Comprehensive analysis of the alteration of plasma miRNA expression level in mice exposed to diesel exhaust

Mixed connective tissue disease (MCTD) is a rare disorder characterized by symptoms that overlap two or more Autoimmune Connective Tissue Diseases (ACTDs). The aim of this study was to determine whether miRNAs participating in the TLRs signaling pathway could serve as biomarkers differentiating MCTD or other ACTD entities from a healthy control group and between groups of patients. Although the selected miRNA expression level was not significantly different between MCTD and control, we observed that miR-126 distinguishes MCTD patients from all other ACTD groups. The expression level of miRNAs was significantly higher in the serum of systemic lupus erythematosus (SLE) and rheumatoid arthritis (RA) patients compared to controls. The miR-145 and -181a levels distinguished RA from other ACDT patients. miR-155 was specific for SLE patients. MiR-132, miR-143, and miR-29a distinguished RA and SLE patients from the systemic sclerosis (SSc) group. Additionally, some clinical parameters were significantly related to the miRNA expression profile in the SLE group. SLE and RA are characterized by a specific serum expression profile of the microRNAs associated with the Toll-like receptors (TLRs) signaling pathway. The analysis showed that their level distinguishes these groups from the control and from other ACTD patients. The present study did not reveal a good biomarker for MCTD patients.

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A PROBABILISTIC FRAMEWORK TO IMPROVE MICRORNA TARGET PREDICTION BY INCORPORATING PROTEOMICS DATA

Journal of Bioinformatics and Computational Biology ◽

10.1142/s021972000900445x ◽

2009 ◽

Vol 07 (06) ◽

pp. 955-972 ◽

Cited By ~ 14

Author(s):

JINGJING LI ◽

RENQIANG MIN ◽

ANTHONY BONNER ◽

ZHAOLEI ZHANG

Keyword(s):

Mrna Expression ◽

Mirna Expression ◽

Probabilistic Model ◽

Expression Level ◽

Sequence Information ◽

Protein Abundance ◽

Underlying Assumption ◽

Mrna Targets ◽

Mirna Expression Level ◽

Sequence Complementarity

Due to the difficulties in identifying microRNA (miRNA) targets experimentally in a high-throughput manner, several computational approaches have been proposed. To this date, most leading algorithms are based on sequence information alone. However, there has been limited overlap between these predictions, implying high false-positive rates, which underlines the limitation of sequence-based approaches. Considering the repressive nature of miRNAs at the mRNA translational level, here we describe a probabilistic model to make predictions by combining sequence complementarity, miRNA expression level, and protein abundance. Our underlying assumption is that, given sequence complementarity between a miRNA and its putative mRNA targets, the miRNA expression level should be high and the protein abundance of the mRNA should be low. Having identified a set of confident predictions, we then built a second probabilistic model to trace back to the mRNA expression of the confident targets to investigate the mechanisms of the miRNA-mediated post-transcriptional regulation. Our results suggest that translational repression (which has no effect on mRNA level), instead of mRNA degradation, is the dominant mechanism in miRNA regulation. This observation explained the previously observed discordant correlation between mRNA expression and protein abundance.

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Identification of miRNA-eQTLs in maize mature leaf by GWAS

BMC Genomics ◽

10.1186/s12864-020-07073-0 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Shu-Yun Chen ◽

Mei-Hsiu Su ◽

Karl A. Kremling ◽

Nicholas K. Lepak ◽

M. Cinta Romay ◽

...

Keyword(s):

