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Alexandre D, Fernandes AR, Baptista PV, Cruz C. Evaluation of miR-155 silencing using a molecular beacon in human lung adenocarcinoma cell line. Talanta 2024; 274:126052. [PMID: 38608633 DOI: 10.1016/j.talanta.2024.126052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/26/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
Lung cancer (LC) is a leading cause of global cancer-related deaths, highlighting the development of innovative methods for biomarker detection improving the early diagnostics. microRNAs (miRs) alterations are known to be involved in the initiation and progression of human cancers and can act as biomarkers for diagnostics and treatment. Herein, we develop the application of molecular beacon (MB) technology to monitor miR-155-3p expression in human lung adenocarcinoma A549 cells without complementary DNA synthesis, amplification, or expensive reagents. Furthermore, we produced gold nanoparticles (AuNPs) for delivering antisense oligonucleotides into A549 cells to reduce miR-155-3p expression, which was subsequently detectable using the MB. The MB was designed and structural characterized by Förster Resonance Energy Transfer (FRET)-melting, Circular Dichroism (CD), Nuclear magnetic resonance (NMR), and fluorometric experiments, and then the hybridization conditions were optimized for an in vitro approach involving the detection of miR-155-3p in total RNA extracted from A549 cell line. The expression profile of miR-155-3p was obtained by RT-qPCR. The results demonstrated that MB was properly designed and showed efficacy in targeting miR-155-3p. Furthermore, a limit of detection down to nanomolar concentration was achieved and the specificity of the biosensor was proved. Moreover, the self-assembly of ASOs with AuNPs exhibited exceptional target specificity, effectively silencing miR-155-3p. Notably, compared to lipid-based transfection agent, AuNPs displayed superior silencing efficiency. We highlighted the ability of MB to detect changes in the target gene expression after gene silencing. Overall, this innovative approach represents a promising tool for detecting various biomarkers at the same time, with potential applications in clinical settings.
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Affiliation(s)
- Daniela Alexandre
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6200-506, Covilhã, Portugal; UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal
| | - Alexandra R Fernandes
- UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; i4HB, Associate Laboratory - Institute for Health and Bioeconomy, FCT-NOVA, Portugal
| | - Pedro V Baptista
- UCIBIO, Department of Life Sciences, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; i4HB, Associate Laboratory - Institute for Health and Bioeconomy, FCT-NOVA, Portugal.
| | - Carla Cruz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6200-506, Covilhã, Portugal; Departamento de Química, Faculdade de Ciências da Universidade da Beira Interior, 6201-001, Covilhã, Portugal.
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2
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Liu X, Jiang H, Wang X. Advances in Cancer Research: Current and Future Diagnostic and Therapeutic Strategies. BIOSENSORS 2024; 14:100. [PMID: 38392019 PMCID: PMC10886776 DOI: 10.3390/bios14020100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024]
Abstract
Cancers of unknown primary (CUP) exhibit significant cellular heterogeneity and malignancy, which poses significant challenges for diagnosis and treatment. Recent years have seen deeper insights into the imaging, pathology, and genetic characteristics of CUP, driven by interdisciplinary collaboration and the evolution of diagnostic and therapeutic strategies. However, due to their insidious onset, lack of evidence-based medicine, and limited clinical understanding, diagnosing and treating CUP remain a significant challenge. To inspire more creative and fantastic research, herein, we report and highlight recent advances in the diagnosis and therapeutic strategies of CUP. Specifically, we discuss advanced diagnostic technologies, including 12-deoxy-2-[fluorine-18]fluoro-D-glucose integrated with computed tomography (18F-FDG PET/CT) or 68Ga-FAPI (fibroblast activation protein inhibitor) PET/CT, liquid biopsy, molecular diagnostics, self-assembling nanotechnology, and artificial intelligence (AI). In particular, the discussion will extend to the effective treatment techniques currently available, such as targeted therapies, immunotherapies, and bio-nanotechnology-based therapeutics. Finally, a novel perspective on the challenges and directions for future CUP diagnostic and therapeutic strategies is discussed.
