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Hayden JP, Wiggins A, Sullivan T, Kalantzakos T, Hooper K, Moinzadeh A, Rieger-Christ K. Use of Droplet Digital Polymerase Chain Reaction to Identify Biomarkers for Differentiation of Benign and Malignant Renal Masses. Cancers (Basel) 2024; 16:787. [PMID: 38398177 PMCID: PMC10886675 DOI: 10.3390/cancers16040787] [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: 01/23/2024] [Revised: 02/08/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Several microRNAs (miRNAs) have been identified as cell-free biomarkers for detecting renal cell carcinoma (RCC). Droplet digital polymerase chain reaction (ddPCR) is a unique technology for nucleic acid quantification. It has the potential for superior precision, reproducibility, and diagnostic performance in identifying circulating miRNA biomarkers compared to conventional quantitative real-time PCR (qRT-PCR). This study aims to evaluate the performance of ddPCR compared to qRT- PCR in identifying miRNA biomarkers that differentiate malignant from benign renal masses. Potential biomarkers of RCC were identified from a literature review. RNA was extracted from the plasma of 56 patients. All the samples underwent analysis via ddPCR as well as qRT-PCR, and expression levels were recorded for the following miRNAs: miR-93, -144, -210, -221, and -222. Tumors were grouped into low-grade ccRCC, high-grade ccRCC, papillary RCC, and benign masses (primarily angiomyolipoma). The miRNA miR-210 (p = 0.034) and the combination of miRs-210 and miR-222 (p = 0.003) were expressed at significantly higher rates among those with RCC than those with benign masses, as measured by ddPCR. Using the combination of miR-210 and miR-222, ddPCR identified significant differences between the subgroups: papillary RCC versus benign (p = 0.03), low-grade ccRCC versus benign (p = 0.026), and high-grade ccRCC versus benign (p = 0.002). The only significant difference between these subgroups using qRT-PCR was between high-grade ccRCC and benign (p = 0.045). All the AUCs were significant when comparing each RCC subgroup with benign for both PCR technologies. Using a combination of miR-210 and miR-222, ddPCR identified significant differences between benign and malignant renal masses that were not identified as significant by conventional qRT-PCR.
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Affiliation(s)
- Joshua P. Hayden
- Department of Urology, Lahey Hospital & Medical Center, Burlington, MA 01805, USA; (J.P.H.); (A.W.); (A.M.)
| | - Adam Wiggins
- Department of Urology, Lahey Hospital & Medical Center, Burlington, MA 01805, USA; (J.P.H.); (A.W.); (A.M.)
| | - Travis Sullivan
- Department of Translational Research, Lahey Hospital & Medical Center, Burlington, MA 01805, USA; (T.S.); (T.K.); (K.H.)
| | - Thomas Kalantzakos
- Department of Translational Research, Lahey Hospital & Medical Center, Burlington, MA 01805, USA; (T.S.); (T.K.); (K.H.)
| | - Kailey Hooper
- Department of Translational Research, Lahey Hospital & Medical Center, Burlington, MA 01805, USA; (T.S.); (T.K.); (K.H.)
| | - Alireza Moinzadeh
- Department of Urology, Lahey Hospital & Medical Center, Burlington, MA 01805, USA; (J.P.H.); (A.W.); (A.M.)
| | - Kimberly Rieger-Christ
- Department of Urology, Lahey Hospital & Medical Center, Burlington, MA 01805, USA; (J.P.H.); (A.W.); (A.M.)
- Department of Translational Research, Lahey Hospital & Medical Center, Burlington, MA 01805, USA; (T.S.); (T.K.); (K.H.)
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Wilczyński J, Paradowska E, Wilczyński M. High-Grade Serous Ovarian Cancer-A Risk Factor Puzzle and Screening Fugitive. Biomedicines 2024; 12:229. [PMID: 38275400 PMCID: PMC10813374 DOI: 10.3390/biomedicines12010229] [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: 11/12/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/27/2024] Open
Abstract
High-grade serous ovarian cancer (HGSOC) is the most lethal tumor of the female genital tract. Despite extensive studies and the identification of some precursor lesions like serous tubal intraepithelial cancer (STIC) or the deviated mutational status of the patients (BRCA germinal mutation), the pathophysiology of HGSOC and the existence of particular risk factors is still a puzzle. Moreover, a lack of screening programs results in delayed diagnosis, which is accompanied by a secondary chemo-resistance of the tumor and usually results in a high recurrence rate after the primary therapy. Therefore, there is an urgent need to identify the substantial risk factors for both predisposed and low-risk populations of women, as well as to create an economically and clinically justified screening program. This paper reviews the classic and novel risk factors for HGSOC and methods of diagnosis and prediction, including serum biomarkers, the liquid biopsy of circulating tumor cells or circulating tumor DNA, epigenetic markers, exosomes, and genomic and proteomic biomarkers. The novel future complex approach to ovarian cancer diagnosis should be devised based on these findings, and the general outcome of such an approach is proposed and discussed in the paper.
