.
Collapse
|
35
|
Lu T, Han Y, Zhang R, Zhang K, Lin G, Li J. Quantitative detection of hepatitis C virus RNA in urine of patients with chronic hepatitis C using a novel real-time PCR assay. J Med Virol 2018; 91:115-123. [PMID: 30091789 DOI: 10.1002/jmv.25280] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/06/2018] [Indexed: 11/09/2022]
Abstract
Hepatitis C virus (HCV) RNA can be detected in body fluids such as urine. However, because of deficiencies in established isolation and detection methods, the actual prevalence and form of HCV RNA in the urine of patients with hepatitis C remain unclear. To more sensitively and accurately measure urine HCV RNA levels, a novel real-time PCR assay with a modified isolation method and short amplicon designed for short HCV RNA fragments was developed in this study. The limit of detection, precision, linearity, and specificity of the assay was evaluated and demonstrated high-quality performance. The prevalence of HCV RNA in the urine of viremic patients infected with HCV was 60% (36/60), as determined by a 62-bp assay. The HCV RNA detection rate and concentration were much lower with a 157-bp assay, and were undetectable with 222- and 304-bp assays. With the 62-bp assay, patients with detectable urine HCV RNA had significantly higher plasma HCV RNA levels ( P < 0.001), and plasma and urine concentrations were significantly positively correlated ( R 2 = 0.708, P < 0.001). The method not only increased the detection rate of urine HCV RNA but also revealed the presence of short HCV RNA fragments in urine, indicating that urine from CHC patients with normal kidney function should not be infectious. In addition, it raised the possibility of urinary HCV RNA as a potential noninvasive marker for therapeutic monitoring of patients with hepatitis C.
Collapse
Affiliation(s)
- Tian Lu
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| |
Collapse
|
36
|
Bijnsdorp IV, Jimenez CR. Large-Scale Urinary Proteome Dataset Across Tumor Types Reveals Candidate Biomarkers for Lung Cancer. EBioMedicine 2018; 30:5-6. [PMID: 29555362 PMCID: PMC5952333 DOI: 10.1016/j.ebiom.2018.03.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 01/25/2023] Open
Affiliation(s)
- Irene V Bijnsdorp
- Dept. of Urology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands.
| | - Connie R Jimenez
- OncoProteomics Laboratory, Dept. of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands.
| |
Collapse
|
37
|
Patel K, Nagel M, Wesolowski M, Dees S, Rivera-Milla E, Geldmacher C, Dheda K, Hoelscher M, Labugger I. Evaluation of a Urine-Based Rapid Molecular Diagnostic Test with Potential to Be Used at Point-of-Care for Pulmonary Tuberculosis: Cape Town Cohort. J Mol Diagn 2017; 20:215-224. [PMID: 29269279 DOI: 10.1016/j.jmoldx.2017.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 10/02/2017] [Accepted: 11/22/2017] [Indexed: 10/18/2022] Open
Abstract
Tuberculosis (TB) diagnosis among sputum-scarce patients is time consuming. Thus, a nonsputum diagnostic alternative is urgently needed. The Mycobacterium tuberculosis-specific transrenal (Tr) DNA from urine is a potential target for TB diagnostics. In this study, a new urine-based Tr-DNA molecular assay was evaluated for diagnosis of pulmonary tuberculosis among 428 adults suspected of having pulmonary TB (164 HIV positive, 263 HIV negative) from Cape Town, South Africa. Tr-DNA was isolated from 4 mL of EDTA urine, and a rapid, double-stranded, primer-based PCR method was performed targeting the Mycobacterium tuberculosis-specific direct repeat region. Each Tr-DNA eluate was tested in triplicate using an automated molecular analyzer with controls included in each test. With liquid culture used as the gold standard, the Tr-DNA assay showed sensitivity of 42.9% (n = 75/175; 95% CI, 35.4%-50.5%) and specificity of 88.6% (n = 210/237; 95% CI, 83.9%-92.4%). Among HIV-infected patients with TB, sensitivity and specificity were 45.2% and 89.0%, respectively. The combination of smear microscopy and Tr-DNA increased the sensitivity to 83.8% (smear microscopy alone, 75.1%), with 96.6% specificity. This study indicates that Tr-DNA has a moderate specificity with low sensitivity for diagnosis of pulmonary TB. Despite low sensitivity, this diagnostic test may have potential in combination with smear microscopy to support TB diagnosis in HIV-endemic regions, where sputum-scarce patients are common.
