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Qvick A, Bratulic S, Carlsson J, Stenmark B, Karlsson C, Nielsen J, Gatto F, Helenius G. Discriminating Benign from Malignant Lung Diseases Using Plasma Glycosaminoglycans and Cell-Free DNA. Int J Mol Sci 2024; 25:9777. [PMID: 39337265 PMCID: PMC11431521 DOI: 10.3390/ijms25189777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 09/05/2024] [Accepted: 09/08/2024] [Indexed: 09/30/2024] Open
Abstract
We aimed to investigate the use of free glycosaminoglycan profiles (GAGomes) and cfDNA in plasma to differentiate between lung cancer and benign lung disease, in a cohort of 113 patients initially suspected of lung cancer. GAGomes were analyzed in all samples using the MIRAM® Free Glycosaminoglycan Kit with ultra-high-performance liquid chromatography and electrospray ionization triple quadrupole mass spectrometry. In a subset of samples, cfDNA concentration and NGS-data was available. We detected two GAGome features, 0S chondroitin sulfate (CS), and 4S CS, with cancer-specific changes. Based on the observed GAGome changes, we devised a model to predict lung cancer. The model, named the GAGome score, could detect lung cancer with 41.2% sensitivity (95% CI: 9.2-54.2%) at 96.4% specificity (95% CI: 95.2-100.0%, n = 113). When we combined the GAGome score with a cfDNA-based model, the sensitivity increased from 42.6% (95% CI: 31.7-60.6%, cfDNA alone) to 70.5% (95% CI: 57.4-81.5%) at 95% specificity (95% CI: 75.1-100%, n = 74). Notably, the combined GAGome and cfDNA testing improved the sensitivity, compared to cfDNA alone, especially in ASCL stage I (55.6% vs 11.1%). Our findings show that plasma GAGome profiles can enhance cfDNA testing performance, highlighting the applicability of a multiomics approach in lung cancer diagnostics.
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Affiliation(s)
- Alvida Qvick
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, 701 82 Örebro, Sweden
| | - Sinisa Bratulic
- Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Jessica Carlsson
- Department of Urology, Faculty of Medicine and Health, Örebro University, 701 82 Örebro, Sweden
| | - Bianca Stenmark
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, 701 82 Örebro, Sweden
| | | | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- BioInnovation Institute, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Francesco Gatto
- Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Department of Oncology-Pathology, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Gisela Helenius
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, 701 82 Örebro, Sweden
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Konoshenko M, Laktionov P, Bryzgunova O. Prostate cancer therapy outcome prediction: are miRNAs a suitable guide for therapeutic decisions? Andrology 2024; 12:705-718. [PMID: 37750354 DOI: 10.1111/andr.13535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/04/2023] [Accepted: 09/09/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Radical prostatectomy, radiotherapy, chemotherapy, and androgen-deprivation therapy are among the most common treatment options for different forms of prostate cancer (PCa). However, making therapeutic decisions is difficult due to the lack of reliable prediction markers indicating therapy outcomes in clinical practice. The involvement of miRNAs in all mechanisms of the PCa development and their easy detection characterize them as attractive PCa biomarkers. Although there are extensive data on the role of miRNAs in PCa therapy resistance and sensitivity development, the issues of whether they could be used as a guide for therapy choice and, if so, how we can progress toward this goal, remain unclear. Thus, generalizable reviews and studies which summarize, compare, and analyze data on miRNA involvement in responses to different types of PCa therapies are required. OBJECTIVES Data on the involvement of miRNAs in therapy responses, on the role of cross-miRNA expression in different therapies, and on miRNA targets were analyzed in order to determine the miRNA-related factors which can lend perspective to the future development of personalized predictors of PCa sensitivity/resistance to therapies. MATERIALS AND METHODS The data available on the miRNAs associated with different PCa therapies (resistance and sensitivity therapies) are summarized and analyzed in this study, including analyses using bioinformatics resources. Special attention was dedicated to the mechanisms of the development of therapy resistance. RESULTS AND DISCUSSION A comprehensive combined analysis of the current data revealed a panel of miRNAs that were shown to be most closely associated with the PCa therapy response and were found to regulate the genes involved in PCa development via cell proliferation regulation, epithelial-mesenchymal transition (EMT), apoptosis, cell-cycle progression, angiogenesis, metastasis and invasion regulation, androgen-independent development, and colony formation. CONCLUSION The selected miRNA-based panel has the potential to be a guide for therapeutic decision making in the effective treatment of PCa.