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Affiliation(s)
- Xiaohui Liu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Hui Jiang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuemei Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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3
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Ma W, Wu H, Chen Y, Xu H, Jiang J, Du B, Wan M, Ma X, Chen X, Lin L, Su X, Bao X, Shen Y, Xu N, Ruan J, Jiang H, Ding Y. New techniques to identify the tissue of origin for cancer of unknown primary in the era of precision medicine: progress and challenges. Brief Bioinform 2024; 25:bbae028. [PMID: 38343328 PMCID: PMC10859692 DOI: 10.1093/bib/bbae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/10/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Despite a standardized diagnostic examination, cancer of unknown primary (CUP) is a rare metastatic malignancy with an unidentified tissue of origin (TOO). Patients diagnosed with CUP are typically treated with empiric chemotherapy, although their prognosis is worse than those with metastatic cancer of a known origin. TOO identification of CUP has been employed in precision medicine, and subsequent site-specific therapy is clinically helpful. For example, molecular profiling, including genomic profiling, gene expression profiling, epigenetics and proteins, has facilitated TOO identification. Moreover, machine learning has improved identification accuracy, and non-invasive methods, such as liquid biopsy and image omics, are gaining momentum. However, the heterogeneity in prediction accuracy, sample requirements and technical fundamentals among the various techniques is noteworthy. Accordingly, we systematically reviewed the development and limitations of novel TOO identification methods, compared their pros and cons and assessed their potential clinical usefulness. Our study may help patients shift from empirical to customized care and improve their prognoses.
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Affiliation(s)
- Wenyuan Ma
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Wu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiran Chen
- Department of Surgical Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongxia Xu
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Junjie Jiang
- Department of Gastroenterology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bang Du
- Real Doctor AI Research Centre, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Mingyu Wan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaolu Ma
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoyu Chen
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lili Lin
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinhui Su
- Department of Nuclear Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xuanwen Bao
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yifei Shen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Nong Xu
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Ruan
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiping Jiang
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongfeng Ding
- Department of Medical Oncology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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4
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Merchant YP, Shetty R. Comment on: "Intraosseous carcinoma of the anterior maxilla identified as the occult primary tumour of carcinoma of unknown primary". Int J Oral Maxillofac Surg 2023; 52:1015-1016. [PMID: 36792422 DOI: 10.1016/j.ijom.2023.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023]
Affiliation(s)
- Y P Merchant
- Department of Oral and Maxillofacial Surgery, Dr. D. Y. Patil Dental College and Hospital, Dr. D. Y. Patil Vidyapeeth, Pimpri, Pune, India.
| | - R Shetty
- Deparment of Head and Neck Surgical Oncology, ACTREC, TMC, Khargar, Navi Mumbai, India.
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Filippini DM, Broseghini E, Carosi F, Molin DD, Riefolo M, Fabbri L, Abeshi A, Fernandez IJ, Ferracin M. A Systematic Review of Diagnostic and Prognostic Biomarkers for Head and Neck Cancer of Unknown Primary: An Unmet Clinical Need. Diagnostics (Basel) 2023; 13:diagnostics13081492. [PMID: 37189593 DOI: 10.3390/diagnostics13081492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/27/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Head and neck cancer of unknown primary (HNCUP) is defined as cervical lymph node metastases without a detectable primary tumor. The management of these patients presents a challenge to clinicians since guidelines in the diagnosis and treatment of HNCUP remain controversial. An accurate diagnostic workup is fundamental for the search for the hidden primary tumor to allow the best adequate treatment strategy. The purpose of this systematic review is to present the currently available data about the diagnostic and prognostic molecular biomarkers for HNCUP. Systematic research in an electronic database was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) protocol and identified 704 articles, of which 23 studies were selected and included in the analysis. Fourteen studies investigated HNCUP diagnostic biomarkers and focused on the human papilloma virus (HPV) and the Epstein-Barr virus (EBV) due to the strong associations with oropharyngeal cancer and nasopharyngeal cancer, respectively. HPV status was shown to possess prognostic value, correlating with longer disease-free survival and overall survival. HPV and EBV are the only available HNCUP biomarkers, and they are already used in clinical practice. A better characterization of the molecular profiling and the development of tissue-of-origin classifiers are necessary to improve the diagnosis, staging, and therapeutic management of patients with HNCUP.
