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Weiss S, Lamy P, Rusan M, Nørgaard M, Ulhøi BP, Knudsen M, Kassentoft CG, Farajzadeh L, Jensen JB, Pedersen JS, Borre M, Sørensen KD. Exploring the tumor genomic landscape of aggressive prostate cancer by whole-genome sequencing of tissue or liquid biopsies. Int J Cancer 2024. [PMID: 38602058 DOI: 10.1002/ijc.34949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/19/2024] [Accepted: 03/12/2024] [Indexed: 04/12/2024]
Abstract
Treatment resistance remains a major issue in aggressive prostate cancer (PC), and novel genomic biomarkers may guide better treatment selection. Circulating tumor DNA (ctDNA) can provide minimally invasive information about tumor genomes, but the genomic landscape of aggressive PC based on whole-genome sequencing (WGS) of ctDNA remains incompletely characterized. Thus, we here performed WGS of tumor tissue (n = 31) or plasma ctDNA (n = 10) from a total of 41 aggressive PC patients, including 11 hormone-naïve, 15 hormone-sensitive, and 15 castration-resistant patients. Across all variant types, we found progressively more altered tumor genomic profiles in later stages of aggressive PC. The potential driver genes most frequently affected by single-nucleotide variants or insertions/deletions included the known PC-related genes TP53, CDK12, and PTEN and the novel genes COL13A1, KCNH3, and SENP3. Etiologically, aggressive PC was associated with age-related and DNA repair-related mutational signatures. Copy number variants most frequently affected 14q11.2 and 8p21.2, where no well-recognized PC-related genes are located, and also frequently affected regions near the known PC-related genes MYC, AR, TP53, PTEN, and BRCA1. Structural variants most frequently involved not only the known PC-related genes TMPRSS2 and ERG but also the less extensively studied gene in this context, PTPRD. Finally, clinically actionable variants were detected throughout all stages of aggressive PC and in both plasma and tissue samples, emphasizing the potential clinical applicability of WGS of minimally invasive plasma samples. Overall, our study highlights the feasibility of using liquid biopsies for comprehensive genomic characterization as an alternative to tissue biopsies in advanced/aggressive PC.
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Affiliation(s)
- Simone Weiss
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Maria Rusan
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Maibritt Nørgaard
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Gødstrup Hospital, Gødstrup, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Michael Borre
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Karina Dalsgaard Sørensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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2
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Van Der Schueren C, Decruyenaere P, Avila Cobos F, Bult J, Deleu J, Dipalo LL, Helsmoortel HH, Hulstaert E, Morlion A, Ramos Varas E, Schoofs K, Trypsteen W, Vanden Eynde E, Van Droogenbroeck H, Verniers K, Vandesompele J, Decock A. Subpar reporting of pre-analytical variables in RNA-focused blood plasma studies. Mol Oncol 2024. [PMID: 38564603 DOI: 10.1002/1878-0261.13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/13/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
Extracellular RNA (cell-free RNA; exRNA) from blood-derived liquid biopsies is an appealing, minimally invasive source of disease biomarkers. As pre-analytical variables strongly influence exRNA measurements, their reporting is essential for meaningful interpretation and replication of results. The aim of this review was to chart to what extent pre-analytical variables are documented, to pinpoint shortcomings and to improve future reporting. In total, 200 blood plasma exRNA studies published in 2018 or 2023 were reviewed for annotation of 22 variables associated with blood collection, plasma preparation, and RNA purification. Our results show that pre-analytical variables are poorly documented, with only three out of 22 variables described in over half of the publications. The percentage of variables reported ranged from 4.6% to 54.6% (mean 24.84%) in 2023 and from 4.6% to 57.1% (mean 28.60%) in 2018. Recommendations and guidelines (i.e., BRISQ, ASCO-CAP, BloodPAC, PPMPT, and CEN standards) have currently not resulted in improved reporting. In conclusion, our results highlight the lack of reporting pre-analytical variables in exRNA studies and advocate for a consistent use of available standards, endorsed by funders and journals.
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Affiliation(s)
| | - Philippe Decruyenaere
- Department of Biomolecular Medicine, Ghent University, Belgium
- Department of Hematology, Ghent University Hospital, Belgium
| | - Francisco Avila Cobos
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Johanna Bult
- Department of Biomolecular Medicine, Ghent University, Belgium
- Department of Hematology, University Medical Center Groningen, The Netherlands
| | - Jill Deleu
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Laudonia Lidia Dipalo
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Hetty Hilde Helsmoortel
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Eva Hulstaert
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
- Department of Dermatology, AZ Sint-Blasius, Belgium
| | - Annelien Morlion
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Elena Ramos Varas
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Kathleen Schoofs
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
- Translational Oncogenomics and Bioinformatics Lab, Cancer Research Institute Ghent (CRIG), Belgium
- Center for Medical Biotechnology, VIB-UGent, Belgium
| | - Wim Trypsteen
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Eveline Vanden Eynde
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Hanne Van Droogenbroeck
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Kimberly Verniers
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
- CellCarta, Belgium
| | - Anneleen Decock
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
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3
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Cortiana V, Van de Kieft A, Chorya H, Gambill J, Park CH, Leyfman Y. Innovations in Thoracic Oncology and the Promise of Liquid Biopsies with Dr. Luis Raez. Cancers (Basel) 2024; 16:799. [PMID: 38398189 PMCID: PMC10886586 DOI: 10.3390/cancers16040799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Thoracic oncology continues to pose a great threat to human health as one of the most common forms of cancer. Liquid biopsies present a transformative approach to treating patients affected by these types of diseases by providing a less invasive genetic overview of the tumor, aiding in both diagnostic and treatment measures. The primary objective of this article is to examine the prospects of liquid biopsies in managing thoracic malignancies and to present barriers to their usage as demonstrated by Dr. Luis Raez. In examining why molecular diagnostics continue to be employed together with more traditional methods, this article presents the next steps in the clinical application of blood-based cancer screening. Future cancer diagnosis and treatment aim to prioritize circulating biomarker analyses based on their potential for the detection and monitoring of thoracic cancers. Liquid biopsies are favored thanks to their reduced invasiveness with respect to traditional treatments. The further study of clinical biomarkers and technological advancements are thus pivotal to enhance the clinical applicability of this method. In conclusion, this blood-based analysis offers a promising route by which the diagnosis, treatments, and outcomes of thoracic cancer can be improved.
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Affiliation(s)
- Viviana Cortiana
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | | | | | | | | | - Yan Leyfman
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Corné J, Quillien V, Godey F, Cherel M, Cochet A, Le Du F, Robert L, Bourien H, Brunot A, Crouzet L, Perrin C, Lefeuvre-Plesse C, Diéras V, De la Motte Rouge T. Plasma-based analysis of ERBB2 mutational status by multiplex digital PCR in a large series of patients with metastatic breast cancer. Mol Oncol 2024. [PMID: 38287892 DOI: 10.1002/1878-0261.13592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/16/2023] [Accepted: 01/15/2024] [Indexed: 01/31/2024] Open
Abstract
Erb-b2 receptor tyrosine kinase 2 (ERBB2)-activating mutations are therapeutically actionable alterations found in various cancers, including metastatic breast cancer (MBC). We developed multiplex digital PCR assays to detect and quantify ERBB2 mutations in circulating tumor DNA from liquid biopsies. We studied the plasma from 272 patients with hormone-receptor-positive, human epidermal growth factor receptor 2-negative (HR+/HER2-) MBC to detect 17 ERBB2 mutations using a screening assay. The assay was developed on the three-color Crystal dPCR™ naica® platform with a two-step strategy for precise mutation identification. We found that nine patients (3.3%) harbored at least one ERBB2 mutation. The mutation rate was higher in patients with lobular histology (5.9%) compared to invasive breast carcinoma of no special type (2.6%). A total of 12 mutations were found with the following frequencies: L755S (25.00%), V777L (25.00%), S310Y (16.67%), L869R (16.67%), S310F (8.33%), and D769H (8.33%). Matched tumor samples from six patients identified the same mutations with an 83% concordance rate. In summary, our highly sensitive multiplex digital PCR assays are well suited for plasma-based monitoring of ERBB2 mutational status in patients with MBC.
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Affiliation(s)
- Julien Corné
- Department of Biology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Véronique Quillien
- Department of Biology, Centre Eugène Marquis, Unicancer, Rennes, France
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
- INSERM U1242, University of Rennes, France
| | - Florence Godey
- Department of Biology, Centre Eugène Marquis, Unicancer, Rennes, France
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
- INSERM U1242, University of Rennes, France
| | - Mathilde Cherel
- Department of Biology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Agathe Cochet
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Fanny Le Du
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Lucie Robert
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Héloïse Bourien
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Angélique Brunot
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Laurence Crouzet
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | - Christophe Perrin
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
| | | | - Véronique Diéras
- Department of Medical Oncology, Centre Eugène Marquis, Unicancer, Rennes, France
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Maansson CT, Thomsen LS, Meldgaard P, Nielsen AL, Sorensen BS. Integration of Cell-Free DNA End Motifs and Fragment Lengths Can Identify Active Genes in Liquid Biopsies. Int J Mol Sci 2024; 25:1243. [PMID: 38279243 PMCID: PMC10815977 DOI: 10.3390/ijms25021243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 01/28/2024] Open
Abstract
Multiple studies have shown that cell-free DNA (cfDNA) from cancer patients differ in both fragment length and fragment end motif (FEM) from healthy individuals, yet there is a lack of understanding of how the two factors combined are associated with cancer and gene transcription. In this study, we conducted cfDNA fragmentomics evaluations using plasma from lung cancer patients (n = 12) and healthy individuals (n = 7). A personal gene expression profile was established from plasma using H3K36me3 cell-free chromatin immunoprecipitation sequencing (cfChIP-seq). The genes with the highest expression displayed an enrichment of short cfDNA fragments (median = 19.99%, IQR: 16.94-27.13%, p < 0.0001) compared to the genes with low expression. Furthermore, distinct GC-rich FEMs were enriched after cfChIP. Combining the frequency of short cfDNA fragments with the presence of distinct FEMs resulted in an even further enrichment of the most expressed genes (median = 37.85%, IQR: 30.10-39.49%, p < 0.0001). An in vitro size selection of <150 bp cfDNA could isolate cfDNA representing active genes and the size-selection enrichment correlated with the cfChIP-seq enrichment (Spearman r range: 0.499-0.882, p < 0.0001). This study expands the knowledge regarding cfDNA fragmentomics and sheds new light on how gene activity is associated with both cfDNA fragment lengths and distinct FEMs.
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Affiliation(s)
- Christoffer Trier Maansson
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark; (C.T.M.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark;
| | - Louise Skov Thomsen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark; (C.T.M.)
| | - Peter Meldgaard
- Department of Oncology, Aarhus University Hospital, 8200 Aarhus, Denmark;
| | | | - Boe Sandahl Sorensen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus, Denmark; (C.T.M.)
- Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
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6
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Đorić I, Šelemetjev S. Challenges and current advances in the methodology of thyroglobulin measurements. Bioanalysis 2024; 16:49-60. [PMID: 37991211 DOI: 10.4155/bio-2023-0149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Thyroglobulin (Tg) is a large protein secreted exclusively by the thyroid gland. In a clinical setting, it is measured for the purpose of follow-up of thyroidectomy patients. However, Tg measurements are often impeded by the presence of Tg autoantibodies and/or heterophylic antibodies that interfere with most measuring platforms. This presents a global problem in thyroid cancer patients who need to be postoperatively monitored for recurrent or residual disease. Therefore, in this paper we offer an overview of the existing methodologies and alternative approaches for Tg measurements that are a focus of research worldwide. These include Tg mRNA measurements, exosomal Tg detection, the use of alternative analytes (liquid biopsies) and the development of new approaches for preanalytical sample treatment.
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Affiliation(s)
- Ilona Đorić
- Department of Endocrinology & Radioimmunology, Institute for the Application of Nuclear Energy - INEP, Banatska 31b, University of Belgrade, Belgrade, 11000, Serbia
| | - Sonja Šelemetjev
- Department of Endocrinology & Radioimmunology, Institute for the Application of Nuclear Energy - INEP, Banatska 31b, University of Belgrade, Belgrade, 11000, Serbia
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Weber DG, Casjens S, Wichert K, Lehnert M, Taeger D, Rihs HP, Brüning T, Johnen G. Tasks and Experiences of the Prospective, Longitudinal, Multicenter MoMar (Molecular Markers) Study for the Early Detection of Mesothelioma in Individuals Formerly Exposed to Asbestos Using Liquid Biopsies. Cancers (Basel) 2023; 15:5896. [PMID: 38136442 PMCID: PMC10742125 DOI: 10.3390/cancers15245896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/07/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Mesothelioma is an aggressive cancer, strongly associated with prior exposure to asbestos. Commonly, tumors are detected at late stages of the disease. Detection at early stages might be meaningful, because therapies might be more effective when the tumor burden is relatively low and the tumor has not spread to distant sites. Circulating biomarkers in blood might be a promising tool to improve the early detection of mesothelioma, but for screening in asymptomatic subjects, candidate biomarkers need to be validated in appropriate studies. This study was conducted to assess the performance of biomarkers in liquid biopsies to detect mesothelioma at early stages. Over a period of 10 years, 2769 volunteers formerly exposed to asbestos were annually examined and liquid biopsies were collected. A follow-up was completed 17 months after the last blood collection. The article provides a detailed overview of our lessons learned and experiences of conducting a prospective, longitudinal, multicenter study. The existing cohort of individuals at risk is highly suitable for the validation of blood-based biomarkers for the early detection of mesothelioma as well as lung cancer.
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Affiliation(s)
- Daniel Gilbert Weber
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Ruhr University Bochum, 44801 Bochum, Germany
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Yim KHW, Krzyzaniak O, Al Hrout A, Peacock B, Chahwan R. Assessing Extracellular Vesicles in Human Biofluids Using Flow-Based Analyzers. Adv Healthc Mater 2023; 12:e2301706. [PMID: 37800440 DOI: 10.1002/adhm.202301706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/02/2023] [Indexed: 10/07/2023]
Abstract
Extracellular vesicles (EVs) are increasingly being analyzed by flow cytometry. Yet their minuscule size and low refractive index cause the scatter intensity of most EVs to fall below the detection limit of most flow cytometers. A new class of devices, known as spectral flow analyzers, are becoming standards in cell phenotyping studies, largely due to their unique capacity to detect a vast panel of markers with higher sensitivity for light scatter detection. Another class of devices, known as nano-analyzers, provides high-resolution detection of sub-micron-sized particles. Here, the EV phenotyping performance between the Aurora (Cytek) spectral cell analyzer and the NanoFCM (nFCM) nanoflow analyzer are compared. These two devices are specifically chosen given their lead in becoming gold standards in their respective fields. Immune cell-derived EVs remain poorly characterized despite their clinical potential. Therefore, B- and T-cell line-derived EVs and donor-matched human biofluid-derived EVs from plasma, urine, and saliva are used in combination with a panel of established immune markers for this comparative study. A comparative evaluation of both cytometry platforms is performed, discussing their potential and suitability for different applications. It is found that nFCM can accurately i) analyze small EVs (40-200 nm) matching the size accuracy of electron microscopy; ii) measure the concentration of a single EV particle per volume; iii) identify underrepresented EV marker subsets; and iv) provide co-localization of EV surface markers. It can also be shown that human sample biofluids have unique EV marker signatures that can have future clinical relevance. Finally, nFCM and Aurora have their unique strength, preferred fashion of data acquisition, and visualization to fit different research interests.
