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Kim SH, Weigelt B. Circulating cell-free (cf)DNA analysis: Current technologies and applications in gynecologic cancer. Gynecol Oncol Rep 2024; 54:101431. [PMID: 38947418 PMCID: PMC11211888 DOI: 10.1016/j.gore.2024.101431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/04/2024] [Accepted: 06/09/2024] [Indexed: 07/02/2024] Open
Abstract
Cell-free DNA (cfDNA) analysis has several promising clinical applications in the management of cancer patients, with clinical validity established in different types of solid tumors (e.g., lung, breast, and colon cancer). Cancers harbor unique genetic alterations that can be detected in the plasma and other bodily fluids of cancer patients, constituting an alternate source of tumor-derived DNA. Technologic advances and wide-spread availability of next-generation sequencing (NGS) have made sequencing analysis of circulating tumor DNA (ctDNA) possible, employing both off-the-shelf and personalized tumor-informed panels. Tumor size, disease burden and high-grade histologic types have been shown to correlate with ctDNA levels across multiple solid cancer types. Detection of tumor-derived genetic alterations in plasma-derived cfDNA can facilitate diagnosis, guide treatment selection, and serve as a biomarker for treatment response and prognostication. Molecular residual disease (MRD) is at the forefront of cfDNA analysis, with implications in treatment de-escalation/ escalation in the neoadjuvant and adjuvant settings. The development of cfDNA analysis in early detection of cancers is under active investigation. Proof-of-principles studies in gynecologic cancers have demonstrated feasibility and potential for innovation in cancers lacking specific biomarkers, including the tracking of human papillomavirus (HPV) cfDNA in patients with cervical cancer. In this review, we outline the assays currently available for cfDNA sequencing/ ctDNA detection, the role of cfDNA analysis in clinical decision-making and the current status and potential clinical uses of cfDNA research in gynecologic cancers.
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Affiliation(s)
- Sarah H Kim
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Yubin LI, Xiaoyan LI. [Advances in Clinical Application of Cerebrospinal Fluid Circulating Tumor DNA
in Leptomeningeal Metastasis of Non-small Cell Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2024; 27:376-382. [PMID: 38880925 PMCID: PMC11183312 DOI: 10.3779/j.issn.1009-3419.2024.102.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Indexed: 06/18/2024]
Abstract
Leptomeningeal metastasis (LM) is a lethal complication of malignant tumors, with an incidence rate of 3%-5% among patients with non-small cell lung cancer (NSCLC). LM poses significant challenges in diagnosis, has poor prognosis, limited treatment options, and lacks standardized criteria for evaluating therapeutic efficacy, making it a difficult aspect of NSCLC management. Circulating tumor DNA (ctDNA), shed from tumor cells and carrying cancer-related information, holds significant value in precision oncology. Cerebrospinal fluid (CSF), present in the subarachnoid space of the brain, the spinal cord, and the central canal, and in direct contact with meningeal tissues, serves as the fluid medium that best reflects the genetic characteristics of LM. In recent years, CSF ctDNA has become a focal point due to its multi-omics features, playing a crucial role in the management of central nervous system (CNS) metastatic tumors. Its applications span the entire continuum of care, including aiding in diagnosis, assessing treatment response, predicting prognosis, and analyzing resistance mechanisms. This article provides a concise overview of CSF ctDNA detection techniques and their clinical applications in patients with NSCLC-LM.
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Spagnolo CC, Pepe F, Ciappina G, Nucera F, Ruggeri P, Squeri A, Speranza D, Silvestris N, Malapelle U, Santarpia M. Circulating biomarkers as predictors of response to immune checkpoint inhibitors in NSCLC: Are we on the right path? Crit Rev Oncol Hematol 2024; 197:104332. [PMID: 38580184 DOI: 10.1016/j.critrevonc.2024.104332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
Immune checkpoints inhibitors (ICIs) have markedly improved the therapeutic management of advanced NSCLC and, more recently, they have demonstrated efficacy also in the early-stage disease. Despite better survival outcomes with ICIs compared to standard chemotherapy, a large proportion of patients can derive limited clinical benefit from these agents. So far, few predictive biomarkers, including the programmed death-ligand 1 (PD-L1), have been introduced in clinical practice. Therefore, there is an urgent need to identify novel biomarkers to select patients for immunotherapy, to improve efficacy and avoid unnecessary toxicity. A deeper understanding of the mechanisms involved in antitumor immunity and advances in the field of liquid biopsy have led to the identification of a wide range of circulating biomarkers that could potentially predict response to immunotherapy. Herein, we provide an updated overview of these circulating biomarkers, focusing on emerging data from clinical studies and describing modern technologies used for their detection.
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Affiliation(s)
- Calogera Claudia Spagnolo
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina 98122, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Via S. Pansini, Naples 80131, Italy
| | - Giuliana Ciappina
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina 98122, Italy
| | - Francesco Nucera
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina 98122, Italy
| | - Paolo Ruggeri
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina 98122, Italy
| | - Andrea Squeri
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina 98122, Italy
| | - Desirèe Speranza
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina 98122, Italy
| | - Nicola Silvestris
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina 98122, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Via S. Pansini, Naples 80131, Italy
| | - Mariacarmela Santarpia
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina 98122, Italy.
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Efthymiou V, Queenan N, Haas M, Naegele S, Goss D, Faden DL. Circulating Tumor DNA in the Immediate Postoperative Setting. Ann Surg Oncol 2024; 31:2319-2325. [PMID: 38190058 DOI: 10.1245/s10434-023-14860-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/17/2023] [Indexed: 01/09/2024]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as an accurate real-time biomarker of disease status across many solid tumor types. Most studies evaluating the utility of ctDNA have focused on time points weeks to months after surgery, which, for many cancer types, is significantly later than decision-making time points for adjuvant treatment. In this systematic review, we summarize the state of the literature on the feasibility of using ctDNA as a biomarker in the immediate postoperative period. METHODS We performed a systematic review evaluating the early kinetics, defined here as 3 days of ctDNA in patients who underwent curative-intent surgery. RESULTS Among the 2057 studies identified, eight cohort studies met the criteria for evaluation. Across six different cancer types, all studies showed an increased risk of cancer recurrence in patients with detectable ctDNA in the immediate postoperative period. CONCLUSION While ctDNA clearance kinetics appear to vary based on tumor type, across all studies detectable ctDNA after surgery was predictive of recurrence, suggesting early postoperative time points could be feasibly used for determining minimal residual disease. However, larger studies need to be performed to better understand the precise kinetics of ctDNA clearance across different cancer types as well as to determine optimal postoperative time points.
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Affiliation(s)
- Vasileios Efthymiou
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Natalia Queenan
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Markus Haas
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Saskia Naegele
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Deborah Goss
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA
| | - Daniel L Faden
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Kim B, Kim Y, Cho JY, Lee KA. Identification of Potential Genomic Alterations Using Pan-Cancer Cell-Free DNA Next-Generation Sequencing in Patients With Gastric Cancer. Ann Lab Med 2024; 44:164-173. [PMID: 37903652 PMCID: PMC10628753 DOI: 10.3343/alm.2023.0187] [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: 05/03/2023] [Revised: 06/27/2023] [Accepted: 09/12/2023] [Indexed: 11/01/2023] Open
Abstract
Background Molecular cancer profiling may lead to appropriate trials for molecularly targeted therapies. Cell-free DNA (cfDNA) is a promising diagnostic and/or prognostic biomarker in gastric cancer (GC). We characterized somatic genomic alterations in cfDNA of patients with GC. Methods Medical records and cfDNA data of 81 patients diagnosed as having GC were reviewed. Forty-nine and 32 patients were tested using the Oncomine Pan-Cancer Cell-Free Assay on the Ion Torrent platform and AlphaLiquid 100 kit on the Illumina platform, respectively. Results Tier I or II alterations were detected in 64.2% (52/81) of patients. Biomarkers for potential targeted therapy were detected in 55.6% of patients (45/81), and clinical trials are underway. ERBB2 amplification is actionable and was detected in 4.9% of patients (4/81). Among biomarkers showing potential for possible targeted therapy, TP53 mutation (38.3%, 35 variants in 31 patients, 31/81) and FGFR2 amplification (6.2%, 5/81) were detected the most. Conclusions Next-generation sequencing of cfDNA is a promising technique for the molecular profiling of GC. Evidence suggests that cfDNA analysis can provide accurate and reliable information on somatic genomic alterations in patients with GC, potentially replacing tissue biopsy as a diagnostic and prognostic tool. Through cfDNA analysis for molecular profiling, it may be possible to translate the molecular classification into therapeutic targets and predictive biomarkers, leading to personalized treatment options for patients with GC in the future.
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Affiliation(s)
- Boyeon Kim
- Division of Biotechnology, Invites BioCore Co. Ltd., Yongin, Korea
- Genome Service Development, Invites Genomics Co. Ltd., Jeju, Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Yong Cho
- Division of Medical Oncology, Department of Internal Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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Aquino IMC, Pascut D. Liquid biopsy: New opportunities for precision medicine in hepatocellular carcinoma care. Ann Hepatol 2024; 29:101176. [PMID: 37972709 DOI: 10.1016/j.aohep.2023.101176] [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: 08/25/2023] [Accepted: 10/18/2023] [Indexed: 11/19/2023]
Abstract
Liquid biopsy, specifically the analysis of circulating tumor DNA (ctDNA), offers a non-invasive approach for hepatocellular carcinoma (HCC) diagnosis and management. However, its implementation in the clinical setting is difficult due to challenges such as low ctDNA yield and difficulty in understanding the mutation signals from background noise. This review highlights the crucial role of artificial intelligence (AI) in addressing these limitations and in improving discoveries in the field of liquid biopsy for HCC care. Combining AI with liquid biopsy data can offer a promising future for the discovery of novel biomarkers and an AI-powered clinical decision support system (CDSS) can turn liquid biopsy into an important tool for personalized management of HCC. Despite the current challenges, the integration of AI shows promise to significantly improve patient outcomes and revolutionize the field of oncology.
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Affiliation(s)
- Inah Marie C Aquino
- College of Medicine, University of the Philippines Manila, Ermita, Manila, Metro Manila 1000, Philippines; Liver Cancer Unit, Fondazione Italiana Fegato - ONLUS, Basovizza, Trieste 34149, Italy
| | - Devis Pascut
- Liver Cancer Unit, Fondazione Italiana Fegato - ONLUS, Basovizza, Trieste 34149, Italy.
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Chantre-Justino M, Figueiredo MC, Alves G, Ornellas MHF. A pilot study on salivary HPV DNA detection to monitor active disease from patients with recurrent respiratory papillomatosis. Am J Otolaryngol 2024; 45:104157. [PMID: 38061173 DOI: 10.1016/j.amjoto.2023.104157] [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: 10/01/2023] [Accepted: 12/04/2023] [Indexed: 03/16/2024]
Abstract
PURPOSE Recurrent respiratory papillomatosis (RRP) is a human papillomavirus (HPV)-related disease affecting the upper airway and saliva could be an important non-invasive sampling source for viral screening and clinical monitoring. We investigated whether HPV DNA could be detected in saliva (cellular pellets and supernatant) from RRP patients and influence on clinical manifestation of the disease. MATERIALS AND METHODS In this pilot study, saliva samples from 14 RRP patients were obtained in preoperative condition (n = 7) and in disease-free interval (DFI; n = 7). Healthy donors (n = 14) were also included. HPV DNA was investigated by polymerase chain reaction (PCR)-based assays. RESULTS From cellular pellets, HPV-positive saliva was only detected from preoperative collections (5/7; 71.4 %) and showed a mean cycle threshold (Ct) value of 24.33 (±1.25), whereas all patients in DFI were HPV-negative (Ct ≥ 32.16), revealing significant difference between these two clinical moments (p = 0.021). Patients in DFI and healthy donors showed similar Ct values. From saliva supernatant, detectable HPV cell-free DNA (cfDNA) occurred in 42.9 % (3/7) and 57.1 % (4/7) of preoperative collections using the commercial cfDNA kits from Norgen and Qiagen, respectively. Salivary cfDNA size distribution obtained by TapeStation analysis showed a predominant size range of 150 to 400 bp in both patients and healthy controls, corresponding to mononucleosomal and dinucleosomal fragments. CONCLUSIONS In conclusion, HPV DNA screening in saliva (both cellular pellets and cfDNA) may have clinical utility to monitor active disease of RRP patients.
