Relevant bibliographies by topics / RNA biomarkers

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'RNA biomarkers'

Author: Grafiati
Published: 19 February 2023

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Journal articles on the topic "RNA biomarkers"

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Zhang, Xueli, Hong Zhang, Chuanwen Fan, Camilla Hildesjö, Bairong Shen, and Xiao-Feng Sun. "Loss of CHGA Protein as a Potential Biomarker for Colon Cancer Diagnosis: A Study on Biomarker Discovery by Machine Learning and Confirmation by Immunohistochemistry in Colorectal Cancer Tissue Microarrays." Cancers 14, no. 11 (May 27, 2022): 2664. http://dx.doi.org/10.3390/cancers14112664.

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Background. The incidence of colorectal cancers has been constantly increasing. Although the mortality has slightly decreased, it is far from satisfaction. Precise early diagnosis for colorectal cancer has been a great challenge in order to improve patient survival. Patients and Methods. We started with searching for protein biomarkers based on our colorectal cancer biomarker database (CBD), finding differential expressed genes (GEGs) and non-DEGs from RNA sequencing (RNA-seq) data, and further predicted new biomarkers of protein–protein interaction (PPI) networks by machine learning (ML) methods. The best-selected biomarker was further verified by a receiver operating characteristic (ROC) test from microarray and RNA-seq data, biological network, and functional analysis, and immunohistochemistry in the tissue arrays from 198 specimens. Results. There were twelve proteins (MYO5A, CHGA, MAPK13, VDAC1, CCNA2, YWHAZ, CDK5, GNB3, CAMK2G, MAPK10, SDC2, and ADCY5) which were predicted by ML as colon cancer candidate diagnosis biomarkers. These predicted biomarkers showed close relationships with reported biomarkers of the PPI network and shared some pathways. An ROC test showed the CHGA protein with the best diagnostic accuracy (AUC = 0.9 in microarray data and 0.995 in RNA-seq data) among these candidate protein biomarkers. Furthermore, immunohistochemistry examination on our colon cancer tissue microarray samples further confirmed our bioinformatical prediction, indicating that CHGA may be used as a potential biomarker for early diagnosis of colon cancer patients. Conclusions. CHGA could be a potential candidate biomarker for diagnosing earlier colon cancer in the patients.
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Zhang, Xueli, Xiao-Feng Sun, Bairong Shen, and Hong Zhang. "Potential Applications of DNA, RNA and Protein Biomarkers in Diagnosis, Therapy and Prognosis for Colorectal Cancer: A Study from Databases to AI-Assisted Verification." Cancers 11, no. 2 (February 1, 2019): 172. http://dx.doi.org/10.3390/cancers11020172.

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In order to find out the most valuable biomarkers and pathways for diagnosis, therapy and prognosis in colorectal cancer (CRC) we have collected the published CRC biomarkers and established a CRC biomarker database (CBD: http://sysbio.suda.edu.cn/CBD/index.html). In this study, we analysed the single and multiple DNA, RNA and protein biomarkers as well as their positions in cancer related pathways and protein-protein interaction (PPI) networks to describe their potential applications in diagnosis, therapy and prognosis. CRC biomarkers were collected from the CBD. The RNA and protein biomarkers were matched to their corresponding DNAs by the miRDB database and the PubMed Gene database, respectively. The PPI networks were used to investigate the relationships between protein biomarkers and further detect the multiple biomarkers. The Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Ontology (GO) annotation were used to analyse biological functions of the biomarkers. AI classification techniques were utilized to further verify the significances of the multiple biomarkers in diagnosis and prognosis for CRC. We showed that a large number of the DNA, RNA and protein biomarkers were associated with the diagnosis, therapy and prognosis in various degrees in the CRC biomarker networks. The CRC biomarkers were closely related to the CRC initiation and progression. Moreover, the biomarkers played critical roles in cellular proliferation, apoptosis and angiogenesis and they were involved in Ras, p53 and PI3K pathways. There were overlaps among the DNA, RNA and protein biomarkers. AI classification verifications showed that the combined multiple protein biomarkers played important roles to accurate early diagnosis and predict outcome for CRC. There were several single and multiple CRC protein biomarkers which were associated with diagnosis, therapy and prognosis in CRC. Further, AI-assisted analysis revealed that multiple biomarkers had potential applications for diagnosis and prognosis in CRC.
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Fyfe, Ian. "RNA biomarkers of Parkinson disease." Nature Reviews Neurology 17, no. 3 (February 9, 2021): 132. http://dx.doi.org/10.1038/s41582-021-00470-3.

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Bustin, Stephen A., and Jamie Murphy. "RNA biomarkers in colorectal cancer." Methods 59, no. 1 (January 2013): 116–25. http://dx.doi.org/10.1016/j.ymeth.2012.10.003.

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Shahjaman, Md, Habiba Akter, Md Mamunur Rashid, Md Ibnul Asifuzzaman, Md Bipul Hossen, and Md Rezanur Rahman. "Robust and efficient identification of biomarkers from RNA-Seq data using median control chart." F1000Research 8 (January 3, 2019): 7. http://dx.doi.org/10.12688/f1000research.17351.1.