Mirna Expression ◽

Target Genes ◽

Genome Wide Association Study ◽

Developmental Stages ◽

Mature Leaf ◽

Plant Genome ◽

Expression Level ◽

Genome Wide ◽

Mirna Expression Level ◽

Next Generation Sequencing Ngs

Abstract Background MiRNAs play essential roles in plant development and response to biotic and abiotic stresses through interaction with their target genes. The expression level of miRNAs shows great variations among different plant accessions, developmental stages, and tissues. Little is known about the content within the plant genome contributing to the variations in plants. This study aims to identify miRNA expression-related quantitative trait loci (miR-QTLs) in the maize genome. Results The miRNA expression level from next generation sequencing (NGS) small RNA libraries derived from mature leaf samples of the maize panel (200 maize lines) was estimated as phenotypes, and maize Hapmap v3.2.1 was chosen as the genotype for the genome-wide association study (GWAS). A total of four significant miR-eQTLs were identified contributing to miR156k-5p, miR159a-3p, miR390a-5p and miR396e-5p, and all of them are trans-eQTLs. In addition, a strong positive coexpression of miRNA was found among five miRNA families. Investigation of the effects of these miRNAs on the expression levels and target genes provided evidence that miRNAs control the expression of their targets by suppression and enhancement. Conclusions These identified significant miR-eQTLs contribute to the diversity of miRNA expression in the maize penal at the developmental stages of mature leaves in maize, and the positive and negative regulation between miRNA and its target genes has also been uncovered.

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Highly Ordered Architecture of MicroRNA Cluster

BioMed Research International ◽

10.1155/2013/463168 ◽

2013 ◽

Vol 2013 ◽

pp. 1-4 ◽

Cited By ~ 3

Author(s):

Bing Shi ◽

Mingxuan Zhu ◽

Shuang Liu ◽

Mandun Zhang

Keyword(s):

Mirna Expression ◽

Expression Patterns ◽

Expression Level ◽

Mirna Cluster ◽

Microrna Cluster ◽

Mirna Clusters ◽

Mirna Expression Level ◽

Cluster A ◽

The Relationship

Although it is known that the placement of genes in a cluster may be critical for proper expression patterns, it remains largely unclear whether the orders of members in an miRNA cluster have biological insights. By investigating the relationship between expression and orders for miRNAs from the oncogenic miR-17-92 cluster, we observed a highly ordered architecture in this cluster. A significant correlation between miRNA expression level and its placement was revealed. More importantly, the placement of these miRNAs is associated with their dysregulation in cancer. Here, we presented the opinion that miRNA clusters are not arranged randomly but show highly ordered architectures, which may have critical roles in physiology and pathology.

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Lack of Conserved miRNA Deregulation in HPV-Induced Squamous Cell Carcinomas

Biomolecules ◽

10.3390/biom11050764 ◽

2021 ◽

Vol 11 (5) ◽

pp. 764

Author(s):

Jaroslav Nunvar ◽

Lucie Pagacova ◽

Zuzana Vojtechova ◽

Nayara Trevisan Doimo de Azevedo ◽

Jana Smahelova ◽

...

Keyword(s):

Squamous Cell ◽

Mirna Expression ◽

Hpv Infection ◽

Squamous Cell Carcinomas ◽

Human Papillomaviruses ◽

Hpv Status ◽

Mirna Expression Level ◽

Cervical Tumors ◽

Mirna Deregulation ◽

Generation Sequencing

Squamous cell carcinomas (SCCs) in the anogenital and head and neck regions are associated with high-risk types of human papillomaviruses (HR-HPV). Deregulation of miRNA expression is an important contributor to carcinogenesis. This study aimed to pinpoint commonly and uniquely deregulated miRNAs in cervical, anal, vulvar, and tonsillar tumors of viral or non-viral etiology, searching for a common set of deregulated miRNAs linked to HPV-induced carcinogenesis. RNA was extracted from tumors and nonmalignant tissues from the same locations. The miRNA expression level was determined by next-generation sequencing. Differential expression of miRNAs was calculated, and the patterns of miRNA deregulation were compared between tumors. The total of deregulated miRNAs varied between tumors of different locations by two orders of magnitude, ranging from 1 to 282. The deregulated miRNA pool was largely tumor-specific. In tumors of the same location, a low proportion of miRNAs were exclusively deregulated and no deregulated miRNA was shared by all four types of HPV-positive tumors. The most significant overlap of deregulated miRNAs was found between tumors which differed in location and HPV status (HPV-positive cervical tumors vs. HPV-negative vulvar tumors). Our results imply that HPV infection does not elicit a conserved miRNA deregulation in SCCs.

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Patterns in circulating microRNA in black (B) versus white (W) patients with triple-negative (TN) breast cancer (BC).