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Affiliation(s)
- Mariana Chantre-Justino
- Circulating Biomarkers Laboratory, Pathology Department, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil; Research Division, National Institute of Traumatology and Orthopaedics (INTO), Rio de Janeiro 20940-070, Brazil.
| | - Marcelo Cardoso Figueiredo
- Respiratory Endoscopy and Head and Neck Surgery Service at Hospital Federal de Bonsucesso, Rio de Janeiro 21041-030, Brazil
| | - Gilda Alves
- Circulating Biomarkers Laboratory, Pathology Department, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | - Maria Helena Faria Ornellas
- Circulating Biomarkers Laboratory, Pathology Department, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
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Ahluwalia P, Ballur K, Leeman T, Vashisht A, Singh H, Omar N, Mondal AK, Vaibhav K, Baban B, Kolhe R. Incorporating Novel Technologies in Precision Oncology for Colorectal Cancer: Advancing Personalized Medicine. Cancers (Basel) 2024; 16:480. [PMID: 38339232 PMCID: PMC10854941 DOI: 10.3390/cancers16030480] [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: 10/31/2023] [Revised: 01/10/2024] [Accepted: 01/13/2024] [Indexed: 02/12/2024] Open
Abstract
Colorectal cancer (CRC) is one of the most heterogeneous and deadly diseases, with a global incidence of 1.5 million cases per year. Genomics has revolutionized the clinical management of CRC by enabling comprehensive molecular profiling of cancer. However, a deeper understanding of the molecular factors is needed to identify new prognostic and predictive markers that can assist in designing more effective therapeutic regimens for the improved management of CRC. Recent breakthroughs in single-cell analysis have identified new cell subtypes that play a critical role in tumor progression and could serve as potential therapeutic targets. Spatial analysis of the transcriptome and proteome holds the key to unlocking pathogenic cellular interactions, while liquid biopsy profiling of molecular variables from serum holds great potential for monitoring therapy resistance. Furthermore, gene expression signatures from various pathways have emerged as promising prognostic indicators in colorectal cancer and have the potential to enhance the development of equitable medicine. The advancement of these technologies for identifying new markers, particularly in the domain of predictive and personalized medicine, has the potential to improve the management of patients with CRC. Further investigations utilizing similar methods could uncover molecular subtypes specific to emerging therapies, potentially strengthening the development of personalized medicine for CRC patients.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Kalyani Ballur
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Tiffanie Leeman
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Ashutosh Vashisht
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Harmanpreet Singh
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Nivin Omar
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Ashis K. Mondal
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
| | - Kumar Vaibhav
- Department of Neurosurgery, Augusta University, Augusta, GA 30912, USA;
| | - Babak Baban
- Departments of Neurology and Surgery, Augusta University, Augusta, GA 30912, USA;
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia at Augusta University, Augusta, GA 30912, USA; (P.A.); (K.B.); (T.L.); (A.V.); (H.S.); (N.O.); (A.K.M.)
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Matsuoka T, Yashiro M. Current status and perspectives of genetic testing in gastrointestinal cancer (Review). Oncol Lett 2024; 27:21. [PMID: 38058469 PMCID: PMC10696628 DOI: 10.3892/ol.2023.14155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/30/2023] [Indexed: 12/08/2023] Open
Abstract
Genetic testing has become widespread in daily medical care for gastrointestinal (GI) cancers. However, unlike breast cancer and non-small cell lung cancer, in which personalized medicine targeting various driver genes is standardized, the incidence of targeted gene abnormalities in GI cancers is low. Nevertheless, such abnormalities may be linked to therapeutic agents and the further development of therapeutic agents for personalized medicine for GI cancers is desired. A liquid biopsy is of great benefit in offering clinical decision support, in applications such as GI cancer screening, surgical interventions, monitoring disease status and enhancing patient survival outcomes, all of which would contribute to personalized medicine. Germline genetic testing is required for several types of GI cancer, which shows clinical indications of hereditary predisposition. The increasing use of multigene panel testing has redefined gene-cancer associations, and consequently the estimate of cancer risk that vary from low to high penetrance. Comprehensive genetic testing can enable the detection of novel treatment targets and the discovery of undefined multiple diagnostic/predictive markers, which may enhance the molecular-level understanding of GI cancers. Genetic testing can also aid the design of more appropriate and adequate genomic-driven therapies for patients who may benefit from other standardized therapeutic methods.
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Affiliation(s)
- Tasuku Matsuoka
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, Osaka 5458585, Japan
| | - Masakazu Yashiro
- Department of Molecular Oncology and Therapeutics, Osaka Metropolitan University Graduate School of Medicine, Osaka 5458585, Japan
- Institute of Medical Genetics, Osaka Metropolitan University, Osaka 5458585, Japan
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10
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Robinson SD, de Boisanger J, Pearl FMG, Critchley G, Rosenfelder N, Giamas G. A brain metastasis liquid biopsy: Where are we now? Neurooncol Adv 2024; 6:vdae066. [PMID: 38770219 PMCID: PMC11102938 DOI: 10.1093/noajnl/vdae066] [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] [Indexed: 05/22/2024] Open
Abstract
Brain metastases remain a challenging and feared complication for patients with cancer and research in this area has lagged behind research into metastases to other organs. Due to their location and the risks associated with neurosurgical biopsies, the biology underpinning brain metastases response to treatment and evolution over time remains poorly understood. Liquid biopsies are proposed to overcome many of the limitations present with tissue biopsies, providing a better representation of tumor heterogeneity, facilitating repeated sampling, and providing a noninvasive assessment of tumor biology. Several different liquid biopsy approaches have been investigated including circulating tumor cells, circulating tumor DNA, extracellular vesicles, and tumor-educated platelets; however, these have generally been less effective in assessing brain metastases compared to metastases to other organs requiring improved techniques to investigate these approaches, studies combining different liquid biopsy approaches and/or novel liquid biopsy approaches. Through this review, we highlight the current state of the art and define key unanswered questions related to brain metastases liquid biopsies.
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Affiliation(s)
- Stephen David Robinson
- Sussex Cancer Centre, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - James de Boisanger
- Neuro-Oncology Unit, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Frances M G Pearl
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
| | - Giles Critchley
- Department of Neurosurgery, University Hospitals Sussex NHS Foundation Trust, Brighton, UK
- Section of Neurosurgery, Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Nicola Rosenfelder
- Neuro-Oncology Unit, The Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Georgios Giamas
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, UK
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11
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Alahdal M, Perera RA, Moschovas MC, Patel V, Perera RJ. Current advances of liquid biopsies in prostate cancer: Molecular biomarkers. Mol Ther Oncolytics 2023; 30:27-38. [PMID: 37575217 PMCID: PMC10415624 DOI: 10.1016/j.omto.2023.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
Prostate cancer (PCa) incidence is increasing and endangers men's lives. Early detection of PCa could improve overall survival (OS) by preventing metastasis. The prostate-specific antigen (PSA) test is a popular screening method. Several advisory groups, however, warn against using the PSA test due to its high false positive rate, unsupported outcome, and limited benefit. The number of disease-related biopsies performed annually far outweighs the number of diagnoses. Thus, there is an urgent need to develop accurate diagnostic biomarkers to detect PCa and distinguish between aggressive and indolent cancers. Recently, non-coding RNA (ncRNA), circulating tumor DNA (ctDNA)/ctRNA, exosomes, and metabolomic biomarkers in the liquid biopsies (LBs) of patients with PCa showed significant differences and clinical benefits in diagnosis, prognosis, and monitoring response to therapy. The analysis of urinary exosomal ncRNA presented a substantial correlation among Exos-miR-375 downregulation, clinical T stage, and bone metastases of PCa. Furthermore, the expression of miR-532-5p in urine samples was a vital predictive biomarker of PCa progression. Thus, this review focuses on promising molecular and metabolomic biomarkers in LBs from patients with PCa. We thoroughly addressed the most recent clinical findings of LB biomarker use in diagnosing and monitoring PCa in early and advanced stages.
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Affiliation(s)
- Murad Alahdal
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
- Department of Oncology, Sydney Kimmel Cancer Center, School of Medicine, Johns Hopkins University, 401 N. Broadway, Baltimore, MD 21287, USA
| | - Roshane A. Perera
- AdventHealth Celebration, 380 Celebration Place, Celebration, FL 34747, USA
| | | | - Vipul Patel
- AdventHealth Celebration, 380 Celebration Place, Celebration, FL 34747, USA
| | - Ranjan J. Perera
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
- Department of Oncology, Sydney Kimmel Cancer Center, School of Medicine, Johns Hopkins University, 401 N. Broadway, Baltimore, MD 21287, USA
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Yuan J, Xu L, Chien CY, Yang Y, Yue Y, Fadera S, Stark AH, Schwetye KE, Nazeri A, Desai R, Athiraman U, Chaudhuri AA, Chen H, Leuthardt EC. First-in-human prospective trial of sonobiopsy in high-grade glioma patients using neuronavigation-guided focused ultrasound. NPJ Precis Oncol 2023; 7:92. [PMID: 37717084 PMCID: PMC10505140 DOI: 10.1038/s41698-023-00448-y] [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: 03/20/2023] [Accepted: 09/05/2023] [Indexed: 09/18/2023] Open
Abstract
Sonobiopsy is an emerging technology that combines focused ultrasound (FUS) with microbubbles to enrich circulating brain disease-specific biomarkers for noninvasive molecular diagnosis of brain diseases. Here, we report the first-in-human prospective trial of sonobiopsy in high-grade glioma patients to evaluate its feasibility and safety in enriching plasma circulating tumor biomarkers. A nimble FUS device integrated with a clinical neuronavigation system was used to perform sonobiopsy following an established clinical workflow for neuronavigation. Analysis of blood samples collected before and after FUS sonication showed that sonobiopsy enriched plasma circulating tumor DNA (ctDNA), including a maximum increase of 1.6-fold for the mononucleosome cell-free DNA (cfDNA) fragments (120-280 bp), 1.9-fold for the patient-specific tumor variant ctDNA level, and 5.6-fold for the TERT mutation ctDNA level. Histological analysis of surgically resected tumors confirmed the safety of the procedure. Transcriptome analysis of sonicated and nonsonicated tumor tissues found that FUS sonication modulated cell physical structure-related genes. Only 2 out of 17,982 total detected genes related to the immune pathways were upregulated. These feasibility and safety data support the continued investigation of sonobiopsy for noninvasive molecular diagnosis of brain diseases.
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Affiliation(s)
- Jinyun Yuan
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Lu Xu
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Chih-Yen Chien
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Yaoheng Yang
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Yimei Yue
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Siaka Fadera
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Andrew H Stark
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
| | - Katherine E Schwetye
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Arash Nazeri
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, Saint Louis, MO, 63110, USA
| | - Rupen Desai
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Umeshkumar Athiraman
- Department of Anesthesia, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Aadel A Chaudhuri
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
- Department of Radiation Oncology, Washington University School of Medicine, Saint Louis, MO, 63108, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Computer Science and Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hong Chen
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Division of Neurotechnology, Department of Neurosurgery, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
| | - Eric C Leuthardt
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Division of Neurotechnology, Department of Neurosurgery, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
- Center for Innovation in Neuroscience and Technology, Washington University School of Medicine, Saint Louis, MO, 63110, USA.
- Department of Mechanical Engineering and Materials Science, Washington University in St. Louis, Saint Louis, MO, 63130, USA.
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13
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Yu SCY, Choy LYL, Lo YMD. 'Longing' for the Next Generation of Liquid Biopsy: The Diagnostic Potential of Long Cell-Free DNA in Oncology and Prenatal Testing. Mol Diagn Ther 2023; 27:563-571. [PMID: 37474843 PMCID: PMC10435595 DOI: 10.1007/s40291-023-00661-2] [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] [Accepted: 06/15/2023] [Indexed: 07/22/2023]
Abstract
Liquid biopsy using cell-free DNA (cfDNA) has gained global interest as a molecular diagnostic tool. However, the analysis of cfDNA in cancer patients and pregnant women has been focused on short DNA molecules (e.g., ≤ 600 bp). With the detection of long cfDNA in the plasma of pregnant women and cancer patients in two recent studies, a new avenue of long cfDNA-based liquid biopsy has been opened. In this review, we summarize our current knowledge in this nascent field of long cfDNA analysis, focusing on the fragmentomic and epigenetic features of long cfDNA. In particular, long-read sequencing enabled single-molecule methylation analysis and subsequent determination of the tissue-of-origin of long cfDNA, which has promising clinical potential in prenatal and cancer testing. We also examine some of the limitations that may hinder the immediate clinical applications of long cfDNA analysis and the current efforts involved in addressing them. With concerted efforts in this area, it is hoped that long cfDNA analysis will add to the expanding armamentarium of liquid biopsy.
