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Zenlander R, Salter H, Gilg S, Eggertsen G, Stål P. MicroRNAs as Plasma Biomarkers of Hepatocellular Carcinoma in Patients with Liver Cirrhosis-A Cross-Sectional Study. Int J Mol Sci 2024; 25:2414. [PMID: 38397091 PMCID: PMC10888674 DOI: 10.3390/ijms25042414] [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: 01/16/2024] [Revised: 02/13/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Ultrasound screening for hepatocellular carcinoma (HCC) in patients with liver cirrhosis has a poor sensitivity for small tumors. Circulating microRNAs (miRNAs) have been explored as HCC biomarkers, but results are diverging. Here, we evaluate if miRNAs up-regulated in HCC tissue can be detected in plasma and used as screening biomarkers for HCC. In this cross-sectional study, plasma, HCC tissue and surrounding non-tumorous liver tissue were collected from liver resections. Tissue miRNAs were identified and quantitated by RNA-sequencing analysis, and the fold-changes between HCC and surrounding liver tissue were calculated. The miRNAs up-regulated in HCCs were then re-analyzed in plasma from the same patients, and the miRNAs with the highest plasma levels were subsequently measured in plasma from an independent cohort of patients with cirrhosis or HCC. In tissues from 84 resected patients, RNA-sequencing detected 197 differentially expressed miRNAs, 40 of which had a raw count above 200 and were analyzed in plasma from the same cohort. Thirty-one miRNAs were selected for further analysis in 200 patients with HCC or cirrhosis. Of these, eleven miRNAs were significantly increased in HCC as compared to cirrhosis patients. Only miR-93-5p and miR-151a-3p were significantly associated with HCC, with an AUC of 0.662. In comparison, alpha-fetoprotein and des-gamma-carboxy prothrombin yielded an AUC of 0.816, which increased to 0.832 if miR-93-5p and miR-151a-3p were added. When including sex and age, the addition of miR-93-5p and miR-151a-3p did not further improve the AUC (from 0.910 to 0.911). In conclusion, micro-RNAs up-regulated in HCCs are detectable in plasma but have a poor performance as screening biomarkers of HCC.
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Affiliation(s)
- Robin Zenlander
- Department of Clinical Chemistry, Karolinska University Hospital, 141 86 Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, 141 52 Stockholm, Sweden
- Department of Medicine, Huddinge, Karolinska Institutet, 141 86 Stockholm, Sweden (P.S.)
| | - Hugh Salter
- Department of Laboratory Medicine, Karolinska Institutet, 141 52 Stockholm, Sweden
| | - Stefan Gilg
- Department of Medicine, Huddinge, Karolinska Institutet, 141 86 Stockholm, Sweden (P.S.)
| | - Gösta Eggertsen
- Department of Clinical Chemistry, Karolinska University Hospital, 141 86 Stockholm, Sweden
- Department of Medicine, Huddinge, Karolinska Institutet, 141 86 Stockholm, Sweden (P.S.)
| | - Per Stål
- Department of Medicine, Huddinge, Karolinska Institutet, 141 86 Stockholm, Sweden (P.S.)
- Division of Hepatology, Department of Upper GI Diseases, Karolinska University Hospital, 141 86 Stockholm, Sweden
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Jeon BS, Lee SH, Hwang SR, Yi H, Bang JH, Tham NTT, Lee HK, Woo GH, Kang HG, Ku HO. Identification of urinary microRNA biomarkers for in vivo gentamicin-induced nephrotoxicity models. J Vet Sci 2020; 21:e81. [PMID: 33263228 PMCID: PMC7710462 DOI: 10.4142/jvs.2020.21.e81] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/20/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Although previous in vivo studies explored urinary microRNA (miRNA), there is no agreement on nephrotoxicity-specific miRNA biomarkers. OBJECTIVES In this study, we assessed whether urinary miRNAs could be employed as biomarkers for nephrotoxicity. METHODS For this, literature-based candidate miRNAs were identified by reviewing the previous studies. Female Sprague-Dawley rats received subcutaneous injections of a single dose or repeated doses (3 consecutive days) of gentamicin (GEN; 137 or 412 mg/kg). The expression of miRNAs was analyzed by real-time reverse transcription-polymerase chain reaction in 16 h pooled urine from GEN-treated rats. RESULTS GEN-induced acute kidney injury was confirmed by the presence of tubular necrosis. We identified let-7g-5p, miR-21-3p, 26b-3p, 192-5p, and 378a-3p significantly upregulated in the urine of GEN-treated rats with the appearance of the necrosis in proximal tubules. Specifically, miR-26-3p, 192-5p, and 378a-3p with highly expressed levels in urine of rats with GEN-induced acute tubular injury were considered to have sensitivities comparable to clinical biomarkers, such as blood urea nitrogen, serum creatinine, and urinary kidney injury molecule protein. CONCLUSIONS These results indicated the potential involvement of urinary miRNAs in chemical-induced nephrotoxicity, suggesting that certain miRNAs could serve as biomarkers for acute nephrotoxicity.