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Affiliation(s)
- Daria Maria Filippini
- Division of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, Università di Bologna, 40138 Bologna, Italy
| | - Elisabetta Broseghini
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, Università di Bologna, 40138 Bologna, Italy
| | - Francesca Carosi
- Division of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Davide Dal Molin
- Department of Otorhinolaryngology-Head and Neck Surgery, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico S. Orsola-Malpighi, 40138 Bologna, Italy
| | - Mattia Riefolo
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Laura Fabbri
- Division of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Andi Abeshi
- Department of Otorhinolaryngology-Head and Neck Surgery, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico S. Orsola-Malpighi, 40138 Bologna, Italy
| | - Ignacio Javier Fernandez
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, Università di Bologna, 40138 Bologna, Italy
- Department of Otorhinolaryngology-Head and Neck Surgery, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Policlinico S. Orsola-Malpighi, 40138 Bologna, Italy
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, Università di Bologna, 40138 Bologna, Italy
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6
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ROSKOVA IVANA, VECERA MAREK, RADOVA LENKA, TRACHTOVA KAROLINA, SIEGL FRANTISEK, HERMANOVA MARKETA, HENDRYCH MICHAL, KREN LEOS, VYBIHAL VACLAV, VALEKOVA HANA, KASPAROVA PETRA, KOLOUSKOVA IVANA, KAZDA TOMAS, SLABY ONDREJ, JANCALEK RADIM, SANA JIRI, SMRCKA MARTIN. Small RNA Sequencing Identifies a Six-MicroRNA Signature Enabling Classification of Brain Metastases According to their Origin. Cancer Genomics Proteomics 2023; 20:18-29. [PMID: 36581345 PMCID: PMC9806667 DOI: 10.21873/cgp.20361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND/AIM Brain metastases (BMs) are the most frequent intracranial tumors in adults and one of the greatest challenges for modern oncology. Most are derived from lung, breast, renal cell, and colorectal carcinomas and melanomas. Up to 14% of patients are diagnosed with BMs of unknown primary, which are commonly characterized by an early and aggressive metastatic spread. It is important to discover novel biomarkers for early identification of BM origin, allowing better management of patients with this disease. Our study focused on microRNAs (miRNAs), which are very stable in frozen native and FFPE tissues and have been shown to be sensitive and specific diagnostic biomarkers of cancer. We aimed to identify miRNAs with significantly different expression in the five most frequent groups of BMs and develop a diagnostic classifier capable of sensitive and specific classification of BMs. MATERIALS AND METHODS Total RNA enriched for miRNAs was isolated using the mirVana miRNA Isolation Kit from 71 fresh-frozen histopathologically confirmed BM tissues originating in 5 cancer types. Sequencing libraries were prepared using the QIAseq miRNA Library Kit and sequenced on the NextSeq 500 platform. MiRNA expression was further validated by RT-qPCR. RESULTS Differential analysis identified 373 miRNAs with significantly different expression between 5 BM groups (p<0.001). A classifier model was developed based on the expression of 6 miRNAs (hsa-miR-141-3p, hsa-miR-141-5p, hsa-miR-146a-5p, hsa-miR-194-5p, hsa-miR-200b-3p and hsa-miR-365b-5p) with the ability to correctly classify 91.5% of samples. Subsequent validation confirmed both significantly different expression of selected miRNAs in 5 BM groups as well as their diagnostic potential. CONCLUSION To date, our study is the first to analyze miRNA expression in various types of BMs using small RNA sequencing to develop a diagnostic classifier and, thus, to help stratify BMs of unknown primary. The presented results confirm the importance of studying the dysregulated expression of miRNAs in BMs and the diagnostic potential of the validated 6-miRNA signature.