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Affiliation(s)
- Stephanie C Y Yu
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Shatin, Hong Kong SAR, China
| | - L Y Lois Choy
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China
| | - Y M Dennis Lo
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China.
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
- Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, New Territories, Shatin, Hong Kong SAR, China.
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, China.
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14
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Santini D, Botticelli A, Galvano A, Iuliani M, Incorvaia L, Gristina V, Taffon C, Foderaro S, Paccagnella E, Simonetti S, Fazio F, Scagnoli S, Pomati G, Pantano F, Perrone G, De Falco E, Russo A, Spinelli GP. Network approach in liquidomics landscape. J Exp Clin Cancer Res 2023; 42:193. [PMID: 37542343 PMCID: PMC10401883 DOI: 10.1186/s13046-023-02743-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/27/2023] [Indexed: 08/06/2023] Open
Abstract
Tissue-based biopsy is the present main tool to explore the molecular landscape of cancer, but it also has many limits to be frequently executed, being too invasive with the risk of side effects. These limits and the ability of cancer to constantly evolve its genomic profile, have recently led to the need of a less invasive and more accurate alternative, such as liquid biopsy. By searching Circulating Tumor Cells and residues of their nucleic acids or other tumor products in body fluids, especially in blood, but also in urine, stools and saliva, liquid biopsy is becoming the future of clinical oncology. Despite the current lack of a standardization for its workflows, that makes it hard to be reproduced, liquid biopsy has already obtained promising results for cancer screening, diagnosis, prognosis, and risk of recurrence.Through a more accessible molecular profiling of tumors, it could become easier to identify biomarkers predictive of response to treatment, such as EGFR mutations in non-small cell lung cancer and KRAS mutations in colorectal cancer, or Microsatellite Instability and Mismatch Repair as predictive markers of pembrolizumab response.By monitoring circulating tumor DNA in longitudinal repeated sampling of blood we could also predict Minimal Residual Disease and the risk of recurrence in already radically resected patients.In this review we will discuss about the current knowledge of limitations and strengths of the different forms of liquid biopsies for its inclusion in normal cancer management, with a brief nod to their newest biomarkers and its future implications.
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Affiliation(s)
- Daniele Santini
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | - Andrea Botticelli
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | - Antonio Galvano
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Michele Iuliani
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Lorena Incorvaia
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valerio Gristina
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Chiara Taffon
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico Di Roma, Rome, Italy
| | - Simone Foderaro
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Elisa Paccagnella
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.So Della Repubblica 79, 04100, Latina, Italy
| | - Sonia Simonetti
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Federico Fazio
- UOC Oncologia Territoriale, Polo Pontino, La Sapienza Università Di Roma, Latina, Italy.
| | - Simone Scagnoli
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | | | - Francesco Pantano
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Giuseppe Perrone
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico Di Roma, Rome, Italy
| | - Elena De Falco
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.So Della Repubblica 79, 04100, Latina, Italy
- Mediterranea Cardiocentro, 80122, Naples, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Gian Paolo Spinelli
- UOC Oncologia Territoriale, Polo Pontino, La Sapienza Università Di Roma, Latina, Italy
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15
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Chen Z, Li C, Zhou Y, Yao Y, Liu J, Wu M, Su J. Liquid biopsies for cancer: From bench to clinic. MedComm (Beijing) 2023; 4:e329. [PMID: 37492785 PMCID: PMC10363811 DOI: 10.1002/mco2.329] [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: 01/11/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 07/27/2023] Open
Abstract
Over the past two decades, liquid biopsy has been increasingly used as a supplement, or even, a replacement to the traditional biopsy in clinical oncological practice, due to its noninvasive and early detectable properties. The detections can be based on a variety of features extracted from tumor‑derived entities, such as quantitative alterations, genetic changes, and epigenetic aberrations, and so on. So far, the clinical applications of cancer liquid biopsy mainly aimed at two aspects, prediction (early diagnosis, prognosis and recurrent evaluation, therapeutic response monitoring, etc.) and intervention. In spite of the rapid development and great contributions achieved, cancer liquid biopsy is still a field under investigation and deserves more clinical practice. To better open up future work, here we systematically reviewed and compared the latest progress of the most widely recognized circulating components, including circulating tumor cells, cell-free circulating DNA, noncoding RNA, and nucleosomes, from their discovery histories to clinical values. According to the features applied, we particularly divided the contents into two parts, beyond epigenetics and epigenetic-based. The latter was considered as the highlight along with a brief overview of the advances in both experimental and bioinformatic approaches, due to its unique advantages and relatively lack of documentation.
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Affiliation(s)
- Zhenhui Chen
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Chenghao Li
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
| | - Yue Zhou
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Yinghao Yao
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
| | - Jiaqi Liu
- State Key Laboratory of Molecular OncologyNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Min Wu
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiangChina
| | - Jianzhong Su
- School of Biomedical EngineeringSchool of Ophthalmology & Optometry and Eye HospitalWenzhou Medical UniversityWenzhouZhejiangChina
- Oujiang LaboratoryZhejiang Lab for Regenerative MedicineVision and Brain HealthWenzhouZhejiangChina
- Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiangChina
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16
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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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17
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Kim IA, Hur JY, Kim HJ, Kim WS, Lee KY. A prospective phase 2 study of expeditious EGFR genotyping and immediate therapeutic initiation through extracellular vesicles (EV)-based bronchoalveolar lavage fluid (BALF) liquid biopsy in advanced NSCLC patients. Transl Lung Cancer Res 2023; 12:1425-1435. [PMID: 37577304 PMCID: PMC10413015 DOI: 10.21037/tlcr-22-892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 05/30/2023] [Indexed: 08/15/2023]
Abstract
Background In our previous study, epidermal growth factor receptor (EGFR) genotyping using extracellular vesicles (EV)-derived DNA isolated from bronchoalveolar lavage fluid (BALF) was proven to be highly concordant with conventional tissue-based genotyping and its turn-around-time (TAT) was only 1-2 days. On this background, we prospectively validated the performance of EV-based BALF liquid biopsy for EGFR genotyping in the real practice of advanced non-small cell lung cancer (NSCLC) patients. Methods After screening 120 newly diagnosed stage III-IV NSCLC patients, 51 cases were detected as EGFR-mutated by EV-based BALF EGFR genotyping and 40 patients were enrolled for gefitinib treatment. BALF EV were isolated by ultracentrifuge method and EGFR genotyping was performed with PCR-based PNA-clamping assisted fluorescence melting curve analysis. The objective response rate, progression-free survival (PFS), TAT, time to treatment initiation (TTI), and concordance rate were analyzed with clinical parameters. Results There was only one false positive case among the 120 screened patients and the overall concordance rate between tissue biopsy and EV-based BALF liquid biopsy was 99.2% including the subtype of EGFR mutations. TAT for EV-based BALF EGFR genotyping was 1.9±1.1 days, while tissue-based TAT was 12.1±7.2 days (P<0.001). EGFR genotyping was determined even before obtaining histopathologic report in most cases. TTI in BALF EGFR genotyping was faster than tissue genotyping (7.8±6.5 vs. 13.8±12.9 days). Therapeutic outcomes of response rate and PFS were almost similar to tissue-based results. Conclusions We demonstrated, for the first time, that EV-based BALF liquid biopsy should be an excellent platform for expeditious EGFR genotyping and rapid therapeutic intervention even before obtaining the result of histopathology in advanced NSCLC patients.
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Affiliation(s)
- In Ae Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
| | - Jae Young Hur
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Hee Joung Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Wan Seop Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
- Department of Pathology, Konkuk University School of Medicine, Seoul, Republic of Korea
| | - Kye Young Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Republic of Korea
- Department of Pulmonary Medicine, Konkuk University School of Medicine, Seoul, Republic of Korea
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18
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Khan SR, Scheffler M, Soomar SM, Rashid YA, Moosajee M, Ahmad A, Raza A, Uddin S. Role of circulating-tumor DNA in the early-stage non-small cell lung carcinoma as a predictive biomarker. Pathol Res Pract 2023; 245:154455. [PMID: 37054576 DOI: 10.1016/j.prp.2023.154455] [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: 03/15/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 04/15/2023]
Abstract
Lung cancer is one of the most common solid malignancies. Tissue biopsy is the standard method for accurately diagnosing lung and many other malignancies over decades. However, molecular profiling of tumors leads to establishing a new horizon in the field of precision medicine, which has now entered the mainstream in clinical practice. In this context, a minimally invasive complementary method has been proposed as a liquid biopsy (LB) which is a blood-based test that is gaining popularity as it provides the opportunity to test genotypes in a unique, less invasive manner. Circulating tumor cells (CTC) captivating the Circulating-tumor DNA (Ct-DNA) are often present in the blood of lung cancer patients and are the fundamental concept behind LB. There are multiple clinical uses of Ct-DNA, including its role in prognostic and therapeutic purposes. The treatment of lung cancer has drastically evolved over time. Therefore, this review article mainly focuses on the current literature on circulating tumor DNA and its clinical implications and future goals in non-small cell lung cancer.
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Affiliation(s)
- Saqib Raza Khan
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan.
| | - Matthias Scheffler
- Internal Medicine Department, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | | | - Yasmin Abdul Rashid
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan
| | - Munira Moosajee
- Medical Oncology Department, Aga Khan University Hospital, Karachi, Pakistan
| | - Aamir Ahmad
- Translational Research Institute & Dermatology Institute, Hamad Medical Corporation, Doha, Qatar
| | - Afsheen Raza
- College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Shahab Uddin
- Translational Research Institute & Dermatology Institute, Hamad Medical Corporation, Doha, Qatar.
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19
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Yuan J, Xu L, Chien CY, Yang Y, Yue Y, Fadera S, Stark AH, Schwetye KE, Nazeri A, Desai R, Athiraman U, Chaudhuri AA, Chen H, Leuthardt EC. First-in-human prospective trial of sonobiopsy in glioblastoma patients using neuronavigation-guided focused ultrasound. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.17.23287378. [PMID: 36993173 PMCID: PMC10055591 DOI: 10.1101/2023.03.17.23287378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Sonobiopsy is an emerging technology that combines focused ultrasound (FUS) with microbubbles to enrich circulating brain disease-specific biomarkers for noninvasive molecular diagnosis of brain diseases. Here, we report the first-in-human prospective trial of sonobiopsy in glioblastoma patients to evaluate its feasibility and safety in enriching circulating tumor biomarkers. A nimble FUS device integrated with a clinical neuronavigation system was used to perform sonobiopsy following an established clinical workflow for neuronavigation. Analysis of blood samples collected before and after FUS sonication showed enhanced plasma circulating tumor biomarker levels. Histological analysis of surgically resected tumors confirmed the safety of the procedure. Transcriptome analysis of sonicated and unsonicated tumor tissues found that FUS sonication modulated cell physical structure-related genes but evoked minimal inflammatory response. These feasibility and safety data support the continued investigation of sonobiopsy for noninvasive molecular diagnosis of brain diseases.