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Affiliation(s)
- MariaYu Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Zhang Y, Liu R, Li J, Ma H, Bao W, Jiang J, Guo C, Tan D, Cheng X, Dai L, Ming Y. Circulating cell-free DNA as a biomarker for diagnosis of Schistosomiasis japonica. Parasit Vectors 2024; 17:114. [PMID: 38449022 PMCID: PMC10918879 DOI: 10.1186/s13071-024-06203-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Schistosomiasis, a neglected tropical disease, remains an important public health problem. Although there are various methods for diagnosing schistosomiasis, many limitations still exist. Early diagnosis and treatment of schistosomiasis can significantly improve survival and prognosis of patients. METHODOLOGY Circulating cell-free (cf)DNA has been widely used in the diagnosis of various diseases. In our study, we evaluated the diagnostic value of circulating cfDNA for schistosomiasis caused by Schistosoma japonicum. We focused on the tandem sequences and mitochondrial genes of S. japonicum to identify highly sensitive and specific targets for diagnosis of Schistosomiasis japonica. RESULTS Through data screening and analysis, we ultimately identified four specific tandem sequences (TD-1, TD-2, TD-3. and TD-4) and six mitochondrial genes (COX1(1), COX1(2), CYTB, ATP6, COX3, and ND5). We designed specific primers to detect the amount of circulating cfDNA in S. japonicum-infected mouse and chronic schistosomiasis patients. Our results showed that the number of tandem sequences was significantly higher than that of the mitochondrial genes. A S. japonicum infection model in mice suggested that infection of S. japonicum can be diagnosed by detecting circulating cfDNA as early as the first week. We measured the expression levels of circulating cfDNA (TD-1, TD-2, and TD-3) at different time points and found that TD-3 expression was significantly higher than that of TD-1 or TD-2. We also infected mice with different quantities of cercariae (20 s and 80 s). The level of cfDNA (TD-3) in the 80 s infection group was significantly higher than in the 20 s infection group. Additionally, cfDNA (TD-3) levels increased after egg deposition. Meanwhile, we tested 42 patients with chronic Schistosomiasis japonica and circulating cfDNA (TD-3) was detected in nine patients. CONCLUSIONS We have screened highly sensitive targets for the diagnosis of Schistosomiasis japonica, and the detection of circulating cfDNA is a rapid and effective method for the diagnosis of Schistosomiasis japonica. The levels of cfDNA is correlated with cercariae infection severity. Early detection and diagnosis of schistosomiasis is crucial for patient treatment and improving prognosis.
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Affiliation(s)
- Yu Zhang
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Engineering and Technology Research Center for Transplantation Medicine, of National Health Commission, Changsha, Hunan, China
- Hunan Province Clinical Research Center for Infectious Diseases, Changsha, Hunan, China
| | - Rangjiao Liu
- Sanway Clinical Laboratories, Changsha, Hunan, China
| | - Junhui Li
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Engineering and Technology Research Center for Transplantation Medicine, of National Health Commission, Changsha, Hunan, China
- Hunan Province Clinical Research Center for Infectious Diseases, Changsha, Hunan, China
| | - Hongchang Ma
- Sansure Biotech Incoporation, Changsha, Hunan, China
| | - Wenjuan Bao
- Sanway Clinical Laboratories, Changsha, Hunan, China
| | - Jie Jiang
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Engineering and Technology Research Center for Transplantation Medicine, of National Health Commission, Changsha, Hunan, China
- Hunan Province Clinical Research Center for Infectious Diseases, Changsha, Hunan, China
| | - Chen Guo
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Engineering and Technology Research Center for Transplantation Medicine, of National Health Commission, Changsha, Hunan, China
- Hunan Province Clinical Research Center for Infectious Diseases, Changsha, Hunan, China
| | - Deyong Tan
- Sansure Biotech Incoporation, Changsha, Hunan, China
| | - Xing Cheng
- Sansure Biotech Incoporation, Changsha, Hunan, China
| | - Lizhong Dai
- Sansure Biotech Incoporation, Changsha, Hunan, China.
| | - Yingzi Ming
- Transplantation Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Engineering and Technology Research Center for Transplantation Medicine, of National Health Commission, Changsha, Hunan, China.
