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Hu K, Gao L, Zhang R, Lu M, Zhou D, Xie S, Fan X, Zhu M. Clinical application of serum seven tumour-associated autoantibodies in patients with pulmonary nodules. Heliyon 2024; 10:e30576. [PMID: 38765082 PMCID: PMC11098830 DOI: 10.1016/j.heliyon.2024.e30576] [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: 05/17/2023] [Revised: 04/25/2024] [Accepted: 04/29/2024] [Indexed: 05/21/2024] Open
Abstract
Background The incidence of pulmonary nodules is increasing because of the promotion and popularisation of low-dose computed tomography (LDCT) screening for populations with suspected lung cancer. However, a high rate of false positives and concerns regarding the radiation-related cancer risk of repeated CT scanning remain major obstacles to its wide application. This study aimed to investigate the clinical value of seven tumour-associated autoantibodies (7-TAAbs) in the differentiation of malignant pulmonary tumours from benign ones and the early detection of lung cancer in routine clinical practice. Methods We included 377 patients who underwent both the 7-TAAbs panel test and LDCT screening, and were diagnosed with pulmonary nodules using LDCT. An enzyme-linked immunosorbent assay (ELISA) was used to measure the serum levels antibodies for P53, PGP9.5, SOX2, GAGE7, GBU4-5, CAGE, and MAGE-A1. The relationships between the positive rates of the 7-TAAbs and the patient sex, and age, and the number, size, and composition of pulmonary nodules were analysed. We then statistically evaluated the clinical application value. Results The positive rates of the 7-TAAbs did not correlate with sex, age, number, size, or composition of pulmonary nodules. The serum antibody level of GBU4-5 in patients with pulmonary nodules tended to increase with age; the serum antibody level of SOX2 tended to increase with nodule size and was the highest among patients with mixed ground-glass opacity (mGGO) nodules. The antibody positive rate for CAGE in female patients with pulmonary nodules was significantly higher than that in male patients (P < 0.05). The positive rate of GBU4-5 antibody in patients aged 60 years and above was higher than that in younger patients (P < 0.05). The positive rate of GAGE7 antibody in patients with pulmonary nodules sized 8-20 mm was also significantly higher than that in patients with pulmonary nodules sized less than 8 mm (P < 0.01). Significant differences were observed in the GAGE7 antibody levels of patients with pulmonary nodules of different compositions (P < 0.01). The positive rate of the 7-TAAbs panel test in patients with lung cancer was significantly higher than in patients with pulmonary nodules (P < 0.01). Serum levels of P53, SOX2, GBU4-5, and MAGE-A1 antibodies were significantly higher in patients with lung cancer than in those with pulmonary nodules (P < 0.05). Conclusion The low positive rates of serum 7-TAAbs in patients with lung cancer and pulmonary nodules may be related to different case selection, population differences, geographical differences, different degrees of progression, and detection methods. The combined detection of 7-TAAbs has some clinical value for screening and early detection of lung cancer.
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Affiliation(s)
- Kaiming Hu
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Lili Gao
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Ruyi Zhang
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Meiyi Lu
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Dangui Zhou
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Siqi Xie
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Xinyue Fan
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
| | - Mei Zhu
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Hefei, China
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Li J, Li M, Wuethrich A, Guan R, Zhao L, Hu C, Trau M, Sun Y. Molecular Stratification and Treatment Monitoring of Lung Cancer Using a Small Extracellular Vesicle-Activated Nanocavity Architecture. Anal Chem 2024; 96:7651-7660. [PMID: 38690989 DOI: 10.1021/acs.analchem.4c00558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Development of molecular diagnostics for lung cancer stratification and monitoring is crucial for the rational planning and timely adjustment of treatments to improve clinical outcomes. In this regard, we propose a nanocavity architecture to sensitively profile the protein signature on small extracellular vesicles (sEVs) to enable accurate, noninvasive staging and treatment monitoring of lung cancer. The nanocavity architecture is formed by molecular recognition through the binding of sEVs with the nanobox-based core-shell surface-enhanced Raman scattering (SERS) barcodes and mirrorlike, asymmetric gold microelectrodes. By imposing an alternating current on the gold microelectrodes, a nanofluidic shear force was stimulated that supported the binding of sEVs and the efficient assembly of the nanoboxes. The binding of sEVs further induced a nanocavity between the nanobox and the gold microelectrode that significantly amplified the electromagnetic field to enable the simultaneous enhancement of Raman signals from four SERS barcodes and generate patient-specific molecular sEV signatures. Importantly, evaluated on a cohort of clinical samples (n = 76) on the nanocavity architecture, the acquired patient-specific sEV molecular signatures achieved accurate identification, stratification, and treatment monitoring of lung cancer patients, highlighting its potential for transition to clinical utility.
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Affiliation(s)
- Junrong Li
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Meiqin Li
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Alain Wuethrich
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rui Guan
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Lihui Zhao
- Wuhan Pulmonary Hospital, Wuhan 430079, P. R. China
| | - Cong Hu
- Guangxi Key Laboratory of Automatic Detecting Technology and Instruments, Guilin University of Electronic Technology, Guilin 541004, P. R. China
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yao Sun
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
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van der Leest P, Rozendal P, Hinrichs J, van Noesel CJM, Zwaenepoel K, Deiman B, Huijsmans CJJ, van Eijk R, Speel EJM, van Haastert RJ, Ligtenberg MJL, van Schaik RHN, Jansen MPHM, Dubbink HJ, de Leng WW, Leers MPG, Tamminga M, van den Broek D, van Kempen LC, Schuuring E. External Quality Assessment on Molecular Tumor Profiling with Circulating Tumor DNA-Based Methodologies Routinely Used in Clinical Pathology within the COIN Consortium. Clin Chem 2024; 70:759-767. [PMID: 38484302 DOI: 10.1093/clinchem/hvae014] [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: 10/02/2023] [Accepted: 12/21/2023] [Indexed: 05/03/2024]
Abstract
BACKGROUND Identification of tumor-derived variants in circulating tumor DNA (ctDNA) has potential as a sensitive and reliable surrogate for tumor tissue-based routine diagnostic testing. However, variations in pre(analytical) procedures affect the efficiency of ctDNA recovery. Here, an external quality assessment (EQA) was performed to determine the performance of ctDNA mutation detection work flows that are used in current diagnostic settings across laboratories within the Dutch COIN consortium (ctDNA on the road to implementation in The Netherlands). METHODS Aliquots of 3 high-volume diagnostic leukapheresis (DLA) plasma samples and 3 artificial reference plasma samples with predetermined mutations were distributed among 16 Dutch laboratories. Participating laboratories were requested to perform ctDNA analysis for BRAF exon 15, EGFR exon 18-21, and KRAS exon 2-3 using their regular circulating cell-free DNA (ccfDNA) analysis work flow. Laboratories were assessed based on adherence to the study protocol, overall detection rate, and overall genotyping performance. RESULTS A broad range of preanalytical conditions (e.g., plasma volume, elution volume, and extraction methods) and analytical methodologies (e.g., droplet digital PCR [ddPCR], small-panel PCR assays, and next-generation sequencing [NGS]) were used. Six laboratories (38%) had a performance score of >0.90; all other laboratories scored between 0.26 and 0.80. Although 13 laboratories (81%) reached a 100% overall detection rate, the therapeutically relevant EGFR p.(S752_I759del) (69%), EGFR p.(N771_H773dup) (50%), and KRAS p.(G12C) (48%) mutations were frequently not genotyped accurately. CONCLUSIONS Divergent (pre)analytical protocols could lead to discrepant clinical outcomes when using the same plasma samples. Standardization of (pre)analytical work flows can facilitate the implementation of reproducible liquid biopsy testing in the clinical routine.
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Affiliation(s)
- Paul van der Leest
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Pim Rozendal
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - John Hinrichs
- Department of Pathology, Symbiant B.V., Alkmaar, the Netherlands
| | - Carel J M van Noesel
- Department of Pathology, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - Karen Zwaenepoel
- Department of Pathology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Birgit Deiman
- Clinical Laboratory, Catharina Hospital Eindhoven, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, the Netherlands
- Department of Biomedical Engineering, Laboratory of Chemical Biology, Eindhoven University of Technology, Eindhoven, the Netherlands
- Expert Center Clinical Chemistry Eindhoven, Eindhoven, the Netherlands
| | - Cornelis J J Huijsmans
- Pathologie-DNA, Laboratory for Molecular Diagnostics, Location Jeroen Bosch Hospital, 's-Hertogenbosch, the Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Ernst Jan M Speel
- Department of Pathology, GROW-School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Rick J van Haastert
- Department of Clinical Chemistry, St. Antonius Hospital, Nieuwegein, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Pathology, Radboud Institute for Medical Innovation, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ron H N van Schaik
- Department of Clinical Chemistry, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Laboratory of Translational Genomics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Wendy W de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mathie P G Leers
- Department of Clinical Chemistry & Hematology, Zuyderland Medical Center, Heerlen, the Netherlands
| | - Menno Tamminga
- Department of Pulmonary Medicine, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Daan van den Broek
- Department of Laboratory Medicine, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Léon C van Kempen
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
- Department of Pathology, Antwerp University Hospital, University of Antwerp, Edegem, Belgium
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
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Laguna JC, Pastor B, Nalda I, Hijazo-Pechero S, Teixido C, Potrony M, Puig-Butillé JA, Mezquita L. Incidental pathogenic germline alterations detected through liquid biopsy in patients with solid tumors: prevalence, clinical utility and implications. Br J Cancer 2024; 130:1420-1431. [PMID: 38532104 PMCID: PMC11059286 DOI: 10.1038/s41416-024-02607-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/25/2024] [Indexed: 03/28/2024] Open
Abstract
Liquid biopsy, a minimally invasive approach for detecting tumor biomarkers in blood, has emerged as a leading-edge technique in cancer precision medicine. New evidence has shown that liquid biopsies can incidentally detect pathogenic germline variants (PGVs) associated with cancer predisposition, including in patients with a cancer for which genetic testing is not recommended. The ability to detect these incidental PGV in cancer patients through liquid biopsy raises important questions regarding the management of this information and its clinical implications. This incidental identification of PGVs raises concerns about cancer predisposition and the potential impact on patient management, not only in terms of providing access to treatment based on the tumor molecular profiling, but also the management of revealing genetic predisposition in patients and families. Understanding how to interpret this information is essential to ensure proper decision-making and to optimize cancer treatment and prevention strategies. In this review we provide a comprehensive summary of current evidence of incidental PGVs in cancer predisposition genes identified by liquid biopsy in patients with cancer. We critically review the methodological considerations of liquid biopsy as a tool for germline diagnosis, clinical utility and potential implications for cancer prevention, treatment, and research.
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Affiliation(s)
- Juan Carlos Laguna
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Belén Pastor
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Irene Nalda
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Sara Hijazo-Pechero
- Preclinical and Experimental Research in Thoracic Tumors (PRETT), Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), l'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Teixido
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
- Department of Pathology, Hospital Clinic of Barcelona, Barcelona, Spain
| | - Miriam Potrony
- Biochemistry and Molecular Genetics Department, Hospital Clínic of Barcelona, IDIBAPS, Barcelona, Spain
- CIBER of Rare Diseases (CIBERER), Barcelona, Spain
| | - Joan Antón Puig-Butillé
- CIBER of Rare Diseases (CIBERER), Barcelona, Spain
- Molecular Biology CORE, Hospital Clínic of Barcelona, IDIBAPS, Barcelona, Spain
| | - Laura Mezquita
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain.
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain.
- Department of Medicine, University of Barcelona, Barcelona, Spain.
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Lee JS, Cho EH, Kim B, Hong J, Kim YG, Kim Y, Jang JH, Lee ST, Kong SY, Lee W, Shin S, Song EY. Clinical Practice Guideline for Blood-based Circulating Tumor DNA Assays. Ann Lab Med 2024; 44:195-209. [PMID: 38221747 PMCID: PMC10813828 DOI: 10.3343/alm.2023.0389] [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: 10/02/2023] [Revised: 12/06/2023] [Accepted: 01/06/2024] [Indexed: 01/16/2024] Open
Abstract
Circulating tumor DNA (ctDNA) has emerged as a promising tool for various clinical applications, including early diagnosis, therapeutic target identification, treatment response monitoring, prognosis evaluation, and minimal residual disease detection. Consequently, ctDNA assays have been incorporated into clinical practice. In this review, we offer an in-depth exploration of the clinical implementation of ctDNA assays. Notably, we examined existing evidence related to pre-analytical procedures, analytical components in current technologies, and result interpretation and reporting processes. The primary objective of this guidelines is to provide recommendations for the clinical utilization of ctDNA assays.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Boram Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Young-gon Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
- Dxome Co. Ltd., Seongnam, Korea
| | - Sun-Young Kong
- Department of Laboratory Medicine, National Cancer Center, Goyang, Korea
| | - Woochang Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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Basthi Mohan P, Lochan R, Shetty S. Biomarker in Hepatocellular Carcinoma. Indian J Surg Oncol 2024; 15:261-268. [PMID: 38817995 PMCID: PMC11133295 DOI: 10.1007/s13193-023-01858-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/29/2023] [Indexed: 06/01/2024] Open
Abstract
Liver cancer is one of the most prevalent types of cancer and a major contributor to the socioeconomic burden worldwide. The pathogenesis of hepatocellular carcinoma (HCC) is contributed by various etiological factors like virus infection, excessive alcohol consumption, exposure to toxins, or metabolic disorders. Majority of patients are diagnosed with late-stage HCC, which restricts its management to only palliative care. HCC, if diagnosed early, increases the survival and quality of life. Currently available biomarker (alpha-fetoproteins) have several limitations, that impede the early diagnosis and staging of cancer. This warrants the continous search in pursuit of a novel biomarker. Several research works in diverse areas have contributed to the identification of various novel biomarkers that have shown multifaceted application in early disease diagnosis, which further aid in targeted and effective therapy that can prevent cancer progression. This improves the overall health status of the patient along with significant reduction in caretaker's burden. With the aid of novel technologies, several biomarkers have been investigated and validated in mutliple preliminary research works. Therefore in this review, we have outlined various novel biomarkers that showed promising outcomes in their trials and we have highlighted the developing areas that act as game changers in cancer diagnosis and management.