Collapse
Affiliation(s)
- Krutarth Patel
- Alere Technologies GmbH, Jena, Germany; Center for International Health, University of Munich, Munich, Germany.
| | | | | | | | | | - Christof Geldmacher
- Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany; German Center for Infection Research, Munich, Germany
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Division of Pulmonology & Clinical Immunology, Department of Medicine and UCT Lung Institute, University of Cape Town, Cape Town, South Africa
| | - Michael Hoelscher
- Center for International Health, University of Munich, Munich, Germany; Division of Infectious Diseases and Tropical Medicine, Medical Center of the University of Munich, Munich, Germany; German Center for Infection Research, Munich, Germany
| | | |
Collapse
|
38
|
Franovic A, Raymond VM, Erlander MG, Reckamp KL. Urine test for EGFR analysis in patients with non-small cell lung cancer. J Thorac Dis 2017; 9:S1323-S1331. [PMID: 29184671 DOI: 10.21037/jtd.2017.06.144] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Precision medicine approaches in oncology are reliant on the accurate genomic characterization of tumors. While tissue remains the mainstay specimen for molecular testing, tumor biopsies are riddled with challenges and limitations due to their invasive and site-specific nature. Tumor inaccessibility and intratumoral heterogeneity, in particular, represent significant obstacles to the identification of actionable genetic alterations and hence effective mono- and combination therapy strategies. Proof-of-concept studies indicate that circulating tumor DNA (ctDNA) released from multiple tumor regions and anatomical locations is more reflective of intra- and intertumoral heterogeneity. Non-invasive liquid biopsy approaches that allow for the analysis of ctDNA are thus being increasingly implemented in routine patient care for the detection and monitoring of cancer-associated mutations. Indeed, the use of plasma testing to screen for epidermal growth factor receptor (EGFR) T790M mutant positive non-small cell lung cancer (NSCLC) patients eligible for treatment with third-generation EGFR inhibitors was recently approved by the U.S. Food and Drug Administration and is incorporated into the most recent version of the National Comprehensive Cancer Center guidelines as an alternative to tissue biopsy. Urine represents another liquid biopsy specimen that is distinguished by its ease of collection, option for home collection, and lack of temporal and volumetric collection restrictions. Importantly, there is an accumulating body of evidence supporting the clinical validity of urinary EGFR mutant testing for the identification and stratification of patients likely to benefit from EGFR-directed therapies and as a means to assess patient response, the presence of residual disease, and emergence of resistant tumor cell populations.
Collapse
|
39
|
Husain H, Melnikova VO, Kosco K, Woodward B, More S, Pingle SC, Weihe E, Park BH, Tewari M, Erlander MG, Cohen E, Lippman SM, Kurzrock R. Monitoring Daily Dynamics of Early Tumor Response to Targeted Therapy by Detecting Circulating Tumor DNA in Urine. Clin Cancer Res 2017; 23:4716-4723. [PMID: 28420725 PMCID: PMC5737735 DOI: 10.1158/1078-0432.ccr-17-0454] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/08/2017] [Accepted: 04/13/2017] [Indexed: 12/25/2022]
Abstract
Purpose: Noninvasive drug biomarkers for the early assessment of tumor response can enable adaptive therapeutic decision-making and proof-of-concept studies for investigational drugs. Circulating tumor DNA (ctDNA) is released into the circulation by tumor cell turnover and has been shown to be detectable in urine.Experimental Design: We tested the hypothesis that dynamic changes in EGFR activating (exon 19del and L858R) and resistance (T790M) mutation levels detected in urine could inform tumor response within days of therapy for advanced non-small cell lung cancer (NSCLC) patients receiving osimertinib, a second-line third-generation anti-EGFR tyrosine kinase inhibitor.Results: Eight of nine evaluable NSCLC patients had detectable T790M-mutant DNA fragments in pretreatment baseline samples. Daily monitoring of mutations in urine indicated a pattern of intermittent spikes throughout week 1, suggesting apoptosis with an overall decrease in fragment numbers from baselines to day 7 preceding radiographic response assessed at 6 to 12 weeks.Conclusions: These findings suggest drug-induced tumor apoptosis within days of initial dosing. Daily sampling of ctDNA may enable early assessment of patient response and proof-of-concept studies for drug development. The modeling of tumor lysis through the day-to-day kinetics of ctDNA released into the blood and then into the urine is demonstrated in this proof-of-concept study in lung cancer patients receiving anti-EGFR tyrosine kinase inhibitors. This strategy may determine the specific clonal populations of cells which undergo apoptosis within the first week of therapy. This has important implications for developing combinational strategies to address inter- and intralesional heterogeneity and characterizing residual disease after initial drug exposure. Clin Cancer Res; 23(16); 4716-23. ©2017 AACR.
