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Igder S, Zamani M, Fakher S, Siri M, Ashktorab H, Azarpira N, Mokarram P. Circulating Nucleic Acids in Colorectal Cancer: Diagnostic and Prognostic Value. Dis Markers 2024; 2024:9943412. [PMID: 38380073 PMCID: PMC10878755 DOI: 10.1155/2024/9943412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/07/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer in the world and the fourth leading cause of cancer-related mortality. DNA (cfDNA/ctDNA) and RNA (cfRNA/ctRNA) in the blood are promising noninvasive biomarkers for molecular profiling, screening, diagnosis, treatment management, and prognosis of CRC. Technological advancements that enable precise detection of both genetic and epigenetic abnormalities, even in minute quantities in circulation, can overcome some of these challenges. This review focuses on testing for circulating nucleic acids in the circulation as a noninvasive method for CRC detection, monitoring, detection of minimal residual disease, and patient management. In addition, the benefits and drawbacks of various diagnostic techniques and associated bioinformatics tools have been detailed.
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Affiliation(s)
- Somayeh Igder
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Fakher
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division and Cancer Center, Howard University College of Medicine, Washington, DC, USA
| | - Negar Azarpira
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokarram
- Autophagy Research Center, Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
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2
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Roberto TM, Jorge MA, Francisco GV, Noelia T, Pilar RG, Andrés C. Strategies for improving detection of circulating tumor DNA using next generation sequencing. Cancer Treat Rev 2023; 119:102595. [PMID: 37390697 DOI: 10.1016/j.ctrv.2023.102595] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/02/2023]
Abstract
Cancer has become a global health issue and liquid biopsy has emerged as a non-invasive tool for various applications. In cancer, circulating tumor DNA (ctDNA) can be detected from cell-free DNA (cfDNA) obtained from plasma and has potential for early diagnosis, treatment, resistance, minimal residual disease detection, and tumoral heterogeneity identification. However, the low frequency of ctDNA requires techniques for accurate analysis. Multitarget assay such as Next Generation Sequencing (NGS) need improvement to achieve limits of detection that can identify the low frequency variants present in the cfDNA. In this review, we provide a general overview of the use of cfDNA and ctDNA in cancer, and discuss techniques developed to optimize NGS as a tool for ctDNA detection. We also summarize the results obtained using NGS strategies in both investigational and clinical contexts.
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Affiliation(s)
- Tébar-Martínez Roberto
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Precision Medicine Unit, INCLIVA Health Research Institute, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain.
| | - Martín-Arana Jorge
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Bioinformatics Unit, INCLIVA Health Research Institute, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain.
| | - Gimeno-Valiente Francisco
- Cancer Evolution and Genome Instability Laboratory, University College of London Cancer Institute, 72 Huntley St, WC1E 6DD London, United Kingdom.
| | - Tarazona Noelia
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Health Institute Carlos III, CIBERONC, C/ Sinesio Delgado, 4, 28029 Madrid, Spain.
| | - Rentero-Garrido Pilar
- Precision Medicine Unit, INCLIVA Health Research Institute, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain.
| | - Cervantes Andrés
- Department of Medical Oncology, INCLIVA Health Research Institute, University of Valencia, C. de Menéndez y Pelayo, 4, 46010 Valencia, Spain; Health Institute Carlos III, CIBERONC, C/ Sinesio Delgado, 4, 28029 Madrid, Spain.