- Hunan Province Clinical Research Center for Infectious Diseases, Changsha, Hunan, China.
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Bergez-Hernández F, Luque-Ortega F, García-Magallanes N, Alvarez-Arrazola M, Arámbula-Meraz E. Deletion in a regulatory region is associated with underexpression of miR-148b‑3p in patients with prostate cancer. Biomed Rep 2024; 20:52. [PMID: 38357236 PMCID: PMC10865175 DOI: 10.3892/br.2024.1740] [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: 09/18/2023] [Accepted: 01/02/2024] [Indexed: 02/16/2024] Open
Abstract
Prostate cancer (PCa) is the leading cause of cancer-related death in men. This pathology is complex and heterogeneous; therefore, elucidating the molecular mechanisms that lead to its origin and progression is imperative. MicroRNAs (miRNAs or miRs) are part of the epigenetic machinery that regulates the expression of human genes, therefore, mutations in the genes that encode them can lead to a dysregulation in their expression, which directly impacts their target genes, which could be oncogenes or tumor suppressor genes. In PCa several dysregulated expression levels of miRNAs are associated with perturbed cellular processes. A differential expression of miRNAs such as miR-145-5p and miR-148-3p has been observed in PCa, possibly due to mutations in regions near the miRNAs. However, the molecular mechanisms that lead to the dysregulation of these miRNAs still need to be clarified. Therefore, the present study aimed to analyze the expression of miRNAs and their relationship with mutations in patients with and without PCa. In total, 71 patients were analyzed: 41 of whom had PCa (CAP group) and 30 with benign pathology (BPD group). Underexpression was observed in miR-145-5p and miR-148b-3p in PCa patients (P=0.03 and P=0.001, respectively). In miR-145-5p, no mutations related to its expression were identified. For miR-148b-3p, a set of mutations were identified in the chr12:54337042/54337043 region, which were grouped into the mutation named DelsAAG. Although this mutation's abnormal allele is related to PCa (P=0.017), a statistically significant difference was observed in the expression of miR-148b-3p between carriers and non-carriers of the mutated allele, identifying a mechanism likely to be involved in the miR-148b-3p dysregulation.
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Affiliation(s)
- Fernando Bergez-Hernández
- Postgraduate in Biomedical Sciences, Faculty of Chemical-Biological Sciences, Autonomous University of Sinaloa, Culiacán, 80010 Sinaloa, México
| | - Fred Luque-Ortega
- Basic Sciences Laboratory, Faculty of Dentistry, Autonomous University of Sinaloa, Culiacán, 80100 Sinaloa, México
| | - Noemí García-Magallanes
- Laboratory of Biomedicine and Molecular Biology, Biotechnology Engineering, Polytechnic University of Sinaloa, Mazatlán, 82199 Sinaloa, México
| | | | - Eliakym Arámbula-Meraz
- Postgraduate in Biomedical Sciences, Faculty of Chemical-Biological Sciences, Autonomous University of Sinaloa, Culiacán, 80010 Sinaloa, México
- Laboratory of Genetics and Molecular Biology, Faculty of Chemical-Biological Sciences, Autonomous University of Sinaloa, Culiacán, 80010 Sinaloa, México
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Keup C, Kimmig R, Kasimir-Bauer S. The Diversity of Liquid Biopsies and Their Potential in Breast Cancer Management. Cancers (Basel) 2023; 15:5463. [PMID: 38001722 PMCID: PMC10670968 DOI: 10.3390/cancers15225463] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Analyzing blood as a so-called liquid biopsy in breast cancer (BC) patients has the potential to adapt therapy management. Circulating tumor cells (CTCs), extracellular vesicles (EVs), cell-free DNA (cfDNA) and other blood components mirror the tumoral heterogeneity and could support a range of clinical decisions. Multi-cancer early detection tests utilizing blood are advancing but are not part of any clinical routine yet. Liquid biopsy analysis in the course of neoadjuvant therapy has potential for therapy (de)escalation.Minimal residual disease detection via serial cfDNA analysis is currently on its way. The prognostic value of blood analytes in early and metastatic BC is undisputable, but the value of these prognostic biomarkers for clinical management is controversial. An interventional trial confirmed a significant outcome benefit when therapy was changed in case of newly emerging cfDNA mutations under treatment and thus showed the clinical utility of cfDNA analysis for therapy monitoring. The analysis of PIK3CA or ESR1 variants in plasma of metastatic BC patients to prescribe targeted therapy with alpesilib or elacestrant has already arrived in clinical practice with FDA-approved tests available and is recommended by ASCO. The translation of more liquid biopsy applications into clinical practice is still pending due to a lack of knowledge of the analytes' biology, lack of standards and difficulties in proving clinical utility.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, 45147 Essen, Germany
