101
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MicroRNAs in the cancer cell-to-cell communication: An insight into biological vehicles. Biomed Pharmacother 2022; 153:113449. [PMID: 36076563 DOI: 10.1016/j.biopha.2022.113449] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/10/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
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102
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Shahsavar K, Shokri E, Hosseini M. Sensitive colorimetric detection of miRNA-155 via G-quadruplex DNAzyme decorated spherical nucleic acid. Mikrochim Acta 2022; 189:357. [PMID: 36038742 DOI: 10.1007/s00604-022-05455-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 08/09/2022] [Indexed: 11/26/2022]
Abstract
Rapid and sensitive detection of biomarkers enables monitoring patients' health status and can enhance the early diagnosis of deadly diseases. In this work, we have developed a new colorimetric platform based on spherical nucleic acid (SNA) and G-quadruplex DNAzymes for the identification of specific miRNAs. The simple hybridization between the target miRNA and two capture probes (capture probe 1 located at AuNP surface and free capture probe 2) is the working principle of this biosensor. The hybridization and duplex formation among probes and miRNAs led to a significant decrease in the intensity of color change. A linear relationship between the decrease of colorimetric signal and the amount of target molecules was witnessed from 1 to 100 nM for miRNA-155. Using this method, we were able to detect concentrations of miRNA-155 as low as 0.7 nM. Furthermore, the proposed sensing platform can be utilized profitably to detect miRNA-155 in real human serum samples. We further investigated the applicability of the proposed method in a microfluidic system which displayed promising results. In this project, A G-quadruplex based SNAzyme was constructed to provide a fast and simple colorimetric method for miRNA detection. The SNAzyme actually employed as both target recognition element and catalytic nano labels for colorimetric detection.
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Affiliation(s)
- Kosar Shahsavar
- Nanobiosensors Lab, Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Ehsan Shokri
- Department of Nanotechnology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Morteza Hosseini
- Nanobiosensors Lab, Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran.
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103
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Takeuchi N, Hiratani M, Kawano R. Pattern Recognition of microRNA Expression in Body Fluids Using Nanopore Decoding at Subfemtomolar Concentrations. JACS AU 2022; 2:1829-1838. [PMID: 36032536 PMCID: PMC9400052 DOI: 10.1021/jacsau.2c00117] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This paper describes a method for detecting microRNA (miRNA) expression patterns using the nanopore-based DNA computing technology. miRNAs have shown promise as markers for cancer diagnosis due to their cancer type specificity, and therefore simple strategies for miRNA pattern recognition are required. We propose a system for pattern recognition of five types of miRNAs overexpressed in bile duct cancer (BDC). The information of miRNAs from BDC is encoded in diagnostic DNAs (dgDNAs) and decoded electrically by nanopore analysis. With this system, we succeeded in the label-free detection of miRNA expression patterns from the plasma of BDC patients. Moreover, our dgDNA-miRNA complexes can be detected at subfemtomolar concentrations, which is a significant improvement compared to previously reported limits of detection (∼10-12 M) for similar analytical platforms. Nanopore decoding of dgDNA-encoded information represents a promising tool for simple and early cancer diagnosis.
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104
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Riddell DO, Hildyard JCW, Harron RCM, Wells DJ, Piercy RJ. Longitudinal assessment of blood-borne musculoskeletal disease biomarkers in the DE50-MD dog model of Duchenne muscular dystrophy. Wellcome Open Res 2022; 6:354. [PMID: 35600245 PMCID: PMC9111359 DOI: 10.12688/wellcomeopenres.17398.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2022] [Indexed: 01/01/2024] Open
Abstract
Background: Duchenne muscular dystrophy (DMD) is a fatal muscle wasting disease caused by mutations in the dystrophin gene. Due to their phenotypic similarity to human patients, large animal models are invaluable tools for pre-clinical trials. The DE50-MD dog is a relatively new model of DMD, and carries a therapeutically-tractable mutation lying within the hotspot for human patients, making it especially valuable. Prior to conducting therapeutic trials using this novel animal model, it is essential to establish a panel of viable biomarkers. Methods: We evaluated a panel of blood-borne biomarkers of musculoskeletal disease in the DE50-MD dog. Venous blood samples were obtained monthly throughout an 18-month study period in DE50-MD (N=18) and wild-type (WT) control (N=14) dogs. A panel of potential plasma/serum biomarkers of DMD was measured and their theoretical utility in future clinical trials determined using sample size calculations. Results: Compared to WT dogs, DE50-MD dogs had substantially higher circulating creatine kinase (CK) activities, myomesin-3 (MYOM3), and the dystromiRs miR-1, miR-133a and miR-206, but significantly lower serum myostatin concentrations. An age-associated pattern, similar to that observed in DMD patients, was seen for CK and MYOM3. Sample size calculations suggested that low cohort sizes (N≤3) could be used to detect up to a 50% improvement in DE50-MD results towards WT levels for each biomarker or a combination thereof (via principal component analysis); as few as N=3 animals should enable detection of a 25% improvement using a combined biomarker approach (alpha 0.05, power 0.8). Conclusions: We have established a panel of blood-borne biomarkers that could be used to monitor musculoskeletal disease or response to a therapeutic intervention in the DE50-MD dog using low numbers of animals. The blood biomarker profile closely mimics that of DMD patients, supporting the hypothesis that this DMD model would be suitable for use in pre-clinical trials.
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Affiliation(s)
- Dominique O. Riddell
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, NW10TU, UK
| | - John C. W. Hildyard
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, NW10TU, UK
| | - Rachel C. M. Harron
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, NW10TU, UK
| | - Dominic J. Wells
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, NW10TU, UK
| | - Richard J. Piercy
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, NW10TU, UK
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105
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Riddell DO, Hildyard JCW, Harron RCM, Wells DJ, Piercy RJ. Longitudinal assessment of blood-borne musculoskeletal disease biomarkers in the DE50-MD dog model of Duchenne muscular dystrophy. Wellcome Open Res 2022; 6:354. [PMID: 35600245 PMCID: PMC9111359 DOI: 10.12688/wellcomeopenres.17398.2] [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] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Duchenne muscular dystrophy (DMD) is a fatal muscle wasting disease caused by mutations in the dystrophin gene. Due to their phenotypic similarity to human patients, large animal models are invaluable tools for pre-clinical trials. The DE50-MD dog is a relatively new model of DMD, and carries a therapeutically-tractable mutation lying within the hotspot for human patients, making it especially valuable. Prior to conducting therapeutic trials using this novel animal model, it is essential to establish a panel of viable biomarkers. Methods: We evaluated a panel of blood-borne biomarkers of musculoskeletal disease in the DE50-MD dog. Venous blood samples were obtained monthly throughout an 18-month study period in DE50-MD (N=18) and wild-type (WT) control (N=14) dogs. A panel of potential plasma/serum biomarkers of DMD was measured and their theoretical utility in future clinical trials determined using sample size calculations. Results: Compared to WT dogs, DE50-MD dogs had substantially higher circulating creatine kinase (CK) activities, myomesin-3 (MYOM3), and the dystromiRs miR-1, miR-133a and miR-206, but significantly lower serum myostatin concentrations. An age-associated pattern, similar to that observed in DMD patients, was seen for CK and MYOM3. Sample size calculations suggested that low cohort sizes (N≤3) could be used to detect up to a 50% improvement in DE50-MD results towards WT levels for each biomarker or a combination thereof (via principal component analysis); as few as N=3 animals should enable detection of a 25% improvement using a combined biomarker approach (alpha 0.05, power 0.8). Conclusions: We have established a panel of blood-borne biomarkers that could be used to monitor musculoskeletal disease or response to a therapeutic intervention in the DE50-MD dog using low numbers of animals. The blood biomarker profile closely mimics that of DMD patients, supporting the hypothesis that this DMD model would be suitable for use in pre-clinical trials.
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Affiliation(s)
- Dominique O. Riddell
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, NW10TU, UK
| | - John C. W. Hildyard
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, NW10TU, UK
| | - Rachel C. M. Harron
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, NW10TU, UK
| | - Dominic J. Wells
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, NW10TU, UK
| | - Richard J. Piercy
- Comparative Neuromuscular Diseases Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London, NW10TU, UK
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106
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Xu N, Zhou X, Shi W, Ye M, Cao X, Chen S, Xu C. Integrative analysis of circulating microRNAs and the placental transcriptome in recurrent pregnancy loss. Front Physiol 2022; 13:893744. [PMID: 35991164 PMCID: PMC9390878 DOI: 10.3389/fphys.2022.893744] [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: 03/23/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Recurrent pregnancy loss (RPL) is a major type of pathological pregnancy that still lacks reliable early diagnosis and effective treatment. The placenta is critical to fetal development and pregnancy success because it participates in critical processes such as early embryo implantation, vascular remodeling, and immunological tolerance. RPL is associated with abnormalities in the biological behavior of placental villous trophoblasts, resulting in aberrant placental function. MicroRNAs (miRNAs) are increasingly being recognized as essential regulators of placental development, as well as potential biomarkers. In this study, plasma miRNAs and placental messenger RNAs (mRNAs) from RPL patients and normal pregnant (NP) controls were sequenced and analyzed. Compared to those in NP controls, 108 circulating miRNAs and 1199 placental mRNAs were differentially expressed in RPL samples. A total of 140 overlapping genes (overlapping between plasma miRNA target genes and actual placental disorder genes) were identified, and functional enrichment analysis showed that these genes were mainly related to cell proliferation, angiogenesis, and cell migration. The regulatory network among miRNAs, overlapping genes, and downstream biological processes was analyzed by protein–protein interactions and Cytoscape. Moreover, enriched mRNAs, which were predictive targets of the differentially expressed plasma miRNAs miR-766-5p, miR-1285-3p, and miR-520a-3p, were accordingly altered in the placenta. These results suggest that circulating miRNAs may be involved in the pathogenesis of RPL and are potential noninvasive biomarkers for RPL.
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Affiliation(s)
- Naixin Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Xuanyou Zhou
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Weihui Shi
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Mujin Ye
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Xianling Cao
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Songchang Chen
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- *Correspondence: Songchang Chen, ; Chenming Xu,
| | - Chenming Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- *Correspondence: Songchang Chen, ; Chenming Xu,
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107
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Biomarkers of Frailty: miRNAs as Common Signatures of Impairment in Cognitive and Physical Domains. BIOLOGY 2022; 11:biology11081151. [PMID: 36009778 PMCID: PMC9405439 DOI: 10.3390/biology11081151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022]
Abstract
The past years have seen an increasing concern about frailty, owing to the growing number of elderly people and the major impact of this syndrome on health and social care. The identification of frail people passes through the use of different tests and biomarkers, whose concerted analysis helps to stratify the populations of patients according to their risk profile. However, their efficiency in prognosis and their capability to reflect the multisystemic impairment of frailty is discussed. Recent works propose the use of miRNAs as biological hallmarks of physiological impairment in different organismal districts. Changes in miRNAs expression have been described in biological processes associated with phenotypic outcomes of frailty, opening intriguing possibilities for their use as biomarkers of fragility. Here, with the aim of finding reliable biomarkers of frailty, while considering its complex nature, we revised the current literature on the field, for uncovering miRNAs shared across physical and cognitive frailty domains. By applying in silico analyses, we retrieved the top-ranked shared miRNAs and their targets, finally prioritizing the most significant ones. From this analysis, ten miRNAs emerged which converge into two main biological processes: inflammation and energy homeostasis. Such markers, if validated, may offer promising capabilities for early diagnosis of frailty in the elderly population.
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108
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Sattar RSA, Verma R, Nimisha, Kumar A, Dar GM, Apurva, Sharma AK, Kumari I, Ahmad E, Ali A, Mahajan B, Saluja SS. Diagnostic and prognostic biomarkers in colorectal cancer and the potential role of exosomes in drug delivery. Cell Signal 2022; 99:110413. [PMID: 35907519 DOI: 10.1016/j.cellsig.2022.110413] [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: 04/14/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/03/2022]
Abstract
Colorectal cancer (CRC) is third most common cancer with second most common cause of death worldwide. One fourth to one fifth of the CRC cases are detected at advance stage. Early detection of colorectal cancer might help in decreasing mortality and morbidity worldwide. CRC being a heterogeneous disease, new non-invasive approaches are needed to complement and improve the screening and management of CRC. Reliable and early detectable biomarkers would improve diagnosis, prognosis, therapeutic responses, and will enable the prediction of drug response and recurrence risk. Over the past decades molecular research has demonstrated the potentials of CTCs, ctDNAs, circulating mRNA, ncRNAs, and exosomes as tumor biomarkers. Non-invasive screening approaches using fecal samples for identification of altered gut microbes in CRC is also gaining attention. Exosomes can be potential candidates that can be employed in the drug delivery system. Further, the integration of in vitro, in vivo and in silico models that involve CRC biomarkers will help to understand the interactions occurring at the cellular level. This review summarizes recent update on CRC biomarkers and their application along with the nanoparticles followed by the application of organoid culture in CRC.