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Affiliation(s)
- Kevin Ho Wai Yim
- Institute of Experimental Immunology, University of Zurich, Zurich, 8057, Switzerland
| | - Olga Krzyzaniak
- Institute of Experimental Immunology, University of Zurich, Zurich, 8057, Switzerland
| | - Ala'a Al Hrout
- Institute of Experimental Immunology, University of Zurich, Zurich, 8057, Switzerland
| | - Ben Peacock
- NanoFCM, ltd., D6 Thane Rd, Nottingham, NG90 6BH, UK
| | - Richard Chahwan
- Institute of Experimental Immunology, University of Zurich, Zurich, 8057, Switzerland
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Brokāne A, Bajo-Santos C, Zayakin P, Belovs A, Jansons J, Lietuvietis V, Martens-Uzunova ES, Jenster GW, Linē A. Validation of potential RNA biomarkers for prostate cancer diagnosis and monitoring in plasma and urinary extracellular vesicles. Front Mol Biosci 2023; 10:1279854. [PMID: 38099195 PMCID: PMC10720733 DOI: 10.3389/fmolb.2023.1279854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/15/2023] [Indexed: 12/17/2023] Open
Abstract
Introduction: Prostate cancer (PCa), one of the most prevalent malignancies affecting men worldwide, presents significant challenges in terms of early detection, risk stratification, and active surveillance. In recent years, liquid biopsies have emerged as a promising non-invasive approach to complement or even replace traditional tissue biopsies. Extracellular vesicles (EVs), nanosized membranous structures released by various cells into body fluids, have gained substantial attention as a source of cancer biomarkers due to their ability to encapsulate and transport a wide range of biological molecules, including RNA. In this study, we aimed to validate 15 potential RNA biomarkers, identified in a previous EV RNA sequencing study, using droplet digital PCR. Methods: The candidate biomarkers were tested in plasma and urinary EVs collected before and after radical prostatectomy from 30 PCa patients and their diagnostic potential was evaluated in a test cohort consisting of 20 benign prostate hyperplasia (BPH) and 20 PCa patients' plasma and urinary EVs. Next, the results were validated in an independent cohort of plasma EVs from 31 PCa and 31 BPH patients. Results: We found that the levels of NKX3-1 (p = 0.0008) in plasma EVs, and tRF-Phe-GAA-3b (p < 0.0001) tRF-Lys-CTT-5c (p < 0.0327), piR-28004 (p = 0.0081) and miR-375-3p (p < 0.0001) in urinary EVs significantly decreased after radical prostatectomy suggesting that the main tissue source of these RNAs is prostate and/or PCa. Two mRNA biomarkers-GLO1 and NKX3-1 showed promising diagnostic potential in distinguishing between PCa and BPH with AUC of 0.68 and 0.82, respectively, in the test cohort and AUC of 0.73 and 0.65, respectively, in the validation cohort, when tested in plasma EVs. Combining these markers in a biomarker model yielded AUC of 0.85 and 0.71 in the test and validation cohorts, respectively. Although the PSA levels in the blood could not distinguish PCa from BPH in our cohort, adding PSA to the mRNA biomarker model increased AUC from 0.71 to 0.76. Conclusion: This study identified two novel EV-enclosed RNA biomarkers-NKX3-1 and GLO1-for the detection of PCa, and highlights the complementary nature of GLO1, NKX3-1 and PSA as combined biomarkers in liquid biopsies of PCa.
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Affiliation(s)
- Agnese Brokāne
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | | | | | | | | | - Guido W. Jenster
- Department of Urology, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Aija Linē
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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Comba A, Li X, Breznik B. Editorial: Brain cancer pathogenesis and data integration. Front Genet 2023; 14:1298285. [PMID: 37900188 PMCID: PMC10613040 DOI: 10.3389/fgene.2023.1298285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/06/2023] [Indexed: 10/31/2023] Open
Affiliation(s)
- Andrea Comba
- Division of Neuropathology, Department of Pathology, Heersink School of Medicine and the O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Xinzhong Li
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom
| | - Barbara Breznik
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Ljubljana, Slovenia
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11
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Lobo J, Acosta AM, Netto GJ. Molecular Biomarkers With Potential Clinical Application in Testicular Cancer. Mod Pathol 2023; 36:100307. [PMID: 37611872 DOI: 10.1016/j.modpat.2023.100307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/28/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]
Abstract
Testicular germ cell tumors (TGCTs) and sex cord-stromal tumors (SCSTs) are the most common testicular neoplasms. The morphologic spectrum of such tumors is wide, with several histologic subtypes within each group. Testicular tumors often represent a diagnostic challenge, requiring proper identification of their biologic potential for accurate risk stratification and selection of therapy. In the era of precision medicine, molecular biomarkers are increasingly assuming a critical role in the management of patients with cancer. Given the overall rarity of certain types of testicular neoplasms, progress in biomarker research has been relatively slow. However, in recent years, we have witnessed a multitude of important contributions, including both tissue-based and liquid biopsy biomarkers, stemming from important discoveries of tumor pathobiology, accurate histopathological analysis, multi-institutional studies, and genome-wide molecular analyses of specific tumor subtypes. In this review, we provide an overview of the progress in molecular biomarkers of TGCTs and SCSTs, focusing on those with greatest potential for clinical application. In TGCTs, developmental biology has been the key to understanding these tumors and identifying clinically useful biomarkers (from classical serum tumor markers to pluripotency factors and circulating microRNAs of the 371-373 cluster). For SCSTs, studies have focused on tissue biomarkers only, and genome-wide investigations have recently contributed to a better understanding of rare phenotypes and the aggressive biological behavior of some tumors within this nosologic category. Several new biomarkers are moving toward clinical implementation in this field. Therefore, the practicing pathologist should be aware of their strengths and limitations in order to utilize them properly and maximize their clinical benefits.
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Affiliation(s)
- João Lobo
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Porto, Portugal; Cancer Biology and Epigenetics Group, IPO Porto Research Center (GEBC CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center Raquel Seruca & RISE@CI-IPOP (Health Research Network), Porto, Portugal; Department of Pathology and Molecular Immunology, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Andres M Acosta
- Department of Pathology, Indiana University, Indianapolis, Indiana
| | - George J Netto
- Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama.
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12
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Chen TY, Mihalopoulos M, Zuluaga L, Rich J, Ganta T, Mehrazin R, Tsao CK, Tewari A, Gonzalez-Kozlova E, Badani K, Dogra N, Kyprianou N. Clinical Significance of Extracellular Vesicles in Prostate and Renal Cancer. Int J Mol Sci 2023; 24:14713. [PMID: 37834162 PMCID: PMC10573190 DOI: 10.3390/ijms241914713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/02/2023] [Accepted: 09/03/2023] [Indexed: 10/15/2023] Open
Abstract
Extracellular vesicles (EVs)-including apoptotic bodies, microvesicles, and exosomes-are released by almost all cell types and contain molecular footprints from their cell of origin, including lipids, proteins, metabolites, RNA, and DNA. They have been successfully isolated from blood, urine, semen, and other body fluids. In this review, we discuss the current understanding of the predictive value of EVs in prostate and renal cancer. We also describe the findings supporting the use of EVs from liquid biopsies in stratifying high-risk prostate/kidney cancer and advanced disease, such as castration-resistant (CRPC) and neuroendocrine prostate cancer (NEPC) as well as metastatic renal cell carcinoma (RCC). Assays based on EVs isolated from urine and blood have the potential to serve as highly sensitive diagnostic studies as well as predictive measures of tumor recurrence in patients with prostate and renal cancers. Overall, we discuss the biogenesis, isolation, liquid-biopsy, and therapeutic applications of EVs in CRPC, NEPC, and RCC.
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Affiliation(s)
- Tzu-Yi Chen
- Department of Pathology & Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.-Y.C.); (A.T.)
| | - Meredith Mihalopoulos
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Laura Zuluaga
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Jordan Rich
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Teja Ganta
- Department of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.G.); (C.-K.T.)
| | - Reza Mehrazin
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Che-Kai Tsao
- Department of Hematology/Oncology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.G.); (C.-K.T.)
| | - Ash Tewari
- Department of Pathology & Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.-Y.C.); (A.T.)
| | - Edgar Gonzalez-Kozlova
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Ketan Badani
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
| | - Navneet Dogra
- Department of Pathology & Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (T.-Y.C.); (A.T.)
| | - Natasha Kyprianou
- Department of Urology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.M.); (L.Z.); (J.R.); (R.M.); (K.B.)
- The Tisch Cancer Institute, Mount Sinai Health, New York, NY 10029, USA
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13
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Lalić N, Lovrenski A, Ilić M, Ivanov O, Bojović M, Lalić I, Popević S, Stjepanović M, Janjić N. Invasive Diagnostic Procedures from Bronchoscopy to Surgical Biopsy-Optimization of Non-Small Cell Lung Cancer Samples for Molecular Testing. Medicina (Kaunas) 2023; 59:1723. [PMID: 37893442 PMCID: PMC10608158 DOI: 10.3390/medicina59101723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023]
Abstract
Background and Objectives: Treatment of advanced lung cancer (LC) has become increasingly personalized over the past decade due to an improved understanding of tumor molecular biology and antitumor immunity. The main task of a pulmonologist oncologist is to establish a tumor diagnosis and, ideally, to confirm the stage of the disease with the least invasive technique possible. Materials and Methods: The paper will summarize published reviews and original papers, as well as published clinical studies and case reports, which studied the role and compared the methods of invasive pulmonology diagnostics to obtain adequate tumor tissue samples for molecular analysis, thereby determining the most effective molecular treatments. Results: Bronchoscopy is often recommended as the initial diagnostic procedure for LC. If the tumor is endoscopically visible, the biopsy sample is susceptible to molecular testing, the same as tumor tissue samples obtained from surgical resection and mediastinoscopy. The use of new sampling methods, such as cryobiopsy for peripheral tumor lesions or cytoblock obtained by ultrasound-guided transbronchial needle aspiration (TBNA), enables obtaining adequate small biopsies and cytological samples for molecular testing, which have until recently been considered unsuitable for this type of analysis. During LC patients' treatment, resistance occurs due to changes in the mutational tumor status or pathohistological tumor type. Therefore, the repeated taking of liquid biopsies for molecular analysis or rebiopsy of tumor tissue for new pathohistological and molecular profiling has recently been mandated. Conclusions: In thoracic oncology, preference should be given to the least invasive diagnostic procedure providing a sample for histology rather than for cytology. However, there is increasing evidence that, when properly processed, cytology samples can be sufficient for both the cancer diagnosis and molecular analyses. A good knowledge of diagnostic procedures is essential for LC diagnosing and treatment in the personalized therapy era.
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Affiliation(s)
- Nensi Lalić
- Faculty of Medicine in Novi Sad, University of Novi Sad, Hajduk Veljkova 3, 21137 Novi Sad, Serbia; (A.L.); (M.I.); (O.I.); (M.B.); (N.J.)
- Institute for Pulmonary Diseases of Vojvodina, 21204 Sremska Kamenica, Serbia
| | - Aleksandra Lovrenski
- Faculty of Medicine in Novi Sad, University of Novi Sad, Hajduk Veljkova 3, 21137 Novi Sad, Serbia; (A.L.); (M.I.); (O.I.); (M.B.); (N.J.)
- Institute for Pulmonary Diseases of Vojvodina, 21204 Sremska Kamenica, Serbia
| | - Miroslav Ilić
- Faculty of Medicine in Novi Sad, University of Novi Sad, Hajduk Veljkova 3, 21137 Novi Sad, Serbia; (A.L.); (M.I.); (O.I.); (M.B.); (N.J.)
- Institute for Pulmonary Diseases of Vojvodina, 21204 Sremska Kamenica, Serbia
| | - Olivera Ivanov
- Faculty of Medicine in Novi Sad, University of Novi Sad, Hajduk Veljkova 3, 21137 Novi Sad, Serbia; (A.L.); (M.I.); (O.I.); (M.B.); (N.J.)
- Clinic of Radiation Oncology, Oncology Institute of Vojvodina, 21204 Sremska Kamenica, Serbia
| | - Marko Bojović
- Faculty of Medicine in Novi Sad, University of Novi Sad, Hajduk Veljkova 3, 21137 Novi Sad, Serbia; (A.L.); (M.I.); (O.I.); (M.B.); (N.J.)
- Clinic of Radiation Oncology, Oncology Institute of Vojvodina, 21204 Sremska Kamenica, Serbia
| | - Ivica Lalić
- Faculty of Pharmacy, University Business Academy in Novi Sad, Trg Mladenaca 5, 21101 Novi Sad, Serbia;
| | - Spasoje Popević
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (S.P.); (M.S.)
- University Hospital of Pulmonology, Clinical Center of Serbia, 11000 Belgrade, Serbia
| | - Mihailo Stjepanović
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (S.P.); (M.S.)
- University Hospital of Pulmonology, Clinical Center of Serbia, 11000 Belgrade, Serbia
| | - Nataša Janjić
- Faculty of Medicine in Novi Sad, University of Novi Sad, Hajduk Veljkova 3, 21137 Novi Sad, Serbia; (A.L.); (M.I.); (O.I.); (M.B.); (N.J.)
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Figaredo G, Martín-Muñoz A, Barrio S, Parrilla L, Campos-Martín Y, Poza M, Rufián L, Algara P, De La Torre M, Jiménez Ubieto A, Martínez-López J, Casado LF, Mollejo M. Genetic Profiling of Cell-Free DNA in Liquid Biopsies: A Complementary Tool for the Diagnosis of B-Cell Lymphomas and the Surveillance of Measurable Residual Disease. Cancers (Basel) 2023; 15:4022. [PMID: 37627050 PMCID: PMC10452485 DOI: 10.3390/cancers15164022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/26/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
PURPOSE To assess the potential value of LiqBio as a complementary tool for diagnosis and surveillance of BCL. METHODS This prospective multi-center study included 78 patients (25 follicular lymphomas (FL) and 53 large B-cell lymphomas (LBCL)). We performed next-generation sequencing (NGS) of cfDNA LiqBio and paired gDNA tissue biopsies at diagnosis and compared the mutational statuses. Also, through NGS of LiqBio, we identified MRD biomarkers and compared this novel LiqBio-MRD method with PET/CT in detecting MRD at follow-up. RESULTS We identified mutations in 71% of LiqBio and 95% of tissue biopsies, and found a correlation between variant allele frequency of somatic mutations. Additionally, we identified mutations in 73% of LiqBio from patients with no available tissue samples or no mutations in them. Regarding the utility of LiqBio-MRD as a dynamic monitoring tool, when compared with the PET/CT method, a lower sensitivity was observed for LiqBio-MRD at 92.3% (vs. 100% for PET/CT), but a higher specificity of 91.3% (vs. 86.9% for PET/CT). CONCLUSION Genetic profiling of tumor cfDNA in plasma LiqBio is a complementary tool for BCL diagnosis and MRD surveillance.
