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Hakami ZH. Biomarker discovery and validation for gastrointestinal tumors: A comprehensive review of colorectal, gastric, and liver cancers. Pathol Res Pract 2024; 255:155216. [PMID: 38401376 DOI: 10.1016/j.prp.2024.155216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
Gastrointestinal (GI) malignancies, encompassing gastric, hepatic, colonic, and rectal cancers, are prevalent forms of cancer globally and contribute substantially to cancer-related mortality. Although there have been improvements in methods for diagnosing and treating GI cancers, the chances of survival for these types of cancers are still extremely low. According to the World Cancer Research International Fund's most recent figures, stomach cancer was responsible for roughly one million deaths worldwide in 2020. This emphasizes the importance of developing more effective tools for detecting, diagnosing, and predicting the outcome of these cancers at an early stage. Biomarkers, quantitative indications of biological processes or disease states, have emerged as promising techniques for enhancing the diagnosis and prognosis of GI malignancies. Recently, there has been a considerable endeavor to discover and authenticate biomarkers for various GI cancers by the utilization of diverse methodologies, including genomics, proteomics, and metabolomics. This review provides a thorough examination of the current state of biomarker research in the field of gastrointestinal malignancies, with a specific emphasis on colorectal, stomach, and liver cancers. A thorough literature search was performed on prominent databases such as PubMed, Scopus, and Web of Science to find pertinent papers published until November, 2023 for the purpose of compiling this review. The diverse categories of biomarkers, encompassing genetic, epigenetic, and protein-based biomarkers, and their potential utility in the fields of diagnosis, prognosis, and treatment selection, are explored. Recent progress in identifying and confirming biomarkers, as well as the obstacles that persist in employing biomarkers in clinical settings are emphasized. The utilization of biomarkers in GI cancers has significant potential in enhancing patient outcomes. Ongoing research is expected to uncover more efficient biomarkers for the diagnosis and prognosis of these cancers.
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Affiliation(s)
- Zaki H Hakami
- Department of Medical Laboratory Technology, Faculty of Applied Medical Science, Jazan University, Jazan 45142, Saudi Arabia.
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New Tools for Precision and Personalized Treatment in Gastrointestinal Cancers. GASTROINTESTINAL DISORDERS 2021. [DOI: 10.3390/gidisord3040019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Precision medicine aims at treating patients with the most tailored treatments based on individual biological and molecular features [...]
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Ratti M, Grizzi G, Passalacqua R, Lampis A, Cereatti F, Grassia R, Hahne JC. NTRK fusions in colorectal cancer: clinical meaning and future perspective. Expert Opin Ther Targets 2021; 25:677-683. [PMID: 34488530 DOI: 10.1080/14728222.2021.1978070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
INTRODUCTION Despite the efforts of the scientific community, the prognosis of metastatic colorectal cancer (mCRC) remains poor. Actionable gene fusions such as Neurotrophic Tropomyosin Receptor Kinases (NTRK) rearrangements are rare but might represent a new target to improve outcomes in this setting. The first-generation TRK inhibitors, larotrectinib and entrectinib, have demonstrated efficacy and safety in mCRC cancer patients exhibiting NTRK pathogenic fusions. Moreover, second-generation molecules are emerging, able to overcome the acquired resistance to NTRK blocking. AREAS COVERED This review aims to report the current knowledge and the available evidence on NTRK fusion in mCRC, with a focus on molecular bases, clinical characteristics, prognostic meaning, and new therapeutic approaches, from the perspective of the clinical oncologist. EXPERT OPINION Considering the limited options associated with the treatment of mCRC patients, the possibility of identifying new molecular biomarkers is an urgent clinical need. The availability of new molecular targets and the combinations of different agents might represent the true breakthrough point, allowing for change in the clinical course of colorectal cancer patients.
