scholarly journals Specific PIWI-interacting small noncoding RNA expression patterns in pulmonary tuberculosis patients

Epigenomics ◽  
2019 ◽  
Vol 11 (16) ◽  
pp. 1779-1794 ◽  
Author(s):  
Xing Zhang ◽  
Zi Liang ◽  
Yunshan Zhang ◽  
Min Zhu ◽  
Yueping Zhu ◽  
...  
Keyword(s):  
Pulmonary Tuberculosis ◽  
Peripheral Blood ◽  
Noncoding Rna ◽  
Target Genes ◽  
Human Peripheral Blood ◽  
Expression Patterns ◽  
Small Rna Sequencing ◽  
Germline Development ◽  
Small Noncoding Rna ◽  
Pirna Pathway

Aim: PIWI-interacting RNAs (piRNAs) play crucial roles in germline development and carcinogenesis. The expression patterns of piRNAs in pulmonary tuberculosis (PTB) are still unclear. Materials & methods: Small RNA sequencing was applied to investigate peripheral blood piRNA expression patterns in PTB patients and healthy individuals. Results: A total of 428 upregulated and 349 downregulated piRNAs were identified from PTB patients. Target genes of dysregulated piRNAs were mainly involved in transcription and protein binding. Dysregulated piRNAs were enriched in many pathways related with immunity. Many target genes were regulated by the same piRNAs. Nucleotide bias of these piRNAs showed that piRNAs in peripheral blood may be formed from the primary biogenesis pathway. Conclusion: Findings demonstrated that the PIWI-piRNA pathway is active in human peripheral blood, where it may represent a new player in the PTB pathogenesis.

scholarly journals Distinct miRNA Signatures and Networks Discern Fetal from Adult Erythroid Differentiation and Primary from Immortalized Erythroid Cells

2021 ◽  
Vol 22 (7) ◽  
pp. 3626
Author(s):  
Panayiota L. Papasavva ◽  
Nikoletta Y. Papaioannou ◽  
Petros Patsali ◽  
Ryo Kurita ◽  
Yukio Nakamura ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Regulatory Networks ◽  
Target Genes ◽  
Human Peripheral Blood ◽  
Expression Patterns ◽  
Erythroid Differentiation ◽  
Erythroid Cell ◽  
Small Rna Sequencing ◽  
Erythroid Cells ◽  
Mirna Regulation

MicroRNAs (miRNAs) are small non-coding RNAs crucial for post-transcriptional and translational regulation of cellular and developmental pathways. The study of miRNAs in erythropoiesis elucidates underlying regulatory mechanisms and facilitates related diagnostic and therapy development. Here, we used DNA Nanoball (DNB) small RNA sequencing to comprehensively characterize miRNAs in human erythroid cell cultures. Based on primary human peripheral-blood-derived CD34+ (hCD34+) cells and two influential erythroid cell lines with adult and fetal hemoglobin expression patterns, HUDEP-2 and HUDEP-1, respectively, our study links differential miRNA expression to erythroid differentiation, cell type, and hemoglobin expression profile. Sequencing results validated by reverse-transcription quantitative PCR (RT-qPCR) of selected miRNAs indicate shared differentiation signatures in primary and immortalized cells, characterized by reduced overall miRNA expression and reciprocal expression increases for individual lineage-specific miRNAs in late-stage erythropoiesis. Despite the high similarity of same-stage hCD34+ and HUDEP-2 cells, differential expression of several miRNAs highlighted informative discrepancies between both cell types. Moreover, a comparison between HUDEP-2 and HUDEP-1 cells displayed changes in miRNAs, transcription factors (TFs), target genes, and pathways associated with globin switching. In resulting TF-miRNA co-regulatory networks, major therapeutically relevant regulators of globin expression were targeted by many co-expressed miRNAs, outlining intricate combinatorial miRNA regulation of globin expression in erythroid cells.

scholarly journals Genome-wide analysis of changes in miRNA and target gene expression reveals key roles in heterosis for Chinese cabbage biomass

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Peirong Li ◽  
Tongbing Su ◽  
Deshuang Zhang ◽  
Weihong Wang ◽  
Xiaoyun Xin ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Leaf Development ◽  
Target Genes ◽  
Expression Patterns ◽  
Seedling Stage ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Leaf Morphogenesis ◽  
Expression Levels ◽  
Parental Lines