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Menna G, Piaser Guerrato G, Bilgin L, Ceccarelli GM, Olivi A, Della Pepa GM. Is There a Role for Machine Learning in Liquid Biopsy for Brain Tumors? A Systematic Review. Int J Mol Sci 2023; 24:9723. [PMID: 37298673 PMCID: PMC10253654 DOI: 10.3390/ijms24119723] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
The paucity of studies available in the literature on brain tumors demonstrates that liquid biopsy (LB) is not currently applied for central nervous system (CNS) cancers. The purpose of this systematic review focused on the application of machine learning (ML) to LB for brain tumors to provide practical guidance for neurosurgeons to understand the state-of-the-art practices and open challenges. The herein presented study was conducted in accordance with the PRISMA-P (preferred reporting items for systematic review and meta-analysis protocols) guidelines. An online literature search was launched on PubMed/Medline, Scopus, and Web of Science databases using the following query: "((Liquid biopsy) AND (Glioblastoma OR Brain tumor) AND (Machine learning OR Artificial Intelligence))". The last database search was conducted in April 2023. Upon the full-text review, 14 articles were included in the study. These were then divided into two subgroups: those dealing with applications of machine learning to liquid biopsy in the field of brain tumors, which is the main aim of this review (n = 8); and those dealing with applications of machine learning to liquid biopsy in the diagnosis of other tumors (n = 6). Although studies on the application of ML to LB in the field of brain tumors are still in their infancy, the rapid development of new techniques, as evidenced by the increase in publications on the subject in the past two years, may in the future allow for rapid, accurate, and noninvasive analysis of tumor data. Thus making it possible to identify key features in the LB samples that are associated with the presence of a brain tumor. These features could then be used by doctors for disease monitoring and treatment planning.
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Terp SK, Stoico MP, Dybkær K, Pedersen IS. Early diagnosis of ovarian cancer based on methylation profiles in peripheral blood cell-free DNA: a systematic review. Clin Epigenetics 2023; 15:24. [PMID: 36788585 PMCID: PMC9926627 DOI: 10.1186/s13148-023-01440-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/05/2023] [Indexed: 02/16/2023] Open
Abstract
Patients diagnosed with epithelial ovarian cancer (OC) have a 5-year survival rate of 49%. For early-stage disease, the 5-year survival rate is above 90%. However, advanced-stage disease accounts for most cases as patients with early stages often are asymptomatic or present with unspecific symptoms, highlighting the need for diagnostic tools for early diagnosis. Liquid biopsy is a minimal invasive blood-based approach that utilizes circulating tumor DNA (ctDNA) shed from tumor cells for real-time detection of tumor genetics and epigenetics. Increased DNA methylation of promoter regions is an early event during tumorigenesis, and the methylation can be detected in ctDNA, accentuating the promise of methylated ctDNA as a biomarker for OC diagnosis. Many studies have investigated multiple methylation biomarkers in ctDNA from plasma or serum for discriminating OC patients from patients with benign diseases of the ovaries and/or healthy females. This systematic review summarizes and evaluates the performance of the currently investigated DNA methylation biomarkers in blood-derived ctDNA for early diagnosis of OC. PubMed's MEDLINE and Elsevier's Embase were systematically searched, and essential results such as methylation frequency of OC cases and controls, performance measures, as well as preanalytical factors were extracted. Overall, 29 studies met the inclusion criteria for this systematic review. The most common method used for methylation analysis was methylation-specific PCR, with half of the studies using plasma and the other half using serum. RASSF1A, BRCA1, and OPCML were the most investigated gene-specific methylation biomarkers, with OPCML having the best performance measures. Generally, methylation panels performed better than single gene-specific methylation biomarkers, with one methylation panel of 103,456 distinct regions and 1,116,720 CpGs having better performance in both training and validation cohorts. However, the evidence is still limited, and the promising methylation panels, as well as gene-specific methylation biomarkers highlighted in this review, need validation in large, prospective cohorts with early-stage asymptomatic OC patients to assess the true diagnostic value in a clinical setting.