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20
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Ghorbanizamani F, Moulahoum H, Guler Celik E, Zihnioglu F, Beduk T, Goksel T, Turhan K, Timur S. Design of Polymeric Surfaces as Platforms for Streamlined Cancer Diagnostics in Liquid Biopsies. BIOSENSORS 2023; 13:400. [PMID: 36979612 PMCID: PMC10046689 DOI: 10.3390/bios13030400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/10/2023] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
Minimally invasive approaches for cancer diagnosis are an integral step in the quest to improve cancer survival. Liquid biopsies such as blood samples are matrices explored to extract valuable information about the tumor and its state through various indicators, such as proteins, peptides, tumor DNA, or circulating tumor cells. Although these markers are scarce, making their isolation and detection in complex matrices challenging, the development in polymer chemistry producing interesting structures, including molecularly imprinted polymers, branched polymers, nanopolymer composites, and hybrids, allowed the development of enhanced platforms with impressive performance for liquid biopsies analysis. This review describes the latest advances and developments in polymer synthesis and their application for minimally invasive cancer diagnosis. The polymer structures improve the operational performances of biosensors through various processes, such as increased affinity for enhanced sensitivity, improved binding, and avoidance of non-specific interactions for enhanced specificity. Furthermore, polymer-based materials can be a tremendous help in signal amplification of usually low-concentrated targets in the sample. The pros and cons of these materials, how the synthesis process affects their performance, and the device applications for liquid biopsies diagnosis will be critically reviewed to show the essentiality of this technology in oncology and clinical biomedicine.
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Affiliation(s)
- Faezeh Ghorbanizamani
- Biochemistry Department, Faculty of Science, Ege University, Bornova, 35100 Izmir, Türkiye
| | - Hichem Moulahoum
- Biochemistry Department, Faculty of Science, Ege University, Bornova, 35100 Izmir, Türkiye
| | - Emine Guler Celik
- Bioengineering Department, Faculty of Engineering, Ege University, Bornova, 35100 Izmir, Türkiye
- EGE SCIENCE PRO Scientific Research Inc., Ege University, IdeEGE Technology Development Zone, Bornova, 35100 Izmir, Türkiye
| | - Figen Zihnioglu
- Biochemistry Department, Faculty of Science, Ege University, Bornova, 35100 Izmir, Türkiye
| | - Tutku Beduk
- Silicon Austria Labs GmbH: Sensor Systems, Europastrasse 12, 9524 Villach, Austria
| | - Tuncay Goksel
- EGE SCIENCE PRO Scientific Research Inc., Ege University, IdeEGE Technology Development Zone, Bornova, 35100 Izmir, Türkiye
- Department of Pulmonary Medicine, Faculty of Medicine, Ege University, Bornova, 35100 Izmir, Türkiye
- EGESAM-Ege University Translational Pulmonary Research Center, Bornova, 35100 Izmir, Türkiye
| | - Kutsal Turhan
- EGE SCIENCE PRO Scientific Research Inc., Ege University, IdeEGE Technology Development Zone, Bornova, 35100 Izmir, Türkiye
- Department of Thoracic Surgery, Faculty of Medicine, Ege University, Bornova, 35100 Izmir, Türkiye
| | - Suna Timur
- Biochemistry Department, Faculty of Science, Ege University, Bornova, 35100 Izmir, Türkiye
- EGE SCIENCE PRO Scientific Research Inc., Ege University, IdeEGE Technology Development Zone, Bornova, 35100 Izmir, Türkiye
- Central Research Testing and Analysis Laboratory Research and Application Center, Ege University, Bornova, 35100 Izmir, Türkiye
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21
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Armakolas A, Kotsari M, Koskinas J. Liquid Biopsies, Novel Approaches and Future Directions. Cancers (Basel) 2023; 15:1579. [PMID: 36900369 PMCID: PMC10000663 DOI: 10.3390/cancers15051579] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/22/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
Cancer is among the leading causes of death worldwide. Early diagnosis and prognosis are vital to improve patients' outcomes. The gold standard of tumor characterization leading to tumor diagnosis and prognosis is tissue biopsy. Amongst the constraints of tissue biopsy collection is the sampling frequency and the incomplete representation of the entire tumor bulk. Liquid biopsy approaches, including the analysis of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating miRNAs, and tumor-derived extracellular vesicles (EVs), as well as certain protein signatures that are released in the circulation from primary tumors and their metastatic sites, present a promising and more potent candidate for patient diagnosis and follow up monitoring. The minimally invasive nature of liquid biopsies, allowing frequent collection, can be used in the monitoring of therapy response in real time, allowing the development of novel approaches in the therapeutic management of cancer patients. In this review we will describe recent advances in the field of liquid biopsy markers focusing on their advantages and disadvantages.
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Affiliation(s)
- Athanasios Armakolas
- Physiology Laboratory, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
- B' Department of Medicine, Hippokration Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - Maria Kotsari
- Physiology Laboratory, Medical School, National and Kapodistrian University of Athens, 115 27 Athens, Greece
| | - John Koskinas
- B' Department of Medicine, Hippokration Hospital, National and Kapodistrian University of Athens, 115 27 Athens, Greece
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22
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Hernandez KM, Bramlett KS, Agius P, Baden J, Cao R, Clement O, Corner AS, Craft J, Dean DA, Dry JR, Grigaityte K, Grossman RL, Hicks J, Higa N, Holzer TR, Jensen J, Johann DJ, Katz S, Kolatkar A, Keynton JL, Lee JSH, Maar D, Martini JF, Meyer CG, Roberts PC, Ryder M, Salvatore L, Schageman JJ, Somiari S, Stetson D, Stern M, Xu L, Leiman LC. Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests: A Blood Profiling Atlas in Cancer (BLOODPAC) Community Study. J Mol Diagn 2023; 25:143-155. [PMID: 36828596 DOI: 10.1016/j.jmoldx.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/21/2022] [Accepted: 12/02/2022] [Indexed: 02/24/2023] Open
Abstract
The Blood Profiling Atlas in Cancer (BLOODPAC) Consortium is a collaborative effort involving stakeholders from the public, industry, academia, and regulatory agencies focused on developing shared best practices on liquid biopsy. This report describes the results from the JFDI (Just Freaking Do It) study, a BLOODPAC initiative to develop standards on the use of contrived materials mimicking cell-free circulating tumor DNA, to comparatively evaluate clinical laboratory testing procedures. Nine independent laboratories tested the concordance, sensitivity, and specificity of commercially available contrived materials with known variant-allele frequencies (VAFs) ranging from 0.1% to 5.0%. Each participating laboratory utilized its own proprietary evaluation procedures. The results demonstrated high levels of concordance and sensitivity at VAFs of >0.1%, but reduced concordance and sensitivity at a VAF of 0.1%; these findings were similar to those from previous studies, suggesting that commercially available contrived materials can support the evaluation of testing procedures across multiple technologies. Such materials may enable more objective comparisons of results on materials formulated in-house at each center in multicenter trials. A unique goal of the collaborative effort was to develop a data resource, the BLOODPAC Data Commons, now available to the liquid-biopsy community for further study. This resource can be used to support independent evaluations of results, data extension through data integration and new studies, and retrospective evaluation of data collection.
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Affiliation(s)
- Kyle M Hernandez
- Department of Medicine, University of Chicago, Chicago, Illinois; Center for Translational Data Science, University of Chicago, Chicago, Illinois
| | | | | | | | - Ru Cao
- Thermo Fisher Scientific, Austin, Texas
| | | | - Adam S Corner
- Digital Biology Group, Bio-Rad Laboratories Inc., Pleasanton, California
| | | | | | | | | | - Robert L Grossman
- Department of Medicine, University of Chicago, Chicago, Illinois; Open Commons Consortium, Chicago, Illinois; Pfizer, San Diego, California
| | - James Hicks
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | - Nikki Higa
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | | | | | - Donald J Johann
- Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Anand Kolatkar
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
| | | | - Jerry S H Lee
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA; Lawrence J. Ellison Institute for Transformative Medicine, Los Angeles, California
| | - Dianna Maar
- Digital Biology Group, Bio-Rad Laboratories Inc., Pleasanton, California
| | | | - Christopher G Meyer
- Center for Translational Data Science, University of Chicago, Chicago, Illinois
| | | | | | | | | | | | | | - Mark Stern
- Bristol Myers Squibb, Newton, New Jersey
| | - Liya Xu
- Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA
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23
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Advances in the Molecular Landscape of Lung Cancer Brain Metastasis. Cancers (Basel) 2023; 15:cancers15030722. [PMID: 36765679 PMCID: PMC9913505 DOI: 10.3390/cancers15030722] [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: 12/23/2022] [Revised: 01/16/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is one of the most frequent tumors that metastasize to the brain. Brain metastasis (BM) is common in advanced cases, being the major cause of patient morbidity and mortality. BMs are thought to arise via the seeding of circulating tumor cells into the brain microvasculature. In brain tissue, the interaction with immune cells promotes a microenvironment favorable to the growth of cancer cells. Despite multimodal treatments and advances in systemic therapies, lung cancer patients still have poor prognoses. Therefore, there is an urgent need to identify the molecular drivers of BM and clinically applicable biomarkers in order to improve disease outcomes and patient survival. The goal of this review is to summarize the current state of knowledge on the mechanisms of the metastatic spread of lung cancer to the brain and how the metastatic spread is influenced by the brain microenvironment, and to elucidate the molecular determinants of brain metastasis regarding the role of genomic and transcriptomic changes, including coding and non-coding RNAs. We also present an overview of the current therapeutics and novel treatment strategies for patients diagnosed with BM from NSCLC.
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24
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Jonak ST, Liu Z, Liu J, Li T, D'Souza BV, Schiaffino JA, Oh S, Xie YH. Analyzing bronchoalveolar fluid derived small extracellular vesicles using single-vesicle SERS for non-small cell lung cancer detection. SENSORS & DIAGNOSTICS 2023; 2:90-99. [PMID: 36741247 PMCID: PMC9850358 DOI: 10.1039/d2sd00109h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/24/2022] [Indexed: 11/07/2022]
Abstract
An emerging body of research by biologists and clinicians has demonstrated the clinical application of small extracellular vesicles (sEVs, also commonly referred to as exosomes) as biomarkers for cancer detections. sEVs isolated from various body fluids such as blood, saliva, urine, and cerebrospinal fluid have been used for biomarker discoveries with highly encouraging outcomes. Among the biomarkers discovered are those responsible for multiple cancer types and immune responses. These biomarkers are recapitulated from the tumor microenvironments. Yet, despite numerous discussions of sEVs in scientific literature, sEV-based biomarkers have so far played only a minor role for cancer diagnostics in the clinical setting, notably less so than other techniques such as imaging and biopsy. In this paper, we report the results of a pilot study (n = 10 from each of the patient and the control group) using bronchoalveolar lavage fluid to determine the presence of sEVs related to non-small cell lung cancer in twenty clinical samples examined using surface enhanced Raman spectroscopy (SERS).
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Affiliation(s)
- Sumita T. Jonak
- NurLabsSan AntonioTX 78201USA,UCLA Biodesign, University of California Los AngelesLos AngelesCA 90095USA
| | - Zirui Liu
- Department of Materials Science and Engineering, University of California Los AngelesLos AngelesCA 90095USA(310) 259 6946
| | - Jun Liu
- Department of Materials Science and Engineering, University of California Los AngelesLos AngelesCA 90095USA(310) 259 6946
| | - Tieyi Li
- Department of Materials Science and Engineering, University of California Los AngelesLos AngelesCA 90095USA(310) 259 6946
| | - Brian V. D'Souza
- NurLabsSan AntonioTX 78201USA,UCLA Biodesign, University of California Los AngelesLos AngelesCA 90095USA
| | - J. Alan Schiaffino
- NurLabsSan AntonioTX 78201USA,UCLA Biodesign, University of California Los AngelesLos AngelesCA 90095USA
| | - Scott Oh
- NurLabsSan AntonioTX 78201USA,UCLA Biodesign, University of California Los AngelesLos AngelesCA 90095USA,UCLA Health System, University of California Los AngelesLos AngelesCA 90095USA
| | - Ya-Hong Xie
- Department of Materials Science and Engineering, University of California Los AngelesLos AngelesCA 90095USA(310) 259 6946,NurLabsSan AntonioTX 78201USA,UCLA Biodesign, University of California Los AngelesLos AngelesCA 90095USA,UCLA Jonsson Comprehensive Cancer Center, University of California, Los AngelesLos AngelesCA 90095USA
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25
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Wu NJW, Aquilina M, Qian BZ, Loos R, Gonzalez-Garcia I, Santini CC, Dunn KE. The Application of Nanotechnology for Quantification of Circulating Tumour DNA in Liquid Biopsies: A Systematic Review. IEEE Rev Biomed Eng 2023; 16:499-513. [PMID: 35302938 DOI: 10.1109/rbme.2022.3159389] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Technologies for quantifying circulating tumour DNA (ctDNA) in liquid biopsies could enable real-time measurements of cancer progression, profoundly impacting patient care. Sequencing methods can be too complex and time-consuming for regular point-of-care monitoring, but nanotechnology offers an alternative, harnessing the unique properties of objects tens to hundreds of nanometres in size. This systematic review was performed to identify all examples of nanotechnology-based ctDNA detection and assess their potential for clinical use. Google Scholar, PubMed, Web of Science, Google Patents, Espacenet and Embase/MEDLINE were searched up to 23rd March 2021. The review identified nanotechnology-based methods for ctDNA detection for which quantitative measures (e.g., limit of detection, LOD) were reported and biologically relevant samples were used. The pre-defined inclusion criteria were met by 66 records. LODs ranged from 10 zM to 50nM. 25 records presented an LOD of 10fM or below. Nanotechnology-based approaches could provide the basis for the next wave of advances in ctDNA diagnostics, enabling analysis at the point-of-care, but none are currently used clinically. Further work is needed in development and validation; trade-offs are expected between different performance measures e.g., number of sequences detected and time to result.