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Background: One of the main goals of RNA-seq data analysis is identification of biomarkers that are differentially expressed (DE) across two or more experimental conditions. RNA-seq uses next generation sequencing technology and it has many advantages over microarrays. Numerous statistical methods have already been developed for identification the biomarkers from RNA-seq data. Most of these methods were based on either Poisson distribution or negative binomial distribution. However, efficient biomarker identification from discrete RNA-seq data is hampered by existing methods when the datasets contain outliers or extreme observations. Specially, the performance of these methods becomes more severe when the data come from a small number of samples in the presence of outliers. Therefore, in this study, an attempt is made to propose an outlier detection and modification approach for RNA-seq data to overcome the aforesaid problems of traditional methods. We make our proposed method facilitate in RNA-seq data by transforming the read count data into continuous data. Methods: We use median control chart to detect and modify the outlying observation in a log-transformed RNA-seq dataset. To investigate the performance of the proposed method in absence and presence of outliers, we employ the five popular biomarker selection methods (edgeR, edgeR_robust, DEseq, DEseq2 and limma) both in simulated and real datasets. Results: The simulation results strongly suggest that the performance of the proposed method improved in the presence of outliers. The proposed method also detected an additional 18 outlying DE genes from a real mouse RNA-seq dataset that were not detected by traditional methods. Using the KEGG pathway and gene ontology analysis results we reveal that these genes may be biomarkers, which require validation in a wet lab. Conclusions: Our proposal is to apply the proposed method for biomarker identification from other RNA-seq data.
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Nikitina, A. S., V. V. Babenko, K. A. Babalyan, A. O. Vasiliev, A. V. Govorov, E. A. Prilepskaya, S. A. Danilenko, O. V. Selezneva, and E. I. Sharova. "Primary candidate RNA biomarker screening by RNA-seq for prostate cancer diagnostics." Biomeditsinskaya Khimiya 61, no. 6 (2015): 781–84. http://dx.doi.org/10.18097/pbmc20156106781.

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The RNA-seq approach for prostate cancer candidate RNA biomarkers screening in plasma and urine obtained by minimally invasive or noninvasive methods is proved to be feasible. Significant amount of RNA biomarkers associated with prostate cancer according to the literature were found in plasma and urine samples obtained from patients with benign prostatic hyperplasia (BPH). The number of detected markers was shown to vary in accordance with method of library preparation used for transcriptome profiling. The detection of known RNA biomarkers for prostate cancer in urine and plasma samples shows the feasibility of such method for minimally invasive diagnostics. The fact of presence of the same RNA biomarkers in samples from patients with BPH suggests their possible lack of specificity and confirms the need for further research in this area.
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Li, Feng, Janice M. Yoshizawa, Kyoung-Mee Kim, Julie Kanjanapangka, Tristan R. Grogan, Xiaoyan Wang, David E. Elashoff, et al. "Discovery and Validation of Salivary Extracellular RNA Biomarkers for Noninvasive Detection of Gastric Cancer." Clinical Chemistry 64, no. 10 (October 1, 2018): 1513–21. http://dx.doi.org/10.1373/clinchem.2018.290569.

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Abstract BACKGROUND Biomarkers are needed for noninvasive early detection of gastric cancer (GC). We investigated salivary extracellular RNA (exRNA) biomarkers as potential clinical evaluation tools for GC. METHODS Unstimulated whole saliva samples were prospectively collected from 294 individuals (163 GC and 131 non-GC patients) who underwent endoscopic evaluation at the Samsung Medical Center in Korea. Salivary transcriptomes of 63 GC and 31 non-GC patients were profiled, and mRNA biomarker candidates were verified with reverse transcription quantitative real-time PCR (RT-qPCR). In parallel, microRNA (miRNA) biomarkers were profiled and verified with saliva samples from 10 GC and 10 non-GC patients. Candidate biomarkers were validated with RT-qPCR in an independent cohort of 100/100 saliva samples from GC and non-GC patients. Validated individual markers were configured into a best performance panel. RESULTS We identified 30 mRNA and 15 miRNA candidates whose expression pattern associated with the presence of GC. Among them, 12 mRNA and 6 miRNA candidates were verified with the discovery cohort by RT-qPCR and further validated with the independent cohort (n = 200). The configured biomarker panel consisted of 3 mRNAs (SPINK7, PPL, and SEMA4B) and 2 miRNAs (MIR140-5p and MIR301a), which were all significantly down-regulated in the GC group, and yielded an area under the ROC curve (AUC) of 0.81 (95% CI, 0.72–0.89). When combined with demographic factors, the AUC of the biomarker panel reached 0.87 (95% CI, 0.80–0.93). CONCLUSIONS We have discovered and validated a panel of salivary exRNA biomarkers with credible clinical performance for the detection of GC. Our study demonstrates the potential utility of salivary exRNA biomarkers in screening and risk assessment for GC.
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Dutton, Gail. "Singling Out RNA Biomarkers in Situ." Genetic Engineering & Biotechnology News 37, no. 6 (March 15, 2017): 4–5. http://dx.doi.org/10.1089/gen.37.06.04.

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Engelhardt, Stefan. "Small RNA Biomarkers Come of Age." Journal of the American College of Cardiology 60, no. 4 (July 2012): 300–303. http://dx.doi.org/10.1016/j.jacc.2012.04.018.

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Chauhan, Ranjit, and Nivedita Lahiri. "Tissue- and Serum-Associated Biomarkers of Hepatocellular Carcinoma." Biomarkers in Cancer 8s1 (January 2016): BIC.S34413. http://dx.doi.org/10.4137/bic.s34413.

