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Pourhamidi R, Moslemi A. Using the Precision Lasso for gene selection in diffuse large B cell lymphoma cancer. J Egypt Natl Canc Inst 2023; 35:19. [PMID: 37357234 DOI: 10.1186/s43046-023-00172-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 04/18/2023] [Indexed: 06/27/2023] Open
Abstract
BACKGROUND Gene selection from gene expression profiles is the appropriate tool for diagnosing and predicting cancers. The aim of this study is to perform a Precision Lasso regression model on gene expression of diffuse large B cell lymphoma patients and to find marker genes related to DLBCL. METHODS In the present case-control study, the dataset included 180 gene expressions from 14 healthy individuals and 17 DLBCL patients. The marker genes were selected by fitting Ridge, Lasso, Elastic Net, and Precision Lasso regression models. RESULTS Based on our findings, the Precision Lasso, the Ridge, the Elastic Net, and the Lasso models choose the most marker genes, respectively. In addition, the top 20 genes are based on models compared with the results of clinical studies. The Precision Lasso and the Ridge models selected the most common genes with the clinical results, respectively. CONCLUSIONS The performance of the Precision Lasso model in selecting related genes could be considered more acceptable rather than other models.
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Affiliation(s)
- Rashed Pourhamidi
- Non Communicable Diseases Research Center, Bam University of Medical Sciences, Bam, Iran
| | - Azam Moslemi
- Department of Biostatistics, School of Medicine, Arak University of Medical Sciences, Sardasht, Basij Square, Arak, Markazi Province, Iran.
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2
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Erikstrup C, Sørensen E, Nielsen KR, Bruun MT, Petersen MS, Rostgaard K, Thørner LW, Larsen M, Mikkelsen S, Dinh KM, Schwinn M, Rigas AS, Didriksen M, Dowsett J, von Stemann JH, Brodersen T, Paulsen IW, Hindhede L, Sækmose SG, Kaspersen KA, Boldsen JK, Kjerulff B, Werge T, Brunak S, Banasik K, Hansen TF, Ullum H, Hjalgrim H, Ostrowski SR, Pedersen OB. Cohort Profile: The Danish Blood Donor Study. Int J Epidemiol 2022:6747973. [PMID: 36194120 DOI: 10.1093/ije/dyac194] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/27/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Kaspar R Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Mie T Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Mikkel S Petersen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Klaus Rostgaard
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Lise W Thørner
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Margit Larsen
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Susan Mikkelsen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Khoa M Dinh
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Schwinn
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Andreas S Rigas
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Joseph Dowsett
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jakob H von Stemann
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thorsten Brodersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Isabella W Paulsen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Lotte Hindhede
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Susanne G Sækmose
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Kathrine A Kaspersen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark.,Danish Big Data Centre for Environment and Health (BERTHA), Aarhus University, Aarhus, Denmark
| | - Jens K Boldsen
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark.,Danish Big Data Centre for Environment and Health (BERTHA), Aarhus University, Aarhus, Denmark
| | - Bertram Kjerulff
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark.,Danish Big Data Centre for Environment and Health (BERTHA), Aarhus University, Aarhus, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark.,LF Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,iPSYCH Initiative, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karina Banasik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas F Hansen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Danish Headache Center, Department of Neurology, Copenhagen University Hospital, Glostrup, Denmark
| | | | - Henrik Hjalgrim
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Danish Cancer Society Research Center, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Haematology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sisse R Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole B Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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3