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Affiliation(s)
- Simone Karlsson Terp
- Department of Molecular Diagnostics, Aalborg University Hospital, 9000, Aalborg, Denmark.
- Department of Clinical Medicine, Aalborg University, 9000, Aalborg, Denmark.
| | - Malene Pontoppidan Stoico
- Department of Molecular Diagnostics, Aalborg University Hospital, 9000, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, 9000, Aalborg, Denmark
| | - Karen Dybkær
- Department of Clinical Medicine, Aalborg University, 9000, Aalborg, Denmark
- Department of Hematology, Aalborg University Hospital, 9000, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, 9000, Aalborg, Denmark
| | - Inge Søkilde Pedersen
- Department of Molecular Diagnostics, Aalborg University Hospital, 9000, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, 9000, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, 9000, Aalborg, Denmark
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Tomeva E, Krammer UDB, Switzeny OJ, Haslberger AG, Hippe B. Sex-Specific miRNA Differences in Liquid Biopsies from Subjects with Solid Tumors and Healthy Controls. EPIGENOMES 2023; 7:epigenomes7010002. [PMID: 36648863 PMCID: PMC9844450 DOI: 10.3390/epigenomes7010002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/22/2022] [Accepted: 01/07/2023] [Indexed: 01/12/2023] Open
Abstract
Dysregulation of epigenetic mechanisms has been recognized to play a crucial role in cancer development, but these mechanisms vary between sexes. Therefore, we focused on sex-specific differences in the context of cancer-based data from a recent study. A total of 12 cell-free DNA methylation targets in CpG-rich promoter regions and 48 miRNAs were analyzed by qPCR in plasma samples from 8 female and 7 male healthy controls as well as 48 female and 80 male subjects with solid tumors of the bladder, brain, colorectal region (CRC), lung, stomach, pancreas, and liver. Due to the small sample size in some groups and/or the non-balanced distribution of men and women, sex-specific differences were evaluated statistically only in healthy subjects, CRC, stomach or pancreas cancer patients, and all cancer subjects combined (n female/male-8/7, 14/14, 8/15, 6/6, 48/80, respectively). Several miRNAs with opposing expressions between the sexes were observed for healthy subjects (miR-17-5p, miR-26b-5p); CRC patients (miR-186-5p, miR-22-3p, miR-22-5p, miR-25-3p, miR-92a-3p, miR-16-5p); stomach cancer patients (miR-133a-3p, miR-22-5p); and all cancer patients combined (miR-126-3p, miR-21-5p, miR-92a-3p, miR-183-5p). Moreover, sex-specific correlations that were dependent on cancer stage were observed in women (miR-27a-3p) and men (miR-17-5p, miR-20a-5p). Our results indicate the complex and distinct role of epigenetic regulation, particularly miRNAs, depending not only on the health status but also on the sex of the patient. The same miRNAs could have diverse effects in different tissues and opposing effects between the biological sexes, which should be considered in biomarker research.