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3
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Filatova AA, Alekseeva LA, Savin IA, Sen'kova AV, Zenkova MA, Mironova NL. The Effect of Cell-Free DNA from Blood Serum of Mice with Metastatic Melanoma on Enhancement of Oncogenic Properties of Melanoma Cells. Biochemistry (Mosc) 2023; 88:995-1007. [PMID: 37751869 DOI: 10.1134/s0006297923070118] [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: 01/31/2023] [Revised: 03/13/2023] [Accepted: 03/13/2023] [Indexed: 09/28/2023]
Abstract
Currently, a significant increase in the levels of circulating cell-free DNA (cfDNA) in the blood of patients is considered as a generally recognized marker of the development of oncological diseases. Although the tumor-associated cfDNA has been well studied, its biological functions remain unclear. In this work, we investigated the effect of cfDNA isolated from the blood serum of the mice with B16-F10 metastatic melanoma on the properties of the B16-F10 melanoma cells in vitro. It was found that the profile of cfDNA isolated from the blood serum of mice with melanoma differs significantly from the cfDNA isolated from the blood serum of healthy mice, and is similar to the genomic DNA of B16 cells with regards to abundance of oncogenes and mobile genetic elements (MGE). It was shown that the cfDNA of mice with melanoma penetrated into B16 cells, resulting in the increase in abundance of oncogenes and MGE fragments, and caused 5-fold increase of the mRNA level of the secreted DNase Dnase1l3 and a slight increase of the mRNA level of the Jun, Fos, Ras, and Myc oncogenes. cfDNA of the healthy mice caused increase of the mRNA level of intracellular regulatory DNase EndoG and 4-fold increase of the mRNA level of Fos and Ras oncogenes, which are well-known triggers of a large number of signal cascades, from apoptosis inhibition to increased tumor cell proliferation. Thus, it is obvious that the circulating cfDNA of tumor origin is able to penetrate into the cells and, despite the fact that no changes were found in the level of viability and migration activity of the tumor cells, cfDNA, even with a single exposure, can cause changes at the cellular level that increase oncogenicity of the recipient cells.
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Affiliation(s)
- Alina A Filatova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Ludmila A Alekseeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Innokenty A Savin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Aleksandra V Sen'kova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Nadezhda L Mironova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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4
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Rubio-Mangas D, García-Arranz M, Suela J, García-Olmo D. New method of clustering colorectal cancer patients using differential presence of exons (DPE) sequencing. Oncoscience 2023; 10:4-5. [PMID: 36968010 PMCID: PMC10037527 DOI: 10.18632/oncoscience.573] [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: 03/17/2023] [Indexed: 03/25/2023] Open
Affiliation(s)
- David Rubio-Mangas
- Correspondence to:David Rubio-Mangas, Genómica y Medicina, NIMGenetics, Madrid, Spain. S. L, Madrid 28108, Spain email:
| | | | | | - Damian García-Olmo
- Correspondence to:Damian García-Olmo, New Therapy Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Madrid 28040, Spain; Department of Surgery, School of Medicine, Universidad Autónoma de Madrid, C. Arzobispo Morcillo, 4, Madrid 28029, Spain; Department of Surgery, Hospital Fundación Jiménez Díaz, Madrid 28040, Spain; Department of Surgery, New Therapies Laboratory, Foundation Health Research Institute-Fundación Jiménez Díaz University Hospital (FIIS-FJD), Universidad Autónoma de Madrid (UAM), Avda. Reyes Católicos, 2, Madrid 28040, Spain email:
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Rubio-Mangas D, García-Arranz M, Torres-Rodriguez Y, León-Arellano M, Suela J, García-Olmo D. Differential presence of exons (DPE): sequencing liquid biopsy by NGS. A new method for clustering colorectal Cancer patients. BMC Cancer 2023; 23:2. [PMID: 36593457 PMCID: PMC9808981 DOI: 10.1186/s12885-022-10459-w] [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: 08/23/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
Differential presence of exons (DPE) by next generation sequencing (NGS) is a method of interpretation of whole exome sequencing. This method has been proposed to design a predictive and diagnostic algorithm with clinical value in plasma from patients bearing colorectal cancer (CRC). The aim of the present study was to determine a common exonic signature to discriminate between different clinical pictures, such as non-metastatic, metastatic and non-disease (healthy), using a sustainable and novel technology in liquid biopsy.Through DPE analysis, we determined the differences in DNA exon levels circulating in plasma between patients bearing CRC vs. healthy, patients bearing CRC metastasis vs. non-metastatic and patients bearing CRC metastasis vs. healthy comparisons. We identified a set of 510 exons (469 up and 41 down) whose differential presence in plasma allowed us to group and classify between the three cohorts. Random forest classification (machine learning) was performed and an estimated out-of-bag (OOB) error rate of 35.9% was obtained and the predictive model had an accuracy of 75% with a confidence interval (CI) of 56.6-88.5.In conclusion, the DPE analysis allowed us to discriminate between different patho-physiological status such as metastatic, non-metastatic and healthy donors. In addition, this analysis allowed us to obtain very significant values with respect to previous published results, since we increased the number of samples in our study. These results suggest that circulating DNA in patient's plasma may be actively released by cells and may be involved in intercellular communication and, therefore, may play a pivotal role in malignant transformation (genometastasis).