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Affiliation(s)
- Real Sumayya Abdul Sattar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Renu Verma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Nimisha
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Arun Kumar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ghulam Mehdi Dar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Apurva
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Abhay Kumar Sharma
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Indu Kumari
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Ejaj Ahmad
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Asgar Ali
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Bhawna Mahajan
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of Biochemistry, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Sundeep Singh Saluja
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India; Department of GI Surgery, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India.
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109
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Coradduzza D, Solinas T, Balzano F, Culeddu N, Rossi N, Cruciani S, Azara E, Maioli M, Zinellu A, De Miglio MR, Madonia M, Falchi M, Carru C. miRNAs as molecular biomarkers for prostate cancer. J Mol Diagn 2022; 24:1171-1180. [PMID: 35835374 DOI: 10.1016/j.jmoldx.2022.05.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/05/2022] [Accepted: 05/23/2022] [Indexed: 01/10/2023] Open
Abstract
MicroRNAs (miRNAs) are short noncoding RNA able to regulate specific mRNA stability, thus influencing target gene expression. Disrupted levels of several miRNA have been associated with prostate cancer, the leading cause of cancer death among men and the fifth leading cause of death worldwide. Here, we investigated whether miR-145, miR-148, and miR-185 circulating levels in plasma could be used as molecular biomarkers, to allow distinguishing between individuals with benign prostatic hyperplasia, precancerous lesion, and prostate cancer. In this study, we recruited 170 urological clinic patients with suspected prostate cancer who underwent prostate biopsy. Total RNA was isolated from plasma, and TaqMan MicroRNA assays were used to analyze miR-145, miR-185, and miR-148 expression. First, differential miRNA expression among patient groups was evaluated. Then, miRNA levels were combined with clinical assessment outcomes, including results from invasive tests, using multivariate analysis to examine their ability in discriminating among the three patient groups. Our results suggest that miRNA is a promising molecular tool for clinical management of at-risk patients.
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Affiliation(s)
| | - Tatiana Solinas
- Urologic Clinic, Dep. of Clinical and Experimental Medicine, University of Sassari
| | - Francesca Balzano
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Nicola Culeddu
- Institute of Biomolecular Chemistry, National Research Council, Sassari, Italy
| | - Niccolò Rossi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Sara Cruciani
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Emanuela Azara
- Institute of Biomolecular Chemistry, National Research Council, Sassari, Italy
| | - Margherita Maioli
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Angelo Zinellu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | | | - Massimo Madonia
- Urologic Clinic, Dep. of Clinical and Experimental Medicine, University of Sassari
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy; University Hospital of Sassari (AOU), Sassari, Italy.
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110
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Orthologs of human circulating miRNAs associated with hepatocellular carcinoma are elevated in mouse plasma months before tumour detection. Sci Rep 2022; 12:10927. [PMID: 35764780 PMCID: PMC9240017 DOI: 10.1038/s41598-022-15061-5] [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: 03/24/2022] [Accepted: 06/17/2022] [Indexed: 11/08/2022] Open
Abstract
Research examining the potential for circulating miRNA to serve as markers for preneoplastic lesions or early-stage hepatocellular carcinoma (HCC) is hindered by the difficulties of obtaining samples from asymptomatic individuals. As a surrogate for human samples, we identified hub miRNAs in gene co-expression networks using HCC-bearing C3H mice. We confirmed 38 hub miRNAs as associated with HCC in F2 hybrid mice derived from radiogenic HCC susceptible and resistant founders. When compared to a panel of 12 circulating miRNAs associated with human HCC, two had no mouse ortholog and 7 of the remaining 10 miRNAs overlapped with the 38 mouse HCC hub miRNAs. Using small RNA sequencing data generated from serially collected plasma samples in F2 mice, we examined the temporal levels of these 7 circulating miRNAs and found that the levels of 4 human circulating markers, miR-122-5p, miR-100-5p, miR-34a-5p and miR-365-3p increased linearly as the time approaching HCC detection neared, suggesting a correlation of miRNA levels with oncogenic progression. Estimation of change points in the kinetics of the 4 circulating miRNAs suggested the changes started 17.5 to 6.8 months prior to HCC detection. These data establish these 4 circulating miRNAs as potential sentinels for preneoplastic lesions or early-stage HCC.
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111
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Smith LD, Nalla S, Kuo CW, Kohli M, Smith AM. Rapid quantification of microRNA-375 through one-pot primer-generating rolling circle amplification. Analyst 2022; 147:2936-2941. [PMID: 35695478 PMCID: PMC11247439 DOI: 10.1039/d2an00263a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
A recent surge of interest in microRNA has been driven by its discovery as a circulating biomarker of disease, with many diagnostic test platforms currently under development. Alternatives to widely used microRNA quantification methods such as quantitative reverse transcriptase PCR (qRT-PCR) are needed for use in portable and point-of-care devices which are incompatible with complex sample processing workflows and thermal cycling. Rolling circle amplification (RCA) is a one-pot assay technique which directly amplifies nucleic acids using sequence-specific microRNA priming to initiate a single-step isothermal reaction that is compatible with simple devices. Sensitivity remains a limitation of RCA methods, however, and detection limits do not typically reach the femtomolar level in which microRNA targets are present in blood. RCA assays have previously been improved by digestion of the amplification products using a nicking endonuclease to exponentially generate new reaction primers. Here we describe how a ligation-free version of this technique performed in a single tube can be used to improve the limit of detection for microRNA-375, an important blood biomarker for prostate cancer. Endonuclease addition changes a linear process into an exponential amplification reaction which results in a 61-fold improvement of the limit of detection (5.9 fM), a dynamic range wider than 5-log(10), and a shorter reaction time. By eliminating the need for microRNA reverse transcription and thermal cycling, this single-step one-pot method provides a more rapid and simplified alternative to qRT-PCR for ultrasensitive microRNA quantification in blood extracts.
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Affiliation(s)
- Lucas D Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Siva Nalla
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Chia-Wei Kuo
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Manish Kohli
- Division of Oncology, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Andrew M Smith
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA.
- Micro and Nanotechnology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Materials Science & Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Carle Illinois College of Medicine, Urbana, Illinois 61801, USA
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112
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Mallette TL, Lakin MR. Protecting Heterochiral DNA Nanostructures against Exonuclease-Mediated Degradation. ACS Synth Biol 2022; 11:2222-2228. [PMID: 35749687 DOI: 10.1021/acssynbio.2c00105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heterochiral DNA nanotechnology employs nucleic acids of both chiralities to construct nanoscale devices for applications in the intracellular environment. Interacting directly with cellular nucleic acids can be done most easily using D-DNA of the naturally occurring right-handed chirality; however, D-DNA is more vulnerable to degradation than enantiometric left-handed L-DNA. Here we report a novel combination of D-DNA and L-DNA nucleotides in triblock heterochiral copolymers, where the L-DNA domains act as protective caps on D-DNA domains. We demonstrate that the D-DNA components of strand displacement-based molecular circuits constructed using this technique resist exonuclease-mediated degradation during extended incubations in serum-supplemented media more readily than similar devices without the L-DNA caps. We show that this protection can be applied to both double-stranded and single-stranded circuit components. Our work enhances the state of the art for robust heterochiral circuit design and could lead to practical applications such as in vivo biomedical diagnostics.
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Affiliation(s)
- Tracy L Mallette
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Matthew R Lakin
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States.,Department of Computer Science, University of New Mexico, Albuquerque, New Mexico 87131, United States.,Department of Chemical & Biological Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
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113
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Mousavi SM, Amin Mahdian SM, Ebrahimi MS, Taghizadieh M, Vosough M, Sadri Nahand J, Hosseindoost S, Vousooghi N, Javar HA, Larijani B, Hadjighassem MR, Rahimian N, Hamblin MR, Mirzaei H. Microfluidics for detection of exosomes and microRNAs in cancer: State of the art. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:758-791. [PMID: 35664698 PMCID: PMC9130092 DOI: 10.1016/j.omtn.2022.04.011] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exosomes are small extracellular vesicles with sizes ranging from 30-150 nanometers that contain proteins, lipids, mRNAs, microRNAs, and double-stranded DNA derived from the cells of origin. Exosomes can be taken up by target cells, acting as a means of cell-to-cell communication. The discovery of these vesicles in body fluids and their participation in cell communication has led to major breakthroughs in diagnosis, prognosis, and treatment of several conditions (e.g., cancer). However, conventional isolation and evaluation of exosomes and their microRNA content suffers from high cost, lengthy processes, difficult standardization, low purity, and poor yield. The emergence of microfluidics devices with increased efficiency in sieving, trapping, and immunological separation of small volumes could provide improved detection and monitoring of exosomes involved in cancer. Microfluidics techniques hold promise for advances in development of diagnostic and prognostic devices. This review covers ongoing research on microfluidics devices for detection of microRNAs and exosomes as biomarkers and their translation to point-of-care and clinical applications.
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Affiliation(s)
- Seyed Mojtaba Mousavi
- Department of Neuroscience and Addiction Studies, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Amin Mahdian
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Saeid Ebrahimi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
- Student Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Mohammad Taghizadieh
- Department of Pathology, School of Medicine, Center for Women’s Health Research Zahra, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 1665659911, Iran
| | - Javid Sadri Nahand
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saereh Hosseindoost
- Pain Research Center, Neuroscience Institute, Tehran University of Medical Science, Tehran, Iran
| | - Nasim Vousooghi
- Department of Applied Cell Sciences, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Research Center for Cognitive and Behavioral Sciences, Tehran University of Medical Sciences, Tehran, Iran
- Iranian National Center for Addiction Studies (INCAS), Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Akbari Javar
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahmoud Reza Hadjighassem
- Department of Neuroscience and Addiction Studies, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Brain and Spinal Cord Research Center, Imam Khomeini Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Neda Rahimian
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Michael R. Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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Chen JW, Dhahbi J. Identification of four serum miRNAs as potential markers to screen for thirteen cancer types. PLoS One 2022; 17:e0269554. [PMID: 35687572 PMCID: PMC9187062 DOI: 10.1371/journal.pone.0269554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/23/2022] [Indexed: 02/07/2023] Open
Abstract
Introduction Cancer consistently remains one of the top causes of death in the United States every year, with many cancer deaths preventable if detected early. Circulating serum miRNAs are a promising, minimally invasive supplement or even an alternative to many current screening procedures. Many studies have shown that different serum miRNAs can discriminate healthy individuals from those with certain types of cancer. Although many of those miRNAs are often reported to be significant in one cancer type, they are also altered in other cancer types. Currently, very few studies have investigated serum miRNA biomarkers for multiple cancer types for general cancer screening purposes. Method To identify serum miRNAs that would be useful in screening multiple types of cancers, microarray cancer datasets were curated, yielding 13 different types of cancer with a total of 3352 cancer samples and 2809 non-cancer samples. The samples were divided into training and validation sets. One hundred random forest models were built using the training set to select candidate miRNAs. The selected miRNAs were then used in the validation set to see how well they differentiate cancer from normal samples in an independent dataset. Furthermore, the interactions between these miRNAs and their target mRNAs were investigated. Result The random forest models achieved an average of 97% accuracy in the training set with 95% bootstrap confidence interval of 0.9544 to 0.9778. The selected miRNAs were hsa-miR-663a, hsa-miR-6802-5p, hsa-miR-6784-5p, hsa-miR-3184-5p, and hsa-miR-8073. Each miRNA exhibited high area under the curve (AUC) value using receiver operating characteristic analysis. Moreover, the combination of four out of five miRNAs achieved the highest AUC value of 0.9815 with high sensitivity of 0.9773, indicating that these miRNAs have a high potential for cancer screening. miRNA-mRNA and protein-protein interaction analysis provided insights into how these miRNAs play a role in cancer.