AbstractHeterosis is a complex phenomenon in which hybrids show better phenotypic characteristics than their parents do. Chinese cabbage (Brassica rapa L. spp. pekinensis) is a popular leafy crop species, hybrids of which are widely used in commercial production; however, the molecular basis of heterosis for biomass of Chinese cabbage is poorly understood. We characterized heterosis in a Chinese cabbage F1 hybrid cultivar and its parental lines from the seedling stage to the heading stage; marked heterosis of leaf weight and biomass yield were observed. Small RNA sequencing revealed 63 and 50 differentially expressed microRNAs (DEMs) at the seedling and early-heading stages, respectively. The expression levels of the majority of miRNA clusters in the F1 hybrid were lower than the mid-parent values (MPVs). Using degradome sequencing, we identified 1,819 miRNA target genes. Gene ontology (GO) analyses demonstrated that the target genes of the MPV-DEMs and low parental expression level dominance (ELD) miRNAs were significantly enriched in leaf morphogenesis, leaf development, and leaf shaping. Transcriptome analysis revealed that the expression levels of photosynthesis and chlorophyll synthesis-related MPV-DEGs (differentially expressed genes) were significantly different in the F1 hybrid compared to the parental lines, resulting in increased photosynthesis capacity and chlorophyll content in the former. Furthermore, expression of genes known to regulate leaf development was also observed at the seedling stage. Arabidopsis plants overexpressing BrGRF4.2 and bra-miR396 presented increased and decreased leaf sizes, respectively. These results provide new insight into the regulation of target genes and miRNA expression patterns in leaf size and heterosis for biomass of B. rapa.

MicroRNAs in domestic livestock

2013 ◽  
Vol 45 (16) ◽  
pp. 685-696 ◽  
Author(s):  
Attia Fatima ◽  
Dermot G. Morris
Keyword(s):  
Posttranscriptional Regulation ◽  
Noncoding Rna ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Noncoding Rna ◽  
Domestic Livestock ◽  
Temporal Expression Pattern ◽  
Mrna Binding

microRNAs (miRNAs) are a class of small noncoding RNA that bind to complementary sequences in the untranslated regions of multiple target mRNAs resulting in posttranscriptional regulation of gene expression. The recent discovery and expression-profiling studies of miRNAs in domestic livestock have revealed both their tissue-specific and temporal expression pattern. In addition, breed-dependent expression patterns as well as single nucleotide polymorphisms in either the miRNA or in the target mRNA binding site have revealed associations with traits of economic importance and highlight the potential use of miRNAs in future genomic selection programs.

scholarly journals The emerging role of microRNAs in bone remodeling and its therapeutic implications for osteoporosis

2018 ◽  
Vol 38 (3) ◽  
Author(s):  
Qianyun Feng ◽  
Sheng Zheng ◽  
Jia Zheng
Keyword(s):  
Bone Remodeling ◽  
Noncoding Rna ◽  
Target Genes ◽  
Epigenetic Modification ◽  
Therapeutic Implications ◽  
Small Noncoding Rna ◽  
Genetic And Environmental Factors ◽  
Underlying Mechanisms ◽  
Post Transcriptional Regulation

Osteoporosis, a common and multifactorial disease, is influenced by genetic factors and environments. However, the pathogenesis of osteoporosis has not been fully elucidated yet. Recently, emerging evidence suggests that epigenetic modifications may be the underlying mechanisms that link genetic and environmental factors with increased risks of osteoporosis and bone fracture. MicroRNA (miRNA), a major category of small noncoding RNA with 20–22 bases in length, is recognized as one important epigenetic modification. It can mediate post-transcriptional regulation of target genes with cell differentiation and apoptosis. In this review, we aimed to profile the role of miRNA in bone remodeling and its therapeutic implications for osteoporosis. A deeper insight into the role of miRNA in bone remodeling and osteoporosis can provide unique opportunities to develop a novel diagnostic and therapeutic approach of osteoporosis.

scholarly journals Curcumin inhibits cancer progression through regulating expression of microRNAs

Tumor Biology ◽  
2017 ◽  
Vol 39 (2) ◽  
pp. 101042831769168 ◽  
Author(s):  
Siying Zhou ◽  
Sijie Zhang ◽  
Hongyu Shen ◽  
Wei Chen ◽  
Hanzi Xu ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Cancer Progression ◽  
Noncoding Rna ◽  
Target Genes ◽  
Therapeutic Potential ◽  
Tumor Biology ◽  
Multiple Cancer ◽  
Small Noncoding Rna ◽  
Cancer Agent ◽  
Regulation Of Cell Cycle