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Affiliation(s)
- David Rubio-Mangas
- Genómica y Medicina, NIMGenetics, Madrid, Spain. S. L, 28108 Madrid, Spain
| | - Mariano García-Arranz
- grid.419651.e0000 0000 9538 1950New Therapy Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, 28040 Madrid, Spain ,grid.5515.40000000119578126Department of Surgery, School of Medicine, Universidad Autónoma de Madrid, C. Arzobispo Morcillo, 4, 28029 Madrid, Spain
| | | | - Miguel León-Arellano
- grid.419651.e0000 0000 9538 1950Department of Surgery, Hospital Fundación Jiménez Díaz, 28040 Madrid, Spain
| | - Javier Suela
- Genómica y Medicina, NIMGenetics, Madrid, Spain. S. L, 28108 Madrid, Spain
| | - Damián García-Olmo
- grid.419651.e0000 0000 9538 1950New Therapy Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, 28040 Madrid, Spain ,grid.5515.40000000119578126Department of Surgery, School of Medicine, Universidad Autónoma de Madrid, C. Arzobispo Morcillo, 4, 28029 Madrid, Spain ,grid.419651.e0000 0000 9538 1950Department of Surgery, Hospital Fundación Jiménez Díaz, 28040 Madrid, Spain ,grid.5515.40000000119578126Department of Surgery, New Therapies Laboratory, Foundation Health Research Institute-Fundación Jiménez Díaz University Hospital (FIIS-FJD), Universidad Autónoma de Madrid (UAM), Avda. Reyes Católicos, 2, 28040 Madrid, Spain
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6
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Gao W, Chen Y, Yang J, Zhuo C, Huang S, Zhang H, Shi Y. Clinical Perspectives on Liquid Biopsy in Metastatic Colorectal Cancer. Front Genet 2021; 12:634642. [PMID: 33584829 PMCID: PMC7876389 DOI: 10.3389/fgene.2021.634642] [Citation(s) in RCA: 6] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 01/04/2021] [Indexed: 02/05/2023] Open
Abstract
Liquid biopsy, which generally refers to the analysis of biological components such as circulating nuclear acids and circulating tumor cells in body fluids, particularly in peripheral blood, has shown good capacity to overcome several limitations faced by conventional tissue biopsies. Emerging evidence in recent decades has confirmed the promising role of liquid biopsy in the clinical management of various cancers, including colorectal cancer, which is one of the most prevalent cancers and the second leading cause of cancer-related deaths worldwide. Despite the challenges and poor clinical outcomes, patients with metastatic colorectal cancer can expect potential clinical benefits with liquid biopsy. Therefore, in this review, we focus on the clinical prospects of liquid biopsy in metastatic colorectal cancer, specifically with regard to the recently discovered various biomarkers identified on liquid biopsy. These biomarkers have been shown to be potentially useful in multiple aspects of metastatic colorectal cancer, such as auxiliary diagnosis of metastasis, prognosis prediction, and monitoring of therapy response.