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Affiliation(s)
- Joe W. Chen
- California University of Science and Medicine, Colton, CA, United States of America
| | - Joseph Dhahbi
- California University of Science and Medicine, Colton, CA, United States of America
- * E-mail:
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Dysregulation of microRNAs and tRNA-derived ncRNAs in mesothelial and mesothelioma cell lines after asbestiform fiber exposure. Sci Rep 2022; 12:9181. [PMID: 35654808 PMCID: PMC9163335 DOI: 10.1038/s41598-022-13044-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/19/2022] [Indexed: 11/09/2022] Open
Abstract
Experimental evidence demonstrated that fluoro-edenite (FE) can develop chronic respiratory diseases and elicit carcinogenic effects. Environmental exposure to FE fibers is correlated with malignant pleural mesothelioma (MPM). An early diagnosis of MPM, and a comprehensive health monitoring of the patients exposed to FE fibers are two clinical issues that may be solved by the identification of specific biomarkers. We reported the microRNA (miRNA) and transfer RNA-derived non coding RNA (tRNA-derived ncRNA) transcriptome in human normal mesothelial and malignant mesothelioma cell lines exposed or not exposed to several concentration FE fibers. Furthermore, an interactive mesothelioma-based network was derived by using NetME tool. In untreated condition, the expression of miRNAs and tRNA-derived ncRNAs in tumor cells was significantly different with respect to non-tumor samples. Moreover, interesting and significant changes were found after the exposure of both cells lines to FE fibers. The network-based pathway analysis showed several signaling and metabolic pathways potentially involved in the pathogenesis of MPM. From papers analyzed by NetME, it is clear that many miRNAs can positively or negatively influence various pathways involved in MPM. For the first time, the analysis of tRNA-derived ncRNAs molecules in the context of mesothelioma has been made by using in vitro systems. Further studies will be designed to test and validate their diagnostic potential in high-risk individuals' liquid biopsies.
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Dogan B, Gumusoglu E, Ulgen E, Sezerman OU, Gunel T. Integrated bioinformatics analysis of validated and circulating miRNAs in ovarian cancer. Genomics Inform 2022; 20:e20. [PMID: 35794700 PMCID: PMC9299562 DOI: 10.5808/gi.21067] [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: 11/04/2021] [Accepted: 01/03/2022] [Indexed: 11/20/2022] Open
Abstract
Recent studies have focused on the early detection of ovarian cancer (OC) using tumor materials by liquid biopsy. The mechanisms of microRNAs (miRNAs) to impact OC and signaling pathways are still unknown. This study aims to reliably perform functional analysis of previously validated circulating miRNAs' target genes by using pathfindR. Also, overall survival and pathological stage analyses were evaluated with miRNAs' target genes which are common in the The Cancer Genome Atlas and GTEx datasets. Our previous studies have validated three downregulated miRNAs (hsa-miR-885-5p, hsa-miR-1909-5p, and hsalet7d-3p) having a diagnostic value in OC patients' sera, with high-throughput techniques. The predicted target genes of these miRNAs were retrieved from the miRDB database (v6.0). Active-subnetwork-oriented Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted by pathfindR using the target genes. Enrichment of KEGG pathways assessed by the analysis of pathfindR indicated that 24 pathways were related to the target genes. Ubiquitin-mediated proteolysis, spliceosome and Notch signaling pathway were the top three pathways with the lowest p-values (p < 0.001). Ninety-three common genes were found to be differentially expressed (p < 0.05) in the datasets. No significant genes were found to be significant in the analysis of overall survival analyses, but 24 genes were found to be significant with pathological stages analysis (p < 0.05). The findings of our study provide in-silico evidence that validated circulating miRNAs' target genes and enriched pathways are related to OC and have potential roles in theranostics applications. Further experimental investigations are required to validate our results which will ultimately provide a new perspective for translational applications in OC management.
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Affiliation(s)
- Berkcan Dogan
- Department of Medical Genetics, Faculty of Medicine, Bursa Uludag University, Bursa 16059, Turkey.,Department of Translational Medicine, Institute of Health Sciences, Bursa Uludag University, Bursa 16059, Turkey
| | - Ece Gumusoglu
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Ege Ulgen
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34750, Turkey
| | - Osman Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul 34750, Turkey
| | - Tuba Gunel
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
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Xu F, Wang Y, Ling Y, Zhou C, Wang H, Teschendorff AE, Zhao Y, Zhao H, He Y, Zhang G, Yang Z. dbDEMC 3.0: Functional Exploration of Differentially Expressed miRNAs in Cancers of Human and Model Organisms. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:446-454. [PMID: 35643191 PMCID: PMC9801039 DOI: 10.1016/j.gpb.2022.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/11/2022] [Accepted: 05/08/2022] [Indexed: 01/26/2023]
Abstract
MicroRNAs (miRNAs) are important regulators in gene expression. The dysregulation of miRNA expression is widely reported in the transformation from physiological to pathological states of cells. A large number of differentially expressed miRNAs (DEMs) have been identified in various human cancers by using high-throughput technologies, such as microarray and miRNA-seq. Through mining of published studies with high-throughput experiment information, the database of DEMs in human cancers (dbDEMC) was constructed with the aim of providing a systematic resource for the storage and query of the DEMs. Here we report an update of the dbDEMC to version 3.0, which contains two-fold more data entries than the second version and now includes also data from mice and rats. The dbDEMC 3.0 contains 3268 unique DEMs in 40 different cancer types. The current datasets for differential expression analysis have expanded to 9 generalized categories. Moreover, the current release integrates functional annotations of DEMs obtained by using experimentally validated targets. The annotations can be of great benefit to the intensive analysis of the roles of DEMs in cancer. In summary, dbDEMC 3.0 provides a valuable resource for characterizing molecular functions and regulatory mechanisms of DEMs in human cancers. The dbDEMC 3.0 is freely accessible at https://www.biosino.org/dbDEMC.
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Affiliation(s)
- Feng Xu
- Center for Medical Research and Innovation of Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 201399, China; Institutes of Biomedical Science, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai 200032, China
| | - Yifan Wang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yunchao Ling
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chenfen Zhou
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haizhou Wang
- Center for Medical Research and Innovation of Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 201399, China; Institutes of Biomedical Science, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai 200032, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yi Zhao
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Haitao Zhao
- Department of Liver Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yungang He
- Institutes of Biomedical Science, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai 200032, China; Shanghai Fifth People's Hospital, Fudan University, Shanghai 200240, China.
| | - Guoqing Zhang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Zhen Yang
- Center for Medical Research and Innovation of Pudong Hospital, Fudan University Pudong Medical Center, Shanghai 201399, China; Institutes of Biomedical Science, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Shanghai 200032, China.
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Muwonge H, Kasujja H, Niyonzima N, Atugonza C, Kasolo J, Lugaajju A, Nfambi J, Fred SL, Damani AM, Kimuli I, Zavuga R, Nakazzi F, Kigozi E, Nakanjako D, Kateete DP, Bwanga F. Unique circulating microRNA profiles in epidemic Kaposi's sarcoma. Noncoding RNA Res 2022; 7:114-122. [PMID: 35570854 PMCID: PMC9065625 DOI: 10.1016/j.ncrna.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/24/2022] [Accepted: 02/12/2022] [Indexed: 11/30/2022] Open
Abstract
Background Human herpesvirus 8 (HHV-8) causes Kaposi's sarcoma (KS). Kaposi sarcoma in HIV/AIDS patients is referred to as epidemic KS and is the most common HIV-related malignancy worldwide. The lack of a diagnostic assay to detect latent and early-stage disease has increased disease morbidity and mortality. Serum miRNAs have previously been used as potential biomarkers of normal physiology and disease. In the current study, we profiled unique serum miRNAs in patients with epidemic KS to generate baseline data to aid in developing a miRNA-based noninvasive biomarker assay for epidemic KS. Methods This was a comparative cross-sectional study involving 27 patients with epidemic KS and 27 HIV-positive adults with no prior diagnosis or clinical manifestation of KS. DNA and RNA were isolated from blood and serum collected from study participants. Nested PCR for circulating HHV-8 DNA was performed on the isolated DNA, whereas miRNA library preparation and sequencing for circulating miRNA were performed on the RNA samples. The miRge2 pipeline and EdgeR were used to analyse the sequencing data. Results Fifteen out of the 27 epidemic KS-positive subjects (55.6%) tested positive for HHV-8 DNA, whereas only 3 (11.1%) out of the 27 HIV-positive, KS-negative subjects tested positive for HHV-8 DNA. Additionally, we found a unique miRNA expression signature in 49 circulating miRNAs in epidemic KS subjects compared to subjects with no epidemic KS, with 41 miRNAs upregulated and 8 miRNAs downregulated. Subjects with latent KS infection had a differential upregulation of circulating miR-193a compared to HIV-positive, KS-negative subjects for whom circulating HHV-8 DNA was not detected. Further analysis of serum from epidemic KS patients revealed a miRNA signature according to KS tumor status and time since first HIV diagnosis. Conclusions This study reveals unique circulating miRNA profiles in the serum of patients with epidemic KS versus HIV-infected subjects with no KS, as well as in subjects with latent KS. Many of the dysregulated miRNAs in epidemic KS patients were previously reported to have crucial roles in KS infection and latency, highlighting their promising roles as potential biomarkers of latent or active KS infection.
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Affiliation(s)
- Haruna Muwonge
- Department of Physiology, School of Biomedical Sciences, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
- Habib Medical School, Islamic University in Uganda (IUIU), Uganda
| | - Hassan Kasujja
- Department of Physiology, School of Biomedical Sciences, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
| | - Nixon Niyonzima
- Uganda Cancer Institute (UCI)-Fred Hutch Collaboration, P. O Box 3935, Kampala, Uganda
| | - Carolyne Atugonza
- Medical and Molecular Laboratories, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
| | - Josephine Kasolo
- Department of Physiology, School of Biomedical Sciences, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
| | - Allan Lugaajju
- Department of Physiology, School of Biomedical Sciences, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
| | - Joshua Nfambi
- Department of Physiology, School of Biomedical Sciences, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
| | - Sembajwe Larry Fred
- Department of Physiology, School of Biomedical Sciences, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
| | - Ali Moses Damani
- Department of Physiology, School of Biomedical Sciences, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
| | - Ivan Kimuli
- Department of Physiology, School of Biomedical Sciences, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
| | - Robert Zavuga
- Uganda Peoples Defence forces (UPDF), P. O Box 123, Bombo, Uganda
| | - Faith Nakazzi
- Medical and Molecular Laboratories, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
| | - Edgar Kigozi
- Medical and Molecular Laboratories, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
| | - Damalie Nakanjako
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
| | - David Patrick Kateete
- Medical and Molecular Laboratories, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
| | - Freddie Bwanga
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, P. O Box 7072, Kampala, Uganda
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Carbon Electrodes with Gold Nanoparticles for the Electrochemical Detection of miRNA 21-5p. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10050189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Extracellular vesicles are involved in many physiological and pathological activities. They transport miRNAs to recipient cells during their role in intercellular communication, making them emerging biomarkers of many diseases. Interest in exosomal miRNAs has grown after they have shown numerous advantages as biomarkers for diagnosis, prognosis, and evaluation of cancer treatment. This work describes the development of a biosensor for the detection of 21-5p miRNA in human serum using screen-printed carbon electrodes modified with gold nanoparticles fabricated in situ, an innovative approach to avoid the use of more expensive gold substrates that provide better analytical outputs. The several variables involved in the assembly of the biosensor were optimized by univariant mode. Under the best conditions, the biosensor showed a linear response from 0.010 fM to 10 pM, with a limit of detection (LOD) of 4.31 aM. The sensitivity was 0.3718 relative Ω per decade concentration in buffered saline solutions, and the standard deviation of the blank is 2.94 Ω. A linear response was also obtained when human serum samples were tested with miRNA 21-5p. Interference from similar miRNA and miss-match miRNA sequences was evaluated and good selectivity for miRNA 21-5p was observed. Overall, the device proposed is an alternative approach to gold substrates, which typically result in more sensitive systems and lower LODs, which compares favorably to current gold-based biosensors for the targeted miRNA. This design may be further extended to other nucleic acids.
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Exploring Endothelial Colony-Forming Cells to Better Understand the Pathophysiology of Disease: An Updated Review. Stem Cells Int 2022; 2022:4460041. [PMID: 35615696 PMCID: PMC9126670 DOI: 10.1155/2022/4460041] [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: 01/06/2022] [Revised: 04/20/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022] Open
Abstract
Endothelial cell (EC) dysfunction has been implicated in a variety of pathological conditions. The collection of ECs from patients is typically conducted postmortem or through invasive procedures, such as surgery and interventional procedures, hampering efforts to clarify the role of ECs in disease onset and progression. In contrast, endothelial colony-forming cells (ECFCs), also termed late endothelial progenitor cells, late outgrowth endothelial cells, blood outgrowth endothelial cells, or endothelial outgrowth cells, are obtained in a minimally invasive manner, namely, by the culture of human peripheral blood mononuclear cells in endothelial growth medium. ECFCs resemble mature ECs phenotypically, genetically, and functionally, making them excellent surrogates for ECs. Numerous studies have been performed that examined ECFC function in conditions such as coronary artery disease, diabetes mellitus, hereditary hemorrhagic telangiectasia, congenital bicuspid aortic valve disease, pulmonary arterial hypertension, venous thromboembolic disease, and von Willebrand disease. Here, we provide an updated review of studies using ECFCs that were performed to better understand the pathophysiology of disease. We also discuss the potential of ECFCs as disease biomarkers and the standardized methods to culture, quantify, and evaluate ECFCs and suggest the future direction of research in this field.