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Affiliation(s)
- Pooja Basthi Mohan
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
| | - Rajiv Lochan
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
- Lead Consultant Surgeon - HPB and Liver transplantation Surgery, Manipal Hospital, Bengaluru, 560017 Karnataka India
| | - Shiran Shetty
- Department of Gastroenterology and Hepatology, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104 Karnataka India
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Flory A, Wilson-Robles H. Noninvasive Blood-Based Cancer Detection in Veterinary Medicine. Vet Clin North Am Small Anim Pract 2024; 54:541-558. [PMID: 38195361 DOI: 10.1016/j.cvsm.2023.12.008] [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] [Indexed: 01/11/2024]
Abstract
The past decade has seen incredible advances in blood-based cancer detection in people and in dogs - yet this represents only a glimpse of the benefits these tests can provide to patients. The clinical uses of this technology range from screening asymptomatic individuals for early detection to use as an aid in diagnosis when cancer is suspected, to cancer monitoring both during and after treatment. This article summarizes the benefits of early cancer detection and examines use cases and methods of blood-based cancer detection in dogs, including quantitative, qualitative, and alternative approaches.
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Affiliation(s)
- Andi Flory
- PetDx, 9310 Athena Circle, Suite 230, La Jolla, CA 92037, USA.
| | - Heather Wilson-Robles
- Volition Veterinary Diagnostics Development, LLC 1489 West Warm Springs Road Suite 110, Henderson, NV 89014, USA; Ethos Discovery, 10435 Sorrento Valley Road, San Diego, CA 92121, USA; The Oncology Service, United Veterinary Health, 6651 Backlick Road, Springfield, VA 22150, USA
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Xu J, Gao H, Guan X, Meng J, Ding S, Long Q, Yi W. Circulating tumor DNA: from discovery to clinical application in breast cancer. Front Immunol 2024; 15:1355887. [PMID: 38745646 PMCID: PMC11091288 DOI: 10.3389/fimmu.2024.1355887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
Breast cancer (BC) stands out as the cancer with the highest incidence of morbidity and mortality among women worldwide, and its incidence rate is currently trending upwards. Improving the efficiency of breast cancer diagnosis and treatment is crucial, as it can effectively reduce the disease burden. Circulating tumor DNA (ctDNA) originates from the release of tumor cells and plays a pivotal role in the occurrence, development, and metastasis of breast cancer. In recent years, the widespread application of high-throughput analytical technology has made ctDNA a promising biomarker for early cancer detection, monitoring minimal residual disease, early recurrence monitoring, and predicting treatment outcomes. ctDNA-based approaches can effectively compensate for the shortcomings of traditional screening and monitoring methods, which fail to provide real-time information and prospective guidance for breast cancer diagnosis and treatment. This review summarizes the applications of ctDNA in various aspects of breast cancer, including screening, diagnosis, prognosis, treatment, and follow-up. It highlights the current research status in this field and emphasizes the potential for future large-scale clinical applications of ctDNA-based approaches.
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Affiliation(s)
- Jiachi Xu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Hongyu Gao
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Xinyu Guan
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Jiahao Meng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Shirong Ding
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Qian Long
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
| | - Wenjun Yi
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Clinical Research Center For Breast Disease In Hunan Province, Changsha, China
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Ríos-Hoyo A, Monzonís X, Vidal J, Linares J, Montagut C. Unveiling acquired resistance to anti-EGFR therapies in colorectal cancer: a long and winding road. Front Pharmacol 2024; 15:1398419. [PMID: 38711991 PMCID: PMC11070789 DOI: 10.3389/fphar.2024.1398419] [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: 03/09/2024] [Accepted: 04/03/2024] [Indexed: 05/08/2024] Open
Abstract
Emergence of acquired resistance limits the efficacy of the anti-EGFR therapies cetuximab and panitumumab in metastatic colorectal cancer. In the last decade, preclinical and clinical cohort studies have uncovered genomic alterations that confer a selective advantage to tumor cells under EGFR blockade, mainly downstream re-activation of RAS-MEK signaling and mutations in the extracellular domain of EGFR (EGFR-ECD). Liquid biopsies (genotyping of ctDNA) have been established as an excellent tool to easily monitor the dynamics of genomic alterations resistance in the blood of patients and to select patients for rechallenge with anti-EGFR therapies. Accordingly, several clinical trials have shown clinical benefit of rechallenge with anti-EGFR therapy in genomically-selected patients using ctDNA. However, alternative mechanisms underpinning resistance beyond genomics -mainly related to the tumor microenvironment-have been unveiled, specifically relevant in patients receiving chemotherapy-based multi-drug treatment in first line. This review explores the complexity of the multifaceted mechanisms that mediate secondary resistance to anti-EGFR therapies and potential therapeutic strategies to circumvent acquired resistance.
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Affiliation(s)
- Alejandro Ríos-Hoyo
- Yale Cancer Center, Yale School of Medicine, Yale University, New Haven, CT, United States
| | - Xavier Monzonís
- Department of Medical Oncology, Hospital del Mar Research Institute, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Joana Vidal
- Department of Medical Oncology, Hospital del Mar Research Institute, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Jenniffer Linares
- Department of Medical Oncology, Hospital del Mar Research Institute, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - Clara Montagut
- Department of Medical Oncology, Hospital del Mar Research Institute, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
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Valladares-Ayerbes M, Safont MJ, González Flores E, García-Alfonso P, Aranda E, Muñoz AML, Falcó Ferrer E, Cirera Nogueras L, Rodríguez-Salas N, Aparicio J, Llanos Muñoz M, Pimentel Cáceres PP, Castillo Trujillo OA, Vidal Tocino R, Salgado Fernández M, Salud-Salvia A, Massuti Sureda B, Garcia-Carbonero R, Vicente Conesa MÁ, Lloansí Vila A. Sequential RAS mutations evaluation in cell-free DNA of patients with tissue RAS wild-type metastatic colorectal cancer: the PERSEIDA (Cohort 2) study. Clin Transl Oncol 2024:10.1007/s12094-024-03487-4. [PMID: 38642257 DOI: 10.1007/s12094-024-03487-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 03/25/2024] [Indexed: 04/22/2024]
Abstract
PURPOSE RAS (KRAS/NRAS) mutational status on a tumor biopsy is mandatory to guide the best treatment in metastatic colorectal cancer (mCRC). Determining the RAS mutational status by tumor-tissue biopsy is essential in guiding the optimal treatment decision for mCRC. RAS mutations are negative predictive factors for the use of EGFR monoclonal antibodies. Cell-free DNA (cfDNA) analysis enables minimally invasive monitoring of tumor evolution. METHODS/PATIENTS PERSEIDA was an observational, prospective study assessing cfDNA RAS, BRAF and EGFR mutations (using Idylla™) in first-line mCRC, RAS wild-type (baseline tumor-tissue biopsy) patients (cohort 2). Plasma samples were collected before first-line treatment, after 20 ± 2 weeks, and at disease progression. RESULTS 117 patients were included (103 received panitumumab + chemotherapy as first-line treatment). At baseline, 7 (6.8%) patients had RAS mutations, 4 (3.9%) BRAF mutations and no EGFR mutations were detected (cfDNA, panitumumab + chemotherapy subpopulation [panitumumab + Ch]). The baseline RAS mutational status concordance between tissue and liquid biopsies was 94.0% (93.2%, panitumumab + Ch). At 20 weeks, only one patient in the study (included in the panitumumab + Ch) had an emerging cfDNA RAS mutation. No emerging BRAF or EGFR mutations were reported. At disease progression, 6 patients had emergent mutations not present at baseline (RAS conversion rate: 13.3% [6/45]; 15.0% [6/40], panitumumab + Ch). CONCLUSIONS The concordance rate between liquid and solid biopsies at baseline was very high, as previously reported, while our results suggest a considerable emergence of RAS mutations during disease progression. Thus, the dynamics of the genomic landscape in ctDNA may provide relevant information for the management of mCRC patients.
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Affiliation(s)
| | - Maria José Safont
- Consorcio Hospital General Universitario de Valencia, Universidad de Valencia, Valencia; CIBERONC, Valencia, Spain
| | | | - Pilar García-Alfonso
- Medical Oncology Service, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Universidad Complutense, Madrid, Spain
| | | | | | | | | | | | - Jorge Aparicio
- Hospital Universitari i Politècnic La Fe, Valencia, Spain
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Korte B, Mathios D. Innovation in Non-Invasive Diagnosis and Disease Monitoring for Meningiomas. Int J Mol Sci 2024; 25:4195. [PMID: 38673779 PMCID: PMC11050588 DOI: 10.3390/ijms25084195] [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: 02/19/2024] [Revised: 03/26/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Meningiomas are tumors of the central nervous system that vary in their presentation, ranging from benign and slow-growing to highly aggressive. The standard method for diagnosing and classifying meningiomas involves invasive surgery and can fail to provide accurate prognostic information. Liquid biopsy methods, which exploit circulating tumor biomarkers such as DNA, extracellular vesicles, micro-RNA, proteins, and more, offer a non-invasive and dynamic approach for tumor classification, prognostication, and evaluating treatment response. Currently, a clinically approved liquid biopsy test for meningiomas does not exist. This review provides a discussion of current research and the challenges of implementing liquid biopsy techniques for advancing meningioma patient care.
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Affiliation(s)
- Brianna Korte
- Department of Neurosurgery, Washington University Medical Campus, St. Louis, MO 63110, USA
| | - Dimitrios Mathios
- Department of Neurosurgery, Washington University Medical Campus, St. Louis, MO 63110, USA
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62
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Mao Z, Dong S, Yan Y, Wang C, Li W, Wang L, Qian C, Song Y, Tong L, Yu W. Diagnosis of malignant body fluids via cancer-universal methylation in cell-free DNA. JCI Insight 2024; 9:e175482. [PMID: 38587071 PMCID: PMC11128206 DOI: 10.1172/jci.insight.175482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 02/14/2024] [Indexed: 04/09/2024] Open
Abstract
BACKGROUNDDifferentiating malignant from nonmalignant body fluids remains a clinical challenge because of the unsatisfying performance of conventional cytology. We aimed to improve the sensitivity and ubiquity of cancer cell detection by assaying universal cancer-only methylation (UCOM) markers in supernatant cell-free DNA (cfDNA).METHODSAn observational prospective cohort including 1,321 nonmalignant and malignant body fluids of multiple cancers was used to develop and validate a cfDNA UCOM methylation diagnostic assay. All samples were divided into 2 portions for cytology and supernatant cfDNA methylation analysis.RESULTSThe significant hypermethylation of a potentially novel UCOM marker, TAGMe, together with the formerly reported PCDHGB7, was identified in the cfDNA of malignant body fluid samples. The combined model, cell-free cancer-universal methylation (CUE), was developed and validated in a prospective multicancer cohort with markedly elevated sensitivity and specificity, and was further verified in a set containing additional types of malignant body fluids and metastases. In addition, it remained hypersensitive in detecting cancer cells in cytologically negative malignant samples.CONCLUSIONcfDNA methylation markers are robust in detecting tumor cells and are applicable to diverse body fluids and tumor types, providing a feasible complement to current cytology-based diagnostic analyses.TRIAL REGISTRATIONThis study was registered at Chictr.org.cn (ChiCTR2200060532).FUNDINGNational Natural Science Foundation of China (32270645, 31872814, 32000505, 82170088), the National Key R&D Program of Ningxia Hui Autonomous region (2022BEG01003), Shanghai Municipal Key Clinical Specialty (shslczdzk02201), Science and Technology Commission of Shanghai Municipality (20DZ2261200, 20DZ2254400), and Major Special Projects of Basic Research of Shanghai Science and Technology Commission (18JC1411101).
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Affiliation(s)
- Zhanrui Mao
- Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Cancer Metastasis Institute, and Department of General Surgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shihua Dong
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Yu Yan
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chengyang Wang
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Wei Li
- Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Cancer Metastasis Institute, and Department of General Surgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lu Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chengchen Qian
- Shanghai Epiprobe Biotechnology Co., Ltd, Shanghai, China
| | - Yuanlin Song
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Respiratory Research Institute, Shanghai, China
| | - Lin Tong
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
- Shanghai Respiratory Research Institute, Shanghai, China
| | - Wenqiang Yu
- Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Cancer Metastasis Institute, and Department of General Surgery, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
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Giudice V, Ianniello M, De Novellis D, Pezzullo L, Petrillo N, Serio B, D'Addona M, Della Corte AM, Rizzo M, Cuffa B, Castaldi MA, Savarese P, Mori A, Castiello R, Fico A, Savarese G, Selleri C. Non-invasive prenatal test identifies circulating cell-free DNA chromosomal abnormalities derived from clonal hematopoiesis in aggressive hematological malignancies. Clin Exp Med 2024; 24:69. [PMID: 38578383 PMCID: PMC10997720 DOI: 10.1007/s10238-024-01313-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/28/2024] [Indexed: 04/06/2024]
Abstract
Liquid biopsy is a minimally invasive diagnostic tool for identification of tumor-related mutations in circulating cell-free DNA (cfDNA). The aim of this study was to investigate feasibility, sensitivity, and specificity of non-invasive prenatal test (NIPT) for identification of chromosomal abnormalities in cfDNA from a total of 77 consecutive patients with non-Hodgkin B-cell lymphomas, Hodgkin lymphoma (HL), or plasma cell dyscrasia. In this case series, half of patients had at least one alteration, more frequently in chromosome 6 (23.1%), chromosome 9 (20.5%), and chromosomes 3 and 18 (16.7%), with losses of chromosome 6 and gains of chromosome 7 negatively impacting on overall survival (OS), with a 5-year OS of 26.9% and a median OS of 14.6 months, respectively (P = 0.0009 and P = 0.0004). Moreover, B-cell lymphomas had the highest NIPT positivity, especially those with aggressive lymphomas, while patients with plasma cell dyscrasia with extramedullary disease had a higher NIPT positivity compared to conventional cytogenetics analysis and a worse outcome. Therefore, we proposed a NIPT-based liquid biopsy a complementary minimally invasive tool for chromosomal abnormality detection in hematological malignancies. However, prospective studies on larger cohorts are needed to validate clinical utility of NIPT-based liquid biopsy in routinely clinical practice.