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Affiliation(s)
- Wei Gao
- Department of Internal Medicine-Oncology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Yigui Chen
- Department of Internal Medicine-Oncology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Jianwei Yang
- Department of Internal Medicine-Oncology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Changhua Zhuo
- Department of Gastrointestinal Surgical Oncology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Sha Huang
- Department of Internal Medicine-Oncology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Hui Zhang
- Department of Hepatopancreatobiliary Surgical Oncology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Yi Shi
- Department of Molecular Pathology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, China
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Navarro S, Cuatrecasas M, Hernández-Losa J, Landolfi S, Musulén E, Ramón Y Cajal S, García-Carbonero R, García-Foncillas J, Pérez-Segura P, Salazar R, Vera R, García-Alfonso P. [Update of the recommendations for the determination of biomarkers in colorectal carcinoma. National Consensus of the Spanish Society of Medical Oncology and the Spanish Society of Pathology]. Rev Esp Patol 2020; 54:41-54. [PMID: 33455693 DOI: 10.1016/j.patol.2020.07.004] [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] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/02/2020] [Accepted: 07/26/2020] [Indexed: 11/25/2022]
Abstract
This update of the consensus of the Spanish Society of Medical Oncology (Sociedad Española de Oncología Médica - SEOM) and the Spanish Society of Pathology (Sociedad Española de Anatomía Patológica - SEAP), reviews the advances in the analysis of biomarkers in advanced colorectal cancer (CRC) as well as susceptibility markers of hereditary CRC and molecular biomarkers of localized CRC. Recently published information on the essential determination of KRAS, NRAS and BRAF mutations and the possible benefits of determining the amplification of human epidermal growth factor receptor 2 (HER2), the expression of proteins in the DNA repair pathway and the study of NTRK fusions are also evaluated. From a pathological point of view, the importance of analysing the tumour budding and poorly differentiated clusters and its prognostic value in CRC is reviewed, as well as the impact of molecular lymph node analysis on lymph node staging in CRC. The incorporation of pan-genomic technologies, such as next-generation sequencing (NGS) and liquid biopsy in the clinical management of patients with CRC is also outlined. All these aspects are developed in this guide which, like the previous one, will be revised when necessary in the future.
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Affiliation(s)
- Samuel Navarro
- Departamento de Patología, Universidad de Valencia, Hospital Clínico Universitario de Valencia, CIBERONC, Valencia, España.
| | | | - Javier Hernández-Losa
- Departamento de Patología, Hospital Universitario Vall d'Hebron, CIBERONC, Barcelona, España
| | - Stefania Landolfi
- Departamento de Patología, Hospital Universitario Vall d'Hebron, CIBERONC, Barcelona, España
| | - Eva Musulén
- Departamento de Patología, Hospital Universitari General de Catalunya, Grupo Quirónsalud, Sant Cugat del Vallès, España; Grupo de Epigenética del Cáncer, Institut de Recerca contra la Leucèmia Josep Carreras, Badalona, España
| | - Santiago Ramón Y Cajal
- Departamento de Patología, Hospital Universitario Vall d'Hebron, CIBERONC, Barcelona, España
| | - Rocío García-Carbonero
- Departamento de Oncología Médica, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), UCM, CNIO, CIBERONC, Madrid, España
| | - Jesús García-Foncillas
- Departamento de Oncología, Hospital Universitario Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, España
| | - Pedro Pérez-Segura
- Departamento de Oncología Médica, Hospital Clínico Universitario San Carlos, CIBERONC, Madrid, España
| | - Ramón Salazar
- Departamento de Oncología Médica, ICO ĹHospitalet, Oncobell Program (IDIBELL), CIBERONC, Hospitalet de Llobregat, España
| | - Ruth Vera
- Departamento de Oncología Médica, Complejo Hospitalario de Navarra, Navarrabiomed, IDISNA, Pamplona, España
