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Alsaab HO, Alzahrani MS, Bahauddin AA, Almutairy B. Circulating tumor DNA (ctDNA) application in investigation of cancer: Bench to bedside. Arch Biochem Biophys 2024; 758:110066. [PMID: 38906310 DOI: 10.1016/j.abb.2024.110066] [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: 04/10/2024] [Revised: 06/02/2024] [Accepted: 06/18/2024] [Indexed: 06/23/2024]
Abstract
Now, genomics forms the core of the precision medicine concept. Comprehensive investigations of tumor genomes have made it possible to characterize tumors at the molecular level and, specifically, to identify the fundamental processes that cause condition. A variety of kinds of tumors have seen better outcomes for patients as a result of the development of novel medicines to tackle these genetic-driving processes. Since therapy may exert selective pressure on cancers, non-invasive methods such as liquid biopsies can provide the opportunity for rich reservoirs of crucial and real-time genetic data. Liquid biopsies depend on the identification of circulating cells from tumors, circulating tumor DNA (ctDNA), RNA, proteins, lipids, and metabolites found in patient biofluids, as well as cell-free DNA (cfDNA), which exists in those with cancer. Although it is theoretically possible to examine biological fluids other than plasma, such as pleural fluid, urine, saliva, stool, cerebrospinal fluid, and ascites, we will limit our discussion to blood and solely cfDNA here for the sake of conciseness. Yet, the pace of wider clinical acceptance has been gradual, partly due to the increased difficulty of choosing the best analysis for the given clinical issue, interpreting the findings, and delaying proof of value from clinical trials. Our goal in this review is to discuss the current clinical value of ctDNA in cancers and how clinical oncology systems might incorporate procedures for ctDNA testing.
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Affiliation(s)
- Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, Taif University, Taif, 21944, Saudi Arabia.
| | - Mohammad S Alzahrani
- Department of Clinical Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia.
| | - Ammar A Bahauddin
- Department of Pharmacology and Toxicology, College of Pharmacy, Taibah University, Medina Al-Munawarah, Saudi Arabia.
| | - Bandar Almutairy
- Department of Pharmacology, College of Pharmacy, Shaqra University, Shaqra 11961, Saudi Arabia.
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2
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Ya N, Zhang D, Wang Y, Zheng Y, Yang M, Wu H, Oudeng G. Recent advances of biocompatible optical nanobiosensors in liquid biopsy: towards early non-invasive diagnosis. NANOSCALE 2024; 16:13784-13801. [PMID: 38979555 DOI: 10.1039/d4nr01719f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Liquid biopsy is a non-invasive diagnostic method that can reduce the risk of complications and offers exceptional benefits in the dynamic monitoring and acquisition of heterogeneous cell population information. Optical nanomaterials with excellent light absorption, luminescence, and photoelectrochemical properties have accelerated the development of liquid biopsy technologies. Owing to the unique size effect of optical nanomaterials, their improved optical properties enable them to exhibit good sensitivity and specificity for mitigating signal interference from various molecules in body fluids. Nanomaterials with biocompatible and optical sensing properties play a crucial role in advancing the maturity and diversification of liquid biopsy technologies. This article offers a comprehensive review of recent advanced liquid biopsy technologies that utilize novel biocompatible optical nanomaterials, including fluorescence, colorimetric, photoelectrochemical, and Raman broad-spectrum-based biosensors. We focused on liquid biopsy for the most significant early biomarkers in clinical medicine, and specifically reviewed reports on the effectiveness of optical nanosensing technology in the detection of real patient samples, which may provide basic evidence for the transition of optical nanosensing technology from engineering design to clinical practice. Furthermore, we introduced the integration of optical nanosensing-based liquid biopsy with modern devices, such as smartphones, to demonstrate the potential of the technology in portable clinical diagnosis.
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Affiliation(s)
- Na Ya
- Pediatric Research Institute, Shenzhen Children's Hospital, Shenzhen, Guangdong, P.R. China
- Department of Biomedical Engineering, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, P.R. China
| | - Dangui Zhang
- Pediatric Research Institute, Shenzhen Children's Hospital, Shenzhen, Guangdong, P.R. China
- Research Center of Translational Medicine, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, P.R. China
| | - Yan Wang
- Department of Biomedical Engineering, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, P.R. China
| | - Yi Zheng
- Department of Biomedical Engineering, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, P.R. China
| | - Mo Yang
- Department of Biomedical Engineering, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, P.R. China
| | - Hao Wu
- Department of Orthopedics, The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong, P.R. China
| | - Gerile Oudeng
- Pediatric Research Institute, Shenzhen Children's Hospital, Shenzhen, Guangdong, P.R. China
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3
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Seyhan AA. Circulating Liquid Biopsy Biomarkers in Glioblastoma: Advances and Challenges. Int J Mol Sci 2024; 25:7974. [PMID: 39063215 DOI: 10.3390/ijms25147974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Gliomas, particularly glioblastoma (GBM), represent the most prevalent and aggressive tumors of the central nervous system (CNS). Despite recent treatment advancements, patient survival rates remain low. The diagnosis of GBM traditionally relies on neuroimaging methods such as magnetic resonance imaging (MRI) or computed tomography (CT) scans and postoperative confirmation via histopathological and molecular analysis. Imaging techniques struggle to differentiate between tumor progression and treatment-related changes, leading to potential misinterpretation and treatment delays. Similarly, tissue biopsies, while informative, are invasive and not suitable for monitoring ongoing treatments. These challenges have led to the emergence of liquid biopsy, particularly through blood samples, as a promising alternative for GBM diagnosis and monitoring. Presently, blood and cerebrospinal fluid (CSF) sampling offers a minimally invasive means of obtaining tumor-related information to guide therapy. The idea that blood or any biofluid tests can be used to screen many cancer types has huge potential. Tumors release various components into the bloodstream or other biofluids, including cell-free nucleic acids such as microRNAs (miRNAs), circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), proteins, extracellular vesicles (EVs) or exosomes, metabolites, and other factors. These factors have been shown to cross the blood-brain barrier (BBB), presenting an opportunity for the minimally invasive monitoring of GBM as well as for the real-time assessment of distinct genetic, epigenetic, transcriptomic, proteomic, and metabolomic changes associated with brain tumors. Despite their potential, the clinical utility of liquid biopsy-based circulating biomarkers is somewhat constrained by limitations such as the absence of standardized methodologies for blood or CSF collection, analyte extraction, analysis methods, and small cohort sizes. Additionally, tissue biopsies offer more precise insights into tumor morphology and the microenvironment. Therefore, the objective of a liquid biopsy should be to complement and enhance the diagnostic accuracy and monitoring of GBM patients by providing additional information alongside traditional tissue biopsies. Moreover, utilizing a combination of diverse biomarker types may enhance clinical effectiveness compared to solely relying on one biomarker category, potentially improving diagnostic sensitivity and specificity and addressing some of the existing limitations associated with liquid biomarkers for GBM. This review presents an overview of the latest research on circulating biomarkers found in GBM blood or CSF samples, discusses their potential as diagnostic, predictive, and prognostic indicators, and discusses associated challenges and future perspectives.
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Affiliation(s)
- Attila A Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
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Erice E, Mitxelena-Iribarren O, Arana S, Lawrie CH, Mujika M. Efficient enrichment of free target sequences in an integrated microfluidic device for point-of-care detection systems. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 61:102771. [PMID: 38960366 DOI: 10.1016/j.nano.2024.102771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/07/2024] [Accepted: 06/23/2024] [Indexed: 07/05/2024]
Abstract
Nucleic acid biomarker detection has great importance in the diagnosis of disease, the monitoring of disease progression and the classification of patients according to treatment decision making. Nucleic acid biomarkers found in the blood of patients have generated a lot of interest due to the possibility of being detected non-invasively which makes them ideal for monitoring and screening tests and particularly amenable to point-of-care (POC) or self-testing. A major challenge to POC molecular diagnostics is the need to enrich the target to optimise detection. In this work, we describe a microfabricated device for the enrichment of short dsDNA target sequences, which is especially valuable for potential detection methods, as it improves the probability of effectively detecting the target in downstream analyses. The device integrated a heating element and a temperature sensor with a microfluidic chamber to carry out the denaturation of the dsDNA combined with blocking-probes to enrich the target. This procedure was validated by fluorescence resonance energy transfer (FRET) technique, labelling DNA with a fluorophore and a quencher. As proof of concept, a 23-mer long dsDNA sequence corresponding to the L858R mutation of the EGFR gene was used. The qualitative results obtained determined that the most optimal blocking rate was obtained with the incorporation of 11/12-mer blocking-probes at a total concentration of 6 μM. This device is a powerful DNA preparation tool, which is an indispensable initial step for subsequent detection of sequences via nucleic acid hybridisation methods.
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Affiliation(s)
- Elisa Erice
- CEIT-Basque Research and Technology Alliance (BRTA), Manuel Lardizabal 15, 20018 Donostia, San Sebastián, Spain; Universidad de Navarra, Tecnun, Manuel Lardizabal 13, 20018 Donostia, San Sebastián, Spain.
| | - Oihane Mitxelena-Iribarren
- CEIT-Basque Research and Technology Alliance (BRTA), Manuel Lardizabal 15, 20018 Donostia, San Sebastián, Spain; Universidad de Navarra, Tecnun, Manuel Lardizabal 13, 20018 Donostia, San Sebastián, Spain; Group of Bioengineering in Regeneration and Cancer, Biogipuzkoa Health Research Institute, San Sebastian, Spain
| | - Sergio Arana
- CEIT-Basque Research and Technology Alliance (BRTA), Manuel Lardizabal 15, 20018 Donostia, San Sebastián, Spain; Universidad de Navarra, Tecnun, Manuel Lardizabal 13, 20018 Donostia, San Sebastián, Spain
| | - Charles H Lawrie
- Molecular Oncology Group, Biogipuzkoa Health Research Institute, San Sebastian, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; Sino-Swiss Institute of Advanced Technology (SSIAT), University of Shanghai, Shanghai, China; Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Maite Mujika
- CEIT-Basque Research and Technology Alliance (BRTA), Manuel Lardizabal 15, 20018 Donostia, San Sebastián, Spain; Universidad de Navarra, Tecnun, Manuel Lardizabal 13, 20018 Donostia, San Sebastián, Spain
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Turabi K, Klute K, Radhakrishnan P. Decoding the Dynamics of Circulating Tumor DNA in Liquid Biopsies. Cancers (Basel) 2024; 16:2432. [PMID: 39001494 PMCID: PMC11240538 DOI: 10.3390/cancers16132432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
Circulating tumor DNA (ctDNA), a fragment of tumor DNA found in the bloodstream, has emerged as a revolutionary tool in cancer management. This review delves into the biology of ctDNA, examining release mechanisms, including necrosis, apoptosis, and active secretion, all of which offer information about the state and nature of the tumor. Comprehensive DNA profiling has been enabled by methods such as whole genome sequencing and methylation analysis. The low abundance of the ctDNA fraction makes alternative techniques, such as digital PCR and targeted next-generation exome sequencing, more valuable and accurate for mutation profiling and detection. There are numerous clinical applications for ctDNA analysis, including non-invasive liquid biopsies for minimal residual disease monitoring to detect cancer recurrence, personalized medicine by mutation profiling for targeted therapy identification, early cancer detection, and real-time evaluation of therapeutic response. Integrating ctDNA analysis into routine clinical practice creates promising avenues for successful and personalized cancer care, from diagnosis to treatment and follow-up.
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Affiliation(s)
- Khadija Turabi
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kelsey Klute
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Division of Oncology and Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Prakash Radhakrishnan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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6
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Mishra M, Ahmed R, Das DK, Pramanik DD, Dash SK, Pramanik A. Recent Advancements in the Application of Circulating Tumor DNA as Biomarkers for Early Detection of Cancers. ACS Biomater Sci Eng 2024. [PMID: 38950521 DOI: 10.1021/acsbiomaterials.4c00606] [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: 07/03/2024]
Abstract
Early detection of cancer is vital for increasing patient survivability chances. The three major techniques used to diagnose cancers are instrumental examination, tissue biopsy, and tumor biomarker detection. Circulating tumor DNA (ctDNA) has gained much attention in recent years due to advantages over traditional technology, such as high sensitivity, high specificity, and noninvasive nature. Through the mechanism of apoptosis, necrosis, and circulating exosome release in tumor cells, ctDNA can spread throughout the circulatory system and carry modifications such as methylations, mutations, gene rearrangements, and microsatellite instability. Traditional gene-detection technology struggles to achieve real-time, low-cost, and portable ctDNA measurement, whereas electrochemical biosensors offer low cost, high specificity alongside sensitivity, and portability for the detection of ctDNA. Therefore, this review focuses on describing the recent advancements in ctDNA biomarkers for various cancer types and biosensor developments for real-time, noninvasive, and rapid ctDNA detection. Further in the review, ctDNA sensors are also discussed in regards to their selections of probes for receptors based on the electrode surface recognition elements.
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Affiliation(s)
- Mahima Mishra
- Amity Institute of Biotechnology, Amity University, Noida 201301, India
| | - Rubai Ahmed
- Department of Physiology, University of Gour Banga, Malda-732103, West Bengal, India
| | - Deepak Kumar Das
- Department of Chemistry and Nanoscience, GLA University, Mathura, 281406 Uttar Pradesh, India
| | | | - Sandeep Kumar Dash
- Department of Physiology, University of Gour Banga, Malda-732103, West Bengal, India
| | - Arindam Pramanik
- Amity Institute of Biotechnology, Amity University, Noida 201301, India
- School of Medicine, University of Leeds, Leeds LS53RL, United Kingdom
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7
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Lee JC, Ray RM, Scott TA. Prospects and challenges of tissue-derived extracellular vesicles. Mol Ther 2024:S1525-0016(24)00408-8. [PMID: 38910325 DOI: 10.1016/j.ymthe.2024.06.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/30/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024] Open
Abstract
Extracellular vesicles (EVs) are considered a vital component of cell-to-cell communication and represent a new frontier in diagnostics and a means to identify pathways for therapeutic intervention. Recently, studies have revealed the importance of tissue-derived EVs (Ti-EVs), which are EVs present in the interstitial spaces between cells, as they better represent the underlying physiology of complex, multicellular tissue microenvironments in biology and disease. EVs are native, lipid bilayer membraned nano-sized particles produced by all cells that are packaged with varied functional biomolecules including proteins, lipids, and nucleic acids. They are implicated in short- and long-range cellular communication and may elicit functional responses in recipient cells. To date, studies have often utilized cultured cells or biological fluids as a source for EVs that do not capture local molecular signatures of the tissue microenvironment. Recent work utilizing Ti-EVs has elucidated novel biomarkers for disease and provided insights into disease mechanisms that may lead to the development of novel therapeutic agents. Still, there are considerable challenges facing current studies. This review explores the vast potential and unique challenges for Ti-EV research and provides considerations for future studies that seek to advance this exciting field.