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Wang G, Yan G, Sang K, Yang H, Sun N, Bai Y, Xu F, Zheng X, Chen Z. Circulating lnc-LOC as a novel noninvasive biomarker in the treatment surveillance of acute promyelocytic leukaemia. BMC Cancer 2022; 22:481. [PMID: 35501730 PMCID: PMC9059359 DOI: 10.1186/s12885-022-09621-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 04/29/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Acute promyelocytic leukaemia (APL) is a unique subtype of acute myeloid leukaemia (AML) characterized by haematopoietic failure caused by the accumulation of abnormal promyelocytic cells in bone marrow (BM). However, indispensable BM biopsy frequently afflicts patients in leukaemia surveillance, which increases the burden on patients and reduces compliance. This study aimed to explore whether the novel circulating long noncoding RNA LOC100506453 (lnc-LOC) could be a target in diagnosis, assess the treatment response and supervise the minimal residual disease (MRD) of APL, thereby blazing a trail in noninvasive lncRNA biomarkers of APL. METHODS Our study comprised 100 patients (40 with APL and 60 with non-APL AML) and 60 healthy donors. BM and peripheral blood (PB) sample collection was accomplished from APL patients at diagnosis and postinduction. Quantitative real-time PCR (qRT-PCR) was conducted to evaluate lnc-LOC expression. A receiver operating characteristic (ROC) analysis was implemented to analyse the value of lnc-LOC in the diagnosis of APL and treatment monitoring. For statistical analysis, the Mann-Whitney U test, a t test, and Spearman's rank correlation test were utilized. RESULTS Our results showed that BM lnc-LOC expression was significantly different between APL and healthy donors and non-APL AML. lnc-LOC was drastically downregulated in APL patients' BM after undergoing induction therapy. Lnc-LOC was upregulated in APL cell lines and downregulated after all-trans retinoic acid (ATRA)-induced myeloid differentiation, preliminarily verifying that lnc-LOC has the potential to be considered a treatment monitoring biomarker. PB lnc-LOC was positively correlated with BM lnc-LOC in APL patients, non-APL AML patients and healthy donors and decreased sharply after complete remission (CR). However, upregulated lnc-LOC was manifested in relapsed-refractory patients. A positive correlation was revealed between PB lnc-LOC and PML-RARα transcript levels in BM samples. Furthermore, we observed a positive correlation between PB lnc-LOC and BM lnc-LOC expression in APL patients, suggesting that lnc-LOC can be utilized as a noninvasive biomarker for MRD surveillance. CONCLUSIONS Our study demonstrated that PB lnc-LOC might serve as a novel noninvasive biomarker in the treatment surveillance of APL, and it innovated the investigation and application of newly found lncRNAs in APL noninvasive biomarkers used in diagnosis and detection.
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MESH Headings
- Biomarkers
- Bone Marrow/pathology
- Case-Control Studies
- Humans
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Promyelocytic, Acute/diagnosis
- Leukemia, Promyelocytic, Acute/drug therapy
- Leukemia, Promyelocytic, Acute/genetics
- Neoplasm, Residual/genetics
- RNA, Long Noncoding/blood
- RNA, Long Noncoding/genetics
- Tretinoin/pharmacology
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Affiliation(s)
- Guiran Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xueyuan Xi Road, Wenzhou, Zhejiang, 325000, P.R. China
| | - Guiling Yan
- Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xueyuan Xi Road, Wenzhou, Zhejiang, 325000, P.R. China
| | - Kanru Sang
- Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xueyuan Xi Road, Wenzhou, Zhejiang, 325000, P.R. China
- The First School of Clinical Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325000, P.R. China
| | - Huijie Yang
- Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xueyuan Xi Road, Wenzhou, Zhejiang, 325000, P.R. China
- Department of Clinical Laboratory, Fengxian Hospital Affiliated to Southern Medical University, Nanfeng Road 6600, Shanghai, 201499, P.R. China
| | - Ni Sun
- Department of Haematology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325000, P.R. China
| | - Yuanyuan Bai
- Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xueyuan Xi Road, Wenzhou, Zhejiang, 325000, P.R. China
| | - Feng Xu
- School of Laboratory Medicine and Life Sciences, The Key Laboratory of Laboratory Medicine, Wenzhou Medical University, Ministry of Education of China, Wenzhou, Zhejiang, 325035, P.R. China
| | - Xiaoqun Zheng
- Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xueyuan Xi Road, Wenzhou, Zhejiang, 325000, P.R. China.
- School of Laboratory Medicine and Life Sciences, The Key Laboratory of Laboratory Medicine, Wenzhou Medical University, Ministry of Education of China, Wenzhou, Zhejiang, 325035, P.R. China.
| | - Zhanguo Chen
- Department of Clinical Laboratory, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xueyuan Xi Road, Wenzhou, Zhejiang, 325000, P.R. China.
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Wang Q, Li F, Liang Z, Liao H, Zhang B, Lin P, Liu X, Hu S, Lee J, Ling D. A K+-sensitive AND-gate dual-mode probe for simultaneous tumor imaging and malignancy identification. Natl Sci Rev 2022; 9:nwac080. [PMID: 35832777 PMCID: PMC9273306 DOI: 10.1093/nsr/nwac080] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/28/2022] [Accepted: 02/14/2022] [Indexed: 11/13/2022] Open
Abstract
Although molecular imaging probes have the potential to non-invasively diagnose a tumor, imaging probes that can detect a tumor and simultaneously identify tumor malignancy remain elusive. Here, we demonstrate a potassium ion (K+) sensitive dual-mode nanoprobe (KDMN) for non-invasive tumor imaging and malignancy identification, which operates via a cascaded ‘AND’ logic gate controlled by inputs of magnetic resonance imaging (MRI) and fluorescence imaging (FI) signals. We encapsulate commercial K+ indicators into the hollow cavities of magnetic mesoporous silica nanoparticles, which are subsequently coated with a K+-selective membrane that exclusively permits the passage of K+ while excluding other cations. The KDMN can readily accumulate in tumors and enhance the MRI contrast after systemic administration. Spatial information of the tumor lesion is thus accessible via MRI and forms the first layer of the ‘AND’ gate. Meanwhile, the KDMN selectively captures K+ and prevents interference from other cations, triggering a K+-activated FI signal as the second layer of the ‘AND’ gate in the case of a malignant tumor with a high extracellular K+ level. This dual-mode imaging approach effectively eliminates false positive or negative diagnostic results and allows for non-invasive imaging of tumor malignancy with high sensitivity and accuracy.
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Affiliation(s)
- Qiyue Wang
- Institute of Pharmaceutics, Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, China
| | - Fangyuan Li
- Institute of Pharmaceutics, Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, China
- WLA Laboratories, Shanghai201203, China
| | - Zeyu Liang
- Institute of Pharmaceutics, Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, China
| | - Hongwei Liao
- Institute of Pharmaceutics, Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, China
| | - Bo Zhang
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
- WLA Laboratories, Shanghai201203, China
| | - Peihua Lin
- Institute of Pharmaceutics, Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, China
| | - Xun Liu
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
- WLA Laboratories, Shanghai201203, China
| | - Shen Hu
- Department of Obstetrics, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou310000, China
| | - Jiyoung Lee
- Institute of Pharmaceutics, Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, China
| | - Daishun Ling
- Institute of Pharmaceutics, Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou310058, China
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai200240, China
- WLA Laboratories, Shanghai201203, China
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Bakhsh T, Alhazmi S, Alburae NA, Farsi A, Alzahrani F, Choudhry H, Bahieldin A. Exosomal miRNAs as a Promising Source of Biomarkers in Colorectal Cancer Progression. Int J Mol Sci 2022; 23:ijms23094855. [PMID: 35563246 PMCID: PMC9103063 DOI: 10.3390/ijms23094855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 01/27/2023] Open
Abstract
Colorectal cancer (CRC) is the third most common type of cancer worldwide amongst males and females. CRC treatment is multidisciplinary, often including surgery, chemotherapy, and radiotherapy. Early diagnosis of CRC can lead to treatment initiation at an earlier stage. Blood biomarkers are currently used to detect CRC, but because of their low sensitivity and specificity, they are considered inadequate diagnostic tools and are used mainly for following up patients for recurrence. It is necessary to detect novel, noninvasive, specific, and sensitive biomarkers for the screening and diagnosis of CRC at earlier stages. The tumor microenvironment (TME) has an essential role in tumorigenesis; for example, extracellular vesicles (EVs) such as exosomes can play a crucial role in communication between cancer cells and different components of TME, thereby inducing tumor progression. The importance of miRNAs that are sorted into exosomes has recently attracted scientists’ attention. Some unique sequences of miRNAs are favorably packaged into exosomes, and it has been illustrated that particular miRNAs can be directed into exosomes by special mechanisms that occur inside the cells. This review illustrates and discusses the sorted and transported exosomal miRNAs in the CRC microenvironment and their impact on CRC progression as well as their potential use as biomarkers.
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Affiliation(s)
- Tahani Bakhsh
- Department of Biology, Faculty of Science, Jeddah University, Jeddah 21589, Saudi Arabia
- Correspondence:
| | - Safiah Alhazmi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.); (N.A.A.); (A.B.)
| | - Najla Ali Alburae
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.); (N.A.A.); (A.B.)
| | - Ali Farsi
- Department of Surgry, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Faisal Alzahrani
- King Fahd Medical Research Center, Embryonic Stem Cells Unit, Department of Biochemistry, Faculty of Science, King AbdulAziz University, Jeddah 21589, Saudi Arabia;
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Hani Choudhry
- Centre of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (S.A.); (N.A.A.); (A.B.)
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Micro-RNA-215 and -375 regulate thymidylate synthase protein expression in pleural mesothelioma and mediate epithelial to mesenchymal transition. Virchows Arch 2022; 481:233-244. [PMID: 35461395 PMCID: PMC9343276 DOI: 10.1007/s00428-022-03321-8] [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: 08/21/2021] [Revised: 04/03/2022] [Accepted: 04/05/2022] [Indexed: 11/15/2022]
Abstract
The standard front-line treatment for pleural mesothelioma (PM) is pemetrexed-based chemotherapy, whose major target is thymidylate synthase (TS). In several cancer models, miR-215 and miR-375 have been shown to target TS, while information on these miRNAs in PM are still limited although suggest their role in epithelial to mesenchymal transition. Seventy-one consecutive PM tissues (4 biphasic, 7 sarcomatoid, and 60 epithelioid types) and 16 commercial and patient-derived PM cell lines were screened for TS, miR-215, and miR-375 expression. REN and 570B cells were selected for miR-215 and miR-375 transient transfections to test TS modulation. ZEB1 protein expression in tumor samples was also tested. Moreover, genetic profile was investigated by means of BAP1 and p53 immunohistochemistry. Expression of both miR-215 and miR-375 was significantly higher in epithelioid histotype. Furthermore, inverse correlation between TS protein and both miR-215 and miR-375 expression was found. Efficiently transfected REN and 570B cell lines overexpressing miR-215 and miR-375 showed decreased TS protein levels. Epithelioid PM with a mesenchymal component highlighted by reticulin stain showed significantly higher TS and ZEB1 protein and lower miRNA expression. A better survival was recorded for BAP1 lost/TS low cases. Our data indicate that miR-215 and miR-375 are involved in TS regulation as well as in epithelial-to-mesenchymal transition in PM.
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125
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Yu SY, Koh EJ, Kim SH, Song B, Lee JS, Son SW, Seo H, Hwang SY. Analysis of multi-omics data on the relationship between epigenetic changes and nervous system disorders caused by exposure to environmentally harmful substances. ENVIRONMENTAL TOXICOLOGY 2022; 37:802-813. [PMID: 34921580 DOI: 10.1002/tox.23444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/12/2021] [Accepted: 12/11/2021] [Indexed: 06/14/2023]
Abstract
Environmentally hazardous substances and exposure to these can cause various diseases. Volatile organic compounds can easily evaporate into the atmosphere, thereby exerting toxic effects through either the skin or respiratory tract exposures. Toluene, a neurotoxin, has been widely used in various industries. However, it has a detrimental effect on the nervous system (such as hallucinations or memory impairment), while data on the mechanism underlaying its harmful effects remain limited. Therefore, this study investigates the effect of toluene on the nervous system via epigenetic and genetic changes of toluene-exposed individuals. We identified significant epigenetic changes and confirmed that the affected abnormally expressed genes negatively influenced the nervous system. In particular, we confirmed that the miR-15 family, upregulated by toluene, downregulated ABL2, which could affect the R as signaling pathway resulting in neuronal structural abnormalities. Our study suggests that miR-15a-5p, miR-15b-5p, miR-16-5p, miR-301a-3p, and lncRNA NEAT1 may represent effective epigenomic markers associated with neurodegenerative diseases caused by toluene.