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Affiliation(s)
- Valentina Giudice
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, Italy
| | | | - Danilo De Novellis
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, Italy
| | - Luca Pezzullo
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | | | - Bianca Serio
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Matteo D'Addona
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, Italy
| | - Anna Maria Della Corte
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Michela Rizzo
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Bianca Cuffa
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | - Maria Antonietta Castaldi
- Gynecology and Obstetrics Unit, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy
| | | | - Alessio Mori
- Ames Center s.r.l, Casalnuovo di Naples, Naples, Italy
| | | | - Antonio Fico
- Ames Center s.r.l, Casalnuovo di Naples, Naples, Italy
| | | | - Carmine Selleri
- Hematology and Transplant Center, University Hospital "San Giovanni di Dio e Ruggi d'Aragona", Salerno, Italy.
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081, Baronissi, Italy.
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Pope B, Park G, Lau E, Belic J, Lach R, George A, McCoy P, Nguyen A, Grima C, Campbell B, Jung CH, Ditter EJ, Zhao H, Wedge DC, Brewer DS, Lynch AG, Dev H, Gnanpragasam VJ, Rosenfeld N, Hovens CM, Corcoran NM, Massie CE. Ultrasensitive Detection of Circulating Tumour DNA enriches for Patients with a Greater Risk of Recurrence of Clinically Localised Prostate Cancer. Eur Urol 2024; 85:407-410. [PMID: 38378299 DOI: 10.1016/j.eururo.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 12/17/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Affiliation(s)
- Bernard Pope
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia; Melbourne Bioinformatics, The University of Melbourne, Carlton, Australia; Department of Medicine, School of Clinical Sciences, Monash University, Melbourne, Australia; Department of Clinical Pathology, The University of Melbourne, Victorian Comprehensive Cancer Centre, Melbourne, Australia.
| | - Gahee Park
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
| | - Edmund Lau
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia; Melbourne Bioinformatics, The University of Melbourne, Carlton, Australia
| | - Jelena Belic
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
| | - Radoslaw Lach
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
| | - Anne George
- Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK; Department of Surgery, Division of Urology, University of Cambridge, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Academic Urology Group, Department of Surgery, University of Cambridge, Cambridge, UK; Cambridge Urology Translational Research and Clinical Trials, Cambridge, UK
| | - Patrick McCoy
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Anne Nguyen
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Corrina Grima
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Bethany Campbell
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia
| | - Chol-Hee Jung
- Melbourne Bioinformatics, The University of Melbourne, Carlton, Australia
| | - Emma-Jane Ditter
- Cancer Research UK Cambridge Centre, Cambridge, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Hui Zhao
- Cancer Research UK Cambridge Centre, Cambridge, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - David C Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, UK
| | - Daniel S Brewer
- Norwich Medical School, University of East Anglia, Norwich, UK; Earlham Institute, Norwich, UK
| | - Andy G Lynch
- School of Medicine, University of St. Andrews, St. Andrews, UK; School of Mathematics and Statistics, University of St. Andrews, St. Andrews, UK
| | - Harveer Dev
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
| | - Vincent J Gnanpragasam
- Department of Surgery, Division of Urology, University of Cambridge, Cambridge, UK; Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Cambridge Urology Translational Research and Clinical Trials, Cambridge, UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Centre, Cambridge, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Christopher M Hovens
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia; Department of Urology, Western Health, Footscray, Australia; Australian Prostate Cancer Research Centre, Melbourne, Australia
| | - Niall M Corcoran
- Department of Surgery, The University of Melbourne, 5th Floor Clinical Sciences Building, Royal Melbourne Hospital, Grattan Street, Parkville, VIC 3050, Australia; Department of Urology, Western Health, Footscray, Australia; Department of Urology, Royal Melbourne Hospital, Parkville, Australia; Victorian Comprehensive Cancer Centre, Parkville, Australia
| | - Charles E Massie
- Early Cancer Institute, University of Cambridge Department of Oncology, Hutchison Research Centre, Cambridge, UK; Cancer Research UK Cambridge Centre, Cambridge, UK; Department of Oncology, University of Cambridge Hutchison-MRC Research Centre, Cambridge, UK
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Splendiani E, Besharat ZM, Covre A, Maio M, Di Giacomo AM, Ferretti E. Immunotherapy in melanoma: Can we predict response to treatment with circulating biomarkers? Pharmacol Ther 2024; 256:108613. [PMID: 38367867 DOI: 10.1016/j.pharmthera.2024.108613] [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: 10/16/2023] [Revised: 01/08/2024] [Accepted: 02/09/2024] [Indexed: 02/19/2024]
Abstract
Melanoma is the most aggressive form of skin cancer, representing approximately 4% of all cutaneous neoplasms and accounting for up to 80% of deaths. Advanced stages of melanoma involve metastatic processes and are associated with high mortality and morbidity, mainly due to the rapid dissemination and heterogeneous responses to current therapies, including immunotherapy. Immune checkpoint inhibitors (ICIs) are currently used in the treatment of metastatic melanoma (MM) and despite being linked to an increase in patient survival, a high percentage of them still do not benefit from it. Accordingly, the number of therapeutic regimens for MM patients using ICIs either alone or in combination with other therapies has increased, together with the need for reliable biomarkers that can both predict and monitor response to ICIs. In this context, circulating biomarkers, such as DNA, RNA, proteins, and cells, have emerged due to their ability to reflect disease status. Moreover, blood tests are minimally invasive and provide an attractive option to detect biomarkers, avoiding stressful medical procedures. This systematic review aims to evaluate the possibility of a non-invasive biomarker signature that can guide therapeutic decisions. The studies reported here offer valuable insight into how circulating biomarkers can have a role in personalized treatments for melanoma patients receiving ICIs therapy, emphasizing the need for rigorous clinical trials to confirm findings and establish standardized procedures.
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Affiliation(s)
- Elena Splendiani
- Department of Experimental Medicine, Sapienza University, Rome, Italy
| | | | - Alessia Covre
- Center for Immuno-Oncology, Medical Oncology and Immunotherapy, Department of Oncology, University Hospital of Siena, 53100 Siena, Italy; Medical Oncology, Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
| | - Michele Maio
- Center for Immuno-Oncology, Medical Oncology and Immunotherapy, Department of Oncology, University Hospital of Siena, 53100 Siena, Italy; Medical Oncology, Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
| | - Anna Maria Di Giacomo
- Center for Immuno-Oncology, Medical Oncology and Immunotherapy, Department of Oncology, University Hospital of Siena, 53100 Siena, Italy; Medical Oncology, Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy
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Pilala KM, Kotronopoulos G, Levis P, Giagkos GC, Stravodimos K, Vassilacopoulou D, Scorilas A, Avgeris M. MIR145 Core Promoter Methylation in Pretreatment Cell-Free DNA: A Liquid Biopsy Tool for Muscle-Invasive Bladder Cancer Treatment Outcome. JCO Precis Oncol 2024; 8:e2300414. [PMID: 38579191 DOI: 10.1200/po.23.00414] [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: 07/29/2023] [Revised: 01/06/2024] [Accepted: 02/13/2024] [Indexed: 04/07/2024] Open
Abstract
PURPOSE The lack of personalized management of bladder cancer (BlCa) results in patients' lifelong post-treatment monitoring with invasive interventions, underlying the urgent need for tailored and minimally invasive health care services. On the basis of our previous findings on miR-143/145 cluster methylation in bladder tumors, we evaluated its clinical significance in pretreatment cell-free DNA (cfDNA) of patients with BlCa. MATERIALS AND METHODS Methylation analysis was performed in our screening cohort (120 patients with BlCa; 20 age-matched healthy donors) by bisulfite-based pyrosequencing. Tumor recurrence/progression for patients with non-muscle-invasive bladder cancer, and progression and mortality for patients with muscle-invasive bladder cancer (MIBC) were used as clinical end point events in survival analysis. Bootstrap analysis was applied for internal validation of Cox regression models and decision curve analysis for assessment of clinical benefit on disease prognosis. RESULTS Decreased methylation of MIR145 core promoter in pretreatment cfDNA was associated with short-term disease progression (multivariate Cox: hazard ratio [HR], 2.027 [95% CI, 1.157 to 3.551]; P = .010) and poor overall survival (multivariate Cox: HR, 2.098 [95% CI, 1.154 to 3.817]; P = .009) of patients with MIBC after radical cystectomy (RC). Multivariate models incorporating MIR145 promoter methylation in cfDNA with tumor stage clearly ameliorated patients' risk stratification, highlighting superior clinical benefit in MIBC prognostication. CONCLUSION Reduced pretreatment cfDNA methylation of MIR145 core promoter was markedly correlated with increased risk for short-term progression and worse survival of patients with MIBC after RC and adjuvant therapy, supporting modern personalized and minimally invasive prognosis. Methylation profiling of MIR145 core promoter in pretreatment cfDNA could serve as a minimally invasive and independent predictor of MIBC treatment outcome and emerge as a promising marker for blood-based test in BlCa.
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Affiliation(s)
- Katerina-Marina Pilala
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Kotronopoulos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Panagiotis Levis
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios-Christos Giagkos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Stravodimos
- First Department of Urology, "Laiko" General Hospital, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Dido Vassilacopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
| | - Margaritis Avgeris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Athens, Greece
- Laboratory of Clinical Biochemistry-Molecular Diagnostics, Second Department of Pediatrics, School of Medicine, National and Kapodistrian University of Athens, "P. & A. Kyriakou" Children's Hospital, Athens, Greece
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67
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Allen TA. The Role of Circulating Tumor Cells as a Liquid Biopsy for Cancer: Advances, Biology, Technical Challenges, and Clinical Relevance. Cancers (Basel) 2024; 16:1377. [PMID: 38611055 PMCID: PMC11010957 DOI: 10.3390/cancers16071377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Cancer remains a leading cause of mortality worldwide, with metastasis significantly contributing to its lethality. The metastatic spread of tumor cells, primarily through the bloodstream, underscores the importance of circulating tumor cells (CTCs) in oncological research. As a critical component of liquid biopsies, CTCs offer a non-invasive and dynamic window into tumor biology, providing invaluable insights into cancer dissemination, disease progression, and response to treatment. This review article delves into the recent advancements in CTC research, highlighting their emerging role as a biomarker in various cancer types. We explore the latest technologies and methods for CTC isolation and detection, alongside novel approaches to characterizing their biology through genomics, transcriptomics, proteomics, and epigenetic profiling. Additionally, we examine the clinical implementation of these findings, assessing how CTCs are transforming the landscape of cancer diagnosis, prognosis, and management. By offering a comprehensive overview of current developments and potential future directions, this review underscores the significance of CTCs in enhancing our understanding of cancer and in shaping personalized therapeutic strategies, particularly for patients with metastatic disease.
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Liu Y, Zhao W, Hodgson J, Egan M, Cooper Pope CN, Hicks G, Nikolinakos PG, Mao L. CTC-Race: Single-Cell Motility Assay of Circulating Tumor Cells from Metastatic Lung Cancer Patients. ACS NANO 2024; 18:8683-8693. [PMID: 38465942 PMCID: PMC10976960 DOI: 10.1021/acsnano.3c09450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 02/26/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
Distinctive subpopulations of circulating tumor cells (CTCs) with increased motility are considered to possess enhanced tumor-initiating potential and contribute to metastasis. Single-cell analysis of the migratory CTCs may increase our understanding of the metastatic process, yet most studies are limited by technical challenges associated with the isolation and characterization of these cells due to their extreme scarcity and heterogeneity. We report a microfluidic method based on CTCs' chemotactic motility, termed as CTC-Race assay, that can analyze migrating CTCs from metastatic non-small-cell lung cancer (NSCLC) patients with advanced tumor stages and enable concurrent biophysical and biochemical characterization of them with single-cell resolution. Analyses of motile CTCs in the CTC-Race assay, in synergy with other single cell characterization techniques, could provide insights into cancer metastasis.
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Affiliation(s)
- Yang Liu
- School
of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
| | - Wujun Zhao
- FCS
Technology, LLC, Athens, Georgia 30602, United States
| | - Jamie Hodgson
- University
Cancer and Blood Center, LLC, Athens, Georgia 30607, United States
| | - Mary Egan
- University
Cancer and Blood Center, LLC, Athens, Georgia 30607, United States
| | | | - Glenda Hicks
- University
Cancer and Blood Center, LLC, Athens, Georgia 30607, United States
| | | | - Leidong Mao
- School
of Electrical and Computer Engineering, College of Engineering, The University of Georgia, Athens, Georgia 30602, United States
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Jia L, Hu W, Yan X, Shao J, Guo Y, Zhang A, Yu L, Zhou Y, Li Y, Ren L, Dong D. Soluble Periostin is a potential surveillance biomarker for early and long-term response to chemotherapy in advanced breast cancer. Cancer Cell Int 2024; 24:109. [PMID: 38504252 PMCID: PMC10953259 DOI: 10.1186/s12935-024-03298-1] [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: 09/03/2023] [Accepted: 03/08/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Noninvasive biomarkers for the assessment of response to chemotherapy in advanced breast cancer (BCa) are essential for optimized therapeutic decision-making. We evaluated the potential of soluble Periostin (POSTN) in circulation as a novel biomarker for chemotherapy efficacy monitoring. METHODS Two hundred and thirty-one patients with different stages of BCa were included. Of those patients, 58 patients with inoperable metastatic disease receiving HER2-targeted or non-targeted chemotherapy were enrolled to assess the performances of markers in recapitulating the chemotherapy efficacy assessed by imaging. POSTN, together with CA153 or CEA at different time points (C0, C2, and C4) were determined. RESULTS POSTN levels were significantly associated with tumor volume (P < 0.0001) and TNM stages (P < 0.0001) of BCa. For early monitoring, dynamics of POSTN could recapitulate the chemotherapy efficacy among all molecular subtypes (Cohen's weighted kappa = 0.638, P < 0.0001), much better than that of carcinoembryonic antigen (CEA) and cancer antigen 153 (CA15-3). For early partial response, superior performance of POSTN was observed (Cohen's weighted kappa = 0.827, P < 0.0001) in cases with baseline levels above 17.19 ng/mL. For long-term monitoring, the POSTN response was observed to be strongly consistent with the course of the disease. Moreover, progression free survival analysis showed that patients experienced a significant early decrease of POSTN tended to obtain more benefits from the treatments. CONCLUSIONS The current study suggests that soluble POSTN is an informative serum biomarker to complement the current clinical approaches for early and long-term chemotherapy efficacy monitoring in advanced BCa.