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Affiliation(s)
- Justin C Lee
- Department of Neurosurgery, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Roslyn M Ray
- Gene Therapy Research, CSL Behring, Pasadena, CA 91106, USA
| | - Tristan A Scott
- Center for Gene Therapy, City of Hope, Beckman Research Institute and Hematological Malignancy and Stem Cell Transplantation Institute, Duarte, CA 91010, USA.
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De Simoni E, Spagnolo F, Gandini S, Gaeta A, Rizzetto G, Molinelli E, Simonetti O, Offidani A, Queirolo P. Circulating tumor DNA-based assessment of molecular residual disease in non-metastatic melanoma. Cancer Treat Rev 2024; 129:102788. [PMID: 38908229 DOI: 10.1016/j.ctrv.2024.102788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/10/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024]
Abstract
In patients with resected non-metastatic melanoma, the liquid biopsy for the assessment of molecular residual disease (MRD) by circulating tumour DNA (ctDNA) represents a promising tool to stratify the risk and to monitor tumour evolution. However, its validation requires the demonstration of analytical validity, clinical validity and utility. Indeed, the development of sensitive and specific assays can optimize prognostication and eventually help clinicians to modulate adjuvant treatments, in order to improve clinical outcomes. Data about ctDNA-guided prognosis stratification is emerging, but clinical trials assessing ctDNA-guided therapeutic decisions are still ongoing. This review aims to depict the role of ctDNA-based MRD assessment in patients with non-metastatic melanoma and to provide a roadmap to face challenges for its introduction into clinical practice.
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Affiliation(s)
- Edoardo De Simoni
- Clinic of Dermatology, Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Francesco Spagnolo
- Skin Cancer Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy; Department of Surgical Sciences and Integrated Diagnostics (DISC), Plastic Surgery Division, University of Genova, Genova, Italy
| | - Sara Gandini
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Aurora Gaeta
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Giulio Rizzetto
- Clinic of Dermatology, Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Elisa Molinelli
- Clinic of Dermatology, Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Oriana Simonetti
- Clinic of Dermatology, Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Annamaria Offidani
- Clinic of Dermatology, Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Paola Queirolo
- Division of Medical Oncology for Melanoma, Sarcoma, and Rare Tumors, European Institute of Oncology IRCCS, Milan, Italy.
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Hou Y, Meng XY, Zhou X. Systematically Evaluating Cell-Free DNA Fragmentation Patterns for Cancer Diagnosis and Enhanced Cancer Detection via Integrating Multiple Fragmentation Patterns. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308243. [PMID: 38881520 DOI: 10.1002/advs.202308243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/12/2024] [Indexed: 06/18/2024]
Abstract
Cell-free DNA (cfDNA) fragmentation patterns have immense potential for early cancer detection. However, the definition of fragmentation varies, ranging from the entire genome to specific genomic regions. These patterns have not been systematically compared, impeding broader research and practical implementation. Here, 1382 plasma cfDNA sequencing samples from 8 cancer types are collected. Considering that cfDNA within open chromatin regions is more susceptible to fragmentation, 10 fragmentation patterns within open chromatin regions as features and employed machine learning techniques to evaluate their performance are examined. All fragmentation patterns demonstrated discernible classification capabilities, with the end motif showing the highest diagnostic value for cross-validation. Combining cross and independent validation results revealed that fragmentation patterns that incorporated both fragment length and coverage information exhibited robust predictive capacities. Despite their diagnostic potential, the predictive power of these fragmentation patterns is unstable. To address this limitation, an ensemble classifier via integrating all fragmentation patterns is developed, which demonstrated notable improvements in cancer detection and tissue-of-origin determination. Further functional bioinformatics investigations on significant feature intervals in the model revealed its impressive ability to identify critical regulatory regions involved in cancer pathogenesis.
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Affiliation(s)
- Yuying Hou
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiang-Yu Meng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Health Science Center, Hubei Minzu University, Enshi, 445000, China
- Hubei Provincial Clinical Medical Research Center for Nephropathy, Hubei Minzu University, Enshi, 445000, China
| | - Xionghui Zhou
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Smart Farming for Agricultural Animals, Ministry of Agriculture and Rural Affairs, Wuhan, 430070, China
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Rendek T, Pos O, Duranova T, Saade R, Budis J, Repiska V, Szemes T. Current Challenges of Methylation-Based Liquid Biopsies in Cancer Diagnostics. Cancers (Basel) 2024; 16:2001. [PMID: 38893121 PMCID: PMC11171112 DOI: 10.3390/cancers16112001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
In current clinical practice, effective cancer testing and screening paradigms are limited to specific types of cancer, exhibiting varying efficiency, acceptance, and adherence. Cell-free DNA (cfDNA) methylation profiling holds promise in providing information about the presence of malignity regardless of its type and location while leveraging blood-based liquid biopsies as a method to obtain analytical samples. However, technical difficulties, costs and challenges resulting from biological variations, tumor heterogeneity, and exogenous factors persist. This method exploits the mechanisms behind cfDNA release but faces issues like fragmentation, low concentrations, and high background noise. This review explores cfDNA methylation's origins, means of detection, and profiling for cancer diagnostics. The critical evaluation of currently available multi-cancer early detection methods (MCEDs) as well as tests targeting single genes, emphasizing their potential and limits to refine strategies for early cancer detection, are explained. The current methodology limitations, workflows, comparisons of clinically approved liquid biopsy-based methylation tests for cancer, their utilization in companion diagnostics as well as the biological limitations of the epigenetics approach are discussed, aiming to help healthcare providers as well as researchers to orient themselves in this increasingly complex and evolving field of diagnostics.
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Affiliation(s)
- Tomas Rendek
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Ondrej Pos
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | | | - Rami Saade
- 2nd Department of Gynaecology and Obstetrics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Jaroslav Budis
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia;
| | - Tomas Szemes
- Geneton Ltd., 841 04 Bratislava, Slovakia; (O.P.); (J.B.); (T.S.)
- Comenius University Science Park, 841 04 Bratislava, Slovakia;
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11
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Fang R, Yuan W, Mao C, Cao J, Chen H, Shi X, Cong H. Human circular RNA hsa_circ_0000231 clinical diagnostic effectiveness as a new tumor marker in gastric cancer. Cancer Rep (Hoboken) 2024; 7:e2081. [PMID: 38703060 PMCID: PMC11069127 DOI: 10.1002/cnr2.2081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Owing to the subtlety of initial symptoms associated with gastric cancer (GC), the majority of patients are diagnosed at later stages. Given the absence of reliable diagnostic markers, it is imperative to identify novel markers that exhibit high sensitivity and specificity. Circular RNA, a non-coding RNA, plays an important role in tumorigenesis and development and is well expressed in body fluids. AIMS In this study, we aimed to identify hsa_circ_0000231 as a new biomarker for the diagnosis of GC and to assess its clinical diagnostic value in serum. METHODS AND RESULTS The stability and correctness of hsa_circ_0000231 was determined by agarose gel electrophoresis, Rnase R assay and Sanger sequencing. Real-time quantitative polymerase chain reaction (qRT-PCR) was designed to discover the expression level of hsa_circ_0000231 and whether it has dynamic serum monitoring capability. The correlation between hsa_circ_0000231 and clinicopathological parameters was analyzed by collecting clinical and pathological data from GC patients. In addition, diagnostic efficacy was assessed by constructing receiver operating characteristic curves (ROC). Hsa_circ_0000231 exhibits a stable and consistently expressed structure. In GC serum, cells, and tissues, it demonstrates reduced expression levels. Elevated expression levels observed postoperatively suggest its potential for dynamic monitoring. Additionally its expression level correlates with TNM staging and neuro/vascular differentiation. The area under ROC curve (AUC) for hsa_circ_0000231 is 0.781, indicating its superior diagnostic value compared to CEA, CA19-9, and CA72-4. The combination of these four indicators enhances diagnostic accuracy, with an AUC of 0.833. CONCLUSIONS The stable expression of hsa_circ_0000231 in the serum of gastric cancer patients holds promise as a novel biomarker for both the diagnosis and dynamic monitoring of GC.
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Affiliation(s)
- Ronghua Fang
- Department of Laboratory MedicineAffiliated Hospital of Nantong UniversityNantongChina
- Department of Clinical MedicineMedical School of Nantong UniversityNantongChina
| | - Wentao Yuan
- Department of Laboratory MedicineAffiliated Hospital of Nantong UniversityNantongChina
- Department of Clinical MedicineMedical School of Nantong UniversityNantongChina
| | - Chunyan Mao
- Department of Laboratory MedicineAffiliated Hospital of Nantong UniversityNantongChina
- Department of Clinical MedicineMedical School of Nantong UniversityNantongChina
| | - Jing Cao
- Department of Blood TransfusionAffiliated Hospital of Nantong UniversityNantongChina
| | - Hongmei Chen
- Vip WardAffiliated Hospital of Nantong UniversityNantongChina
| | - Xiuying Shi
- Department of Laboratory MedicineAffiliated Hospital of Nantong UniversityNantongChina
| | - Hui Cong
- Department of Laboratory MedicineAffiliated Hospital of Nantong UniversityNantongChina
- Department of Blood TransfusionAffiliated Hospital of Nantong UniversityNantongChina
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12
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Rashid S, Sun Y, Ali Khan Saddozai U, Hayyat S, Munir MU, Akbar MU, Khawar MB, Ren Z, Ji X, Ihsan Ullah Khan M. Circulating tumor DNA and its role in detection, prognosis and therapeutics of hepatocellular carcinoma. Chin J Cancer Res 2024; 36:195-214. [PMID: 38751441 PMCID: PMC11090798 DOI: 10.21147/j.issn.1000-9604.2024.02.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is considered the fifth most prevalent cancer among all types of cancers and has the third most morbidity value. It has the most frequent duplication time and a high recurrence rate. Recently, the most unique technique used is liquid biopsies, which carry many markers; the most prominent is circulating tumor DNA (ctDNA). Varied methods are used to investigate ctDNA, including various forms of polymerase chain reaction (PCR) [emulsion PCR (ePCR), digital PCR (dPCR), and bead, emulsion, amplification, magnetic (BEAMing) PCR]. Hence ctDNA is being recognized as a potential biomarker that permits early cancer detection, treatment monitoring, and predictive data on tumor burden are subjective to therapy or surgery. Numerous ctDNA biomarkers have been investigated based on their alterations such as 1) single nucleotide variations (either insertion or deletion of a nucleotide) markers including TP53, KRAS, and CCND1; 2) copy number variations which include markers such as CDK6, EFGR, MYC and BRAF; 3) DNA methylation (RASSF1A, SEPT9, KMT2C and CCNA2); 4) homozygous mutation includes ctDNA markers as CDKN2A, AXIN1; and 5) gain or loss of function of the genes, particularly for HCC. Various researchers have conducted many studies and gotten fruitful results. Still, there are some drawbacks to ctDNA namely low quantity, fragment heterogeneity, less stability, limited mutant copies and standards, and differential sensitivity. However, plenty of investigations demonstrate ctDNA's significance as a polyvalent biomarker for cancer and can be viewed as a future diagnostic, prognostic and therapeutic agent. This article overviews many conditions in genetic changes linked to the onset and development of HCC, such as dysregulated signaling pathways, somatic mutations, single-nucleotide polymorphisms, and genomic instability. Additionally, efforts are also made to develop treatments for HCC that are molecularly targeted and to unravel some of the genetic pathways that facilitate its early identification.
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Affiliation(s)
- Sana Rashid
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore 54590, Pakistan
| | - Yingchuan Sun
- Department of Internal Oncology (Section I), Xuchang Municipal Central Hospital, Xuchang 461000, China
| | - Umair Ali Khan Saddozai
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China
| | - Sikandar Hayyat
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore 54590, Pakistan
| | - Muhammad Usman Munir
- Australian Institute for Bioengineering & Nanotechnology, the University of Queensland, Brisbane 4072, Australia
| | - Muhammad Usman Akbar
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan
| | - Muhammad Babar Khawar
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore 54590, Pakistan
- Applied Molecular Biology and Biomedicine Lab, Department of Zoology, University of Narowal, Narowal Punjab 51600, Pakistan
| | - Zhiguang Ren
- Kaifeng Municipal Key Laboratory for Infection and Biosafety, Henan International Joint Laboratory of Nuclear Protein Regulation, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Xinying Ji
- Faculty of Basic Medical Subjects, Shu-Qing Medical College of Zhengzhou, Zhengzhou 450064, China
- Department of Medicine, Huaxian County People’s Hospital, Huaxian 456400, China
| | - Malik Ihsan Ullah Khan
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore 54590, Pakistan
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Singhto N, Pongphitcha P, Jinawath N, Hongeng S, Chutipongtanate S. Extracellular Vesicles for Childhood Cancer Liquid Biopsy. Cancers (Basel) 2024; 16:1681. [PMID: 38730633 PMCID: PMC11083250 DOI: 10.3390/cancers16091681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Liquid biopsy involves the utilization of minimally invasive or noninvasive techniques to detect biomarkers in biofluids for disease diagnosis, monitoring, or guiding treatments. This approach is promising for the early diagnosis of childhood cancer, especially for brain tumors, where tissue biopsies are more challenging and cause late detection. Extracellular vesicles offer several characteristics that make them ideal resources for childhood cancer liquid biopsy. Extracellular vesicles are nanosized particles, primarily secreted by all cell types into body fluids such as blood and urine, and contain molecular cargos, i.e., lipids, proteins, and nucleic acids of original cells. Notably, the lipid bilayer-enclosed structure of extracellular vesicles protects their cargos from enzymatic degradation in the extracellular milieu. Proteins and nucleic acids of extracellular vesicles represent genetic alterations and molecular profiles of childhood cancer, thus serving as promising resources for precision medicine in cancer diagnosis, treatment monitoring, and prognosis prediction. This review evaluates the recent progress of extracellular vesicles as a liquid biopsy platform for various types of childhood cancer, discusses the mechanistic roles of molecular cargos in carcinogenesis and metastasis, and provides perspectives on extracellular vesicle-guided therapeutic intervention. Extracellular vesicle-based liquid biopsy for childhood cancer may ultimately contribute to improving patient outcomes.