Collapse
Affiliation(s)
- Hatim Husain
- University of California San Diego, Moores Cancer Center, La Jolla, California.
| | | | | | - Brian Woodward
- University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Soham More
- University of California San Diego, Moores Cancer Center, La Jolla, California
| | | | - Elizabeth Weihe
- University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Ben Ho Park
- Johns Hopkins Sidney Kimmel Cancer, Baltimore, Maryland
| | | | | | - Ezra Cohen
- University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Scott M Lippman
- University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- University of California San Diego, Moores Cancer Center, La Jolla, California
| |
Collapse
|
40
|
Siravegna G, Sartore-Bianchi A, Mussolin B, Cassingena A, Amatu A, Novara L, Buscarino M, Corti G, Crisafulli G, Bartolini A, Tosi F, Erlander M, Di Nicolantonio F, Siena S, Bardelli A. Tracking aCAD-ALK gene rearrangement in urine and blood of a colorectal cancer patient treated with an ALK inhibitor. Ann Oncol 2017; 28:1302-1308. [DOI: 10.1093/annonc/mdx095] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
|
41
|
Kao HW, Pan CY, Lai CH, Wu CW, Fang WL, Huang KH, Lin WC. Urine miR-21-5p as a potential non-invasive biomarker for gastric cancer. Oncotarget 2017; 8:56389-56397. [PMID: 28915598 PMCID: PMC5593569 DOI: 10.18632/oncotarget.16916] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/14/2017] [Indexed: 12/12/2022] Open
Abstract
Many reports have implicated that microRNAs involve in cancer development and progression, such as miR-155 in breast cancers and miR-196 in gastric cancers. Furthermore, microRNAs are more stable than typical protein-coding gene mRNAs in varieties of clinical samples including body fluids. This suggests that they are potentially valuable biomarkers for cancer monitoring. In this study, we have used urine samples of gastric cancer patients to demonstrate the feasibility of urine microRNAs for gastric cancer detection. Urine samples of gastric cancer patients were extracted for total RNA, which were examined for the expression of miR-21-5p using quantitative stem-loop PCR. Our results demonstrated that miR-21-5p could be detected in small amounts of urine samples with good stability, and the expression levels of miR-21-5p were reduced following surgical removal of gastric cancer tissues. These results implicate that urine miR-21-5p could be utilized as a novel non-invasive biomarker of gastric cancer detection and monitoring.
Collapse
Affiliation(s)
- Hsiao-Wei Kao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chao-Yu Pan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Chun-Hung Lai
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chew-Wun Wu
- Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan
| | - Wen-Liang Fang
- Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan
| | - Kuo-Hung Huang
- Department of Surgery, Veterans General Hospital and National Yang-Ming University, Taipei, Taiwan
| | - Wen-Chang Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| |
Collapse
|
42
|
Abstract
During cancer progression and treatment, multiple subclonal populations of tumour cells compete with one another, with selective pressures leading to the emergence of predominant subclones that replicate and spread most proficiently, and are least susceptible to treatment. At present, the molecular landscapes of solid tumours are established using surgical or biopsy tissue samples. Tissue-based tumour profiles are, however, subject to sampling bias, provide only a snapshot of tumour heterogeneity, and cannot be obtained repeatedly. Genomic profiles of circulating cell-free tumour DNA (ctDNA) have been shown to closely match those of the corresponding tumours, with important implications for both molecular pathology and clinical oncology. Analyses of circulating nucleic acids, commonly referred to as 'liquid biopsies', can be used to monitor response to treatment, assess the emergence of drug resistance, and quantify minimal residual disease. In addition to blood, several other body fluids, such as urine, saliva, pleural effusions, and cerebrospinal fluid, can contain tumour-derived genetic information. The molecular profiles gathered from ctDNA can be further complemented with those obtained through analysis of circulating tumour cells (CTCs), as well as RNA, proteins, and lipids contained within vesicles, such as exosomes. In this Review, we examine how different forms of liquid biopsies can be exploited to guide patient care and should ultimately be integrated into clinical practice, focusing on liquid biopsy of ctDNA - arguably the most clinically advanced approach.