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Hepatocellular carcinoma (HCC), one of the leading causes of cancer deaths in the world, is offering a challenge to human beings, with the current modes of treatment being a palliative approach. Lack of proper curative or preventive treatment methods encouraged extensive research around the world with an aim to detect a vaccine or therapeutic target biomolecule that could lead to development of a drug or vaccine against HCC. Biomarkers or biological disease markers have emerged as a potential tool as drug/vaccine targets, as they can accurately diagnose, predict, and even prevent the diseases. Biomarker expression in tissue, serum, plasma, or urine can detect tumor in very early stages of its development and monitor the cancer progression and also the effect of therapeutic interventions. Biomarker discoveries are driven by advanced techniques, such as proteomics, transcriptomics, whole genome sequencing, micro- and micro-RNA arrays, and translational clinics. In this review, an overview of the potential of tissue- and serum-associated HCC biomarkers as diagnostic, prognostic, and therapeutic targets for drug development is presented. In addition, we highlight recently developed micro-RNA, long noncoding RNA biomarkers, and single-nucleotide changes, which may be used independently or as complementary biomarkers. These active investigations going on around the world aimed at conquering HCC might show a bright light in the near future.
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Dissertations / Theses on the topic "RNA biomarkers"

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Yazbek, Hanna Marcelino. "Exosomal RNA as a source of urine biomarkers for prostate cancer." Thesis, University of East Anglia, 2017. https://ueaeprints.uea.ac.uk/66563/.

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Introduction: In this study we exploited the recent development of methods that have enabled the analysis of RNA present in urine exosomes of prostate cancer patients. We report RNA expression patterns that contain diagnostic and prognostic information for prostate cancer, and association with response to hormone treatment. Methods: First catch urine following digital rectal examination were collected from 662 men. 3 groups of patients were used: Low, Intermediate, and High-risk according to NICE stratification criteria, and two control groups: benign and advanced disease. 50-gene transcript expression analysis using NanoString technology was performed on 192 samples. Exosomal RNA Next-Generation Sequencing was performed on 18 samples for novel biomarker discovery. Results: Expression analysis showed that PCa-specific transcripts such as TMPRSS2/ERG fusion transcripts were identifiable in exosomes from PCa urine samples. LPD analysis highlighted expression levels of 15 transcripts with diagnostic potential (significantly up-regulated in cancer samples in comparison to benign control) and 17 transcripts with prognostic potential (differentialy expressed in high risk and advanced disease in comparison to lower grade disease). I also report two gene transcripts (SERPINB5/Maspin, HPRT) that were significantly differentially expressed in patients who failed to respond to hormone deprivation therapy for high risk/metastatic disease. Three genes (STEAP4, ARexons4_8 and NAALADL2) were significantly differentially expressed in patients who relapsed within 12 months of hormone treatment initiation. Next-Generation Sequencing of twenty samples identified 45 genes to be significantly differentially expressed between non-cancer and cancer samples (28 were up regulated and 17 down regulated). 33 out of the 45 genes showed a significant linear trend in association with cancer risk. Conclusions: Urine Exosomal RNA contains PCa specific transcripts. Gene expression analysis and Next Generation Sequencing identified genes that are significantly differentially expressed between cancer and non-cancer cases as well as prognostic genes and genes that can predict response to hormone treatment.
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Islam, Nazmul. "Engineering translational approaches for molecular diagnostics of cancer: Multifunctional nanomaterials and electrochemical sensors for clinically relevant RNA biomarker detection." Thesis, Griffith University, 2018. http://hdl.handle.net/10072/374754.