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Affiliation(s)
- Nilubon Singhto
- Ramathibodi Comprehensive Cancer Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Pongpak Pongphitcha
- Bangkok Child Health Center, Bangkok Hospital Headquarters, Bangkok 10130, Thailand;
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan 10540, Thailand
- Integrative Computational Biosciences Center, Mahidol University, Nakon Pathom 73170, Thailand
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Somchai Chutipongtanate
- MILCH and Novel Therapeutics Laboratory, Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Extracellular Vesicle Working Group, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
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Lee MR, Woo SM, Kim MK, Han S, Park S, Lee WJ, Lee D, Choi SI, Choi W, Yoon K, Chun JW, Kim Y, Kong S. Application of plasma circulating KRAS mutations as a predictive biomarker for targeted treatment of pancreatic cancer. Cancer Sci 2024; 115:1283-1295. [PMID: 38348576 PMCID: PMC11007020 DOI: 10.1111/cas.16104] [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: 09/12/2023] [Revised: 01/11/2024] [Accepted: 01/27/2024] [Indexed: 04/12/2024] Open
Abstract
Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations in circulating tumor deoxyribonucleic acid (ctDNA) have been reported as representative noninvasive prognostic markers for pancreatic ductal adenocarcinoma (PDAC). Here, we aimed to evaluate single KRAS mutations as prognostic and predictive biomarkers, with an emphasis on potential therapeutic approaches to PDAC. A total of 128 patients were analyzed for multiple or single KRAS mutations (G12A, G12C, G12D, G12R, G12S, G12V, and G13D) in their tumors and plasma using droplet digital polymerase chain reaction (ddPCR). Overall, KRAS mutations were detected by multiplex ddPCR in 119 (93%) of tumor DNA and 68 (53.1%) of ctDNA, with a concordance rate of 80% between plasma ctDNA and tumor DNA in the metastatic stage, which was higher than the 44% in the resectable stage. Moreover, the prognostic prediction of both overall survival (OS) and progression-free survival (PFS) was more relevant using plasma ctDNA than tumor DNA. Further, we evaluated the selective tumor-suppressive efficacy of the KRAS G12C inhibitor sotorasib in a patient-derived organoid (PDO) from a KRAS G12C-mutated patient using a patient-derived xenograft (PDX) model. Sotorasib showed selective inhibition in vitro and in vivo with altered tumor microenvironment, including fibroblasts and macrophages. Collectively, screening for KRAS single mutations in plasma ctDNA and the use of preclinical models of PDO and PDX with genetic mutations would impact precision medicine in the context of PDAC.
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Affiliation(s)
- Mi Rim Lee
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Molecular Imaging Branch, Division of Convergence TechnologyResearch Institute of National Cancer CenterGoyangKorea
| | - Sang Myung Woo
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer CenterGoyangKorea
- Immuno‐Oncology Branch, Division of Rare and Refractory CenterResearch Institute of National Cancer CenterGoyangKorea
| | - Min Kyeong Kim
- Targeted Therapy Branch, Division of Rare and Refractory CenterResearch Institute of National Cancer CenterGoyangKorea
| | - Sung‐Sik Han
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer CenterGoyangKorea
| | - Sang‐Jae Park
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer CenterGoyangKorea
| | - Woo Jin Lee
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer CenterGoyangKorea
- Interventional Medicine Branch, Division of Clinical ResearchResearch Institute of National Cancer CenterGoyangKorea
| | - Dong‐eun Lee
- Biostatistics Collaboration TeamResearch Core Center, National Cancer CenterGoyangKorea
| | - Sun Il Choi
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Molecular Imaging Branch, Division of Convergence TechnologyResearch Institute of National Cancer CenterGoyangKorea
- Henan Key Laboratory of Brain Targeted Bio‐Nanomedicine, School of Life Sciences & School of PharmacyHenan UniversityKaifengHenanChina
| | - Wonyoung Choi
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Center for Clinical Trials, Hospital, National Cancer CenterGoyangKorea
- Cancer Molecular Biology Branch, Division of Cancer BiologyResearch Institute of National Cancer CenterGoyangKorea
| | - Kyong‐Ah Yoon
- College of Veterinary MedicineKonkuk UniversitySeoulKorea
| | - Jung Won Chun
- Center for Liver and Pancreatobiliary Cancer, Hospital, National Cancer CenterGoyangKorea
- Interventional Medicine Branch, Division of Clinical ResearchResearch Institute of National Cancer CenterGoyangKorea
| | - Yun‐Hee Kim
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Molecular Imaging Branch, Division of Convergence TechnologyResearch Institute of National Cancer CenterGoyangKorea
| | - Sun‐Young Kong
- Department of Cancer Biomedical ScienceNational Cancer Center Graduate School of Cancer Science and PolicyGoyangKorea
- Targeted Therapy Branch, Division of Rare and Refractory CenterResearch Institute of National Cancer CenterGoyangKorea
- Department of Laboratory MedicineHospital, National Cancer CenterGoyangKorea
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Martins-de-Barros AV, da Costa Araújo FA, Barros AMI, Dos Santos EGF, Barbosa Neto AG, da Silva HAM, de Lima ELS, Muniz MTC, Neves RFSN, de Hollanda Valente RO, de Oliveira E Silva ED, de Vasconcelos Carvalho M. It was not possible to detect BRAF V600E mutation in circulating cell-free DNA from patients with ameloblastoma: A diagnostic accuracy study. J Oral Pathol Med 2024; 53:258-265. [PMID: 38494749 DOI: 10.1111/jop.13529] [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: 11/15/2023] [Revised: 01/30/2024] [Accepted: 03/05/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND The objective of this study is to evaluate the diagnostic accuracy of plasma-based liquid biopsy for the detection of the BRAF V600E mutation in circulating cell-free DNA from patients with ameloblastoma. METHODS This is a prospective diagnostic accuracy study conducted based on the Standards for Reporting Diagnostic Accuracy recommendations. The index test was the plasma-based liquid biopsy, whereas the reference standard was the conventional tissue biopsy. The target condition was the detection of BRAF V600E mutation. The study population consisted of individuals with ameloblastoma recruited from three tertiary hospitals from Brazil. A negative control group composed of three individuals with confirmed wild-type BRAF lesions were included. The participants underwent plasma circulating cell-free DNA and tumor tissue DNA isolation, and both were submitted to using competitive allele-specific TaqMan™ real-time polymerase chain reaction technology mutation detection assays. Sensitivity and specificity measures and positive and negative predictive values were calculated. RESULTS Twelve patients with conventional ameloblastoma were included. BRAF V600E mutation was detected in 11/12 (91.66%) ameloblastoma tissue samples. However, the mutation was not detected in any of the plasma-based liquid biopsy circulating cell-free DNA samples in both ameloblastomas and negative control group. The sensitivity and specificity of plasma-based liquid biopsy for the detection of the BRAF V600E mutation in circulating cell-free DNA was 0.0 and 1.0, respectively. The agreement between index test and reference standard results was 26.66%. CONCLUSION Plasma-based liquid biopsy does not seem to be an accurate method for the detection of the BRAF V600E mutation in circulating circulating cell-free DNA from patients with ameloblastoma, regardless of tumor size, anatomic location, recurrence status, and other clinicopathological features.
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Affiliation(s)
- Allan Vinícius Martins-de-Barros
- School of Dentistry, Post-Graduation Program in Dentistry, University of Pernambuco (UPE), Recife, Pernambuco, Brazil
- Centro Integrado de Anatomia Patológica (CIAP), Hospital Universitário Oswaldo Cruz (HUOC/UPE), Recife, Pernambuco, Brazil
| | - Fábio Andrey da Costa Araújo
- School of Dentistry, Post-Graduation Program in Dentistry, University of Pernambuco (UPE), Recife, Pernambuco, Brazil
- Department of Oral and Maxillofacial Surgery, Hospital Universitário Oswaldo Cruz (HUOC/UPE), Recife, Pernambuco, Brazil
| | - Ana Maria Ipólito Barros
- School of Dentistry, Post-Graduation Program in Dentistry, University of Pernambuco (UPE), Recife, Pernambuco, Brazil
- Centro Integrado de Anatomia Patológica (CIAP), Hospital Universitário Oswaldo Cruz (HUOC/UPE), Recife, Pernambuco, Brazil
| | | | - Adauto Gomes Barbosa Neto
- Instituto de Ciências Biológicas (ICB/UPE), University of Pernambuco (UPE), Recife, Pernambuco, Brazil
| | | | - Elker Lene Santos de Lima
- Instituto de Ciências Biológicas (ICB/UPE), University of Pernambuco (UPE), Recife, Pernambuco, Brazil
| | | | | | | | - Emanuel Dias de Oliveira E Silva
- School of Dentistry, Post-Graduation Program in Dentistry, University of Pernambuco (UPE), Recife, Pernambuco, Brazil
- Department of Oral and Maxillofacial Surgery, Hospital Universitário Oswaldo Cruz (HUOC/UPE), Recife, Pernambuco, Brazil
| | - Marianne de Vasconcelos Carvalho
- School of Dentistry, Post-Graduation Program in Dentistry, University of Pernambuco (UPE), Recife, Pernambuco, Brazil
- Centro Integrado de Anatomia Patológica (CIAP), Hospital Universitário Oswaldo Cruz (HUOC/UPE), Recife, Pernambuco, Brazil
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16
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Pomerantz T, Brooks R. Circulating Tumor DNA (ctDNA) and Its Role in Gynecologic Malignancies. Curr Treat Options Oncol 2024; 25:510-522. [PMID: 38472567 DOI: 10.1007/s11864-024-01180-w] [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] [Accepted: 01/10/2024] [Indexed: 03/14/2024]
Abstract
OPINION STATEMENT Circulating tumor DNA (ctDNA) refers to small fragments of DNA released into the bloodstream by cancer cells. It is obtained through "liquid biopsy;" which most commonly refers to plasma or blood samples, but can be obtained from a number of bodily fluids including ascitic fluid, saliva, and even urine and stool. ctDNA is detected via polymerase chain reaction (PCR) or next-generation sequencing (NGS). The DNA from these samples is analyzed for the detection of point mutations, copy-number alterations, gene fusion, and DNA methylation. These results have the potential for use in cancer diagnosis, determining prognosis, targeting gene-specific therapies, and monitoring for/predicting disease recurrence and response to treatment. ctDNA offers an alternative to tissue biopsy; it is less invasive and can be monitored serially over time without multiple procedures. Moreover it may have the ability to detect disease recurrence or predict behavior in a way that solid tissue biopsies, tumor marker surveillance, and imaging cannot. Recent explosion in interest in ctDNA shows promising developments for widespread adoption of these techniques in cancer care. However, the use of ctDNA in diagnosis and treatment of gynecologic malignancies is currently limited, compared to adoption in other solid-organ tumors such as breast and colorectal cancers. Compared to other cancer types, there appear to be fewer comprehensive studies and clinical validations specifically focusing on the use of ctDNA in gynecologic cancers. More research is needed in this area to advance the potential for use of ctDNA in ovarian, endometrial, and cervical cancers before this can be routinely adopted to improve care for patients with gynecologic malignancies.
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Affiliation(s)
- Tali Pomerantz
- University of California Davis Medical Center, 4860 Y Street, Suite 2500, Sacramento, CA, 95817, USA.
| | - Rebecca Brooks
- University of California Davis Medical Center, 4860 Y Street, Suite 2500, Sacramento, CA, 95817, USA
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Gupta S, Singh B, Abhishek R, Gupta S, Sachan M. The emerging role of liquid biopsy in oral squamous cell carcinoma detection: advantages and challenges. Expert Rev Mol Diagn 2024; 24:311-331. [PMID: 38607339 DOI: 10.1080/14737159.2024.2340997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/05/2024] [Indexed: 04/13/2024]
Abstract
INTRODUCTION Oral Squamous Cell Carcinoma (OSCC), the sixth most widespread malignancy in the world, accounts for 90% of all cases of oral cancer. The primary risk factors are tobacco chewing, alcohol consumption, viral infection, and genetic modifications. OSCC has a high morbidity rate due to the lack of early diagnostic methods. Nowadays, liquid biopsy plays a vital role in the initial diagnosis of oral cancer. ctNAs extracted from saliva and serum/plasma offer meaningful insights into tumor genetics and dynamics. The interplay of these elements in saliva and serum/plasma showcases their significance in advancing noninvasive, effective OSCC detection and monitoring. AREAS COVERED This review mainly focused on the role of liquid biopsy as an emerging point in the diagnosis and prognosis of OSCC and the current advancements and challenges associated with liquid biopsy. EXPERT OPINION Liquid biopsy is regarded as a new, minimally invasive, real-time monitoring tool for cancer diagnosis and prognosis. Many biomolecules found in bodily fluids, including ctDNA, ctRNA, CTCs, and EVs, are significant biomarkers to identify cancer in its early stages. Despite these groundbreaking strides, challenges persist. Standardization of sample collection, isolation, processing, and detection methods is imperative for ensuring result reproducibility across diverse studies.
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Affiliation(s)
- Sudha Gupta
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, India
| | - Brijesh Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, India
| | - Rajul Abhishek
- Department of Surgical Oncology, Motilal Nehru Medical College, Prayagraj, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, India
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Scaini MC, Catoni C, Poggiana C, Pigozzo J, Piccin L, Leone K, Scarabello I, Facchinetti A, Menin C, Elefanti L, Pellegrini S, Aleotti V, Vidotto R, Schiavi F, Fabozzi A, Chiarion-Sileni V, Rosato A. A multiparameter liquid biopsy approach allows to track melanoma dynamics and identify early treatment resistance. NPJ Precis Oncol 2024; 8:78. [PMID: 38548846 PMCID: PMC10978909 DOI: 10.1038/s41698-024-00567-0] [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: 06/14/2023] [Accepted: 03/14/2024] [Indexed: 04/01/2024] Open
Abstract
Melanoma heterogeneity is a hurdle in metastatic disease management. Although the advent of targeted therapy has significantly improved patient outcomes, the occurrence of resistance makes monitoring of the tumor genetic landscape mandatory. Liquid biopsy could represent an important biomarker for the real-time tracing of disease evolution. Thus, we aimed to correlate liquid biopsy dynamics with treatment response and progression by devising a multiplatform approach applied to longitudinal melanoma patient monitoring. We conceived an approach that exploits Next Generation Sequencing (NGS) and droplet digital PCR, as well as the FDA-cleared platform CellSearch, to analyze circulating tumor DNA (ctDNA) trend and circulating melanoma cell (CMC) count, together with their customized genetic and copy number variation analysis. The approach was applied to 17 stage IV melanoma patients treated with BRAF/MEK inhibitors, followed for up to 28 months. BRAF mutations were detected in the plasma of 82% of patients. Single nucleotide variants known or suspected to confer resistance were identified in 70% of patients. Moreover, the amount of ctDNA, both at baseline and during response, correlated with the type and duration of the response itself, and the CMC count was confirmed to be a prognostic biomarker. This work provides proof of principle of the power of this approach and paves the way for a validation study aimed at evaluating early ctDNA-guided treatment decisions in stage IV melanoma. The NGS-based molecular profile complemented the analysis of ctDNA trend and, together with CMC analysis, revealed to be useful in capturing tumor evolution.