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Affiliation(s)
- IVANA ROSKOVA
- Department of Neurosurgery, University Hospital Brno, Brno, Czech Republic,Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - MAREK VECERA
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - LENKA RADOVA
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - KAROLINA TRACHTOVA
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - FRANTISEK SIEGL
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - MARKETA HERMANOVA
- Faculty of Medicine, Masaryk University, Brno, Czech Republic,First Department of Pathology, St. Anne’s University Hospital, Brno, Czech Republic
| | - MICHAL HENDRYCH
- Faculty of Medicine, Masaryk University, Brno, Czech Republic,First Department of Pathology, St. Anne’s University Hospital, Brno, Czech Republic
| | - LEOS KREN
- Department of Pathology, University Hospital Brno, Brno, Czech Republic
| | - VACLAV VYBIHAL
- Department of Neurosurgery, University Hospital Brno, Brno, Czech Republic
| | - HANA VALEKOVA
- Faculty of Medicine, Masaryk University, Brno, Czech Republic,Department of Neurosurgery, St. Anne’s University Hospital, Brno, Czech Republic
| | - PETRA KASPAROVA
- The Fingerland Department of Pathology, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | | | - TOMAS KAZDA
- Faculty of Medicine, Masaryk University, Brno, Czech Republic,Department of Radiation Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - ONDREJ SLABY
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - RADIM JANCALEK
- Faculty of Medicine, Masaryk University, Brno, Czech Republic,Department of Neurosurgery, St. Anne’s University Hospital, Brno, Czech Republic
| | - JIRI SANA
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - MARTIN SMRCKA
- Department of Neurosurgery, University Hospital Brno, Brno, Czech Republic,Faculty of Medicine, Masaryk University, Brno, Czech Republic
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7
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Miglietta S, Girolimetti G, Marchio L, Sollazzo M, Laprovitera N, Coluccelli S, De Biase D, De Leo A, Santini D, Kurelac I, Iommarini L, Ghelli A, Campana D, Ferracin M, Perrone AM, Gasparre G, Porcelli AM. MicroRNA and Metabolic Profiling of a Primary Ovarian Neuroendocrine Carcinoma Pulmonary-Type Reveals a High Degree of Similarity with Small Cell Lung Cancer. Noncoding RNA 2022; 8:ncrna8050064. [PMID: 36287116 PMCID: PMC9611163 DOI: 10.3390/ncrna8050064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 11/25/2022] Open
Abstract
Small cell neuroendocrine carcinoma is most frequently found in the lung (SCLC), but it has been also reported, albeit with a very low incidence, in the ovary. Here, we analyze a case of primary small cell carcinoma of the ovary of pulmonary type (SCCOPT), a rare and aggressive tumor with poor prognosis, whose biology and molecular features have not yet been thoroughly investigated. The patient affected by SCCOPT had a residual tumor following chemotherapy which displayed pronounced similarity with neuroendocrine tumors and lung cancer in terms of its microRNA expression profile and mTOR-downstream activation. By analyzing the metabolic markers of the neoplastic lesion, we established a likely glycolytic signature. In conclusion, this in-depth characterization of SCCOPT could be useful for future diagnoses, possibly aided by microRNA profiling, allowing clinicians to adopt the most appropriate therapeutic strategy.