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Affiliation(s)
- Li Jia
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huanhuxi Road, Hexi District, Tianjin, 300060, PR China
| | - Wenwei Hu
- Department of Gastroenterology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing, 100088, PR China
| | - Xu Yan
- Department of Anesthesiology, Chinese People's Liberation Army Rocket Force Characteristic Medical Center, Beijing, 100088, PR China
| | - Jie Shao
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huanhuxi Road, Hexi District, Tianjin, 300060, PR China
| | - Yuhong Guo
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Tianjin, 300060, PR China
| | - Aimin Zhang
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huanhuxi Road, Hexi District, Tianjin, 300060, PR China
| | - Lianzi Yu
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huanhuxi Road, Hexi District, Tianjin, 300060, PR China
| | - Yunli Zhou
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huanhuxi Road, Hexi District, Tianjin, 300060, PR China
| | - Yueguo Li
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huanhuxi Road, Hexi District, Tianjin, 300060, PR China.
| | - Li Ren
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huanhuxi Road, Hexi District, Tianjin, 300060, PR China.
| | - Dong Dong
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Tianjin's Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University, Ministry of Education, Huanhuxi Road, Hexi District, Tianjin, 300060, PR China.
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Zhao Y, Ma C, Cai R, Xin L, Li Y, Ke L, Ye W, Ouyang T, Liang J, Wu R, Lin Y. NMR and MS reveal characteristic metabolome atlas and optimize esophageal squamous cell carcinoma early detection. Nat Commun 2024; 15:2463. [PMID: 38504100 PMCID: PMC10951220 DOI: 10.1038/s41467-024-46837-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024] Open
Abstract
Metabolic changes precede malignant histology. However, it remains unclear whether detectable characteristic metabolome exists in esophageal squamous cell carcinoma (ESCC) tissues and biofluids for early diagnosis. Here, we conduct NMR- and MS-based metabolomics on 1,153 matched ESCC tissues, normal mucosae, pre- and one-week post-operative sera and urines from 560 participants across three hospitals, with machine learning and WGCNA. Aberrations in 'alanine, aspartate and glutamate metabolism' proved to be prevalent throughout the ESCC evolution, consistently identified by NMR and MS, and reflected in 16 serum and 10 urine metabolic signatures in both discovery and validation sets. NMR-based simplified panels of any five serum or urine metabolites outperform clinical serological tumor markers (AUC = 0.984 and 0.930, respectively), and are effective in distinguishing early-stage ESCC in test set (serum accuracy = 0.994, urine accuracy = 0.879). Collectively, NMR-based biofluid screening can reveal characteristic metabolic events of ESCC and be feasible for early detection (ChiCTR2300073613).
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Affiliation(s)
- Yan Zhao
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Central Laboratory, Clinical Research Center, Shantou Central Hospital, Shantou, Guangdong, China
| | - Changchun Ma
- Radiation Oncology Department, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Rongzhi Cai
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Lijing Xin
- Animal Imaging and Technology Core, Center for Biomedical Imaging, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Yongsheng Li
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, China
| | - Lixin Ke
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Wei Ye
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Ting Ouyang
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Jiahao Liang
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Renhua Wu
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
| | - Yan Lin
- Radiology Department, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
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71
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Murakami H, Takahama S, Akita H, Kobayashi S, Masuta Y, Nagatsuka Y, Higashiguchi M, Tomokuni A, Yoshida K, Takahashi H, Doki Y, Eguchi H, Matsuura N, Yamamoto T. Circulating tumor-associated antigen-specific IFNγ +4-1BB + CD8 + T cells as peripheral biomarkers of treatment outcomes in patients with pancreatic cancer. Front Immunol 2024; 15:1363568. [PMID: 38550601 PMCID: PMC10972947 DOI: 10.3389/fimmu.2024.1363568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 02/22/2024] [Indexed: 04/02/2024] Open
Abstract
CD8+ T cells affect the outcomes of pancreatic ductal adenocarcinoma (PDAC). Using tissue samples at pre-treatment to monitor the immune response is challenging, while blood samples are beneficial in overcoming this limitation. In this study, we measured peripheral antigen-specific CD8+ T cell responses against four different tumor-associated antigens (TAAs) in PDAC using flow cytometry and investigated their relationships with clinical features. We analyzed the optimal timing within the treatment course for effective immune checkpoint inhibition in vitro. We demonstrated that the frequency of TAA-specific IFNγ+4-1BB+ CD8+ T cells was correlated with a fold reduction in CA19-9 before and after neoadjuvant therapy. Moreover, patients with TAA-specific IFNγ+4-1BB+ CD8+ T cells after surgery exhibited a significantly improved disease-free survival. Anti-PD-1 treatment in vitro increased the frequency of TAA-specific IFNγ+4-1BB+ CD8+ T cells before neoadjuvant therapy in patients, suggesting the importance of the timing of anti-PD-1 inhibition during the treatment regimen. Our results indicate that peripheral immunophenotyping, combined with highly sensitive identification of TAA-specific responses in vitro as well as detailed CD8+ T cell subset profiling via ex vivo analysis, may serve as peripheral biomarkers to predict treatment outcomes and therapeutic efficacy of immunotherapy plus neoadjuvant chemotherapy.
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Affiliation(s)
- Hirotomo Murakami
- Laboratory of Precision Immunology, Center for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shokichi Takahama
- Laboratory of Precision Immunology, Center for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Hirofumi Akita
- Laboratory of Precision Immunology, Center for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Department of Gastroenterological Surgery, Osaka International Cancer Institute, Osaka, Japan
- Next-Generation Precision Medicine Research Center, Osaka International Cancer Institute, Osaka, Japan
| | - Shogo Kobayashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuji Masuta
- Laboratory of Precision Immunology, Center for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Yuta Nagatsuka
- Laboratory of Precision Immunology, Center for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Masaya Higashiguchi
- Laboratory of Precision Immunology, Center for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Akira Tomokuni
- Department of Gastroenterological Surgery, Osaka General Medical Center, Osaka, Japan
| | - Keiichi Yoshida
- Next-Generation Precision Medicine Research Center, Osaka International Cancer Institute, Osaka, Japan
| | - Hidenori Takahashi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hidetoshi Eguchi
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Nariaki Matsuura
- Department of Gastroenterological Surgery, Osaka International Cancer Institute, Osaka, Japan
| | - Takuya Yamamoto
- Laboratory of Precision Immunology, Center for Intractable Diseases and ImmunoGenomics, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
- Next-Generation Precision Medicine Research Center, Osaka International Cancer Institute, Osaka, Japan
- Laboratory of Aging and Immune Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
- Department of Virology and Immunology, Graduate School of Medicine, Osaka University, Osaka, Japan
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72
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Wever BMM, Steenbergen RDM. Unlocking the potential of tumor-derived DNA in urine for cancer detection: methodological challenges and opportunities. Mol Oncol 2024. [PMID: 38462745 DOI: 10.1002/1878-0261.13628] [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: 10/17/2023] [Revised: 12/20/2023] [Accepted: 01/27/2024] [Indexed: 03/12/2024] Open
Abstract
High cancer mortality rates and the rising cancer burden worldwide drive the development of innovative methods in order to advance cancer diagnostics. Urine contains a viable source of tumor material and allows for self-collection from home. Biomarker testing in this liquid biopsy represents a novel approach that is convenient for patients and can be effective in detecting cancer at a curable stage. Here, we set out to provide a detailed overview of the rationale behind urine-based cancer detection, with a focus on non-urological cancers, and its potential for cancer diagnostics. Moreover, evolving methodological challenges and untapped opportunities for urine biomarker testing are discussed, particularly emphasizing DNA methylation of tumor-derived cell-free DNA. We also provide future recommendations for technical advancements in urine-based cancer detection and elaborate on potential mechanisms involved in the transrenal transport of cell-free DNA.
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Affiliation(s)
- Birgit M M Wever
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, The Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, The Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, The Netherlands
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73
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Wang B, Wang M, Lin Y, Zhao J, Gu H, Li X. Circulating tumor DNA methylation: a promising clinical tool for cancer diagnosis and management. Clin Chem Lab Med 2024; 0:cclm-2023-1327. [PMID: 38443752 DOI: 10.1515/cclm-2023-1327] [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: 11/23/2023] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Cancer continues to pose significant challenges to the medical community. Early detection, accurate molecular profiling, and adequate assessment of treatment response are critical factors in improving the quality of life and survival of cancer patients. Accumulating evidence shows that circulating tumor DNA (ctDNA) shed by tumors into the peripheral blood preserves the genetic and epigenetic information of primary tumors. Notably, DNA methylation, an essential and stable epigenetic modification, exhibits both cancer- and tissue-specific patterns. As a result, ctDNA methylation has emerged as a promising molecular marker for noninvasive testing in cancer clinics. In this review, we summarize the existing techniques for ctDNA methylation detection, describe the current research status of ctDNA methylation, and present the potential applications of ctDNA-based assays in the clinic. The insights presented in this article could serve as a roadmap for future research and clinical applications of ctDNA methylation.
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Affiliation(s)
- Binliang Wang
- Department of Respiratory Medicine, Huangyan Hospital Affiliated to Wenzhou Medical University, Taizhou, P.R. China
| | - Meng Wang
- Institute of Health Education, Hangzhou Center for Disease Control and Prevention, Hangzhou, P.R. China
| | - Ya Lin
- Zhejiang University of Chinese Medicine, Hangzhou, P.R. China
| | - Jinlan Zhao
- Scientific Research Department, Zhejiang Shengting Medical Company, Hangzhou, P.R. China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P.R. China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, P.R. China
| | - Xiangjuan Li
- Department of Gynaecology, Hangzhou Obstetrics and Gynecology Hospital, Hangzhou, P.R. China
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74
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Zhang Y, Liu R, Li J, Ma H, Bao W, Jiang J, Guo C, Tan D, Cheng X, Dai L, Ming Y. Circulating cell-free DNA as a biomarker for diagnosis of Schistosomiasis japonica. Parasit Vectors 2024; 17:114. [PMID: 38449022 PMCID: PMC10918879 DOI: 10.1186/s13071-024-06203-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Schistosomiasis, a neglected tropical disease, remains an important public health problem. Although there are various methods for diagnosing schistosomiasis, many limitations still exist. Early diagnosis and treatment of schistosomiasis can significantly improve survival and prognosis of patients. METHODOLOGY Circulating cell-free (cf)DNA has been widely used in the diagnosis of various diseases. In our study, we evaluated the diagnostic value of circulating cfDNA for schistosomiasis caused by Schistosoma japonicum. We focused on the tandem sequences and mitochondrial genes of S. japonicum to identify highly sensitive and specific targets for diagnosis of Schistosomiasis japonica. RESULTS Through data screening and analysis, we ultimately identified four specific tandem sequences (TD-1, TD-2, TD-3. and TD-4) and six mitochondrial genes (COX1(1), COX1(2), CYTB, ATP6, COX3, and ND5). We designed specific primers to detect the amount of circulating cfDNA in S. japonicum-infected mouse and chronic schistosomiasis patients. Our results showed that the number of tandem sequences was significantly higher than that of the mitochondrial genes. A S. japonicum infection model in mice suggested that infection of S. japonicum can be diagnosed by detecting circulating cfDNA as early as the first week. We measured the expression levels of circulating cfDNA (TD-1, TD-2, and TD-3) at different time points and found that TD-3 expression was significantly higher than that of TD-1 or TD-2. We also infected mice with different quantities of cercariae (20 s and 80 s). The level of cfDNA (TD-3) in the 80 s infection group was significantly higher than in the 20 s infection group. Additionally, cfDNA (TD-3) levels increased after egg deposition. Meanwhile, we tested 42 patients with chronic Schistosomiasis japonica and circulating cfDNA (TD-3) was detected in nine patients. CONCLUSIONS We have screened highly sensitive targets for the diagnosis of Schistosomiasis japonica, and the detection of circulating cfDNA is a rapid and effective method for the diagnosis of Schistosomiasis japonica. The levels of cfDNA is correlated with cercariae infection severity. Early detection and diagnosis of schistosomiasis is crucial for patient treatment and improving prognosis.