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Affiliation(s)
- Margherita Ratti
- Department of Medical Oncology, Azienda Socio Sanitaria Territoriale of Cremona, Cremona, Italy
| | - Giulia Grizzi
- Department of Medical Oncology, Azienda Socio Sanitaria Territoriale of Cremona, Cremona, Italy
| | - Rodolfo Passalacqua
- Department of Medical Oncology, Azienda Socio Sanitaria Territoriale of Cremona, Cremona, Italy
| | - Andrea Lampis
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Fabrizio Cereatti
- Department of Medical Oncology, Azienda Socio Sanitaria Territoriale of Cremona, Cremona, Italy
| | - Roberto Grassia
- Department of Medical Oncology, Azienda Socio Sanitaria Territoriale of Cremona, Cremona, Italy
| | - Jens Claus Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
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Abidi A, Gorris MAJ, Brennan E, Jongmans MCJ, Weijers DD, Kuiper RP, de Voer RM, Hoogerbrugge N, Schreibelt G, de Vries IJM. Challenges of Neoantigen Targeting in Lynch Syndrome and Constitutional Mismatch Repair Deficiency Syndrome. Cancers (Basel) 2021; 13:2345. [PMID: 34067951 PMCID: PMC8152233 DOI: 10.3390/cancers13102345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/28/2021] [Accepted: 04/30/2021] [Indexed: 12/11/2022] Open
Abstract
Lynch syndrome (LS) and constitutional mismatch repair deficiency (CMMRD) are hereditary disorders characterised by a highly increased risk of cancer development. This is due to germline aberrations in the mismatch repair (MMR) genes, which results in a high mutational load in tumours of these patients, including insertions and deletions in genes bearing microsatellites. This generates microsatellite instability and cause reading frameshifts in coding regions that could lead to the generation of neoantigens and opens up avenues for neoantigen targeting immune therapies prophylactically and therapeutically. However, major obstacles need to be overcome, such as the heterogeneity in tumour formation within and between LS and CMMRD patients, which results in considerable variability in the genes targeted by mutations, hence challenging the choice of suitable neoantigens. The machine-learning methods such as NetMHC and MHCflurry that predict neoantigen- human leukocyte antigen (HLA) binding affinity provide little information on other aspects of neoantigen presentation. Immune escape mechanisms that allow MMR-deficient cells to evade surveillance combined with the resistance to immune checkpoint therapy make the neoantigen targeting regimen challenging. Studies to delineate shared neoantigen profiles across patient cohorts, precise HLA binding algorithms, additional therapies to counter immune evasion and evaluation of biomarkers that predict the response of these patients to immune checkpoint therapy are warranted.
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Affiliation(s)
- Asima Abidi
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (A.A.); (M.A.J.G.); (E.B.); (G.S.)
| | - Mark A. J. Gorris
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (A.A.); (M.A.J.G.); (E.B.); (G.S.)
| | - Evan Brennan
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (A.A.); (M.A.J.G.); (E.B.); (G.S.)
| | - Marjolijn C. J. Jongmans
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (M.C.J.J.); (D.D.W.); (R.P.K.)
- Department of Genetics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Dilys D. Weijers
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (M.C.J.J.); (D.D.W.); (R.P.K.)
| | - Roland P. Kuiper
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, The Netherlands; (M.C.J.J.); (D.D.W.); (R.P.K.)
- Department of Genetics, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Richarda M. de Voer
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.M.d.V.); (N.H.)
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (R.M.d.V.); (N.H.)
| | - Gerty Schreibelt
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (A.A.); (M.A.J.G.); (E.B.); (G.S.)
| | - I. Jolanda M. de Vries
- Department of Tumor Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (A.A.); (M.A.J.G.); (E.B.); (G.S.)
- Department of Medical Oncology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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Bahreini F, Saidijam M, Mousivand Z, Najafi R, Afshar S. Assessment of lncRNA DANCR, miR-145-5p and NRAS axis as biomarkers for the diagnosis of colorectal cancer. Mol Biol Rep 2021; 48:3541-3547. [PMID: 33956301 DOI: 10.1007/s11033-021-06373-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/23/2021] [Indexed: 12/21/2022]
Abstract
Recent evidence reveals that miRNA sponges neutralize miRNAs activity by binding to miRNAs and sequester them from their relevant targets to regulate expression. The detailed mechanisms of sponge RNAs in colorectal cancer remain to be exactly determined. In this study DANCR, miR-145-5p, NRAS axis was evaluated and the diagnostic value of these targets was assessed in colorectal cancer patients. A case-control study was carried out on 40 samples of tumor tissues and 40 adjacent tissues. Total RNA was extracted, and then, the expression level of DANCR, miR-145-5p and NRAS was evaluated using qRT-PCR. In addition, the sensitivity and specificity of these markers were evaluated by receiver operating characteristic (ROC) curve analysis. Our results revealed that the expression level of DANCR was significantly upregulated in colorectal cancer tissues (p < 0.001). It was demonstrated that DANCR could regulate NRAS expression by sponging miR-145-5 in colorectal cancer patients. Furthermore, the mean expression of miR-145-5p (p < 0.001) and NRAS (p < 0.001) was significantly different between tumor and normal tissue. A significant correlation was observed between DANCR and miR-145-5p (p = 0.001), and also between miR-145-5p and NRAS (p < 0.001). Sensitivity and specificity value for DANCR, miR-145-5p and NRAS were (0.875 and 0.725), (0.875 and 0.745), and (0.877 and 0.694), respectively. According to the values of sensitivities and specificity of DANCR, miR-145-5p and NRAS, confirmed with ROC curve analysis, these biomarkers may be useful in the screening and differentiating between tumor and control sample in colorectal neoplasm.