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Affiliation(s)
- Stefano Miglietta
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
| | - Giulia Girolimetti
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Lorena Marchio
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Manuela Sollazzo
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
| | - Noemi Laprovitera
- Unit of Transplant immunobiology and Advanced Cell Therapy, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Sara Coluccelli
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
| | - Dario De Biase
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Antonio De Leo
- Department of Experimental Diagnostic and Specialized Medicine (DIMES), University of Bologna, 40138 Bologna, Italy
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Donatella Santini
- Pathology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Ivana Kurelac
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
- Centro Studi E Ricerca Sulle Neoplasie Ginecologiche (CSR), University of Bologna, 40138 Bologna, Italy
| | - Luisa Iommarini
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
- Centro Studi E Ricerca Sulle Neoplasie Ginecologiche (CSR), University of Bologna, 40138 Bologna, Italy
| | - Anna Ghelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
| | - Davide Campana
- Department of Experimental Diagnostic and Specialized Medicine (DIMES), University of Bologna, 40138 Bologna, Italy
- Division of Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Manuela Ferracin
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
- Department of Experimental Diagnostic and Specialized Medicine (DIMES), University of Bologna, 40138 Bologna, Italy
| | - Anna Myriam Perrone
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
- Centro Studi E Ricerca Sulle Neoplasie Ginecologiche (CSR), University of Bologna, 40138 Bologna, Italy
- Division of Oncologic Gynecology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Giuseppe Gasparre
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy
- Centro Studi E Ricerca Sulle Neoplasie Ginecologiche (CSR), University of Bologna, 40138 Bologna, Italy
- Correspondence: (G.G.); (A.M.P.); Tel.: +39-051-2094747 (G.G.); +39-051-2091282 (A.M.P.)
| | - Anna Maria Porcelli
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy
- Centro Studi E Ricerca Sulle Neoplasie Ginecologiche (CSR), University of Bologna, 40138 Bologna, Italy
- Interdepartmental Center of Industrial Research (CIRI) Life Science and Health Technologies, University of Bologna, 40064 Ozzano dell’Emilia, Italy
- Correspondence: (G.G.); (A.M.P.); Tel.: +39-051-2094747 (G.G.); +39-051-2091282 (A.M.P.)
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8
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Emerging digital PCR technology in precision medicine. Biosens Bioelectron 2022; 211:114344. [DOI: 10.1016/j.bios.2022.114344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/23/2022] [Accepted: 05/03/2022] [Indexed: 12/20/2022]
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9
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Dobre EG, Constantin C, Neagu M. Skin Cancer Research Goes Digital: Looking for Biomarkers within the Droplets. J Pers Med 2022; 12:jpm12071136. [PMID: 35887633 PMCID: PMC9323323 DOI: 10.3390/jpm12071136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
Skin cancer, which includes the most frequent malignant non-melanoma carcinomas (basal cell carcinoma, BCC, and squamous cell carcinoma, SCC), along with the difficult to treat cutaneous melanoma (CM), pose important worldwide issues for the health care system. Despite the improved anti-cancer armamentarium and the latest scientific achievements, many skin cancer patients fail to respond to therapies, due to the remarkable heterogeneity of cutaneous tumors, calling for even more sophisticated biomarker discovery and patient monitoring approaches. Droplet digital polymerase chain reaction (ddPCR), a robust method for detecting and quantifying low-abundance nucleic acids, has recently emerged as a powerful technology for skin cancer analysis in tissue and liquid biopsies (LBs). The ddPCR method, being capable of analyzing various biological samples, has proved to be efficient in studying variations in gene sequences, including copy number variations (CNVs) and point mutations, DNA methylation, circulatory miRNome, and transcriptome dynamics. Moreover, ddPCR can be designed as a dynamic platform for individualized cancer detection and monitoring therapy efficacy. Here, we present the latest scientific studies applying ddPCR in dermato-oncology, highlighting the potential of this technology for skin cancer biomarker discovery and validation in the context of personalized medicine. The benefits and challenges associated with ddPCR implementation in the clinical setting, mainly when analyzing LBs, are also discussed.
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Affiliation(s)
- Elena-Georgiana Dobre
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Correspondence:
| | - Carolina Constantin
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Monica Neagu
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
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10
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Nguyen L, Van Hoeck A, Cuppen E. Machine learning-based tissue of origin classification for cancer of unknown primary diagnostics using genome-wide mutation features. Nat Commun 2022; 13:4013. [PMID: 35817764 PMCID: PMC9273599 DOI: 10.1038/s41467-022-31666-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 06/23/2022] [Indexed: 12/25/2022] Open
Abstract
Cancers of unknown primary (CUP) origin account for ∼3% of all cancer diagnoses, whereby the tumor tissue of origin (TOO) cannot be determined. Using a uniformly processed dataset encompassing 6756 whole-genome sequenced primary and metastatic tumors, we develop Cancer of Unknown Primary Location Resolver (CUPLR), a random forest TOO classifier that employs 511 features based on simple and complex somatic driver and passenger mutations. CUPLR distinguishes 35 cancer (sub)types with ∼90% recall and ∼90% precision based on cross-validation and test set predictions. We find that structural variant derived features increase the performance and utility for classifying specific cancer types. With CUPLR, we could determine the TOO for 82/141 (58%) of CUP patients. Although CUPLR is based on machine learning, it provides a human interpretable graphical report with detailed feature explanations. The comprehensive output of CUPLR complements existing histopathological procedures and can enable improved diagnostics for CUP patients.