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Affiliation(s)
- Maria Chiara Scaini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy.
| | - Cristina Catoni
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Cristina Poggiana
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy.
| | - Jacopo Pigozzo
- Medical Oncology 2, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Luisa Piccin
- Medical Oncology 2, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Kevin Leone
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Ilaria Scarabello
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Antonella Facchinetti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), Oncology Section, University of Padua, Padua, Italy
| | - Chiara Menin
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Lisa Elefanti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Stefania Pellegrini
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Valentina Aleotti
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Riccardo Vidotto
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Francesca Schiavi
- Familial Cancer Clinic, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | - Alessio Fabozzi
- Oncology Unit 3, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
| | | | - Antonio Rosato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology - IOV IRCCS, Padua, Italy
- Department of Surgery, Oncology and Gastroenterology (DiSCOG), Oncology Section, University of Padua, Padua, Italy
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Díaz del Arco C, Fernández Aceñero MJ, Ortega Medina L. Liquid biopsy for gastric cancer: Techniques, applications, and future directions. World J Gastroenterol 2024; 30:1680-1705. [PMID: 38617733 PMCID: PMC11008373 DOI: 10.3748/wjg.v30.i12.1680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/01/2024] [Accepted: 03/08/2024] [Indexed: 03/28/2024] Open
Abstract
After the study of circulating tumor cells in blood through liquid biopsy (LB), this technique has evolved to encompass the analysis of multiple materials originating from the tumor, such as nucleic acids, extracellular vesicles, tumor-educated platelets, and other metabolites. Additionally, research has extended to include the examination of samples other than blood or plasma, such as saliva, gastric juice, urine, or stool. LB techniques are diverse, intricate, and variable. They must be highly sensitive, and pre-analytical, patient, and tumor-related factors significantly influence the detection threshold, diagnostic method selection, and potential results. Consequently, the implementation of LB in clinical practice still faces several challenges. The potential applications of LB range from early cancer detection to guiding targeted therapy or immunotherapy in both early and advanced cancer cases, monitoring treatment response, early identification of relapses, or assessing patient risk. On the other hand, gastric cancer (GC) is a disease often diagnosed at advanced stages. Despite recent advances in molecular understanding, the currently available treatment options have not substantially improved the prognosis for many of these patients. The application of LB in GC could be highly valuable as a non-invasive method for early diagnosis and for enhancing the management and outcomes of these patients. In this comprehensive review, from a pathologist's perspective, we provide an overview of the main options available in LB, delve into the fundamental principles of the most studied techniques, explore the potential utility of LB application in the context of GC, and address the obstacles that need to be overcome in the future to make this innovative technique a game-changer in cancer diagnosis and treatment within clinical practice.
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Affiliation(s)
- Cristina Díaz del Arco
- Department of Surgical Pathology, Health Research Institute of the Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid 28040, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - M Jesús Fernández Aceñero
- Department of Surgical Pathology, Health Research Institute of the Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid 28040, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Luis Ortega Medina
- Department of Surgical Pathology, Health Research Institute of the Hospital Clínico San Carlos, Hospital Clínico San Carlos, Madrid 28040, Spain
- Department of Legal Medicine, Psychiatry and Pathology, Universidad Complutense de Madrid, Madrid 28040, Spain
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20
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Napiórkowska-Mastalerz M, Wybranowski T, Bosek M, Kruszewski S, Rhone P, Ruszkowska-Ciastek B. A Preliminary Evaluation of Advanced Oxidation Protein Products (AOPPs) as a Potential Approach to Evaluating Prognosis in Early-Stage Breast Cancer Patients and Its Implication in Tumour Angiogenesis: A 7-Year Single-Centre Study. Cancers (Basel) 2024; 16:1068. [PMID: 38473424 DOI: 10.3390/cancers16051068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/28/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
Breast cancer (BrC) is a highly prevalent tumour among women. The high incidence and mortality rate of BrC prompts researchers to search for new markers that will provide information on the possible impact of the therapy on the risk of cancer-related events. This study aimed to investigate whether the level of advanced oxidation protein products (AOPPs) may have a potential impact on disease-free (DFS) and overall survival (OS) in BrC patients with early-stage cancer. Additionally, we tried to assess the relationship between AOPPs and angiogenic parameters. In this study, the pre- and post-treatment AOPP levels were examined in the serum of 70 newly diagnosed BrC women. The receiver operating characteristic curve identified pre- and post-treatment AOPPs to be above 9.37 μM and 10.39 μM, respectively, as the best cut-off values to predict the risk of cancer relapse. Additionally, Kaplan-Meier survival analysis indicated that pre- and post-treatment AOPPs above 9.37 μM and 10.39 μM were associated with significantly poorer OS. The uni- and multivariate Cox regression analysis highlighted that lower levels of pre- and post-treatment AOPPs were associated with a longer duration without relapse or cancer-related death. A positive correlation between concentrations of pre-treatment AOPPs and vascular endothelial growth factor A, and negative correlations with levels of soluble forms of vascular endothelial growth factor receptor type 1 and 2, were found. In conclusion, AOPPs appear to have an important role in predicting cancer-related events and may potentially serve as a simple prognostic marker in clinical practice.
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Affiliation(s)
- Marta Napiórkowska-Mastalerz
- Department of Biophysics, Faculty of Pharmacy, Nicolaus Copernicus University, Collegium Medicum, 85-067 Bydgoszcz, Poland
| | - Tomasz Wybranowski
- Department of Biophysics, Faculty of Pharmacy, Nicolaus Copernicus University, Collegium Medicum, 85-067 Bydgoszcz, Poland
| | - Maciej Bosek
- Department of Biophysics, Faculty of Pharmacy, Nicolaus Copernicus University, Collegium Medicum, 85-067 Bydgoszcz, Poland
| | - Stefan Kruszewski
- Department of Biophysics, Faculty of Pharmacy, Nicolaus Copernicus University, Collegium Medicum, 85-067 Bydgoszcz, Poland
| | - Piotr Rhone
- Clinical Ward of Breast Cancer and Reconstructive Surgery, Oncology Centre Prof. F. Łukaszczyk Memorial Hospital, 85-796 Bydgoszcz, Poland
| | - Barbara Ruszkowska-Ciastek
- Department of Pathophysiology, Faculty of Pharmacy, Nicolaus Copernicus University, Collegium Medicum, 85-094 Bydgoszcz, Poland
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21
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Dubey AK, Kaur I, Madaan R, Raheja S, Bala R, Garg M, Kumar S, Lather V, Mittal V, Pandita D, Gundamaraju R, Singla RK, Sharma R. Unlocking the potential of oncology biomarkers: advancements in clinical theranostics. Drug Metab Pers Ther 2024; 39:5-20. [PMID: 38469723 DOI: 10.1515/dmpt-2023-0056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/11/2024] [Indexed: 03/13/2024]
Abstract
INTRODUCTION Cancer biomarkers have revolutionized the field of oncology by providing valuable insights into tumor changes and aiding in screening, diagnosis, prognosis, treatment prediction, and risk assessment. The emergence of "omic" technologies has enabled biomarkers to become reliable and accurate predictors of outcomes during cancer treatment. CONTENT In this review, we highlight the clinical utility of biomarkers in cancer identification and motivate researchers to establish a personalized/precision approach in oncology. By extending a multidisciplinary technology-based approach, biomarkers offer an alternative to traditional techniques, fulfilling the goal of cancer therapeutics to find a needle in a haystack. SUMMARY AND OUTLOOK We target different forms of cancer to establish a dynamic role of biomarkers in understanding the spectrum of malignancies and their biochemical and molecular characterization, emphasizing their prospective contribution to cancer screening. Biomarkers offer a promising avenue for the early detection of human cancers and the exploration of novel technologies to predict disease severity, facilitating maximum survival and minimum mortality rates. This review provides a comprehensive overview of the potential of biomarkers in oncology and highlights their prospects in advancing cancer diagnosis and treatment.
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Affiliation(s)
- Ankit Kumar Dubey
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, 34753 Sichuan University , Chengdu, P.R. China
- iGlobal Research and Publishing Foundation, New Delhi, India
| | - Ishnoor Kaur
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Reecha Madaan
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Shikha Raheja
- Jan Nayak Ch. Devi Lal Memorial College of Pharmacy, Sirsa, Haryana, India
| | - Rajni Bala
- Chitkara College of Pharmacy, 154025 Chitkara University Punjab , Rajpura, India
| | - Manoj Garg
- Amity Institute of Molecular Medicine & Stem Cell Research, 77282 Amity University, Sector-125 , Noida, India
| | - Suresh Kumar
- Department of Pharmaceutical Sciences and Drug Research, 429174 Punjabi University Patiala , Patiala, India
| | - Viney Lather
- Amity Institute of Pharmacy, 77282 Amity University , Noida, India
| | - Vineet Mittal
- Department of Pharmaceutical Sciences, 29062 Maharshi Dayanand University , Rohtak, Haryana, India
| | - Deepti Pandita
- Department of Pharmaceutics, Delhi Pharmaceutical Sciences and Research University, PushpVihar, 633274 Govt. of NCT of Delhi , New Delhi, India
- Centre for Advanced Formulation and Technology (CAFT), Delhi Pharmaceutical Sciences and Research University, PushpVihar, Govt. of NCT of Delhi, New Delhi, India
| | - Rohit Gundamaraju
- ER Stress and Mucosal Immunology Lab, School of Health Sciences, 8785 University of Tasmania , Launceston, Tasmania, Australia
- School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rajeev K Singla
- Joint Laboratory of Artificial Intelligence for Critical Care Medicine, Department of Critical Care Medicine and Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, 34753 Sichuan University , Chengdu, P.R. China
- School of Pharmaceutical Sciences, 34753 Lovely Professional University , Phagwara, Punjab, India
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, 80095 Banaras Hindu University , Varanasi, Uttar Pradesh, India
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22
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Grant CR, Benjamin DJ, Cramer S, Rezazadeh Kalebasty A. A remnant never forgotten: the utility of circulating tumor DNA in treatment guidance of urachal cancer. Ther Adv Med Oncol 2024; 16:17588359241230743. [PMID: 38425988 PMCID: PMC10903217 DOI: 10.1177/17588359241230743] [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: 09/14/2023] [Accepted: 01/17/2024] [Indexed: 03/02/2024] Open
Abstract
Urachal cancer is a rare malignancy of the urachus that is treated with surgical resection if localized and systemic chemotherapy for metastatic disease. Circulating tumor DNA (ctDNA) is a single-stranded or double-stranded DNA released by tumor cells into the blood and harbored the mutations of the original tumor, shedding new light on molecular diagnosis and monitoring of cancer. We report a case of resected localized urachal cancer with clear surgical margins and negative lymph node dissection but elevated ctDNA that progressed to metastatic disease. We also highlight the possibility of using ctDNA levels to assist in adjuvant therapy.
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Affiliation(s)
- Christopher Ryan Grant
- Department of Medicine, University of California Irvine Medical Center, UC Irvine Health, 200 S Manchester Avenue, Room 423, Orange, CA 92868, USA
| | | | - Scott Cramer
- Department of Radiology, University of California Irvine Medical Center, Orange, CA, USA
| | - Arash Rezazadeh Kalebasty
- Division of Hematology/Oncology, Department of Medicine, University of California Irvine Medical Center, Orange, CA, USA
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23
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Shbeer AM, Robadi IA. liquid biopsy holds a promising approach for the early detection of cancer: Current information and future perspectives. Pathol Res Pract 2024; 254:155082. [PMID: 38246032 DOI: 10.1016/j.prp.2023.155082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/24/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024]
Abstract
Cancer is becoming a global pandemic, and its occurrence is increasing rapidly, putting a strain on people's families, health systems, and finances, in addition to their physical, mental, and emotional well-being. Many cancer types lack screening programs, and many people at high risk of developing cancer do not follow recommended medical screening regimens because of the nature of currently available screening tests and other compliance issues, despite cancer being the second leading cause of death worldwide. Furthermore, a lot of liquid biopsy methods for early cancer screening are not sensitive enough to catch cancer early. Cancer treatment costs increase with the time it takes to diagnose the disease; therefore, early detection is essential to enhance the quality of life and survival rates. The current status of the liquid biopsy sector is examined in this paper.
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Affiliation(s)
- Abdullah M Shbeer
- Department of Surgery, Faculty of Medicine, Jazan University, Jazan, Saudi Arabia.
| | - Ibrahim Ahmed Robadi
- Department of Pathology, Faculty of Medicine, Jazan University, Jazan, Saudi Arabia.
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24
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Wang X, Wang L, Lin H, Zhu Y, Huang D, Lai M, Xi X, Huang J, Zhang W, Zhong T. Research progress of CTC, ctDNA, and EVs in cancer liquid biopsy. Front Oncol 2024; 14:1303335. [PMID: 38333685 PMCID: PMC10850354 DOI: 10.3389/fonc.2024.1303335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/04/2024] [Indexed: 02/10/2024] Open
Abstract
Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and extracellular vehicles (EVs) have received significant attention in recent times as emerging biomarkers and subjects of transformational studies. The three main branches of liquid biopsy have evolved from the three primary tumor liquid biopsy detection targets-CTC, ctDNA, and EVs-each with distinct benefits. CTCs are derived from circulating cancer cells from the original tumor or metastases and may display global features of the tumor. ctDNA has been extensively analyzed and has been used to aid in the diagnosis, treatment, and prognosis of neoplastic diseases. EVs contain tumor-derived material such as DNA, RNA, proteins, lipids, sugar structures, and metabolites. The three provide different detection contents but have strong complementarity to a certain extent. Even though they have already been employed in several clinical trials, the clinical utility of three biomarkers is still being studied, with promising initial findings. This review thoroughly overviews established and emerging technologies for the isolation, characterization, and content detection of CTC, ctDNA, and EVs. Also discussed were the most recent developments in the study of potential liquid biopsy biomarkers for cancer diagnosis, therapeutic monitoring, and prognosis prediction. These included CTC, ctDNA, and EVs. Finally, the potential and challenges of employing liquid biopsy based on CTC, ctDNA, and EVs for precision medicine were evaluated.