Curcumin, a major yellow pigment and spice in turmeric and curry, is a powerful anti-cancer agent. The anti-tumor activities of curcumin include inhibition of tumor proliferation, angiogenesis, invasion and metastasis, induction of tumor apoptosis, increase of chemotherapy sensitivity, and regulation of cell cycle and cancer stem cell, indicating that curcumin maybe a strong therapeutic potential through modulating various cancer progression. It has been reported that microRNAs as small noncoding RNA molecules are related to cancer progression, which can be regulated by curcumin. Dysregulated microRNAs play vital roles in tumor biology via regulating expressions of target genes and then influencing multiple cancer-related signaling pathways. In this review, we focused on the inhibition effect of curcumin on various cancer progression by regulating expression of multiple microRNAs. Curcumin-induced dysregulation of microRNAs may activate or inactivate a set of signaling pathways, such as Akt, Bcl-2, PTEN, p53, Notch, and Erbb signaling pathways. A better understanding of the relation between curcumin and microRNAs may provide a potential therapeutic target for various cancers.

Circulating Small Noncoding RNA Biomarkers of Response to Triple Disease-modifying Antirheumatic Drug Therapy in White Women With Early Rheumatoid Arthritis

2020 ◽  
Vol 47 (12) ◽  
pp. 1746-1751
Author(s):  
Andrew D. Foers ◽  
Alexandra L. Garnham ◽  
Gordon K. Smyth ◽  
Susanna M. Proudman ◽  
Lesley Cheng ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Early Rheumatoid Arthritis ◽  
Noncoding Rna ◽  
Differential Expression Analysis ◽  
Antirheumatic Drug ◽  
Small Rna Sequencing ◽  
Dmard Therapy ◽  
Small Noncoding Rna ◽  
Disease Modifying ◽  
Disease Modifying Antirheumatic Drug

ObjectiveTo identify small noncoding RNA (sncRNA) serum biomarkers that predict response to triple disease-modifying antirheumatic drug (DMARD) therapy in patients with early rheumatoid arthritis (RA).MethodsEarly RA patients entered into a treat-to-target management algorithm, with triple DMARD therapy (methotrexate, sulfasalazine, hydroxychloroquine). Patients were assessed following 6 months of therapy and classified as European League Against Rheumatism responders or nonresponders. RNA was isolated from 42 archived serum samples, collected prior to commencement of triple DMARD therapy. Small RNA sequencing was performed and the reads mapped to annotations in a database of human sncRNA. Differential expression analysis was performed, comparing responders (n = 24) and nonresponders (n = 18).ResultsPretreatment levels of 4 sncRNA were significantly increased in nonresponders: chr1. tRNA131-GlyCCC (4.1-fold, adjusted P = 0.01), chr2.tRNA13-AlaCGC (2.2-fold, adjusted P = 0.02), U2-L166 (6.6-fold, adjusted P = 0.02), and piR-35982 (2.4-fold, adjusted P = 0.03). 5S-L612 was the only sncRNA significantly increased in responders (3.3-fold; adjusted P = 0.01). Reads for chr1. tRNA131-GlyCCC and chr2.tRNA13-AlaCGC mapped to the 5′ end of each tRNA gene and were truncated at the anticodon loop, consistent with these sncRNA having roles as 5′ translation interfering tRNA halves (tiRNA).ConclusionPretreatment levels of specific serum sncRNA might facilitate identification of patients more likely to respond to triple DMARD therapy.

scholarly journals MicroRNAs in endometriosis: biological function and emerging biomarker candidates†

2019 ◽  
Vol 101 (6) ◽  
pp. 1167-1178 ◽  
Author(s):  
Sarah Bjorkman ◽  
Hugh S Taylor
Keyword(s):  
Noncoding Rna ◽  
Target Genes ◽  
Biological Function ◽  
Transcriptional Regulators ◽  
Circulating Mirnas ◽  
Common Chronic Disease ◽  
Rna Molecules ◽  
Small Noncoding Rna ◽  
Reproductive Aged Women ◽  
Delayed Time