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Affiliation(s)
- Jacek Wilczyński
- Department of Gynecological Surgery and Gynecological Oncology, Medical University of Lodz, 4 Kosciuszki Str., 90-419 Lodz, Poland
| | - Edyta Paradowska
- Laboratory of Virology, Institute of Medical Biology of the Polish Academy of Sciences, 106 Lodowa Str., 93-232 Lodz, Poland;
| | - Miłosz Wilczyński
- Department of Surgical, Endoscopic and Gynecological Oncology, Polish Mother’s Health Center—Research Institute, 281/289 Rzgowska Str., 93-338 Lodz, Poland;
- Department of Surgical and Endoscopic Gynecology, Medical University of Lodz, 4 Kosciuszki Str., 90-419 Lodz, Poland
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Frisk NLS, Sørensen AE, Pedersen OBV, Dalgaard LT. Circulating microRNAs for Early Diagnosis of Ovarian Cancer: A Systematic Review and Meta-Analysis. Biomolecules 2023; 13:biom13050871. [PMID: 37238740 DOI: 10.3390/biom13050871] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/10/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
In this study, we conducted a systematic review and meta-analysis to summarize and evaluate the global research potential of different circulating miRNAs as an early diagnostic biomarker for OC. A systematic literature search for relevant studies was conducted in June 2020 and followed up in November 2021. The search was conducted in English databases (PubMed, ScienceDirect). The primary search resulted in a total of 1887 articles, which were screened according to the prior established inclusion and exclusion criteria. We identified 44 relevant studies, of which 22 were eligible for the quantitative meta-analysis. Statistical analysis was performed using the Meta-package in Rstudio. Standardized mean differences (SMD) of relative levels between control subjects and OC patients were used to evaluate the differential expression. All studies were quality evaluated using a Newcastle-Ottawa Scale. Based on the meta-analysis, nine miRNAs were identified as dysregulated in OC patients compared to controls. Nine were upregulated in OC patients compared to controls (miR-21, -125, -141, -145, -205, -328, -200a, -200b, -200c). Furthermore, miR-26, -93, -106 and -200a were analyzed, but did not present an overall significant difference between OC patients and controls. These observations should be considered when performing future studies of circulating miRNAs in relation to OC: sufficient size of clinical cohorts, development of consensus guidelines for circulating miRNA measurements, and coverage of previously reported miRNAs.
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Affiliation(s)
- Nanna Lond Skov Frisk
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Ringstedgade 77B, 4700 Næstved, Denmark
| | - Anja Elaine Sørensen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Ole Birger Vesterager Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Ringstedgade 77B, 4700 Næstved, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Science, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark
| | - Louise Torp Dalgaard
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
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Insight on Non-Coding RNAs from Biofluids in Ovarian Tumors. Cancers (Basel) 2023; 15:cancers15051539. [PMID: 36900328 PMCID: PMC10001105 DOI: 10.3390/cancers15051539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
Ovarian tumors are the most frequent adnexal mass, raising diagnostic and therapeutic issues linked to a large spectrum of tumors, with a continuum from benign to malignant. Thus far, none of the available diagnostic tools have proven efficient in deciding strategy, and no consensus exists on the best strategy between "single test", "dual testing", "sequential testing", "multiple testing options" and "no testing". In addition, there is a need for prognostic tools such as biological markers of recurrence and theragnostic tools to detect women not responding to chemotherapy in order to adapt therapies. Non-coding RNAs are classified as small or long based on their nucleotide count. Non-coding RNAs have multiple biological functions such as a role in tumorigenesis, gene regulation and genome protection. These ncRNAs emerge as new potential tools to differentiate benign from malignant tumors and to evaluate prognostic and theragnostic factors. In the specific setting of ovarian tumors, the goal of the present work is to offer an insight into the contribution of biofluid non-coding RNAs (ncRNA) expression.