Collapse
|
43
|
Bardelli A, Pantel K. Liquid Biopsies, What We Do Not Know (Yet). Cancer Cell 2017; 31:172-179. [PMID: 28196593 DOI: 10.1016/j.ccell.2017.01.002] [Citation(s) in RCA: 345] [Impact Index Per Article: 49.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 10/28/2016] [Accepted: 01/05/2017] [Indexed: 12/21/2022]
Abstract
The inherent molecular heterogeneity of metastatic tumors and the ability of cancer genomes to dynamically evolve are not properly captured by tissue specimens. Analysis of cell-free DNA and circulating tumor cells has the potential to change clinical practice by exploiting blood rather than tissue as a source of information. Liquid biopsies are already used to monitor disease response and track the emergence of drug resistance. The suitability of blood-based molecular profiles for early detection and monitoring minimal residual disease is being evaluated. In this review, we address open questions in this fast-evolving field of research.
Collapse
Affiliation(s)
- Alberto Bardelli
- University of Torino, Department of Oncology, SP 142, Km 3.95, 10060 Candiolo, Torino, Italy; Candiolo Cancer Institute - FPO, IRCCS, Candiolo, Torino, Italy.
| | - Klaus Pantel
- Department of Tumor Biology, Center of Experimental Medicine, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Martinistraβe 52, 20246 Hamburg, Germany.
| |
Collapse
|
44
|
T Oligo-Primed Polymerase Chain Reaction (TOP-PCR): A Robust Method for the Amplification of Minute DNA Fragments in Body Fluids. Sci Rep 2017; 7:40767. [PMID: 28094343 PMCID: PMC5240146 DOI: 10.1038/srep40767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/12/2016] [Indexed: 01/09/2023] Open
Abstract
Body fluid DNA sequencing is a powerful noninvasive approach for the diagnosis of genetic defects, infectious agents and diseases. The success relies on the quantity and quality of the DNA samples. However, numerous clinical samples are either at low quantity or of poor quality due to various reasons. To overcome these problems, we have developed T oligo-primed polymerase chain reaction (TOP-PCR) for full-length nonselective amplification of minute quantity of DNA fragments. TOP-PCR adopts homogeneous “half adaptor” (HA), generated by annealing P oligo (carrying a phosphate group at the 5′ end) and T oligo (carrying a T-tail at the 3′ end), for efficient ligation to target DNA and subsequent PCR amplification primed by the T oligo alone. Using DNA samples from body fluids, we demonstrate that TOP-PCR recovers minute DNA fragments and maintains the DNA size profile, while enhancing the major molecular populations. Our results also showed that TOP-PCR is a superior method for detecting apoptosis and outperforms the method adopted by Illumina for DNA amplification.
Collapse
|
45
|
Jaswani P, Prakash S, Dhar A, Sharma RK, Prasad N, Agrawal S. MicroRNAs Involvement in Renal Pathophysiology: A Bird's Eye View. Indian J Nephrol 2017; 27:337-341. [PMID: 28904427 PMCID: PMC5590408 DOI: 10.4103/ijn.ijn_264_16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
MicroRNAs (miRNAs) are known to suppress gene expression by binding to messenger RNAs and in turn regulate different pathophysiological processes. Transforming growth factor-β, mitogen-activated protein kinase signaling, and Wnt signaling-like major pathways associated with miRNAs are involved with kidney diseases. The discovery of miRNAs has provided new insights into kidney pathologies and may provide effective therapeutic strategies. Research has demonstrated the role of miRNAs in a variety of kidney diseases including diabetic nephropathy, lupus nephritis, hypertension, nephritic syndrome, acute kidney injury, renal cell carcinoma, and renal fibrosis. miRNAs are implicated as playing a role in these diseases due to their role in apoptosis, cell proliferation, differentiation, and development. As miRNAs have been detected in a stable condition in different biological fluids, they have the potential to be tools to study the pathogenesis of human diseases with a great potential to be used in disease diagnosis and prognosis. The purpose of this review is to examine the role of miRNA in kidney disease.