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Affiliation(s)
- Byung Suk Jeon
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Soo Ho Lee
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - So Ryeon Hwang
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Hee Yi
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Ji Hyun Bang
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Nga Thi Thu Tham
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Hyun Kyoung Lee
- Animal Pathodiagnostic Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Gye Hyeong Woo
- Department of Clinical Laboratory Science, Semyung University, Jecheon 27136, Korea
| | - Hwan Goo Kang
- Department of Clinical Laboratory Science, Semyung University, Jecheon 27136, Korea.
| | - Hyun Ok Ku
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea.
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Zhuang W, Camacho L, Silva CS, Hong H. Reproducibility challenges for biomarker detection with uncertain but informative experimental data. Biomark Med 2020; 14:1255-1263. [PMID: 33021389 DOI: 10.2217/bmm-2019-0599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Recent studies have revealed that circulating microRNAs are promising biomarkers for detecting toxicity or disease. Quantitative real-time polymerase chain reaction (qPCR) is often used to measure the levels of microRNAs. Besides complete and certain data, investigators inevitably have observed technically incomplete or uncertain qPCR data. Investigators usually set incomplete observations equal to the maximum quality number of qPCR cycles, apply the complete-observation method, or choose not to analyze targets with incomplete observations. Using biostatistical knowledge and published studies, we show that three commonly applied methods tend to cause biased inference and decrease reproducibility in biomarker detection. More efforts are needed to address the challenges to identify and detect reliable, novel circulating biomarkers in liquid biopsies.
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Affiliation(s)
- Wei Zhuang
- Division of Bioinformatics & Biostatistics, NCTR, US FDA, Jefferson, AR 72079, USA
| | - Luísa Camacho
- Division of Biochemical Toxicology, NCTR, US FDA, Jefferson, AR 72079, USA
| | - Camila S Silva
- Division of Biochemical Toxicology, NCTR, US FDA, Jefferson, AR 72079, USA
| | - Huixiao Hong
- Division of Bioinformatics & Biostatistics, NCTR, US FDA, Jefferson, AR 72079, USA
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Balasubramanian S, Gunasekaran K, Sasidharan S, Jeyamanickavel Mathan V, Perumal E. MicroRNAs and Xenobiotic Toxicity: An Overview. Toxicol Rep 2020; 7:583-595. [PMID: 32426239 PMCID: PMC7225592 DOI: 10.1016/j.toxrep.2020.04.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/13/2020] [Accepted: 04/19/2020] [Indexed: 12/27/2022] Open
Abstract
The advent of new technologies has paved the rise of various chemicals that are being employed in industrial as well as consumer products. This leads to the accumulation of these xenobiotic compounds in the environment where they pose a serious threat to both target and non-target species. miRNAs are one of the key epigenetic mechanisms that have been associated with toxicity by modulating the gene expression post-transcriptionally. Here, we provide a comprehensive view on miRNA biogenesis, their mechanism of action and, their possible role in xenobiotic toxicity. Further, we review the recent in vitro and in vivo studies involved in xenobiotic exposure induced miRNA alterations and the mRNA-miRNA interactions. Finally, we address the challenges associated with the miRNAs in toxicological studies.
