scholarly journals miRNAome expression profiles in the gonads of adultMelopsittacus undulatus

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4615 ◽  
Author(s):  
Lan Jiang ◽  
Qingqing Wang ◽  
Jue Yu ◽  
Vinita Gowda ◽  
Gabriel Johnson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Early Development ◽  
Expression Profiles ◽  
Critical Role ◽  
Genomic Research ◽  
Go Annotation ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Mirnas Expression ◽  
Paired End Sequencing

The budgerigar (Melopsittacus undulatus) is one of the most widely studied parrot species, serving as an excellent animal model for behavior and neuroscience research. Until recently, it was unknown how sexual differences in the behavior, physiology, and development of organisms are regulated by differential gene expression. MicroRNAs (miRNAs) are endogenous short non-coding RNA molecules that can post-transcriptionally regulate gene expression and play a critical role in gonadal differentiation as well as early development of animals. However, very little is known about the role gonadal miRNAs play in the early development of birds. Research on the sex-biased expression of miRNAs in avian gonads are limited, and little is known aboutM. undulatus. In the current study, we sequenced two small non-coding RNA libraries made from the gonads of adult male and female budgerigars using Illumina paired-end sequencing technology. We obtained 254 known and 141 novel miRNAs, and randomly validated five miRNAs. Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research.

scholarly journals Genome-wide miRNA profiling of villus and decidua of recurrent spontaneous abortion patients

Reproduction ◽  
2014 ◽  
Vol 148 (1) ◽  
pp. 33-41 ◽  
Author(s):  
Fulu Dong ◽  
Yuan Zhang ◽  
Fei Xia ◽  
Yi Yang ◽  
Sidong Xiong ◽  
...  
Keyword(s):  
Spontaneous Abortion ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Expression Profiles ◽  
Normal Pregnancy ◽  
Recurrent Spontaneous Abortion ◽  
Future Research ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Transcriptional Gene Regulation

MicroRNAs (miRNAs) are non-coding RNA molecules of about 22 nucleotides that involved in post-transcriptional gene regulation. Evidence indicates that miRNAs play essential roles in endometriosis, pre-eclampsia, infertility and other reproductive system diseases. However, whether miRNAs are involved in recurrent spontaneous abortion (RSA) is unclear. In this work, we analysed the miRNA expression profiles in six pairs of villus or decidua from RSA patients and normal pregnancy (NP) women using a human miRNA microarray. Some of the chip results were confirmed by RT-qPCR. In the villi of RSA patients, expression of hsa-miR-184, hsa-miR-187 and hsa-miR-125b-2 was significantly higher, while expression of hsa-miR-520f, hsa-miR-3175 and hsa-miR-4672 was significantly lower, comparing with those of NP control. As well, a total of five miRNAs (hsa-miR-517c, hsa-miR-519a-1, hsa-miR-522, hsa-miR-520h and hsa-miR-184) were upregulated in the decidua of RSA patients. The target genes of these differentially expressed miRNAs were predicted by miRWalk, and we speculate a network of miRNA regulating RSA by target genes function on adhesion, apoptosis and angiogenesis. Our study may help clarify the molecular mechanisms which are involved in the progression of RSA, and provide a reference for future research.

Comprehensive Analysis of Differential Expression Profiles of Long Non-coding RNAs with Associated Co-expression and Competing Endogenous RNA Networks in the Hippocampus of Patients with Alzheimer's Disease

2021 ◽  
Vol 18 ◽  
Author(s):  
Jian-Jun Zhang ◽  
Ze-Xuan-Zhu ◽  
Guang-Min-Xu ◽  
Peng Su ◽  
Qian Lei ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Expression Profiles ◽  
Gene Expression Omnibus ◽  
Competing Endogenous Rna ◽  
Pathogenic Genes ◽  
Non Coding Rna ◽  
Using Data ◽  
Trans Regulation