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Affiliation(s)
- Xiaoling Wang
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Lijuan Wang
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Haihong Lin
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Yifan Zhu
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Defa Huang
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Mi Lai
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xuxiang Xi
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Junyun Huang
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Wenjuan Zhang
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
| | - Tianyu Zhong
- Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- The First School of Clinical Medicine, Gannan Medical University, Ganzhou, China
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25
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Witz A, Dardare J, Betz M, Gilson P, Merlin JL, Harlé A. Tumor-derived cell-free DNA and circulating tumor cells: partners or rivals in metastasis formation? Clin Exp Med 2024; 24:2. [PMID: 38231464 PMCID: PMC10794481 DOI: 10.1007/s10238-023-01278-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 01/18/2024]
Abstract
The origin of metastases is a topic that has sparked controversy. Despite recent advancements, metastatic disease continues to pose challenges. The first admitted model of how metastases develop revolves around cells breaking away from the primary tumor, known as circulating tumor cells (CTCs). These cells survive while circulating through the bloodstream and subsequently establish themselves in secondary organs, a process often referred to as the "metastatic cascade". This intricate and dynamic process involves various steps, but all the mechanisms behind metastatic dissemination are not yet comprehensively elucidated. The "seed and soil" theory has shed light on the phenomenon of metastatic organotropism and the existence of pre-metastatic niches. It is now established that these niches can be primed by factors secreted by the primary tumor before the arrival of CTCs. In particular, exosomes have been identified as important contributors to this priming. Another concept then emerged, i.e. the "genometastasis" theory, which challenged all other postulates. It emphasizes the intriguing but promising role of cell-free DNA (cfDNA) in metastasis formation through oncogenic formation of recipient cells. However, it cannot be ruled out that all these theories are intertwined. This review outlines the primary theories regarding the metastases formation that involve CTCs, and depicts cfDNA, a potential second player in the metastasis formation. We discuss the potential interrelationships between CTCs and cfDNA, and propose both in vitro and in vivo experimental strategies to explore all plausible theories.
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Affiliation(s)
- Andréa Witz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France.
| | - Julie Dardare
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Margaux Betz
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Pauline Gilson
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Jean-Louis Merlin
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
| | - Alexandre Harlé
- Département de Biopathologie, Institut de Cancérologie de Lorraine, CNRS UMR 7039 CRAN-Université de Lorraine, 6 avenue de Bourgogne, 54519, Vandœuvre-lès-Nancy Cedex, France
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26
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Najafi S, Majidpoor J, Mortezaee K. Liquid biopsy in colorectal cancer. Clin Chim Acta 2024; 553:117674. [PMID: 38007059 DOI: 10.1016/j.cca.2023.117674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Liquid biopsy refers to a set of pathological samples retrieved from non-solid sources, such as blood, cerebrospinal fluid, urine, and saliva through non-invasive or minimally invasive approaches. In the recent decades, an increasing number of studies have focused on clinical applications and improving technological investigation of liquid biopsy biosources for diagnostic goals particularly in cancer. Materials extracted from these sources and used for medical evaluations include cells like circulating tumor cells (CTCs), tumor-educated platelets (TEPs), cell-free nucleic acids released by cells, such as circulating tumor DNA (ctDNA), cell-free DNA (cfDNA), cell-free RNA (cfRNA), and exosomes. Playing significant roles in the pathogenesis of human malignancies, analysis of these sources can provide easier access to genetic and transcriptomic information of the cancer tissue even better than the conventional tissue biopsy. Notably, they can represent the inter- and intra-tumoral heterogeneity and accordingly, liquid biopsies demonstrate strengths for improving diagnosis in early detection and screening, monitoring and follow-up after therapies, and personalization of therapeutical strategies in various types of human malignancies. In this review, we aim to discuss the roles, functions, and analysis approaches of liquid biopsy sources and their clinical implications in human malignancies with a focus on colorectal cancer.
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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
| | - Jamal Majidpoor
- Department of Anatomy, School of Medicine, Infectious Diseases Research Center, Gonabad University of Medical Sciences, Gonabad, Iran
| | - Keywan Mortezaee
- Department of Anatomy, School of Medicine, Kurdistan University of Medical Sciences, Sanandaj, Iran.
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27
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Rassomakhina NV, Ryazanova AY, Likhov AR, Bruskin SA, Maloshenok LG, Zherdeva VV. Tumor Organoids: The Era of Personalized Medicine. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S127-S147. [PMID: 38621748 DOI: 10.1134/s0006297924140086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/01/2023] [Accepted: 11/09/2023] [Indexed: 04/17/2024]
Abstract
The strategies of future medicine are aimed to modernize and integrate quality approaches including early molecular-genetic profiling, identification of new therapeutic targets and adapting design for clinical trials, personalized drug screening (PDS) to help predict and individualize patient treatment regimens. In the past decade, organoid models have emerged as an innovative in vitro platform with the potential to realize the concept of patient-centered medicine. Organoids are spatially restricted three-dimensional clusters of cells ex vivo that self-organize into complex functional structures through genetically programmed determination, which is crucial for reconstructing the architecture of the primary tissue and organs. Currently, there are several strategies to create three-dimensional (3D) tumor systems using (i) surgically resected patient tissue (PDTOs, patient-derived tumor organoids) or (ii) single tumor cells circulating in the patient's blood. Successful application of 3D tumor models obtained by co-culturing autologous tumor organoids (PDTOs) and peripheral blood lymphocytes have been demonstrated in a number of studies. Such models simulate a 3D tumor architecture in vivo and contain all cell types characteristic of this tissue, including immune system cells and stem cells. Components of the tumor microenvironment, such as fibroblasts and immune system cells, affect tumor growth and its drug resistance. In this review, we analyzed the evolution of tumor models from two-dimensional (2D) cell cultures and laboratory animals to 3D tissue-specific tumor organoids, their significance in identifying mechanisms of antitumor response and drug resistance, and use of these models in drug screening and development of precision methods in cancer treatment.
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Affiliation(s)
- Natalia V Rassomakhina
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Alexandra Yu Ryazanova
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Astemir R Likhov
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
| | - Sergey A Bruskin
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Liliya G Maloshenok
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Victoria V Zherdeva
- Bach Institute of Biochemistry, Federal Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
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28
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Paul T, Palaniyandi K, Gnanasampanthapandian D. Therapeutic Approaches to Increase the Survival Rate of Cancer Patients in the Younger and Older Population. Curr Aging Sci 2024; 17:16-30. [PMID: 38062658 DOI: 10.2174/0118746098241507231127114248] [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: 01/25/2023] [Revised: 06/25/2023] [Accepted: 09/22/2023] [Indexed: 05/18/2024]
Abstract
Various developments have been observed in the treatment of cancer patients, such as higher survival rates and better treatment outcomes. However, expecting similar outcomes in older patients remains a challenge. The main reason for this conclusion is the exclusion of older people from clinical trials for cancer drugs, as well as other factors, such as comorbidity, side effects, age-related frailties and their willingness to undergo multiple treatments. However, the discovery of new techniques and drug combinations has led to a significant improvement in the survival of the elderly population after the onset of the disease. On the other hand, cancer treatments have not become more complex for the younger population when compared to the older population, as the younger population tends to respond well to treatment trials and their physiological conditions are stable in response to treatments. In summary, this review correlates recent cancer treatment strategies and the corresponding responses and survival outcomes of older and younger patients.
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Affiliation(s)
- Tharrun Paul
- Cancer Science Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu, India
| | - Kanagaraj Palaniyandi
- Cancer Science Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu, India
| | - Dhanavathy Gnanasampanthapandian
- Cancer Science Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu, India
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29
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Hua H, Zhou Y, Li W, Zhang J, Deng Y, Khoo BL. Microfluidics-based patient-derived disease detection tool for deep learning-assisted precision medicine. BIOMICROFLUIDICS 2024; 18:014101. [PMID: 38223546 PMCID: PMC10787641 DOI: 10.1063/5.0172146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024]
Abstract
Cancer spatial and temporal heterogeneity fuels resistance to therapies. To realize the routine assessment of cancer prognosis and treatment, we demonstrate the development of an Intelligent Disease Detection Tool (IDDT), a microfluidic-based tumor model integrated with deep learning-assisted algorithmic analysis. IDDT was clinically validated with liquid blood biopsy samples (n = 71) from patients with various types of cancers (e.g., breast, gastric, and lung cancer) and healthy donors, requiring low sample volume (∼200 μl) and a high-throughput 3D tumor culturing system (∼300 tumor clusters). To support automated algorithmic analysis, intelligent decision-making, and precise segmentation, we designed and developed an integrative deep neural network, which includes Mask Region-Based Convolutional Neural Network (Mask R-CNN), vision transformer, and Segment Anything Model (SAM). Our approach significantly reduces the manual labeling time by up to 90% with a high mean Intersection Over Union (mIoU) of 0.902 and immediate results (<2 s per image) for clinical cohort classification. The IDDT can accurately stratify healthy donors (n = 12) and cancer patients (n = 55) within their respective treatment cycle and cancer stage, resulting in high precision (∼99.3%) and high sensitivity (∼98%). We envision that our patient-centric IDDT provides an intelligent, label-free, and cost-effective approach to help clinicians make precise medical decisions and tailor treatment strategies for each patient.
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Affiliation(s)
| | - Yunlan Zhou
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | | | - Jing Zhang
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
| | - Yanlin Deng
- Department of Biomedical Engineering, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong 999077, China
| | - Bee Luan Khoo
- Authors to whom correspondence should be addressed:; ; and
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30
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Dai L, Jing Z, Zhu Y, Deng K, Ma L. Genome-wide analysis of circulating tumor DNA methylation profiles in cerebrospinal fluid: a clinical trial of oncolytic virus for glioblastoma. Am J Cancer Res 2023; 13:5950-5965. [PMID: 38187045 PMCID: PMC10767359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/11/2023] [Indexed: 01/09/2024] Open
Abstract
Glioblastoma (GBM) is a common malignant tumor of the central nervous system with a poor prognosis and a short survival period. A novel tumor oncolytic virus, Ad-TD-nsIL-12, has manifested anti-tumor properties in preclinical studies. However, the genetic changes caused by Ad-TD-nsIL-12 after GBM treatment are unclear. Therefore, we collected cerebrospinal fluid and tumor tissues from patients injected with Ad-TD-nsIL-12 at different time points and analyzed the methylation and expression profiles of cerebrospinal fluid-derived circulating tumor DNA (ctDNA). The differential genes were screened using the least absolute selection and shrinkage operator (LASSO) and Cox regression analyses. The CIBERSORT algorithm was used to assess the abundance of glioma immune cell infiltration in The Cancer Genome Atlas (TCGA) dataset. The role of hub genes in the diagnosis, prognosis, and immune cell correlation was analyzed using R software, SPSS software, and GraphPad Prism. The results showed that after Ad-TD-nsIL-12 injection, 3631 differential methylation regions (DMRs) were up-regulated and 497 DMRs were down-regulated. The methylation levels of these DMRs recovered within 70 to 82 days. Combined with the TCGA dataset, 8 key genes were selected for the construction of diagnostic and prognostic models. There was a significant correlation between core genes and immune cells. The results revealed that the hub genes in CSF could be used as a biomarker for the diagnosis and prognosis of GBM and led us to speculate the effect of the hub gene on the immune mechanism underlying Ad-TD-nsIL-12.
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Affiliation(s)
- Lin Dai
- Department of Neurosurgery, Binzhou Medical University HospitalBinzhou 256603, Shandong, P. R. China
| | - Zixuan Jing
- Department of Neurosurgery, Binzhou Medical University HospitalBinzhou 256603, Shandong, P. R. China
| | - Yi Zhu
- Department of Neurosurgery, Binzhou Medical University HospitalBinzhou 256603, Shandong, P. R. China
| | - Kaihan Deng
- Department of Neurosurgery, Binzhou Medical University HospitalBinzhou 256603, Shandong, P. R. China
| | - Lixin Ma
- Department of Neurosurgery, Beijing Chaoyang Hospital, Capital Medical UniversityBeijing 100020, P. R. China
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical UniversityBeijing 100093, P. R. China
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31
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Kalashnikova E, Aushev VN, Malashevich AK, Tin A, Krinshpun S, Salari R, Scalise CB, Ram R, Malhotra M, Ravi H, Sethi H, Sanchez S, Hagelstrom RT, Brevnov M, Rabinowitz M, Moshkevich S, Zimmermann BG, Liu MC, Aleshin A. Correlation between variant allele frequency and mean tumor molecules with tumor burden in patients with solid tumors. Mol Oncol 2023. [PMID: 38037739 DOI: 10.1002/1878-0261.13557] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 10/03/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023] Open
Abstract
Several studies have demonstrated the prognostic value of circulating tumor DNA (ctDNA); however, the correlation of mean tumor molecules (MTM)/ml of plasma and mean variant allele frequency (mVAF; %) with clinical parameters is yet to be understood. In this study, we analyzed ctDNA data in a pan-cancer cohort of 23 543 patients who had ctDNA testing performed using a personalized, tumor-informed assay (Signatera™, mPCR-NGS assay). For ctDNA-positive patients, the correlation between MTM/ml and mVAF was examined. Two subanalyses were performed: (a) to establish the association of ctDNA with tumor volume and (b) to assess the correlation between ctDNA dynamics and patient outcomes. On a global cohort, a positive correlation between MTM/ml and mVAF was observed. Among 18 426 patients with longitudinal ctDNA measurements, 13.3% had discordant trajectories between MTM/ml and mVAF at subsequent time points. In metastatic patients receiving immunotherapy (N = 51), changes in ctDNA levels expressed both in MTM/ml and mVAF showed a statistically significant association with progression-free survival; however, the correlation with MTM/ml was numerically stronger.
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Cheng M, Zheng X, Wei J, Liu M. Current state and challenges of emerging biomarkers for immunotherapy in hepatocellular carcinoma (Review). Exp Ther Med 2023; 26:586. [PMID: 38023367 PMCID: PMC10665984 DOI: 10.3892/etm.2023.12285] [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: 03/22/2023] [Accepted: 08/29/2023] [Indexed: 12/01/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most prevalent form of primary liver cancer. According to the American Cancer Society, among patients diagnosed with advanced liver cancer, HCC has the sixth-highest incident rate, resulting in a poor prognosis. Surgery, radiofrequency ablation, transcatheter arterial chemoembolization, radiation, chemotherapy, targeted therapy and immunotherapy are the current treatment options available. Immunotherapy, which has emerged as an innovative treatment strategy over the past decade, is serving a vital role in the treatment of advanced liver cancer. Since only a small number of individuals can benefit from immunotherapy, biomarkers are required to help clinicians identify the target populations for this precision medicine. These biomarkers, such as PD-1/PD-L1, tumor mutational burden and circulating tumor DNA, can be used to investigate interactions between immune checkpoint inhibitors and tumors. The present review summarizes information on the currently available biomarkers used for immunotherapy and the challenges that are present.