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Affiliation(s)
- Gloria Figaredo
- Department of Haematology, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain; (L.P.); (M.D.L.T.); (L.-F.C.)
| | - Alejandro Martín-Muñoz
- Altum Sequencing SL, Av. Gregorio Peces Barba, 1, 28919 Madrid, Spain; (A.M.-M.); (S.B.); (L.R.)
| | - Santiago Barrio
- Altum Sequencing SL, Av. Gregorio Peces Barba, 1, 28919 Madrid, Spain; (A.M.-M.); (S.B.); (L.R.)
- Computational Science Department, Carlos III University, Ronda de Toledo, 1, 28005 Madrid, Spain
| | - Laura Parrilla
- Department of Haematology, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain; (L.P.); (M.D.L.T.); (L.-F.C.)
| | - Yolanda Campos-Martín
- Biobank Department, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain;
| | - María Poza
- Haematology Department, Hospital Universitario 12 de Octubre, Avda. de Córdoba, s/n, 28041 Madrid, Spain; (M.P.); (A.J.U.); (J.M.-L.)
| | - Laura Rufián
- Altum Sequencing SL, Av. Gregorio Peces Barba, 1, 28919 Madrid, Spain; (A.M.-M.); (S.B.); (L.R.)
- Haematology Department, Hospital Universitario 12 de Octubre, Avda. de Córdoba, s/n, 28041 Madrid, Spain; (M.P.); (A.J.U.); (J.M.-L.)
| | - Patrocinio Algara
- Genetics Department, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain;
| | - Marina De La Torre
- Department of Haematology, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain; (L.P.); (M.D.L.T.); (L.-F.C.)
| | - Ana Jiménez Ubieto
- Haematology Department, Hospital Universitario 12 de Octubre, Avda. de Córdoba, s/n, 28041 Madrid, Spain; (M.P.); (A.J.U.); (J.M.-L.)
| | - Joaquín Martínez-López
- Haematology Department, Hospital Universitario 12 de Octubre, Avda. de Córdoba, s/n, 28041 Madrid, Spain; (M.P.); (A.J.U.); (J.M.-L.)
| | - Luis-Felipe Casado
- Department of Haematology, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain; (L.P.); (M.D.L.T.); (L.-F.C.)
| | - Manuela Mollejo
- Anatomopathology Department, Hospital Universitario de Toledo, Av. del Río Guadiana, 45007 Toledo, Spain;
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15
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Britze TE, Jakobsen KK, Grønhøj C, von Buchwald C. A systematic review on the role of biomarkers in liquid biopsies and saliva samples in the monitoring of salivary gland cancer. Acta Otolaryngol 2023; 143:709-713. [PMID: 37534452 DOI: 10.1080/00016489.2023.2238757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/16/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND Salivary gland cancer is a rare disease, and approximately 20% of tumors in the salivary glands are malignant. Reliable biomarkers may have a role in monitoring salivary gland cancer. AIM To review the current literature on the role of biomarkers in liquid biopsies and saliva samples in the monitoring of salivary gland cancer. MATERIALS AND METHOD This study systematically reviewed the literature on studies detecting salivary gland cancer by biomarkers in liquid biopsies and saliva samples by systematically searching PubMed and Embase between 1 January 2013 and 7 March 2023. RESULTS Five studies covering 64 malignant cases of salivary gland cancer were included, which considered inflammatory biomarkers or markers of genetic material in either blood or saliva. In saliva, there were demonstrated elevations of CA-19-9 in malignant cases, and elevations of miRNA in malignant and benign cases. In blood, there were demonstrated elevations of IL-33 in malignant and benign cases, elevations of ctDNA in malignant cases, and elevations of CTC in malignant cases. CONCLUSION AND SIGNIFICANCE The studies indicate that there is potential in the detection method. The studies detecting genetic material by liquid biopsies showed the most promising results. At present, there is still progression to be made before the method can be implemented for diagnostic use.
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Affiliation(s)
- Theresa Emilia Britze
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kathrine Kronberg Jakobsen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Christian Grønhøj
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, University Hospital Rigshospitalet, Copenhagen, Denmark
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Parker J. Uncovering cancer's secrets: could liquid biopsies and artificial intelligence hold the answers? Future Oncol 2023. [PMID: 37317873 DOI: 10.2217/fon-2023-0428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023] Open
Abstract
Tweetable abstract How are #liquidbiopsies and #AI pushing us closer to the goal of early cancer detection for all? Plus, what more needs to be done to truly deciphers cancer's secrets? Find out in this editorial by @JadeParkerB.
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17
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Mishra S, Kumar A, Kim S, Su Y, Singh S, Sharma M, Almousa S, Rather HA, Jain H, Lee J, Furdui CM, Ahmad S, Ferrario CM, Punzi HA, Chuang CC, Wabitsch M, Kritchevsky SB, Register TC, Deep G. A Liquid Biopsy-Based Approach to Isolate and Characterize Adipose Tissue-Derived Extracellular Vesicles from Blood. ACS Nano 2023; 17:10252-10268. [PMID: 37224410 DOI: 10.1021/acsnano.3c00422] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Obesity is a major risk factor for multiple chronic diseases. Anthropometric and imaging approaches are primarily used to assess adiposity, and there is a dearth of techniques to determine the changes in adipose tissue (AT) at the molecular level. Extracellular vesicles (EVs) have emerged as a novel and less invasive source of biomarkers for various pathologies. Furthermore, the possibility of enriching cell or tissue-specific EVs from the biofluids based on their unique surface markers has led to classifying these vesicles as "liquid biopsies", offering valuable molecular information on hard-to-access tissues. Here, we isolated small EVs from AT (sEVAT) of lean and diet-induced obese (DIO) mice, identified unique surface proteins on sEVAT by surface shaving followed by mass spectrometry, and developed a signature of five unique proteins. Using this signature, we pulled out sEVAT from the blood of mice and validated the specificity of isolated sEVAT by measuring the expression of adiponectin, 38 adipokines on an array, and several adipose tissue-related miRNAs. Furthermore, we provided evidence of sEV applicability in disease prediction by characterizing sEVAT from the blood of lean and DIO mice. Interestingly, sEVAT-DIO cargo showed a stronger pro-inflammatory effect on THP1 monocytes compared to sEVAT-Lean and a significant increase in obesity-associated miRNA expression. Equally important, sEVAT cargo revealed an obesity-associated aberrant amino acid metabolism that was subsequently validated in the corresponding AT. Lastly, we show a significant increase in inflammation-related molecules in sEVAT isolated from the blood of nondiabetic obese (>30 kg/m2) individuals. Overall, the present study offers a less-invasive approach to characterize AT.
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Affiliation(s)
- Shalini Mishra
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Ashish Kumar
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Susy Kim
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Yixin Su
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Sangeeta Singh
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Mitu Sharma
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Sameh Almousa
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Hilal A Rather
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Heetanshi Jain
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Jingyun Lee
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina 27157, United States
| | - Cristina M Furdui
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina 27157, United States
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Sarfaraz Ahmad
- Laboratory of Translational Hypertension, Department of General Surgery, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Carlos M Ferrario
- Laboratory of Translational Hypertension, Department of General Surgery, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Henry A Punzi
- Punzi Medical Center, Punzi Institute of Medicine, Carrollton, Texas 75006, United States
- UT Southwestern Medical Center, Dallas, Texas, 75390, United States
| | - Chia-Chi Chuang
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Martin Wabitsch
- Department of Pediatrics and Adolescent Medicine, Center for Rare Endocrine Diseases, Ulm University Medical Centre, Ulm 89069, Germany
| | - Stephen B Kritchevsky
- Department of Internal Medicine-Gerontology and Geriatric Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
- Sticht Center for Healthy Aging and Alzheimer's Prevention, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Thomas C Register
- Sticht Center for Healthy Aging and Alzheimer's Prevention, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
- Department of Pathology, Section on Comparative Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
| | - Gagan Deep
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
- Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, North Carolina 27157, United States
- Sticht Center for Healthy Aging and Alzheimer's Prevention, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27157, United States
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Vlataki K, Antonouli S, Kalyvioti C, Lampri E, Kamina S, Mauri D, Harissis HV, Magklara A. Circulating Tumor DNA in the Management of Early-Stage Breast Cancer. Cells 2023; 12:1573. [PMID: 37371043 DOI: 10.3390/cells12121573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Liquid biopsies refer to the isolation and analysis of tumor-derived biological material from body fluids, most commonly blood, in order to provide clinically valuable information for the management of cancer patients. Their non-invasive nature allows to overcome the limitations of tissue biopsy and complement the latter in guiding therapeutic decision-making. In the past years, several studies have demonstrated that circulating tumor DNA (ctDNA) detection can be used in the clinical setting to improve patient prognosis and monitor therapy response, especially in metastatic cancers. With the advent of significant technological advances in assay development, ctDNA can now be accurately and reliably identified in early-stage cancers despite its low levels in the bloodstream. In this review, we discuss the most important studies that highlight the potential clinical utility of ctDNA in early-stage breast cancer focusing on early diagnosis, detection of minimal residual disease and prediction of metastatic relapse. We also offer a concise description of the most sensitive techniques that are deemed appropriate for ctDNA detection in early-stage cancer and we examine their advantages and disadvantages, as they have been employed in various studies. Finally, we discuss future perspectives on how ctDNA could be better integrated into the everyday oncology practice.
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Affiliation(s)
- Katerina Vlataki
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Sevastiani Antonouli
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
| | - Christina Kalyvioti
- Breast Unit, Department of Surgery, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Evangeli Lampri
- Department of Pathology, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Sevasti Kamina
- Department of Pathology, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Davide Mauri
- Department of Medical Oncology, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Haralampos V Harissis
- Breast Unit, Department of Surgery, University Hospital of Ioannina, 45500 Ioannina, Greece
| | - Angeliki Magklara
- Department of Clinical Chemistry, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
- Biomedical Research Institute, Foundation for Research and Technology, 45110 Ioannina, Greece
- Institute of Biosciences, University Research Center of Ioannina (URCI), 45110 Ioannina, Greece
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Hofste LS, Geerlings MJ, Kamping EJ, Kouwenhoven ND, von Rhein D, Jansen EA, Garms LM, Nagtegaal ID, van der Post RS, de Wilt JH, Klarenbeek BR, Ligtenberg MJ. Clinical Validity of Tumor-Informed Circulating Tumor DNA Analysis in Patients Undergoing Surgery of Colorectal Metastases. Dis Colon Rectum 2023; 66:796-804. [PMID: 35857852 PMCID: PMC10191207 DOI: 10.1097/dcr.0000000000002443] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Accurate biomarkers to monitor tumor load and response in metastatic colorectal cancer patients undergoing surgery could optimize treatment regimens. OBJECTIVE This study aimed to explore the clinical validity of tumor-informed quantification of circulating tumor DNA in blood using ultradeep sequencing. DESIGN Resection specimens from 53 colorectal cancer patients were analyzed for tumor-specific mutations in 15 genes. These mutations were used to measure the presence of circulating tumor DNA in preoperatively collected plasma samples using hybrid capture-based sequencing. Additional postoperative measurements were performed 1 week after surgery in 16 patients. SETTINGS The study was conducted at the Radboud University Medical Center. PATIENTS A total of 53 colorectal cancer patients undergoing surgery of metastases were included. MAIN OUTCOME MEASURES The detection of circulating tumor DNA. RESULTS At least 1 tumor-specific mutation was detected in all tumor samples. In preoperative plasma samples, circulating tumor DNA was detected in 88% (37/42) of systemic treatment-naïve patients and in 55% (6/11) of patients who received preoperative chemotherapy. More specifically, circulating tumor DNA was detected in 0% (0/3) of cases with a subtotal or partial pathologic response and in 75% (6/8) of cases without a pathologic response in the resection specimen ( p = 0.06). In postoperative plasma samples, circulating tumor DNA was detected in 80% (4/5) of patients with an incomplete resection and in 0% (0/11) of those with a complete resection ( p = 0.003). LIMITATIONS The study was limited by the heterogeneity of the cohort and the small number of postoperative plasma samples. CONCLUSIONS These data indicate that tumor-informed circulating tumor DNA detection in the plasma of patients undergoing surgery for metastatic colorectal cancer is feasible and may have clinical value in response monitoring and predicting residual disease. Prospective studies are needed to establish the clinical utility of circulating tumor DNA analysis to guide treatment decisions in these patients. See Video Abstract at http://links.lww.com/DCR/B990 . VALIDEZ CLNICA DEL ANLISIS DE ADN DEL TUMOR CIRCULANTE INFORMADO POR EL TUMOR EN PACIENTES SOMETIDOS A CIRUGA DE METSTASIS COLORRECTALES ANTECEDENTES:Los biomarcadores precisos para monitorear la carga tumoral y la respuesta en pacientes con cáncer colorrectal metastásico que se someten a cirugía podrían optimizar los regímenes de tratamiento.OBJETIVO:Este estudio explora la validez clínica de la cuantificación informada por el tumor del ADN tumoral circulante en sangre mediante secuenciación ultraprofunda.DISEÑO:Se analizaron muestras de resección de 53 pacientes con cáncer colorrectal en busca de mutaciones específicas del tumor en quince genes. Estas mutaciones se usaron para medir la presencia de ADN tumoral circulante en muestras de plasma recolectadas antes de la operación usando secuenciación basada en captura híbrida. Se realizaron mediciones postoperatorias adicionales una semana después de la cirugía en dieciséis pacientes.AJUSTES:El estudio se realizó en el centro médico de la universidad de Radboud.PACIENTES:Se incluyeron un total de 53 pacientes con cáncer colorrectal sometidos a cirugía de metástasis.PRINCIPALES MEDIDAS DE RESULTADO:La detección de ADN tumoral circulante.RESULTADOS:Se detectó al menos una mutación específica de tumor en todas las muestras de tumor. En muestras de plasma preoperatorias, se detectó ADN tumoral circulante en el 88% (37/42) de los pacientes sin tratamiento sistémico previo y en el 55% (6/11) de los pacientes que recibieron quimioterapia preoperatoria. Más concretamente, en el 0% (0/3) de los casos con respuesta patológica subtotal o parcial y en el 75% (6/8) de los casos sin respuesta patológica en la pieza de resección ( p = 0,06). En muestras de plasma postoperatorio se detectó ADN tumoral circulante en el 80% (4/5) de los pacientes con una resección incompleta y en el 0% (0/11) de los que tenían resección completa ( p = 0,003).LIMITACIONES:El estudio estuvo limitado por la heterogeneidad de la cohorte y el pequeño número de muestras de plasma postoperatorias.CONCLUSIONES:Estos datos indican que la detección de ADN tumoral circulante informado por el tumor en el plasma de pacientes sometidos a cirugía por cáncer colorrectal metastásico es factible y puede tener valor clínico en el control de la respuesta y la predicción de la enfermedad residual. Se necesitan estudios prospectivos para establecer la utilidad clínica del análisis de ADN tumoral circulante para guiar las decisiones de tratamiento en estos pacientes. Consulte Video Resumen en http://links.lww.com/DCR/B990 . (Traducción-Dr. Mauricio Santamaria ).