| | - Pilar García-Alfonso
- Departamento de Oncología Médica, Hospital General Universitario Gregorio Marañón, Madrid, España
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Gasparello J, Papi C, Allegretti M, Giordani E, Carboni F, Zazza S, Pescarmona E, Romania P, Giacomini P, Scapoli C, Gambari R, Finotti A. A Distinctive microRNA (miRNA) Signature in the Blood of Colorectal Cancer (CRC) Patients at Surgery. Cancers (Basel) 2020; 12:cancers12092410. [PMID: 32854257 PMCID: PMC7564483 DOI: 10.3390/cancers12092410] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 07/01/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Liquid biopsy (LB) provides an examination of the peripheral blood of cancer patients for circulating tumor cells, cell-free nucleic acids and microRNAs (miRNAs) and is an established tool of precision medicine. Unlike most previous LB studies that focused on advanced metastatic colorectal cancer (CRC), we assessed miRNA dysregulation in blood samples obtained on the day of surgery from patients with primary CRC lesions but no clinical evidence of extra-colonic diffusion. In this study, plasma preparation included miRNAs associated to exosomes, but excluded large macrovesicles from the preparation. Methods: The miRNA profile in plasma isolated from a cohort of 35 CRC patients at the day of surgery was analyzed by Next Generation Sequencing (NGS) and further confirmed by droplet digital RT-PCR (dd-RT-PCR). Results: A miR-141-3p/miR-221-3p/miR-222-3p upregulation signature previously described in advanced CRC did not discriminate the analyzed early-CRC cohort from six tumor-free donors (Tf-D). In contrast, NGS-based miRNome analysis of a training cohort of five CRC and three tumor-free donors identified a novel, distinct nine miRNA signature comprising five up-regulated and four down-regulated miRNAs, six of which could be confirmed in the full CRC and tumor-free donor validation dataset by dd-RT-PCR. Additionally, a KRAS (Kirsten Rat Sarcoma Viral Oncogene Homolog) mutant status was correlated with the plasma content of three identified miRNAs. Conclusions: When the data obtained were comparatively evaluated, at least one of the miRNAs belonging to the signature list was found to be dysregulated in 34/35 (97.1%) of our early-CRC plasma samples. The miRNA list provides diagnostic markers as well as possible molecular targets for protocols focusing on “microRNA therapeutics”.
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Affiliation(s)
- Jessica Gasparello
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy; (J.G.); (C.P.); (C.S.)
| | - Chiara Papi
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy; (J.G.); (C.P.); (C.S.)
| | - Matteo Allegretti
- Oncogenomics and Epigenetics, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy; (M.A.); (E.G.); (P.R.); (P.G.)
| | - Elena Giordani
- Oncogenomics and Epigenetics, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy; (M.A.); (E.G.); (P.R.); (P.G.)
| | - Fabio Carboni
- Digestive Surgery, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy; (F.C.); (S.Z.)
| | - Settimio Zazza
- Digestive Surgery, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy; (F.C.); (S.Z.)
| | - Edoardo Pescarmona
- Pathology, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy;
| | - Paolo Romania
- Oncogenomics and Epigenetics, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy; (M.A.); (E.G.); (P.R.); (P.G.)
| | - Patrizio Giacomini
- Oncogenomics and Epigenetics, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Regina Elena National Cancer Institute, 00144 Rome, Italy; (M.A.); (E.G.); (P.R.); (P.G.)
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy; (J.G.); (C.P.); (C.S.)
| | - Roberto Gambari
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy; (J.G.); (C.P.); (C.S.)
- Correspondence: (R.G.); (A.F.); Tel.: +39-0532-974443 (R.G.); +39-0532-974510 (A.F.); Fax: +39-0532-974500 (R.G. & A.F.)
| | - Alessia Finotti
- Department of Life Sciences and Biotechnology, Ferrara University, 44121 Ferrara, Italy; (J.G.); (C.P.); (C.S.)
- Correspondence: (R.G.); (A.F.); Tel.: +39-0532-974443 (R.G.); +39-0532-974510 (A.F.); Fax: +39-0532-974500 (R.G. & A.F.)