Background: Alzheimer's disease (AD) is still one of the major threats to human health. Although a satisfactory treatment for AD has not yet been discovered, it is necessary to continue to search for novel approaches to deal with this insidious and debilitating disease. Although numerous studies have shown that long non-coding RNA (lncRNA) occupy a significant role in a variety of diseases, their roles in AD remain unclear. Objectives: Using data analysis to explore the role of lncRNA in the course of AD, to further our understanding of AD, and to look forward to finding a new breakthrough for the treatment of AD. Methods: We downloaded and screened expression data of the hippocampal regions of patients with AD from the Gene Expression Omnibus database. We generated lncRNA-miRNA-mRNA networks based on the competing endogenous RNA (ceRNA) hypothesis, and according to gene expression level, we constructed a coding-noncoding co-expression (CNC) network and then executed cis- and trans-regulation analyses. Results: Through comprehensive and systematic analyses, we found that lncRNAs MALAT1, OIP5-AS1, LINC00657, and lnc-NUMB-1 regulated the expression of the key AD pathogenic genes APP, PSEN1, BACE1; and that these lncRNAs may promote the distribution of β-amyloid (Aβ protein) in the brain through exosomes. In addition, lncRNAs were found to adjust viral transcriptional expression, thereby further supporting viral pathogenesis for AD. Conclusions: The lncRNAs MALAT1, OIP5-AS1, LINC00657, and lnc-NUMB-1 that are present in the hippocampus of AD patients exert an important influence on the development of this disease.

The characteristics of mesenteric adipose tissue attached to different intestinal segments and their roles in immune regulation

2022 ◽  
Author(s):  
Haowei Zhang ◽  
Yujin Ding ◽  
Qin Zeng ◽  
Dandan Wang ◽  
Ganglei Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Adipose Tissue ◽  
Immune Regulation ◽  
Expression Profiles ◽  
Critical Role ◽  
Gene Expression Profiles ◽  
Rna Seq ◽  
Mesenteric Adipose Tissue ◽  
Cell Components ◽  
Subsequent Effect

Background: Mesenteric adipose tissue (MAT) plays a critical role in the intestinal physiological ecosystems. Small and large intestines have evidently intrinsic and distinct characteristics. However, whether there exist any mesenteric differences adjacent to the small and large intestines (SMAT and LMAT) has not been properly characterized. We studied the important facets of these differences, such as morphology, gene expression, cell components and immune regulation of MATs, to characterize the mesenteric differences. Methods: The SMAT and LMAT of mice were utilized for comparison of tissue morphology. Paired mesenteric samples were analyzed by RNA-seq to clarify gene expression profiles. MAT partial excision models were constructed to illustrate the immune regulation roles of MATs, and 16S-seq was applied to detect the subsequent effect on microbiota. Results: Our data show that different segments of mesenteries have different morphological structures. SMAT not only has smaller adipocytes but also contains more fat-associated lymphoid clusters than LMAT. The gene expression profile is also discrepant between these two MATs in mice. B-cell markers were abundantly expressed in SMAT, while development-related genes were highly expressed in LMAT. Adipose-derived stem cells of LMAT exhibited higher adipogenic potential and lower proliferation rates than those of SMAT. In addition, SMAT and LMAT play different roles in immune regulation and subsequently affect microbiota components. Finally, our data clarified the described differences between SMAT and LMAT in humans. Conclusions: There were significant differences in cell morphology, gene expression profiles, cell components, biological characteristics, and immune and microbiota regulation roles between regional MATs.

scholarly journals Molecular Mechanisms, Diagnostic Aspects and Therapeutic Opportunities of Micro Ribonucleic Acids in Atrial Fibrillation

2020 ◽  
Vol 21 (8) ◽  
pp. 2742 ◽  
Author(s):  
Allan Böhm ◽  
Marianna Vachalcova ◽  
Peter Snopek ◽  
Ljuba Bacharova ◽  
Dominika Komarova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Atrial Fibrillation ◽  
Molecular Mechanisms ◽  
Wide Spectrum ◽  
Regulation Of Gene Expression ◽  
Review Article ◽  
Ribonucleic Acids ◽  
Rna Molecules ◽  
Diagnostic Aspects ◽  
Non Coding Rna

Micro ribonucleic acids (miRNAs) are short non-coding RNA molecules responsible for regulation of gene expression. They are involved in many pathophysiological processes of a wide spectrum of diseases. Recent studies showed their involvement in atrial fibrillation. They seem to become potential screening biomarkers for atrial fibrillation and even treatment targets for this arrhythmia. The aim of this review article was to summarize the latest knowledge about miRNA and their molecular relation to the pathophysiology, diagnosis and treatment of atrial fibrillation.