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Affiliation(s)
- Lisa S.M. Hofste
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maartje J. Geerlings
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eveline J. Kamping
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Daniel von Rhein
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erik A.M. Jansen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Linda M. Garms
- Department of Surgery, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Iris D. Nagtegaal
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | | | | | - Marjolijn J.L. Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
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20
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LaPlante EL, Stürchler A, Fullem R, Chen D, Starner AC, Esquivel E, Alsop E, Jackson AR, Ghiran I, Pereira G, Rozowsky J, Chang J, Gerstein MB, Alexander RP, Roth ME, Franklin JL, Coffey RJ, Raffai RL, Mansuy IM, Stavrakis S, deMello AJ, Laurent LC, Wang YT, Tsai CF, Liu T, Jones J, Van Keuren-Jensen K, Van Nostrand E, Mateescu B, Milosavljevic A. exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers. Cell Genom 2023; 3:100303. [PMID: 37228754 PMCID: PMC10203258 DOI: 10.1016/j.xgen.2023.100303] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 01/01/2023] [Accepted: 03/24/2023] [Indexed: 05/27/2023]
Abstract
Although the role of RNA binding proteins (RBPs) in extracellular RNA (exRNA) biology is well established, their exRNA cargo and distribution across biofluids are largely unknown. To address this gap, we extend the exRNA Atlas resource by mapping exRNAs carried by extracellular RBPs (exRBPs). This map was developed through an integrative analysis of ENCODE enhanced crosslinking and immunoprecipitation (eCLIP) data (150 RBPs) and human exRNA profiles (6,930 samples). Computational analysis and experimental validation identified exRBPs in plasma, serum, saliva, urine, cerebrospinal fluid, and cell-culture-conditioned medium. exRBPs carry exRNA transcripts from small non-coding RNA biotypes, including microRNA (miRNA), piRNA, tRNA, small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), Y RNA, and lncRNA, as well as protein-coding mRNA fragments. Computational deconvolution of exRBP RNA cargo reveals associations of exRBPs with extracellular vesicles, lipoproteins, and ribonucleoproteins across human biofluids. Overall, we mapped the distribution of exRBPs across human biofluids, presenting a resource for the community.
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Affiliation(s)
- Emily L. LaPlante
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alessandra Stürchler
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Robert Fullem
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anne C. Starner
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 76706, USA
| | - Emmanuel Esquivel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Alsop
- Neurogenomics Division, TGen, Phoenix, AZ 85004, USA
| | - Andrew R. Jackson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ionita Ghiran
- Department of Anesthesia, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Getulio Pereira
- Department of Anesthesia, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Joel Rozowsky
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Justin Chang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mark B. Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Matthew E. Roth
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey L. Franklin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Robert J. Coffey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37235, USA
| | - Robert L. Raffai
- Department of Veterans Affairs, Surgical Service (112G), San Francisco VA Medical Center, San Francisco, CA 94121, USA
- Division of Endovascular and Vascular Surgery, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Isabelle M. Mansuy
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Stavros Stavrakis
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Andrew J. deMello
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive Sciences and Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Jennifer Jones
- Laboratory of Pathology Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Eric Van Nostrand
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX 76706, USA
- Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bogdan Mateescu
- Institute for Chemical and Bioengineering, ETH Zürich, 8093 Zürich, Switzerland
- Brain Research Institute, University of Zürich, 8057 Zürich, Switzerland
| | - Aleksandar Milosavljevic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
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21
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Gautam SK, Khan P, Natarajan G, Atri P, Aithal A, Ganti AK, Batra SK, Nasser MW, Jain M. Mucins as Potential Biomarkers for Early Detection of Cancer. Cancers (Basel) 2023; 15:1640. [PMID: 36980526 PMCID: PMC10046558 DOI: 10.3390/cancers15061640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/25/2023] [Accepted: 02/27/2023] [Indexed: 03/10/2023] Open
Abstract
Early detection significantly correlates with improved survival in cancer patients. So far, a limited number of biomarkers have been validated to diagnose cancers at an early stage. Considering the leading cancer types that contribute to more than 50% of deaths in the USA, we discuss the ongoing endeavors toward early detection of lung, breast, ovarian, colon, prostate, liver, and pancreatic cancers to highlight the significance of mucin glycoproteins in cancer diagnosis. As mucin deregulation is one of the earliest events in most epithelial malignancies following oncogenic transformation, these high-molecular-weight glycoproteins are considered potential candidates for biomarker development. The diagnostic potential of mucins is mainly attributed to their deregulated expression, altered glycosylation, splicing, and ability to induce autoantibodies. Secretory and shed mucins are commonly detected in patients' sera, body fluids, and tumor biopsies. For instance, CA125, also called MUC16, is one of the biomarkers implemented for the diagnosis of ovarian cancer and is currently being investigated for other malignancies. Similarly, MUC5AC, a secretory mucin, is a potential biomarker for pancreatic cancer. Moreover, anti-mucin autoantibodies and mucin-packaged exosomes have opened new avenues of biomarker development for early cancer diagnosis. In this review, we discuss the diagnostic potential of mucins in epithelial cancers and provide evidence and a rationale for developing a mucin-based biomarker panel for early cancer detection.
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Affiliation(s)
- Shailendra K. Gautam
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Gopalakrishnan Natarajan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Pranita Atri
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Abhijit Aithal
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Apar K. Ganti
- Fred & Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Division of Oncology-Hematology, Department of Internal Medicine, VA Nebraska Western Iowa Health Care System, University of Nebraska Medical Center, Omaha, NE 68105, USA
| | - Surinder K. Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd W. Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred & Pamela Buffett Cancer Center, Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
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22
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Schneider L, Dansranjav T, Neumann E, Yan H, Pilatz A, Schuppe HC, Wagenlehner F, Schagdarsurengin U. Post-prostatic-massage urine exosomes of men with chronic prostatitis/chronic pelvic pain syndrome carry prostate-cancer-typical microRNAs and activate proto-oncogenes. Mol Oncol 2023; 17:445-468. [PMID: 36321189 PMCID: PMC9980307 DOI: 10.1002/1878-0261.13329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 10/05/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022] Open
Abstract
Chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) has a high prevalence of up to 15% and accounts for 90-95% of prostatitis diagnoses, and yet its etiopathogenesis and link to prostate cancer (PCa) are still unclear. Here, we investigated microRNAs in exosomes isolated from blood and post-prostatic-massage urine of CP/CPPS type IIIb patients and healthy men. THP-1 monocytes (human leukemia monocytic cell line) were treated with exosomes and subjected to mRNA arrays "Cancer Inflammation and Immunity Crosstalk" and "Transcription Factors." Using The Cancer Genome Atlas, the expression of CP/CPPS-associated microRNAs was analyzed in PCa and normal prostate tissue. In silico functional studies were carried out to explore the disease ontology of CP/CPPS. In CP/CPPS, urine exosomes exhibited significant upregulation of eight PCa-specific microRNAs (e.g., hsa-miR-501, hsa-miR-20a, and hsa-miR-106), whose target genes were significantly enriched for GO terms, hallmark gene sets, and pathways specific for carcinogenesis. In THP-1 monocytes, CP/CPPS-derived urine exosomes induced upregulation of PCa-associated proinflammatory genes (e.g., CCR2 and TLR2) and proto-oncogene transcription factors (e.g., MYB and JUNB). In contrast, CP/CPPS-derived blood exosomes exhibited molecular properties similar to those of healthy men. Thus, CP/CPPS exhibits molecular changes that constitute a risk for PCa and should be considered in the development of PCa biomarkers and cancer screening programs.
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Affiliation(s)
- Laura Schneider
- Clinic of Urology, Pediatric Urology and Andrology, Justus-Liebig-University Giessen, Germany.,Working Group "Epigenetics of the Urogenital System," Clinic of Urology, Pediatric Urology and Andrology, Justus-Liebig-University Giessen, Germany
| | - Temuujin Dansranjav
- Clinic of Urology, Pediatric Urology and Andrology, Justus-Liebig-University Giessen, Germany
| | - Elena Neumann
- Department of Rheumatology and Clinical Immunology, Campus Kerckhoff, Justus-Liebig-University of Giessen, Bad Nauheim, Germany
| | - Hang Yan
- Clinic of Urology, Pediatric Urology and Andrology, Justus-Liebig-University Giessen, Germany.,Working Group "Epigenetics of the Urogenital System," Clinic of Urology, Pediatric Urology and Andrology, Justus-Liebig-University Giessen, Germany
| | - Adrian Pilatz
- Clinic of Urology, Pediatric Urology and Andrology, Justus-Liebig-University Giessen, Germany
| | - Hans-Christian Schuppe
- Clinic of Urology, Pediatric Urology and Andrology, Justus-Liebig-University Giessen, Germany
| | - Florian Wagenlehner
- Clinic of Urology, Pediatric Urology and Andrology, Justus-Liebig-University Giessen, Germany
| | - Undraga Schagdarsurengin
- Clinic of Urology, Pediatric Urology and Andrology, Justus-Liebig-University Giessen, Germany.,Working Group "Epigenetics of the Urogenital System," Clinic of Urology, Pediatric Urology and Andrology, Justus-Liebig-University Giessen, Germany
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23
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Abstract
Tumor cells release extracellular vesicles (EVs) that can function as mediators of intercellular communication in the tumor microenvironment. EVs contain a host of bioactive cargo, including membrane, cytosolic, and nuclear proteins, in addition to noncoding RNAs, other RNA types, and double-stranded DNA fragments. These shed vesicles may deposit paracrine information and can also be taken up by stromal cells, causing the recipient cells to undergo phenotypic changes that profoundly impact diverse facets of cancer progression. For example, this unique form of cellular cross talk helps condition the premetastatic niche, facilitates evasion of the immune response, and promotes invasive and metastatic activity. These findings, coupled with those demonstrating that the number and content of EVs produced by tumors can vary depending on their tumor of origin, disease stage, or response to therapy, have raised the exciting possibility that EVs can be used for risk stratification, diagnostic, and even prognostic purposes. We summarize recent developments and the current knowledge of EV cargoes, their impact on disease progression, and implementation of EV-based liquid biopsies as tumor biomarkers.
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Affiliation(s)
- James W Clancy
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA; ,
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24
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Costa B, Li Calzi M, Castellano M, Blanco V, Cuevasanta E, Litvan I, Ivanov P, Witwer K, Cayota A, Tosar JP. Nicked tRNAs are stable reservoirs of tRNA halves in cells and biofluids. Proc Natl Acad Sci U S A 2023; 120:e2216330120. [PMID: 36652478 DOI: 10.1073/pnas.2216330120] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Nonvesicular extracellular RNAs (nv-exRNAs) constitute the majority of the extracellular RNAome, but little is known about their stability, function, and potential use as disease biomarkers. Herein, we measured the stability of several naked RNAs when incubated in human serum, urine, and cerebrospinal fluid (CSF). We identified extracellularly produced tRNA-derived small RNAs (tDRs) with half-lives of several hours in CSF. Contrary to widespread assumptions, these intrinsically stable small RNAs are full-length tRNAs containing broken phosphodiester bonds (i.e., nicked tRNAs). Standard molecular biology protocols, including phenol-based RNA extraction and heat, induce the artifactual denaturation of nicked tRNAs and the consequent in vitro production of tDRs. Broken bonds are roadblocks for reverse transcriptases, preventing amplification and/or sequencing of nicked tRNAs in their native state. To solve this, we performed enzymatic repair of nicked tRNAs purified under native conditions, harnessing the intrinsic activity of phage and bacterial tRNA repair systems. Enzymatic repair regenerated an RNase R-resistant tRNA-sized band in northern blot and enabled RT-PCR amplification of full-length tRNAs. We also separated nicked tRNAs from tDRs by chromatographic methods under native conditions, identifying nicked tRNAs inside stressed cells and in vesicle-depleted human biofluids. Dissociation of nicked tRNAs produces single-stranded tDRs that can be spontaneously taken up by human epithelial cells, positioning stable nv-exRNAs as potentially relevant players in intercellular communication pathways.
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25
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Macedo-Silva C, Constâncio V, Miranda-Gonçalves V, Leite-Silva P, Salta S, Lobo J, Guimarães R, Carvalho-Maia C, Gigliano D, Farinha M, Sousa O, Henrique R, Jerónimo C. DNA methylation biomarkers accurately detect esophageal cancer prior and post neoadjuvant chemoradiation. Cancer Med 2023; 12:8777-8788. [PMID: 36670548 PMCID: PMC10134363 DOI: 10.1002/cam4.5623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Esophageal cancer (ECa) is associated with high mortality, mostly due to late diagnosis, precluding curativeintent surgery. Hence, neoadjuvant chemoradiation (ChRT) is recommended in most patients regardless of histological subtype. A proportion of these patients, however, achieve complete disease remission and might be spared of radical surgery. The lack of reliable, minimally invasive biomarkers able to detect post-ChRT disease persistence is, nonetheless, a major drawback. We have previously shown that miRNA promotor methylation enables accurate cancer detection in tissues and liquid biopsies but has been seldom explored in ECa patients. AIMS Herein, we sought to unveil and validate novel candidate biomarkers able to detect ECa prior and post ChRT. MATERIALS AND METHODS Promoter methylation of miR129-2, miR124-3 and ZNF569 was assessed, using quantitative methylation-specific PCR (qMSP), in tissue samples from normal esophagus, treatment-naïve and post-ChRT ECa, as well as in liquid biopsies from ECa patients. RESULTS All genes disclosed significantly different promoter methylation levels between ECa and normal esophagus, accurately detecting post-ChRT disease, especially for adenocarcinoma. Remarkably, miR129-2me /ZNF569me methylation panel identified ECa in liquid samples with 53% sensitivity and 87% specificity. DISCUSSION MiR129-2me , miR124-3me and ZNF569me accurately discriminate ECa, either pre- or post-ChRT, from normal tissue, enabling ECa detection. Furthermore, circulalting methylation-based biomarkers are promising minimally invasive tools to detect post-ChRT residual ECa. CONCLUSION Overall, our results encourage the use of miRNA methylation biomarkers as accurate ECa detection tools as a novel approach for ChRT response monitoring.
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Affiliation(s)
- Catarina Macedo-Silva
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - Vera Constâncio
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - Vera Miranda-Gonçalves
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Pedro Leite-Silva
- Cancer Epidemiology Group, Research Center & Department of Epidemiology of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - Sofia Salta
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - João Lobo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Rita Guimarães
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Carina Carvalho-Maia
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal
| | - Davide Gigliano
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Mónica Farinha
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Olga Sousa
- Department of Radiation Oncology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Rui Henrique
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
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Debattista J, Grech L, Scerri C, Grech G. Copy Number Variations as Determinants of Colorectal Tumor Progression in Liquid Biopsies. Int J Mol Sci 2023; 24. [PMID: 36675253 DOI: 10.3390/ijms24021738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Over the years, increasing evidence has shown that copy number variations (CNVs) play an important role in the pathogenesis and prognosis of Colorectal Cancer (CRC). Colorectal adenomas are highly prevalent lesions, but only 5% of these adenomas ever progress to carcinoma. This review summarizes the different CNVs associated with adenoma-carcinoma CRC progression and with CRC staging. Characterization of CNVs in circulating free-RNA and in blood-derived exosomes augers well with the potential of using such assays for patient management and early detection of metastasis. To overcome the limitations related to tissue biopsies and tumor heterogeneity, using CNVs to characterize tumor-derived materials in biofluids provides less invasive sampling methods and a sample that collectively represents multiple tumor sites in heterogeneous samples. Liquid biopsies provide a source of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), tumor-derived exosomes (TDE), circulating free RNA, and non-coding RNA. This review provides an overview of the current diagnostic and predictive models from liquid biopsies.