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Chokeshaiusaha K, Sananmuang T, Puthier D, Nguyen C. A novel cross-species differential tumor classification method based on exosome-derived microRNA biomarkers established by human-dog lymphoid and mammary tumor cell lines' transcription profiles. Vet World 2022; 15:1163-1170. [PMID: 35765483 PMCID: PMC9210832 DOI: 10.14202/vetworld.2022.1163-1170] [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: 12/11/2021] [Accepted: 03/17/2022] [Indexed: 11/22/2022] Open
Abstract
Background and Aim: Exosome-derived microRNA (miRNA) has been widely studied as a non-invasive candidate biomarker for tumor diagnosis in humans and dogs. Its application, however, was primarily focused on intraspecies usage for individual tumor type diagnosis. This study aimed to gain insight into its application as a cross-species differential tumor diagnostic tool; we demonstrated the process of identifying and using exosome-derived miRNA as biomarkers for the classification of lymphoid and mammary tumor cell lines in humans and dogs. Materials and Methods: Exosome-derived miRNA sequencing data from B-cell lymphoid tumor cell lines (n=13), mammary tumor cell lines (n=8), and normal mammary epithelium cultures (n=4) were pre-processed in humans and dogs. F-test and rank product (RP) analyses were used to select candidate miRNA orthologs for tumor cell line classification. The classification was carried out using an optimized support vector machine (SVM) with various kernel classifiers, including linear SVM, polynomial SVM, and radial basis function SVM. The receiver operating characteristic and precision-recall curves were used to assess the performance of all models. Results: MIR10B, MIR21, and MIR30E were chosen as the candidate orthologs from a total of 236 human-dog miRNA orthologs (p≤0.01, F-test score ≥10, and RP score ≤10). Their use of polynomial SVM provided the best performance in classifying samples from various tumor cell lines and normal epithelial culture. Conclusion: The study successfully demonstrated a method for identifying and utilizing candidate human-dog exosome-derived miRNA orthologs for differential tumor cell line classification. Such findings shed light on a novel non-invasive tumor diagnostic tool that could be used in both human and veterinary medicine in the future.
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Affiliation(s)
- Kaj Chokeshaiusaha
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chon Buri, Thailand
| | - Thanida Sananmuang
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chon Buri, Thailand
| | - Denis Puthier
- Aix-Marseille University, INSERM UMR 1090, TAGC, Marseille, France
| | - Catherine Nguyen
- Aix-Marseille University, INSERM UMR 1090, TAGC, Marseille, France
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4
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Fidler G, Szilágyi-Rácz AA, Dávid P, Tolnai E, Rejtő L, Szász R, Póliska S, Biró S, Paholcsek M. Circulating microRNA sequencing revealed miRNome patterns in hematology and oncology patients aiding the prognosis of invasive aspergillosis. Sci Rep 2022; 12:7144. [PMID: 35504997 PMCID: PMC9065123 DOI: 10.1038/s41598-022-11239-z] [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: 09/09/2021] [Accepted: 04/18/2022] [Indexed: 11/20/2022] Open
Abstract
Invasive aspergillosis (IA) may occur as a serious complication of hematological malignancy. Delays in antifungal therapy can lead to an invasive disease resulting in high mortality. Currently, there are no well-established blood circulating microRNA biomarkers or laboratory tests which can be used to diagnose IA. Therefore, we aimed to define dysregulated miRNAs in hematology and oncology (HO) patients to identify biomarkers predisposing disease. We performed an in-depth analysis of high-throughput small transcriptome sequencing data obtained from the whole blood samples of our study cohort of 50 participants including 26 high-risk HO patients and 24 controls. By integrating in silico bioinformatic analyses of small noncoding RNA data, 57 miRNAs exhibiting significant expression differences (P < 0.05) were identified between IA-infected patients and non-IA HO patients. Among these, we found 36 differentially expressed miRNAs (DEMs) irrespective of HO malignancy. Of the top ranked DEMs, we found 14 significantly deregulated miRNAs, whose expression levels were successfully quantified by qRT-PCR. MiRNA target prediction revealed the involvement of IA related miRNAs in the biological pathways of tumorigenesis, the cell cycle, the immune response, cell differentiation and apoptosis.