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26
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Hammad A, Ahmed O, Connell PP, Olson D, Balach T. Team Approach: Management of Pathologic Fractures. JBJS Rev 2023; 11:01874474-202301000-00004. [PMID: 36722819 DOI: 10.2106/jbjs.rvw.22.00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
» Optimal care for pathologic fractures centers on the use of a multidisciplinary team; thus, whenever there is a concern for pathologic fracture and proper workup is unable to be performed, prompt referral to a center equipped to manage these injuries should occur. » Fixation strategies for pathologic fractures must take into account patient characteristics, cancer subtypes, and overall goals of treatment. » As the treatments of cancers improve, patient life expectancy with disease will improve as well. This will lead to an increase in the incidence of impending or completed pathologic fractures. The broader subspecialties of orthopaedics must be aware of general principles in the diagnosis and management of these injuries.
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Affiliation(s)
- Aws Hammad
- Department of Orthopaedic Surgery and Rehabilitation Medicine, The University of Chicago Medicine & Biological Sciences, Chicago, Illinois
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27
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Singh S, Podder PS, Russo M, Henry C, Cinti S. Tailored point-of-care biosensors for liquid biopsy in the field of oncology. LAB ON A CHIP 2022; 23:44-61. [PMID: 36321747 DOI: 10.1039/d2lc00666a] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In the field of cancer detection, technologies to analyze tumors using biomarkers circulating in fluids such as blood have developed rapidly based on liquid biopsy. A proactive approach to early cancer detection can lead to more effective treatments with minimal side effects and better long-term patient survival. However, early detection of cancer is hindered by the existing limitations of conventional cancer diagnostic methods. To enable early diagnosis and regular monitoring and improve automation, the development of integrated point-of-care (POC) and biosensors is needed. This is expected to fundamentally change the diagnosis, management, and monitoring of response to treatment of cancer. POC-based techniques will provide a way to avoid complications that occur after invasive tissue biopsy, such as bleeding, infection, and pain. The aim of this study is to provide a comprehensive view of biosensors and their clinical relevance in oncology for the detection of biomarkers with liquid biopsies of proteins, miRNA, ctDNA, exosomes, and cancer cells. The preceding discussion also illustrates the changing landscape of liquid biopsy-based cancer diagnosis through nanomaterials, machine learning, artificial intelligence, wearable devices, and sensors, many of which apply POC design principles. With the advent of sensitive, selective, and timely detection of cancer, we see the field of POC technology for cancer detection and treatment undergoing a positive paradigm shift in the foreseeable future.
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Affiliation(s)
- Sima Singh
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy.
| | - Pritam Saha Podder
- Department of Pharmacy, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Matt Russo
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523-1872, USA
| | - Charles Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523-1872, USA
| | - Stefano Cinti
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy.
- BAT Center-Interuniversity Center for Studies on Bioinspired Agro-Environmental Technology, University of Napoli Federico II, 80055 Naples, Italy
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28
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Gezer U, Bronkhorst AJ, Holdenrieder S. The Clinical Utility of Droplet Digital PCR for Profiling Circulating Tumor DNA in Breast Cancer Patients. Diagnostics (Basel) 2022; 12:diagnostics12123042. [PMID: 36553049 PMCID: PMC9776872 DOI: 10.3390/diagnostics12123042] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/07/2022] Open
Abstract
Breast cancer is the most common cancer affecting women worldwide. It is a malignant and heterogeneous disease with distinct molecular subtypes, which has prognostic and predictive implications. Circulating tumor DNA (ctDNA), cell-free fragmented tumor-derived DNA in blood plasma, is an invaluable source of specific cancer-associated mutations and holds great promise for the development of minimally invasive diagnostic tests. Furthermore, serial monitoring of ctDNA over the course of systemic and targeted therapies not only allows unparalleled efficacy assessments but also enables the identification of patients who are at risk of progression or recurrence. Droplet digital PCR (ddPCR) is a powerful technique for the detection and monitoring of ctDNA. Due to its relatively high accuracy, sensitivity, reproducibility, and capacity for absolute quantification, it is increasingly used as a tool for managing cancer patients through liquid biopsies. In this review paper, we gauge the clinical utility of ddPCR as a technique for mutational profiling in breast cancer patients and focus on HER2, PIK3CA, ESR1, and TP53, which represent the most frequently mutated genes in breast cancers.
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Affiliation(s)
- Ugur Gezer
- Institute of Oncology, Department of Basic Oncology, Istanbul University, Istanbul 34093, Turkey
| | - Abel J. Bronkhorst
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Munich Technical University Munich, 80636 München, Germany
| | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Center Munich Technical University Munich, 80636 München, Germany
- Correspondence:
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29
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Montella M, Ciani G, Granata V, Fusco R, Grassi F, Ronchi A, Cozzolino I, Franco R, Zito Marino F, Urraro F, Monti R, Sirica R, Savarese G, Chianese U, Nebbioso A, Altucci L, Vietri MT, Nardone V, Reginelli A, Grassi R. Preliminary Experience of Liquid Biopsy in Lung Cancer Compared to Conventional Assessment: Light and Shadows. J Pers Med 2022; 12:jpm12111896. [PMID: 36422072 PMCID: PMC9698369 DOI: 10.3390/jpm12111896] [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: 08/31/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
Purpose: To assess the qualitative relationship between liquid biopsy and conventional tissue biopsy. As a secondary target, we evaluated the relationship between the liquid biopsy results and the T stage, N stage, M stage, and compared to grading. Methods: The Local Ethics Committee of the “Università degli Studi della Campania Luigi Vanvitelli”, with the internal resolution number 24997/2020 of 12.11.2020, approved this spontaneous prospective study. According to the approved protocol, patients with lung cancer who underwent Fine-Needle Aspiration Cytology (FNAC), CT-guided biopsy, and liquid biopsy were enrolled. A Yates chi-square test was employed to analyze differences in percentage values of categorical variables. A p-value < 0.05 was considered statistically significant. Data analysis was performed using the Matlab Statistic Toolbox (The MathWorks, Inc., Natick, MA, USA). Results: When a genetic mutation is present on the pathological examination, this was also detected on the liquid biopsy. ROS1 and PDL1 mutations were found in 2/29 patients, while EGFR Exon 21 was identified in a single patient. At liquid biopsy, 26 mutations were identified in the analyzed samples. The mutations with the highest prevalence rate in the study populations were: ALK (Ile1461Val), found in 28/29 patients (96.6%), EML4 (Lys398Arg), identified in 16/29 (55.2%) patients, ALK (Asp1529Glu), found in 14/29 (48.3%) patients, EGFR (Arg521Lys), found in 12/29 (41.4%) patients, ROS (Lys2228Gln), identified in 11/29 (37.9%) patients, ROS (Arg167Gln) and ROS (Ser2229Cys), identified in 10/29 (34.5%) patients, ALK (Lys1491Arg) and PIK3CA (Ile391Met), identified in 8/29 (27.6%) patients, ROS (Thr145Pro), identified in 6/29 (20.7%) patients, and ROS (Ser1109Leu), identified in 4/29 (13.8%) patients. No statistically significant differences can be observed in the mutation rate between the adenocarcinoma population and the squamous carcinoma population (p > 0.05, Yates chi-square test). Conclusions: We showed that, when a genetic mutation was detected in pathological examination, this was always detected by liquid biopsy, demonstrating a very high concordance rate of genomic testing between tissues and their corresponding mutations obtained by liquid biopsy, without cases of false-negative results. In addition, in our study, liquid biopsy highlighted 26 mutations, with the prevalence of ALK mutation in 96.6% of patients, supporting the idea that this approach could be an effective tool in cases with insufficient tumor tissue specimens or in cases where tissue specimens are not obtainable.
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Affiliation(s)
- Marco Montella
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Giovanni Ciani
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Vincenza Granata
- Division of Radiology, Istituto Nazionale Tumori IRCCS Fondazione Pascale-IRCCS di Napoli, 80131 Naples, Italy
| | - Roberta Fusco
- Medical Oncology Division, Igea SpA, 80013 Napoli, Italy
| | - Francesca Grassi
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
- Correspondence:
| | - Andrea Ronchi
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Immacolata Cozzolino
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Renato Franco
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Federica Zito Marino
- Pathology Unit, Department of Mental and Physical Health and Preventive Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Fabrizio Urraro
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Riccardo Monti
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Roberto Sirica
- AMES-Centro Polidiagnostico Strumentale, SRL, 80013 Naples, Italy
| | | | - Ugo Chianese
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Angela Nebbioso
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Lucia Altucci
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Maria Teresa Vietri
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Valerio Nardone
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Alfonso Reginelli
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Roberta Grassi
- Department of Precision Medicine, Università degli Studi della Campania “Luigi Vanvitelli”, 80138 Naples, Italy
- Italian Society of Medical and Interventional Radiology (SIRM), SIRM Foundation, 20122 Milan, Italy
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30
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Short SC, Noushmehr H. Unmet need for liquid biomarkers and the Brain-Liquid Biopsy Consortium. Neurooncol Adv 2022; 4:ii1-ii3. [PMID: 36380869 PMCID: PMC9650471 DOI: 10.1093/noajnl/vdac020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023] Open
Affiliation(s)
- Susan C Short
- Department of Oncology, Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Health System, Detroit, Michigan, USA
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31
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Fang X, Yu S, Jiang Y, Xiang Y, Lu K. Circulating tumor DNA detection in MRD assessment and diagnosis and treatment of non-small cell lung cancer. Front Oncol 2022; 12:1027664. [PMID: 36387176 PMCID: PMC9646858 DOI: 10.3389/fonc.2022.1027664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022] Open
Abstract
Circulating tumor DNA (ctDNA) has contributed immensely to the management of hematologic malignancy and is now considered a valuable detection tool for solid tumors. ctDNA can reflect the real-time tumor burden and be utilized for analyzing specific cancer mutations via liquid biopsy which is a non-invasive procedure that can be used with a relatively high frequency. Thus, many clinicians use ctDNA to assess minimal residual disease (MRD) and it serves as a prognostic and predictive biomarker for cancer therapy, especially for non-small cell lung cancer (NSCLC). Advanced methods have been developed to detect ctDNA, and recent clinical trials have shown the rationality and feasibility of ctDNA for identifying mutations and guiding treatments in NSCLC. Here, we have reviewed recently developed ctDNA detection methods and the importance of sequence analyses of ctDNA in NSCLC.