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Over the past several years, the human transcriptome has been repeatedly interrogated, and with the recent breakthrough in sequencing technologies, ribonucleic acids (RNAs) comprising different coding and noncoding transcripts, such as messenger RNA (mRNA), microRNA (miRNA), and long-noncoding RNA (lncRNA), are becoming progressively crucial for revolutionising personalised cancer management. Improved diagnostics, prognostics and streamlined therapeutic potentiality makes them an excellent choice as biomarkers. Non-coding RNAs are key regulators of the gene expression network and are involved in the control of a range of important cellular pathways, such as cell cycle, cell proliferation, differentiation, apoptosis, and post-transcriptional regulation. Abnormalities in the expression of these RNAs can affect one or several of these cellular pathways, which might contribute towards initiation and progression of cancer. Despite recent advances in RNA-based fundamental research, their detection approaches are largely confined to laboratory-based molecular biology techniques, such as quantitative reverse transcription polymerase chain reaction (RT-qPCR), microarrays, and RNA sequencing. Although the analytical performance and reliability of these methods are excellent, most of these methods require enzymatic amplification, cumbersome sample pre-treatment, multi-step assay protocol, high maintenance cost, and technical expertise. The development of a simple, sensitive, and low cost method that can be used for rapid detection of RNA biomarkers for a meaningful clinical application at the time and place of patient care (i.e., point-of-care) is of great importance to clinical and translational research. This PhD project endeavours to engineer such translational approaches to circumvent the aforementioned challenges for developing an inexpensive, sensitive, specific, and portable biosensor platform. This thesis initially studies the biogenesis, diagnostic, and prognostic potential of RNA biomarkers followed by a comprehensive appraisal of recent progress in the development of RNA biosensors with a special emphasis on electrochemical-detection approaches. We then report on the development of a biosensing platform consisting of four novel readout schemes for the simple, rapid, and inexpensive analysis of various RNA biomarkers (i.e., mRNAs, miRNAs and lncRNAs). First, employing the nucleotides’ affinity towards gold, we developed an amplification-free electrochemical assay for the detection of tumour-specific mRNAs. This straightforward sensor adopted differential pulse voltammetry to enable the readout using simple direct adsorption of magnetically isolated analytes on unmodified disposable electrodes. Subsequent to the development of this proof of concept sensor, we attempted to address the increasing demand for detecting the ultralow levels of RNAs from the complex biological sample via introducing two novel readout strategies for detecting miRNAs. Utilising the coupling of electrocatalytic strength of two in-house synthesised porous graphene oxide-loaded iron oxide (GO/IO hybrid material), gold-loaded nanoporous ferric oxide nanocubes (Au-NPFe2O3NC), and [Ru(NH3)6]3+/[Fe(CN)6]3- electrocatalytic cycle, two ultrasensitive assays were reported, where the detection was achieved by chronocoulometric (CC) charge measurement of surface bound cationic [Ru(NH3)6]3+, which was electrostatically attached to the anionic phosphate backbone of target RNAs. In our final readout strategies, we extended our approach towards a translational- focused assay platform which enabled naked-eye, colorimetric and electrochemical interrogation of lncRNA via 3,3′,5,5′-tetramethylbenzidine (TMB)/Horseradish peroxidase (HRP)-based colorimetric assay. All of the readout platforms reported herein have shown excellent analytical performance with high sensitivity (LOD for mRNA and miRNA = picomolar to attomolar level, LOD for lncRNA = single cell approaching) and specificity. The applicability of the assays was also demonstrated in complex biological samples (a cohort of cancer cell lines and patient samples) with high reproducibility. The analytical performance of the assays was also validated with the standard RT-qPCR approach. We believe that our research efforts will lead to the development of a translational-focused point-of-care platform for RNA analysis, which in turn will not only hold the potential to improve patient care and outcomes but might also prove to be a venture of immense commercial significance.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Natural Sciences
Science, Environment, Engineering and Technology
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Liu, Ming-lai, and 廖明麗. "Roles of microRNAs in hepatocellular carcinoma: biomarkers, matabolisms and pathway regulators." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46918929.

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Götschke, Jeremias [Verfasser], and Susanne [Akademischer Betreuer] Krauss-Etschmann. "Beschreibung eines potentiellen micro-RNA-basierten Biomarkers für allergisches Asthma / Jeremias Götschke ; Betreuer: Susanne Krauss-Etschmann." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2018. http://d-nb.info/115653352X/34.

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Franklin, Oskar. "Stromal components and micro-RNAs as biomarkers in pancreatic cancer." Doctoral thesis, Umeå universitet, Kirurgi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-128000.

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Background Pancreatic ductal adenocarcinoma (PDAC) patients have the poorest 5-year survival rates of all cancer forms. It is difficult to diagnose at early disease stages, tumour relapse after surgery is common, and current chemotherapies are ineffective. Carbohydrate antigen 19-9 (Ca 19-9), the only clinically implemented PDAC biomarker, is insufficient for diagnostic and screening purposes. PDAC tumours are characterised by a voluminous stroma that is rich in extracellular matrix (ECM) molecules such as collagens, hyaluronan (HA) and matricellular proteins. These stromal components have been suggested to promote PDAC cell migration, proliferation, evasion of apoptosis and chemotherapy resistance. Those events are mediated via interactions with adhesion receptors, such as integrins and CD44 receptors expressed on cancer cell surfaces. Micro-RNAs (miRNA) post-transcriptionally regulate gene expression in health and disease. At the time of PDAC diagnosis, miRNA levels are altered both in plasma and tumour tissue. Before PDAC diagnosis, tissue miRNA levels are altered in precursor lesions, raising the possibility that plasma miRNAs might aid in early detection. In this thesis, it is hypothesised that stromal components and miRNAs can serve as tissue or blood based biomarkers in PDAC. The aims are: (1) to characterise the expression of stromal components and their receptors in normal and cancerous tissue; (2) to find potential stroma-associated tissue and blood-based biomarkers for diagnosis and prognosis estimates; (3) to determine the cellular effects of type IV collagen (Col IV) in PDAC; (4) to determine if plasma miRNAs that are altered in manifest PDAC can be used to diagnose PDAC earlier. Methods The expression patterns of Col IV, Col IV-binding integrin subunits (α1, α2, β1), Endostatin, Osteopontin (OPN) and Tenascin C (TNC) were analysed in frozen PDAC and normal pancreatic tissue. A tissue microarray (TMA) was constructed using formalin-fixed, paraffin-embedded primary tumours and lymph node metastases. The TMA was used to study the expression levels and associations with survival of the standard CD44 receptor (CD44s), its variant isoform 6 (CD44v6), HA, OPN and Col IV. Circulating levels of HA, Col IV, Endostatin, OPN and TNC were measured in PDAC patients and healthy individuals, and compared with conventional tumour markers (Ca 19-9, CEA, Ca 125 and TPS). The functional roles of Col IV were studied in PDAC cell lines by: (1) growth on different matrices (2) blocking Col IV binding integrin subunits, (3) blocking the Col IV domains 7s, CB3 and NC1, and (4) by down regulation of PDAC cell synthesis of Col IV using siRNA transfection. Plasma miRNAs alterations were screened for in samples from patients with manifest disease, using real-time quantitative PCR (RT-qPCR). To find early miRNA alterations, levels of those miRNAs that were altered at diagnosis were measured in prediagnostic plasma samples. Results High tissue expression of both the standard CD44 receptor (CD44s) and its variant isoform CD44v6 as well as low expression of stromal OPN were associated with poor survival. In addition, high CD44s and low OPN predicted poor survival independent of established prognostic factors. Circulating Col IV, Endostatin, OPN, TNC and HA were increased in preoperative samples from PDAC patients. Preoperatively, higher levels of serum-HA and plasma-Endostatin were associated with shorter survival. Postoperatively, higher levels of Col IV, Endostatin and OPN were associated with shorter survival. On the contrary, only one of the conventional tumour markers was associated with survival (Ca 125). Col IV stimulated PDAC cell proliferation and migration and inhibited apoptosis in vitro, dependent on the collagenous domain (CB3) of Col IV and the Col IV binding integrin subunit β1. Reduced endogenous Col IV synthesis inhibited these effects, suggesting that PDAC cells synthesise Col IV to stimulate tumour-promoting events via a newly discovered autocrine loop. 15 miRNAs were altered in early stage PDAC patients and the combination of these markers outperformed Ca 19-9 in discriminating patients from healthy individuals. However, none of the miRNAs were altered in prediagnostic samples, suggesting that plasma miRNA alterations appear late in the disease course. Conclusions Up regulated stromal components in PDAC tumours are detectable in blood samples and are potential diagnostic and prognostic biomarkers in PDAC. High circulating levels of Col IV, Endostatin, OPN and HA predict poor survival, as well as high expression of CD44s and CD44v6 and low expression of OPN in tumour tissue. PDAC cells synthesise Col IV, which forms BM-like structures close to cancer cells and promote tumour progression in vitro via an autocrine loop. Several plasma-miRNAs are altered in PDAC, but are not useful for early discovery.
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Sohiya, Yotsukura. "Computational Framework for the Dissection of Cancer Genomic Architecture and its Association in Different Biomarkers." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/217149.