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Affiliation(s)
- Mo Cheng
- Department of Medical Oncology, Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiufeng Zheng
- Department of Medical Oncology, Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Jing Wei
- Department of Medical Oncology, Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ming Liu
- Department of Medical Oncology, Gastric Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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Temilola DO, Adeola HA, Grobbelaar J, Chetty M. Liquid Biopsy in Head and Neck Cancer: Its Present State and Future Role in Africa. Cells 2023; 12:2663. [PMID: 37998398 PMCID: PMC10670726 DOI: 10.3390/cells12222663] [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: 10/10/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
The rising mortality and morbidity rate of head and neck cancer (HNC) in Africa has been attributed to factors such as the poor state of health infrastructures, genetics, and late presentation resulting in the delayed diagnosis of these tumors. If well harnessed, emerging molecular and omics diagnostic technologies such as liquid biopsy can potentially play a major role in optimizing the management of HNC in Africa. However, to successfully apply liquid biopsy technology in the management of HNC in Africa, factors such as genetic, socioeconomic, environmental, and cultural acceptability of the technology must be given due consideration. This review outlines the role of circulating molecules such as tumor cells, tumor DNA, tumor RNA, proteins, and exosomes, in liquid biopsy technology for the management of HNC with a focus on studies conducted in Africa. The present state and the potential opportunities for the future use of liquid biopsy technology in the effective management of HNC in resource-limited settings such as Africa is further discussed.
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Affiliation(s)
- Dada Oluwaseyi Temilola
- Department of Craniofacial Biology, Faculty of Dentistry, University of the Western Cape, Tygerberg Hospital, Cape Town 7505, South Africa;
| | - Henry Ademola Adeola
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, University of the Western Cape, Tygerberg Hospital, Cape Town 7505, South Africa;
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town 7925, South Africa
| | - Johan Grobbelaar
- Division of Otorhinolaryngology, Department of Surgical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, Cape Town 7505, South Africa;
| | - Manogari Chetty
- Department of Craniofacial Biology, Faculty of Dentistry, University of the Western Cape, Tygerberg Hospital, Cape Town 7505, South Africa;
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34
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Lu Y, Chen Y, Jiang Z, Ge Y, Yao R, Geng S, Zhang J, Chen F, Wang Y, Chen G, Yang D. Research progress of ferroptosis in Parkinson's disease: a bibliometric and visual analysis. Front Aging Neurosci 2023; 15:1278323. [PMID: 38035275 PMCID: PMC10682076 DOI: 10.3389/fnagi.2023.1278323] [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: 08/16/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023] Open
Abstract
Background In recent years, the role of ferroptosis in Parkinson's disease (PD) has become a research hotspot based on evidence of abnormal iron deposition and lipid peroxidation damage in the brains of PD patients. This study aims to examine the relevant research on ferroptosis and PD from a bibliometric perspective. Methods Original research and review articles related to ferroptosis and PD were retrieved from the Web of Science Core Collection (WOSCC) database. Statistical analysis and visualization of information including countries, institutions, authors, journals, and keywords of the included studies were conducted using the R software package "bibliometrix." Results A total of 414 articles met the inclusion criteria, averaging 37.86 citations per article. From 2012 to 2022, the average annual growth rate of research in this area was 63.44%. The corresponding authors of published articles were mainly affiliated with institutions in China, the United States, and Australia. Shanghai Jiao Tong University in China and the University of Melbourne in Australia emerged as the most active and influential institutions. The journal with the highest H-index and publication output was Free Radical Biology and Medicine. "Ferroptosis," "immunotherapy," "prognosis" and "microenvironment" were identified as high-frequency keywords, indicating current and future research directions in this field. Conclusion This bibliometric study provides insights into current research hotspots and emerging trends in the growing field of ferroptosis research related to PD. The high-frequency keywords identified highlight active areas of investigation involving methods, mechanisms, and populations of interest.
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Affiliation(s)
- Yangguang Lu
- The First School of Medicine, School of Information and Engineering, Wenzhou Medical University, Wenzhou, China
| | - Yiqun Chen
- The First School of Medicine, School of Information and Engineering, Wenzhou Medical University, Wenzhou, China
| | - Zihan Jiang
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yaoying Ge
- The First School of Medicine, School of Information and Engineering, Wenzhou Medical University, Wenzhou, China
| | - Ruotong Yao
- The First School of Medicine, School of Information and Engineering, Wenzhou Medical University, Wenzhou, China
| | - Shangze Geng
- The First School of Medicine, School of Information and Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jinxiu Zhang
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Feng Chen
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yukai Wang
- The Second School of Medicine, Wenzhou Medical University, Wenzhou, China
| | - Guangyong Chen
- Department of Neurology, The Third Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dehao Yang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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35
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Runkel A, Braig D, Bogner B, Schmid A, Lausch U, Boneberg A, Brugger Z, Eisenhardt A, Kiefer J, Pauli T, Boerries M, Fuellgraf H, Kurowski K, Bronsert P, Scholber J, Grosu AL, Rovedo P, Bamberg F, Eisenhardt SU, Jung M. Non-invasive monitoring of neoadjuvant radiation therapy response in soft tissue sarcomas by multiparametric MRI and quantification of circulating tumor DNA-A study protocol. PLoS One 2023; 18:e0285580. [PMID: 37910565 PMCID: PMC10619790 DOI: 10.1371/journal.pone.0285580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/03/2023] [Indexed: 11/03/2023] Open
Abstract
BACKGROUND Wide resection remains the cornerstone of localized soft-tissue sarcomas (STS) treatment. Neoadjuvant radiation therapy (NRT) may decrease the risk of local recurrences; however, its effectiveness for different histological STS subtypes has not been systematically investigated. The proposed prospective study evaluates the NRT response in STS using liquid biopsies and the correlation of multiparametric magnetic resonance imaging (mpMRI) with histopathology and immunohistochemistry. METHODS Patients with localized high-grade STS, who qualify for NRT, are included in this study. LIQUID BIOPSIES Quantification of circulating tumor DNA (ctDNA) in patient blood samples is performed by targeted next-generation sequencing. Soft-tissue sarcoma subtype-specific panel sequencing in combination with patient-specific exome sequencing allows the detection of individual structural variants and point mutations. Circulating free DNA is isolated from peritherapeutically collected patient plasma samples and ctDNA quantified therein. Identification of breakpoints is carried out using FACTERA. Bioinformatic analysis is performed using samtools, picard, fgbio, and the MIRACUM Pipeline. MPMRI Combination of conventional MRI sequences with diffusion-weighted imaging, intravoxel-incoherent motion, and dynamic contrast enhancement. Multiparametric MRI is performed before, during, and after NRT. We aim to correlate mpMRI data with the resected specimen's macroscopical, histological, and immunohistochemical findings. RESULTS Preliminary data support the notion that quantification of ctDNA in combination with tumor mass characterization through co-registration of mpMRI and histopathology can predict NRT response of STS. CLINICAL RELEVANCE The methods presented in this prospective study are necessary to assess therapy response in heterogeneous tumors and lay the foundation of future patient- and tumor-specific therapy concepts. These methods can be applied to various tumor entities. Thus, the participation and support of a wider group of oncologic surgeons are needed to validate these findings on a larger patient cohort.
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Affiliation(s)
- Alexander Runkel
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Berta-Ottenstein-Programme, University of Freiburg, Freiburg, Germany
| | - David Braig
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
- Division of Hand, Plastic and Aesthetic Surgery, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Balazs Bogner
- Faculty of Medicine, Department of Radiology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Adrian Schmid
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Ute Lausch
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Anika Boneberg
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Zacharias Brugger
- Faculty of Medicine, Department of Medicine I, Medical Center—University of Freiburg, Freiburg, Germany
| | - Anja Eisenhardt
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Jurij Kiefer
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Thomas Pauli
- Faculty of Medicine, Institute of Medical Bioinformatics, Medical Center—University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Faculty of Medicine, Institute of Medical Bioinformatics, Medical Center—University of Freiburg, Freiburg, Germany
| | - Hannah Fuellgraf
- Faculty of Medicine, Institute of Surgical Pathology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Konrad Kurowski
- Faculty of Medicine, Institute of Surgical Pathology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Faculty of Medicine, Institute of Surgical Pathology, Medical Center—University of Freiburg, Freiburg, Germany
- Tumorbank Comprehensive Cancer Center Freiburg, Medical Center—University of Freiburg, Freiburg, Germany
- Core Facility for Histopathology and Digital Pathology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Jutta Scholber
- Faculty of Medicine, Department of Radiation Oncology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Anca-Ligia Grosu
- Faculty of Medicine, Department of Radiation Oncology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Philipp Rovedo
- Faculty of Medicine, Department of Radiology, Medical Physics, Medical Center-University of Freiburg, Freiburg, Germany
| | - Fabian Bamberg
- Faculty of Medicine, Department of Radiology, Medical Center—University of Freiburg, Freiburg, Germany
| | - Steffen Ulrich Eisenhardt
- Faculty of Medicine, Department of Plastic and Hand Surgery, Medical Center—University of Freiburg, Freiburg, Germany
| | - Matthias Jung
- Faculty of Medicine, Berta-Ottenstein-Programme, University of Freiburg, Freiburg, Germany
- Faculty of Medicine, Department of Radiology, Medical Center—University of Freiburg, Freiburg, Germany
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Mun B, Kim R, Jeong H, Kang B, Kim J, Son HY, Lim J, Rho HW, Lim EK, Haam S. An immuno-magnetophoresis-based microfluidic chip to isolate and detect HER2-Positive cancer-derived exosomes via multiple separation. Biosens Bioelectron 2023; 239:115592. [PMID: 37603987 DOI: 10.1016/j.bios.2023.115592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/31/2023] [Accepted: 08/10/2023] [Indexed: 08/23/2023]
Abstract
Exosomes are useful for cancer diagnosis and monitoring. However, clinical samples contain impurities that complicate direct analyses of cancer-derived exosomes. Therefore, a microfluidic chip-based magnetically labeled exosome isolation system (MEIS-chip) was developed as a lab-on-a-chip platform for human epidermal growth factor receptor 2 (HER2)-positive cancer diagnosis and monitoring. Various magnetic nanoclusters (MNCs) were synthesized with different degrees of magnetization, and antibodies were introduced to capture HER2-overexpressing and common exosomes using immunoaffinity. MNC-bonded exosomes were separated into different exits according to their magnetization degrees. The MEIS-chip efficiently separated HER2-overexpressing exosomes from common exosomes that did not contain disease-related information. The simultaneous separation of HER2-and non-HER2-overexpressing exosomes provided a means of analyzing high-purity HER2-overexpressing exosomes while minimizing the contribution of non-target exosomes, reducing misdiagnosis risk. Notably, common exosomes served as a negative control for monitoring real-time changes in HER2 expression. These findings support the application of MEIS-chip for cancer diagnosis and treatment monitoring via effective exosome isolation.
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Affiliation(s)
- Byeonggeol Mun
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Ryunhyung Kim
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hyein Jeong
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Byunghoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Genetics and Aging Research Unit, McCance Center for Brain Health, Mass General Institute for Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, 114 16th Street, Charlestown, MA, 02129, USA
| | - Jinyoung Kim
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Hye Young Son
- Department of Radiology College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Jaewoo Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Medical Device Development Center, Osong Medical innovation foundation, 123, Osongsaengmyeong-ro, Chungcheongbuk-do, 28160, Republic of Korea
| | - Hyun Wook Rho
- Department of Radiology College of Medicine, Yonsei University, 50-1 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea; Department of Nanobiotechnology, KRIBB School of Biotechnology, University of Science and Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea; School of Pharmacy, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Seungjoo Haam
- Department of Chemical and Biomolecular Engineering, College of Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea.
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Leenanitikul J, Chanchaem P, Mankhong S, Denariyakoon S, Fongchaiya V, Arayataweegool A, Angspatt P, Wongchanapai P, Prapanpoj V, Chatamra K, Pisitkun T, Sriswasdi S, Wongkongkathep P. Concordance between whole exome sequencing of circulating tumor DNA and tumor tissue. PLoS One 2023; 18:e0292879. [PMID: 37878600 PMCID: PMC10599540 DOI: 10.1371/journal.pone.0292879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/02/2023] [Indexed: 10/27/2023] Open
Abstract
Next generation sequencing of circulating tumor DNA (ctDNA) has been used as a noninvasive alternative for cancer diagnosis and characterization of tumor mutational landscape. However, low ctDNA fraction and other factors can limit the ability of ctDNA analysis to capture tumor-specific and actionable variants. In this study, whole-exome sequencings (WES) were performed on paired ctDNA and tumor biopsy in 15 cancer patients to assess the extent of concordance between mutational profiles derived from the two source materials. We found that up to 16.4% ctDNA fraction can still be insufficient for detecting tumor-specific variants and that good concordance with tumor biopsy is consistently achieved at higher ctDNA fractions. Most importantly, ctDNA analysis can consistently capture tumor heterogeneity and detect key cancer-related genes even in a patient with both primary and metastatic tumors.
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Affiliation(s)
- Julanee Leenanitikul
- Bioinformatics and Computational Biology Program, Chulalongkorn University, Bangkok, Thailand
| | - Prangwalai Chanchaem
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Suwanan Mankhong
- Research Unit of Systems Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sikrit Denariyakoon
- The Queen Sirikit Center for Breast Cancer, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Valla Fongchaiya
- The Queen Sirikit Center for Breast Cancer, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Areeya Arayataweegool
- The Queen Sirikit Center for Breast Cancer, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Pattama Angspatt
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and the King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Ploytuangporn Wongchanapai
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine, Chulalongkorn University and the King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | | | - Kris Chatamra
- The Queen Sirikit Center for Breast Cancer, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Trairak Pisitkun
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sira Sriswasdi
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Computational Molecular Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Piriya Wongkongkathep
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Kiełbowski K, Żychowska J, Becht R. Anaplastic lymphoma kinase inhibitors-a review of anticancer properties, clinical efficacy, and resistance mechanisms. Front Pharmacol 2023; 14:1285374. [PMID: 37954850 PMCID: PMC10634320 DOI: 10.3389/fphar.2023.1285374] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023] Open
Abstract
Fusions and mutations of anaplastic lymphoma kinase (ALK), a tyrosine kinase receptor, have been identified in several neoplastic diseases. Rearranged ALK is a driver of tumorigenesis, which activates various signaling pathway associated with proliferation and survival. To date, several agents that target and inhibit ALK have been developed. The most studied ALK-positive disease is non-small cell lung cancer, and three generations of ALK tyrosine kinase inhibitors (TKIs) have been approved for the treatment of metastatic disease. Nevertheless, the use of ALK-TKIs is associated with acquired resistance (resistance mutations, bypass signaling), which leads to disease progression and may require a substitution or introduction of other treatment agents. Understanding of the complex nature and network of resistance mutations may allow to introduce sequential and targeted therapies. In this review, we aim to summarize the efficacy and safety profile of ALK inhibitors, describe off-target anticancer effects, and discuss resistance mechanisms in the context of personalized oncology.