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Affiliation(s)
- Yu Zhang
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Engineering and Technology Research Center for Transplantation Medicine, of National Health Commission, Changsha, Hunan, China
- Hunan Province Clinical Research Center for Infectious Diseases, Changsha, Hunan, China
| | - Rangjiao Liu
- Sanway Clinical Laboratories, Changsha, Hunan, China
| | - Junhui Li
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Engineering and Technology Research Center for Transplantation Medicine, of National Health Commission, Changsha, Hunan, China
- Hunan Province Clinical Research Center for Infectious Diseases, Changsha, Hunan, China
| | - Hongchang Ma
- Sansure Biotech Incoporation, Changsha, Hunan, China
| | - Wenjuan Bao
- Sanway Clinical Laboratories, Changsha, Hunan, China
| | - Jie Jiang
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Engineering and Technology Research Center for Transplantation Medicine, of National Health Commission, Changsha, Hunan, China
- Hunan Province Clinical Research Center for Infectious Diseases, Changsha, Hunan, China
| | - Chen Guo
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Engineering and Technology Research Center for Transplantation Medicine, of National Health Commission, Changsha, Hunan, China
- Hunan Province Clinical Research Center for Infectious Diseases, Changsha, Hunan, China
| | - Deyong Tan
- Sansure Biotech Incoporation, Changsha, Hunan, China
| | - Xing Cheng
- Sansure Biotech Incoporation, Changsha, Hunan, China
| | - Lizhong Dai
- Sansure Biotech Incoporation, Changsha, Hunan, China.
| | - Yingzi Ming
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Engineering and Technology Research Center for Transplantation Medicine, of National Health Commission, Changsha, Hunan, China.
- Hunan Province Clinical Research Center for Infectious Diseases, Changsha, Hunan, China.
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Fei X, Du X, Wang J, Liu J, Gong Y, Zhao Z, Cao Z, Fu Q, Zhu Y, Dong L, Dong B, Pan J, Sun W, Xie S, Xue W. Precise diagnosis and risk stratification of prostate cancer by comprehensive serum metabolic fingerprints: a prediction model study. Int J Surg 2024; 110:1450-1462. [PMID: 38181121 PMCID: PMC10942223 DOI: 10.1097/js9.0000000000001033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
OBJECTIVES Prostate cancer (PCa) is one of the most common malignancies in men worldwide and has caused increasing clinical morbidity and mortality, making timely diagnosis and accurate staging crucial. The authors introduced a novel approach based on mass spectrometry for precise diagnosis and stratification of PCa to facilitate clinical decision-making. METHODS Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry analysis of trace blood samples was combined with machine learning algorithms to construct diagnostic and stratification models. A total of 367 subjects, comprising 181 with PCa and 186 with non-PCa were enrolled. Additional 60 subjects, comprising 30 with PCa and 30 with non-PCa were enrolled as an external cohort for validation. Subsequent metabolomic analysis was carried out using Autoflex MALDI-TOF, and the mass spectra were introduced into various algorithms to construct different models. RESULTS Serum metabolic fingerprints were successfully obtained from 181 patients with PCa and 186 patients with non-PCa. The diagnostic model based on the eight signals demonstrated a remarkable area under curve of 100% and was validated in the external cohort with the area under curve of 87.3%. Fifteen signals were selected for enrichment analysis, revealing the potential metabolic pathways that facilitate tumorigenesis. Furthermore, the stage prediction model with an overall accuracy of 85.9% precisely classified subjects with localized disease and those with metastasis. The risk stratification model, with an overall accuracy of 89.6%, precisely classified the subjects as low-risk and high-risk. CONCLUSIONS Our study facilitated the timely diagnosis and risk stratification of PCa and provided new insights into the underlying mechanisms of metabolic alterations in PCa.
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Affiliation(s)
| | | | | | | | | | - Zejun Zhao
- Department of Ultrasound, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine
| | - Zhibin Cao
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong, People’s Republic of China
| | - Qibo Fu
- Medical Science and Technology Innovation Center, Shandong First Medical University and Shandong Academy of Medical Sciences, Shandong, People’s Republic of China
| | | | | | | | | | - Wenshe Sun
- Department of Urology, Jiading District Central Hospital, Shanghai University of Medicine and Health Sciences, Shanghai
| | - Shaowei Xie
- Department of Ultrasound, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine
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Franceschini GM, Quaini O, Mizuno K, Orlando F, Ciani Y, Ku SY, Sigouros M, Rothmann E, Alonso A, Benelli M, Nardella C, Auh J, Freeman D, Hanratty B, Adil M, Elemento O, Tagawa ST, Feng FY, Caffo O, Buttigliero C, Basso U, Nelson PS, Corey E, Haffner MC, Attard G, Aparicio A, Demichelis F, Beltran H. Noninvasive Detection of Neuroendocrine Prostate Cancer through Targeted Cell-free DNA Methylation. Cancer Discov 2024; 14:424-445. [PMID: 38197680 PMCID: PMC10905672 DOI: 10.1158/2159-8290.cd-23-0754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/31/2023] [Accepted: 12/15/2023] [Indexed: 01/11/2024]
Abstract
Castration-resistant prostate cancer (CRPC) is a heterogeneous disease associated with phenotypic subtypes that drive therapy response and outcome differences. Histologic transformation to castration-resistant neuroendocrine prostate cancer (CRPC-NE) is associated with distinct epigenetic alterations, including changes in DNA methylation. The current diagnosis of CRPC-NE is challenging and relies on metastatic biopsy. We developed a targeted DNA methylation assay to detect CRPC-NE using plasma cell-free DNA (cfDNA). The assay quantifies tumor content and provides a phenotype evidence score that captures diverse CRPC phenotypes, leveraging regions to inform transcriptional state. We tested the design in independent clinical cohorts (n = 222 plasma samples) and qualified it achieving an AUC > 0.93 for detecting pathology-confirmed CRPC-NE (n = 136). Methylation-defined cfDNA tumor content was associated with clinical outcomes in two prospective phase II clinical trials geared towards aggressive variant CRPC and CRPC-NE. These data support the application of targeted DNA methylation for CRPC-NE detection and patient stratification. SIGNIFICANCE Neuroendocrine prostate cancer is an aggressive subtype of treatment-resistant prostate cancer. Early detection is important, but the diagnosis currently relies on metastatic biopsy. We describe the development and validation of a plasma cell-free DNA targeted methylation panel that can quantify tumor fraction and identify patients with neuroendocrine prostate cancer noninvasively. This article is featured in Selected Articles from This Issue, p. 384.
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Affiliation(s)
- Gian Marco Franceschini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Orsetta Quaini
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Kei Mizuno
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Francesco Orlando
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Yari Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Sheng-Yu Ku
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Michael Sigouros
- Institute for Computational Biomedicine and Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Emily Rothmann
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Alicia Alonso
- Institute for Computational Biomedicine and Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | | | - Caterina Nardella
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Joonghoon Auh
- Institute for Computational Biomedicine and Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Dory Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Brian Hanratty
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mohamed Adil
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Olivier Elemento
- Institute for Computational Biomedicine and Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York
| | - Scott T. Tagawa
- Department of Medicine, Division of Medical Oncology, Weill Cornell Medicine, New York, New York
| | - Felix Y. Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Orazio Caffo
- Department of Medical Oncology, Santa Chiara Hospital, Trento, Italy
| | - Consuelo Buttigliero
- Department of Oncology, University of Turin, San Luigi Gonzaga Hospital, Orbassano, Turin, Italy
| | - Umberto Basso
- Department of Oncology, Istituto Oncologico Veneto IOV - IRCCS, Padua, Italy
| | | | - Eva Corey
- University of Washington, Seattle, Washington
| | - Michael C. Haffner
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- University of Washington, Seattle, Washington
| | - Gerhardt Attard
- Cancer Institute and University College London Hospitals, University College London, London, United Kingdom
| | - Ana Aparicio
- Department of GU Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Francesca Demichelis
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Himisha Beltran
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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77
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Wang H, Yang S, Chen L, Li Y, He P, Wang G, Dong H, Ma P, Ding G. Tumor diagnosis using carbon-based quantum dots: Detection based on the hallmarks of cancer. Bioact Mater 2024; 33:174-222. [PMID: 38034499 PMCID: PMC10684566 DOI: 10.1016/j.bioactmat.2023.10.004] [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: 06/28/2023] [Revised: 09/15/2023] [Accepted: 10/05/2023] [Indexed: 12/02/2023] Open
Abstract
Carbon-based quantum dots (CQDs) have been shown to have promising application value in tumor diagnosis. Their use, however, is severely hindered by the complicated nature of the nanostructures in the CQDs. Furthermore, it seems impossible to formulate the mechanisms involved using the inadequate theoretical frameworks that are currently available for CQDs. In this review, we re-consider the structure-property relationships of CQDs and summarize the current state of development of CQDs-based tumor diagnosis based on biological theories that are fully developed. The advantages and deficiencies of recent research on CQDs-based tumor diagnosis are thus explained in terms of the manifestation of nine essential changes in cell physiology. This review makes significant progress in addressing related problems encountered with other nanomaterials.
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Affiliation(s)
- Hang Wang
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- CAS Center for Excellence in Superconducting Electronics (CENSE), Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Siwei Yang
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Liangfeng Chen
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Yongqiang Li
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Peng He
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Gang Wang
- Department of Microelectronic Science and Engineering, School of Physical Science and Technology, Ningbo University, Ningbo, 315211, PR China
| | - Hui Dong
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- CAS Center for Excellence in Superconducting Electronics (CENSE), Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, PR China
| | - Guqiao Ding
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
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78
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Giannini LAA, Boers RG, van der Ende EL, Poos JM, Jiskoot LC, Boers JB, van IJcken WFJ, Dopper EG, Pijnenburg YAL, Seelaar H, Meeter LH, van Rooij JGJ, Scheper W, Gribnau J, van Swieten JC. Distinctive cell-free DNA methylation characterizes presymptomatic genetic frontotemporal dementia. Ann Clin Transl Neurol 2024; 11:744-756. [PMID: 38481040 DOI: 10.1002/acn3.51997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/01/2023] [Accepted: 12/27/2023] [Indexed: 03/27/2024] Open
Abstract
OBJECTIVE Methylation of plasma cell-free DNA (cfDNA) has potential as a marker of brain damage in neurodegenerative diseases such as frontotemporal dementia (FTD). Here, we study methylation of cfDNA in presymptomatic and symptomatic carriers of genetic FTD pathogenic variants, next to healthy controls. METHODS cfDNA was isolated from cross-sectional plasma of 10 presymptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), 10 symptomatic carriers (4 C9orf72, 4 GRN, and 2 MAPT), and 9 healthy controls. Genome-wide methylation of cfDNA was determined using a high-resolution sequencing technique (MeD-seq). Cumulative scores based on the identified differentially methylated regions (DMRs) were estimated for presymptomatic carriers (vs. controls and symptomatic carriers), and reevaluated in a validation cohort (8 presymptomatic: 3 C9orf72, 3 GRN, and 2 MAPT; 26 symptomatic: 7 C9orf72, 6 GRN, 12 MAPT, and 1 TARDBP; 13 noncarriers from genetic FTD families). RESULTS Presymptomatic carriers showed a distinctive methylation profile compared to healthy controls and symptomatic carriers. Cumulative DMR scores in presymptomatic carriers enabled to significantly differentiate presymptomatic carriers from healthy controls (p < 0.001) and symptomatic carriers (p < 0.001). In the validation cohort, these scores differentiated presymptomatic carriers from symptomatic carriers (p ≤ 0.007) only. Transcription-start-site methylation in presymptomatic carriers, generally associated with gene downregulation, was enriched for genes involved in ubiquitin-dependent processes, while gene body methylation, generally associated with gene upregulation, was enriched for genes involved in neuronal cell processes. INTERPRETATION A distinctive methylation profile of cfDNA characterizes the presymptomatic stage of genetic FTD, and could reflect neuronal death in this stage.
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Affiliation(s)
- Lucia A A Giannini
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ruben G Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Emma L van der Ende
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Clinical Chemistry, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Jackie M Poos
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lize C Jiskoot
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joachim B Boers
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Elise G Dopper
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Yolande A L Pijnenburg
- Alzheimer Center Amsterdam, Neurology, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
| | - Harro Seelaar
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lieke H Meeter
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen G J van Rooij
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wiep Scheper
- Amsterdam Neuroscience, Neurodegeneration, Amsterdam, The Netherlands
- Department of Functional Genomics, Center for Neurogenomics and Cognitive Research, Faculty of Science, Vrije Universiteit, Amsterdam, The Netherlands
- Department of Human Genetics, Vrije Universiteit, Amsterdam UMC location Vumc, Amsterdam, The Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - John C van Swieten
- Department of Neurology, Alzheimer Center Erasmus MC, Erasmus University Medical Center, Rotterdam, The Netherlands
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79
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Valcz G, Buzás EI, Gatenby RA, Újvári B, Molnár B. Small extracellular vesicles from surviving cancer cells as multiparametric monitoring tools of measurable residual disease and therapeutic efficiency. Biochim Biophys Acta Rev Cancer 2024; 1879:189088. [PMID: 38387823 DOI: 10.1016/j.bbcan.2024.189088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/13/2023] [Accepted: 02/18/2024] [Indexed: 02/24/2024]
Abstract
Although conventional anti-cancer therapies remove most cells of the tumor mass, small surviving populations may evolve adaptive resistance strategies, which lead to treatment failure. The size of the resistant population initially may not reach the threshold of clinical detection (designated as measurable residual disease/MRD) thus, its investigation requires highly sensitive and specific methods. Here, we discuss that the specific molecular fingerprint of tumor-derived small extracellular vesicles (sEVs) is suitable for longitudinal monitoring of MRD. Furthermore, we present a concept that exploiting the multiparametric nature of sEVs may help early detection of recurrence and the design of dynamic, evolution-adjusted treatments.