AbstractMicroRNAs (miRNAs), a class of small noncoding RNA molecules, have been recognized as key post-transcriptional regulators associated with a multitude of human diseases. Global expression profiling studies have uncovered hundreds of miRNAs that are dysregulated in several diseases, and yielded many candidate biomarkers. This review will focus on miRNAs in endometriosis, a common chronic disease affecting nearly 10% of reproductive-aged women, which can cause pelvic pain, infertility, and a myriad of other symptoms. Endometriosis has delayed time to diagnosis when compared to other chronic diseases, as there is no current accurate, easily accessible, and noninvasive tool for diagnosis. Specific miRNAs have been identified as potential biomarkers for this disease in multiple studies. These and other miRNAs have been linked to target genes and functional pathways in disease-specific pathophysiology. Highlighting investigations into the roles of tissue and circulating miRNAs in endometriosis, published through June 2018, this review summarizes new connections between miRNA expression and the pathophysiology of endometriosis, including impacts on fertility. Future applications of miRNA biomarkers for precision medicine in diagnosing and managing endometriosis treatment are also discussed.

scholarly journals MicroRNAs as Regulator of Signaling Networks in Metastatic Colon Cancer

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Jian Wang ◽  
Yong Du ◽  
Xiaoming Liu ◽  
William C. Cho ◽  
Yinxue Yang
Keyword(s):  
Colon Cancer ◽  
Noncoding Rna ◽  
Cancer Metastasis ◽  
Target Genes ◽  
Signaling Networks ◽  
Metastatic Colon Cancer ◽  
Rna Molecules ◽  
Small Noncoding Rna ◽  
P53 Signaling ◽  
Colon Cancer Metastasis

MicroRNAs (miRNAs) are a class of small, noncoding RNA molecules capable of regulating gene expression translationally and/or transcriptionally. A large number of evidence have demonstrated that miRNAs have a functional role in both physiological and pathological processes by regulating the expression of their target genes. Recently, the functionalities of miRNAs in the initiation, progression, angiogenesis, metastasis, and chemoresistance of tumors have gained increasing attentions. Particularly, the alteration of miRNA profiles has been correlated with the transformation and metastasis of various cancers, including colon cancer. This paper reports the latest findings on miRNAs involved in different signaling networks leading to colon cancer metastasis, mainly focusing on miRNA profiling and their roles in PTEN/PI3K, EGFR, TGFβ, and p53 signaling pathways of metastatic colon cancer. The potential of miRNAs used as biomarkers in the diagnosis, prognosis, and therapeutic targets in colon cancer is also discussed.

scholarly journals Investigation and Identification of let-7a Related Functional Proteins in Gastric Carcinoma by Proteomics

2012 ◽  
Vol 35 (4) ◽  
pp. 285-295 ◽  
Author(s):  
Yimin Zhu ◽  
Xingyuan Xiao ◽  
Lairong Dong ◽  
Zhiming Liu
Keyword(s):  
Gastric Carcinoma ◽  
Noncoding Rna ◽  
Target Genes ◽  
Rho Gtpase ◽  
Two Dimensional Gel Electrophoresis ◽  
Gastric Carcinoma Cell ◽  
Rna Molecules ◽  
Small Noncoding Rna

MicroRNAs are small noncoding RNA molecules that control expression of target genes. Our previous studies show that let-7a decreased in gastric carcinoma and that up-regulation of let-7a by gene augmentation inhibited gastric carcinoma cell growth bothin vitroandin vivo, whereas it remains largely unclear as to how let-7a affects tumor growth. In this study, proteins associated with the function of let-7a were detected by high throughout screening. The cell line of SGC-7901 stablely overexpressing let-7a was successfully established by gene cloning. Two-dimensional gel electrophoresis (2-DEy was used to separate the total proteins of SGC-7901/let-7a, SGC-7901/EV and SGC-7901, and PDQuest software was applied to analyze 2-DE images. Ten different protein spots were identified by MALDI-TOF-MS, and they may be the proteins associated with let-7a function. The overexpressed proteins included Antioxidant protein 2, Insulin–like growth factor binding protein 2, Protein disulfide isomerase A2, C-1-tetrahydrofolate synthase, Cyclin-dependent kinase inhibitor1 (CDKN1) and Rho–GTPase activating protein 4. The underexpressed proteins consisted of S-phase kinase-associated protein 2 (Spk2), Platelet membrane glycoprotein, Fibronectin and Cks1 protein. Furthermore, the different expression levels of the partial proteins (CDKN1, Spk2 and Fibronectin) were confirmed by western blot analysis. The data suggest that these differential proteins are involved in a novel let-7a signal pathway and these findings provide the basis to investigate the functional mechanisms of let-7a in gastric carcinoma.

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