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32
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Tsering T, Li M, Chen Y, Nadeau A, Laskaris A, Abdouh M, Bustamante P, Burnier JV. EV-ADD, a database for EV-associated DNA in human liquid biopsy samples. J Extracell Vesicles 2022; 11:e12270. [PMID: 36271888 PMCID: PMC9587709 DOI: 10.1002/jev2.12270] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/20/2022] [Accepted: 09/06/2022] [Indexed: 11/06/2022] Open
Abstract
Extracellular vesicles (EVs) play a key role in cellular communication both in physiological conditions and in pathologies such as cancer. Emerging evidence has shown that EVs are active carriers of molecular cargo (e.g. protein and nucleic acids) and a powerful source of biomarkers and targets. While recent studies on EV‐associated DNA (EV‐DNA) in human biofluids have generated a large amount of data, there is currently no database that catalogues information on EV‐DNA. To fill this gap, we have manually curated a database of EV‐DNA data derived from human biofluids (liquid biopsy) and in‐vitro studies, called the Extracellular Vesicle‐Associated DNA Database (EV‐ADD). This database contains validated experimental details and data extracted from peer‐reviewed published literature. It can be easily queried to search for EV isolation methods and characterization, EV‐DNA isolation techniques, quality validation, DNA fragment size, volume of starting material, gene names and disease context. Currently, our database contains samples representing 23 diseases, with 13 different types of EV isolation techniques applied on eight different human biofluids (e.g. blood, saliva). In addition, EV‐ADD encompasses EV‐DNA data both representing the whole genome and specifically including oncogenes, such as KRAS, EGFR, BRAF, MYC, and mitochondrial DNA (mtDNA). An EV‐ADD data metric system was also integrated to assign a compliancy score to the MISEV guidelines based on experimental parameters reported in each study. While currently available databases document the presence of proteins, lipids, RNA and metabolites in EVs (e.g. Vesiclepedia, ExoCarta, ExoBCD, EVpedia, and EV‐TRACK), to the best of our knowledge, EV‐ADD is the first of its kind to compile all available EV‐DNA datasets derived from human biofluid samples. We believe that this database provides an important reference resource on EV‐DNA‐based liquid biopsy research, serving as a learning tool and to showcase the latest developments in the EV‐DNA field. EV‐ADD will be updated yearly as newly published EV‐DNA data becomes available and it is freely available at www.evdnadatabase.com.
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Affiliation(s)
- Thupten Tsering
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Mingyang Li
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Yunxi Chen
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Amélie Nadeau
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Alexander Laskaris
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Mohamed Abdouh
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Prisca Bustamante
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
| | - Julia V. Burnier
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealQuebecCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealQuebecCanada
- Experimental Pathology UnitDepartment of PathologyMcGill UniversityMontrealQuebecCanada
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33
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Geng Y, Jin L, Tang G, Zhao Z, Gu Y, Yang D. LiqBioer: a manually curated database of cancer biomarkers in body fluid. Database (Oxford) 2022; 2022:6687198. [PMID: 36053554 PMCID: PMC9438745 DOI: 10.1093/database/baac077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/15/2022] [Accepted: 08/27/2022] [Indexed: 11/14/2022]
Abstract
Cancer biomarkers are measurable indicators that play vital roles in clinical applications. Biomarkers in body fluids have gained considerable attention since the development of liquid biopsy, and their data volume is rapidly increasing. Nevertheless, current research lacks the compilation of published cancer body fluid biomarkers into a centralized and sustainable repository for researchers and clinicians, despite a handful of small-scale and specific data resources. To fulfill this purpose, we developed liquid biomarker (LiqBioer) containing 6231 manually curated records from 3447 studies, covering 3056 biomarkers and 74 types of cancer in 22 tissues. LiqBioer allows users to browse and download comprehensive information on body liquid biomarkers, including cancer types, source studies and clinical usage. As a comprehensive resource for body fluid biomarkers of cancer, LiqBioer is a powerful tool for researchers and clinicians to query and retrieve biomarkers in liquid biopsy.
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Affiliation(s)
- Yiding Geng
- Department of Biochemistry and Molecular Biology, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, China
| | - Lu Jin
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, China
| | - Guangjue Tang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, China
| | - Zhangxiang Zhao
- The Sino-Russian Medical Research Centre, The Institute of Chronic Disease, The First Affiliated Hospital, Jinan University , Guangzhou, Guangdong 510630, China
| | - Yunyan Gu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, China
| | - Dan Yang
- Department of Biochemistry and Molecular Biology, Harbin Medical University , 157 Baojian Road, Nangang District, Harbin 150081, China
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34
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Ren Y, Cao L, You M, Ji J, Gong Y, Ren H, Xu F, Guo H, Hu J, Li Z. “SMART” digital nucleic acid amplification technologies for lung cancer monitoring from early to advanced stages. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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35
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Liquid biopsy and non-small cell lung cancer: are we looking at the tip of the iceberg? Br J Cancer 2022; 127:383-393. [PMID: 35264788 PMCID: PMC9345955 DOI: 10.1038/s41416-022-01777-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
The possibility to analyse the tumour genetic material shed in the blood is undoubtedly one of the main achievements of translational research in the latest years. In the modern clinical management of advanced non-small cell lung cancer, molecular characterisation plays an essential role. In parallel, immunotherapy is widely employed, but reliable predictive markers are not available yet. Liquid biopsy has the potential to face the two issues and to increase its role in advanced NSCLC in the next future. The aim of this review is to summarise the main clinical applications of liquid biopsy in advanced non-small cell lung cancer, underlining both its potential and limitations from a clinically driven perspective.
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Zhang S, Gao J, Niu R, Ye J, Ma J, Jiang L, Shao X. Association between squamous cell carcinoma antigen level and EGFR mutation status in Chinese lung adenocarcinoma patients. J Clin Lab Anal 2022; 36:e24613. [PMID: 35838003 PMCID: PMC9459300 DOI: 10.1002/jcla.24613] [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: 05/23/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 12/24/2022] Open
Abstract
Background To investigate the association between squamous cell carcinoma antigen (SCCAg) level and epidermal growth factor receptor (EGFR) mutation status in Chinese lung adenocarcinoma patients. Methods We retrospectively analyzed 293 patients with lung adenocarcinoma, divided into EGFR mutant group (n = 178) and EGFR wild‐type group (n = 115). The general data and laboratory parameters of the two groups were compared. We used univariable and multivariable logistic regression to analyze the association between SCCAg level and EGFR mutation. Generalized additive model was used for curve fitting, and a hierarchical binary logistic regression model was used for interaction analysis. Results Squamous cell carcinoma antigen level in the EGFR wild‐type group was significantly higher than that in the mutant group (p < 0.001). After adjusting for confounding factors, we found that elevated SCCAg was associated with a lower probability of EGFR mutation, with an OR of 0.717 (95% CI: 0.543–0.947, p = 0.019). For the tripartite SCCAg groups, the increasing trend of SCCAg was significantly associated with the decreasing probability of EGFR mutation (p for trend = 0.015), especially for Tertile 3 versus Tertile 1 (OR = 0.505; 95% CI: 0.258–0.986; p = 0.045). Curve fitting showed that there was an approximate linear negative relationship between continuous SCCAg and EGFR mutation probability (p = 0.020), which was first flattened and then decreased (p < 0.001). The association between the two was consistent among different subgroups, suggesting no interaction (all p > 0.05). Conclusion There is a negative association between SCCAg level and EGFR mutation probability in Chinese lung adenocarcinoma patients.
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Affiliation(s)
- Shuying Zhang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Jianxiong Gao
- Department of Nuclear Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Changzhou Key Laboratory of Molecular Imaging, Changzhou, China
| | - Rong Niu
- Department of Nuclear Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Changzhou Key Laboratory of Molecular Imaging, Changzhou, China
| | - Jiru Ye
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Jinhong Ma
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Lijuan Jiang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Xiaonan Shao
- Department of Nuclear Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Changzhou Key Laboratory of Molecular Imaging, Changzhou, China
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Kapeleris J, Müller Bark J, Ranjit S, Irwin D, Hartel G, Warkiani ME, Leo P, O'Leary C, Ladwa R, O'Byrne K, Hughes BGM, Punyadeera C. Prognostic value of integrating circulating tumour cells and cell-free DNA in non-small cell lung cancer. Heliyon 2022; 8:e09971. [PMID: 35874074 PMCID: PMC9305346 DOI: 10.1016/j.heliyon.2022.e09971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/11/2022] [Accepted: 07/13/2022] [Indexed: 11/30/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) often presents at an incurable stage, and majority of patients will be considered for palliative treatment at some point in their disease. Despite recent advances, the prognosis remains poor, with a median overall survival of 12–18 months. Liquid biopsy-based biomarkers have emerged as potential candidates for predicting prognosis and response to therapy in NSCLC patients. This pilot study evaluated whether combining circulating tumour cells and clusters (CTCs) and cell-free DNA (cfDNA) can predict progression-free survival (PFS) in NSCLC patients. Methods CTC and cfDNA/ctDNA from advanced stage NSCLC patients were measured at study entry (T0) and 3-months post-treatment (T1). CTCs were enriched using a spiral microfluidic chip and characterised by immunofluorescence. ctDNA was assessed using an UltraSEEK® Lung Panel. Kaplan-Meier plots were generated to investigate the contribution of the presence of CTC/CTC clusters and cfDNA for PFS. Cox proportional hazards analysis compared time to progression versus CTC/CTC cluster counts and cfDNA levels. Results Single CTCs were found in 14 out of 25 patients, while CTC clusters were found in 8 out of the 25 patients at T0. At T1, CTCs were found in 7 out of 18 patients, and CTC clusters in 1 out of the 18 patients. At T0, CTC presence and the combination of CTC cluster counts with cfDNA levels were associated with shorter PFS, p = 0.0261, p = 0.0022, respectively. Conclusions Combining CTC cluster counts and cfDNA levels could improve PFS assessment in NSCLC patients. Our results encourage further investigation on the combined effect of CTC/cfDNA as a prognostic biomarker in a large cohort of advanced stage NSCLC patients.
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Affiliation(s)
- Joanna Kapeleris
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Centre for Biomedical Technologies, Saliva and Liquid Biopsy Translational Laboratory Kelvin Grove, QLD, Australia.,Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - Juliana Müller Bark
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Centre for Biomedical Technologies, Saliva and Liquid Biopsy Translational Laboratory Kelvin Grove, QLD, Australia.,Translational Research Institute, Woolloongabba, Brisbane, Australia.,Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Shanon Ranjit
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Centre for Biomedical Technologies, Saliva and Liquid Biopsy Translational Laboratory Kelvin Grove, QLD, Australia
| | - Darryl Irwin
- Agena Biosciences, Bowen Hills, Brisbane, QLD, Australia
| | - Gunter Hartel
- QIMR Berghofer Medical Research Institute, Herston Road, Herston, QLD, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Ultimo NSW, Australia
| | - Paul Leo
- Translational Research Institute, Woolloongabba, Brisbane, Australia.,Australian Translational Genomics Centre, Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Woolloongabba, Australia
| | - Connor O'Leary
- Translational Research Institute, Woolloongabba, Brisbane, Australia.,Department of Medical Oncology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Rahul Ladwa
- Department of Medical Oncology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia.,School of Medicine, University of Queensland, Herston, Brisbane, Queensland, Australia
| | - Kenneth O'Byrne
- Translational Research Institute, Woolloongabba, Brisbane, Australia.,Department of Medical Oncology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Brett G M Hughes
- School of Medicine, University of Queensland, Herston, Brisbane, Queensland, Australia.,The Royal Brisbane and Women's Hospital, Herston, Brisbane, Queensland, Australia
| | - Chamindie Punyadeera
- Translational Research Institute, Woolloongabba, Brisbane, Australia.,Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia.,Menzies Health Institute, Griffith University, Gold-Coast, Australia
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38
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Filianoti A, Costantini M, Bove AM, Anceschi U, Brassetti A, Ferriero M, Mastroianni R, Misuraca L, Tuderti G, Ciliberto G, Simone G. Volatilome Analysis in Prostate Cancer by Electronic Nose: A Pilot Monocentric Study. Cancers (Basel) 2022; 14:cancers14122927. [PMID: 35740593 PMCID: PMC9220860 DOI: 10.3390/cancers14122927] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 01/27/2023] Open
Abstract
Urine analysis via an electronic nose provides volatile organic compounds easily usable in the diagnosis of urological diseases. Although challenging and highly expensive for health systems worldwide, no useful markers are available in clinical practice that aim to anticipate prostate cancer (PCa) diagnosis in the early stages in the context of wide population screening. Some previous works suggested that dogs trained to smell urine could recognize several types of cancers with various success rates. We hypothesized that urinary volatilome profiling may distinguish PCa patients from healthy controls. In this study, 272 individuals, 133 patients, and 139 healthy controls participated. Urine samples were collected, stabilized at 37 °C, and analyzed using a commercially available electronic nose (Cyranose C320). Statistical analysis of the sensor responses was performed off-line using principal component (PCA) analyses, discriminant analysis (CDA), and ROC curves. Principal components best discriminating groups were identified with univariable ANOVA analysis. groups were identified with univariable ANOVA analysis. Here, 110/133 and 123/139 cases were correctly identified in the PCa and healthy control cohorts, respectively (sensitivity 82.7%, specificity 88.5%; positive predictive value 87.3%, negative predictive value 84.2%). The Cross Validated Accuracy (CVA 85.3%, p < 0.001) was calculated. Using ROC analysis, the area under the curve was 0.9. Urine volatilome profiling via an electronic nose seems a promising non-invasive diagnostic tool.
