scholarly journals Region-specific expression of androgen and growth factor pathway genes in the rat epididymis and the effects of dual 5α-reductase inhibition

2006 ◽  
Vol 190 (3) ◽  
pp. 779-791 ◽  
Author(s):  
Natali Anne Henderson ◽  
Gerard M Cooke ◽  
Bernard Robaire
Keyword(s):  
Gene Expression ◽  
Androgen Receptor ◽  
Expression Profiles ◽  
Gene Array ◽  
Sperm Maturation ◽  
Male Rats ◽  
Pcr Analysis ◽  
Specific Expression ◽  
Signaling Systems ◽  
Reductase Inhibitors

Dihydrotestosterone (DHT) is the primary androgen acting in the epididymis, the site of sperm maturation. Previously, we showed that the treatment of male rats with PNU157706, an inhibitor that acts on both isoforms of 5α-reductase to prevent DHT formation, has effects on the expression of genes implicated in processes that create the optimal luminal microenvironment required for sperm maturation, and on sperm maturation itself. However, signaling pathways involved in regulating or mediating DHT actions in the epididymis remain largely unknown. The goals of this study were to determine the expression profiles of potential signaling systems in the epididymis and assess their DHT-dependence using two different dual 5α-reductase inhibitors. Rats were untreated or gavaged with vehicle, 10 mg/kg per day PNU157706 or 32 mg/kg per day FK143 for 28 days and epididymal gene expression was analyzed. Gene array analysis revealed analogous effects of FK143 on overall epididymal gene expression when compared with previous PNU157706 studies. Quantitative RT-PCR analysis of the expression of the 5α-reductase isozymes, androgen receptor, and members of the IGF, FGF, TGF, and VEGF families revealed novel region-specific expression profiles in the epididymis that were differentially affected by 5α-reductase inhibition; the two inhibitors had parallel effects. Specifically, in proximal regions, 5α-reductase 1, androgen receptor, and TGF-β1 expression increased after treatment, while in distal regions expression of IGF-I, IGFBP-5, IGFBP-6, and FGF-10 decreased. These results provide insight into epididymal signaling mechanisms and indicate potential candidates acting either upstream or downstream of DHT to regulate and/or mediate its actions in the epididymis.

scholarly journals Study on the region-specific expression of epididymis mRNA in the rams

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245933
Author(s):  
Cuiling Wu ◽  
Chunxin Wang ◽  
Bo Zhai ◽  
Yunhui Zhao ◽  
Zhuo Zhao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Sperm Maturation ◽  
Sequencing Technology ◽  
Specific Expression ◽  
Data Resource ◽  
Specific Expression Pattern ◽  
One Year

The epididymis is divided into three regions including the caput, corpus and cauda. Gene expression profiles in different regions indicate the different functions of epididymis which are crucial for sperm maturation. In this study, three one-year-old rams was used as the experimental animal. Transcriptome sequencing technology was used to sequence mRNA in the caput, corpus and cauda of the epididymis. Based on the spatiotemporal-specific expression pattern in the epididymis, the mRNA expression profiles of the three parts of the epididymis were analysed. Region-specifically expressed genes were analysed by GO and KEGG analyses to screen the key genes involved in sheep sperm maturation. We obtained 129, 54 and 99 specifically expressed genes in the caput, corpus and cauda, respectively. And twenty specific expressed genes related to sperm maturation were used to construct functional networks. The heatmap showed that 6 genes of LCN protein family were highly expressed in the head of epididymis of sheep. We infer that sperm maturation is gradual in the epididymis and that there are significant differences in epididymal gene expression patterns between different species. This provides a data resource for analysing the regulatory mechanism of epididymis genes related to sperm maturation in rams.

scholarly journals Comparison of Stemness and Gene Expression between Gingiva and Dental Follicles in Children

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Chung-Min Kang ◽  
Seong-Oh Kim ◽  
Mijeong Jeon ◽  
Hyung-Jun Choi ◽  
Han-Sung Jung ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Pcr Analysis ◽  
Expression Levels ◽  
Qrt Pcr ◽  
Stem Cell Source ◽  
Regenerative Dentistry ◽  
Induced Pluripotent