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Sundaramurthy, Gopinath. "A Probabilistic Approach for Automated Discovery of Biomarkers using Expression Data from Microarray or RNA-Seq Datasets." University of Cincinnati / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1459528594.

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Bajak, Edyta Zofia. "Genotoxic stress: novel biomarkers and detection methods : uncovering RNAs role in epigenetics of carcinogenesis /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-415-5/.

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Tong, Chiu-hung, and 唐朝虹. "MiR-143 and its downstream targets: possible biomarkers for cervical cancer and precursors." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46579436.

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Alvarez, Michelle. "PHYSICAL CHARACTERISTICS OF AN INDIVIDUAL: THE IDENTIFICATION OF BIOMARKERS FOR BIOLOGICAL AGE DETERMINATION." Doctoral diss., University of Central Florida, 2007. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/4198.

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It is now a matter of routine for the forensic scientist to obtain the genetic profile of an individual from DNA recovered from a biological stain deposited at a crime scene. Potential contributors of the stain must either be known to investigators (i.e. a developed suspect) or the questioned profile must be searched against a database of DNA profiles such as those maintained in the CODIS National DNA database. However, in those instances where there is no developed suspect and no match is obtained after interrogation of appropriate DNA databases, the DNA profile per se presently provides no meaningful information to investigators, with the notable exception of gender determination. In these situations it would be advantageous to the investigation, if additional probative information could be obtained from the biological stain. A useful biometric that could provide important probative information, and one that may be amenable to molecular genetic analysis, is the biological age of an individual. The ability to provide investigators with information as to whether a DNA donor is a newborn, infant, toddler, child, adolescent, adult, middle-aged or elderly individual could be useful in certain cases, particularly those involving young children such as kidnappings or in providing additional intelligence during terrorist investigations. Currently no validated molecular assays exist for age determination. Biological human ageing can be defined by two distinct processes, degenerative and developmental ageing. The degenerative process of ageing is based on theories which identify an increase or decrease in physiological conditions with increasing age. In contrast, the developmental process of ageing is based on the theory that as individuals increase in chronological age, there will be subtle corresponding molecular based biological changes, each requiring genes to be expressed or silenced, indicative of that particular stage of life. We investigated the degenerative process of chromosomal telomere shortening, as well as the developmental process of gene expression profiling analysis, in an attempt to identify biomarkers of biological age in a self-renewing tissue such as blood. While telomere length analysis was an ineffective method for age determination; gene expression analysis revealed three gene transcripts expressed in an age-dependent physiological manner. These species namely- COL1A2, HBE1 and IGFBP3, were found to be expressed at elevated levels in younger individuals, newborns, or post-pubertal individuals, respectively. The biological process of hemoglobin switching was also investigated for the possibility of determining human age. While experimenting with the potential of using the gamma-hemoglobin chains, as newborn specific gene candidates, we serendipitously discovered four novel truncated transcripts, which we have termed HBG1n1, HBG1n2, HBG2n2 and HBG2n3; whose expression was restricted to whole-blood newborn samples and specific fetal tissues. The molecular origin of these transcripts appears to be at the RNA level, being produced by specific rearrangement events occurring in the standard gamma hemoglobin transcripts (HBG1 and HBG2), which yield these new isoforms that are expressed in a highly regulated tissue specific manner.
Ph.D.
Department of Biomolecular Science
Burnett College of Biomedical Sciences
Biomolecular Sciences PhD
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Books on the topic "RNA biomarkers"

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Slabý, Ondřej. MicroRNAs in solid cancer: From biomarkers to therapeutic targets. Hauppauge, N.Y: Nova Science, 2011.