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Affiliation(s)
- Gábor Fidler
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
| | - Anna Anita Szilágyi-Rácz
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
| | - Péter Dávid
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
| | - Emese Tolnai
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
| | - László Rejtő
- Department of Hematology, Jósa András Teaching Hospital, Nyíregyháza, Hungary
| | - Róbert Szász
- Division of Hematology, Institute of Internal Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Szilárd Póliska
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Sándor Biró
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary
| | - Melinda Paholcsek
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Egyetem tér 1., 4032, Debrecen, Hungary.
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5
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Mesnage R, Ibragim M, Mandrioli D, Falcioni L, Tibaldi E, Belpoggi F, Brandsma I, Bourne E, Savage E, Mein CA, Antoniou MN. Comparative Toxicogenomics of Glyphosate and Roundup Herbicides by Mammalian Stem Cell-Based Genotoxicity Assays and Molecular Profiling in Sprague-Dawley Rats. Toxicol Sci 2022; 186:83-101. [PMID: 34850229 PMCID: PMC8883356 DOI: 10.1093/toxsci/kfab143] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Whether glyphosate-based herbicides (GBHs) are more potent than glyphosate alone at activating cellular mechanisms, which drive carcinogenesis remain controversial. As GBHs are more cytotoxic than glyphosate, we reasoned they may also be more capable of activating carcinogenic pathways. We tested this hypothesis by comparing the effects of glyphosate with Roundup GBHs both in vitro and in vivo. First, glyphosate was compared with representative GBHs, namely MON 52276 (European Union), MON 76473 (United Kingdom), and MON 76207 (United States) using the mammalian stem cell-based ToxTracker system. Here, MON 52276 and MON 76473, but not glyphosate and MON 76207, activated oxidative stress and unfolded protein responses. Second, molecular profiling of liver was performed in female Sprague-Dawley rats exposed to glyphosate or MON 52276 (at 0.5, 50, and 175 mg/kg bw/day glyphosate) for 90 days. MON 52276 but not glyphosate increased hepatic steatosis and necrosis. MON 52276 and glyphosate altered the expression of genes in liver reflecting TP53 activation by DNA damage and circadian rhythm regulation. Genes most affected in liver were similarly altered in kidneys. Small RNA profiling in liver showed decreased amounts of miR-22 and miR-17 from MON 52276 ingestion. Glyphosate decreased miR-30, whereas miR-10 levels were increased. DNA methylation profiling of liver revealed 5727 and 4496 differentially methylated CpG sites between the control and glyphosate and MON 52276 exposed animals, respectively. Apurinic/apyrimidinic DNA damage formation in liver was increased with glyphosate exposure. Altogether, our results show that Roundup formulations cause more biological changes linked with carcinogenesis than glyphosate.
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Affiliation(s)
- Robin Mesnage
- Gene Expression and Therapy Group, Department of Medical and Molecular Genetics, Faculty of Life Sciences & Medicine, Guy’s Hospital, King’s College London, London SE1 9RT, UK
| | - Mariam Ibragim
- Gene Expression and Therapy Group, Department of Medical and Molecular Genetics, Faculty of Life Sciences & Medicine, Guy’s Hospital, King’s College London, London SE1 9RT, UK
| | - Daniele Mandrioli
- Cesare Maltoni Cancer Research Center, Ramazzini Institute (RI), Bentivoglio, Bologna 40010, Italy
| | - Laura Falcioni
- Cesare Maltoni Cancer Research Center, Ramazzini Institute (RI), Bentivoglio, Bologna 40010, Italy
| | - Eva Tibaldi
- Cesare Maltoni Cancer Research Center, Ramazzini Institute (RI), Bentivoglio, Bologna 40010, Italy
| | - Fiorella Belpoggi
- Cesare Maltoni Cancer Research Center, Ramazzini Institute (RI), Bentivoglio, Bologna 40010, Italy
| | | | - Emma Bourne