Journal of Clinical Oncology ◽

10.1200/jco.2012.30.15_suppl.1046 ◽

2012 ◽

Vol 30 (15_suppl) ◽

pp. 1046-1046

Author(s):

Iuliana Shapira ◽

Annette Lee ◽

Michaela Oswald ◽

Lora Rose Weiselberg ◽

David Ballard ◽

...

Keyword(s):

Breast Cancer ◽

Cancer Patients ◽

Mirna Expression ◽

Triple Negative ◽

Stage Iii ◽

Striking Difference ◽

Circulating Microrna ◽

Survival Difference ◽

Plasma Mirna ◽

Normal Controls

1046 Background: Breast cancer is by far more common in W than in B women. Black women have more aggressive disease that occurs almost a decade earlier, it is usually triple negative and has a lower survival. Objectives to determine 1) if plasma miRNA expression differs between B and W women, and 2) if variation in miRs may explain the observed survival difference in TNBC in W compared to B women. Methods: We determined miRNA profiles in plasma collected before removal of breast tumors in three groups of W and B women: 1) normal controls (N), 2) TN and 2) ER/PR positive BC. Expression miRNA profiling of 754 miRNAs on the ABI Open Array detected 101miRNAs in plasma. We compared miRNA expression in cancer patients and race-matched controls. A moderated t-statistic through the R/Bioconductor 'limma' was used to compare the mean response between subject factors of interest. Results with a p<0.05 were considered statistically significant. Characteristics: 32 patients were included in this analysis (mean age 50 years; range 31-68), 10 had stage III TNBC (5 B & 5 W); 10 had stage III ER/PR+BC (5 B, 5 W); and 12 were controls (6 B, 6 W) Results: W TNBC patients overexpressed (15 fold higher than normal) 20 miRs in plasma (let-7d, let7g, miR-103, -10a, 15a, -9, -99b, -181a, -18a, -502, -187, -365 and others), these miRs were not found in any of the B patients. Six microRNAs (such as miR-34a, -127 and others) were 15 fold higher than normal controls in B cancer patients, these miRs were not detected in W patients with TNBC. Four miRs in B and 8 miRs in W were not previously reported in association with breast cancer suggesting that they may be connected to the host response. Conclusions: The striking difference in the patterns of plasma miRNA expression between B and W patients may provide the key to the large difference in outcome between these groups when receiving similar treatments, the worse prognosis group may carry the miRs that promote metastasis. The seed-soil hypothesis may explain the better prognosis in W patients. W women may carry those miRNAs that support an “exaggerated” response to systemic treatment, while the B may have the miRs that favour metastasis.

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Genome-Wide Analysis of Human MicroRNA Stability

BioMed Research International ◽

10.1155/2013/368975 ◽

2013 ◽

Vol 2013 ◽

pp. 1-12 ◽

Cited By ~ 7

Author(s):

Yang Li ◽

Zhixin Li ◽

Shixin Zhou ◽

Jinhua Wen ◽

Bin Geng ◽

...

Keyword(s):

Cell Types ◽

Biological Molecules ◽

Expression Level ◽

Action Mode ◽

Status Transition ◽

Genome Wide ◽

Mirna Expression Level ◽

High Dynamics ◽

The Stability ◽

Slow Turnover

Increasing studies have shown that microRNA (miRNA) stability plays important roles in physiology. However, the global picture of miRNA stability remains largely unknown. Here, we had analyzed genome-wide miRNA stability across 10 diverse cell types using miRNA arrays. We found that miRNA stability shows high dynamics and diversity both within individual cells and across cell types. Strikingly, we observed a negative correlation between miRNA stability and miRNA expression level, which is different from current findings on other biological molecules such as proteins and mRNAs that show positive and not negative correlations between stability and expression level. This finding indicates that miRNA has a distinct action mode, which we called “rapid production, rapid turnover; slow production, slow turnover.” This mode further suggests that high expression miRNAs normally degrade fast and may endow the cell with special properties that facilitate cellular status-transition. Moreover, we revealed that the stability of miRNAs is affected by cohorts of factors that include miRNA targets, transcription factors, nucleotide content, evolution, associated disease, and environmental factors. Together, our results provided an extensive description of the global landscape, dynamics, and distinct mode of human miRNA stability, which provide help in investigating their functions in physiology and pathophysiology.