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Affiliation(s)
- Fatemeh Bahreini
- Department of Molecular Medicine and Genetics, Faculty of Medicine, Hamadan University of Medical Sciences, 6517838695, Hamadan, Iran. .,Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Street of Mahdieh, 6517838695, Hamadan, Iran.
| | - Masoud Saidijam
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Street of Mahdieh, 6517838695, Hamadan, Iran
| | | | - Rezvan Najafi
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Street of Mahdieh, 6517838695, Hamadan, Iran
| | - Saeid Afshar
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Street of Mahdieh, 6517838695, Hamadan, Iran
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Kyriazi AA, Papiris E, Kitsos Kalyvianakis K, Sakellaris G, Baritaki S. Dual Effects of Non-Coding RNAs (ncRNAs) in Cancer Stem Cell Biology. Int J Mol Sci 2020; 21:ijms21186658. [PMID: 32932969 PMCID: PMC7556003 DOI: 10.3390/ijms21186658] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/04/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022] Open
Abstract
The identification of cancer stem cells (CSCs) as initiators of carcinogenesis has revolutionized the era of cancer research and our perception for the disease treatment options. Additional CSC features, including self-renewal and migratory and invasive capabilities, have further justified these cells as putative diagnostic, prognostic, and therapeutic targets. Given the CSC plasticity, the identification of CSC-related biomarkers has been a serious burden in CSC characterization and therapeutic targeting. Over the past decades, a compelling amount of evidence has demonstrated critical regulatory functions of non-coding RNAs (ncRNAs) on the exclusive features of CSCs. We now know that ncRNAs may interfere with signaling pathways, vital for CSC phenotype maintenance, such as Notch, Wnt, and Hedgehog. Here, we discuss the multifaceted contribution of microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), as representative ncRNA classes, in sustaining the CSC-like traits, as well as the underlying molecular mechanisms of their action in various CSC types. We further discuss the use of CSC-related ncRNAs as putative biomarkers of high diagnostic, prognostic, and therapeutic value.
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Affiliation(s)
- Athina A. Kyriazi
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71500 Heraklion, Greece; (A.A.K.); (E.P.); (K.K.K.)
| | - Efstathios Papiris
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71500 Heraklion, Greece; (A.A.K.); (E.P.); (K.K.K.)
| | - Konstantinos Kitsos Kalyvianakis
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71500 Heraklion, Greece; (A.A.K.); (E.P.); (K.K.K.)
| | - George Sakellaris
- Surgery Unit, University General Hospital, 71500 Heraklion (PAGNH), Greece;
| | - Stavroula Baritaki
- Laboratory of Experimental Oncology, Division of Surgery, School of Medicine, University of Crete, 71500 Heraklion, Greece; (A.A.K.); (E.P.); (K.K.K.)
- Correspondence: ; Tel.: +30-2810394727
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Vacante M, Ciuni R, Basile F, Biondi A. The Liquid Biopsy in the Management of Colorectal Cancer: An Overview. Biomedicines 2020; 8:E308. [PMID: 32858879 PMCID: PMC7555636 DOI: 10.3390/biomedicines8090308] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023] Open
Abstract
Currently, there is a crucial need for novel diagnostic and prognostic biomarkers with high specificity and sensitivity in patients with colorectal cancer. A "liquid biopsy" is characterized by the isolation of cancer-derived components, such as circulating tumor cells, circulating tumor DNA, microRNAs, long non-coding RNAs, and proteins, from peripheral blood or other body fluids and their genomic or proteomic assessment. The liquid biopsy is a minimally invasive and repeatable technique that could play a significant role in screening and diagnosis, and predict relapse and metastasis, as well as monitoring minimal residual disease and chemotherapy resistance in colorectal cancer patients. However, there are still some practical issues that need to be addressed before liquid biopsy can be widely used in clinical practice. Potential challenges may include low amounts of circulating tumor cells and circulating tumor DNA in samples, lack of pre-analytical and analytical consensus, clinical validation, and regulatory endorsement. The aim of this review was to summarize the current knowledge of the role of liquid biopsy in the management of colorectal cancer.
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Affiliation(s)
- Marco Vacante
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Via S. Sofia 78, 95123 Catania, Italy; (R.C.); (F.B.); (A.B.)
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