- Genome Centre, Barts and the London School of Medicine and Dentistry, Blizard Institute, London E1 2AT, UK
| | - Emanuel Savage
- Genome Centre, Barts and the London School of Medicine and Dentistry, Blizard Institute, London E1 2AT, UK
| | - Charles A Mein
- Genome Centre, Barts and the London School of Medicine and Dentistry, Blizard Institute, London E1 2AT, UK
| | - Michael N Antoniou
- Gene Expression and Therapy Group, Department of Medical and Molecular Genetics, Faculty of Life Sciences & Medicine, Guy’s Hospital, King’s College London, London SE1 9RT, UK
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6
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Wen P, Xie Y, Wang L. The Role of microRNA in Pathogenesis, Diagnosis, Different Variants, Treatment and Prognosis of Mycosis Fungoides. Front Oncol 2021; 11:752817. [PMID: 34966672 PMCID: PMC8710607 DOI: 10.3389/fonc.2021.752817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/12/2021] [Indexed: 02/05/2023] Open
Abstract
Mycosis fungoides (MF) is the most common type of cutaneous T-cell lymphoma (CTCL), accounting for approximately 50% of all CTCLs. Although various molecular changes in MF have been described in existing studies, no obvious disease-specific changes have been found thus far. microRNAs (miRs) are short, noncoding RNA molecules that play roles in the post-transcriptional regulation of oncogenes and tumor suppressor genes in various diseases. Recently, there has been rapidly expanding experimental evidence for the role of miRs in the progression, early diagnosis, prognosis prediction for MF. Efforts to improve early diagnosis and develop personalized therapy options have become more important in recent years. Here, we provide an overview and update of recent advances regarding miRs associated with MF. Furthermore, we provide insights into future opportunities for miR-based therapies.
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Affiliation(s)
- Pengfei Wen
- Department of Dermatovenerology, West China Hospital, Sichuan University, Chengdu, China
| | - Yao Xie
- Department of Dermatovenerology, West China Hospital, Sichuan University, Chengdu, China
| | - Lin Wang
- Department of Dermatovenerology, West China Hospital, Sichuan University, Chengdu, China
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7
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Fernandes M, Marques H, Teixeira AL, Medeiros R. Competitive Endogenous RNA Network Involving miRNA and lncRNA in Non-Hodgkin Lymphoma: Current Advances and Clinical Perspectives. Biomedicines 2021; 9:1934. [PMID: 34944752 PMCID: PMC8698845 DOI: 10.3390/biomedicines9121934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 11/18/2022] Open
Abstract
Non-Hodgkin lymphoma (NHL) is a heterogeneous malignancy with variable patient outcomes. There is still a lack of understanding about the different players involved in lymphomagenesis, and the identification of new diagnostic and prognostic biomarkers is urgent. MicroRNAs and long non-coding RNAs emerged as master regulators of B-cell development, and their deregulation has been associated with the initiation and progression of lymphomagenesis. They can function by acting alone or, as recently proposed, by creating competing endogenous RNA (ceRNA) networks. Most studies have focused on individual miRNAs/lncRNAs function in lymphoma, and there is still limited data regarding their interactions in lymphoma progression. The study of miRNAs' and lncRNAs' deregulation in NHL, either alone or as ceRNAs networks, offers new insights into the molecular mechanisms underlying lymphoma pathogenesis and opens a window of opportunity to identify potential diagnostic and prognostic biomarkers. In this review, we summarized the current knowledge regarding the role of miRNAs and lncRNAs in B-cell lymphoma, including their interactions and regulatory networks. Finally, we summarized the studies investigating the potential of miRNAs and lncRNAs as clinical biomarkers, with a special focus on the circulating profiles, to be applied as a non-invasive, easy-to-obtain, and reproducible liquid biopsy for dynamic management of NHL patients.