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Shang, Desi, Wei Jiang, Yan Gu, and Huihui Fan, eds. Non-coding RNA as Prognostic and Diagnostic Biomarkers in Thoracic Oncology. Frontiers Media SA, 2022. http://dx.doi.org/10.3389/978-2-88974-631-6.

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Reckman, Yolan J., and Yigal M. Pinto. The role of non-coding RNA/microRNAs in cardiac disease. Edited by José Maria Pérez-Pomares, Robert G. Kelly, Maurice van den Hoff, José Luis de la Pompa, David Sedmera, Cristina Basso, and Deborah Henderson. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198757269.003.0031.

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In the past two decades, our knowledge about non-coding DNA has increased tremendously. While non-coding DNA was initially discarded as ‘junk DNA’, we are now aware of the important and often crucial roles of RNA transcripts that do not translate into protein. Non-coding RNAs (ncRNAs) play important functions in normal cellular homeostasis and also in many diseases across all organ systems. Among the different ncRNAs, microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) have been studied the most. In this chapter we discuss the role of miRNAs and lncRNAs in cardiac disease. We present examples of miRNAs with fundamental roles in cardiac development (miR-1), hypertrophy (myomiRs, miR-199, miR-1/133), fibrosis (miR-29, miR-21), myocardial infarction (miR-15, miR17~92), and arrhythmias/conduction (miR-1). We provide examples of lncRNAs related to cardiac hypertrophy (MHRT, CHRF), myocardial infarction (ANRIL, MIAT), and arrhythmias (KCNQ1OT1). We also discuss miRNAs and lncRNAs as potential therapeutic targets or biomarkers in cardiac disease.
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Cummings, Jeffrey L., and Jagan A. Pillai. Neurodegenerative Diseases. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780190233563.003.0001.

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Neurodegenerative diseases (NDDs) are growing in frequency and represent a major threat to public health. Advances in scientific progress have made it clear that NDDs share many underlying processes, including shared intracellular mechanisms such as protein misfolding and aggregation, cell-to-cell prion-like spread, growth factor signaling abnormalities, RNA and DNA disturbances, glial cell changes, and neuronal loss. Transmitter deficits are shared across many types of disorders. Means of studying NDDs with human iPS cells and transgenic models are similar. The progression of NDDs through asymptomatic, prodromal, and manifest stages is shared across disorders. Clinical features of NDDs, including cognitive impairment, disease progression, age-related effects, terminal stages, neuropsychiatric manifestations, and functional disorders and disability, have many common elements. Clinical trials, biomarkers, brain imaging, and regulatory aspects of NDD can share information across NDDs. Disease-modifying and transmitter-based therapeutic interventions, clinical trials, and regulatory approaches to treatments for NDDs are also similar.
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Kirchman, David L. Elements, biochemicals, and structures of microbes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0002.

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Microbiologists focus on the basic biochemical make-up of microbes, such as relative amounts of protein, RNA, and DNA in cells, while ecologists and biogeochemists use elemental ratios, most notably, the ratio of carbon to nitrogen (C:N), to explore biogeochemical processes and to connect up the carbon cycle with the cycle of other elements. Microbial ecologists make use of both types of data and approaches. This chapter combines both and reviews all things, from elements to macromolecular structures, that make up bacteria and other microbes. The most commonly used elemental ratio was discovered by Alfred Redfield who concluded that microbes have a huge impact on the chemistry of the oceans because of the similarity in nitrogen-to-phosphorus ratios for organisms and nitrate-to-phosphate ratios in the deep oceans. Although statistically different, the C:N ratios in soil microbes are remarkably similar to the ratios of aquatic microbes. The chapter moves on to discussing the macromolecular composition of bacteria and other microbes. This composition gives insights into the growth state of microbes in nature. Geochemists use specific compounds, “biomarkers”, to trace sources of organic material in ecosystems. The last section of the chapter is a review of extracellular polymers, pili, and flagella, which serve a variety of functions, from propelling microbes around to keeping them stuck in one place.
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K. Gautam, Rupesh, Lokesh Deb, and Kamal Dua, eds. Natural Products for the Management of Arthritic Disorders. BENTHAM SCIENCE PUBLISHERS, 2022. http://dx.doi.org/10.2174/97898150507761220101.