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Affiliation(s)
- So Yeon Yu
- Department of Molecular & Life Science, Hanyang University, Ansan, South Korea
| | - Eun Jung Koh
- Department of Bionano Engineering, Hanyang University, Ansan, South Korea
| | - Seung Hwan Kim
- Department of Bionano Engineering, Hanyang University, Ansan, South Korea
| | - Byeongwook Song
- Department of Molecular & Life Sciences, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, South Korea
| | - Ji Su Lee
- Department of Molecular & Life Science, Hanyang University, Ansan, South Korea
| | - Sang Wook Son
- Department of Dermatology, Korea University College of Medicine, Seoul, South Korea
| | - Hyemyung Seo
- Department of Molecular & Life Sciences, Center for Bionano Intelligence Education and Research, Hanyang University, Ansan, South Korea
| | - Seung Yong Hwang
- Department of Molecular & Life Science, Hanyang University, Ansan, South Korea
- Department of Applied Artificial Intelligence, Hanyang University, Ansan, South Korea
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Petroušková P, Hudáková N, Maloveská M, Humeník F, Cizkova D. Non-Exosomal and Exosome-Derived miRNAs as Promising Biomarkers in Canine Mammary Cancer. Life (Basel) 2022; 12:life12040524. [PMID: 35455015 PMCID: PMC9032658 DOI: 10.3390/life12040524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/06/2023] Open
Abstract
Canine mammary cancer (CMC), similar to human breast cancer (HBC) in many aspects, is the most common neoplasm associated with significant mortality in female dogs. Due to the limited therapy options, biomarkers are highly desirable for early clinical diagnosis or cancer progression monitoring. Since the discovery of microRNAs (miRNAs or miRs) as post-transcriptional gene regulators, they have become attractive biomarkers in oncological research. Except for intracellular miRNAs and cell-free miRNAs, exosome-derived miRNAs (exomiRs) have drawn much attention in recent years as biomarkers for cancer detection. Analysis of exosomes represents a non-invasive, pain-free, time- and money-saving alternative to conventional tissue biopsy. The purpose of this review is to provide a summary of miRNAs that come from non-exosomal sources (canine mammary tumor, mammary tumor cell lines or canine blood serum) and from exosomes as promising biomarkers of CMC based on the current literature. As is discussed, some of the miRNAs postulated as diagnostic or prognostic biomarkers in CMC were also altered in HBC (such as miR-21, miR-29b, miR-141, miR-429, miR-200c, miR-497, miR-210, miR-96, miR-18a, miR19b, miR-20b, miR-93, miR-101, miR-105a, miR-130a, miR-200c, miR-340, miR-486), which may be considered as potential disease-specific biomarkers in both CMC and HBC.
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Affiliation(s)
- Patrícia Petroušková
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Nikola Hudáková
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Marcela Maloveská
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Filip Humeník
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
| | - Dasa Cizkova
- Centre of Experimental and Clinical Regenerative Medicine, The University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice, Slovakia; (P.P.); (N.H.); (M.M.); (F.H.)
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dúbravská Cesta 9, 845 10 Bratislava, Slovakia
- Correspondence: ; Tel.: +421-918-752-157
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127
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Mirzajani E, Vahidi S, Norollahi SE, Samadani AA. Novel biomarkers of microRNAs in gastric cancer; an overview from diagnosis to treatment. Microrna 2022; 11:12-24. [PMID: 35319404 DOI: 10.2174/2211536611666220322160242] [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: 09/22/2021] [Revised: 12/06/2021] [Accepted: 12/28/2021] [Indexed: 11/22/2022]
Abstract
The fourth frequent disease in the world and the second cause of cancer-related death is gastric cancer (GC). In this way, over 80% of diagnoses are made in the middle to advanced degrees of the disease, underscoring the requirement for innovative biomarkers that can be identified quickly. Meaningly, biomarkers that can complement endoscopic diagnosis and be used to detect patients with a high risk of GC are desperately needed. These biomarkers will allow for the accurate prediction of therapy response and prognosis in GC patients, as well as the development of an optimal treatment strategy for each individual. Conspicoiusly, microRNAs (miRNAs) and small noncoding RNA regulates the expression of target mRNA and thereby modifies critical biological mechanisms. According to the data, abnormally miRNAs expression in GC is linked to tumor growth, carcinogenesis, aggression and distant metastasis. Importantly, miRNA expression patterns and next-generation sequencing (NGS) can also be applied to analyze kinds of tissues and cancers. Given the high death rates and poor prognosis of GC, and the absence of a clinical diagnostic factor that is adequately sensitive to GC, research into novel sensitive and specific markers for GC diagnosis is critical. In this review,we evaluate the latest research findings that suggest the feasibility and clinical utility of miRNAs in GC.
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Affiliation(s)
- Ebrahim Mirzajani
- Department of Biochemistry, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Cellular and Molecular Research Center, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Sogand Vahidi
- Clinical Research Development Unit of Poursina Hospital, Guilan University of Medical Sciences, Rasht, Iran
| | - Seyedeh Elham Norollahi
- Cancer Research Center and Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Guilan University of Medical Sciences, Rasht, Iran
- Clinical Research Development Unit of Poursina Hospital, Guilan University of Medical Sciences, Rasht, Iran
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128
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Bagheri M, Sarabi PZ, Mondanizadeh M. The role of miRNAs as a big master regulator of signaling pathways involved in lymphoblastic leukemia. J Cell Physiol 2022; 237:2128-2139. [PMID: 35315068 DOI: 10.1002/jcp.30720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/02/2022] [Accepted: 02/18/2022] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) belong to small noncoding RNAs, which have long attracted researchers' attention because of their potency in acting either as oncogenes or tumor-suppressors in cancers. acute lymphocytic leukemia (ALL) and chronic lymphocytic leukemia (CLL) are two known types of leukemia with high mortality rates in adults and children. On a molecular basis, various signaling pathways are active in both types, making researchers consider the potential role of miRNAs in activating or suppressing these pathways to further hinder cancer development. In this review, we summarized the potential miRNAs, especially circulating ones, involved in essential signaling pathways in the ALL and CLL patients which serve as biomarkers and valuable targets in the treatment fields.
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Affiliation(s)
- Malihe Bagheri
- Department of Biotechnology and Molecular Medicine, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Parisa Zia Sarabi
- Department of Biotechnology and Molecular Medicine, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
| | - Mahdieh Mondanizadeh
- Department of Biotechnology and Molecular Medicine, Faculty of Medicine, Arak University of Medical Sciences, Arak, Iran
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Stojkovic G, Jovanovic I, Dimitrijevic M, Jovanovic J, Tomanovic N, Stankovic A, Arsovic N, Boricic I, Zeljic K. The meta-signature guided investigation of miRNA candidates as potential biomarkers of oral cancer. Oral Dis 2022; 29:1550-1564. [PMID: 35262985 DOI: 10.1111/odi.14185] [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: 09/29/2021] [Revised: 02/25/2022] [Accepted: 03/04/2022] [Indexed: 11/30/2022]
Abstract
OBJECTIVES This study aimed to experimentally validate dysregulated expression of miRNA candidates selected through updated meta-analysis of most commonly deregulated miRNAs in oral cancer and to explore their diagnostic and prognostic potential. MATERIALS AND METHODS Five miRNAs (miR-31-3p, miR-135b-5p, miR-18a-5p, miR-30a-5p, miR-139-5p) from updated meta-signature were selected for validation by qRT-PCR method in 35 oral cancer clinical specimens and adjacent non-cancerous tissue. RESULTS Updated meta-analysis has identified 13 most commonly deregulated miRNAs in oral cancer. Seven miRNAs were consistently up-regulated (miR-21-5p, miR-31-3p, miR-135b-5p, miR-31-5p, miR-424-5p, miR-18a-5p, miR-21-3p), while five were down-regulated (miR-139-5p, miR-30a-3p, miR-375-3p, miR-376c-3p, miR-30a-5p). Increased expression of miR-31-3p, miR-135b-5p, as well as decreased expression of miR-139-5p and miR-30a-5p were confirmed in oral cancer compared to adjacent non-cancerous tissue. A three-miRNAs combination (miR-31-3p, miR-139-5p, miR-30a-5p) gave the most promising diagnostic potential for discriminating oral cancer from non-cancerous tissue (AUC: 0.780 (95% CI: 0.673-0.886), p<0.0005, sensitivity 94.3%, specificity 51.4%). High expression of miR-135b-5p, miR-18a-5p and miR-30a-5p was associated with poor survival (p=0.003, p=0.048, p=0.016, respectively). CONCLUSION miR-31-3p, miR-139-5p, miR-30a-5p panel was confirmed as a potential diagnostic biomarker when distinguishing oral cancer from non-cancerous tissue. miR-135b-5p, miR-18a-5p and miR-30a-5p might serve as potential biomarkers of poor survival of oral cancer patients.
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Affiliation(s)
- Goran Stojkovic
- Clinic for Otorhinolaryngology and Maxillofacial Surgery, University Clinical Center Serbia, Belgrade, Serbia.,Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivan Jovanovic
- VINČA" Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Milovan Dimitrijevic
- Clinic for Otorhinolaryngology and Maxillofacial Surgery, University Clinical Center Serbia, Belgrade, Serbia.,Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Nada Tomanovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Aleksandra Stankovic
- VINČA" Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Nenad Arsovic
- Clinic for Otorhinolaryngology and Maxillofacial Surgery, University Clinical Center Serbia, Belgrade, Serbia.,Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Ivan Boricic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Katarina Zeljic
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
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130
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Chakraborty A, Ghosh S, Biswas B, Pramanik S, Nriagu J, Bhowmick S. Epigenetic modifications from arsenic exposure: A comprehensive review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 810:151218. [PMID: 34717984 DOI: 10.1016/j.scitotenv.2021.151218] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 06/13/2023]
Abstract
Arsenic is a notorious element with the potential to harm exposed individuals in ways that include cancerous and non-cancerous health complications. Millions of people across the globe (especially in South and Southeast Asian countries including China, Vietnam, India and Bangladesh) are currently being unknowingly exposed to precarious levels of arsenic. Among the diverse effects associated with such arsenic levels of exposure is the propensity to alter the epigenome. Although a large volume of literature exists on arsenic-induced genotoxicity, cytotoxicity, and inter-individual susceptibility due to active research on these subject areas from the last millennial, it is only recently that attention has turned on the ramifications and mechanisms of arsenic-induced epigenetic changes. The present review summarizes the possible mechanisms involved in arsenic induced epigenetic alterations. It focuses on the mechanisms underlying epigenome reprogramming from arsenic exposure that result in improper cell signaling and dysfunction of various epigenetic components. The mechanistic information articulated from the review is used to propose a number of novel therapeutic strategies with a potential for ameliorating the burden of worldwide arsenic poisoning.
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Affiliation(s)
- Arijit Chakraborty
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute (NEERI), Kolkata, West Bengal 700107, India
| | - Soma Ghosh
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute (NEERI), Kolkata, West Bengal 700107, India
| | - Bratisha Biswas
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute (NEERI), Kolkata, West Bengal 700107, India
| | - Sreemanta Pramanik
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute (NEERI), Kolkata, West Bengal 700107, India
| | - Jerome Nriagu
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, 109 Observatory Street, Ann Arbor, MI 48109-2029, USA
| | - Subhamoy Bhowmick
- Kolkata Zonal Center, CSIR-National Environmental Engineering Research Institute (NEERI), Kolkata, West Bengal 700107, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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131
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Desai S, Dharavath B, Manavalan S, Rane A, Redhu A, Sunder R, Butle A, Mishra R, Joshi A, Togar T, Apte S, Bala P, Chandrani P, Chopra S, Bashyam M, Banerjee A, Prabhash K, Nair S, Dutt A. Fusobacterium nucleatum is associated with inflammation and poor survival in early-stage HPV-negative tongue cancer. NAR Cancer 2022; 4:zcac006. [PMID: 35252868 PMCID: PMC8894079 DOI: 10.1093/narcan/zcac006] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/03/2022] [Accepted: 02/16/2022] [Indexed: 02/05/2023] Open
Abstract
Persistent pathogen infection is a known cause of malignancy, although with sparse systematic evaluation across tumor types. We present a comprehensive landscape of 1060 infectious pathogens across 239 whole exomes and 1168 transcriptomes of breast, lung, gallbladder, cervical, colorectal, and head and neck tumors. We identify known cancer-associated pathogens consistent with the literature. In addition, we identify a significant prevalence of Fusobacterium in head and neck tumors, comparable to colorectal tumors. The Fusobacterium-high subgroup of head and neck tumors occurs mutually exclusive to human papillomavirus, and is characterized by overexpression of miRNAs associated with inflammation, elevated innate immune cell fraction and nodal metastases. We validate the association of Fusobacterium with the inflammatory markers IL1B, IL6 and IL8, miRNAs hsa-mir-451a, hsa-mir-675 and hsa-mir-486-1, and MMP10 in the tongue tumor samples. A higher burden of Fusobacterium is also associated with poor survival, nodal metastases and extracapsular spread in tongue tumors defining a distinct subgroup of head and neck cancer.