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Allam S, Nasr K, Khalid F, Shah Z, Khan Suheb MZ, Mulla S, Vikash S, Bou Zerdan M, Anwer F, Chaulagain CP. Liquid biopsies and minimal residual disease in myeloid malignancies. Front Oncol 2023; 13:1164017. [PMID: 37213280 PMCID: PMC10196237 DOI: 10.3389/fonc.2023.1164017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/25/2023] [Indexed: 05/23/2023] Open
Abstract
Minimal residual disease (MRD) assessment through blood component sampling by liquid biopsies (LBs) is increasingly being investigated in myeloid malignancies. Blood components then undergo molecular analysis by flow cytometry or sequencing techniques and can be used as a powerful tool for prognostic and predictive purposes in myeloid malignancies. There is evidence and more is evolving about the quantification and identification of cell-based and gene-based biomarkers in myeloid malignancies to monitor treatment response. MRD based acute myeloid leukemia protocol and clinical trials are currently incorporating LB testing and preliminary results are encouraging for potential widespread use in clinic in the near future. MRD monitoring using LBs are not standard in myelodysplastic syndrome (MDS) but this is an area of active investigation. In the future, LBs can replace more invasive techniques such as bone marrow biopsies. However, the routine clinical application of these markers continues to be an issue due to lack of standardization and limited number of studies investigating their specificities. Integrating artificial intelligence (AI) could help simplify the complex interpretation of molecular testing and reduce errors related to operator dependency. Though the field is rapidly evolving, the applicability of MRD testing using LB is mostly limited to research setting at this time due to the need for validation, regulatory approval, payer coverage, and cost issues. This review focuses on the types of biomarkers, most recent research exploring MRD and LB in myeloid malignancies, ongoing clinical trials, and the future of LB in the setting of AI.
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Affiliation(s)
- Sabine Allam
- Department of Medicine and Medical Sciences, University of Balamand, Dekwaneh, Lebanon
| | - Kristina Nasr
- Department of Medicine and Medical Sciences, University of Balamand, Dekwaneh, Lebanon
| | - Farhan Khalid
- Department of Internal Medicine, Monmouth Medical Center, Long Branch, NJ, United States
| | - Zunairah Shah
- Department of Internal Medicine, Weiss Memorial Hospital, Chicago, IL, United States
| | | | - Sana Mulla
- Department of Internal Medicine, St Mary’s Medical Center, Apple Valley, CA, United States
| | - Sindhu Vikash
- Department of Medicine, Jacobi Medical center/AECOM Bronx, Bronx, NY, United States
| | - Maroun Bou Zerdan
- Department of Internal Medicine, SUNY Upstate Medical University, New York, NY, United States
| | - Faiz Anwer
- Department of Hematology and Oncology, Taussig Cancer Center, Cleveland Clinic, Cleveland, OH, United States
| | - Chakra P. Chaulagain
- Department of Hematology and Oncology, Maroone Cancer Center, Cleveland Clinic Florida, Weston, FL, United States
- *Correspondence: Chakra P. Chaulagain,
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Cerón R, Martínez A, Ramos C, De la Cruz A, García A, Mendoza I, Palmeros G, Montaño Figueroa EH, Navarrete J, Jiménez-Morales S, Martinez-Murillo C, Olarte I. Overexpression of BCL2, BCL6, VEGFR1 and TWIST1 in Circulating Tumor Cells Derived from Patients with DLBCL Decreases Event-Free Survival. Onco Targets Ther 2022; 15:1583-1595. [PMID: 36606244 PMCID: PMC9809418 DOI: 10.2147/ott.s386562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/08/2022] [Indexed: 12/31/2022] Open
Abstract
Purpose Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous malignant lymphoid neoplasm and is the most common subtype of non-Hodgkin lymphoma in adults. More than half of patients with DLBCL can achieve remission with standard R-CHOP regimes; however, approximately 30-40% of patients are still failing this standard therapy, which remains as an important cause of progression and mortality of this disease. It is necessary to have diagnostic and monitoring tools that allow us to improve the accuracy of prognosis in these patients. Circulating tumor cells (CTCs) identification through molecular biomarkers is one of the novel strategies that have been used in other types of cancer, and we aim to use this tool to analyze the potential role in DLBCL. Patients and Methods We analyzed 138 blood samples of patients with DLBCL, of which CTCs were isolated by density gradient for subsequent detection and quantitation of molecular biomarkers using RT-qPCR with TaqMan probes. Survival analysis was performed using Kaplan-Meier curves. Results We found overexpression of ABCB1, αSMA, BCL2, BCL6 and VEGFR1 genes, as well as the presence of CK19, EpCAM, KI67, MAGE-A4, SNAIL and TWIST1 genes. CK19 and EpCAM expression were associated with a minor OS (85.7% vs 98.1%, p = 0.002). The overexpression of BCL2, BCL6, VEGFR1 and TWIST1 was related to a minor EFS (p = 0.001). Conclusion This study showed that in liquid biopsies analyzed, the presence of CTCs can be confirmed through molecular biomarkers, and it has an impact on OS and EFs, making this detection useful in the follow-up and prognosis of patients with DLBCL.
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Affiliation(s)
- Rafael Cerón
- Posgrado en Ciencias Biológicas, Biomedicina, UNAM, CDMX, México,Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Adolfo Martínez
- Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Christian Ramos
- Department of Medical Hematology, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Adrián De la Cruz
- Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Anel García
- Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Iveth Mendoza
- Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Goujon Palmeros
- Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | | | - Juan Navarrete
- Department of Hematopathology, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Silvia Jiménez-Morales
- Laboratory of Cancer Genomics, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Carlos Martinez-Murillo
- Department of Medical Hematology, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico
| | - Irma Olarte
- Department of Molecular Biology, Hematology Service, Hospital General de México, “Dr. Eduardo Liceaga”, Mexico City, Mexico,Correspondence: Irma Olarte, Dr. Balmis 148, Col. Doctores, Alc. Cuauhtémoc, Mexico City, ZC. 06726, Mexico, Tel +525527892000 Ext. 1609, Email
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M Silva S, Langley DP, Cossins LR, Samudra AN, Quigley AF, Kapsa RMI, Tothill RW, Greene GW, Moulton SE. Rapid Point-of-Care Electrochemical Sensor for the Detection of Cancer Tn Antigen Carbohydrate in Whole Unprocessed Blood. ACS Sens 2022; 7:3379-3388. [PMID: 36374944 DOI: 10.1021/acssensors.2c01460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Improving outcomes for cancer patients during treatment and monitoring for cancer recurrence requires personalized care which can only be achieved through regular surveillance for biomarkers. Unfortunately, routine detection for blood-based biomarkers is cost-prohibitive using currently specialized laboratories. Using a rapid self-assembly sensing interface amenable to methods of mass production, we demonstrate the ability to detect and quantify a small carbohydrate-based cancer biomarker, Tn antigen (αGalNAc-Ser/Thr) in a small volume of blood, using a test format strip reminiscent of a blood glucose test. The detection of Tn antigen at picomolar levels is achieved through a new transduction mechanism based on the impact of Tn antigen interactions on the molecular dynamic motion of a lectin cross-linked lubricin antifouling brush. In tests performed on retrospective blood plasma samples from patients presenting three different tumor types, differentiation between healthy and diseased patients was achieved, highlighting the clinical potential for cancer monitoring.
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Affiliation(s)
- Saimon M Silva
- ARC Centre of Excellence for Electromaterials Science, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn3122, Victoria, Australia.,The Aikenhead Centre for Medical Discovery, St Vincent's Hospital Melbourne, Melbourne3065, Victoria, Australia.,Iverson Health Innovation Research Institute, Swinburne University of Technology, Hawthorn3122, Victoria, Australia
| | | | | | | | - Anita F Quigley
- School of Electrical and Biomedical Engineering, RMIT University, Melbourne3001, Victoria, Australia.,Department of Medicine, University of Melbourne, St. Vincent's Hospital, Melbourne3065, Victoria, Australia.,The Aikenhead Centre for Medical Discovery, St Vincent's Hospital Melbourne, Melbourne3065, Victoria, Australia
| | - Robert M I Kapsa
- School of Electrical and Biomedical Engineering, RMIT University, Melbourne3001, Victoria, Australia.,Department of Medicine, University of Melbourne, St. Vincent's Hospital, Melbourne3065, Victoria, Australia.,The Aikenhead Centre for Medical Discovery, St Vincent's Hospital Melbourne, Melbourne3065, Victoria, Australia
| | - Richard W Tothill
- Peter MacCallum Cancer Centre, Department of Clinical Pathology, University of Melbourne, Melbourne3010, Victoria, Australia
| | - George W Greene
- Institute for Frontier Materials and ARC Centre of Excellence for Electromaterials Science, Deakin University, Waurn Ponds3216, Victoria, Australia
| | - Simon E Moulton
- ARC Centre of Excellence for Electromaterials Science, School of Science, Computing and Engineering Technologies, Swinburne University of Technology, Hawthorn3122, Victoria, Australia.,The Aikenhead Centre for Medical Discovery, St Vincent's Hospital Melbourne, Melbourne3065, Victoria, Australia.,Iverson Health Innovation Research Institute, Swinburne University of Technology, Hawthorn3122, Victoria, Australia
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30
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Seneviratne C, Shetty AC, Geng X, McCracken C, Cornell J, Mullins K, Jiang F, Stass S. A Pilot Analysis of Circulating cfRNA Transcripts for the Detection of Lung Cancer. Diagnostics (Basel) 2022; 12:diagnostics12122897. [PMID: 36552904 PMCID: PMC9776862 DOI: 10.3390/diagnostics12122897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/20/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022] Open
Abstract
Lung cancers are the leading cause of cancer-related deaths worldwide. Studies have shown that non-small cell lung cancer (NSCLC), which constitutes the majority of lung cancers, is significantly more responsive to early-stage interventions. However, the early stages are often asymptomatic, and current diagnostic methods are limited in their precision and safety. The cell-free RNAs (cfRNAs) circulating in plasma (liquid biopsies) offer a non-invasive detection of spatial and temporal changes occurring in primary tumors since the early stages. To address gaps in the current cfRNA knowledge base, we conducted a pilot study for the comprehensive analysis of transcriptome-wide changes in plasma cfRNA in NSCLC patients. Total cfRNA was extracted from archived plasma collected from NSCLC patients (N = 12), cancer-free former smokers (N = 12), and non-smoking healthy volunteers (N = 12). Plasma cfRNA expression levels were quantified by using a tagmentation-based library preparation and sequencing. The comparisons of cfRNA expression levels between patients and the two control groups revealed a total of 2357 differentially expressed cfRNAs enriched in 123 pathways. Of these, 251 transcripts were previously reported in primary NSCLCs. A small subset of genes (N = 5) was validated in an independent sample (N = 50) using qRT-PCR. Our study provides a framework for developing blood-based assays for the early detection of NSCLC and warrants further validation.
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Affiliation(s)
- Chamindi Seneviratne
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Correspondence: (C.S.); (S.S.)
| | - Amol Carl Shetty
- The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Xinyan Geng
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Carrie McCracken
- The Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jessica Cornell
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Kristin Mullins
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Laboratories of Pathology, University of Maryland Medical Center, Baltimore, MD 21201, USA
| | - Feng Jiang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Sanford Stass
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Laboratories of Pathology, University of Maryland Medical Center, Baltimore, MD 21201, USA
- Correspondence: (C.S.); (S.S.)
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31
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Vera J, Lai X, Baur A, Erdmann M, Gupta S, Guttà C, Heinzerling L, Heppt MV, Kazmierczak PM, Kunz M, Lischer C, Pützer BM, Rehm M, Ostalecki C, Retzlaff J, Witt S, Wolkenhauer O, Berking C. Melanoma 2.0. Skin cancer as a paradigm for emerging diagnostic technologies, computational modelling and artificial intelligence. Brief Bioinform 2022; 23:6761961. [PMID: 36252807 DOI: 10.1093/bib/bbac433] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/28/2022] [Accepted: 09/08/2022] [Indexed: 12/19/2022] Open
Abstract
We live in an unprecedented time in oncology. We have accumulated samples and cases in cohorts larger and more complex than ever before. New technologies are available for quantifying solid or liquid samples at the molecular level. At the same time, we are now equipped with the computational power necessary to handle this enormous amount of quantitative data. Computational models are widely used helping us to substantiate and interpret data. Under the label of systems and precision medicine, we are putting all these developments together to improve and personalize the therapy of cancer. In this review, we use melanoma as a paradigm to present the successful application of these technologies but also to discuss possible future developments in patient care linked to them. Melanoma is a paradigmatic case for disruptive improvements in therapies, with a considerable number of metastatic melanoma patients benefiting from novel therapies. Nevertheless, a large proportion of patients does not respond to therapy or suffers from adverse events. Melanoma is an ideal case study to deploy advanced technologies not only due to the medical need but also to some intrinsic features of melanoma as a disease and the skin as an organ. From the perspective of data acquisition, the skin is the ideal organ due to its accessibility and suitability for many kinds of advanced imaging techniques. We put special emphasis on the necessity of computational strategies to integrate multiple sources of quantitative data describing the tumour at different scales and levels.
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Affiliation(s)
- Julio Vera
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Xin Lai
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Andreas Baur
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Michael Erdmann
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock 18051, Germany
| | - Cristiano Guttà
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Lucie Heinzerling
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany.,Department of Dermatology, LMU University Hospital, Munich, Germany
| | - Markus V Heppt
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | | | - Manfred Kunz
- Department of Dermatology, Venereology and Allergology, University of Leipzig, 04103 Leipzig, Germany
| | - Christopher Lischer
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Brigitte M Pützer
- Institute of Experimental Gene Therapy and Cancer Research, Rostock University Medical Center, 18057 Rostock, Germany
| | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, 70569 Stuttgart, Germany.,Stuttgart Research Center Systems Biology, University of Stuttgart, 70569 Stuttgart, Germany
| | - Christian Ostalecki
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | - Jimmy Retzlaff
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
| | | | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, Institute of Computer Science, University of Rostock, Rostock 18051, Germany
| | - Carola Berking
- Department of Dermatology, FAU Erlangen-Nürnberg, Universitätsklinikum Erlangen, Comprehensive Cancer Center Erlangen and Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany
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Lee SC, Leung KKC, Chung ACY, Wong ESY, Meehan KL, Chan JYK. Fluid Biomarkers in HPV and Non-HPV Related Oropharyngeal Carcinomas: From Diagnosis and Monitoring to Prognostication-A Systematic Review. Int J Mol Sci 2022; 23. [PMID: 36430813 DOI: 10.3390/ijms232214336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/22/2022] Open
Abstract
Biomarkers are crucial in oncology, from detection and monitoring to guiding management and predicting treatment outcomes. Histological assessment of tissue biopsies is currently the gold standard for oropharyngeal cancers, but is technically demanding, invasive, and expensive. This systematic review aims to review current markers that are detectable in biofluids, which offer promising non-invasive alternatives in oropharyngeal carcinomas (OPCs). A total of 174 clinical trials from the PubMed search engine in the last 5 years were identified and screened by 4 independent reviewers. From these, 38 eligible clinical trials were found and subsequently reviewed. The biomarkers involved, categorized by human papillomavirus (HPV)-status, were further divided according to molecular and cellular levels. Recent trials investigating biomarkers for both HPV-positive and HPV-negative OPCs have approaches from various levels and different biofluids including plasma, oropharyngeal swabs, and oral rinse. Promising candidates have been found to aid in detection, staging, and predicting prognosis, in addition to well-established factors including HPV-status, drinking and smoking status. These studies also emphasize the possibility of enhancing prediction results and increasing statistical significance by multivariate analyses. Liquid biopsies offer promising assistance in enhancing personalized medicine for cancer treatment, from lowering barriers towards early screening, to facilitating de-escalation of treatment. However, further research is needed, and the combination of liquid biopsies with pre-existing methods, including in vivo imaging and invasive techniques such as neck dissections, could also be explored in future trials.