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Key Words
- ADAMTS9, A disintegrin and metalloproteinase with thrombospondin motifs 9
- AHR, Aryl Hydrocarbon Receptor
- AMPK, Adenosine Monophosphate-activated protein kinase
- ARRB1, Arrestin beta 1
- Ag, Silver
- Al2O3, Aluminium oxide
- Au, Gold
- Aβ, Amyloid Beta
- BCB, Blood-cerebrospinal fluid barrier
- BNIP3−3, BCL2/adenovirus E1B 19 kDa protein-interacting protein 3
- BaP, Benzo[a]pyrene
- Biomarkers
- CCNB1, Cyclin B1
- CDC25A, M-phase inducer phosphatase 1
- CDC25C, M-phase inducer phosphatase 3
- CDK, Cyclin-dependent Kinase
- CDK1, Cyclin-dependent kinase 1
- CDK6, Cyclin-dependent kinase 6
- CDKN1b, Cyclin-dependent kinase Inhibitor 1B
- CEC, Contaminants of Emerging Concern
- COPD, Chronic obstructive pulmonary disease
- COX2, Cyclooxygenase-2
- CTGF, Connective Tissue Growth Factor
- DGCR8, DiGeorge syndrome chromosomal [or critical] region 8
- DNA, Deoxy ribonucleic acid
- DON, Deoxynivalenol
- ER, Endoplasmic Reticulum
- Environment
- Epigenetics
- Fadd, Fas-associated protein with death domain
- GTP, Guanosine triphosphate
- Gene regulation
- Grp78/BIP, Binding immunoglobulin protein
- HSPA1A, Heat shock 70 kDa protein 1
- Hpf, Hours post fertilization
- IL-6, Interleukin 6
- IL1R1, Interleukin 1 receptor, type 1
- LIN28B, Lin-28 homolog B
- LRP-1-, Low density lipoprotein receptor-related protein 1
- MAPK, Mitogen Activated Protein Kinase
- MC-LR, Microcystin-Leucine Arginine
- MC-RR, Microcystin-Arginine Arginine
- MRE, MicroRNA Response Elements
- Mn, Manganese
- NASH, Non-alcoholic steatohepatitis
- NET1, Neuroepithelial Cell Transforming 1
- NF- ҡB, Nuclear Factor kappa-light-chain-enhancer of activated B cells
- NFKBAP, NFKB Activating protein-1
- NMDAR, N-methyl-d-aspartate receptor
- NPs, Nanoparticles
- Non-coding RNAs
- Nrf2, Nuclear factor erythroid 2-related factor 2
- PDCD4, Programmed cell death protein 4
- PFAS, Poly-fluoroalkyl substances
- PM2.5, Particulate Matter2.5
- RISC, RNA-induced silencing complex
- RNA, Ribonucleic acid
- RNAi, RNA interference
- RNase III, Ribonuclease III
- SEMA6D, Semaphorin-6D
- SOLiD, Sequencing by Oligonucleotide Ligation and Detection
- SPIONs, Superparamagnetic Iron Oxide Nanoparticles
- SiO2, Silicon dioxide
- TCDD, 2,3,7,8-Tetrachlorodibenzodioxin
- TNF-α, Tumor necrosis factor – alpha
- TP53, Tumor protein 53
- TRBP, Transactivation Response RNA Binding Protein
- Toxicity
- UTR, Untranslated region
- WHO, World Health Organization
- Wnt, Wingless-related integration site
- ZEA, Zearalanone
- Zn, Zinc
- bcl2l11, B-cell lymphoma-2-like protein 11
- ceRNA, Competing endogenous RNA
- lncRNAs, Long non-coding RNA
- mRNA, Messenger RNA
- miRNA, MicroRNA
- qRT-PCR, quantitative Real Time-Polymerase Chain Reaction
- ripk 1, Receptor-interacting serine/threonine-protein kinase 1
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Affiliation(s)
| | - Kanmani Gunasekaran
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641 046, India
| | - Saranyadevi Sasidharan
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641 046, India
| | | | - Ekambaram Perumal
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, 641 046, India
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Bushel PR, Caiment F, Wu H, O'Lone R, Day F, Calley J, Smith A, Li J, Harrill AH. RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs for discerning baseline expression exclusivity of candidate biomarkers. RNA Biol 2020; 17:630-636. [PMID: 32009518 DOI: 10.1080/15476286.2020.1724715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small RNAs that regulate mRNA expression and have been targeted as biomarkers of organ damage and disease. To explore the utility of miRNAs to assess injury to specific tissues, a tissue atlas of miRNA abundance was constructed. The Rat Atlas of Tissue-specific and Enriched miRNAs (RATEmiRs) catalogues miRNA sequencing data from 21 and 23 tissues in male and female Sprague-Dawley rats, respectively. RATEmiRs identifies tissue-enriched (TE), tissue-specific (TS), or organ-specific (OS) miRNAs via comparisons of one or more tissue or organ vs others. We provide a brief overview of RATEmiRs and present how to use it to detect miRNA expression abundance of candidate biomarkers as well as to compare the expression of miRNAs between rat and human. The database is available at https://www.niehs.nih.gov/ratemirs/.
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Affiliation(s)
- Pierre R Bushel
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA.,Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA
| | - Florian Caiment
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Han Wu
- Department of Discovery and Development Statistics, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN, USA
| | - Raegan O'Lone
- eSTAR, Health and Environmental Sciences Institute, Washington, DC, USA
| | - Frank Day
- Office of Scientific Computing, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA
| | - John Calley
- Department of TTX Bioinformatics, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN, USA
| | - Aaron Smith
- Department of Investigative Toxicology, Non-Clinical Safety Assessment and Pathology, Lilly Research Laboratories, Lilly Corporate Center, Indianapolis, IN, USA
| | - Jianying Li
- Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA.,Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA.,Kelly Government Solutions, Research Triangle Park, Durham, NC, USA
| | - Alison H Harrill
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA
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