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Affiliation(s)
- Alessio Filianoti
- Department of Urology, IRCCS—“Regina Elena” National Cancer Institute, 00144 Rome, Italy; (A.F.); (M.C.); (A.M.B.); (U.A.); (A.B.); (M.F.); (R.M.); (L.M.); (G.T.)
- Department of Urology, San Filippo Neri Hospital, 00135 Rome, Italy
| | - Manuela Costantini
- Department of Urology, IRCCS—“Regina Elena” National Cancer Institute, 00144 Rome, Italy; (A.F.); (M.C.); (A.M.B.); (U.A.); (A.B.); (M.F.); (R.M.); (L.M.); (G.T.)
| | - Alfredo Maria Bove
- Department of Urology, IRCCS—“Regina Elena” National Cancer Institute, 00144 Rome, Italy; (A.F.); (M.C.); (A.M.B.); (U.A.); (A.B.); (M.F.); (R.M.); (L.M.); (G.T.)
| | - Umberto Anceschi
- Department of Urology, IRCCS—“Regina Elena” National Cancer Institute, 00144 Rome, Italy; (A.F.); (M.C.); (A.M.B.); (U.A.); (A.B.); (M.F.); (R.M.); (L.M.); (G.T.)
| | - Aldo Brassetti
- Department of Urology, IRCCS—“Regina Elena” National Cancer Institute, 00144 Rome, Italy; (A.F.); (M.C.); (A.M.B.); (U.A.); (A.B.); (M.F.); (R.M.); (L.M.); (G.T.)
| | - Mariaconsiglia Ferriero
- Department of Urology, IRCCS—“Regina Elena” National Cancer Institute, 00144 Rome, Italy; (A.F.); (M.C.); (A.M.B.); (U.A.); (A.B.); (M.F.); (R.M.); (L.M.); (G.T.)
| | - Riccardo Mastroianni
- Department of Urology, IRCCS—“Regina Elena” National Cancer Institute, 00144 Rome, Italy; (A.F.); (M.C.); (A.M.B.); (U.A.); (A.B.); (M.F.); (R.M.); (L.M.); (G.T.)
| | - Leonardo Misuraca
- Department of Urology, IRCCS—“Regina Elena” National Cancer Institute, 00144 Rome, Italy; (A.F.); (M.C.); (A.M.B.); (U.A.); (A.B.); (M.F.); (R.M.); (L.M.); (G.T.)
| | - Gabriele Tuderti
- Department of Urology, IRCCS—“Regina Elena” National Cancer Institute, 00144 Rome, Italy; (A.F.); (M.C.); (A.M.B.); (U.A.); (A.B.); (M.F.); (R.M.); (L.M.); (G.T.)
| | - Gennaro Ciliberto
- Scientific Direction, “Regina Elena” National Cancer Institute, 00144 Rome, Italy;
| | - Giuseppe Simone
- Department of Urology, IRCCS—“Regina Elena” National Cancer Institute, 00144 Rome, Italy; (A.F.); (M.C.); (A.M.B.); (U.A.); (A.B.); (M.F.); (R.M.); (L.M.); (G.T.)
- Correspondence:
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Liu S, Wang J. Current and Future Perspectives of Cell-Free DNA in Liquid Biopsy. Curr Issues Mol Biol 2022; 44:2695-2709. [PMID: 35735625 PMCID: PMC9222159 DOI: 10.3390/cimb44060184] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
A liquid biopsy is a minimally invasive or non-invasive method to analyze a range of tumor material in blood or other body fluids, including circulating tumor cells (CTCs), cell-free DNA (cfDNA), messenger RNA (mRNA), microRNA (miRNA), and exosomes, which is a very promising technology. Among these cancer biomarkers, plasma cfDNA is the most widely used in clinical practice. Compared with a tissue biopsy of traditional cancer diagnosis, in assessing tumor heterogeneity, a liquid biopsy is more reliable because all tumor sites release cfDNA into the blood. Therefore, a cfDNA liquid biopsy is less invasive and comprehensive. Moreover, the development of next-generation sequencing technology makes cfDNA sequencing more sensitive than a tissue biopsy, with higher clinical applicability and wider application. In this publication, we aim to review the latest perspectives of cfDNA liquid biopsy clinical significance and application in cancer diagnosis, treatment, and prognosis. We introduce the sequencing techniques and challenges of cfDNA detection, analysis, and clinical applications, and discuss future research directions.
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40
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Pirosa MC, Borchmann S, Jardin F, Gaidano G, Rossi D. Controversies in the Interpretation of Liquid Biopsy Data in Lymphoma. Hemasphere 2022; 6:e727. [PMID: 35747846 PMCID: PMC9208882 DOI: 10.1097/hs9.0000000000000727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/21/2022] [Indexed: 11/25/2022] Open
Abstract
The rapid evolution of genomic technologies over the last years has led to the development of different methods for the detection, measurement and analysis of cell-free DNA fragments (cfDNA) which are shed into the bloodstream by apoptotic cells and circulate at a low concentration in plasma. In cancer patients, the proportion of tumor-derived cfDNA is defined as circulating tumor DNA. This analysis, commonly known as liquid biopsy, allows to access tumor DNA through a simple blood sampling and therefore without the need of an invasive tissue biopsy. For this reason, this tool may have several clinical applications in terms of diagnosis, prognosis, and monitoring of minimal residual disease. However, there are still several critical issues that need to be resolved. In this review, we will discuss some of the controversies around this method and its potential clinical applications.
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Lin AA, Nimgaonkar V, Issadore D, Carpenter EL. Extracellular Vesicle-Based Multianalyte Liquid Biopsy as a Diagnostic for Cancer. Annu Rev Biomed Data Sci 2022; 5:269-292. [PMID: 35562850 DOI: 10.1146/annurev-biodatasci-122120-113218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Liquid biopsy is the analysis of materials shed by tumors into circulation, such as circulating tumor cells, nucleic acids, and extracellular vesicles (EVs), for the diagnosis and management of cancer. These assays have rapidly evolved with recent FDA approvals of single biomarkers in patients with advanced metastatic disease. However, they have lacked sensitivity or specificity as a diagnostic in early-stage cancer, primarily due to low concentrations in circulating plasma. EVs, membrane-enclosed nanoscale vesicles shed by tumor and other cells into circulation, are a promising liquid biopsy analyte owing to their protein and nucleic acid cargoes carried from their mother cells, their surface proteins specific to their cells of origin, and their higher concentrations over other noninvasive biomarkers across disease stages. Recently, the combination of EVs with non-EV biomarkers has driven improvements in sensitivity and accuracy; this has been fueled by the use of machine learning (ML) to algorithmically identify and combine multiple biomarkers into a composite biomarker for clinical prediction. This review presents an analysis of EV isolation methods, surveys approaches for and issues with using ML in multianalyte EV datasets, and describes best practices for bringing multianalyte liquid biopsy to clinical implementation. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Andrew A Lin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; .,Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vivek Nimgaonkar
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - David Issadore
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Erica L Carpenter
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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Doculara L, Trahair TN, Bayat N, Lock RB. Circulating Tumor DNA in Pediatric Cancer. Front Mol Biosci 2022; 9:885597. [PMID: 35647029 PMCID: PMC9133724 DOI: 10.3389/fmolb.2022.885597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
The measurement of circulating tumor DNA (ctDNA) has gained increasing prominence as a minimally invasive tool for the detection of cancer-specific markers in plasma. In adult cancers, ctDNA detection has shown value for disease-monitoring applications including tumor mutation profiling, risk stratification, relapse prediction, and treatment response evaluation. To date, there are ctDNA tests used as companion diagnostics for adult cancers and it is not understood why the same cannot be said about childhood cancer, despite the marked differences between adult and pediatric oncology. In this review, we discuss the current understanding of ctDNA as a disease monitoring biomarker in the context of pediatric malignancies, including the challenges associated with ctDNA detection in liquid biopsies. The data and conclusions from pediatric cancer studies of ctDNA are summarized, highlighting treatment response, disease monitoring and the detection of subclonal disease as applications of ctDNA. While the data from retrospective studies highlight the potential of ctDNA, large clinical trials are required for ctDNA analysis for routine clinical use in pediatric cancers. We outline the requirements for the standardization of ctDNA detection in pediatric cancers, including sample handling and reproducibility of results. With better understanding of the advantages and limitations of ctDNA and improved detection methods, ctDNA analysis may become the standard of care for patient monitoring in childhood cancers.
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Affiliation(s)
- Louise Doculara
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Toby N. Trahair
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW, Australia
| | - Narges Bayat
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Richard B. Lock
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
- *Correspondence: Richard B. Lock,
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Rehman AU, Khan P, Maurya SK, Siddiqui JA, Santamaria-Barria JA, Batra SK, Nasser MW. Liquid biopsies to occult brain metastasis. Mol Cancer 2022; 21:113. [PMID: 35538484 PMCID: PMC9088117 DOI: 10.1186/s12943-022-01577-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/19/2022] [Indexed: 02/08/2023] Open
Abstract
Brain metastasis (BrM) is a major problem associated with cancer-related mortality, and currently, no specific biomarkers are available in clinical settings for early detection. Liquid biopsy is widely accepted as a non-invasive method for diagnosing cancer and other diseases. We have reviewed the evidence that shows how the molecular alterations are involved in BrM, majorly from breast cancer (BC), lung cancer (LC), and melanoma, with an inception in how they can be employed for biomarker development. We discussed genetic and epigenetic changes that influence cancer cells to breach the blood-brain barrier (BBB) and help to establish metastatic lesions in the uniquely distinct brain microenvironment. Keeping abreast with the recent breakthroughs in the context of various biomolecules detections and identifications, the circulating tumor cells (CTC), cell-free nucleotides, non-coding RNAs, secretory proteins, and metabolites can be pursued in human body fluids such as blood, serum, cerebrospinal fluid (CSF), and urine to obtain potential candidates for biomarker development. The liquid biopsy-based biomarkers can overlay with current imaging techniques to amplify the signal viable for improving the early detection and treatments of occult BrM.
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Affiliation(s)
- Asad Ur Rehman
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | - Jawed A Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA
| | | | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68108, USA. .,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68108, USA.
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Zaytseva M, Usman N, Salnikova E, Sanakoeva A, Valiakhmetova A, Chervova A, Papusha L, Novichkova G, Druy A. Methodological Challenges of Digital PCR Detection of the Histone H3 K27M Somatic Variant in Cerebrospinal Fluid. Pathol Oncol Res 2022; 28:1610024. [PMID: 35498161 PMCID: PMC9039021 DOI: 10.3389/pore.2022.1610024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 03/23/2022] [Indexed: 11/13/2022]
Abstract
Cell-free DNA (cfDNA) in body fluids is invaluable for cancer diagnostics. Despite the impressive potential of liquid biopsies for the diagnostics of central nervous system (CNS) tumors, a number of challenges prevent introducing this approach into routine laboratory practice. In this study, we adopt a protocol for sensitive detection of the H3 K27M somatic variant in cerebrospinal fluid (CSF) by using digital polymerase chain reaction (dPCR). Optimization of the protocol was carried out stepwise, including preamplification of the H3 target region and adjustment of dPCR conditions. The optimized protocol allowed detection of the mutant allele starting from DNA quantities as low as 9 picograms. Analytical specificity was tested using a representative group of tumor tissue samples with known H3 K27M status, and no false-positive cases were detected. The protocol was applied to a series of CSF samples collected from patients with CNS tumors (n = 18) using two alternative dPCR platforms, QX200 Droplet Digital PCR system (Bio-Rad) and QIAcuity Digital PCR System (Qiagen). In three out of four CSF specimens collected from patients with H3 K27M-positive diffuse midline glioma, both platforms allowed detection of the mutant allele. The use of ventricular access for CSF collection appears preferential, as lumbar CSF samples may produce ambiguous results. All CSF samples collected from patients with H3 wild-type tumors were qualified as H3 K27M-negative. High agreement of the quantitative data obtained with the two platforms demonstrates universality of the approach.