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Comprehensive analysis of the differentially expressed receptor-like kinase genes in responding to pollination in A. thaliana and B. napus

10.21203/rs.2.9786/v1 ◽

2019 ◽

Author(s):

Qiguo Gao ◽

Yupeng Jiang ◽

Xingyu Chen ◽

Yuming Dong ◽

Chen Kuang ◽

...

Keyword(s):

Comprehensive Analysis ◽

Differentially Expressed ◽

Expression Level ◽

Flowering Plant ◽

Level Change ◽

Mature Flower ◽

Receptor Like Kinase ◽

Change Tendency ◽

Differently Expressed Genes

Abstract Background Successful sexual reproduction in flowering plant requires extensive communications between male and female organs and tissues. Although RLKs have been proved to play critical roles in these communications, so far the identified RLKs are still limited. Here we performed a comprehensive analysis on differentially expressed RLKs in responding to pollination in Arabidopsis thaliana and Brassica napus to contibute to further analysis on RLKs’ function in male-female communication. Result In this study, a total of 2,583 B. napus AtRLK orthologs were obtained. 89 AtRLKs showed obvious expression level changes after pollination in A. thaliana or in B. napus. Although 30 differentially expressed AtRLKs were opened anthers and anthers of mature flower before opening preferentially expressed or hydrated pollen-enriched, up to 79 AtRLKs corresponding to 129 B. napus orthologs showed obvious expression level changes at different time points after pollination. Among 89 differentially expressed AtRLKs after pollination, only 7 AtRLKs were shared by differently expressed genes during in vitro pollen tube growth, 3 of 7 AtRLKs’ expression level change tendency after pollination and during PTG were different. Conclusions Amount to 89 AtRLKs were differentially expressed in responding to pollination in A. thaliana and B. napus, and their expression level changes should be mainly induced by pollen-stigma interaction, several of them had been proved to function in male-female communication in the former reports.

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MicroRNA in refined diagnosis of choroidal melanoma

Acta biomedica scientifica ◽

10.29413/abs.2021-6.6-1.8 ◽

2021 ◽

Vol 6 (6-1) ◽

pp. 65-73

Author(s):

A. F. Brovkina ◽

N. D. Tsybikova

Keyword(s):

Cell Proliferation ◽

Differential Diagnosis ◽

Mirna Expression ◽

Real Time Pcr ◽

Malignant Tumors ◽

Choroidal Melanoma ◽

Accurate Diagnosis ◽

Control Group ◽

Plasma Mirna

Epigenetic studies of the level of microRNAs in human oncogenesis indicate their signifi cant role in the development and growth of malignant tumors of various origins. The fi rst works on the role of microRNAs in patients with uveal melanoma appeared in 2008.The aim: to analyze the expression level of miRNA-126 and miRNA-223 in the plasma blood of patients and to determine their signifi cance in the refi ned diagnosis of choroidal melanoma. Materials and methods. We examined 84 patients with choroidal melanoma (CM), mean age – 63.4 ± 1.2 (35–86 y.o.). Localization – a single CM node with a thickness of 0.77–17.19 mm. The control group consisted of 28 volunteers, age – 62.9 ± 1.42 (45–78 y.o.). Plasma miRNA expression levels were determined by real-time PCR.Results. An increase in the level of expression of miRNA-223 and miRNA-126 in blood plasma was confi rmed in all 84 patients with choroidal melanoma N0M0 compared with the control group. An increase in the expression of miRNA-223 and miRNA-126 was proved with an increase in tumor prominence.Conclusion. The obtained results of an increase in the expression of miRNA-223 indicate an increase in cell proliferation, and an increase in the expression of miRNA-126 on the activation of angiogenesis in a growing tumor, which makes it possible to recommend a study of the level of miRNA-223 and miRNA-126 for a more accurate diagnosis of small CM in cases of difficulty of differential diagnosis with other tumor-like diseases of the choroid.

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