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Affiliation(s)
| | | | - Rafał Becht
- Department of Clinical Oncology, Chemotherapy and Cancer Immunotherapy, Pomeranian Medical University, Szczecin, Poland
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39
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Farncombe KM, Wong D, Norman ML, Oldfield LE, Sobotka JA, Basik M, Bombard Y, Carile V, Dawson L, Foulkes WD, Malkin D, Karsan A, Parkin P, Penney LS, Pollett A, Schrader KA, Pugh TJ, Kim RH. Current and new frontiers in hereditary cancer surveillance: Opportunities for liquid biopsy. Am J Hum Genet 2023; 110:1616-1627. [PMID: 37802042 PMCID: PMC10577078 DOI: 10.1016/j.ajhg.2023.08.014] [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: 04/14/2023] [Revised: 08/15/2023] [Accepted: 08/22/2023] [Indexed: 10/08/2023] Open
Abstract
At least 5% of cancer diagnoses are attributed to a causal pathogenic or likely pathogenic germline genetic variant (hereditary cancer syndrome-HCS). These individuals are burdened with lifelong surveillance monitoring organs for a wide spectrum of cancers. This is associated with substantial uncertainty and anxiety in the time between screening tests and while the individuals are awaiting results. Cell-free DNA (cfDNA) sequencing has recently shown potential as a non-invasive strategy for monitoring cancer. There is an opportunity for high-yield cancer early detection in HCS. To assess clinical validity of cfDNA in individuals with HCS, representatives from eight genetics centers from across Canada founded the CHARM (cfDNA in Hereditary and High-Risk Malignancies) Consortium in 2017. In this perspective, we discuss operationalization of this consortium and early data emerging from the most common and well-characterized HCSs: hereditary breast and ovarian cancer, Lynch syndrome, Li-Fraumeni syndrome, and Neurofibromatosis type 1. We identify opportunities for the incorporation of cfDNA sequencing into surveillance protocols; these opportunities are backed by examples of earlier cancer detection efficacy in HCSs from the CHARM Consortium. We seek to establish a paradigm shift in early cancer surveillance in individuals with HCSs, away from highly centralized, regimented medical screening visits and toward more accessible, frequent, and proactive care for these high-risk individuals.
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Affiliation(s)
- Kirsten M Farncombe
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Derek Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Maia L Norman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Leslie E Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Julia A Sobotka
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Mark Basik
- Department of Surgery, McGill University Medical School, Montreal, QC, Canada; Department of Oncology, McGill University Medical School, Montreal, QC, Canada
| | - Yvonne Bombard
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada; Genomics Health Services Research Program, Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Victoria Carile
- Jewish General Hospital Stroll Cancer Prevention Centre, Montreal, QC, Canada
| | - Lesa Dawson
- Memorial University, St. John's, NL, Canada; Eastern Health Authority, St. John's, NL, Canada
| | - William D Foulkes
- Jewish General Hospital Stroll Cancer Prevention Centre, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - David Malkin
- Division of Hematology-Oncology, Hospital for Sick Children, Toronto, ON, Canada; Department of Pediatrics, University of Toronto, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | | | - Patricia Parkin
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada; Division of Pediatric Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | | | | | - Kasmintan A Schrader
- BC Cancer, Vancouver, BC, Canada; University of British Columbia, Vancouver, BC, Canada
| | - Trevor J Pugh
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
| | - Raymond H Kim
- Ontario Institute for Cancer Research, Toronto, ON, Canada; Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Sinai Health System, Toronto, ON, Canada; Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada; Department of Medicine, University of Toronto, Toronto, ON, Canada.
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40
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Wahab MRA, Palaniyandi T, Ravi M, Viswanathan S, Baskar G, Surendran H, Gangadharan SGD, Rajendran BK. Biomarkers and biosensors for early cancer diagnosis, monitoring and prognosis. Pathol Res Pract 2023; 250:154812. [PMID: 37741139 DOI: 10.1016/j.prp.2023.154812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/22/2023] [Accepted: 09/08/2023] [Indexed: 09/25/2023]
Abstract
Cancers continue to be of major concern due to their serious global socioeconomic impact, apart from the continued increase in the incidence of various cancer types. A major challenge that this disease poses is due to the low "early detection" rates which limit the therapeutic outcomes for the affected individuals. Current research has highlighted the discovering biomarkers that help in early cancer detection and the development of technologies for the detection and quantification of such biomarkers. Biomarkers range from proteins to nucleic acids, and can be specific to a particular cancer type. Detection and quantification of such biomarkers at low levels from biological samples is being made possible by the advent of developing biosensors and by using biomedical engineering technologies such as tumor-on-a-chip models. Here, we present biomarkers that can be helpful for the early detection of breast, colorectal, esophageal, lung, liver, ovarian, and prostate cancer. In addition, we discuss the potential of circulating tumor cell DNA (ctDNA) as an early diagnostic marker. Finally, biosensors available for the detection of cancer biomarkers, which is a recent advancement in this area of research, are discussed.
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Affiliation(s)
| | - Thirunavukkarasu Palaniyandi
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Chennai 600095; Department of Anatomy, Biomedical Research Unit and Laboratory Animal Centre, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Science, Saveetha University, Chennai, Tamil Nadu, India.
| | - Maddaly Ravi
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116, Tamil Nadu, India
| | - Sandhiya Viswanathan
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Chennai 600095
| | - Gomathy Baskar
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Chennai 600095
| | - Hemapreethi Surendran
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Chennai 600095
| | - S G D Gangadharan
- Department of Medical Oncology, Madras Medical College, R. G. G. G. H., Chennai, Tamil Nadu, India
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Yang T, Wang N, Wang F, Liu H, Shen F, Lv G. Refinement and validation of a comprehensive clinical diagnostic model (GAMAD) based on gender, age, multitarget circulating tumour DNA methylation signature and commonly used serological biomarkers for early detection of hepatocellular carcinoma: a multicentre, prospective observational study protocol. BMJ Open 2023; 13:e076467. [PMID: 37723113 PMCID: PMC10510880 DOI: 10.1136/bmjopen-2023-076467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/30/2023] [Indexed: 09/20/2023] Open
Abstract
INTRODUCTION Prompt detection of hepatocellular carcinoma (HCC) in patients with chronic liver diseases is critical for enhancing prognosis. Existing imaging techniques and serum markers fall short of clinical needs. This study aims to establish a non-invasive diagnostic model for early HCC detection in the Chinese population. METHODS AND ANALYSIS This prospective, multicentre, observational study will enrol 2000 participants, including HCC patients, those with chronic liver diseases (hepatitis, cirrhosis and benign liver space-occupying lesions), and healthy individuals. The study will collect demographic data and blood samples, which will be used to test α-fetoprotein (AFP), des-γ-carboxy-prothrombin (DCP) and circulating tumour DNA (ctDNA) methylation. The GAMAD (Gender+Age+Methylation+AFP+DCP) model involving gender, age, ctDNA methylation signature, AFP and DCP will be developed and blindly validated in training and validation sets (1400 and 600 cases, respectively). Primary endpoints include sensitivity, specificity and accuracy (receiver operating characteristic curves; area under the curve value) of GAMAD for HCC and/or high-risk HCC groups. Secondary endpoints involve comparing GAMAD with the established GALAD (Gender+Age+AFP-L3+AFP+DCP) model and each blood index (AFP, DCP and methylation signature) to evaluate: (1) GAMAD's clinical utility for HCC patients in all stages according to different staging systems; (2) GAMAD's discrimination ability for patients in various subgroups, including liver cirrhosis (LC) related HCC and LC, hepatitis B virus (HBV) related HCC and HBV, hepatitis C virus (HCV) related HCC and HCV, and non-alcoholic fatty liver disease (NAFLD) related HCC and NAFLD. ETHICS AND DISSEMINATION This trial has been approved by the Medical Ethics Committees of the First Hospital of Jilin University (#22K073-001), the Eastern Hepatobiliary Surgery Hospital, Naval Medical University (#EHBHKY2023-H0003-P001) and Tianjin Third Central Hospital (#IRB2023-007-01). All participants in the trial will provide written informed consent. Results of this study will be disseminated in peer-reviewed scientific journals and at conferences nationally and internationally. TRIAL REGISTRATION NUMBER NCT05626985.
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Affiliation(s)
- Tian Yang
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Nanya Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Fengmei Wang
- Department of Gastroenterology and Hepatology, Tianjin Third Central Hospital, Tianjin, China
| | - Hongmei Liu
- Department of Medical Affairs, Singlera Genomics (Shanghai) Ltd, Shanghai, China
| | - Feng Shen
- Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
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Dean EA, Kimmel GJ, Frank MJ, Bukhari A, Hossain NM, Jain MD, Dahiya S, Miklos DB, Altrock PM, Locke FL. Circulating tumor DNA adds specificity to PET after axicabtagene ciloleucel in large B-cell lymphoma. Blood Adv 2023; 7:4608-4618. [PMID: 37126659 PMCID: PMC10448428 DOI: 10.1182/bloodadvances.2022009426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 03/07/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023] Open
Abstract
We examined the meaning of metabolically active lesions on 1-month restaging nuclear imaging of patients with relapsed/refractory large B-cell lymphoma receiving axicabtagene ciloleucel (axi-cel) by assessing the relationship between total metabolic tumor volume (MTV) on positron emission tomography (PET) scans and circulating tumor DNA (ctDNA) in the plasma. In this prospective multicenter sample collection study, MTV was retrospectively calculated via commercial software at baseline, 1, and 3 months after chimeric antigen receptor (CAR) T-cell therapy; ctDNA was available before and after axi-cel administration. Spearman correlation coefficient (rs) was used to study the relationship between the variables, and a mathematical model was constructed to describe tumor dynamics 1 month after CAR T-cell therapy. The median time between baseline scan and axi-cel infusion was 33 days (range, 1-137 days) for all 57 patients. For 41 of the patients with imaging within 33 days of axi-cel or imaging before that time but no bridging therapy, the correlation at baseline became stronger (rs, 0.61; P < .0001) compared with all patients (rs, 0.38; P = .004). Excluding patients in complete remission with no measurable residual disease, ctDNA and MTV at 1 month did not correlate (rs, 0.28; P = .11) but correlated at 3 months (rs, 0.79; P = .0007). Modeling of tumor dynamics, which incorporated ctDNA and inflammation as part of MTV, recapitulated the outcomes of patients with positive radiologic 1-month scans. Our results suggested that nonprogressing hypermetabolic lesions on 1-month PET represent ongoing treatment responses, and their composition may be elucidated by concurrently examining the ctDNA.
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Affiliation(s)
- Erin A. Dean
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer and Research Institute, Tampa, FL
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, FL
| | - Gregory J. Kimmel
- Department of Integrated Mathematical Oncology, Moffitt Research Institute, Tampa, FL
| | - Matthew J. Frank
- Division of Blood and Stem Cell Transplantation, Department of Medicine, Stanford University, Stanford, CA
| | - Ali Bukhari
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD
- Division of Hematology and Oncology, Department of Internal Medicine, Wright-Patterson Medical Center, Wright-Patterson Air Force Base, OH
| | - Nasheed M. Hossain
- Cell Therapy and Transplant Program, Division of Hematology/Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Michael D. Jain
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer and Research Institute, Tampa, FL
| | - Saurabh Dahiya
- Division of Blood and Stem Cell Transplantation, Department of Medicine, Stanford University, Stanford, CA
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD
| | - David B. Miklos
- Division of Blood and Stem Cell Transplantation, Department of Medicine, Stanford University, Stanford, CA
| | - Philipp M. Altrock
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Ploen, Germany
| | - Frederick L. Locke
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer and Research Institute, Tampa, FL
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Biglari N, Soltani-Zangbar MS, Mohammadian J, Mehdizadeh A, Abbasi K. ctDNA as a novel and promising approach for cancer diagnosis: a focus on hepatocellular carcinoma. EXCLI JOURNAL 2023; 22:752-780. [PMID: 37720239 PMCID: PMC10502204 DOI: 10.17179/excli2023-6277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 07/26/2023] [Indexed: 09/19/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most prevalent forms of cancer worldwide. Therefore, it is essential to diagnose and treat HCC patients promptly. As a novel discovery, circulating tumor DNA (ctDNA) can be used to analyze the tumor type and the cancer location. Additionally, ctDNA assists the cancer stage determination, which enables medical professionals to provide patients with the most appropriate treatment. This review will discuss the HCC-related mutated genes diagnosed by ctDNA. In addition, we will introduce the different and the most appropriate ctDNA diagnosis approaches based on the facilities.
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Affiliation(s)
- Negin Biglari
- Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mohammad Sadegh Soltani-Zangbar
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jamal Mohammadian
- School of Advanced Medical Science, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Mehdizadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khadijeh Abbasi
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Shegekar T, Vodithala S, Juganavar A. The Emerging Role of Liquid Biopsies in Revolutionising Cancer Diagnosis and Therapy. Cureus 2023; 15:e43650. [PMID: 37719630 PMCID: PMC10505053 DOI: 10.7759/cureus.43650] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 08/17/2023] [Indexed: 09/19/2023] Open
Abstract
A potential non-invasive technique for identifying and tracking cancer is a liquid biopsy. This review article provides a comprehensive overview of the principles, applications, and challenges associated with liquid biopsies. The circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), exosomes, and microRNAs are just a few of the biomarkers we cover in this article that are discovered in liquid biopsies. The clinical application of liquid biopsies in many stages of cancer management, including early cancer identification, therapy selection and response monitoring, and minimum residual illness, is also investigated. The technical advancements in liquid biopsy techniques, including digital polymerase chain reaction (dPCR) and next-generation sequencing (NGS), have improved the sensitivity and specificity of biomarker identification. Liquid biopsies require assistance with cost-effectiveness, sensitivity, and standardisation despite the potential benefits. We talk about these restrictions and potential solutions. In conclusion, liquid biopsies revolutionise personalised therapies and cancer diagnostics by providing a real-time, non-invasive tool for characterising and monitoring tumours. It will be possible to expand the use of liquid biopsies in clinical practises by having a better understanding of their current state and predicted future developments.