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Vilella-Figuerola A, Padró T, Roig E, Mirabet S, Badimon L. New factors in heart failure pathophysiology: Immunity cells release of extracellular vesicles. Front Cardiovasc Med 2022; 9:939625. [PMID: 36407432 PMCID: PMC9669903 DOI: 10.3389/fcvm.2022.939625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/12/2022] [Indexed: 07/30/2023] Open
Abstract
Leukocyte-shed extracellular vesicles (EVs) can play effector roles in the pathophysiological mechanisms of different diseases. These EVs released by membrane budding of leukocytes have been found in high amounts locally in inflamed tissues and in the circulation, indicating immunity cell activation. These EVs secreted by immune cell subsets have been minimally explored and deserve further investigation in many areas of disease. In this study we have investigated whether in heart failure there is innate and adaptive immune cell release of EVs. Patients with chronic heart failure (cHF) (n = 119) and in sex- and age-matched controls without this chronic condition (n = 60). Specifically, EVs were quantified and phenotypically characterized by flow cytometry and cell-specific monoclonal antibodies. We observed that even in well medically controlled cHF patients (with guideline-directed medical therapy) there are higher number of blood annexin-V+ (phosphatidylserine+)-EVs carrying activated immunity cell-epitopes in the circulation than in controls (p < 0.04 for all cell types). Particularly, EVs shed by monocytes and neutrophils (innate immunity) and by T-lymphocytes and natural-killer cells (adaptive immunity) are significantly higher in cHF patients. Additionally, EVs-shed by activated leukocytes/neutrophils (CD11b+, p = 0.006; CD29+/CD15+, p = 0.048), and T-lymphocytes (CD3+/CD45+, p < 0.02) were positively correlated with cHF disease severity (NYHA classification). Interestingly, cHF patients with ischemic etiology had the highest levels of EVs shed by lymphocytes and neutrophils (p < 0.045, all). In summary, in cHF patients there is a significant immune cell activation shown by high-release of EVs that is accentuated by clinical severity of cHF. These activated innate and adaptive immunity cell messengers may contribute by intercellular communication to the progression of the disease and to the common affectation of distant organs in heart failure (paracrine regulation) that contribute to the clinical deterioration of cHF patients.
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Affiliation(s)
- Alba Vilella-Figuerola
- Cardiovascular-Program ICCC, IR-Hospital Santa Creu i Sant Pau, IIB-Sant Pau, Barcelona, Spain
- Department of Biochemical and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Teresa Padró
- Cardiovascular-Program ICCC, IR-Hospital Santa Creu i Sant Pau, IIB-Sant Pau, Barcelona, Spain
- Centro de Investigación Biomédica en Red Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain
| | - Eulàlia Roig
- Heart Failure Group, Department of Cardiology, Hospital Santa Creu i Sant Pau, Barcelona, Spain
| | - Sònia Mirabet
- Centro de Investigación Biomédica en Red Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain
- Heart Failure Group, Department of Cardiology, Hospital Santa Creu i Sant Pau, Barcelona, Spain
| | - Lina Badimon
- Cardiovascular-Program ICCC, IR-Hospital Santa Creu i Sant Pau, IIB-Sant Pau, Barcelona, Spain
- Centro de Investigación Biomédica en Red Cardiovascular, Instituto de Salud Carlos III, Madrid, Spain
- UAB-Chair Cardiovascular Research, Barcelona, Spain
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Pedraz-Valdunciel C, Giannoukakos S, Giménez-Capitán A, Fortunato D, Filipska M, Bertran-Alamillo J, Bracht JWP, Drozdowskyj A, Valarezo J, Zarovni N, Fernández-Hilario A, Hackenberg M, Aguilar-Hernández A, Molina-Vila MÁ, Rosell R. Multiplex Analysis of CircRNAs from Plasma Extracellular Vesicle-Enriched Samples for the Detection of Early-Stage Non-Small Cell Lung Cancer. Pharmaceutics 2022; 14:2034. [PMID: 36297470 PMCID: PMC9610636 DOI: 10.3390/pharmaceutics14102034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND The analysis of liquid biopsies brings new opportunities in the precision oncology field. Under this context, extracellular vesicle circular RNAs (EV-circRNAs) have gained interest as biomarkers for lung cancer (LC) detection. However, standardized and robust protocols need to be developed to boost their potential in the clinical setting. Although nCounter has been used for the analysis of other liquid biopsy substrates and biomarkers, it has never been employed for EV-circRNA analysis of LC patients. METHODS EVs were isolated from early-stage LC patients (n = 36) and controls (n = 30). Different volumes of plasma, together with different number of pre-amplification cycles, were tested to reach the best nCounter outcome. Differential expression analysis of circRNAs was performed, along with the testing of different machine learning (ML) methods for the development of a prognostic signature for LC. RESULTS A combination of 500 μL of plasma input with 10 cycles of pre-amplification was selected for the rest of the study. Eight circRNAs were found upregulated in LC. Further ML analysis selected a 10-circRNA signature able to discriminate LC from controls with AUC ROC of 0.86. CONCLUSIONS This study validates the use of the nCounter platform for multiplexed EV-circRNA expression studies in LC patient samples, allowing the development of prognostic signatures.
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Affiliation(s)
- Carlos Pedraz-Valdunciel
- Department of Cancer Biology and Precision Medicine, Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
- Department of Biochemistry, Molecular Biology and Biomedicine, Autonomous University of Barcelona, Campus de Bellaterra, 08193 Barcelona, Spain
- Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
| | - Stavros Giannoukakos
- Department of Genetics, Facultad de Ciencias, Campus Fuentenueva s/n, Universidad de Granada, 18071 Granada, Spain
| | - Ana Giménez-Capitán
- Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
| | | | - Martyna Filipska
- Department of Cancer Biology and Precision Medicine, Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
- B Cell Biology Group, Hospital del Mar Biomedical Research Park (IMIM), Barcelona Biomedical Research Park (PRBB), 08003 Barcelona, Spain
| | - Jordi Bertran-Alamillo
- Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
| | - Jillian W. P. Bracht
- Vesicle Observation Centre, Laboratory of Experimental Clinical Chemistry, Department of Clinical Chemistry, Amsterdam UMC location University of Amsterdam, 1105AZ Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, 1105AZ Amsterdam, The Netherlands
| | - Ana Drozdowskyj
- Oncology Institute Dr. Rosell (IOR), Dexeus University Institute, 08028 Barcelona, Spain
| | - Joselyn Valarezo
- Laboratory of Oncology, Pangaea Oncology, Dexeus University Hospital, 08028 Barcelona, Spain
| | | | - Alberto Fernández-Hilario
- Department of Computer Science and Artificial Intelligence, DaSCI., University of Granada, 18071 Granada, Spain
| | - Michael Hackenberg
- Department of Genetics, Facultad de Ciencias, Campus Fuentenueva s/n, Universidad de Granada, 18071 Granada, Spain
| | | | | | - Rafael Rosell
- Department of Cancer Biology and Precision Medicine, Germans Trias I Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain
- Oncology Institute Dr. Rosell (IOR), Dexeus University Institute, 08028 Barcelona, Spain
- Catalan Institute of Oncology, Campus Can Ruti, 08916 Badalona, Spain
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Hofste LSM, Geerlings MJ, von Rhein D, Tolmeijer SH, Weiss MM, Gilissen C, Hofste T, Garms LM, Janssen MJR, Rütten H, Rosman C, van der Post RS, Klarenbeek BR, Ligtenberg MJL. Circulating Tumor DNA-Based Disease Monitoring of Patients with Locally Advanced Esophageal Cancer. Cancers (Basel) 2022; 14:cancers14184417. [PMID: 36139577 PMCID: PMC9497103 DOI: 10.3390/cancers14184417] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary The standard of care for patients diagnosed with locally advanced esophageal cancer is neoadjuvant chemoradiotherapy followed by surgery. There is a high clinical need to monitor response to neoadjuvant treatment and recognize patients at risk for recurrence to enable individual treatment strategies. Ultradeep sequencing-based detection of circulating tumor DNA in preoperative plasma of patients with locally advanced esophageal cancer can predict which patients have a high risk of recurrence after neoadjuvant chemoradiotherapy and surgery. Circulating tumor DNA-based prediction of the presence of distant metastasis might eventually be used to reconsider surgery and its associated morbidity in patients with detected circulating tumor DNA or stratify patients for adjuvant treatment. Abstract Patients diagnosed with locally advanced esophageal cancer are often treated with neoadjuvant chemoradiotherapy followed by surgery. This study explored whether detection of circulating tumor DNA (ctDNA) in plasma can be used to predict residual disease during treatment. Diagnostic tissue biopsies from patients with esophageal cancer receiving neoadjuvant chemoradiotherapy and surgery were analyzed for tumor-specific mutations. These tumor-informed mutations were used to measure the presence of ctDNA in serially collected plasma samples using hybrid capture-based sequencing. Plasma samples were obtained before chemoradiotherapy, and prior to surgery. The association between ctDNA detection and progression-free and overall survival was measured. Before chemoradiotherapy, ctDNA was detected in 56% (44/78) of patients and detection was associated with tumor stage and volume (p = 0.05, Fisher exact and p = 0.02, Mann-Whitney, respectively). After chemoradiotherapy, ctDNA was detected in 10% (8/78) of patients. This preoperative detection of ctDNA was independently associated with recurrent disease (hazard ratio 2.8, 95% confidence interval 1.1–6.8, p = 0.03, multivariable Cox-regression) and worse overall survival (hazard ratio 2.9, 95% confidence interval 1.2–7.1, p = 0.02, multivariable Cox-regression).Ultradeep sequencing-based detection of ctDNA in preoperative plasma of patients with locally advanced esophageal cancer may help to assess which patients have a high risk of recurrence after neoadjuvant chemoradiotherapy and surgery.
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Affiliation(s)
- Lisa S. M. Hofste
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Maartje J. Geerlings
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Daniel von Rhein
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Sofie H. Tolmeijer
- Department of Medical Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Marjan M. Weiss
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Tom Hofste
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Linda M. Garms
- Department of Surgery, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Marcel J. R. Janssen
- Department of Radiology and Nuclear Medicine, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Heidi Rütten
- Department of Radiation Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Camiel Rosman
- Department of Surgery, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Rachel S. van der Post
- Department of Pathology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Bastiaan R. Klarenbeek
- Department of Surgery, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Marjolijn J. L. Ligtenberg
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Department of Pathology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Correspondence: ; Tel.: +31-0024-3617-749
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Einoch Amor R, Zinger A, Broza YY, Schroeder A, Haick H. Artificially Intelligent Nanoarray Detects Various Cancers by Liquid Biopsy of Volatile Markers. Adv Healthc Mater 2022; 11:e2200356. [PMID: 35765713 DOI: 10.1002/adhm.202200356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/24/2022] [Indexed: 01/27/2023]
Abstract
Cancer is usually not symptomatic in its early stages. However, early detection can vastly improve prognosis. Liquid biopsy holds great promise for early detection, although it still suffers from many disadvantages, mainly searching for specific cancer biomarkers. Here, a new approach for liquid biopsies is proposed, based on volatile organic compound (VOC) patterns in the blood headspace. An artificial intelligence nanoarray based on a varied set of chemi-sensitive nano-based structured films is developed and used to detect and stage cancer. As a proof-of-concept, three cancer models are tested showing high incidence and mortality rates in the population: breast cancer, ovarian cancer, and pancreatic cancer. The nanoarray has >84% accuracy, >81% sensitivity, and >80% specificity for early detection and >97% accuracy, 100% sensitivity, and >88% specificity for metastasis detection. Complementary mass spectrometry analysis validates these results. The ability to analyze such a complex biological fluid as blood, while considering data of many VOCs at a time using the artificially intelligent nanoarray, increases the sensitivity of predictive models and leads to a potential efficient early diagnosis and disease-monitoring tool for cancer.
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Affiliation(s)
- Reef Einoch Amor
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Assaf Zinger
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Yoav Y Broza
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Avi Schroeder
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Hossam Haick
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
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Xie Y, Xu X, Lin J, Xu Y, Wang J, Ren Y, Wu A. Effective Separation of Cancer-Derived Exosomes in Biological Samples for Liquid Biopsy: Classic Strategies and Innovative Development. Glob Chall 2022; 6:2100131. [PMID: 36176940 PMCID: PMC9463520 DOI: 10.1002/gch2.202100131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/28/2022] [Indexed: 05/26/2023]
Abstract
Liquid biopsy has remarkably facilitated clinical diagnosis and surveillance of cancer via employing a non-invasive way to detect cancer-derived components, such as circulating tumor DNA and circulating tumor cells from biological fluid samples. The cancer-derived exosomes, which are nano-sized vesicles secreted by cancer cells have been investigated in liquid biopsy as their important roles in intracellular communication and disease development have been revealed. Given the challenges posed by the complicated humoral microenvironment, which contains a variety of different cells and macromolecular substances in addition to the exosomes, it has attracted a large amount of attention to effectively isolate exosomes from collected samples. In this review, the authors aim to analyze classic strategies for separation of cancer-derived exosomes, giving an extensive discussion of advantages and limitations of these methods. Furthermore, the innovative multi-strategy methods to realize efficient isolation of cancer-derived exosomes in practical applications are also presented. Additionally, the possible development trends of exosome separation in to the future is discussed in this review.