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Affiliation(s)
- Gábor Valcz
- HUN-REN-SU Translational Extracellular Vesicle Research Group, Budapest, Hungary; Department of Image Analysis, 3DHISTECH Ltd, Budapest, Hungary.
| | - Edit I Buzás
- HUN-REN-SU Translational Extracellular Vesicle Research Group, Budapest, Hungary; Institute of Genetics, Cell- and Immunobiology, Semmelweis University, Budapest, Hungary; HCEMM-SU Extracellular Vesicles Research Group, Budapest, Hungary
| | - Robert A Gatenby
- Cancer Biology and Evolution Program, Moffitt Cancer Center, Tampa, FL, USA
| | - Beáta Újvári
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds, VIC, Australia
| | - Béla Molnár
- Department of Image Analysis, 3DHISTECH Ltd, Budapest, Hungary; Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
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80
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Sender R, Noor E, Milo R, Dor Y. What fraction of cellular DNA turnover becomes cfDNA? eLife 2024; 12:RP89321. [PMID: 38407214 PMCID: PMC10942627 DOI: 10.7554/elife.89321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
Cell-free DNA (cfDNA) tests use small amounts of DNA in the bloodstream as biomarkers. While it is thought that cfDNA is largely released by dying cells, the proportion of dying cells' DNA that reaches the bloodstream is unknown. Here, we integrate estimates of cellular turnover rates to calculate the expected amount of cfDNA. By comparing this to the actual amount of cell type-specific cfDNA, we estimate the proportion of DNA reaching plasma as cfDNA. We demonstrate that <10% of the DNA from dying cells is detectable in plasma, and the ratios of measured to expected cfDNA levels vary a thousand-fold among cell types, often reaching well below 0.1%. The analysis suggests that local clearance, presumably via phagocytosis, takes up most of the dying cells' DNA. Insights into the underlying mechanism may help to understand the physiological significance of cfDNA and improve the sensitivity of liquid biopsies.
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Affiliation(s)
- Ron Sender
- Weizmann Institute of ScienceRehovotIsrael
| | - Elad Noor
- Weizmann Institute of ScienceRehovotIsrael
| | - Ron Milo
- Weizmann Institute of ScienceRehovotIsrael
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel Canada, the Hebrew University-Hadassah Medical SchoolJerusalemIsrael
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81
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Kong H, Yi K, Mintz RL, Wang B, Xu Y, Lao YH, Tao Y, Li M. CRISPR/Cas detection with nanodevices: moving deeper into liquid biopsy. Chem Commun (Camb) 2024; 60:2301-2319. [PMID: 38251733 DOI: 10.1039/d3cc05375j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
The emerging field of liquid biopsy has garnered significant interest in precision diagnostics, offering a non-invasive and repetitive method for analyzing bodily fluids to procure real-time diagnostic data. The precision and accuracy offered by the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas) technology have advanced and broadened the applications of liquid biopsy. Significantly, when combined with swiftly advancing nanotechnology, CRISPR/Cas-mediated nanodevices show vast potential in precise liquid biopsy applications. However, persistent challenges are still associated with off-target effects, and the current platforms also constrain the performance of the assays. In this review, we highlight the merits of CRISPR/Cas systems in liquid biopsy, tracing the development of CRISPR/Cas systems and their current applications in disease diagnosis particularly in liquid biopsies. We also outline ongoing efforts to design nanoscale devices with improved sensing and readout capabilities, aiming to enhance the performance of CRISPR/Cas detectors in liquid biopsy. Finally, we identify the critical obstacles hindering the widespread adoption of CRISPR/Cas liquid biopsy and explore potential solutions. This feature article presents a comprehensive overview of CRISPR/Cas-mediated liquid biopsies, emphasizing the progress in integrating nanodevices to improve specificity and sensitivity. It also sheds light on future research directions in employing nanodevices for CRISPR/Cas-based liquid biopsies in the realm of precision medicine.
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Affiliation(s)
- Huimin Kong
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Ke Yi
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Rachel L Mintz
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Bin Wang
- Department of Infectious Diseases, Center of Infectious Diseases and Pathogen Biology, Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, The First Hospital of Jilin University, Changchun 130061, China
| | - Yanteng Xu
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Yeh-Hsing Lao
- Department of Pharmaceutical Sciences, University at Buffalo, The State University of New York, Buffalo, NY, 14214, USA
| | - Yu Tao
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Mingqiang Li
- Laboratory of Biomaterials and Translational Medicine, Center for Nanomedicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
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82
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Wang HY, Lin WY, Zhou C, Yang ZA, Kalpana S, Lebowitz MS. Integrating Artificial Intelligence for Advancing Multiple-Cancer Early Detection via Serum Biomarkers: A Narrative Review. Cancers (Basel) 2024; 16:862. [PMID: 38473224 DOI: 10.3390/cancers16050862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 02/08/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
The concept and policies of multicancer early detection (MCED) have gained significant attention from governments worldwide in recent years. In the era of burgeoning artificial intelligence (AI) technology, the integration of MCED with AI has become a prevailing trend, giving rise to a plethora of MCED AI products. However, due to the heterogeneity of both the detection targets and the AI technologies, the overall diversity of MCED AI products remains considerable. The types of detection targets encompass protein biomarkers, cell-free DNA, or combinations of these biomarkers. In the development of AI models, different model training approaches are employed, including datasets of case-control studies or real-world cancer screening datasets. Various validation techniques, such as cross-validation, location-wise validation, and time-wise validation, are used. All of the factors show significant impacts on the predictive efficacy of MCED AIs. After the completion of AI model development, deploying the MCED AIs in clinical practice presents numerous challenges, including presenting the predictive reports, identifying the potential locations and types of tumors, and addressing cancer-related information, such as clinical follow-up and treatment. This study reviews several mature MCED AI products currently available in the market, detecting their composing factors from serum biomarker detection, MCED AI training/validation, and the clinical application. This review illuminates the challenges encountered by existing MCED AI products across these stages, offering insights into the continued development and obstacles within the field of MCED AI.
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Affiliation(s)
- Hsin-Yao Wang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33343, Taiwan
- School of Medicine, National Tsing Hua University, Hsinchu 300044, Taiwan
- 20/20 GeneSystems, Gaithersburg, MD 20877, USA
| | - Wan-Ying Lin
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33343, Taiwan
| | | | - Zih-Ang Yang
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33343, Taiwan
| | - Sriram Kalpana
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan 33343, Taiwan
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83
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Ding T, Diao Y, Zeng X, Zhou L, Wu G, Liu J, Hao X. Influential factors on urine EV DNA methylation detection and its diagnostic potential in prostate cancer. Front Genet 2024; 15:1338468. [PMID: 38440192 PMCID: PMC10909848 DOI: 10.3389/fgene.2024.1338468] [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: 11/16/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024] Open
Abstract
The value of Extracellular vesicles (EVs) diagnostic markers is widely recognized. However, current research on EV DNA remains limited. This study investigates the biological properties, preprocessing factors, and diagnostic potential of EV DNA. We found that DNA positive vesicles account for 23.3% ± 6.7% of the urine total EV, with a large amount of DNA attached to the outside. EV DNA fragments are large, there is no significant effect on uEV DNA when store urine less than 6 h at 4°C. In addition, the influence of different EV extraction methods on methylation detection is also minor. More importantly, RASSF1A methylation in urine total EV DNA can distinguish between PCa and BPH, with an AUC of 0.874. Our results suggest the potential of urine EV DNA as a novel marker for PCa diagnosis. This provides a new idea for the study of urinary tumor markers.
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Affiliation(s)
- Ting Ding
- Fourth Military Medical University (Air Force Medical University), Xi’an, China
- School of Medicine, Northwest University, Xi’an, China
| | - Yanjun Diao
- Fourth Military Medical University (Air Force Medical University), Xi’an, China
| | - Xianfei Zeng
- School of Medicine, Northwest University, Xi’an, China
- Shanxi Lifegen Co., Ltd., Xi’an, China
| | - Lei Zhou
- Fourth Military Medical University (Air Force Medical University), Xi’an, China
| | - Guojun Wu
- School of Medicine, Northwest University, Xi’an, China
- Department of Urology, Xi’an People’s Hospital(Xi’an Fourth Hospital), Xi’an, China
| | - Jiayun Liu
- Fourth Military Medical University (Air Force Medical University), Xi’an, China
| | - Xiaoke Hao
- Fourth Military Medical University (Air Force Medical University), Xi’an, China
- School of Medicine, Northwest University, Xi’an, China
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84
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Wang Z, Wang Q, Qin F, Chen J. Exosomes: a promising avenue for cancer diagnosis beyond treatment. Front Cell Dev Biol 2024; 12:1344705. [PMID: 38419843 PMCID: PMC10900531 DOI: 10.3389/fcell.2024.1344705] [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: 11/26/2023] [Accepted: 01/31/2024] [Indexed: 03/02/2024] Open
Abstract
Exosomes, extracellular vesicles secreted by cells, have garnered significant attention in recent years for their remarkable therapeutic potential. These nanoscale carriers can be harnessed for the targeted delivery of therapeutic agents, such as pharmaceuticals, proteins, and nucleic acids, across biological barriers. This versatile attribute of exosomes is a promising modality for precision medicine applications, notably in the realm of cancer therapy. However, despite their substantial therapeutic potential, exosomes still confront challenges tied to standardization and scalability that impede their practice in clinical applications. Moreover, heterogeneity in isolation methodologies and limited cargo loading mechanisms pose obstacles to ensuring consistent outcomes, thereby constraining their therapeutic utility. In contrast, exosomes exhibit a distinct advantage in cancer diagnosis, as they harbor specific signatures reflective of the tumor's genetic and proteomic profile. This characteristic endows them with the potential to serve as valuable liquid biopsies for non-invasive and real-time monitoring, making possible early cancer detection for the development of personalized treatment strategies. In this review, we provide an extensive evaluation of the advancements in exosome research, critically examining their advantages and limitations in the context of cancer therapy and early diagnosis. Furthermore, we present a curated overview of the most recent technological innovations utilizing exosomes, with a focus on enhancing the efficacy of early cancer detection.
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Affiliation(s)
- Zhu Wang
- Breast Center, West China Hospital, Sichuan University, Chengdu, China
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Institute for Breast Health Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Qianqian Wang
- Department of Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng Qin
- School of Basic Medicine, Dali University, Dali, Yunnan, China
| | - Jie Chen
- Breast Center, West China Hospital, Sichuan University, Chengdu, China
- Department of General Surgery, West China Hospital, Sichuan University, Chengdu, China
- Institute for Breast Health Medicine, West China Hospital, Sichuan University, Chengdu, China
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85
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Riedl JM, Moik F, Esterl T, Kostmann SM, Gerger A, Jost PJ. Molecular diagnostics tailoring personalized cancer therapy-an oncologist's view. Virchows Arch 2024; 484:169-179. [PMID: 37982847 PMCID: PMC10948510 DOI: 10.1007/s00428-023-03702-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 10/27/2023] [Accepted: 11/04/2023] [Indexed: 11/21/2023]
Abstract
Medical oncology is rapidly evolving with the implementation of personalized, targeted therapies. Advances in molecular diagnostics and the biologic understanding of cancer pathophysiology led to the identification of specific genetic alterations as drivers of cancer progression. Further, improvements in drug development enable the direct interference with these pathways, which allow tailoring personalized treatments based on a distinct molecular characterization of tumors. Thereby, we are currently experiencing a paradigm-shift in the treatment of cancers towards cancer-type agnostic, molecularly targeted, personalized therapies. However, this concept has several important hurdles and limitations to overcome to ultimately increase the proportion of patients benefitting from the precision oncology approach. These include the assessment of clinical relevancy of identified alterations, capturing and interpreting levels of heterogeneity based on intra-tumoral or time-dependent molecular evolution, and challenges in the practical implementation of precision oncology in routine clinical care. In the present review, we summarize the current state of cancer-agnostic precision oncology, discuss the concept of molecular tumor boards, and consider current limitations of personalized cancer therapy. Further, we provide an outlook towards potential future developments including the implementation of functionality assessments of identified genetic alterations and the broader use of liquid biopsies in order to obtain more comprehensive and longitudinal genetic information that might guide personalized cancer therapy in the future.
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Affiliation(s)
- Jakob M Riedl
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Florian Moik
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Tamara Esterl
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Sarah M Kostmann
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Armin Gerger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Philipp J Jost
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria.
- Medical Department III for Haematology and Oncology, School of Medicine, Technical University of Munich, Munich, Germany.
- BioTechMed-Graz, Graz, Austria.
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86
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Zhang K, Fu R, Liu R, Su Z. Circulating cell-free DNA-based multi-cancer early detection. Trends Cancer 2024; 10:161-174. [PMID: 37709615 DOI: 10.1016/j.trecan.2023.08.010] [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: 07/03/2023] [Revised: 08/03/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023]
Abstract
Patients benefit considerably from early detection of cancer. Existing single-cancer tests have various limitations, which could be effectively addressed by circulating cell-free DNA (cfDNA)-based multi-cancer early detection (MCED). With sensitive detection and accurate localization of multiple cancer types at a very low and fixed false-positive rate (FPR), MCED has great potential to revolutionize early cancer detection. Herein, we review state-of-the-art approaches for cfDNA-based MCED and their limitations and discuss both technical and clinical challenges in the development and application of MCED tests. Given the constant improvements in technology and understanding of cancer biology, we propose that a cfDNA-based targeted sequencing assay that integrates multimodal features should be optimized for MCED.
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Affiliation(s)
- Kai Zhang
- Department of Cancer Prevention, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 17 South Panjiayuan Lane, Chaoyang District, Beijing 100021, China
| | - Ruiqing Fu
- Singlera Genomics Ltd, Shanghai 201203, China
| | - Rui Liu
- Singlera Genomics Ltd, Shanghai 201203, China
| | - Zhixi Su
- Singlera Genomics Ltd, Shanghai 201203, China.