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Rheumatoid arthritis (RA) is the most common inflammatory complication and affects approximately 1 % of the global population. It affects three times more women than men. RA is an autoimmune disorder elicited by exposure of genetic factors from the host to unknown antigens causing arthritogenic complaints. It also includes the activation of lymphocytes as well as CD4+ helper T cells along with local release of chronic inflammatory mediators and cytokines like tumor necrosis factor (TNF α) and various cytokines like interleukins (IL) that enormously affect the joints. The available allopathic therapies for RA are not a cure for the complications, and antibody therapy and surgical procedures are expensive. However, in the present era, researchers and healthcare professionals have moved toward natural medicines obtained from plants and other natural sources. Research based on developments in phytomedicine has progressed steadily. Evidence has been collected to show the massive therapeutic potential of medicinal plants used in various traditional systems against many pathological complications. Researchers have focused on the therapeutic potential of natural products used for treatment and counteracting various disorders along with their complications having negligible adverse effects. Natural Products for the Management of Arthritic Disorders compiles current knowledge about the bioactive compounds and herbal formulations useful in the treatment of rheumatoid arthritis. 11 chapters explain the role of natural products in the management of rheumatoid arthritis. Topics have been contributed by experts in medicinal chemistry and rheumatology. The book first introduces the reader to rheumatoid arthritis before delving into conventional and alternative therapies for the disease. The editors have also included special topics such as the biomarkers for RA, cytokines and anti-inflammatory mediators, preclinical and clinical studies. The range of topics should provide a comprehensive overview of natural remedies for arthritis and the role of natural products in anti-arthritic drug development. The information will be useful for many readers including medical and pharmacology students, multidisciplinary research scholars, scientists, pharma / herbal / food industrialists, and policy makers.
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Book chapters on the topic "RNA biomarkers"

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de Souza, Daniel Martins, and Emmanuel Dias-Neto. "RNA Biomarkers in Schizophrenia." In Biomarkers for Psychiatric Disorders, 97–127. Boston, MA: Springer US, 2008. http://dx.doi.org/10.1007/978-0-387-79251-4_5.

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Reggiardo, Roman E., Sreelakshmi Velandi Maroli, and Daniel H. Kim. "LncRNA Biomarkers of Inflammation and Cancer." In Long Noncoding RNA, 121–45. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-92034-0_7.

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Vilar, Eduardo, and Josep Tabernero. "Biomarker Discovery Strategies: DNA, RNA, and Protein." In Biomarkers in Oncology, 401–16. New York, NY: Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4419-9755-5_17.

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Bartlett, Michael G., Babak Basiri, and Ning Li. "LC-MS of RNA Biomarkers." In Targeted Biomarker Quantitation by LC-MS, 407–23. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2017. http://dx.doi.org/10.1002/9781119413073.ch26.

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Hahn, Stephan A., Hannah Zoellner, Abdelouahid Maghnouj, and Deepak B. Vangala. "U2 Small Nuclear RNA as a Biomarker in Cancer." In Biomarkers in Cancer, 233–50. Dordrecht: Springer Netherlands, 2015. http://dx.doi.org/10.1007/978-94-007-7681-4_6.

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Hahn, Stephan A., Hannah Zoellner, Abdelouahid Maghnouj, and Deepak B. Vangala. "U2 Small Nuclear RNA as a Biomarker in Cancer." In Biomarkers in Cancer, 1–15. Dordrecht: Springer Netherlands, 2014. http://dx.doi.org/10.1007/978-94-007-7744-6_6-1.

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Song, Qianqian, and Liang Liu. "Single-Cell RNA-Seq Technologies and Computational Analysis Tools: Application in Cancer Research." In Cancer Biomarkers, 245–55. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-1896-7_23.

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Loi, Eleonora, and Patrizia Zavattari. "CpG Islands Methylation Alterations in Cancer: Functionally Intriguing Security Locks, Useful Early Tumor Biomarkers." In RNA Technologies, 53–62. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-14792-1_3.

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Mlcochova, Hana, Renata Hezova, Albano C. Meli, and Ondrej Slaby. "Urinary MicroRNAs as a New Class of Noninvasive Biomarkers in Oncology, Nephrology, and Cardiology." In RNA Interference, 439–63. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-1538-5_26.

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Juracek, Jaroslav, and Ondrej Slaby. "Urinary MicroRNAs as Emerging Class of Noninvasive Biomarkers." In RNA Interference and CRISPR Technologies, 221–47. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0290-4_13.

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Conference papers on the topic "RNA biomarkers"

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Goel, Ajay. "Abstract IA18: Noncoding RNA biomarkers in gastrointestinal cancers." In Abstracts: AACR Special Conference: Colorectal Cancer: From Initiation to Outcomes; September 17-20, 2016; Tampa, FL. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.crc16-ia18.

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Hardikar, Anandwardhan A. "Non-coding RNA Biomarkers Of Diabetes And Metabolic Health." In Qatar Foundation Annual Research Conference Proceedings. Hamad bin Khalifa University Press (HBKU Press), 2014. http://dx.doi.org/10.5339/qfarc.2014.hbpp0302.

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Orjalo, Arturo V., and Hans E. Johansson. "Abstract A2-44: Stellaris® RNA fluorescence in situ hybridization (RNA FISH) for the detection of long non coding RNA biomarkers." In Abstracts: AACR Special Conference: Translation of the Cancer Genome; February 7-9, 2015; San Francisco, CA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.transcagen-a2-44.

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Pangilinan, J., M. Tennis, M. New, and R. L. Keith. "Micro-RNA Profiles as Potential Biomarkers in Prostacyclin Lung Cancer Chemoprevention." In American Thoracic Society 2021 International Conference, May 14-19, 2021 - San Diego, CA. American Thoracic Society, 2021. http://dx.doi.org/10.1164/ajrccm-conference.2021.203.1_meetingabstracts.a4838.