Inhibition of Elastase or SDF-1/CXCR4 Axis Promotes Differentiation of Human AML Cells.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1891-1891
Author(s):  
Sigal Tavor ◽  
Jasmine Jacob-Hirsch ◽  
Manny Eisenbach ◽  
Sigi Kay ◽  
Shoshana Baron ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Critical Role ◽  
Marker Genes ◽  
Granulocytic Differentiation ◽  
Elastase Inhibitor ◽  
Granule Proteins ◽  
Cxcr4 Axis

Abstract Elastase, along with other azurophil granule proteins like proteinase 3 regulates normal and leukemic granulopoiesis in an un-defined mechanism. We have recently showed that human acute myeloid leukemic (AML) cells constitutively express and secrete stromal derived factor 1 (SDF-1) dependent cell surface elastase, which regulates their migration and proliferation. To elucidate the molecular events and genes regulated by elastase and SDF-1/CXCR4 axis in AML cells, we examined gene expression of U937 AML cell line treated with neutralizing anti-CXCR4 Abs or elastase inhibitor (EI) compared to untreated cells, using DNA microarray technology. Unsupervised hierarchical clustering analysis showed very similar gene expression profiles of EI and anti CXCR4 Abs treated cells as compared to control. 230 of 8400 genes interrogated were repressed, and 164 were induced after culturing AML cells in the presence of EI or anti CXCR4 Abs at different time points as compared to untreated cells. Inhibition of elastase or CXCR4 was accompanied by down regulation of the transcripts of primary granule proteins. Functional classification of elastase or SDF-1/CXCR4 axis regulated genes revealed downregulation of HOXA9, HOXA10, ETS2, as well as other transcription factors that are over expressed in AML and are important for the development of leukemia. Whereas, transcriptional factors and regulators known to be induced during myeloid differentiation like C/EBPε, ID1, RUNX3 and HHEX were up-regulated in treated cells. Expression patterns of apoptosis genes indicated decline in death control by the p53 dependent pathway and a more prominent control by mitochondrial mediated apoptotic pathway like bcl2 related genes. In addition, receptors for interleukins, growth factors (G-CSFR and GM-CSF), complement component (C1QR1) were upregulated in the treated cells. In contrast, FLT-3, a growth factor receptor stimulating growth of early progenitor cells and AML blasts, was down regulated in AML cell treated with EI or anti CXCR4 Abs. These data were confirmed by real time PCR for selected marker genes of granulocytic differentiation. Interestingly, many of the differentially expressed genes were common to the transcriptional program of normal terminal granulocytic differentiation (Theilgaard-Monch & Borregarrd 2005. Blood 105:1785) suggesting that inhibition of elastase may induce differentiation in AML cells. Thus we further analyzed the effect of elastase inhibition on AML cell differentiation and growth. Treatment of HL60 AML cell line with EI triggered a proliferative arrest, apoptosis and mimicked terminal granulocytic differentiation, including morphologic changes, increased CD11b expression, and the ability to produce oxidative bursts. In summary, our study showed that inhibition of elastase or SDF-1/CXCR4 axis in AML cells affects similar pathways related to differentiation and malignant transformation, implying a critical role for those molecules in regulating leukemic development. Repression of elastase decreases proliferation and induces differentiation of AML cells, suggesting a potential new therapeutic approach for AML.

The critical role of surgical pathology in personalized medicine: The impact of biopsy cavities in breast cancer samples on recurrence risk when assessed by quantitative RT-PCR

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e22016-e22016
Author(s):  
F. L. Baehner ◽  
J. Anderson ◽  
C. Millward ◽  
C. Sangli ◽  
C. Quale ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Expression Profiles ◽  
Critical Role ◽  
Recurrence Score ◽  
Pcr Analysis ◽  
Breast Cancers ◽  
Rt Pcr ◽  
Poorly Differentiated ◽  
The Impact