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Affiliation(s)
- Yujiao Xie
- Cixi Institute of Biomedical EngineeringInternational Cooperation Base of Biomedical MaterialsTechnology and ApplicationChinese Academy of Science (CAS) Key Laboratory of Magnetic Materials and Devices and Zhejiang Engineering Research Center for Biomedical MaterialsNingbo Institute of Materials Technology and EngineeringCASNingbo315201P. R. China
- Advanced Energy Science and Technology Guangdong LaboratoryHuizhou516000P. R. China
- Research Group for Fluids and Thermal EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
- Department of MechanicalMaterials and Manufacturing EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
| | - Xiawei Xu
- Cixi Institute of Biomedical EngineeringInternational Cooperation Base of Biomedical MaterialsTechnology and ApplicationChinese Academy of Science (CAS) Key Laboratory of Magnetic Materials and Devices and Zhejiang Engineering Research Center for Biomedical MaterialsNingbo Institute of Materials Technology and EngineeringCASNingbo315201P. R. China
- Advanced Energy Science and Technology Guangdong LaboratoryHuizhou516000P. R. China
- Research Group for Fluids and Thermal EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
- Department of MechanicalMaterials and Manufacturing EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
| | - Jie Lin
- Cixi Institute of Biomedical EngineeringInternational Cooperation Base of Biomedical MaterialsTechnology and ApplicationChinese Academy of Science (CAS) Key Laboratory of Magnetic Materials and Devices and Zhejiang Engineering Research Center for Biomedical MaterialsNingbo Institute of Materials Technology and EngineeringCASNingbo315201P. R. China
- Advanced Energy Science and Technology Guangdong LaboratoryHuizhou516000P. R. China
| | - Yanping Xu
- Cixi Institute of Biomedical EngineeringInternational Cooperation Base of Biomedical MaterialsTechnology and ApplicationChinese Academy of Science (CAS) Key Laboratory of Magnetic Materials and Devices and Zhejiang Engineering Research Center for Biomedical MaterialsNingbo Institute of Materials Technology and EngineeringCASNingbo315201P. R. China
- Advanced Energy Science and Technology Guangdong LaboratoryHuizhou516000P. R. China
| | - Jing Wang
- Department of Electrical and Electronic EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
- Key Laboratory of More Electric Aircraft Technology of Zhejiang ProvinceUniversity of Nottingham Ningbo ChinaNingbo315100China
- Nottingham Ningbo China Beacons of Excellence Research and Innovation InstituteNingbo315040China
| | - Yong Ren
- Research Group for Fluids and Thermal EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
- Department of MechanicalMaterials and Manufacturing EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
- Nottingham Ningbo China Beacons of Excellence Research and Innovation InstituteNingbo315040China
- Key Laboratory of Carbonaceous Wastes Processing and Process Intensification Research of Zhejiang ProvinceUniversity of Nottingham Ningbo ChinaNingbo315100China
| | - Aiguo Wu
- Cixi Institute of Biomedical EngineeringInternational Cooperation Base of Biomedical MaterialsTechnology and ApplicationChinese Academy of Science (CAS) Key Laboratory of Magnetic Materials and Devices and Zhejiang Engineering Research Center for Biomedical MaterialsNingbo Institute of Materials Technology and EngineeringCASNingbo315201P. R. China
- Advanced Energy Science and Technology Guangdong LaboratoryHuizhou516000P. R. China
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Ponzini E, Santambrogio C, De Palma A, Mauri P, Tavazzi S, Grandori R. Mass spectrometry-based tear proteomics for noninvasive biomarker discovery. Mass Spectrom Rev 2022; 41:842-860. [PMID: 33759206 PMCID: PMC9543345 DOI: 10.1002/mas.21691] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 05/05/2023]
Abstract
The lacrimal film has attracted increasing interest in the last decades as a potential source of biomarkers of physiopathological states, due to its accessibility, moderate complexity, and responsiveness to ocular and systemic diseases. High-performance liquid chromatography-mass spectrometry (LC-MS) has led to effective approaches to tear proteomics, despite the intrinsic limitations in sample amounts. This review focuses on the recent progress in strategy and technology, with an emphasis on the potential for personalized medicine. After an introduction on lacrimal-film composition, examples of applications to biomarker discovery are discussed, comparing approaches based on pooled-sample and single-tear analysis. Then, the most critical steps of the experimental pipeline, that is, tear collection, sample fractionation, and LC-MS implementation, are discussed with reference to proteome-coverage optimization. Advantages and challenges of the alternative procedures are highlighted. Despite the still limited number of studies, tear quantitative proteomics, including single-tear investigation, could offer unique contributions to the identification of low-invasiveness, sustained-accessibility biomarkers, and to the development of personalized approaches to therapy and diagnosis.
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Affiliation(s)
- Erika Ponzini
- Materials Science DepartmentUniversity of Milano‐BicoccaMilanItaly
| | - Carlo Santambrogio
- Department of Biotechnology and BiosciencesUniversity of Milano‐BicoccaMilanItaly
| | - Antonella De Palma
- Institute for Biomedical TechnologiesNational Research Council (ITB‐CNR)Segrate (MI)Italy
| | - Pierluigi Mauri
- Institute for Biomedical TechnologiesNational Research Council (ITB‐CNR)Segrate (MI)Italy
| | - Silvia Tavazzi
- Materials Science DepartmentUniversity of Milano‐BicoccaMilanItaly
- COMiBUniversity of Milano‐BicoccaMilanItaly
| | - Rita Grandori
- Department of Biotechnology and BiosciencesUniversity of Milano‐BicoccaMilanItaly
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Abstract
Extracellular vesicles (EVs) are complex lipid membrane vehicles with variable expressions of molecular cargo, composed of diverse subpopulations that participate in the intercellular signaling of biological responses in disease. EV-based liquid biopsies demonstrate invaluable clinical potential for overhauling current practices of disease management. Yet, EV heterogeneity is a major needle-in-a-haystack challenge to translate their use into clinical practice. In this review, existing digital assays will be discussed to analyze EVs at a single vesicle resolution, and future opportunities to optimize the throughput, multiplexing, and sensitivity of current digital EV assays will be highlighted. Furthermore, this review will outline the challenges and opportunities that impact the clinical translation of single EV technologies for disease diagnostics and treatment monitoring.
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Affiliation(s)
- Renee-Tyler T Morales
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jina Ko
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Sauer CM, Heider K, Belic J, Boyle SE, Hall JA, Couturier D, An A, Vijayaraghavan A, Reinius MAV, Hosking K, Vias M, Rosenfeld N, Brenton JD. Longitudinal monitoring of disease burden and response using ctDNA from dried blood spots in xenograft models. EMBO Mol Med 2022; 14:e15729. [PMID: 35694774 PMCID: PMC9358392 DOI: 10.15252/emmm.202215729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 12/29/2022] Open
Abstract
Whole-genome sequencing (WGS) of circulating tumour DNA (ctDNA) is now a clinically important biomarker for predicting therapy response, disease burden and disease progression. However, the translation of ctDNA monitoring into vital preclinical PDX models has not been possible owing to low circulating blood volumes in small rodents. Here, we describe the longitudinal detection and monitoring of ctDNA from minute volumes of blood in PDX mice. We developed a xenograft Tumour Fraction (xTF) metric using shallow WGS of dried blood spots (DBS), and demonstrate its application to quantify disease burden, monitor treatment response and predict disease outcome in a preclinical study of PDX mice. Further, we show how our DBS-based ctDNA assay can be used to detect gene-specific copy number changes and examine the copy number landscape over time. Use of sequential DBS ctDNA assays could transform future trial designs in both mice and patients by enabling increased sampling and molecular monitoring.
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Affiliation(s)
- Carolin M Sauer
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Katrin Heider
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Jelena Belic
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Samantha E Boyle
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - James A Hall
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Dominique‐Laurent Couturier
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Medical Research Council Biostatistics UnitUniversity of CambridgeCambridgeUK
| | - Angela An
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Aadhitthya Vijayaraghavan
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Marika AV Reinius
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Karen Hosking
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Maria Vias
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
| | - James D Brenton
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Cancer Research UK Major Centre–CambridgeUniversity of CambridgeCambridgeUK
- Cambridge University Hospitals NHS Foundation Trust and National Institute for Health Research Cambridge Biomedical Research CentreAddenbrooke's HospitalCambridgeUK
- Department of OncologyUniversity of CambridgeCambridgeUK
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Constâncio V, Tavares NT, Henrique R, Jerónimo C, Lobo J. MiRNA biomarkers in cancers of the male reproductive system: are we approaching clinical application? Andrology 2022; 11:651-667. [PMID: 35930290 DOI: 10.1111/andr.13258] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Specific cancer types face specific clinical management challenges. Owing to their stability, robustness and fast, easy, and cost-effective detection, microRNAs (miRNAs) are attractive candidate biomarkers to the clinic. OBJECTIVES Based on a comprehensive review of the relevant literature in the field, we explore the potential of miRNAs as biomarkers to answer relevant clinical dilemmas inherent to cancers of the male reproductive tract (prostate (PCa), testis (TGCTs) and penis (PeCa)) and identify some of the challenges/limitations hampering their widely application. RESULTS AND DISCUSSION We conclude that the use of miRNAs as biomarkers is at different stages for these distinct cancer types. While for TGCTs, miRNA-371a-3p is universally accepted to fill in important clinicals gaps and is moving fast towards clinical implementation, for PCa almost no overlap of miRNAs exists between studies, denoting the absence of a consistent miRNA biomarker, and for PeCa the field of miRNAs has just recently started, with only a few studies attempting to explore their clinical usefulness. CONCLUSION Technological advances influencing miRNA detection and quantification will be instrumental to continue to move forward with implementation of miRNAs in the clinic as biomarkers for non-invasive diagnosis, risk stratification, treatment monitoring and follow-up. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Vera Constâncio
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Centre (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, 4200-072, Portugal.,Doctoral Programme in Biomedical Sciences, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, 4050-513, Portugal
| | - Nuno Tiago Tavares
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Centre (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, 4200-072, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Centre (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, 4200-072, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto / Porto Comprehensive Cancer Centre (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, 4200-072, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, 4050-513, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Centre (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, 4200-072, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, 4050-513, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Centre (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, 4200-072, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto / Porto Comprehensive Cancer Centre (Porto.CCC), R. Dr. António Bernardino de Almeida, Porto, 4200-072, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, Porto, 4050-513, Portugal
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Pedersen JG, Sokac M, Sørensen BS, Luczak AA, Aggerholm-Pedersen N, Birkbak NJ, Øllegaard TH, Jakobsen MR. Increased Soluble PD-1 Predicts Response to Nivolumab plus Ipilimumab in Melanoma. Cancers (Basel) 2022; 14:cancers14143342. [PMID: 35884403 PMCID: PMC9322974 DOI: 10.3390/cancers14143342] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Checkpoint inhibitors have revolutionized the treatment of metastatic melanoma, yielding long-term survival in a considerable proportion of the patients. Yet, 40-60% of patients do not achieve a long-term benefit from such therapy, emphasizing the urgent need to identify biomarkers that can predict response to immunotherapy and guide patients for the best possible treatment. Here, we exploited an unsupervised machine learning approach to identify potential inflammatory cytokine signatures from liquid biopsies, which could predict response to immunotherapy in melanoma. METHODS We studied a cohort of 77 patients diagnosed with unresectable advanced-stage melanoma undergoing treatment with first-line nivolumab plus ipilimumab or pembrolizumab. Baseline and on-treatment plasma samples were tested for levels of PD-1, PD-L1, IFNγ, IFNβ, CCL20, CXCL5, CXCL10, IL6, IL8, IL10, MCP1, and TNFα and analyzed by Uniform Manifold Approximation and Projection (UMAP) dimension reduction method and k-means clustering analysis. RESULTS Interestingly, using UMAP analysis, we found that treatment-induced cytokine changes measured as a ratio between baseline and on-treatment samples correlated significantly to progression-free survival (PFS). For patients treated with nivolumab plus ipilimumab we identified a group of patients with superior PFS that were characterized by significantly higher baseline-to-on-treatment increments of PD-1, PD-L1, IFNγ, IL10, CXCL10, and TNFα compared to patients with worse PFS. Particularly, a high PD-1 increment was a strong individual predictor for superior PFS (HR = 0.13; 95% CI 0.034-0.49; p = 0.0026). In contrast, decreasing levels of IFNγ and IL6 and increasing levels of CXCL5 were associated with superior PFS in the pembrolizumab group, although none of the cytokines were individually predictors for PFS. CONCLUSIONS In short, our study demonstrates that a high increment of PD-1 is associated with superior PFS in advanced-stage melanoma patients treated with nivolumab plus ipilimumab. In contrast, decreasing levels of IFNγ and IL6, and increasing levels of CXCL5 are associated with response to pembrolizumab. These results suggest that using serial samples to monitor changes in cytokine levels early during treatment is informative for treatment response.
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Affiliation(s)
| | - Mateo Sokac
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, 8200 Aarhus N, Denmark; (M.S.); (N.J.B.)
| | - Boe Sandahl Sørensen
- Department of Clinical Biochemistry, Aarhus University Hospital, 8200 Aarhus N, Denmark;
| | | | | | - Nicolai Juul Birkbak
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, 8200 Aarhus N, Denmark; (M.S.); (N.J.B.)
- Department of Clinical Medicine, Aarhus University, 8200 Aarhus N, Denmark
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus C, Denmark
| | - Trine Heide Øllegaard
- Department of Oncology, Aarhus University Hospital, 8200 Aarhus N, Denmark;
- Correspondence: (T.H.Ø); (M.R.J.)
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Sequeira JP, Lobo J, Constâncio V, Brito-Rocha T, Carvalho-Maia C, Braga I, Maurício J, Henrique R, Jerónimo C. DigiMir Test: Establishing a Novel Pipeline for MiR-371a Quantification Using Droplet Digital PCR in Liquid Biopsies From Testicular Germ Cell Tumor Patients. Front Oncol 2022; 12:876732. [PMID: 35756620 PMCID: PMC9226402 DOI: 10.3389/fonc.2022.876732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/03/2022] [Indexed: 01/19/2023] Open
Abstract
Testicular germ cell tumors (TGCTs) are the most common cancers in young-adult male patients aged between 15 and 39 years. Hsa-miR-371a-3p is currently the most reliable biomarker for diagnosis and monitoring of these patients non-invasively in liquid biopsies, and it is destined to be introduced in the clinic due to improved performance compared to the classical serum tumor markers available. Current studies have focused on real-time quantitative PCR (RT-qPCR) protocols for its determination; still, some challenges remain, since these protocols often require preamplification steps (costly and time-consuming), and report relative levels normalized to a housekeeping microRNA, not always performed the same way. Droplet digital PCR (ddPCR) shows the promise to overcome these challenges, skipping normalization and preamplifications, but has hardly been explored in the field of TGCTs. In this work, we provide a report of a ddPCR-based pipeline for the quantification of hsa-miR-371a-3p (the DigiMir pipeline) and compare it with two RT-qPCR protocols. A total of 107 plasma samples were investigated in the validation setting. The DigiMir pipeline detected TGCTs in a manner representative of tumor burden, with a sensitivity and specificity of 94% and 100%, respectively, outperforming the combined sensitivity of all three classical serum tumor markers (61.5%). Therefore, in this proof-of-concept investigation, we have shown that the DigiMir pipeline constitutes a new promising methodology to accurately report hsa-miR-371a-3p in the clinical setting.