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Affiliation(s)
- Sanket Desai
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Bhasker Dharavath
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Sujith Manavalan
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Aishwarya Rane
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Archana Kumari Redhu
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Roma Sunder
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Ashwin Butle
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Rohit Mishra
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Asim Joshi
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Trupti Togar
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Shruti Apte
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Pratyusha Bala
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad500039, Telangana, India
| | - Pratik Chandrani
- Integrated Cancer Genomics Laboratory, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
| | - Supriya Chopra
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, Maharashtra, India
- Department of Radiation Oncology, Advanced Centre for Treatment, Research, and Education in Cancer, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Murali Dharan Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad500039, Telangana, India
| | - Anirban Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Kumar Prabhash
- Department of Medical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai 400012, Maharashtra, India
| | - Sudhir Nair
- Division of Head and Neck Oncology, Department of Surgical Oncology, Tata Memorial Hospital, Tata Memorial Centre, Mumbai 400012, Maharashtra, India
| | - Amit Dutt
- To whom correspondence should be addressed. Tel: +91 22 27405056/30435056;
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A Review of Biosensors for Detecting Tumor Markers in Breast Cancer. Life (Basel) 2022; 12:life12030342. [PMID: 35330093 PMCID: PMC8955405 DOI: 10.3390/life12030342] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 12/21/2022] Open
Abstract
Breast cancer has the highest cancer incidence rate in women. Early screening of breast cancer can effectively improve the treatment effect of patients. However, the main diagnostic techniques available for the detection of breast cancer require the corresponding equipment, professional practitioners, and expert analysis, and the detection cost is high. Tumor markers are a kind of active substance that can indicate the existence and growth of the tumor. The detection of tumor markers can effectively assist the diagnosis and treatment of breast cancer. The conventional detection methods of tumor markers have some shortcomings, such as insufficient sensitivity, expensive equipment, and complicated operations. Compared with these methods, biosensors have the advantages of high sensitivity, simple operation, low equipment cost, and can quantitatively detect all kinds of tumor markers. This review summarizes the biosensors (2013–2021) for the detection of breast cancer biomarkers. Firstly, the various reported tumor markers of breast cancer are introduced. Then, the development of biosensors designed for the sensitive, stable, and selective recognition of breast cancer biomarkers was systematically discussed, with special attention to the main clinical biomarkers, such as human epidermal growth factor receptor-2 (HER2) and estrogen receptor (ER). Finally, the opportunities and challenges of developing efficient biosensors in breast cancer diagnosis and treatment are discussed.
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Sousa DA, Carneiro M, Ferreira D, Moreira FTC, Sales MGFV, Rodrigues LR. Recent advances in the selection of cancer-specific aptamers for the development of biosensors. Curr Med Chem 2022; 29:5850-5880. [PMID: 35209816 DOI: 10.2174/0929867329666220224155037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/30/2021] [Accepted: 12/19/2021] [Indexed: 11/22/2022]
Abstract
An early diagnosis has the potential to greatly decrease cancer mortality. For that purpose, specific cancer biomarkers have been molecularly targeted by aptamer sequences to enable an accurate and rapid detection. Aptamer-based biosensors for cancer diagnostics are a promising alternative to those using antibodies, due to their high affinity and specificity to the target molecules and advantageous production. Synthetic nucleic acid aptamers are generated by in vitro Systematic Evolution of Ligands by Exponential enrichment (SELEX) methodologies that have been improved over the years to enhance the efficacy and to shorten the selection process. Aptamers have been successfully applied in electrochemical, optical, photoelectrochemical and piezoelectrical-based detection strategies. These aptasensors comprise a sensitive, accurate and inexpensive option for cancer detection being used as point-of-care devices. This review highlights the recent advances in cancer biomarkers, achievements and optimizations made in aptamer selection, as well as the different aptasensors developed for the detection of several cancer biomarkers.
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Affiliation(s)
- Diana A Sousa
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- MIT-Portugal Program, Lisbon, Portugal
| | - Mariana Carneiro
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- BioMark@ISEP, School of Engineering, Polytechnic of Porto, Porto, Portugal
| | - Débora Ferreira
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- MIT-Portugal Program, Lisbon, Portugal
| | - Felismina T C Moreira
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- BioMark@ISEP, School of Engineering, Polytechnic of Porto, Porto, Portugal
| | - Maria Goreti F V Sales
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- MIT-Portugal Program, Lisbon, Portugal
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Lígia R Rodrigues
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
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Soleimani M, Kollmannsberger C, Nappi L. Emerging Role of Biomarkers in Testicular Germ Cell Tumors. Curr Oncol Rep 2022; 24:437-442. [PMID: 35142973 DOI: 10.1007/s11912-022-01231-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 01/01/2023]
Abstract
PURPOSE OF REVIEW This review will focus on biomarkers in testicular germ cell tumors (TGCT), focusing on microRNAs with high potential clinical application to drive management of TGCT. We explore the mechanism of action of microRNAs, literature to date, and how microRNAs may be incorporated into clinical practice in the near future. RECENT FINDINGS MicroRNAs are small non-coding RNAs found in blood which play an important role in post-transcriptional gene regulation and have been explored in TGCT for the past 15 years. More recently, results show they are promising biomarkers for diagnosis with impressive sensitivity and specificity, while also being cost-effective. MicroRNAs will likely play a critical role in areas of unmet need in GCT in the next decade, as they have many of the characteristics of an ideal biomarker. Ongoing prospective clinical trials evaluating microRNA-371 will be eagerly awaited and will help inform decision-making in real-world application.
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Affiliation(s)
- Maryam Soleimani
- BC Cancer, Division of Medical Oncology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christian Kollmannsberger
- BC Cancer, Division of Medical Oncology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lucia Nappi
- BC Cancer, Division of Medical Oncology, University of British Columbia, Vancouver, British Columbia, Canada. .,Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
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Errafii K, Jayyous A, Arredouani A, Khatib H, Azizi F, Mohammad RM, Abdul-Ghani M, Chikri M. Comprehensive analysis of circulating miRNA expression profiles in insulin resistance and type 2 diabetes in Qatari population. ALL LIFE 2022. [DOI: 10.1080/26895293.2022.2033853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Khaoula Errafii
- Biochemistry and Clinical Neuroscience Laboratory, Faculty of Medicine and Pharmacy of Fez, Sidi Mohammad Ben Abdullah University, Fes, Morocco
- African Genome Center, Mohamed IV Polytechnic, Benguerir, Morocco
- Qatar Biomedical Research Institute, Hamad Ben Khalifa University, HBKU, Doha, Qatar
| | - Amin Jayyous
- Diabetes and Obesity Clinical Research Center, Hamad General Hospital, Doha, Qatar
| | - Abdelillah Arredouani
- Qatar Biomedical Research Institute, Hamad Ben Khalifa University, HBKU, Doha, Qatar
| | - Hasan Khatib
- Department of Animal Sciences, University of Wisconsin–Madison, Madison, WI, USA
| | - Fouad Azizi
- Interim Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Ramzi M. Mohammad
- Interim Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Muhammad Abdul-Ghani
- Diabetes and Obesity Clinical Research Center, Hamad General Hospital, Doha, Qatar
- Department of Animal Sciences, University of Wisconsin–Madison, Madison, WI, USA
- Interim Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Mohamed Chikri
- Biochemistry and Clinical Neuroscience Laboratory, Faculty of Medicine and Pharmacy of Fez, Sidi Mohammad Ben Abdullah University, Fes, Morocco
- Qatar Biomedical Research Institute, Hamad Ben Khalifa University, HBKU, Doha, Qatar
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Bone Regeneration and Oxidative Stress: An Updated Overview. Antioxidants (Basel) 2022; 11:antiox11020318. [PMID: 35204201 PMCID: PMC8868092 DOI: 10.3390/antiox11020318] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 01/27/2022] [Accepted: 02/02/2022] [Indexed: 11/17/2022] Open
Abstract
Bone tissue engineering is a complex domain that requires further investigation and benefits from data obtained over past decades. The models are increasing in complexity as they reveal new data from co-culturing and microfluidics applications. The in vitro models now focus on the 3D medium co-culturing of osteoblasts, osteoclasts, and osteocytes utilizing collagen for separation; this type of research allows for controlled medium and in-depth data analysis. Oxidative stress takes a toll on the domain, being beneficial as well as destructive. Reactive oxygen species (ROS) are molecules that influence the differentiation of osteoclasts, but over time their increasing presence can affect patients and aid the appearance of diseases such as osteoporosis. Oxidative stress can be limited by using antioxidants such as vitamin K and N-acetyl cysteine (NAC). Scaffolds and biocompatible coatings such as hydroxyapatite and bioactive glass are required to isolate the implant, protect the zone from the metallic, ionic exchange, and enhance the bone regeneration by mimicking the composition and structure of the body, thus enhancing cell proliferation. The materials can be further functionalized with growth factors that create a better response and higher chances of success for clinical use. This review highlights the vast majority of newly obtained information regarding bone tissue engineering, such as new co-culturing models, implant coatings, scaffolds, biomolecules, and the techniques utilized to obtain them.
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Dey A, Kundu M, Das S, Jena BC, Mandal M. Understanding the function and regulation of Sox2 for its therapeutic potential in breast cancer. Biochim Biophys Acta Rev Cancer 2022; 1877:188692. [PMID: 35122882 DOI: 10.1016/j.bbcan.2022.188692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/11/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022]
Abstract
Sox family of transcriptional factors play essential functions in development and are implicated in multiple clinical disorders, including cancer. Sox2 being their most prominent member and performing a critical role in reprogramming differentiated adult cells to an embryonic phenotype is frequently upregulated in multiple cancers. High Sox2 levels are detected in breast tumor tissues and correlate with a worse prognosis. In addition, Sox2 expression is connected with resistance to conventional anticancer therapy. Together, it can be said that inhibiting Sox2 expression can reduce the malignant features associated with breast cancer, including invasion, migration, proliferation, stemness, and chemoresistance. This review highlights the critical roles played by the Sox gene family members in initiating or suppressing breast tumor development, while primarily focusing on Sox2 and its role in breast tumor initiation, maintenance, and progression, elucidates the probable mechanisms that control its activity, and puts forward potential therapeutic strategies to inhibit its expression.
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Affiliation(s)
- Ankita Dey
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
| | - Moumita Kundu
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
| | - Subhayan Das
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
| | - Bikash Chandra Jena
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
| | - Mahitosh Mandal
- Cancer Biology Lab, School of Medical Science and Technology, Indian Institute of Technology Kharagpur (IIT Kharagpur), Kharagpur, West Bengal, India..