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Affiliation(s)
| | - Ulrike D. B. Krammer
- HealthBioCare GmbH, A-1090 Vienna, Austria
- Department of Nutritional Science, University of Vienna, A-1090 Vienna, Austria
| | | | | | - Berit Hippe
- HealthBioCare GmbH, A-1090 Vienna, Austria
- Department of Nutritional Science, University of Vienna, A-1090 Vienna, Austria
- Correspondence:
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He W, Xiao Y, Yan S, Zhu Y, Ren S. Cell-free DNA in the management of prostate cancer: Current status and future prospective. Asian J Urol 2022. [PMID: 37538150 PMCID: PMC10394290 DOI: 10.1016/j.ajur.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Objective With the escalating prevalence of prostate cancer (PCa) in China, there is an urgent demand for novel diagnostic and therapeutic approaches. Extensive investigations have been conducted on the clinical implementation of circulating free DNA (cfDNA) in PCa. This review aims to provide a comprehensive overview of the present state of cfDNA as a biomarker for PCa and to examine its merits and obstacles for future clinical utilization. Methods Relevant peer-reviewed manuscripts on cfDNA as a PCa marker were evaluated by PubMed search (2010-2022) to evaluate the roles of cfDNA in PCa diagnosis, prognosis, and prediction, respectively. Results cfDNA is primarily released from cells undergoing necrosis and apoptosis, allowing for non-invasive insight into the genomic, transcriptomic, and epigenomic alterations within various PCa disease states. Next-generation sequencing, among other detection methods, enables the assessment of cfDNA abundance, mutation status, fragment characteristics, and epigenetic modifications. Multidimensional analysis based on cfDNA can facilitate early detection of PCa, risk stratification, and treatment monitoring. However, standardization of cfDNA detection methods is still required to expedite its clinical application. Conclusion cfDNA provides a non-invasive, rapid, and repeatable means of acquiring multidimensional information from PCa patients, which can aid in guiding clinical decisions and enhancing patient management. Overcoming the application barriers of cfDNA necessitates increased data sharing and international collaboration.
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Matulić M, Gršković P, Petrović A, Begić V, Harabajsa S, Korać P. miRNA in Molecular Diagnostics. Bioengineering (Basel) 2022; 9:bioengineering9090459. [PMID: 36135005 PMCID: PMC9495386 DOI: 10.3390/bioengineering9090459] [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: 07/16/2022] [Revised: 08/05/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
MicroRNAs are a class of small non-coding RNA molecules that regulate gene expression on post-transcriptional level. Their biogenesis consists of a complex series of sequential processes, and they regulate expression of many genes involved in all cellular processes. Their function is essential for maintaining the homeostasis of a single cell; therefore, their aberrant expression contributes to development and progression of many diseases, especially malignant tumors and viral infections. Moreover, they can be associated with certain states of a specific disease, obtained in the least invasive manner for patients and analyzed with basic molecular methods used in clinical laboratories. Because of this, they have a promising potential to become very useful biomarkers and potential tools in personalized medicine approaches. In this review, miRNAs biogenesis, significance in cancer and infectious diseases, and current available test and methods for their detection are summarized.
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Affiliation(s)
- Maja Matulić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Paula Gršković
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Andreja Petrović
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Institute of Clinical Pathology and Cytology, Merkur University Hospital, 10000 Zagreb, Croatia
| | - Valerija Begić
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Primary School “Sesvetski Kraljevec”, 10361 Sesvetski Kraljevec, Croatia
| | - Suzana Harabajsa
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Department of Pathology and Cytology, Division of Pulmonary Cytology Jordanovac, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Petra Korać
- Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-1-4606-278
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11
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Bergez-Hernández F, Arámbula-Meraz E, Alvarez-Arrazola M, Irigoyen-Arredondo M, Luque-Ortega F, Martínez-Camberos A, Cedano-Prieto D, Contreras-Gutiérrez J, Martínez-Valenzuela C, García-Magallanes N. Expression Analysis of miRNAs and Their Potential Role as Biomarkers for Prostate Cancer Detection. Am J Mens Health 2022; 16:15579883221120989. [PMID: 36082407 PMCID: PMC9465588 DOI: 10.1177/15579883221120989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Prostate cancer (PCa) is the second most frequent cancer diagnosed in men worldwide. The detection methods for PCa are either unreliable, like prostate-specific antigen (PSA), or extremely invasive, such as in the case of biopsies. Therefore, there is an urgent necessity for reliable and less invasive detection procedures that can differentiate between patients with benign diseases and those with cancer. In this matter, microRNAs (miRNAs) are suggested as potential biomarkers for cancer. MiRNAs have been found to be dysregulated in several different cancers, and these genetic alterations may present specific signatures for a given malignancy. Here, we examined the expression of miR141-3p, miR145-5p, miR146a-5p, and miR148b-3p in human tissue samples of PCa (n = 41) and benign prostatic diseases (BPD) (n = 30) using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). We combined the expression results with patient clinicopathological characteristics in logistic regression models to create accurate PCa predictive models. A model including information of miR148b-3p and patient age showed relevant prediction results (area under the curve [AUC] = 0.818, precision = 0.763, specificity = 0.762, and accuracy = 0.762). A model including all four miRNAs and patient age presented outstanding prediction results (AUC = 0.918, precision = 0.861, specificity = 0.861, and accuracy = 0.857). Our results represent a potential novel procedure based on logistic regression models that utilize miRNA expressions and patient age to assist with PCa diagnosis.