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87
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Mishra S, Srivastava P, Pandey A, Shukla S, Agarwal A, Husain N. Diagnostic Utility of Next-Generation Sequencing in Circulating Free DNA and a Comparison With Matched Tissue in Gallbladder Carcinoma. J Transl Med 2024; 104:100301. [PMID: 38092180 DOI: 10.1016/j.labinv.2023.100301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/15/2023] [Accepted: 12/05/2023] [Indexed: 01/14/2024] Open
Abstract
Mutation detection for therapy monitoring in cell-free DNA (cfDNA) is used clinically for some malignancies. Gallbladder carcinoma (GBC) presents a diagnostic challenge and has limited late-stage treatment options. To our knowledge, this novel study examines, for the first time, genomic alterations in cfDNA from GBC to assess diagnostic accuracy and therapeutic options. The concordance of somatic genomic changes in cfDNA and DNA from paired tumor tissue was analyzed. Paired serum and tissue samples from 40 histologically proven GBC, 20 cholecystitis, and 4 normal (noninflamed gallbladder) controls were included. Targeted next-generation sequencing with a 22-gene panel (Colon and Lung Cancer Research Panel v2, Thermo Scientific) in cfDNA and tumor tissue with high depth and uniform coverage on ION Personal Genome Machine (ION, PGM) was performed. A spectrum of 223 mutations in cfDNA and 225 mutations in formalin-fixed paraffin-embedded tissue DNA were identified in 22 genes. Mutations ranged from 1 to 17 per case. In cfDNA frequent alterations were in TP53 (85.0%), EGFR (52.5%), MET (35%) CTNNB1, SMAD4, BRAF (32.5%), PTEN (30%), FGFR3 and PIK3CA (27.5%), NOTCH1 (25.0%), and FBXW7 and ERBB4 (22.5%). At least one clinically actionable mutation was identified in all cfDNA samples. Paired samples shared 149 of 225 genetic abnormalities (66.2%). Individual gene mutation concordance ranged from 44.44% to 82.0% and was highest for EGFR (82.0%), BRAF and NOTCH1 (80.0%), TP53 (73.08%), MET (72.22%), and ERBB4 (71.42%) with a significant level of correlation (Spearman r = 0.91, P ≤ .0001). The sensitivity and specificity of the TP53 gene at the gene level was the highest (94.44% and 100.0%, respectively). Overall survival was higher for ERBB4 and ERBB2 mutant tumors. The adenocarcinoma subtype revealed specific genetic changes in ERBB4, SMAD4, ERBB2, PTEN, KRAS, and NRAS. NGS-based cfDNA mutation profiling can be used to diagnose GBC before surgery to guide treatment decisions. Targeted therapy identified in GBC included SMAD4, ERBB2, ERBB4, EGFR, KRAS, BRAF, PIK3CA, MET, and NRAS.
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Affiliation(s)
- Sridhar Mishra
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Pallavi Srivastava
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Anshuman Pandey
- Department of Gastrosurgery, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Saumya Shukla
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Akash Agarwal
- Department of Surgical Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Nuzhat Husain
- Department of Pathology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, India.
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88
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Li L, Jiang H, Zeng B, Wang X, Bao Y, Chen C, Ma L, Yuan J. Liquid biopsy in lung cancer. Clin Chim Acta 2024; 554:117757. [PMID: 38184141 DOI: 10.1016/j.cca.2023.117757] [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: 10/23/2023] [Revised: 12/29/2023] [Accepted: 12/31/2023] [Indexed: 01/08/2024]
Abstract
Lung cancer is a highly prevalent malignancy worldwide and the primary cause of mortality. The absence of systematic and standardized diagnostic approaches for identifying potential pulmonary nodules, early-stage cancers, and indeterminate tumors has led clinicians to consider tissue biopsy and pathological sections as the preferred method for clinical diagnosis, often regarded as the gold standard. The conventional tissue biopsy is an invasive procedure that does not adequately capture the diverse characteristics and evolving nature of tumors. Recently, the concept of 'liquid biopsy' has gained considerable attention as a promising solution. Liquid biopsy is a non-invasive approach that facilitates repeated analysis, enabling real-time monitoring of tumor recurrence, metastasis, and response to treatment. Currently, liquid biopsy includes circulating tumor cells, circulating cell-free DNA, circulating tumor DNA, circulating cell-free RNA, extracellular vesicles, and other proteins and metabolites. With rapid progress in molecular technology, liquid biopsy has emerged as a highly promising and intriguing approach, yielding compelling results. This article critically examines the significant role and potential clinical implications of liquid biopsy in the diagnosis, treatment, and prognosis of lung cancer.
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Affiliation(s)
- Lan Li
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Haixia Jiang
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China
| | - Bingjie Zeng
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China
| | - Xianzhao Wang
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China
| | - Yunxia Bao
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China
| | - Changqiang Chen
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China.
| | - Lifang Ma
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China.
| | - Jin Yuan
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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89
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Farooq M, Leevan E, Ahmed J, Ko B, Shin S, De Souza A, Takebe N. Blood-based multi-cancer detection: A state-of-the-art update. Curr Probl Cancer 2024; 48:101059. [PMID: 38181630 DOI: 10.1016/j.currproblcancer.2023.101059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/12/2023] [Accepted: 12/26/2023] [Indexed: 01/07/2024]
Abstract
The early detection of cancer is a key goal of the National Cancer Plan formally released by the National Institutes of Health's (NIH) National Cancer Institute (NCI) in April 2023. To support this effort, many laboratories and vendors are developing multi-cancer detection (MCD) assays that interrogate blood and other bodily fluids for cancer-related biomarkers, most commonly circulating tumor DNA (ctDNA). While this approach holds promise for non-invasively detecting early signals of multiple different cancers and potentially reducing cancer-related mortality, there is a dearth of prospective clinical data to inform the deployment of MCD assays for cancer screening in the general adult population. In this review we highlight differing technologies that underpin various MCD assays in clinical development, the importance of achieving adequate performance specifications for MCD assays, ongoing clinical studies investigating the utility of MCD assays in cancer screening and detection, and efforts by the NCI's Division of Cancer Prevention (DCP) to establish a network infrastructure that has the capacity to comprehensively address the scientific and logistical challenges of evaluating blood-based MCD approaches and other cancer screening tools.
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Affiliation(s)
- Maria Farooq
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elyse Leevan
- Division of Cancer Prevention, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jibran Ahmed
- Developmental Therapeutics Clinic, Early Phase Clinical Trials Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian Ko
- Developmental Therapeutics Clinic, Early Phase Clinical Trials Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sarah Shin
- Developmental Therapeutics Clinic, Early Phase Clinical Trials Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andre De Souza
- Developmental Therapeutics Clinic, Early Phase Clinical Trials Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Naoko Takebe
- Developmental Therapeutics Clinic, Early Phase Clinical Trials Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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90
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Soliman N, Saharia A, Abdelrahim M, Connor AA. Molecular profiling in the management of hepatocellular carcinoma. Curr Opin Organ Transplant 2024; 29:10-22. [PMID: 38038621 DOI: 10.1097/mot.0000000000001124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to both summarize the current knowledge of hepatocellular carcinoma molecular biology and to suggest a framework in which to prospectively translate this knowledge into patient care. This is timely as recent guidelines recommend increased use of these technologies to advance personalized liver cancer care. RECENT FINDINGS The main themes covered here address germline and somatic genetic alterations recently discovered in hepatocellular carcinoma, largely owing to next generation sequencing technologies, and nascent efforts to translate these into contemporary practice. SUMMARY Early efforts of translating molecular profiling to hepatocellular carcinoma care demonstrate a growing number of potentially actionable alterations. Still lacking are a consensus on what biomarkers and technologies to adopt, at what scale and cost, and how to integrate them most effectively into care.
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91
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Zhu L, Qin J. Predictive biomarkers for immunotherapy response in extensive-stage SCLC. J Cancer Res Clin Oncol 2024; 150:22. [PMID: 38245636 PMCID: PMC10799815 DOI: 10.1007/s00432-023-05544-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/13/2023] [Indexed: 01/22/2024]
Abstract
BACKGROUND Small cell lung cancer (SCLC) accounts for about 13-15% of all lung cancers, and about 70% of SCLC patients have developed extensive-stage small cell lung cancer (ES-SCLC) at the time of diagnosis because of its highgrade malignancy, easy invasion, and metastasis. In recent years, immunotherapy combined with chemotherapy has become the standard first-line treatment for ES-SCLC. However, SCLC is a relatively immune-cold lung cancer subtype with a limited number of beneficiaries and a short benefit period. Therefore, the use of biomarkers to identify populations with significant benefits from immunotherapy will help improve the efficacy and survival benefits of immunotherapy. However, predictive biomarkers suitable for clinical practice have not been established in the field of SCLC. PURPOSE In order to find the predictive biomarkers of immunotherapy for ES-SCLC, we summarized the research progress of traditional biomarkers, such as programmed cell death ligand 1 (PD-L1) and tumor mutation burden (TMB), and summarizes the research of potential biomarkers associated with prognosis, such as molecular subtypes, special gene expression, expression of major histocompatibility complex (MHC) I and II classes, tumor immune microenvironment (TIME), and circulating tumor DNA (ctDNA) .We aim to provide new insights on biomarkers. CONCLUSION The exploration of biomarkers for immunotherapy of SCLC is still very difficult, and it is clear that conventional predictive biomarkers are not suitable for SCLC. At present, the molecular subtypes defined from transcription factors may have some guiding significance, which still needs to be confirmed by prospective clinical studies. In addition, the ctDNA positivity rate of SCLC is higher than that of other tumor types, which can also solve the dilemma of the difficulty of obtaining specimens of SCLC tissues. And the dynamic change of ctDNA also has great potential to predict the curative effect of SCLC, which is worth further clinical exploration.
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Affiliation(s)
- Lin Zhu
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China
| | - Jing Qin
- Department of Thoracic Medical Oncology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China.
- Zhejiang Key Laboratory of Diagnosis and Treatment Technology on Thoracic Oncology (Lung and Esophagus), Zhejiang Cancer Hospital, Hangzhou, 310022, People's Republic of China.
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92
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Moser T, Heitzer E. Surpassing sensitivity limits in liquid biopsy. Science 2024; 383:260-261. [PMID: 38236970 DOI: 10.1126/science.adn1886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Attenuation of cell-free DNA clearance in vivo is an alternative strategy to maximize recovery.
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Affiliation(s)
- Tina Moser
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
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93
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Martin-Alonso C, Tabrizi S, Xiong K, Blewett T, Sridhar S, Crnjac A, Patel S, An Z, Bekdemir A, Shea D, Wang ST, Rodriguez-Aponte S, Naranjo CA, Rhoades J, Kirkpatrick JD, Fleming HE, Amini AP, Golub TR, Love JC, Bhatia SN, Adalsteinsson VA. Priming agents transiently reduce the clearance of cell-free DNA to improve liquid biopsies. Science 2024; 383:eadf2341. [PMID: 38236959 DOI: 10.1126/science.adf2341] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 12/01/2023] [Indexed: 01/23/2024]
Abstract
Liquid biopsies enable early detection and monitoring of diseases such as cancer, but their sensitivity remains limited by the scarcity of analytes such as cell-free DNA (cfDNA) in blood. Improvements to sensitivity have primarily relied on enhancing sequencing technology ex vivo. We sought to transiently augment the level of circulating tumor DNA (ctDNA) in a blood draw by attenuating its clearance in vivo. We report two intravenous priming agents given 1 to 2 hours before a blood draw to recover more ctDNA. Our priming agents consist of nanoparticles that act on the cells responsible for cfDNA clearance and DNA-binding antibodies that protect cfDNA. In tumor-bearing mice, they greatly increase the recovery of ctDNA and improve the sensitivity for detecting small tumors.
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Affiliation(s)
- Carmen Martin-Alonso
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Shervin Tabrizi
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothy Blewett
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Andjela Crnjac
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sahil Patel
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Division of Pulmonary and Critical Care, Department of Medicine, Massachusetts General Hospital, Boston, MA 02124, USA
| | - Zhenyi An
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ahmet Bekdemir
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Douglas Shea
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shih-Ting Wang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sergio Rodriguez-Aponte
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Naranjo
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Justin Rhoades
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jesse D Kirkpatrick
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Heather E Fleming
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ava P Amini
- Microsoft Research, Cambridge, MA 02142, USA
| | - Todd R Golub
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Wyss Institute at Harvard University, Boston, MA 02215, USA
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
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Horgan D, den Bulcke MV, Malapelle U, Normanno N, Capoluongo ED, Prelaj A, Rizzari C, Stathopoulou A, Singh J, Kozaric M, Dube F, Ottaviano M, Boccia S, Pravettoni G, Cattaneo I, Malats N, Buettner R, Lekadir K, de Lorenzo F, Blanc P, Alix-Panabieres C, Badreh S, Hofman P, Solary E, De Maria R. Aligning Cancer Research Priorities in Europe with Recommendations for Conquering Cancer: A Comprehensive Analysis. Healthcare (Basel) 2024; 12:259. [PMID: 38275541 PMCID: PMC10815829 DOI: 10.3390/healthcare12020259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
Improvements in cancer care require a new degree of collaboration beyond the purely medical sphere, extending deeply into the world of other stakeholders-preeminently patients but also the other stakeholders in the hardware and software of care. Cancer remains a global health challenge, necessitating collaborative efforts to understand, prevent, and treat this complex disease. To achieve this goal, a comprehensive analysis was conducted, aligning the prioritization of cancer research measures in 13 European countries with 13 key recommendations for conquering cancer in the region. The study utilized a survey involving both patients and citizens, alongside data from IQVIA, a global healthcare data provider, to assess the availability and access to single-biomarker tests in multiple European countries. The results revealed a focused approach toward understanding, preventing, and treating cancer, with each country emphasizing specific research measures tailored to its strengths and healthcare objectives. This analysis highlights the intricate relationship between research priorities, access to biomarker tests, and financial support. Timely access to tests and increased availability positively influence research areas such as cancer prevention, early detection, ageing, and data utilization. The alignment of these country-specific measures with 13 recommendations for conquering cancer in Europe underscores the importance of tailored strategies for understanding, preventing, and treating cancer.
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Affiliation(s)
- Denis Horgan
- European Alliance for Personalised Medicine, 1040 Brussels, Belgium; (J.S.); (M.K.)