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Affiliation(s)
- Margarita Zaytseva
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Natalia Usman
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Ekaterina Salnikova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Agunda Sanakoeva
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Andge Valiakhmetova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Almira Chervova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell Biology, Institut Pasteur, Paris, France
| | - Ludmila Papusha
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alexander Druy
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Research Institute of Medical Cell Technologies, Yekaterinburg, Russia
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Poellmann MJ, Rawding P, Kim D, Bu J, Kim Y, Hong S. Branched, dendritic, and hyperbranched polymers in liquid biopsy device design. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1770. [PMID: 34984833 PMCID: PMC9480505 DOI: 10.1002/wnan.1770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/02/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022]
Abstract
The development of minimally invasive tests for cancer diagnosis and prognosis will aid in the research of new treatments and improve survival rates. Liquid biopsies seek to derive actionable information from tumor material found in routine blood samples. The relative scarcity of tumor material in this complex mixture makes isolating and detecting cancerous material such as proteins, circulating tumor DNA, exosomes, and whole circulating tumor cells a challenge for device engineers. This review describes the chemistry and applications of branched and hyperbranched to improve the performance of liquid biopsy devices. These polymers can improve the performance of a liquid biopsy through several mechanisms. For example, polymers designed to increase the affinity of capture enhance device sensitivity. On the other hand, polymers designed to increase binding avidity or repel nonspecific adsorption enhance device specificity. Branched and hyperbranched polymers can also be used to amplify the signal from small amounts of detected material. The further development of hyperbranched polymers in liquid biopsy applications will enhance device capabilities and help these critical technologies reach the oncology clinic where they are sorely needed. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices.
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Affiliation(s)
- Michael J Poellmann
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA.,Capio Biosciences, Madison, Wisconsin, USA
| | - Piper Rawding
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - DaWon Kim
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - Jiyoon Bu
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA
| | - YoungSoo Kim
- Department of Pharmacy, Yonsei University, Incheon, South Korea
| | - Seungpyo Hong
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, Wisconsin, USA.,Capio Biosciences, Madison, Wisconsin, USA.,Department of Pharmacy, Yonsei University, Incheon, South Korea.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Carbone Cancer Center, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Wisconsin Center for NanoBioSystems, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Kwon M, Ku BM, Olsen S, Park S, Lefterova M, Odegaard J, Jung HA, Sun JM, Lee SH, Ahn JS, Park K, Ahn MJ. Longitudinal monitoring by next-generation sequencing of plasma cell-free DNA in ALK rearranged NSCLC patients treated with ALK tyrosine kinase inhibitors. Cancer Med 2022; 11:2944-2956. [PMID: 35437925 PMCID: PMC9359877 DOI: 10.1002/cam4.4663] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 11/30/2021] [Accepted: 12/03/2021] [Indexed: 12/11/2022] Open
Abstract
Background Patients with ALK‐rearranged non‐small cell lung cancer (ALK+ NSCLC) inevitably acquire resistance to ALK inhibitors. Longitudinal monitoring of cell‐free plasma DNA (cfDNA) next‐generation sequencing (NGS) could predict the response and resistance to tyrosine kinase inhibitor (TKI) therapy in ALK+ NSCLC. Methods Patients with ALK+ NSCLC determined by standard tissue testing and planned to undergo TKI therapy were prospectively recruited. Plasma was collected at pretreatment, 2 months‐post therapy, and at progression for cfDNA‐NGS analysis, Guardant 360. Results Among 92 patients enrolled, circulating tumor DNA (ctDNA) was detected in 69 baseline samples (75%): 43 ALK fusions (62.3%) and two ALK mutations without fusion (2.8%). Two patients showed ALK‐resistance mutations after ceritinib; G1202R, and co‐occurring G1202R and T1151R. Eight patients developed ALK resistance mutations after crizotinib therapy; L1196M (n = 5), G1269A (n = 1), G1202R (n = 1), and co‐occurring F1174L, G1202R, and G1269A (n = 1). Absence of ctDNA at baseline was significantly associated with longer progression‐free survival (PFS; median 36.1 vs. 11.4 months, p = 0.0049) and overall survival (OS; not reached vs. 29.3 months, p = 0.0200). ctDNA clearance at 2 months (n = 29) was associated with significantly longer PFS (25.4 vs. 11.6 months, p = 0.0012) and OS (not reached vs. 26.1 months, p = 0.0307) than those without clearance (n = 22). Patients with co‐occurring TP53 alterations and ALK fusions at baseline (n = 16) showed significantly shorter PFS (7.28 vs. 13.0 months, p = 0.0307) than those without TP53 alterations (n = 25). Conclusions cfDNA‐NGS facilitates detection of ALK fusions and resistance mutations, assessment of prognosis, and monitoring dynamic changes of genomic alterations in ALK+ NSCLC treated with ALK‐TKI.
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Affiliation(s)
- Minsuk Kwon
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Hematology-Oncology, Ajou University School of Medicine, Suwon, South Korea
| | - Bo Mi Ku
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Steve Olsen
- Department of Medical and Clinical Affairs, Guardant Health AMEA, Singapore, Singapore
| | - Sehhoon Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Martina Lefterova
- Department of Medical and Clinical Affairs, Guardant Health AMEA, Singapore, Singapore
| | - Justin Odegaard
- Department of Medical and Clinical Affairs, Guardant Health AMEA, Singapore, Singapore
| | - Hyun-Ae Jung
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong-Mu Sun
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jin Seok Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Keunchil Park
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Myung-Ju Ahn
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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The potential of liquid biopsy in the management of cancer patients. Semin Cancer Biol 2022; 84:69-79. [DOI: 10.1016/j.semcancer.2022.03.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 03/06/2022] [Accepted: 03/17/2022] [Indexed: 02/07/2023]
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Ye X, Li W, Zhang L, Yu J. Clinical Significance of Circulating Cell-Free DNA Detection in Multiple Myeloma: A Meta-Analysis. Front Oncol 2022; 12:852573. [PMID: 35252019 PMCID: PMC8894433 DOI: 10.3389/fonc.2022.852573] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) detection, a non-invasive method, appears promising for genetic analyses as well as quantitative assessment of tumor burden in patients with cancer. Although the analysis of cfDNA for clinical prognosis and monitoring disease burden in multiple myeloma (MM) has been recently studied, the results are unclear. In this meta-analysis, we explored the clinical significance of circulating cfDNA detection in patients with MM. We searched PubMed, Embase, and the Cochrane Library for eligible studies published up until July 25, 2021. Diagnostic accuracy variables were calculated and analyzed using Meta-Disc, and prognostic data were analyzed using Review Manager. Overall, seven studies comprising 235 myeloma patients met our inclusion criteria. The overall sensitivity and specificity of cfDNA to detect minimal residual disease (MRD) were 0.58 and 0.91, respectively. Moreover, higher levels of cfDNA were associated with worse progression-free survival as well as with poor overall survival. Our meta-analysis revealed that ctDNA detection has an obvious advantage in terms of MRD detection specificity, but it showed no superiority over bone marrow assessment in terms of MRD detection sensitivity, and higher levels of cfDNA were indicative of worse prognosis in patients with MM. cfDNA detection is a non-invasive method and thus shows promise as a good alternative to BM biopsies for monitoring clonal evolution and tumor burden so as to guide the treatment of patients with MM.
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Affiliation(s)
- Xueshi Ye
- Department of Hematology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- *Correspondence: Xueshi Ye,
| | - Wanli Li
- Department of Orthopedics, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lifei Zhang
- Department of Hematology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Junyao Yu
- Department of Hematology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
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Zou W, Yaung SJ, Fuhlbrück F, Ballinger M, Peters E, Palma JF, Shames DS, Gandara D, Jiang Y, Patil NS. ctDNA Predicts Overall Survival in Patients With NSCLC Treated With PD-L1 Blockade or With Chemotherapy. JCO Precis Oncol 2022; 5:827-838. [PMID: 34994614 DOI: 10.1200/po.21.00057] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Identification of predictors for overall survival (OS) allows timely detection of clinical efficacy signals and therefore facilitates treatment decisions. We assessed the association between circulating tumor DNA (ctDNA) metrics and the primary end point of OS in a subset of previously treated patients with locally advanced or metastatic non-small-cell lung cancer, who underwent atezolizumab or docetaxel treatment in the open-label randomized phase III OAK trial. MATERIALS AND METHODS Plasma from 94 patients at baseline and at subsequent cycles of therapy every 3 weeks was analyzed retrospectively for ctDNA. ctDNA was measured by allele frequency and mutant molecules per milliliter (MMPM). Concordance between various per-sample metrics and clinical outcome were assessed using C index. RESULTS Of all the ctDNA metrics tested, the association of median MMPM at 6 weeks with OS in patients treated with atezolizumab or docetaxel had a C index > 0.7. The OS hazard ratios relative to high ctDNA above median MMPM within each arm were 0.28 (95% CI, 0.11 to 0.75) for atezolizumab and 0.19 (95% CI, 0.08 to 0.48) for docetaxel. For patients who had ctDNA median MMPM levels of < 4.79, the median survival time was more than 17 months in docetaxel-treated patients and the median survival time was not reached in the atezolizumab-treated patients. CONCLUSION ctDNA MMPM levels measured at 6 weeks post-treatment are associated with OS in advanced non-small-cell lung cancer. Our results suggest that ctDNA has the potential for a noninvasive early liquid biopsy predictor for OS that warrants further studies to demonstrate its utility in clinical development.
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Affiliation(s)
- Wei Zou
- Genentech, South San Francisco, CA
| | | | | | | | | | | | | | | | - Yuqiu Jiang
- Roche Sequencing Solutions, Inc, Pleasanton, CA
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Pacia CP, Yuan J, Yue Y, Xu L, Nazeri A, Desai R, Gach HM, Wang X, Talcott MR, Chaudhuri AA, Dunn GP, Leuthardt EC, Chen H. Sonobiopsy for minimally invasive, spatiotemporally-controlled, and sensitive detection of glioblastoma-derived circulating tumor DNA. Am J Cancer Res 2022; 12:362-378. [PMID: 34987650 PMCID: PMC8690937 DOI: 10.7150/thno.65597] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/06/2021] [Indexed: 12/12/2022] Open
Abstract
Though surgical biopsies provide direct access to tissue for genomic characterization of brain cancer, they are invasive and pose significant clinical risks. Brain cancer management via blood-based liquid biopsies is a minimally invasive alternative; however, the blood-brain barrier (BBB) restricts the release of brain tumor-derived molecular biomarkers necessary for sensitive diagnosis. Methods: A mouse glioblastoma multiforme (GBM) model was used to demonstrate the capability of focused ultrasound (FUS)-enabled liquid biopsy (sonobiopsy) to improve the diagnostic sensitivity of brain tumor-specific genetic mutations compared with conventional blood-based liquid biopsy. Furthermore, a pig GBM model was developed to characterize the translational implications of sonobiopsy in humans. Magnetic resonance imaging (MRI)-guided FUS sonication was performed in mice and pigs to locally enhance the BBB permeability of the GBM tumor. Contrast-enhanced T1-weighted MR images were acquired to evaluate the BBB permeability change. Blood was collected immediately after FUS sonication. Droplet digital PCR was used to quantify the levels of brain tumor-specific genetic mutations in the circulating tumor DNA (ctDNA). Histological staining was performed to evaluate the potential for off-target tissue damage by sonobiopsy. Results: Sonobiopsy improved the detection sensitivity of EGFRvIII from 7.14% to 64.71% and TERT C228T from 14.29% to 45.83% in the mouse GBM model. It also improved the diagnostic sensitivity of EGFRvIII from 28.57% to 100% and TERT C228T from 42.86% to 71.43% in the porcine GBM model. Conclusion: Sonobiopsy disrupts the BBB at the spatially-targeted brain location, releases tumor-derived DNA into the blood circulation, and enables timely collection of ctDNA. Converging evidence from both mouse and pig GBM models strongly supports the clinical translation of sonobiopsy for the minimally invasive, spatiotemporally-controlled, and sensitive molecular characterization of brain cancer.
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