The aim of this study was to compare the differential gene expression and stemness in the human gingiva and dental follicles (DFs) according to their biological characteristics. Gingiva (n=9) and DFs (n=9) were collected from 18 children. Comparative gene expression profiles were collected using cDNA microarray. The expression of development, chemotaxis, mesenchymal stem cells (MSCs), and induced pluripotent stem cells (iPSs) related genes was assessed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Histological analysis was performed using hematoxylin-eosin and immunohistochemical staining. Gingiva had greater expression of genes related to keratinization, ectodermal development, and chemotaxis whereas DFs exhibited higher expression levels of genes related to tooth and embryo development. qRT-PCR analysis showed that the expression levels of iPSc factors includingSOX2,KLF4, andC-MYCwere58.5±26.3,12.4±3.5, and12.2±1.9times higher in gingiva andVCAM1(CD146) andALCAM(CD166) were33.5±6.9and4.3±0.8times higher in DFs. Genes related to MSCs markers includingCD13,CD34,CD73,CD90, andCD105were expressed at higher levels in DFs. The results of qRT-PCR and IHC staining supported the microarray analysis results. Interestingly, this study demonstrated transcription factors of iPS cells were expressed at higher levels in the gingiva. Given the minimal surgical discomfort and simple accessibility, gingiva is a good candidate stem cell source in regenerative dentistry.

Expression profiles of metamorphosis-related genes during natural transformations in tadpoles of wild Wood Frogs (Lithobates sylvaticus)

2012 ◽  
Vol 90 (9) ◽  
pp. 1059-1071 ◽  
Author(s):  
Laia Navarro-Martín ◽  
Chantal Lanctôt ◽  
Christopher Edge ◽  
Jeff Houlahan ◽  
Vance L. Trudeau
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Rana Sylvatica ◽  
Fold Increase ◽  
Gonadal Development ◽  
Specific Expression ◽  
Wood Frogs ◽  
Lithobates Sylvaticus ◽  
Expression Levels ◽  
Gene Expression Levels

Numerous studies using laboratory-reared tadpoles have shown the importance of thyroid hormones (TH), thyroid receptors (TR), and deiodinase (Dio) enzymes during anuran metamorphosis. Our study focuses on the analysis of thyroid-related genes in tadpoles of wild Wood Frogs ( Lithobates sylvaticus (LeConte, 1825); also known as Rana sylvatica (Cope, 1889)) during metamorphosis. Results showed that, in concordance with laboratory-reared studies, thyroid receptor beta (trb) gene expression profiles presented the most marked changes. At climax and compared with premetamorphic stages, brains, tails, and gonad–mesonephros complex (GMC) tissues increased trb expression levels 5-, 21-, and 41-fold, respectively (p < 0.05). In addition, gene expression levels of brain deiodinase type II and III showed opposite trends, where 3-fold decrease and 10-fold increase were, respectively, found. This finding supports the idea that thyroid hormone, as it has been demonstrated in laboratory-reared tadpoles, is also involved in natural metamorphosis in wild tadpoles. Interestingly, and contrary to our predictions, we observed that whole brain corticotropin-releasing factor (crf) and crf receptor 1 (crfr1) gene expression levels significantly decrease through metamorphosis in wild L. sylvaticus tadpoles. Further analyses are required to determine if a role of TH in the timing of anuran gonadal development exists, as well as the importance of cell-specific and tissue-specific expression of crf and crfr1 to metamorphosis.