e22016 Background: Tumor gene expression analysis using the Recurrence Score (RS) assay is frequently used in ER+ breast cancer. Manual microdissection is performed in cases where biopsy cavities (BxC) are present in the submitted specimen. The objective of this was to characterize by quantitative RT-PCR the impact of BxC on 21 gene expression profiles and the RS. Methods: 48 (15 well, 18 moderate, and 15 poorly differentiated) breast cancers were evaluated for gene expression differences between whole sections (WS; containing BxC) and enriched tumor (ET; BxC excluded). Standardized quantitative RT-PCR analysis for the 21 Oncotype DX genes was performed; reference normalized gene expression measurements ranged from 0 to 15, where each 1-unit reflects an approximate 2-fold change in RNA. Analyses of individual genes and the RS were performed on the entire sample set and stratified by tumor grade. Correlation analyses used Pearson's R, concordance analysis used Lin's sample concordance and paired t- tests to characterize differences. Results: There were statistically significant differences in reference normalized gene expression between ET and WS in 6 genes: BAG1 (ET-WS: 0.13 units, p=0.0025), CD68 (ET-WS: -0.64 units, p<0.0001), ER (ET-WS: 0.29 units, p=0.0012), GSTM1 (ET-WS: 0.18 units p=0.0025), STK15 (ET-WS: -0.18 units, p=0.0041) and STMY3 (ET-WS: 0.62 units, p<0.0001). Expression of the macrophage marker CD68 was higher and expression of ER was lower in WS containing BxC. The correlation (0.95) and concordance (0.92) were generally high between WS and ET for RS overall however among moderately differentially tumors, there was a statistically significant mean increase in RS for WS of 3.3 units (p = 0.0012) while among poorly differentiated tumors there was a trend toward a statistically significant decrease in RS for WS of 2.2 units (p=0.0569). Conclusions: Histologic identification of invasive carcinoma and exclusion of BxC is essential for precise RS assessment. Inclusion of BxC in breast cancer specimens is associated with significant changes in the expression of individual genes and impacts the RS. Removal of BxC from breast cancer specimens assessed for gene expression levels is warranted. [Table: see text]

scholarly journals Gene expression profiling of gilthead sea bream during early development and detection of stress-related genes by the application of cDNA microarray technology

2005 ◽  
Vol 23 (2) ◽  
pp. 182-191 ◽  
Author(s):  
Elena Sarropoulou ◽  
Georgios Kotoulas ◽  
Deborah M. Power ◽  
Robert Geisler
Keyword(s):  
Gene Expression ◽  
Early Development ◽  
Cdna Microarray ◽  
Evolutionary Biology ◽  
Large Scale ◽  
Expression Profiles ◽  
Gilthead Sea Bream ◽  
Sea Bream ◽  
Regulatory Pathways ◽  
Study Gene Expression

Large-scale gene expression studies were performed for one of the main European aquaculture species, the gilthead sea bream Sparus auratus L. For this purpose, a cDNA microarray containing 10,176 clones from a cDNA library of mixed embryonic and larval stages was constructed. In addition to its importance for aquaculture, the taxonomic position and the relatively small genome size of sea bream makes it a prospective model for evolutionary biology and comparative genomics. However, so far, no large-scale analysis of gene expression exists for this species. In the present study, gene expression was analyzed in gilthead sea bream during early development, a significant period in the determination of quantitative traits and therefore of considerable interest for aquaculture. Synexpression groups expressed primarily early and late in development were determined and were composed of both known and novel genes. Furthermore, it was possible to identify stress response genes induced by cortisol injections using the cDNA microarray generated. The creation of gene expression profiles for sea bream by microarray hybridization will accelerate identification of candidate genes involved in multifactorial traits and certain regulatory pathways and will also contribute to a better understanding of the genetic background of fish physiology, which may help to improve aquaculture practices.

MicroRNA profiling in cancer

2011 ◽  
Vol 121 (4) ◽  
pp. 141-158 ◽  
Author(s):  
Reinhold Munker ◽  
George A. Calin
Keyword(s):  
Gene Expression ◽  
Expression Profiling ◽  
Cell Biology ◽  
Human Cancer ◽  
Rare Tumour ◽  
Rna Molecules ◽  
Future Developments ◽  
Microrna Profiling ◽  
Non Coding Rna ◽  
Diagnosis Of Cancer