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García-Olmo DC, Peiró-Pastor R, Picazo MG, Olmedillas-López S, García-Arranz M, Aguado B, García-Olmo D. Liquid biopsy by NGS: Differential presence of exons (DPE) is related to metastatic potential in a colon-cancer model in the rat. Transl Oncol 2020; 13:100837. [PMID: 32736333 PMCID: PMC7393324 DOI: 10.1016/j.tranon.2020.100837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/09/2020] [Accepted: 07/16/2020] [Indexed: 11/17/2022] Open
Abstract
Differential presence of exons (DPE) is a method of interpretation of exome sequencing, which has been proposed to design a predictive algorithm with clinical value in patients with colorectal cancer (CRC). The goal of the present study was to examine the reproducibility in a rat model of metastatic colon cancer. DHD/K12-TRb cells were injected in syngenic immunocompetent BD-IX rats. Cells were from two stocks with low and normal metastatic potential, and injected into two separate groups of rats. Five to ten weeks after injection, blood samples were taken prior euthanasia and whole exome sequencing performed. Through DPE analysis, we identified a set of exons whose differential presence in plasma allowed us to compare both groups of tumor-bearing animals. A verification test was performed to confirm that the algorithm was able to classify extracted samples into their corresponding groups of origin. The highest mean probability was 0.8954. In conclusion, the DPE analysis in tumor-bearing animals was able to discriminate between different disease status, which fully supports previous results in CRC patients.
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Affiliation(s)
- Dolores C García-Olmo
- Centre de Recerca Experimental Biomédica Aplicada (CREBA), IRBLleida, Lleida, Spain; Experimental Research Unit, University Hospital of Albacete, Spain
| | - Ramón Peiró-Pastor
- Genomics and NGS Service, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid, Spain
| | - María G Picazo
- Experimental Research Unit, University Hospital of Albacete, Spain
| | - Susana Olmedillas-López
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid, Spain
| | - Mariano García-Arranz
- New Therapies Laboratory, Health Research Institute-Fundación Jiménez Díaz University Hospital (IIS-FJD), Madrid, Spain
| | - Begoña Aguado
- Genomics and NGS Service, Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM, Madrid, Spain
| | - Damián García-Olmo
- Department of Surgery, Fundación Jiménez Díaz University Hospital, Madrid, Spain.
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10
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García-Alfonso P, García-Carbonero R, García-Foncillas J, Pérez-Segura P, Salazar R, Vera R, Ramón Y Cajal S, Hernández-Losa J, Landolfi S, Musulén E, Cuatrecasas M, Navarro S. Update of the recommendations for the determination of biomarkers in colorectal carcinoma: National Consensus of the Spanish Society of Medical Oncology and the Spanish Society of Pathology. Clin Transl Oncol 2020; 22:1976-1991. [PMID: 32418154 PMCID: PMC7505870 DOI: 10.1007/s12094-020-02357-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 12/18/2019] [Accepted: 04/28/2020] [Indexed: 12/16/2022]
Abstract
In this update of the consensus of the Spanish Society of Medical Oncology (Sociedad Española de Oncología Médica—SEOM) and the Spanish Society of Pathology (Sociedad Española de Anatomía Patológica—SEAP), advances in the analysis of biomarkers in advanced colorectal cancer (CRC) as well as susceptibility markers of hereditary CRC and molecular biomarkers of localized CRC are reviewed. Recently published information on the essential determination of KRAS, NRAS and BRAF mutations and the convenience of determining the amplification of human epidermal growth factor receptor 2 (HER2), the expression of proteins in the DNA repair pathway and the study of NTRK fusions are also evaluated. From the pathological point of view, the importance of analysing the tumour budding and poorly differentiated clusters, and its prognostic value in CRC is reviewed, as well as the impact of molecular lymph node analysis on lymph node staging in CRC. The incorporation of pan-genomic technologies, such as next-generation sequencing (NGS) and liquid biopsy in the clinical management of patients with CRC is also outlined. All these aspects are developed in this guide, which, like the previous one, will remain open to any necessary revision in the future.
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Affiliation(s)
- P García-Alfonso
- Departament of Medical Oncology, Hospital General Universitario Gregorio Marañón, Madrid, Spain.