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]

Age-related changes in the transcriptional profile of mouse RPE/choroid

2003 ◽  
Vol 15 (3) ◽  
pp. 258-262 ◽  
Author(s):  
Hisashi Ida ◽  
Sharon A. Boylan ◽  
Andrea L. Weigel ◽  
Leonard M. Hjelmeland
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Cdna Probe ◽  
Gene Expression Profiles ◽  
Age Related Macular Degeneration ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Mouse Cdna ◽  
Age Related ◽  
Age Related Changes

To evaluate the age-related changes in gene expression occurring in the complex of retinal pigmented epithelium, Bruch’s membrane, and choroid (RPE/choroid), we examined the gene expression profiles of young adult (2 mo) and old (24 mo) male C57BL/6 mice. cDNA probe sets from individual animals were synthesized using total RNA isolated from the RPE/choroid of each animal. Probes were amplified using the Clontech SMART system, radioactively labeled, and hybridized to two different Clontech Atlas mouse cDNA arrays. From each age group, three independent triplicates were hybridized to the arrays. Statistical analyses were performed using the Significance Analysis of Microarrays program (SAM version 1.13; Stanford University). Selected array results were confirmed by semi-quantitative RT-PCR analysis. Of 2,340 genes represented on the arrays, ∼60% were expressed in young and/or old mouse RPE/choroid. A moderate fraction (12%) of all expressed genes exhibited a statistically significant change in expression with age. Of these 150 genes, all but two, HMG14 and carboxypeptidase E, were upregulated with age. Many of these upregulated genes can be grouped into several broad functional categories: immune response, proteases and protease inhibitors, stress response, and neovascularization. RT-PCR results from six of six genes examined confirmed the differential change in expression with age of these genes. Our study provides likely candidate genes to further study their role in the development of age-related macular degeneration and other aging diseases affecting the RPE/choroid.

Systematic assessment of the human osteoblast transcriptome in resting and induced primary cells

2008 ◽  
Vol 33 (3) ◽  
pp. 301-311 ◽  
Author(s):  
Elin Grundberg ◽  
Helena Brändström ◽  
Kevin C. L. Lam ◽  
Scott Gurd ◽  
Bing Ge ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Biology ◽  
Gene Networks ◽  
Cell Function ◽  
Expression Profiles ◽  
Bone Cell ◽  
Specific Gene ◽  
Molecular Physiology ◽  
Specific Expression ◽  
Vast Number

Osteoblasts are key players in bone remodeling. The accessibility of human primary osteoblast-like cells (HObs) from bone explants makes them a lucrative model for studying molecular physiology of bone turnover, for discovering novel anabolic therapeutics, and for mesenchymal cell biology in general. Relatively little is known about resting and dynamic expression profiles of HObs, and to date no studies have been conducted to systematically assess the osteoblast transcriptome. The aim of this study was to characterize HObs and investigate signaling cascades and gene networks with genomewide expression profiling in resting and bone morphogenic protein (BMP)-2- and dexamethasone-induced cells. In addition, we compared HOb gene expression with publicly available samples from the Gene Expression Omnibus. Our data show a vast number of genes and networks expressed predominantly in HObs compared with closely related cells such as fibroblasts or chondrocytes. For instance, genes in the insulin-like growth factor (IGF) signaling pathway were enriched in HObs ( P = 0.003) and included the binding proteins (IGFBP-1, -2, -5) and IGF-II and its receptor. Another HOb-specific expression pattern included leptin and its receptor ( P < 10−8). Furthermore, after stimulation of HObs with BMP-2 or dexamethasone, the expression of several interesting genes and pathways was observed. For instance, our data support the role of peripheral leptin signaling in bone cell function. In conclusion, we provide the landscape of tissue-specific and dynamic gene expression in HObs. This resource will allow utilization of osteoblasts as a model to study specific gene networks and gene families related to human bone physiology and diseases.

scholarly journals RNA-seq Analysis Reveals Gene Expression Profiling of Female Fertile and Sterile Ovules of Pinus Tabulaeformis Carr. during Free Nuclear Mitosis of the Female Gametophyte