The diagnosis of cancer has undergone major changes in the last 40 years. Once based purely on morphology, diagnosis has come to incorporate immunological, cytogenetic and molecular methods. Many cancers, especially leukaemias, are now defined by molecular markers. Gene expression profiling based on mRNA has led to further refinement of the classification and diagnosis of cancer. More recently, miRNAs (microRNAs), among other small non-coding RNA molecules, have been discovered and found to be major players in cell biology. miRNAs, having both oncogenic and tumour-suppressive functions, are dysregulated in many types of cancer. miRNAs also interfere with metastasis, apoptosis and invasiveness of cancer cells. In the present review, we discuss recent advances in miRNA profiling in human cancer. We discuss both frequent and rare tumour types and give an outlook on future developments.

scholarly journals Distinct properties in ventral pallidum projection neuron subtypes

2021 ◽  
Author(s):  
Nimrod Bernat ◽  
Rianne Campbell ◽  
Hyungwoo Nam ◽  
Mahashweta Basu ◽  
Tal Odesser ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Critical Role ◽  
Gene Expression Profiles ◽  
Cell Types ◽  
Projection Neuron ◽  
Brain Regions ◽  
Ventral Pallidum ◽  
Lateral Habenula

The ventral pallidum (VP), a major component of the basal ganglia, plays a critical role in motivational disorders. It sends projections to many different brain regions but it is not yet known whether and how these projections differ in their cellular properties, gene expression patterns, connectivity and role in reward seeking. In this study, we focus on four major outputs of the VP - to the lateral hypothalamus (LH), ventral tegmental area (VTA), mediodorsal thalamus (MDT), and lateral habenula (LHb) - and examine the differences between them in 1) baseline gene expression profiles using projection-specific RNA-sequencing; 2) physiological parameters using whole-cell patch clamp; and 3) their influence on cocaine reward using chemogenetic tools. We show that these four VP efferents differ in all three aspects and highlight specifically differences between the projections to the LH and the VTA. These two projections originate largely from separate populations of neurons, express distinct sets of genes related to neurobiological functions, and show opposite physiological and behavioral properties. Collectively, our data demonstrates for the first time that VP neurons exhibit distinct molecular and cellular profiles in a projection-specific manner, suggesting that they represent different cell types.

scholarly journals Our First Experience with Magnetic Separation of Platelets for Analyses of Platelet MicroRNA in Patients with Sticky Platelet Syndrome

2019 ◽  
Vol 19 (3) ◽  
pp. 88-94
Author(s):  
L Vadelova ◽  
J Ivankova ◽  
J Sokol ◽  
M Skerenova ◽  
J Zolkova ◽  
...  
Keyword(s):  
Magnetic Separation ◽  
Platelet Reactivity ◽  
Platelet Rich Plasma ◽  
Expression Profiles ◽  
Adenosine Diphosphate ◽  
Blood Samples ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Low Concentrations ◽  
Post Transcriptional Regulation

Abstract Introduction: Sticky platelet syndrome (SPS) is referred to as a platelet hyperaggregability triggered by low concentrations of platelet agonists adenosine diphosphate (ADP) and/or epinephrine (EPI). Platelet aggregation with other inducers (collagen, arachidonic acid, ristocetin, and thrombin) remains within a normal range. MicroRNAs (miRNAs) are small, non-coding RNA molecules that play an important role in post-transcriptional regulation of protein expression. More recently, several studies show that the platelets are an abundant source of miRNAs and that the miRNA expression profiles within platelets correlate with the platelet reactivity. Aim: The principle objective of this article is to describe the method which we developed for the preparation of the pure platelet samples and report the results of this method. These final pure platelet samples are intended to be the first step for the platelet miRNA testing. Methods: The blood samples from 50 subjects were examined in the study. Then, the platelet rich plasma (PRP) samples obtained by centrifugation of the patient blood samples were used for our experiments. Subsequently, the erythrocytes and leucocytes remaining in PRP sample were magnetically labelled by CD45 Microbeads and CD235a Microbeads. After incubation the PRP sample passed through the magnetic separation system and the magnetically labelled cells (erythrocytes and leucocytes) were retained within the column of separator. The number of cells in the final PRP samples was measured by the blood cell analyser. Results and conclusion: We successfully developed and optimized the effective and reproducible method for magnetic separation of platelets, resulting in the leukocyte-depleted and erythrocyte-depleted platelet samples, which can be used for further genetic analyses.

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