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Affiliation(s)
- Tejas Shegekar
- Department of Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Sahitya Vodithala
- Department of Pathology and Laboratory Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
| | - Anup Juganavar
- Department of Medicine, Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education and Research, Wardha, IND
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Liu X, Zhang M, Shao C, Sun H, Zhang B, Guo Z, Sun J, Qi F, Zhang Y, Niu H, Sun W. Blood- and Urine-Based Liquid Biopsy for Early-Stage Cancer Investigation: Taken Clear Renal Cell Carcinoma as a Model. Mol Cell Proteomics 2023; 22:100603. [PMID: 37348606 PMCID: PMC10416070 DOI: 10.1016/j.mcpro.2023.100603] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 06/12/2023] [Accepted: 06/18/2023] [Indexed: 06/24/2023] Open
Abstract
Liquid biopsy is a noninvasive technique that can provide valuable information for disease characterization by using biofluids as a source of biomarkers. Proteins found in biofluids can offer a wealth of information for understanding pathological processes. In this study, we used early-stage clear cell renal cell carcinoma (ccRCC) as a model to explore the proteomic relationships among tissue, plasma, and urine. We analyzed samples of tumor tissue, plasma, and urine from a cohort of 27 ccRCC patients with T1-2 stage and 27 matched healthy controls, using liquid chromatography-mass spectrometry (LC-MS) for proteomic analysis. We integrated the differential proteins found in the three types of samples to explore ccRCC-associated molecular changes. Our results showed that both plasma and urine proteomes could reflect functional changes in tumor tissue. In plasma, cytoskeletal proteins and metabolic enzymes were differentially expressed, while in urine, adhesion molecules and defense proteins showed differential levels. The differential proteins found in plasma and urine both reflect the binding and catalytic activity of tumor tissue. Additionally, proteins only changed in biofluids could reflect body immune response changes, with plasma proteins involved in actin cytoskeleton and oxidative stress, and urine proteins involved in granulocyte adhesion and leukocyte extravasation signaling. Plasma and urine proteins could effectively distinguish RCC from control, with good performances (plasma/urine: 92.6%/92.6% specificity, 96.3%/92.6% sensitivity, and an area under the curve of 0.981/0.97). In conclusion, biofluids could not only reflect functional changes in tumor tissue but also reflect changes in the body's immune response. These findings will benefit the understanding of body biomarkers in tumors and the discovery of potential disease biomarkers.
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Affiliation(s)
- Xiaoyan Liu
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Mingxin Zhang
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Chen Shao
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China; Bioinformatics Department, DeepKinase Biotechnologies, Ltd, Beijing, China
| | - Haidan Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Binbin Zhang
- Department of Pharmacy, No.79 Army Group Hospital of People's Liberation Army Ground Force, Liaoyang, China
| | - Zhengguang Guo
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Jiameng Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Feng Qi
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Yushi Zhang
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
| | - Haitao Niu
- Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China.
| | - Wei Sun
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China.
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Tran TO, Lam LHT, Le NQK. Hyper-methylation of ABCG1 as an epigenetics biomarker in non-small cell lung cancer. Funct Integr Genomics 2023; 23:256. [PMID: 37523012 DOI: 10.1007/s10142-023-01185-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/01/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most prevalent histological type of lung cancer and the leading cause of death globally. Patients with NSCLC have a poor prognosis for various factors, and a late diagnosis is one of them. The DNA methylation of CpG island sequences found in the promoter regions of tumor suppressor genes has recently received attention as a potential biomarker of human cancer. In this study, we report DNA methylation changes of the adenosine triphosphate (ATP)-binding cassette transporter G1 (ABCG1), which belongs to the ATP cassette transporter family in NSCLC patients. Our results demonstrate that ABCG1 is hyper-methylation in NSCLC samples, and these changes are negatively correlated to gene and protein expression. Furthermore, the expression of the ABCG1 gene is significantly associated with the survival time of lung adenocarcinoma (LUAD) patients; however, it did not show a correlation to overall survival (OS) of lung squamous cell carcinoma (LUSC) patients. Notably, we found ABCG1 methylation status at locus cg20214535 is strongly associated with the survival time and consistently observed hyper-methylation in LUAD samples. This novel finding suggests ABCG1 is a potential candidate for targeted therapy in lung cancer via this specific probe. In addition, we illustrate the protein-protein interaction (PPI) of ABCG1 with other proteins and the strong communication of ABCG1 with immune cells.
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Affiliation(s)
- Thi-Oanh Tran
- International Ph.D. Program in Cell Therapy and Regenerative Medicine, College of Medicine, Taipei Medical University, 110, Taipei, Taiwan
- AIBioMed Research Group, Taipei Medical University, Taipei, 110, Taiwan
- Hematology and Blood Transfusion Center, Bach Mai Hospital, No. 78, Giai Phong street, Hanoi, Vietnam
| | - Luu Ho Thanh Lam
- Department of Pediatrics, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Khanh Le
- AIBioMed Research Group, Taipei Medical University, Taipei, 110, Taiwan.
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan.
- Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei, 110, Taiwan.
- Translational Imaging Research Center, Taipei Medical University Hospital, Taipei, 110, Taiwan.
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Goyal R, Wassie MM, Winter JM, Lathlean TJ, Young GP, Symonds EL. Progress in the field of noninvasive diagnostics for colorectal cancer: a systematic review for the accuracy of blood-based biomarkers for detection of advanced pre-cancerous lesions. Expert Rev Mol Diagn 2023; 23:1233-1250. [PMID: 38044883 DOI: 10.1080/14737159.2023.2290646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/22/2023] [Indexed: 12/05/2023]
Abstract
BACKGROUND Early detection of pre-cancerous adenomas through screening can reduce colorectal cancer (CRC) incidence. Fecal immunochemical tests are commonly used, but have limited sensitivity for pre-cancerous lesions. Blood-based screening may improve test sensitivity. This systematic review and meta-analysis was conducted to evaluate the accuracy of blood-based biomarkers for detection of advanced pre-cancerous lesions. RESEARCH DESIGN AND METHODS We present the accuracy of blood-based biomarkers for the detection of advanced pre-cancerous lesions. EMBASE, Web of Science and PubMed databases were searched, with study populations limited to adults diagnosed with advanced pre-cancerous lesions at colonoscopy, who had a blood-based biomarker test analyzed with reports of sensitivity and specificity. RESULTS 69 studies were identified, which assessed 133 unique biomarkers sets. The best performing test was a panel of 6 miRNAs, with a sensitivity of 95% and specificity of 90% for advanced pre-cancerous lesions. Only 6 biomarkers demonstrated sensitivity ≥ 50% and specificity ≥ 90% for the detection of advanced pre-cancerous lesions. CONCLUSION Many different blood-based biomarkers have been assessed for detection of advanced pre-cancerous lesions, but few have progressed beyond the discovery stage. While some biomarkers have reported high sensitivity and specificity, larger prospective studies in unbiased intended-use screening populations are required for validation.
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Affiliation(s)
- Rishabh Goyal
- Department of Medicine, College of Medicine and Public Health, Flinders University, Bedford Park, Australia
| | - Molla M Wassie
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
| | - Jean M Winter
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
| | - Timothy Jh Lathlean
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
- ROSA Research Centre, South Australian Health and Medical Research Institue, Adelaide, Australia
| | - Graeme P Young
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
| | - Erin L Symonds
- Cancer Research, Flinders Health and Medical Research Institute, Flinders University, Bedford Park, Australia
- Gastroenterology Department, Flinders Medical Centre, Bedford Park, Australia
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Raei N, Safaralizadeh R, Latifi-Navid S. Clinical application of circulating tumor DNA in metastatic cancers. Expert Rev Mol Diagn 2023; 23:1209-1220. [PMID: 37797209 DOI: 10.1080/14737159.2023.2268008] [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: 04/07/2023] [Accepted: 10/04/2023] [Indexed: 10/07/2023]
Abstract
INTRODUCTION Advances in genomics have facilitated the application of cell-free DNA (cfDNA) and circulating tumor DNA (ctDNA) in phase II and phase III clinical trials. The various mutations of cfDNA/ctDNA have been correlated with clinical features. Advances in next-generation sequencing (NGS) and digital droplet PCR have paved the way for identifying cfDNA/ctDNA mutations. AREAS COVERED Herein, the biology of ctDNA and its function in clinical application in metastasis, which may lead to improved clinical management of metastatic cancer patients, are comprehensively reviewed. EXPERT OPINION Metastatic cancer ctDNA shows the greatest frequency of mutations in TP53, HER-2, KRAS, and EGFR genes (alteration frequency of > 50%). Therefore, identifying key mutations frequently present in metastatic cancers can help identify patients with pre-malignant tumors before cancer progression. Studying ctDNA can help determine the prognosis and select appropriate treatments for affected patients. Nevertheless, the obstacles to detecting and analyzing ctDNA should be addressed before translation into routine practice. Also, more clinical trials should be conducted to study the significance of ctDNA in commonly diagnosed malignancies. Given the recent advances in personalized anti-neoplastic treatments, further studies are needed to detect a panel of ctDNA and patient-specific ctDNA for various cancers.
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Affiliation(s)
- Negin Raei
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Reza Safaralizadeh
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
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Ahmad A, Imran M, Ahsan H. Biomarkers as Biomedical Bioindicators: Approaches and Techniques for the Detection, Analysis, and Validation of Novel Biomarkers of Diseases. Pharmaceutics 2023; 15:1630. [PMID: 37376078 DOI: 10.3390/pharmaceutics15061630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
A biomarker is any measurable biological moiety that can be assessed and measured as a potential index of either normal or abnormal pathophysiology or pharmacological responses to some treatment regimen. Every tissue in the body has a distinct biomolecular make-up, which is known as its biomarkers, which possess particular features, viz., the levels or activities (the ability of a gene or protein to carry out a particular body function) of a gene, protein, or other biomolecules. A biomarker refers to some feature that can be objectively quantified by various biochemical samples and evaluates the exposure of an organism to normal or pathological procedures or their response to some drug interventions. An in-depth and comprehensive realization of the significance of these biomarkers becomes quite important for the efficient diagnosis of diseases and for providing the appropriate directions in case of multiple drug choices being presently available, which can benefit any patient. Presently, advancements in omics technologies have opened up new possibilities to obtain novel biomarkers of different types, employing genomic strategies, epigenetics, metabolomics, transcriptomics, lipid-based analysis, protein studies, etc. Particular biomarkers for specific diseases, their prognostic capabilities, and responses to therapeutic paradigms have been applied for screening of various normal healthy, as well as diseased, tissue or serum samples, and act as appreciable tools in pharmacology and therapeutics, etc. In this review, we have summarized various biomarker types, their classification, and monitoring and detection methods and strategies. Various analytical techniques and approaches of biomarkers have also been described along with various clinically applicable biomarker sensing techniques which have been developed in the recent past. A section has also been dedicated to the latest trends in the formulation and designing of nanotechnology-based biomarker sensing and detection developments in this field.
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Affiliation(s)
- Anas Ahmad
- Julia McFarlane Diabetes Research Centre (JMDRC), Department of Microbiology, Immunology and Infectious Diseases, Snyder Institute for Chronic Diseases, Hotchkiss Brain Institute, Cumming School of Medicine, Foothills Medical Centre, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mohammad Imran
- Therapeutics Research Group, Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane 4102, Australia
| | - Haseeb Ahsan
- Department of Biochemistry, Faculty of Dentistry, Jamia Millia Islamia, New Delhi 110025, India
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Li M, Liu T, Cheng W, Jin H, Wang X. A test of miR-128-3p and miR-33a-5p in serum exosome as biomarkers for auxiliary diagnosis of non-small cell lung cancer. J Thorac Dis 2023; 15:2616-2626. [PMID: 37324093 PMCID: PMC10267929 DOI: 10.21037/jtd-23-398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 05/10/2023] [Indexed: 06/17/2023]
Abstract
Background Lung cancer is the malignant tumor with the highest incidence and mortality rate in the world today, and non-small cell lung cancer (NSCLC) is its most common type. However, there is still a paucity of specific tumor markers for lung cancer screening. Herein, we detected and compared the levels of miR-128-3p and miR-33a-5p in serum exosomes of NSCLC patients and healthy volunteers, with the aim of identifying suitable exosomal microRNAs (miRNAs) as tumor biomarkers, and explored their value in the auxiliary diagnosis of NSCLC. Methods All participants were recruited from September 1, 2022 to December 30, 2022, and met the inclusion criteria. The case group included 20 patients with lung nodules who were highly suspected of having lung cancer (two cases were excluded). A total of 18 healthy volunteers (control group) were also enrolled. Blood samples were collected in both the case group before surgery and in the control group. Quantitative real-time polymerase chain reaction method was used to detect the expression of miR-128-3p and miR-33a-5p in serum exosomes. The main indicators of statistical analysis included the area under the receiver operating characteristic curve (AUC), sensitivity, and specificity. Results Compared with the healthy control group, the NSCLC case group had significantly lower expression levels of serum exosome miR-128-3p and miR-33a-5p (P<0.01, P<0.001), and there was a significant positive correlation between the two exosome miRNAs (r=0.848, P<0.01). The AUC values of miR-128-3p alone and miR-33a-5p alone in distinguishing case group and control group were 0.789 [95% confidence interval (CI): 0.637-0.940; sensitivity: 61.1%; specificity: 94.4%; P=0.003] and 0.821 (95% CI: 0.668-0.974; sensitivity: 77.8%; specificity: 83.3%; and P=0.001), respectively. The combination of miR-128-3p and miR-33a-5p had an AUC of 0.855 (95% CI: 0.719-0.991; P<0.001) for distinguishing case group and control group, which was greater than the AUC values of miR-128-3p alone and miR-33a-5p alone (cut-off value: 0.034; sensitivity: 83.3%; and specificity: 88.9%). However, there was no significant difference in the AUC among these three groups (P>0.05). Conclusions Serum exosome miR-128-3p and miR-33a-5p showed good performance in NSCLC screening and may be used as new biomarkers for large-scale NSCLC screening.
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Affiliation(s)
- Mengxing Li
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Tao Liu
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Wen Cheng
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Hai Jin
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Xiaowei Wang
- Department of Thoracic Surgery, Changhai Hospital, Second Military Medical University, Shanghai, China
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