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Affiliation(s)
- Mara Fernandes
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- Research Department of the Portuguese League against Cancer Regional Nucleus of the North (LPCC-NRN), 4200-177 Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Herlander Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal;
- ICVS/3B’s–PT Government Associate Laboratory, 4805-017 Braga/Guimarães, Portugal
- Department of Oncology, Hospital de Braga, 4710-243 Braga, Portugal
- CINTESIS, Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, 4200-450 Porto, Portugal
| | - Ana Luísa Teixeira
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-513 Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology and Viral Pathology Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC), 4200-072 Porto, Portugal; (M.F.); (A.L.T.)
- Research Department of the Portuguese League against Cancer Regional Nucleus of the North (LPCC-NRN), 4200-177 Porto, Portugal
- Faculty of Medicine, University of Porto (FMUP), 4200-319 Porto, Portugal
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-513 Porto, Portugal
- Biomedical Research Center (CEBIMED), Faculty of Health Sciences of Fernando Pessoa University (UFP), 4249-004 Porto, Portugal
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Kos IA, Thurner L, Bittenbring JT, Christofyllakis K, Kaddu-Mulindwa D. Advances in Lymphoma Molecular Diagnostics. Diagnostics (Basel) 2021; 11:diagnostics11122174. [PMID: 34943410 PMCID: PMC8699850 DOI: 10.3390/diagnostics11122174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/15/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
Lymphomas encompass a diverse group of malignant lymphoid neoplasms. Over recent years much scientific effort has been undertaken to identify and understand molecular changes in lymphomas, resulting in a wide range of genetic alterations that have been reported across all types of lymphomas. As many of these changes are now incorporated into the World Health Organization’s defined criteria for the diagnostic evaluation of patients with lymphoid neoplasms, their accurate identification is crucial. Even if many alterations are not routinely evaluated in daily clinical practice, they may still have implications in risk stratification, treatment, prognosis or disease monitoring. Moreover, some alterations can be used for targeted treatment. Therefore, these advances in lymphoma molecular diagnostics in some cases have led to changes in treatment algorithms. Here, we give an overview of and discuss advances in molecular techniques in current clinical practice, as well as highlight some of them in a clinical context.
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Decruyenaere P, Offner F, Vandesompele J. Circulating RNA biomarkers in diffuse large B-cell lymphoma: a systematic review. Exp Hematol Oncol 2021; 10:13. [PMID: 33593440 PMCID: PMC7885416 DOI: 10.1186/s40164-021-00208-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 02/06/2021] [Indexed: 12/31/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is the most common histological subtype of non-Hodgkin's lymphomas (NHL). DLBCL is an aggressive malignancy that displays a great heterogeneity in terms of morphology, genetics and biological behavior. While a sustained complete remission is obtained in the majority of patients with standard immunochemotherapy, patients with refractory of relapsed disease after first-line treatment have a poor prognosis. This patient group represents an important unmet need in lymphoma treatment. In recent years, improved understanding of the underlying molecular pathogenesis had led to new classification and prognostication tools, including the development of cell-free biomarkers in liquid biopsies. Although the majority of studies have focused on the use of cell-free fragments of DNA (cfDNA), there has been an increased interest in circulating-free coding and non-coding RNA, including messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA) and circular RNA (circRNA), as well as RNA encapsulated in extracellular vesicles or tumor-educated platelets (TEPs). We performed a systematic search in PubMed to identify articles that evaluated circulating RNA as diagnostic, subtype, treatment response or prognostic biomarkers in a human DLBCL population. A total of 35 articles met the inclusion criteria. The aim of this systematic review is to present the current understanding of circulating RNA molecules as biomarker in DLBCL and to discuss their future potential.
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Affiliation(s)
- Philippe Decruyenaere
- Department of Hematology, Ghent University Hospital, 9K12, Campus UZ Ghent, Corneel Heymanslaan 10, 9000 Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Fritz Offner
- Department of Hematology, Ghent University Hospital, 9K12, Campus UZ Ghent, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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