Collapse
Affiliation(s)
- P Jaswani
- Department of Nephrology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - S Prakash
- Department of Nephrology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - A Dhar
- Department of Immunology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - R K Sharma
- Department of Nephrology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - N Prasad
- Department of Nephrology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - S Agrawal
- Department of Hematology, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| |
Collapse
|
46
|
Salvi S, Martignano F, Molinari C, Gurioli G, Calistri D, De Giorgi U, Conteduca V, Casadio V. The potential use of urine cell free DNA as a marker for cancer. Expert Rev Mol Diagn 2016; 16:1283-1290. [PMID: 27796148 DOI: 10.1080/14737159.2016.1254551] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Although the role of circulating cell free DNA in cancer has been widely demonstrated, less is known about the role of urine cell free DNA (UcfDNA). UcfDNA can serve as a 'liquid biopsy' for urological and non-urological tumors, as it carries information on DNA from cells exfoliated in urine and from circulation. Areas covered: We review the studies on UcfDNA as a source of biomarkers for cancer, focusing on the new techniques and the differences between urological and non-urological tumors. We searched Pubmed for articles published between 1998 and 2016 with the following key words and phrases: 'urine' and 'cell free DNA' or 'liquid biopsy' or 'cancer'. Expert commentary: Despite the few papers published on this topic, UcfDNA is an important component of 'liquid biopsy', a useful and non-invasive tool for cancer diagnosis, prognosis and treatment monitoring, containing a wide range of genetic information.
Collapse
Affiliation(s)
- Samanta Salvi
- a Biosciences Laboratory , Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS , Meldola , Italy
| | - Filippo Martignano
- a Biosciences Laboratory , Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS , Meldola , Italy
| | - Chiara Molinari
- a Biosciences Laboratory , Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS , Meldola , Italy
| | - Giorgia Gurioli
- a Biosciences Laboratory , Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS , Meldola , Italy
| | - Daniele Calistri
- a Biosciences Laboratory , Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS , Meldola , Italy
| | - Ugo De Giorgi
- b Department of Medical Oncology , Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS , Meldola , Italy
| | - Vincenza Conteduca
- b Department of Medical Oncology , Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS , Meldola , Italy
| | - Valentina Casadio
- a Biosciences Laboratory , Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS , Meldola , Italy
| |
Collapse
|
47
|
Leierer J, Mayer G, Kronbichler A. Primary focal segmental glomerulosclerosis: miRNAs and targeted therapies. Eur J Clin Invest 2016; 46:954-964. [PMID: 27651302 DOI: 10.1111/eci.12676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 09/07/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Primary focal segmental glomerulosclerosis (FSGS) is a common cause of nephrotic syndrome. AIMS The pathogenic steps leading to primary FSGS are still obscure, although evidence suggests that circulatory factor(s) are involved in the onset of disease. RESULTS Recent technical advances allow the analysis of miRNA expression in tissues and body fluids, leading to reports of miRNAs involved in the molecular mechanisms of FSGS-aetiopathogenesis. Moreover, investigations have also highlighted miRNAs that might serve as biomarkers for primary FSGS. DISCUSSION/CONCLUSIONS The aim of this review was to summarize reports showing a direct relation between miRNAs and primary FSGS. In addition, the impact of identified miRNAs on treatment response, prediction of the disease onset as well as the regulation in different disease activities is summarized.