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138
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De Silva K, Demmer RT, Jönsson D, Mousa A, Forbes A, Enticott J. A data-driven biocomputing pipeline with meta-analysis on high throughput transcriptomics to identify genome-wide miRNA markers associated with type 2 diabetes. Heliyon 2022; 8:e08886. [PMID: 35169647 PMCID: PMC8829580 DOI: 10.1016/j.heliyon.2022.e08886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/23/2021] [Accepted: 01/29/2022] [Indexed: 12/12/2022] Open
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Johnson K, Leary PJ, Govaere O, Barter MJ, Charlton SH, Cockell SJ, Tiniakos D, Zatorska M, Bedossa P, Brosnan MJ, Cobbold JF, Ekstedt M, Aithal GP, Clément K, Schattenberg JM, Boursier J, Ratziu V, Bugianesi E, Anstee QM, Daly AK. Increased serum miR-193a-5p during non-alcoholic fatty liver disease progression: Diagnostic and mechanistic relevance. JHEP Rep 2022; 4:100409. [PMID: 35072021 PMCID: PMC8762473 DOI: 10.1016/j.jhepr.2021.100409] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 10/08/2021] [Accepted: 11/09/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND & AIMS Serum microRNA (miRNA) levels are known to change in non-alcoholic fatty liver disease (NAFLD) and may serve as useful biomarkers. This study aimed to profile miRNAs comprehensively at all NAFLD stages. METHODS We profiled 2,083 serum miRNAs in a discovery cohort (183 cases with NAFLD representing the complete NAFLD spectrum and 10 population controls). miRNA libraries generated by HTG EdgeSeq were sequenced by Illumina NextSeq. Selected serum miRNAs were profiled in 372 additional cases with NAFLD and 15 population controls by quantitative reverse transcriptase PCR. RESULTS Levels of 275 miRNAs differed between cases and population controls. Fewer differences were seen within individual NAFLD stages, but miR-193a-5p consistently showed increased levels in all comparisons. Relative to NAFL/non-alcoholic steatohepatitis (NASH) with mild fibrosis (stage 0/1), 3 miRNAs (miR-193a-5p, miR-378d, and miR378d) were increased in cases with NASH and clinically significant fibrosis (stages 2-4), 7 (miR193a-5p, miR-378d, miR-378e, miR-320b, miR-320c, miR-320d, and miR-320e) increased in cases with NAFLD activity score (NAS) 5-8 compared with lower NAS, and 3 (miR-193a-5p, miR-378d, and miR-378e) increased but 1 (miR-19b-3p) decreased in steatosis, activity, and fibrosis (SAF) activity score 2-4 compared with lower SAF activity. The significant findings for miR-193a-5p were replicated in the additional cohort with NAFLD. Studies in Hep G2 cells showed that following palmitic acid treatment, miR-193a-5p expression decreased significantly. Gene targets for miR-193a-5p were investigated in liver RNAseq data for a case subgroup (n = 80); liver GPX8 levels correlated positively with serum miR-193a-5p. CONCLUSIONS Serum miR-193a-5p levels correlate strongly with NAFLD activity grade and fibrosis stage. MiR-193a-5p may have a role in the hepatic response to oxidative stress and is a potential clinically tractable circulating biomarker for progressive NAFLD. LAY SUMMARY MicroRNAs (miRNAs) are small pieces of nucleic acid that may turn expression of genes on or off. These molecules can be detected in the blood circulation, and their levels in blood may change in liver disease including non-alcoholic fatty liver disease (NAFLD). To see if we could detect specific miRNA associated with advanced stages of NAFLD, we carried out miRNA sequencing in a group of 183 patients with NAFLD of varying severity together with 10 population controls. We found that a number of miRNAs showed changes, mainly increases, in serum levels but that 1 particular miRNA miR-193a-5p consistently increased. We confirmed this increase in a second group of cases with NAFLD. Measuring this miRNA in a blood sample may be a useful way to determine whether a patient has advanced NAFLD without an invasive liver biopsy.
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Key Words
- ALT, alanine aminotransferase
- AST, aspartate aminotransferase
- AUROC, area under the receiver operating characteristic
- Biomarker
- CPM, counts per million
- Ct, cycle threshold
- ER, endoplasmic reticulum
- FC, fold change
- FIB-4, fibrosis-4
- FLIP, fatty liver inhibition of progression
- GTEx, Genotype-Tissue Expression
- MicroRNA
- NAFL, non-alcoholic fatty liver
- NAFLD, non-alcoholic fatty liver disease
- NAS, NAFLD activity score
- NASH, non-alcoholic steatohepatitis
- Non-alcoholic fatty liver disease
- PCA, principal component analysis
- SAF, steatosis–activity–fibrosis
- Sequencing
- TGF-β, transforming growth factor-beta
- cDNA, complementary DNA
- logFC, log2 fold change
- miRNA, microRNA
- qPCR, quantitative PCR
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Affiliation(s)
- Katherine Johnson
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Peter J. Leary
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Olivier Govaere
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Matthew J. Barter
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Sarah H. Charlton
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Simon J. Cockell
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Dina Tiniakos
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Michalina Zatorska
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Pierre Bedossa
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - M. Julia Brosnan
- Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA
| | - Jeremy F. Cobbold
- Oxford Liver Unit, NIHR Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Mattias Ekstedt
- Division of Diagnostics and Specialist Medicine, Department of Health, Medicine, and Caring Sciences, Linköping University, Linköping, Sweden
| | - Guruprasad P. Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Karine Clément
- Institute of Cardiometabolism and Nutrition, Pitié Salpêtrière Hospital, Paris, France
- Assistance Publique – Hopitaux de Paris, Paris, France
| | - Jörn M. Schattenberg
- Metabolic Liver Research Program, I. Department of Medicine, University Medical Center of Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Jerome Boursier
- Hepatology Department, Angers University Hospital, Angers, France
| | - Vlad Ratziu
- Institute of Cardiometabolism and Nutrition, Pitié Salpêtrière Hospital, Paris, France
- Assistance Publique – Hopitaux de Paris, Paris, France
| | - Elisabetta Bugianesi
- Division of Gastroenterology, Department of Medical Sciences, University of Turin, Turin, Italy
| | - Quentin M. Anstee
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
| | - Ann K. Daly
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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The Role of Androgen Receptor and microRNA Interactions in Androgen-Dependent Diseases. Int J Mol Sci 2022; 23:ijms23031553. [PMID: 35163477 PMCID: PMC8835816 DOI: 10.3390/ijms23031553] [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] [Received: 12/28/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 12/31/2022] Open
Abstract
The androgen receptor (AR) is a member of the steroid hormone receptor family of nuclear transcription factors. It is present in the primary/secondary sexual organs, kidneys, skeletal muscles, adrenal glands, skin, nervous system, and breast. Abnormal AR functioning has been identified in numerous diseases, specifically in prostate cancer (PCa). Interestingly, recent studies have indicated a relationship between the AR and microRNA (miRNA) crosstalk and cancer progression. MiRNAs are small, endogenous, non-coding molecules that are involved in crucial cellular processes, such as proliferation, apoptosis, or differentiation. On the one hand, AR may be responsible for the downregulation or upregulation of specific miRNA, while on the other hand, AR is often a target of miRNAs due to their regulatory function on AR gene expression. A deeper understanding of the AR–miRNA interactions may contribute to the development of better diagnostic tools as well as to providing new therapeutic approaches. While most studies usually focus on the role of miRNAs and AR in PCa, in this review, we go beyond PCa and provide insight into the most recent discoveries about the interplay between AR and miRNAs, as well as about other AR-associated and AR-independent diseases.
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141
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Guz M, Jeleniewicz W, Cybulski M. An Insight into miR-1290: An Oncogenic miRNA with Diagnostic Potential. Int J Mol Sci 2022; 23:ijms23031234. [PMID: 35163157 PMCID: PMC8835968 DOI: 10.3390/ijms23031234] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 12/12/2022] Open
Abstract
For more than two decades, the view of the roles of non-coding RNAs (ncRNAs) has been radically changing. These RNA molecules that are transcribed from our genome do not have the capacity to encode proteins, but are critical regulators of gene expression at different levels. Our knowledge is constantly enriched by new reports revealing the role of these new molecular players in the development of many pathological conditions, including cancer. One of the ncRNA classes includes short RNA molecules called microRNAs (miRNAs), which are involved in the post-transcriptional control of gene expression affecting various cellular processes. The aberrant expression of miRNAs with oncogenic and tumor-suppressive function is associated with cancer initiation, promotion, malignant transformation, progression and metastasis. Oncogenic miRNAs, also known as oncomirs, mediate the downregulation of tumor-suppressor genes and their expression is upregulated in cancer. Nowadays, miRNAs show promising application in diagnosis, prediction, disease monitoring and therapy response. Our review presents a current view of the oncogenic role of miR-1290 with emphasis on its properties as a cancer biomarker in clinical medicine.
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142
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Singh S, Srivastava PN, Meena A, Luqman S. Dietary flavonoid narirutin as a prospective antagonist of oncogenic pri/pre-microRNAs. Phytother Res 2022; 36:963-983. [PMID: 35040205 DOI: 10.1002/ptr.7367] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 12/02/2021] [Accepted: 12/11/2021] [Indexed: 12/13/2022]
Abstract
MicroRNAs (miRNAs) are involved in cancer progression via translational degradation in a sequence-specific manner of the 3'-untranslated region (3'UTR) of messenger RNA (mRNA). The involvement of miRNA in the biological progression of various cancer types is considered to be a potential target. Primary miRNA (pri-miRNA) and precursor-miRNA (pre-miRNA) synthesize the miRNA by dicer-catalyzed processes thus targeting pri/pre-miRNA by phytochemicals is amongst the appropriate approaches for anticancer therapies. Flavonoids category of phytochemicals is well-known for its chemotherapeutic and chemopreventive potential against multiple cancer types. However, the molecular interactions of flavonoids with miRNAs are not reported so far. Thus, this study aims to identify the promising flavonoids as the antagonist of miRNAs (pre-miR21, pri-miR-208a, pri-miR-378a, pri-miR320b, pri-miR-300, pri-miR-19b, and pre-miR-20b) using molecular docking simulations studies. Among the tested flavonoids, narirutin showed highest binding energy (-11.7 kcal/mol) against pri-miR19b followed by pri-miR-378a (-11.4 kcal/mol) > pri-miR320b (-11.2 kcal/mol) = pri-miR-300 (-11.2 kcal/mol) > pri-miR-208a (-9.0 kcal/mol) > pre-miR-20b (- 8.3 kcal/mol). The molecular dynamic simulation experiment confirmed that narirutin destabilizes the tertiary structure of pri-miRNA in comparison to apo-RNA. The finding indicates that narirutin binding with pre-miRNA causes disruption of pri-RNA structure that creates a loss of DICER-pre-miRNA interactions by hindering the pre-miRNA synthesis, thereby affecting miRNA processing. Further pharmacokinetics and toxicity prediction revealed that it is non-carcinogenic, non-mutagenic, and does not inhibit the CYPs activity. Thus, narirutin could be a possible antagonist of oncogenic miRNAs, therefore could be useful for miRNA-targeted cancer prevention and treatment.
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Affiliation(s)
- Shilpi Singh
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Pratik Narain Srivastava
- Molecular Microbiology and Immunology Division, CSIR-Central Drug Research Institute, Jankipuram Extension, Lucknow, India
| | - Abha Meena
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Suaib Luqman
- Bioprospection and Product Development Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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143
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Novel Diagnostic Biomarkers in Colorectal Cancer. Int J Mol Sci 2022; 23:ijms23020852. [PMID: 35055034 PMCID: PMC8776048 DOI: 10.3390/ijms23020852] [Citation(s) in RCA: 77] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/27/2021] [Accepted: 01/03/2022] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is still a leading cause of cancer death worldwide. Less than half of cases are diagnosed when the cancer is locally advanced. CRC is a heterogenous disease associated with a number of genetic or somatic mutations. Diagnostic markers are used for risk stratification and early detection, which might prolong overall survival. Nowadays, the widespread use of semi-invasive endoscopic methods and feacal blood tests characterised by suboptimal accuracy of diagnostic results has led to the detection of cases at later stages. New molecular noninvasive tests based on the detection of CRC alterations seem to be more sensitive and specific then the current methods. Therefore, research aiming at identifying molecular markers, such as DNA, RNA and proteins, would improve survival rates and contribute to the development of personalized medicine. The identification of “ideal” diagnostic biomarkers, having high sensitivity and specificity, being safe, cheap and easy to measure, remains a challenge. The purpose of this review is to discuss recent advances in novel diagnostic biomarkers for tumor tissue, blood and stool samples in CRC patients.
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144
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Oskouie AA, Ahmadi MS, Taherkhani A. Identification of Prognostic Biomarkers in Papillary Thyroid Cancer and Developing Non-Invasive Diagnostic Models Through Integrated Bioinformatics Analysis. Microrna 2022; 11:73-87. [PMID: 35068400 DOI: 10.2174/2211536611666220124115445] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/21/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Papillary thyroid cancer (PTC) is the most frequent subtype of thyroid carcinoma, mainly detected in patients with benign thyroid nodules (BTN). Due to the invasiveness of accurate diagnostic tests, there is a need to discover applicable biomarkers for PTC. So, in this study, we aimed to identify the genes associated with prognosis in PTC. Besides, we performed a machine learning tool to develop a non-invasive diagnostic approach for PTC. METHODS For the study purposes, the miRNA dataset GSE130512 was downloaded from the GEO database and then analyzed to identify the common differentially expressed miRNAs in patients with non-metastatic PTC (nm-PTC)/metastatic PTC (m-PTC) compared with BTNs. The SVM was also applied to differentiate patients with PTC from those patients with BTN using the common DEMs. A protein-protein interaction network was also constructed based on the targets of the common DEMs. Next, functional analysis was performed, the hub genes were determined, and survival analysis was then executed. RESULTS A total of three common miRNAs were found to be differentially expressed among patients with nm-PTC/m-PTC compared with BTNs. In addition, it was established that the autophagosome maturation, ciliary basal body-plasma membrane docking, antigen processing as ubiquitination & proteasome degradation, and class I MHC mediated antigen processing & presentation are associated with the pathogenesis of PTC. Furthermore, it was illustrated that RPS6KB1, CCNT1, SP1, and CHD4 might serve as new potential biomarkers for PTC prognosis. CONCLUSION RPS6KB1, CCNT1, SP1, and CHD4 may be considered new potential biomarkers used for prognostic aims in PTC. However, performing validation tests is inevitable in the future.