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Affiliation(s)
- Luan Nguyen
- University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Arne Van Hoeck
- University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Edwin Cuppen
- University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands. .,Hartwig Medical Foundation, Science Park 408, 1098 XH, Amsterdam, The Netherlands.
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Ding Y, Jiang J, Xu J, Chen Y, Zheng Y, Jiang W, Mao C, Jiang H, Bao X, Shen Y, Li X, Teng L, Xu N. Site-specific therapy in cancers of unknown primary site: a systematic review and meta-analysis. ESMO Open 2022; 7:100407. [PMID: 35248824 PMCID: PMC8897579 DOI: 10.1016/j.esmoop.2022.100407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 12/01/2022] Open
Abstract
Background Cancer of unknown primary site (CUP) is a term applied to characterize pathologically confirmed metastatic cancer with unknown primary tumor origin. It remains uncertain whether patients with CUP benefit from site-specific therapy guided by molecular profiling. Patients and methods A systematic search in PubMed, Web of Science, Embase, Cochrane Library, and ClinicalTrials.gov, and of conference abstracts from January 1976 to January 2021 was performed to identify studies investigating the efficacy of site-specific therapy on patients with CUP. The quality of included studies was evaluated using the Cochrane risk of bias tool and Newcastle–Ottawa scale. Eligible studies were weighted and pooled for meta-analysis. Hazard ratios (HRs) for overall survival (OS) and progression-free survival (PFS) were assessed to compare the efficacy of site-specific therapy with empiric therapy in patients with CUP. In addition, subgroup analyses were conducted. Results Five studies comprising 1114 patients were identified, of which 454 patients received site-specific therapy, and 660 patients received empiric therapy. Our meta-analysis revealed that site-specific therapy was not significantly associated with improved PFS [HR 0.93, 95% confidence interval (CI) 0.74-1.17, P = 0.534] and OS (HR 0.75, 95% CI 0.55-1.03, P = 0.069), compared with empiric therapy. However, during subgroup analysis significantly improved OS was associated with site-specific therapy in the high-accuracy predictive assay subgroup (HR 0.46, 95% CI 0.26-0.81, P = 0.008) compared with the low accuracy predictive assay subgroup (HR 0.93, 95% CI 0.75-1.15, P = 0.509). Furthermore, compared with patients with less responsive tumor types, more survival benefit from site-specific therapy was found in patients with more responsive tumors (HR 0.67, 95% CI 0.46-0.97, P = 0.037). Conclusions Our results suggest that site-specific therapy is not significantly associated with improved survival outcomes; however, it might benefit patients with CUP with responsive tumor types. Studies evaluating the role of site-specific therapy guided by molecular profiling in CUP provided contradictory results. Site-specific therapy is not significantly associated with improved survival outcomes in the overall CUP population. Molecularly defined site-specific therapy may improve OS only when high-accuracy assays assign CUP to responsive tumor types.
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Affiliation(s)
- Y Ding
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - J Jiang
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - J Xu
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Y Chen
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Y Zheng
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - W Jiang
- Department of Colorectal Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou; China
| | - C Mao
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - H Jiang
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - X Bao
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Y Shen
- Centre of Clinical Laboratory, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou; China; Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou; China; Institute of Laboratory Medicine, Zhejiang University, Hangzhou; China
| | - X Li
- Department of Surgery, The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - L Teng
- Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
| | - N Xu
- Department of Medical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
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