2018 ◽  
Vol 19 (8) ◽  
pp. 2246 ◽  
Author(s):  
Yang Yao ◽  
Rui Han ◽  
Zaixin Gong ◽  
Caixia Zheng ◽  
Yuanyuan Zhao
Keyword(s):  
Gene Expression ◽  
Female Gametophyte ◽  
Expression Profiles ◽  
Signal Transduction Pathway ◽  
Gene Expression Profiles ◽  
Pinus Tabulaeformis ◽  
Cdna Libraries ◽  
Pcr Analysis ◽  
Transcriptional Networks ◽  
Ovule Development

The development of the female gametophyte (FG) is one of the key processes of life cycle alteration between the haploid gametophyte and the diploid sporophytes in plants and it is required for successful seed development after fertilization. It is well demonstrated that free nuclear mitosis (FNM) of FG is crucial for the development of the ovule. However, studies of the molecular mechanism of ovule and FG development focused mainly on angiosperms, such as Arabidopsis thaliana and further investigation of gymnosperms remains to be completed. Here, Illumina sequencing of six transcriptomic libraries obtained from developing and abortive ovules at different stages during free nuclear mitosis of magagametophyte (FNMM) was used to acquire transcriptome data and gene expression profiles of Pinus tabulaeformis. Six cDNA libraries generated a total of 71.0 million high-quality clean reads that aligned with 63,449 unigenes and the comparison between developing and abortive ovules identified 7174 differentially expressed genes (DEGs). From the functional annotation results, DEGs involved in the cell cycle and phytohormone regulation were highlighted to reveal their biological importance in ovule development. Furthermore, validation of DEGs from the phytohormone signal transduction pathway was performed using quantitative real-time PCR analysis, revealing the dynamics of transcriptional networks and potential key components in the regulation of FG development in P. tabulaeformis were identified. These findings provide new insights into the regulatory mechanisms of ovule development in woody gymnosperms.

scholarly journals A computational method for direct imputation of cell type-specific expression profiles and cellular compositions from bulk-tissue RNA-Seq in brain disorders

2020 ◽  
Author(s):  
Abolfazl Doostparast Torshizi ◽  
Jubao Duan ◽  
Kai Wang
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Complex Diseases ◽  
Specific Gene ◽  
Cellular Composition ◽  
Rna Seq ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

AbstractThe importance of cell type-specific gene expression in disease-relevant tissues is increasingly recognized in genetic studies of complex diseases. However, the vast majority of gene expression studies are conducted on bulk tissues, necessitating computational approaches to infer biological insights on cell type-specific contribution to diseases. Several computational methods are available for cell type deconvolution (that is, inference of cellular composition) from bulk RNA-Seq data, but cannot impute cell type-specific expression profiles. We hypothesize that with external prior information such as single cell RNA-seq (scRNA-seq) and population-wide expression profiles, it can be a computationally tractable and identifiable to estimate both cellular composition and cell type-specific expression from bulk RNA-Seq data. Here we introduce CellR, which addresses cross-individual gene expression variations by employing genome-wide tissue-wise expression signatures from GTEx to adjust the weights of cell-specific gene markers. It then transforms the deconvolution problem into a linear programming model while taking into account inter/intra cellular correlations, and uses a multi-variate stochastic search algorithm to estimate the expression level of each gene in each cell type. Extensive analyses on several complex diseases such as schizophrenia, Alzheimer’s disease, Huntington’s disease, and type 2 diabetes validated efficiency of CellR, while revealing how specific cell types contribute to different diseases. We conducted numerical simulations on human cerebellum to generate pseudo-bulk RNA-seq data and demonstrated its efficiency in inferring cell-specific expression profiles. Moreover, we inferred cell-specific expression levels from bulk RNA-seq data on schizophrenia and computed differentially expressed genes within certain cell types. Using predicted gene expression profile on excitatory neurons, we were able to reproduce our recently published findings on TCF4 being a master regulator in schizophrenia and showed how this gene and its targets are enriched in excitatory neurons. In summary, CellR compares favorably (both accuracy and stability of inference) against competing approaches on inferring cellular composition from bulk RNA-seq data, but also allows direct imputation of cell type-specific gene expression, opening new doors to re-analyze gene expression data on bulk tissues in complex diseases.

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