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Affiliation(s)
- Afsaneh Arefi Oskouie
- Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Saeed Ahmadi
- Department of Otorhinolaryngology, Besat Hospital, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Amir Taherkhani
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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145
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Sivanantham A, Lee H, Jin Y. Direct Detection of Extracellular Vesicle miRNAs Using a Single-Step RT-qPCR Assay. Methods Mol Biol 2022; 2504:137-145. [PMID: 35467284 DOI: 10.1007/978-1-0716-2341-1_10] [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] [Indexed: 10/18/2022]
Abstract
Extracellular vesicles (EVs) are biological carriers, and EV-associated miRNAs (EV-miRNAs) are considered as a novel biomarker in multiple diseases. Currently, the column-based purification method is used to purify miRNAs from EVs. However, this method of purification is complex, time-consuming, and expensive. Therefore, a simple and cost-effective single-step quantitative reverse transcription-polymerase chain reaction (RT-qPCR) method is required to detect the expression of EV-miRNAs. This chapter describes a protocol for directly analyzing the EV-miRNAs expression from mouse bronchoalveolar lavage fluid (BALF) and serum without going for an RNA isolation and purification step from EVs. It is an efficient method in several terms such as cost-wise, time, low expertise, and accuracy in results. This method may be helpful in diagnostic blood tests used in medical centers or research laboratories.
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Affiliation(s)
- Ayyanar Sivanantham
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, MA, USA
| | - Heedoo Lee
- Department of Biology and Chemistry, Changwon National University, Changwon, Korea
| | - Yang Jin
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Boston University, Boston, MA, USA.
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146
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Bakhtiari-Nezhad S, Rejali L, Hadizadeh M, Taleghani MY, Aghdaei HA, Young C, Khanabadi B, Nazemalhosseini-Mojarad E, Bonab MA. Up regulation of long non-coding RNAs BACE1 and down regulation of LINC-PINT are associated with CRC clinicopathological characteristics. Mol Biol Rep 2022; 49:10259-10267. [PMID: 36087249 PMCID: PMC9618545 DOI: 10.1007/s11033-022-07707-4] [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: 02/24/2022] [Accepted: 06/14/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Long non-coding RNAs (LncRNAs) are known to have regulatory consequences for aberrant gene expression in cancers. The aim of this study was to evaluate the expression levels of long non-encoding RNAs, BACE1 (β-secretase1) and LINC-PINT (Long Intergenic Non-Protein Coding RNA, P53 Induced Transcript), in colorectal cancer (CRC) with clinicopathological parameters. METHODS AND RESULTS Bioinformatics analysis defining effectual signalling pathways Wnt. A total of 130 tissue samples (50 fresh CRC tissues with parallel adjacent normal tissues (ADJ) accompanied with 30 normal healthy control tissue samples) were collected from the Iranian population. mRNA expression analysis was performed via Real Time Q-PCR. Statistical analysis for comparing CRC expression levels with ADJ and normal healthy tissues were carried out using Kruskal-Wallis tests. The Receiver Operating Characteristic (ROC) curve was plotted for each LNC, separately. We discovered that PINT and BACE1 expression levels were decreased and increased respectively in CRC tumour samples compared with ADJ normal and healthy tissues. Clinicopathological parameter assessment revealed a significant relationship between PINT expression, tumour location, staging and distant metastasis (p < 0.009, p < 0.014, p < 0.008, respectively). Also, BACE1 over expression was significantly associated with tumour site (p < 0.009), metastasis (p < 0.017) and histological differentiation (p < 0.028) and staging (p < 0.017). Furthermore, ROC curve plotting showed LINC-PINT LNC-BACE1 may distinguish between early and late-stage of CRC, highlighting the value of both BACE1 and PINT as CRC progression biomarkers. CONCLUSION We investigated two LNCRNAs (PINT and BACE1) as potential CRC prognostic biomarkers, which are imperative for early and effective medical intervention in CRC. Expression levels of PINT and BACE1 in CRC tissue samples may serve to identify metastasis earlier, increasing patient survival rates and expediating clinical treatment options.
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Affiliation(s)
- Sara Bakhtiari-Nezhad
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shaheed Beheshti University of Medical Sciences, Tehran, Iran
| | - Leili Rejali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shaheed Beheshti University of Medical Sciences, Tehran, Iran
| | - Mahrooyeh Hadizadeh
- Faculty of Health and Wellbeing, Canterbury Christ Church University, North Holmes Road, Canterbury, CT1 1QU UK
| | - Mohammad Yaghob Taleghani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shaheed Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shaheed Beheshti University of Medical Sciences, Tehran, Iran
| | - Chris Young
- Leicester School of Allied Health Sciences, Faculty of Health and Life Sciences, De Montfort University, Leicester, LE1 9BH UK
| | - Binazir Khanabadi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shaheed Beheshti University of Medical Sciences, Tehran, Iran
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Centre, Research Institute for Gastroenterology and Liver Diseases, Shaheed Beheshti University of Medical Sciences, Tehran, Iran
| | - Maziar Ashrafian Bonab
- Kent and Medway Medical School, Pears Building, Park Wood Road, Canterbury, Kent CT2 7FS UK
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147
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Zhao Y, Xiang J, Cheng H, Liu X, Li F. Flexible photoelectrochemical biosensor for ultrasensitive microRNA detection based on concatenated multiplex signal amplification. Biosens Bioelectron 2021; 194:113581. [PMID: 34461568 DOI: 10.1016/j.bios.2021.113581] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/19/2021] [Accepted: 08/22/2021] [Indexed: 12/13/2022]
Abstract
Precise microRNA (miRNA) analysis is significant importance for early disease diagnosis. Herein, a novel flexible photoelectrochemical (PEC) biosensor for miRNA determination was developed by employing CdS NPs-modified carbon cloth (CC) on polyimide (PI) film as photoelectric material to provide the PEC responses and an efficient four-stage reaction system as the target recognition and signal amplification unit to improve the analytical performance. In this PEC biosensor, the presence of target miR-21 would trigger the catalytic hairpin assembly (CHA) and the following hybridization chain reaction (HCR) to produce a long dsDNA labeled with numerous biotins, which would further capture a large amount of alkaline phosphatase (ALP) for catalyzing the generation of ascorbic acid (AA). As an efficient electron donor, AA could be oxidized by the photoelectrode, which would initiate a redox cycling amplification process to regenerate AA, resulting in the enhancement of the photocurrent response. Benefitting from the synergistic nucleic acid-based, enzyme catalytic, and chemical signal amplification strategies, the proposed biosensing strategy enabled ultrasensitive miRNA determination. As expected, the PEC biosensor performed satisfactory analytical performances with a linear range of 1 fM to 1 nM and the detection limit down to 0.41 fM. Furthermore, the PEC biosensing strategy exhibited recommendable selectivity, stability, flexibility, and practical applicability. Therefore, this sensing platform provides promising potential for application in bioassay and early diagnosis of disease.
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Affiliation(s)
- Yuecan Zhao
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Junzhu Xiang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Hao Cheng
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China
| | - Xiaojuan Liu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China.
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, People's Republic of China.
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148
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Pottoo FH, Iqubal A, Iqubal MK, Salahuddin M, Rahman JU, AlHajri N, Shehadeh M. miRNAs in the Regulation of Cancer Immune Response: Effect of miRNAs on Cancer Immunotherapy. Cancers (Basel) 2021; 13:6145. [PMID: 34885253 PMCID: PMC8656569 DOI: 10.3390/cancers13236145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/22/2021] [Accepted: 11/24/2021] [Indexed: 02/07/2023] Open
Abstract
In the last few decades, carcinogenesis has been extensively explored and substantial research has identified immunogenic involvement in various types of cancers. As a result, immune checkpoint blockers and other immune-based therapies were developed as novel immunotherapeutic strategies. However, despite being a promising therapeutic option, immunotherapy has significant constraints such as a high cost of treatment, unpredictable toxicity, and clinical outcomes. miRNAs are non-coding, small RNAs actively involved in modulating the immune system's multiple signalling pathways by binding to the 3'-UTR of target genes. miRNAs possess a unique advantage in modulating multiple targets of either the same or different signalling pathways. Therefore, miRNA follows a 'one drug multiple target' hypothesis. Attempts are made to explore the therapeutic promise of miRNAs in cancer so that it can be transported from bench to bedside for successful immunotherapeutic results. Therefore, in the current manuscript, we discussed, in detail, the mechanism and role of miRNAs in different types of cancers relating to the immune system, its diagnostic and therapeutic aspect, the effect on immune escape, immune-checkpoint molecules, and the tumour microenvironment. We have also discussed the existing limitations, clinical success and the prospective use of miRNAs in cancer.
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Affiliation(s)
- Faheem Hyder Pottoo
- Department of Pharmacology, College of Clinical Pharmacy, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia;
| | - Ashif Iqubal
- Department of Pharmacology, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India;
- Department of Pharmacology, Delhi Pharmaceutical Sciences and Research University, New Delhi 110017, India
| | - Mohammad Kashif Iqubal
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard, New Delhi 110062, India;
- Product Development Department, Sentiss Research Centre, Sentiss Pharma Pvt Ltd., Gurugram 122001, India
| | - Mohammed Salahuddin
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia;
| | - Jawad Ur Rahman
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia;
| | - Noora AlHajri
- Mayo Clinic, Sheikh Shakhbout Medical City (SSMC), Abu Dhabi 127788, United Arab Emirates
| | - Mustafa Shehadeh
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
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149
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Boucher AC, Caldwell KJ, Crispino JD, Flerlage JE. Clinical and biological aspects of myeloid leukemia in Down syndrome. Leukemia 2021; 35:3352-3360. [PMID: 34518645 PMCID: PMC8639661 DOI: 10.1038/s41375-021-01414-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 02/08/2023]
Abstract
Children with Down syndrome are at an elevated risk of leukemia, especially myeloid leukemia (ML-DS). This malignancy is frequently preceded by transient abnormal myelopoiesis (TAM), which is self-limited expansion of fetal liver-derived megakaryocyte progenitors. An array of international studies has led to consensus in treating ML-DS with reduced-intensity chemotherapy, leading to excellent outcomes. In addition, studies performed in the past 20 years have revealed many of the genetic and epigenetic features of the tumors, including GATA1 mutations that are arguably associated with all cases of both TAM and ML-DS. Despite these advances in understanding the clinical and biological aspects of ML-DS, little is known about the mechanisms of relapse. Upon relapse, patients face a poor outcome, and there is no consensus on treatment. Future studies need to be focused on this challenging aspect of leukemia in children with DS.
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Affiliation(s)
- Austin C Boucher
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kenneth J Caldwell
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - John D Crispino
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Jamie E Flerlage
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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150
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An AC electrokinetics-based electrochemical aptasensor for the rapid detection of microRNA-155. Biosens Bioelectron 2021; 199:113847. [PMID: 34902642 DOI: 10.1016/j.bios.2021.113847] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/12/2021] [Accepted: 11/25/2021] [Indexed: 12/21/2022]
Abstract
Traditional immunosensors are often limited by low sensitivity and long detection times, for they usually depend on passive diffusion-dominated transport of target analytes for the binding reaction with a bio-recognition element such as enzymes, antibodies, and aptamers. Numerous studies rely on electric field manipulation by using alternating current (AC) electrokinetics to enhance the hybridization rate and reduce the hybridization time for faster and more efficient detection. This study demonstrated a rapid electrochemical aptasensor integrated with an AC electroosmotic (ACEO) flow phenomenon for the enhanced target hybridization of microRNA-155 (miR-155). Optimization of the electrokinetic conditions for target collection resulted in a saturation point after 75 s miR-155 was detected within the range of 1 aM-10 pM with a detection limit of 1 aM, which is 100 times lower and about 50 times faster compared with the conventional diffusion-dependent detection done for 1 h. The detection was also done in spiked serum samples, and a concentration range within the required detection range was obtained. The highly sensitive and specific results allow for the rapid and real-time sensing of target biomarkers, which can be used for the early detection of infection.
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