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Affiliation(s)
- Fernando Bergez-Hernández
- Posgrado en Ciencias Biomédicas,
Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa,
Culiacán Rosales, México
| | - Eliakym Arámbula-Meraz
- Laboratorio de Genética y
Biología Molecular, Facultad de Ciencias Químico Biológicas, Universidad
Autónoma de Sinaloa, Culiacán Rosales, México
| | | | - Martín Irigoyen-Arredondo
- Posgrado en Ciencias Biomédicas,
Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa,
Culiacán Rosales, México
| | - Fred Luque-Ortega
- Laboratorio de Ciencias Básicas,
Facultad de Odontología, Universidad Autónoma de Sinaloa, Culiacán Rosales,
México
| | - Alejandra Martínez-Camberos
- Posgrado en Ciencias Biomédicas,
Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa,
Culiacán Rosales, México
| | - Dora Cedano-Prieto
- Laboratorio de Genética y
Biología Molecular, Facultad de Ciencias Químico Biológicas, Universidad
Autónoma de Sinaloa, Culiacán Rosales, México
| | - José Contreras-Gutiérrez
- Centro de Investigación y
Docencia en Ciencias de la Salud, Hospital Civil de Culiacán, Universidad
Autónoma de Sinaloa, Culiacán Rosales, México
| | - Carmen Martínez-Valenzuela
- Laboratorio de Genotoxicología
“Dr Jesus Kumate Rodriguez,” Unidad de Investigación en Ambiente y Salud,
Universidad Autónoma de Occidente, Los Mochis, México
| | - Noemí García-Magallanes
- Laboratorio de Biomedicina y
Biología Molecular, Ingeniería en Biotecnología, Universidad Politécnica de
Sinaloa, Mazatlán, México,Noemí García Magallanes,
Laboratorio de Biomedicina y Biología Molecular, Ingeniería en
Biotecnología, Universidad Politécnica de Sinaloa, Carretera Municipal
Libre Mazatlán-Higueras s/n 3km col. Genaro Estrada, 82199 Mazatlán,
Sinaloa, México.