| | - R García-Carbonero
- Departament of Medical Oncology, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), UCM, CNIO, CIBERONC, Madrid, Spain
| | - J García-Foncillas
- Departament of Medical Oncology, Hospital Universitario Fundación Jiménez Díaz, Universidad Autónoma de Madrid, Madrid, Spain
| | - P Pérez-Segura
- Departament of Medical Oncology, Hospital Clínico Universitario San Carlos, CIBERONC, Madrid, Spain
| | - R Salazar
- Departament of Medical Oncology, ICO L'Hospitalet, Oncobell Program (IDIBELL), CIBERONC, Hospitalet de Llobregat, Spain
| | - R Vera
- Departament of Medical Oncology, Complejo Hospitalario de Navarra; Navarrabiomed, IDISNA, Pamplona, Spain
| | - S Ramón Y Cajal
- Department of Pathology, Hospital Universitario Vall D'Hebron, CIBERONC, Barcelona, Spain
| | - J Hernández-Losa
- Department of Pathology, Hospital Universitario Vall D'Hebron, CIBERONC, Barcelona, Spain
| | - S Landolfi
- Department of Pathology, Hospital Universitario Vall D'Hebron, CIBERONC, Barcelona, Spain
| | - E Musulén
- Department of Pathology, Hospital Universitari General de Catalunya, Grupo Quirónsalud, Sant Cugat del Vallès, Spain.,Cancer Epigenetics Group, Institut de Recerca Contra La Leucèmia Josep Carreras, Badalona, Spain
| | - M Cuatrecasas
- Department of Pathology, Hospital Clinic, CIBERehd, Barcelona, Spain
| | - S Navarro
- Department of Pathology, University of Valencia, Hospital Clínico Universitario de Valencia, CIBERONC, Valencia, Spain
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11
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Otandault A, Anker P, Al Amir Dache Z, Guillaumon V, Meddeb R, Pastor B, Pisareva E, Sanchez C, Tanos R, Tousch G, Schwarzenbach H, Thierry AR. Recent advances in circulating nucleic acids in oncology. Ann Oncol 2020; 30:374-384. [PMID: 30753271 DOI: 10.1093/annonc/mdz031] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [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: 12/19/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) is one of the fastest growing and most exciting areas in oncology in recent years. Its potential clinical uses cover now each phase of cancer patient management care (predictive information, detection of the minimal residual disease, early detection of resistance, treatment monitoring, recurrence surveillance, and cancer early detection/screening). This review relates the recent advances in the application of circulating DNA or RNA in oncology building on unpublished or initial findings/work presented at the 10th international symposium on circulating nucleic acids in plasma and serum held in Montpellier from the 20th to the 22nd of September 2017. This year, presenters revealed their latest data and crucial observations notably in relation to (i) the circulating cell-free (cfDNA) structure and implications regarding their optimal detection; (ii) their role in the metastatic or immunological processes; (iii) evaluation of miRNA panels for cancer patient follow up; (iv) the detection of the minimal residual disease; (v) the evaluation of a screening tests for cancer using cfDNA analysis; and (vi) elements of preanalytical guidelines. This work reviews the recent progresses in the field brought to light in the meeting, as well as in the most important reports from the literature, past and present. It proposes a broader picture of the basic research and its potential, and of the implementation and current challenges in the use of circulating nucleic acids in oncology.
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Affiliation(s)
- A Otandault
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - P Anker
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - Z Al Amir Dache
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - V Guillaumon
- Regional Institute of Cancer of Montpellier, Montpellier; SIRIC, Integrated Cancer Research Site, Montpellier, France
| | - R Meddeb
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - B Pastor
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - E Pisareva
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - C Sanchez
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - R Tanos
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - G Tousch
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier
| | - H Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - A R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier; INSERM, U1194, Montpellier; Department of Oncology, Montpellier University, Montpellier; Regional Institute of Cancer of Montpellier, Montpellier.