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Beg A, Parveen R, Fouad H, Yahia ME, Hassanein AS. Identification of Driver Genes and miRNAs in Ovarian Cancer through an Integrated In-Silico Approach. BIOLOGY 2023; 12:biology12020192. [PMID: 36829472 PMCID: PMC9952540 DOI: 10.3390/biology12020192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/25/2022] [Accepted: 01/05/2023] [Indexed: 01/28/2023]
Abstract
Ovarian cancer is the eighth-most common cancer in women and has the highest rate of death among all gynecological malignancies in the Western world. Increasing evidence shows that miRNAs are connected to the progression of ovarian cancer. In the current study, we focus on the identification of miRNA and its associated genes that are responsible for the early prognosis of patients with ovarian cancer. The microarray dataset GSE119055 used in this study was retrieved via the publicly available GEO database by NCBI for the analysis of DEGs. The miRNA GSE119055 dataset includes six ovarian carcinoma samples along with three healthy/primary samples. In our study, DEM analysis of ovarian carcinoma and healthy subjects was performed using R Software to transform and normalize all transcriptomic data along with packages from Bioconductor. Results: We identified miRNA and its associated hub genes from the samples of ovarian cancer. We discovered the top five upregulated miRNAs (hsa-miR-130b-3p, hsa-miR-18a-5p, hsa-miR-182-5p, hsa-miR-187-3p, and hsa-miR-378a-3p) and the top five downregulated miRNAs (hsa-miR-501-3p, hsa-miR-4324, hsa-miR-500a-3p, hsa-miR-1271-5p, and hsa-miR-660-5p) from the network and their associated genes, which include seven common genes (SCN2A, BCL2, MAF, ZNF532, CADM1, ELAVL2, and ESRRG) that were considered hub genes for the downregulated network. Similarly, for upregulated miRNAs we found two hub genes (PRKACB and TAOK1).
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Affiliation(s)
- Anam Beg
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
- Correspondence: or (A.B.); (R.P.); Tel.: +91-965-049-3477 (R.P.)
| | - Rafat Parveen
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
- Correspondence: or (A.B.); (R.P.); Tel.: +91-965-049-3477 (R.P.)
| | - Hassan Fouad
- Applied Medical Science Department, CC, King Saud University, Riyadh 11433, Saudi Arabia
| | - M. E. Yahia
- Faculty of Engineering and Natural Sciences, International University of Sarajevo, Hrasnička Cesta 15, Ilidža, 71210 Sarajevo, Bosnia and Herzegovina
| | - Azza S. Hassanein
- Biomedical Engineering Department, Faculty of Engineering, Helwan University, Cairo 11792, Egypt
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Tang F, Liu Y, Sun Y, Xiong Y, Gu Y, Zhou J, Ouyang Y, Zhang S. Construction of a serum diagnostic signature based on m5C-related miRNAs for cancer detection. Front Endocrinol (Lausanne) 2023; 14:1099703. [PMID: 36777349 PMCID: PMC9911864 DOI: 10.3389/fendo.2023.1099703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/13/2023] [Indexed: 01/28/2023] Open
Abstract
Currently, no clinically relevant non-invasive biomarkers are available for screening of multiple cancer types. In this study, we developed a serum diagnostic signature based on 5-methylcytosine (m5C)-related miRNAs (m5C-miRNAs) for multiple-cancer detection. Serum miRNA expression data and the corresponding clinical information of patients were collected from the Gene Expression Omnibus database. Serum samples were then randomly assigned to the training or validation cohort at a 1:1 ratio. Using the identified m5C-miRNAs, an m5C-miRNA signature for cancer detection was established using a support vector machine algorithm. The constructed m5C-miRNA signature displayed excellent accuracy, and its areas under the curve were 0.977, 0.934, and 0.965 in the training cohort, validation cohort, and combined training and validation cohort, respectively. Moreover, the diagnostic capability of the m5C-miRNA signature was unaffected by patient age or sex or the presence of noncancerous disease. The m5C-miRNA signature also displayed satisfactory performance for distinguishing tumor types. Importantly, in the detection of early-stage cancers, the diagnostic performance of the m5C-miRNA signature was obviously superior to that of conventional tumor biomarkers. In summary, this work revealed the value of serum m5C-miRNAs in cancer detection and provided a new strategy for developing non-invasive and cost effective tools for large-scale cancer screening.
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Affiliation(s)
- Fuzhou Tang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yang Liu
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yichi Sun
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yu Xiong
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
| | - Yan Gu
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
| | - Jing Zhou
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
- *Correspondence: Jing Zhou, ; Yan Ouyang, ; Shichao Zhang,
| | - Yan Ouyang
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Engineering Research Center of Cellular Immunotherapy of Guizhou Province, Guizhou Medical University, Guiyang, China
- *Correspondence: Jing Zhou, ; Yan Ouyang, ; Shichao Zhang,
| | - Shichao Zhang
- Immune Cells and Antibody Engineering Research Center of Guizhou Province, Key Laboratory of Biology and Medical Engineering, Guizhou Medical University, Guiyang, China
- *Correspondence: Jing Zhou, ; Yan Ouyang, ; Shichao Zhang,
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A novel circulating miRNA panel for non-invasive ovarian cancer diagnosis and prognosis. Br J Cancer 2022; 127:1550-1556. [PMID: 35931806 PMCID: PMC9553930 DOI: 10.1038/s41416-022-01925-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 12/12/2022] Open
Abstract
Background Ovarian cancer (OC) is an aggressive disease, primarily diagnosed in late stages with only 20% of patients surviving more than 5 years after diagnosis. There is a pending need to improve current diagnostics and prognostics. Methods In this study, we investigated total circulating cell-free microRNA (cf-miRNA) levels as well as a panel of cf-miRNAs in the plasma of OC patients (n = 100), patients with benign lesions (n = 45) and healthy controls (n = 99). Results High levels of cf-miRNAs correlated with unfavourable clinical features and were an independent prognosticator of patient survival. By mining NGS data, we identified a signature panel of seven individual cf-miRNAs which could distinguish controls from benign cases with an AUC of 0.77 and controls from cancer cases with an AUC of 0.87. Importantly, in combination with the current gold-standard marker, CA-125, the panel could predict early OC with an AUC of 0.93. Conclusion Our findings highlight the potential of cf-miRNA levels as well as individual cf-miRNAs for OC diagnosis and prognosis that warrants further clinical evaluation.