Collapse
Affiliation(s)
- Johannes Leierer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria.
| | - Gert Mayer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Andreas Kronbichler
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| |
Collapse
|
48
|
Guerrero-Preston R, Valle BL, Jedlicka A, Turaga N, Folawiyo O, Pirini F, Lawson F, Vergura A, Noordhuis M, Dziedzic A, Pérez G, Renehan M, Guerrero-Diaz C, De Jesus Rodríguez E, Diaz-Montes T, Rodríguez Orengo J, Méndez K, Romaguera J, Trock BJ, Florea L, Sidransky D. Molecular Triage of Premalignant Lesions in Liquid-Based Cervical Cytology and Circulating Cell-Free DNA from Urine, Using a Panel of Methylated Human Papilloma Virus and Host Genes. Cancer Prev Res (Phila) 2016; 9:915-924. [DOI: 10.1158/1940-6207.capr-16-0138] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/23/2016] [Accepted: 09/07/2016] [Indexed: 11/16/2022]
|
49
|
Reckamp KL, Melnikova VO, Karlovich C, Sequist LV, Camidge DR, Wakelee H, Perol M, Oxnard GR, Kosco K, Croucher P, Samuelsz E, Vibat CR, Guerrero S, Geis J, Berz D, Mann E, Matheny S, Rolfe L, Raponi M, Erlander MG, Gadgeel S. A Highly Sensitive and Quantitative Test Platform for Detection of NSCLC EGFR Mutations in Urine and Plasma. J Thorac Oncol 2016; 11:1690-700. [PMID: 27468937 DOI: 10.1016/j.jtho.2016.05.035] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/24/2016] [Indexed: 01/19/2023]
Abstract
INTRODUCTION In approximately 60% of patients with NSCLC who are receiving EGFR tyrosine kinase inhibitors, resistance develops through the acquisition of EGFR T790M mutation. We aimed to demonstrate that a highly sensitive and quantitative next-generation sequencing analysis of EGFR mutations from urine and plasma specimens is feasible. METHODS Short footprint mutation enrichment next-generation sequencing assays were used to interrogate EGFR activating mutations and the T790M resistance mutation in urine or plasma specimens from patients enrolled in TIGER-X (NCT01526928), a phase 1/2 clinical study of rociletinib in previously treated patients with EGFR mutant-positive advanced NSCLC. RESULTS Of 63 patients, 60 had evaluable tissue specimens. When the tissue result was used as a reference, the sensitivity of EGFR mutation detection in urine was 72% (34 of 47 specimens) for T790M, 75% (12 of 16) for L858R, and 67% (28 of 42) for exon 19 deletions. With specimens that met a recommended volume of 90 to 100 mL, the sensitivity was 93% (13 of 14 specimens) for T790M, 80% (four of five) for L858R, and 83% (10 of 12) for exon 19 deletions. A comparable sensitivity of EGFR mutation detection was observed in plasma: 93% (38 of 41 specimens) for T790M, 100% (17 of 17) for L858R, and 87% (34 of 39) for exon 19 deletions. Together, urine and plasma testing identified 12 additional T790M-positive cases that were either undetectable or inadequate by tissue test. In nine patients monitored while receiving treatment with rociletinib, a rapid decrease in urine T790M levels was observed by day 21. CONCLUSIONS DNA derived from NSCLC tumors can be detected with high sensitivity in urine and plasma, enabling diagnostic detection and monitoring of therapeutic response from these noninvasive "liquid biopsy" samples.
Collapse
Affiliation(s)
- Karen L Reckamp
- City of Hope Comprehensive Cancer Center, Duarte, California.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - David Berz
- Beverly Hills Cancer Center, Beverly Hills, CA; City of Hope, Duarte, California
| | | | | | | | | | | | | |
Collapse
|
50
|
Kausar A, Osman EA, Gadzikwa T, Gibbs-Davis JM. The presence of a 5'-abasic lesion enhances discrimination of single nucleotide polymorphisms while inducing an isothermal ligase chain reaction. Analyst 2016; 141:4272-7. [PMID: 27326790 DOI: 10.1039/c6an00614k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Lesion-induced DNA amplification (LIDA) has been employed in the detection of single nucleotide polymorphisms (SNPs). Due to the presence of the proximal abasic lesion, T4 DNA ligase exhibits greater intolerance to basepair mismatches when compared with mismatch ligation in the absence of the abasic lesion. Moreover the presence of the abasic group also results in an isothermal ligase chain reaction enabling SNP detection with great discrimination and sensitivity. Specifically, at forty minutes, the ratio of amplified product from the matched and mismatched initiated reactions are 7-12 depending on the mismatch. The ease of implementation of our method is demonstrated by real-time analysis of DNA amplification using a fluorescent plate reader.
Collapse
Affiliation(s)
- Abu Kausar
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada.
| | | | | | | |
Collapse
|