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12
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Bos MK, Angus L, Nasserinejad K, Jager A, Jansen MPHM, Martens JWM, Sleijfer S. Whole exome sequencing of cell-free DNA - A systematic review and Bayesian individual patient data meta-analysis. Cancer Treat Rev 2019; 83:101951. [PMID: 31874446 DOI: 10.1016/j.ctrv.2019.101951] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 10/17/2019] [Revised: 12/09/2019] [Accepted: 12/11/2019] [Indexed: 12/21/2022]
Abstract
Molecular profiling of tumor derived cell free DNA (cfDNA) is gaining ground as a prognostic and predictive biomarker. However to what extent cfDNA reflects the full metastatic landscape as currently determined by tumor tissue analysis remains controversial. Though technically challenging, whole exome sequencing (WES) of cfDNA enables thorough evaluation of somatic alterations. Here, we review the feasibility of WES of cfDNA and determine the sensitivity of WES-detected single nucleotide variants (SNVs) in cfDNA on individual patient data level using paired tumor tissue as reference (sharedSNVsAlltissueSNVs×100%). The pooled sensitivity was 50% (95% credible interval (CI): 29-72%). The tissue mutant allele frequency (MAF) of variants exclusively identified in tissue was significantly lower (12.5%, range: 0.5-18%) than the tissue MAF of variants identified in both tissue and cfDNA (23.9%, range: 17-38%), p = 0.004. The overall agreement (sharedSNVsAllSNVs×100%)between SNVs in cfDNA and tumor tissue was 31% (95% CI: 15-49%). The number of detected SNVs was positively correlated with circulating tumor DNA (ctDNA) fraction (p = 0.016). A sub analysis of samples with ctDNA fractions ≥ 25% improved the sensitivity to 69% (95% CI: 46-89%) and agreement to 46% (95% CI: 36-59%), suggesting that WES is mainly feasible for patients with high ctDNA fractions. Pre- and post-analytical procedures were highly variable between studies rendering comparisons problematic. In conclusion, various aspects of WES of cfDNA are largely in its investigative phase, standardization of methodologies is highly needed to bring this promising technique to its clinical potential.
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Affiliation(s)
- Manouk K Bos
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
| | - Lindsay Angus
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Kazem Nasserinejad
- HOVON Data Center, Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Agnes Jager
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Stefan Sleijfer
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
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13
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Abstract
Genetic material derived from tumours is constantly shed into the circulation of cancer patients both in the form of circulating free nucleic acids and within circulating cells or extracellular vesicles. Monitoring cancer-specific genomic alterations, particularly mutant allele frequencies, in circulating nucleic acids allows for a non-invasive liquid biopsy for detecting residual disease and response to therapy. The advent of molecular targeted treatments and immunotherapies with increasing effectiveness requires corresponding effective molecular biology methods for the detection of biomarkers such as circulating nucleic acid to monitor and ultimately personalise therapy. The use of polymerase chain reaction (PCR)-based methods, such as droplet digital PCR, allows for a very sensitive analysis of circulating tumour DNA, but typically only a limited number of gene mutations can be detected in parallel. In contrast, next-generation sequencing allows for parallel analysis of multiple mutations in many genes. The development of targeted next-generation sequencing cancer gene panels optimised for the detection of circulating free DNA now provides both the flexibility of multiple mutation analysis coupled with a sensitivity that approaches or even matches droplet digital PCR. In this review, we discuss the advantages and disadvantages of these current molecular technologies in conjunction with how this field is evolving in the context of melanoma diagnosis, prognosis, and monitoring of response to therapy.
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14
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Toma SC, Ungureanu BS, Patrascu S, Surlin V, Georgescu I. Colorectal Cancer Biomarkers - A New Trend in Early Diagnosis. Curr Health Sci J 2018; 44:140-6. [PMID: 30746161 DOI: 10.12865/CHSJ.44.02.08] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 03/27/2018] [Indexed: 12/12/2022]
Abstract
Colorectal cancer (CRC) is one of the most widespread malignancy, posing as a great challenge due to its high incidence and mortality in both genders. Yet, it also stands as one of the most preventable diseases because of its known malignant transformation mostly from tubular adenomas or serrated polyps, therefore offering a strong incentive to the screening programs that are being developed for this disease. Current diagnosis of CRC has surely evolved along with the evolutionary step in gastrointestinal technology of flexible endoscopy. These innovations have promoted colonoscopy as a primary choice for screening programs of colonic lesions, proving to be of great benefit for patient’s well-being. In this review, we present the current status of CRC screening methods from the non-invasive options to the long developed colonoscopic and imaging techniques. We search through PubMed and Medline databases and chose relevant articles on CRC with focus on blood based biomarkers and stool based tests. Additional relevant publications were also according to the reference lists of firstly identified articles.
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