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Abstract
Recent studies have revealed the significant dysregulation of m6A level in peripheral blood in several cancer types and its value in diagnosis. Nonetheless, a biomarker for accurate screening of multiple cancer types has not been established based on the perspective of m6A modification. In this study, we aimed to develop a serum diagnostic signature based on the m6A target miRNAs for the mass detection of cancer. A total of 14965 serum samples with 12 cancer types were included. Based on training cohort (n=7299), we developed the m6A-miRNAs signature using a support vector machine algorithm for cancer detection. The m6A-miRNAs signature showed high accuracy, and its area under the curve (AUC) in the training, internal validation and external validation cohort reached 0.979 (95%CI 0.976 - 0.982), 0.976 (95%CI 0.973 - 0.979) and 0.936 (95%CI 0.922 - 0.951), respectively. In the performance of distinguishing cancer types, the m6A-miRNAs signature showed superior sensitivity in each cancer type and presented a satisfactory AUC in identifying lung cancer, gastric cancer and hepatocellular carcinoma. Additionally, the diagnostic performance of m6A-miRNAs was not interfered by the gender, age and benign disease. In short, this study revealed the value of serum circulating m6A miRNAs in cancer detection and provided a new direction and strategy for the development of novel biomarkers with high accuracy, low cost and less invasiveness for mass cancer screening, such as RNA modification.
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ElShelmani H, Brennan I, Kelly DJ, Keegan D. Differential Circulating MicroRNA Expression in Age-Related Macular Degeneration. Int J Mol Sci 2021; 22:ijms222212321. [PMID: 34830203 PMCID: PMC8625913 DOI: 10.3390/ijms222212321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 02/06/2023] Open
Abstract
This study explored the expression of several miRNAs reported to be deregulated in age-related macular degeneration (AMD). Total RNA was isolated from sera from patients with dry AMD (n = 12), wet AMD (n = 14), and controls (n = 10). Forty-two previously investigated miRNAs were selected based on published data and their role in AMD pathogenesis, such as angiogenic and inflammatory effects, and were co-analysed using a miRCURY LNA miRNA SYBR® Green PCR kit via quantitative real-time polymerase chain reaction (qRT-PCR) to validate their presence. Unsupervised hierarchical clustering indicated that AMD serum specimens have a different miRNA profile to healthy controls. We successfully validated the differentially regulated miRNAs in serum from AMD patients versus controls. Eight miRNAs (hsa-let-7a-5p, hsa-let-7d-5p, hsa-miR-23a-3p, hsa-miR-301a-3p, hsa-miR-361-5p, hsa-miR-27b-3p, hsa-miR-874-3p, hsa-miR-19b-1-5p) showed higher expression in the serum of dry AMD patients than wet AMD patients and compared with healthy controls. Increased quantities of certain miRNAs in the serum of AMD patients indicate that these miRNAs could potentially serve as diagnostic AMD biomarkers and might be used as future AMD treatment targets. The discovery of significant serum miRNA biomarkers in AMD patients would provide an easy screening tool for at-risk populations.
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Affiliation(s)
- Hanan ElShelmani
- Mater Misericordiae University Hospital, Eccles St., Dublin 7, Ireland; (H.E.); (I.B.)
| | - Ian Brennan
- Mater Misericordiae University Hospital, Eccles St., Dublin 7, Ireland; (H.E.); (I.B.)
- University College Cork, College Road, Cork, Ireland
| | - David J. Kelly
- Zoology Department, School of Natural Sciences, Trinity College Dublin, University of Dublin, Dublin 2, Ireland;
| | - David Keegan
- Mater Misericordiae University Hospital, Eccles St., Dublin 7, Ireland; (H.E.); (I.B.)
- Correspondence:
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