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Faculty of Engineering and Technology, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj 211007, India
| | | | - Umberto Malapelle
- Department of Public Health, University Federico II of Naples, 80138 Naples, Italy;
| | - Nicola Normanno
- Istituto Nazionale Tumori “Fondazione G. Pascale”—IRCCS, 80131 Naples, Italy;
| | - Ettore D. Capoluongo
- Dipartimento di Eccellenza in Medicina Molecolare e Biotecnologie Mediche, Università Federico II, 80138 Naples, Italy;
- Department of Clinical Pathology and Genomics, Azienda Ospedaliera Per L’Emergenza Cannizzaro, 95126 Catania, Italy
| | - Arsela Prelaj
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Tumori, 20133 Milan, Italy;
| | - Carmelo Rizzari
- Unità di Ematologia Pediatrica, Fondazione MBBM, Università di Milano-Bicocca, 20126 Monza, Italy;
| | - Aliki Stathopoulou
- European Cancer Patient Coalition, 1000 Brussels, Belgium; (A.S.); (F.d.L.)
| | - Jaya Singh
- European Alliance for Personalised Medicine, 1040 Brussels, Belgium; (J.S.); (M.K.)
| | - Marta Kozaric
- European Alliance for Personalised Medicine, 1040 Brussels, Belgium; (J.S.); (M.K.)
| | - France Dube
- Astra Zeneca, Concord Pike, Wilmington, DE 19803, USA;
| | - Manuel Ottaviano
- Departamento de Tecnología Fotónica y Bioingeniería, Universidad Politècnica de Madrid, 28040 Madrid, Spain;
| | - Stefania Boccia
- Section of Hygiene, Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 20123 Rome, Italy;
- Departments of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Gabriella Pravettoni
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy;
- Applied Research Division for Cognitive and Psychological Science, European Institute of Oncology (IEO) IRCCS, 20139 Milan, Italy
| | | | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain;
| | - Reinhard Buettner
- Lung Cancer Group Cologne, Institute of Pathology and Medical Faculty, Center for Integrated Oncology Cologne/Bonn, University Hospital Cologne, 50937 Cologne, Germany;
| | - Karim Lekadir
- Artificial Intelligence in Medicine Lab (BCN-AIM), Universitat de Barcelona, 08007 Barcelona, Spain;
| | | | | | - Catherine Alix-Panabieres
- Laboratory of Rare Human Circulating Cells, University Medical Center of Montpellier, 34093 Montpellier, France;
| | - Sara Badreh
- Cancer Childhood International, 1200 Vienna, Austria;
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France;
| | - Eric Solary
- INSERM U1287, Gustave Roussy Cancer Campus, 94805 Villejuif, France;
- Faculty of Medicine, Université Paris-Sud, Le Kremlin-Bicêtre, 91405 Île-de-France, France
- Department of Hematology, Gustave Roussy Cancer Campus, 94805 Paris, France
| | - Ruggero De Maria
- Institute of General Pathology, Catholic University of the Sacred Heart, 20123 Rome, Italy;
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95
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Mansur A, Radovanovic I. The expansion of liquid biopsies to vascular care: an overview of existing principles, techniques and potential applications to vascular malformation diagnostics. Front Genet 2024; 15:1348096. [PMID: 38304336 PMCID: PMC10832994 DOI: 10.3389/fgene.2024.1348096] [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: 12/01/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Vascular malformations are congenital lesions that occur due to mutations in major cellular signalling pathways which govern angiogenesis, cell proliferation, motility, and cell death. These pathways have been widely studied in oncology and are substrates for various small molecule inhibitors. Given their common molecular biology, there is now a potential to repurpose these cancer drugs for vascular malformation care; however, a molecular diagnosis is required in order to tailour specific drugs to the individual patient's mutational profile. Liquid biopsies (LBs), emerging as a transformative tool in the field of oncology, hold significant promise in this feat. This paper explores the principles and technologies underlying LBs and evaluates their potential to revolutionize the management of vascular malformations. The review begins by delineating the fundamental principles of LBs, focusing on the detection and analysis of circulating biomarkers such as cell-free DNA, circulating tumor cells, and extracellular vesicles. Subsequently, an in-depth analysis of the technological advancements driving LB platforms is presented. Lastly, the paper highlights the current state of research in applying LBs to various vascular malformations, and uses the aforementioned principles and techniques to conceptualize a liquid biopsy framework that is unique to vascular malformation research and clinical care.
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Affiliation(s)
- Ann Mansur
- Division of Neurosurgery, Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, School of Graduate Studies, University of Toronto, Toronto, ON, Canada
| | - Ivan Radovanovic
- Division of Neurosurgery, Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Division of Neurosurgery, Department of Surgery, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
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96
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Cheng S, Zhang C, Hu X, Zhu Y, Shi H, Tan W, Luo X, Xian Y. Ultrasensitive determination of surface proteins on tumor-derived small extracellular vesicles for breast cancer identification based on lanthanide-activated signal amplification strategy. Talanta 2024; 267:125189. [PMID: 37714039 DOI: 10.1016/j.talanta.2023.125189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
Small extracellular vesicles (sEVs) carrying multiple tumor-associated proteins inherited from parental cells play crucial roles in noninvasive breast cancer (BC) diagnosis. However, it is challenging to assess the subtle variations of surface proteins on sEV membranes due to the highly heterogeneous BC. Therefore, a simple and ultrasensitive assay based on lanthanide (Ln3+)-activated luminescence signal amplification was developed to detect multiple surface proteins on BC-derived sEVs. Multiple protein biomarkers on sEVs can be well identified with high sensitivity and specificity through dissolution-amplified luminescence of the NaEuF4 nanoparticle-based nanoprobe. We employ linear discriminant analysis to successfully discriminate triple negative BC cell (MDA-MB-231 cell) derived sEVs from other breast cell lines (MCF-7, SK-BR-3, BT474 and MCF-10A cell). Furthermore, the strategy enables high accuracy for districting the progression stages of BC patients and healthy donors. The simple and sensitive signal amplification strategy exhibits great potential for early clinic diagnosis by precise protein profiling of sEVs.
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Affiliation(s)
- Shasha Cheng
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Cuiling Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China.
| | - Xinyu Hu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Yingxin Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Hui Shi
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, Institute of Stem Cell, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Wenqiao Tan
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Xianzhu Luo
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Yuezhong Xian
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China.
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97
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Yang L, Gu X, Liu J, Wu L, Qin Y. Functionalized nanomaterials-based electrochemiluminescent biosensors and their application in cancer biomarkers detection. Talanta 2024; 267:125237. [PMID: 37757698 DOI: 10.1016/j.talanta.2023.125237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
To detect a range of trace biomarkers associated with human diseases, researchers have been focusing on developing biosensors that possess high sensitivity and specificity. Electrochemiluminescence (ECL) biosensors have emerged as a prominent research tool in recent years, owing to their potential superiority in low background signal, high sensitivity, straightforward instrumentation, and ease of operation. Functional nanomaterials (FNMs) exhibit distinct advantages in optimizing electrical conductivity, increasing reaction rate, and expanding specific surface area due to their small size effect, quantum size effect, and surface and interface effects, which can significantly improve the stability, reproducibility, and sensitivity of the biosensors. Thereby, various nanomaterials (NMs) with excellent properties have been developed to construct efficient ECL biosensors. This review provides a detailed summary and discussion of FNMs-based ECL biosensors and their applications in cancer biomarkers detection.
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Affiliation(s)
- Luxia Yang
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Xijuan Gu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China
| | - Jinxia Liu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Li Wu
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
| | - Yuling Qin
- Nantong Key Laboratory of Public Health and Medical Analysis, School of Public Health, Nantong University, Nantong, Jiangsu, 226019, PR China.
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98
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Zhang N, Li Y, Zhang H, Dong Y, Zhang C, Du W, Long C, Xing X, Li K, Liu Z, Chen X, Zhang L, Xu F, Fu Y, Tan J, She B, Che N. Performance of SHOX2 and RASSF1A methylation assay in supernatants and matched cell pellets for the diagnosis of malignant pleural effusion. Clin Chim Acta 2024; 553:117699. [PMID: 38072300 DOI: 10.1016/j.cca.2023.117699] [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: 05/08/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND It is difficult to distinguish between malignant pleural effusion (MPE) and benign pleural effusion (BPE). The purpose of this study was to determine the best specimen type by evaluating the DNA methylation status of SHOX2 and RASSF1A in 3 matched PE components. METHODS In total, 94 patients were enrolled, including 45 MPE, 35 BPE, and 14 undefined PE (UPE) with malignancies. PE samples were processed into supernatants, fresh-cell pellets, and formalin-fixed and paraffin-embedded (FFPE) cell blocks, respectively. A quantitative real-time PCR was used to detect the methylation status of SHOX2 and RASSF1A. RESULTS SHOX2 and RASSF1A methylation levels were significantly higher in the 3 MPE sample types than those of BPE (P < 0.05). The area under the curve using cell-free DNA (cf-DNA) was the highest. The detection sensitivity of SHOX2 and RASSF1A in fresh-cell DNA, cf-DNA and FFPE cell-block were 71.1% (32/45), 97.8% (44/45) and 66.7% (28/42), respectively, with specificities of 97.1% (34/35), 94.3% (33/35), and 96.9% (31/32). Notably, a combination of the cytological analysis and cf-DNA methylation assay showed an increase in positivity rate from 75.6% to 100%. CONCLUSIONS The SHOX2 and RASSF1A methylation assay using cf-DNA, the primary recommended specimen type, can excellently increase the diagnostic sensitivity of MPE. A combination of methylation assay with cytological analysis can be used for auxiliary diagnosis of PE.
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Affiliation(s)
- Nana Zhang
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Yongmeng Li
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Haoran Zhang
- Biobank of Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Yujie Dong
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Chen Zhang
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Weili Du
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Chaolian Long
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Xuya Xing
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Kun Li
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Zichen Liu
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Xuejing Chen
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Lili Zhang
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Fudong Xu
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Yuhong Fu
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Jing Tan
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China
| | - Bin She
- Academic Development, Tellgen Corporation, Shanghai, China
| | - Nanying Che
- Department of Pathology, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing 101149, China; Biobank of Beijing Chest Hospital, Capital Medical University, Beijing 101149, China.
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99
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Li JH, Zhang DY, Zhu JM, Dong L. Clinical applications and perspectives of circulating tumor DNA in gastric cancer. Cancer Cell Int 2024; 24:13. [PMID: 38184573 PMCID: PMC10770949 DOI: 10.1186/s12935-024-03209-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/02/2024] [Indexed: 01/08/2024] Open
Abstract
Gastric cancer remains a leading cause of cancer-related death worldwide, largely due to inadequate screening methods, late diagnosis, and limited treatment options. Liquid biopsy has emerged as a promising non-invasive approach for cancer screening and prognosis by detecting circulating tumor components like circulating tumor DNA (ctDNA) in the blood. Numerous gastric cancer-specific ctDNA biomarkers have now been identified. CtDNA analysis provides insight into genetic and epigenetic alterations in tumors, holding promise for predicting treatment response and prognosis in gastric cancer patients. This review summarizes current research on ctDNA biology and detection technologies, while highlighting clinical applications of ctDNA for gastric cancer diagnosis, prognosis, and guiding treatment decisions. Current challenges and future perspectives for ctDNA analysis are also discussed.
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Affiliation(s)
- Jing-Han Li
- Department of Gastroenterology and Hepatology and Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Dan-Ying Zhang
- Department of Gastroenterology and Hepatology and Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Ji-Min Zhu
- Department of Gastroenterology and Hepatology and Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Ling Dong
- Department of Gastroenterology and Hepatology and Shanghai Institute of Liver Diseases, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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100
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Rayamajhi S, Sipes J, Tetlow AL, Saha S, Bansal A, Godwin AK. Extracellular Vesicles as Liquid Biopsy Biomarkers across the Cancer Journey: From Early Detection to Recurrence. Clin Chem 2024; 70:206-219. [PMID: 38175602 DOI: 10.1093/clinchem/hvad176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 09/26/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Cancer is a dynamic process and thus requires highly informative and reliable biomarkers to help guide patient care. Liquid-based biopsies have emerged as a clinical tool for tracking cancer dynamics. Extracellular vesicles (EVs), lipid bilayer delimited particles secreted by cells, are a new class of liquid-based biomarkers. EVs are rich in selectively sorted biomolecule cargos, which provide a spatiotemporal fingerprint of the cell of origin, including cancer cells. CONTENT This review summarizes the performance characteristics of EV-based biomarkers at different stages of cancer progression, from early malignancy to recurrence, while emphasizing their potential as diagnostic, prognostic, and screening biomarkers. We discuss the characteristics of effective biomarkers, consider challenges associated with the EV biomarker field, and report guidelines based on the biomarker discovery pipeline. SUMMARY Basic science and clinical trial studies have shown the potential of EVs as precision-based biomarkers for tracking cancer status, with promising applications for diagnosing disease, predicting response to therapy, and tracking disease burden. The multi-analyte cargos of EVs enhance the performance characteristics of biomarkers. Recent technological advances in ultrasensitive detection of EVs have shown promise with high specificity and sensitivity to differentiate early-cancer cases vs healthy individuals, potentially outperforming current gold-standard imaging-based cancer diagnosis. Ultimately, clinical translation will be dictated by how these new EV biomarker-based platforms perform in larger sample cohorts. Applying ultrasensitive, scalable, and reproducible EV detection platforms with better design considerations based upon the biomarker discovery pipeline should guide the field towards clinically useful liquid biopsy biomarkers.
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Affiliation(s)
- Sagar Rayamajhi
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Jared Sipes
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Ashley L Tetlow
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
| | - Souvik Saha
- Division of Gastroenterology and Hepatology, University of Kansas Health System, Kansas City, KS, United States
| | - Ajay Bansal
- Division of Gastroenterology and Hepatology, University of Kansas Health System, Kansas City, KS, United States
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, United States
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, United States
- The University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS, United States
- Division of Genomic Diagnostics, University of Kansas Health System, Kansas City, KS, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, United States
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