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Tian, Song, Hong Xu, Mohammad Nezami Ranjbar, Frank Reinecke, Xiujing Gu, Raghavendra Padmanabhan, Jixin Deng, et al. "Abstract 753: Profiling of multiple RNA-based biomarkers for cancer identification." In Proceedings: AACR Annual Meeting 2020; April 27-28, 2020 and June 22-24, 2020; Philadelphia, PA. American Association for Cancer Research, 2020. http://dx.doi.org/10.1158/1538-7445.am2020-753.

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Sreebunpeng, Kritsada, Jonathan H. Chan, and Asawin Meechai. "Identification of Gene Subnetwork Biomarkers of Lung Cancer from RNA-seq Data." In CSBio2020: The 11th International Conference on Computational Systems-Biology and Bioinformatics. New York, NY, USA: ACM, 2020. http://dx.doi.org/10.1145/3429210.3429212.

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Cai, Jia-Hua, Yu-Ching Chen, Hsueh-Ting Chu, and Jeffrey J. P. Tsai. "Identification of Potential Long Non-coding RNA Biomarkers for Breast Cancer Patients with Somatic BRCA1 Mutations from RNA-Seq Datasets." In 2018 IEEE 18th International Conference on Bioinformatics and Bioengineering (BIBE). IEEE, 2018. http://dx.doi.org/10.1109/bibe.2018.00060.

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Johansson, Hans E., Arturo V. Orjalo, Sally R. Coassin, and Raymund Yin. "Abstract 3399: Detection and validation of novel RNA cancer biomarkers by single molecule RNA fluorescence in situ hybridization (smRNA FISH)." In Proceedings: AACR Annual Meeting 2014; April 5-9, 2014; San Diego, CA. American Association for Cancer Research, 2014. http://dx.doi.org/10.1158/1538-7445.am2014-3399.

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Antonello, Jenny, Jakub Chudziak, Alan Redfern, Victoria Foy, Shambhavi Srivastava, Adnan Syed, Deborah Burt, et al. "Abstract 5685: An evaluation of DNA and RNA based blood biomarkers in prostate cancer." In Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC. American Association for Cancer Research, 2017. http://dx.doi.org/10.1158/1538-7445.am2017-5685.

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Zhou, Yuehan, Hong Liang, and Jianzhi Deng. "Bioinformatics analysis of competing endogenous RNA and screening of biomarkers in childhood wilms tumor." In ICIIP 2019: 2019 4th International Conference on Intelligent Information Processing. New York, NY, USA: ACM, 2019. http://dx.doi.org/10.1145/3378065.3378156.

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Reports on the topic "RNA biomarkers"

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Xu, Jianhao, Fang Cao, Yongwei Hu, and Zaichang Chen. Circulating long noncoding RNAs as potential biomarkers for stomach cancer: A systematic review and meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, February 2021. http://dx.doi.org/10.37766/inplasy2021.2.0079.

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Liu, Miao, Tihong Liang, Fengyan Wang, Hua Yang, Xu Ning, and Hong Sun. Prognostic value of long non-coding RNA PVT1 as a potential biomarker in osteosarcoma: A protocol for systematic review and meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, September 2020. http://dx.doi.org/10.37766/inplasy2020.9.0050.

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Sun, Lina, Yanan Han, Hua Wang, Huanyu Liu, Shan Liu, Hongbin Yang, Xiaoxia Ren, and Ying Fang. MicroRNAs as Potential Biomarkers for the Diagnosis of Inflammatory Bowel Disease: A Systematic Review and Meta-analysis. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, February 2022. http://dx.doi.org/10.37766/inplasy2022.2.0027.

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Review question / Objective: The purpose of this systematic review was to systematically review the clinical studies regarding miRNAs as diagnostic biomarkers for inflammatory bowel disease and assess the overall diagnostic accuracy of miRNAs. Condition being studied: The symptoms of inflammatory bowel disease (IBD) are highly variable. The diagnosis of IBD must be made through medical history, physical, laboratory, radiologic, endoscopic, and histological examinations. However, these diagnostic techniques are not specific and sometimes even equivocal. Therefore, reliable biomarkers are urgently needed in the diagnosis of IBD. Several clinical and preclinical researches have shown that dysregulated microRNAs (miRNAs) play a crucial role in IBD development. miRNAs, as single-stranded noncoding RNAs that contain 22-24 nucleotides, can post-transcriptionally regulate gene expression by blocking mRNA translation or degrading target mRNAs. miRNAs are widely involved in physiological and pathological cellular processes, such as differentiation, proliferation and apoptosis. Besides, they are stable, noninvasive, and resistant to degradation by ribonucleases, making them valuable targets in the diagnosis, monitoring, prognosis, and treatment of diseases. To date, inconsistent results have been found about miRNA expression profiling in the patients with IBD. Moreover, the diagnostic accuracy of miRNAs for IBD has not been reported in any meta-analysis.
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Zhou, Xuefeng, Wenjing Liu, Zhenhuan Yang, Wei'e Zhou, and Ping Li. Long non-coding RNAs, one of candidate biomarkers in diabetic kidney disease A systematic review protocol of profiling studies. INPLASY - International Platform of Registered Systematic Review and Meta-analysis Protocols, November 2020. http://dx.doi.org/10.37766/inplasy2020.11.0136.

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