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Affiliation(s)
- José Pedro Sequeira
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal.,Master in Oncology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - João Lobo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Vera Constâncio
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal.,Doctoral Programme in Biomedical Sciences, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Tiago Brito-Rocha
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal.,Master in Oncology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Carina Carvalho-Maia
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal
| | - Isaac Braga
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal.,Department of Urology and Urology Clinics, Portuguese Oncology Institute of Porto (IPOP), Porto, Portugal
| | - Joaquina Maurício
- Department of Medical Oncology and Urology Clinics, Portuguese Oncology Institute of Porto (IPOP), Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPOP), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Centre (Porto.CCC), Porto, Portugal.,Department of Pathology and Molecular Immunology, School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
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44
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Al Sulaiman D, Juthani N, Doyle PS. Quantitative and Multiplex Detection of Extracellular Vesicle-Derived MicroRNA via Rolling Circle Amplification within Encoded Hydrogel Microparticles. Adv Healthc Mater 2022; 11:e2102332. [PMID: 35029040 PMCID: PMC9117410 DOI: 10.1002/adhm.202102332] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/06/2022] [Indexed: 12/11/2022]
Abstract
Extracellular vesicle-derived microRNA (EV-miRNA) represent a promising cancer biomarker for disease diagnosis and monitoring. However, existing techniques to detect EV-miRNA rely on complex, bias-prone strategies, and preprocessing steps, making absolute quantification highly challenging. This work demonstrates the development and application of a method for quantitative and multiplex detection of EV-miRNA, via rolling circle amplification within encoded hydrogel particles. By a one-pot extracellular vesicle lysis and microRNA capture step, the bias and losses associated with standard RNA extraction techniques is avoided. The system offers a large dynamic range (3 orders of magnitude), ease of multiplexing, and a limit of detection down to 2.3 zmol (46 × 10-18 m), demonstrating its utility in clinical applications based on liquid biopsy tests. Furthermore, orthogonal measurements of EV concentrations coupled with the direct, absolute quantification of miRNA in biological samples results in quantitative measurements of miRNA copy numbers per volume sample, and per extracellular vesicle.
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Affiliation(s)
- Dana Al Sulaiman
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02142 USA
- Division of Physical Science and Engineering King Abdullah University of Science and Technology Thuwal 23955‐6900 Kingdom of Saudi Arabia
| | - Nidhi Juthani
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02142 USA
| | - Patrick S. Doyle
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA 02142 USA
- Harvard Medical School Initiative for RNA Medicine Boston MA 02115 USA
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Mendelaar PAJ, Robbrecht DGJ, Rijnders M, de Wit R, de Weerd V, Deger T, Westgeest HM, Aarts MJB, Voortman J, Martens JWM, van der Veldt AAM, Nakauma‐González JA, Wilting SM, Lolkema M. Genome-wide aneuploidy detected by mFast-SeqS in circulating cell-free DNA is associated with poor response to pembrolizumab in patients with advanced urothelial cancer. Mol Oncol 2022; 16:2086-2097. [PMID: 35181986 PMCID: PMC9120908 DOI: 10.1002/1878-0261.13196] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 01/18/2022] [Accepted: 02/17/2022] [Indexed: 12/02/2022] Open
Abstract
Second-line treatment with immune checkpoint inhibition in patients with metastatic urothelial cancer (mUC) has a low success rate (~ 20%). Circulating tumour-derived DNA (ctDNA) levels may guide patient stratification, provided that an affordable and robust assay is available. Here, we investigate whether the modified fast aneuploidy screening test-sequencing system (mFast-SeqS) may provide such an assay. To this end, mFast-SeqS was performed on cell-free DNA (cfDNA) from 74 patients with mUC prior to treatment with pembrolizumab. Results were associated with corresponding tissue-based profiles, plasma-based variant allele frequencies (VAFs) and clinical response. We found that plasma-derived mFast-SeqS-based aneuploidy scores significantly correlated with those observed in the corresponding tumour tissue as well as with the ctDNA level in the plasma. In multivariate logistic regression analysis, a high aneuploidy score was independently associated with lack of clinical benefit from treatment with pembrolizumab. In conclusion, mFast-SeqS provides a patient-friendly, high-throughput and affordable method to estimate ctDNA level. Following independent validation, this test could be used to stratify mUC patients for response prior to the initiation of treatment with pembrolizumab.
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Affiliation(s)
| | | | - Maud Rijnders
- Department of Medical OncologyErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Ronald de Wit
- Department of Medical OncologyErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Vanja de Weerd
- Department of Medical OncologyErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Teoman Deger
- Department of Medical OncologyErasmus MC Cancer InstituteRotterdamThe Netherlands
| | | | - Maureen J. B. Aarts
- Department of Medical OncologyGROW School for Oncology and Developmental BiologyMaastricht University Medical Center+The Netherlands
| | - Jens Voortman
- Department of Medical OncologyCancer Center AmsterdamAmsterdam UMC, Vrije Universiteit AmsterdamThe Netherlands
| | - John W. M. Martens
- Department of Medical OncologyErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Astrid A. M. van der Veldt
- Department of Medical OncologyErasmus MC Cancer InstituteRotterdamThe Netherlands
- Department of Radiology & Nuclear MedicineErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - José Alberto Nakauma‐González
- Department of Medical OncologyErasmus MC Cancer InstituteRotterdamThe Netherlands
- Department of Cancer Computational Biology CenterErasmus MC Cancer InstituteRotterdamThe Netherlands
- Department of UrologyErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Saskia M. Wilting
- Department of Medical OncologyErasmus MC Cancer InstituteRotterdamThe Netherlands
| | - Martijn Lolkema
- Department of Medical OncologyErasmus MC Cancer InstituteRotterdamThe Netherlands
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46
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Ciobanu OA, Martin S, Fica S. Perspectives on the diagnostic, predictive and prognostic markers of neuroendocrine neoplasms (Review). Exp Ther Med 2021; 22:1479. [PMID: 34765020 PMCID: PMC8576627 DOI: 10.3892/etm.2021.10914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/23/2021] [Indexed: 12/15/2022] Open
Abstract
Neuroendocrine neoplasms (NENs) are a heterogeneous group of rare tumors with different types of physiology and prognosis. Therefore, prognostic information, including morphological differentiation, grade, tumor stage and primary location, are invaluable and contribute to the formulation of treatment decisions. Biomarkers that are currently used, including chromogranin A (CgA), serotonin and neuron-specific enolase, are singular parameters that cannot be used to accurately predict variables associated with tumor growth, including proliferation, metabolic rate and metastatic potential. In addition, site-specific biomarkers, such as insulin and gastrin, cannot be applied to all types of NENs. The clinical application of broad-spectrum markers, as it is the case for CgA, remains controversial despite being widely used. Due to limitations of the currently available mono-analyte biomarkers, recent studies were conducted to explore novel parameters for NEN diagnosis, prognosis, therapy stratification and evaluation of treatment response. Identification of prognostic factors for predicting NEN outcome is a critical requirement for the planning of adequate clinical management. Advances in ‘liquid’ biopsies and genomic analysis techniques, including microRNA, circulating tumor DNA or circulating tumor cells and sophisticated biomathematical analysis techniques, such as NETest or molecular image-based biomarkers, are currently under investigation as potentially novel tools for the management of NENs in the future. Despite these recent findings yielding promising observations, further research is necessary. The present review therefore summarizes the existing knowledge and recent advancements in the exploration of biochemical markers for NENs, with focus on gastroenteropancreatic-neuroendocrine tumors.
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Affiliation(s)
- Oana Alexandra Ciobanu
- Department of Endocrinology and Diabetes, Elias Hospital, 011461 Bucharest, Romania.,Department of Endocrinology, Carol Davila University of Medicine and Pharmacy, 20021 Bucharest, Romania
| | - Sorina Martin
- Department of Endocrinology and Diabetes, Elias Hospital, 011461 Bucharest, Romania.,Department of Endocrinology, Carol Davila University of Medicine and Pharmacy, 20021 Bucharest, Romania
| | - Simona Fica
- Department of Endocrinology and Diabetes, Elias Hospital, 011461 Bucharest, Romania.,Department of Endocrinology, Carol Davila University of Medicine and Pharmacy, 20021 Bucharest, Romania
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Huang J, Soupir AC, Schlick BD, Teng M, Sahin IH, Permuth JB, Siegel EM, Manley BJ, Pellini B, Wang L. Cancer Detection and Classification by CpG Island Hypermethylation Signatures in Plasma Cell-Free DNA. Cancers (Basel) 2021; 13:cancers13225611. [PMID: 34830765 PMCID: PMC8616264 DOI: 10.3390/cancers13225611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/01/2021] [Accepted: 11/06/2021] [Indexed: 01/12/2023] Open
Abstract
Simple Summary The detection of DNA methylation changes in blood has emerged as a promising approach for cancer diagnosis and management. Our group has previously optimized a blood DNA methylation profiling technology that is based on affinity capture of methylated DNA, termed cfMBD-seq. The aim of this study was to assess the potential clinical feasibility of cfMBD-seq. We applied cfMBD-seq to the blood samples of cancer patients and identified methylation signatures that can not only discriminate cancer patients from cancer-free individuals but can also enable accurate multi-cancer classification. Our findings will help to expand on existing blood-based molecular diagnostic tests and identify novel methylation biomarkers for early cancer detection and classification. Abstract Cell-free DNA (cfDNA) methylation has emerged as a promising biomarker for early cancer detection, tumor type classification, and treatment response monitoring. Enrichment-based cfDNA methylation profiling methods such as cfMeDIP-seq have shown high accuracy in the classification of multiple cancer types. We have previously optimized another enrichment-based approach for ultra-low input cfDNA methylome profiling, termed cfMBD-seq. We reported that cfMBD-seq outperforms cfMeDIP-seq in the enrichment of high-CpG-density regions, such as CpG islands. However, the clinical feasibility of cfMBD-seq is unknown. In this study, we applied cfMBD-seq to profiling the cfDNA methylome using plasma samples from cancer patients and non-cancer controls. We identified 1759, 1783, and 1548 differentially hypermethylated CpG islands (DMCGIs) in lung, colorectal, and pancreatic cancer patients, respectively. Interestingly, the vast majority of DMCGIs were overlapped with aberrant methylation changes in corresponding tumor tissues, indicating that DMCGIs detected by cfMBD-seq were mainly driven by tumor-specific DNA methylation patterns. From the overlapping DMCGIs, we carried out machine learning analyses and identified a set of discriminating methylation signatures that had robust performance in cancer detection and classification. Overall, our study demonstrates that cfMBD-seq is a powerful tool for sensitive detection of tumor-derived epigenomic signals in cfDNA.
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Affiliation(s)
- Jinyong Huang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (J.H.); (A.C.S.)
| | - Alex C. Soupir
- Department of Tumor Biology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (J.H.); (A.C.S.)
| | - Brian D. Schlick
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Mingxiang Teng
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Ibrahim H. Sahin
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Jennifer B. Permuth
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (J.B.P.); (E.M.S.)
| | - Erin M. Siegel
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (J.B.P.); (E.M.S.)
| | - Brandon J. Manley
- Department of Genitourinary Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Bruna Pellini
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA;
- Department of Oncologic Sciences, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: (B.P.); (L.W.)
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA; (J.H.); (A.C.S.)
- Correspondence: (B.P.); (L.W.)
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48
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Sequeira JP, Constâncio V, Lobo J, Henrique R, Jerónimo C. Unveiling the World of Circulating and Exosomal microRNAs in Renal Cell Carcinoma. Cancers (Basel) 2021; 13:5252. [PMID: 34771419 DOI: 10.3390/cancers13215252] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/18/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Liquid biopsies have emerged as a new tool for early diagnosis. In renal cell carcinoma, this need is also evident and may represent an improvement in disease management. Hence, in this review we discuss the most updated advances in the assessment of miRNAs in liquid biopsies. Moreover, we explore the potential of circulating or exosome miRNAs in renal cell carcinoma to overcome the tissue biopsies limitations. Abstract Renal cell carcinoma is the third most common urological cancer. Despite recent advances, late diagnosis and poor prognosis of advanced-stage disease remain a major problem, entailing the need for novel early diagnosis tools. Liquid biopsies represent a promising minimally invasive clinical tool, providing real-time feedback of tumor behavior and biological potential, addressing its clonal evolution and representing its heterogeneity. In particular, the study of circulating microRNAs and exosomal microRNAs in liquid biopsies experienced an exponential increase in recent years, considering the potential clinical utility and available technology that facilitates implementation. Herein, we provide a systematic review on the applicability of these biomarkers in the context of renal cell carcinoma. Issues such as additional benefit from extracting microRNAs transported in extracellular vesicles, use for subtyping and representation of different histological types, correlation with tumor burden, and prediction of patient outcome are also addressed. Despite the need for more conclusive research, available data indicate that exosomal microRNAs represent a robust minimally invasive biomarker for renal cell carcinoma. Thus, innovative research on microRNAs and novel detection techniques are likely to provide clinically relevant biomarkers, overcome current clinical challenges, and improve patient management.
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Blomain ES, Moding EJ. Liquid Biopsies for Molecular Biology-Based Radiotherapy. Int J Mol Sci 2021; 22:11267. [PMID: 34681925 PMCID: PMC8538046 DOI: 10.3390/ijms222011267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022] Open
Abstract
Molecular alterations drive cancer initiation and evolution during development and in response to therapy. Radiotherapy is one of the most commonly employed cancer treatment modalities, but radiobiologic approaches for personalizing therapy based on tumor biology and individual risks remain to be defined. In recent years, analysis of circulating nucleic acids has emerged as a non-invasive approach to leverage tumor molecular abnormalities as biomarkers of prognosis and treatment response. Here, we evaluate the roles of circulating tumor DNA and related analyses as powerful tools for precision radiotherapy. We highlight emerging work advancing liquid biopsies beyond biomarker studies into translational research investigating tumor clonal evolution and acquired resistance.
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Affiliation(s)
- Erik S. Blomain
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA;
| | - Everett J. Moding
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA;
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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50
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Killingsworth B, Welsh JA, Jones JC. EV Translational Horizons as Viewed Across the Complex Landscape of Liquid Biopsies. Front Cell Dev Biol 2021; 9:556837. [PMID: 34616722 PMCID: PMC8488153 DOI: 10.3389/fcell.2021.556837] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 03/04/2021] [Indexed: 12/16/2022] Open
Abstract
Extracellular Vesicle (EV)-based diagnostic and therapeutic tools are an area of intensive study and substantial promise, but EVs as liquid biopsies have advanced years ahead of EVs as therapeutic tools. EVs are emerging as a promising approach for detecting tumors, evaluating the molecular profiles of known disease, and monitoring treatment responses. Although correlative assays based on liquid biopsies are already having an impact on translational studies and clinical practice, much remains to be learned before these assays will be optimized for clinical correlations, functional biological studies, and therapeutic use. What follows is an overview of current evidence supporting the investigation and use of liquid biopsies, organized by specific liquid biopsy components available for analysis, along with a summary of what challenges must be overcome before these assays will provide functional biological insights into the pathogenesis and treatment of disease. The same challenges must also be overcome before it will be feasible to measure and monitor the dosing, distribution, pharmacokinetics, and delivery of EV therapeutics and their cargo in complex biofluids where EVs and circulate with and are co-isolated with a number of other nanoscale materials, including lipoproteins (LPPs), ribonucleoprotein complexes (RNPs), and cell free nucleic acids (cfNA).
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Affiliation(s)
- Bryce Killingsworth
- Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Joshua A Welsh
- Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jennifer C Jones
- Translational Nanobiology Section, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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