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12
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Wang S, Liu C, Li Y, Qiao J, Chen X, Bao J, Li R, Xing Y. LINC00665 affects the malignant biological behavior of ovarian cancer via the miR-148b-3p/KLF5. Syst Biol Reprod Med 2022; 68:370-383. [PMID: 36016468 DOI: 10.1080/19396368.2022.2101961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
This study investigated the expression and clinical significance of long intergenic noncoding RNA 00665 (LINC00665) in ovarian cancer (OC), as well as its effect on the malignant biological behavior of OC cells. The expression of LINC00665, miR-148b-3p, and Krüppel-like factor 5 (KLF5) in OC tissues and cells were determined by RT-qPCR. Western blot was used to detect the protein expression of KLF5. The expression patterns of LINC00665 in nuclear and cytoplasm fractions were undertaken using RT-qPCR. In addition, CCK-8 assay, clone formation assay, transwell, scratch test, and flow cytometry were respectively used to detect the cell activity, proliferation, invasiveness, healing of cells, and apoptosis rate of OC cells. Furthermore, the interactions between LINC00665 and miR-148b-3p and between miR-148b-3p and KLF5 were verified by the luciferase reporter assay, and the correlations among these three genes were analyzed. LINC00665 expression was upregulated both in OC cell lines and tissues. Si-LINC00665 inhibited cell proliferation, invasion, and migration and induced apoptosis to a certain extent. The subcellular fraction assay revealed LINC00665 to be located mainly in the cytoplasm. miR-148b-3p was a target of LINC00665, and KLF5 was directly targeted by miR-148b-3p. Si-LINC00665 inhibited KLF5 expression, miR-148b-3p inhibitor promoted KLF5 expression, and si-KLF5 inhibited LINC00665 expression. Interestingly, the expression of LINC00665 was reversely associated with miR-148b-3p expression but positively correlated with KLF5. Furthermore, miR-148b-3p expression was negatively correlated with KLF5. In addition, si-KLF5 inhibited the malignant biological behavior of OC cells, whereas miR-148b-3p inhibitor had the opposite effect. Most importantly, the si-LINC00665 could reverse the promotion effect of the miR-148b-3p inhibitor on the malignant biological behavior of OC cells. LINC00665 can be used as an effective prognostic indicator of OC, which has the potential to be a new therapeutic target.
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Affiliation(s)
- Shenglan Wang
- Department of Pathophysiology, Medical College of Qinghai University, Qinghai, P.R. China
| | - Chuanchuan Liu
- Key Laboratory of Hydatidosis Research, Qinghai University Affiliated Hospital, Qinghai, P.R. China
| | - Yongchuan Li
- Department of Gynaecology, Qinghai Red Cross Hospital, Qinghai, P.R. China
| | - Jinwan Qiao
- Department of Scientific Research and Teaching, the Fifth People's Hospital of Qinghai Province, Qinghai, P.R. China
| | - Xinling Chen
- Basic Medical Sciences, Qinghai University, Qinghai, P.R. China
| | - Jin Bao
- Basic Medical Sciences, Qinghai University, Qinghai, P.R. China
| | - Ran Li
- Basic Medical Sciences, Qinghai University, Qinghai, P.R. China
| | - Yanxia Xing
- Department of Gynaecology, the Fifth People's Hospital of Qinghai Province, Qinghai, P.R. China
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13
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Keup C, Kimmig R, Kasimir-Bauer S. Combinatorial Power of cfDNA, CTCs and EVs in Oncology. Diagnostics (Basel) 2022; 12:870. [PMID: 35453918 PMCID: PMC9031112 DOI: 10.3390/diagnostics12040870] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 01/01/2023] Open
Abstract
Liquid biopsy is a promising technique for clinical management of oncological patients. The diversity of analytes circulating in the blood useable for liquid biopsy testing is enormous. Circulating tumor cells (CTCs), cell-free DNA (cfDNA) and extracellular vesicles (EVs), as well as blood cells and other soluble components in the plasma, were shown as liquid biopsy analytes. A few studies directly comparing two liquid biopsy analytes showed a benefit of one analyte over the other, while most authors concluded the benefit of the additional analyte. Only three years ago, the first studies to examine the value of a characterization of more than two liquid biopsy analytes from the same sample were conducted. We attempt to reflect on the recent development of multimodal liquid biopsy testing in this review. Although the analytes and clinical purposes of the published multimodal studies differed significantly, the additive value of the analytes was concluded in almost all projects. Thus, the blood components, as liquid biopsy reservoirs, are complementary rather than competitive, and orthogonal data sets were even shown to harbor synergistic effects. The unmistakable potential of multimodal liquid biopsy testing, however, is dampened by its clinical utility, which is yet to be proven, the lack of methodical standardization and insufficiently mature reimbursement, logistics and data handling.
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Affiliation(s)
- Corinna Keup
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Rainer Kimmig
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
| | - Sabine Kasimir-Bauer
- Department of Gynecology and Obstetrics, University Hospital of Essen, Hufelandstr. 55, 45122 Essen, Germany
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