Transcriptomic changes in the pituitary of female mice with androgen excess through dihydrotestosterone (DHT) treatment

Mapping Intimacies ◽

10.1101/2021.12.31.474680 ◽

2022 ◽

Author(s):

Serene Joseph ◽

Sara Divall ◽

Sheng Wu

Keyword(s):

Factor Analysis ◽

Transcriptional Factor ◽

Rna Seq ◽

Androgen Excess ◽

Female Mice ◽

Transcriptomic Changes

Androgen excess in women is associated with the development of PCOS and its abnormalities. The Hypothalamus Pituitary Ovarian axis signaling is altered with excessed androgens, leading to anovulation and infertility. Previous studies have shown that AR signaling in the pituitary alters gonadotrophin release. Hence, the present pioneering study was an approach to determine the transcriptomic changes responsible to the phenotype seen with DHT excess. RNA seq data showed that 583 genes were differentially regulated by DHT in pituitary, of which 344 were upregulated and 239 downregulated. Meanwhile, Transcriptional factor analysis showed that majority of the genes changed had Androgen responsive elements.

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Transcriptome Profile Alterations with Carbon Nanotubes, Quantum Dots, and Silver Nanoparticles: A Review

Genes ◽

10.3390/genes12060794 ◽

2021 ◽

Vol 12 (6) ◽

pp. 794

Author(s):

Cullen Horstmann ◽

Victoria Davenport ◽

Min Zhang ◽

Alyse Peters ◽

Kyoungtae Kim

Keyword(s):

Carbon Nanotubes ◽

Quantum Dots ◽

High Throughput Sequencing ◽

The Body ◽

Rna Seq ◽

Mechanisms Of Toxicity ◽

Promising Tool ◽

Engineered Nanomaterial ◽

Next Generation Sequencing Ngs ◽

Transcriptomic Changes

Next-generation sequencing (NGS) technology has revolutionized sequence-based research. In recent years, high-throughput sequencing has become the method of choice in studying the toxicity of chemical agents through observing and measuring changes in transcript levels. Engineered nanomaterial (ENM)-toxicity has become a major field of research and has adopted microarray and newer RNA-Seq methods. Recently, nanotechnology has become a promising tool in the diagnosis and treatment of several diseases in humans. However, due to their high stability, they are likely capable of remaining in the body and environment for long periods of time. Their mechanisms of toxicity and long-lasting effects on our health is still poorly understood. This review explores the effects of three ENMs including carbon nanotubes (CNTs), quantum dots (QDs), and Ag nanoparticles (AgNPs) by cross examining publications on transcriptomic changes induced by these nanomaterials.

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Differential Expression Analysis of Phytohormone-Related Genes of Korean Wheat (Triticum aestivum) in Response to Preharvest Sprouting and Abscisic Acid (ABA)

Applied Sciences ◽

10.3390/app11083562 ◽

2021 ◽

Vol 11 (8) ◽

pp. 3562

Author(s):

Yong Jin Lee ◽

Sang Yong Park ◽

Dae Yeon Kim ◽

Jae Yoon Kim

Keyword(s):

Abscisic Acid ◽

Differential Expression Analysis ◽

Preharvest Sprouting ◽

Global Changes ◽

Rna Seq ◽

Hormone Metabolism ◽

Global Issue ◽

End Use ◽

Transcriptomic Changes

Preharvest sprouting (PHS) is a key global issue in production and end-use quality of cereals, particularly in regions where the rainfall season overlaps the harvest. To investigate transcriptomic changes in genes affected by PHS-induction and ABA-treatment, RNA-seq analysis was performed in two wheat cultivars that differ in PHS tolerance. A total of 123 unigenes related to hormone metabolism and signaling for abscisic acid (ABA), gibberellic acid (GA), indole-3-acetic acid (IAA), and cytokinin were identified and 1862 of differentially expressed genes were identified and divided into 8 groups by transcriptomic analysis. DEG analysis showed the majority of genes were categorized in sugar related processes, which interact with ABA signaling in PHS tolerant cultivar under PHS-induction. Thus, genes related to ABA are key regulators of dormancy and germination. Our results give insight into global changes in expression of plant hormone related genes in response to PHS.

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Developmental androgen excess programs sympathetic tone and adipose tissue dysfunction and predisposes to a cardiometabolic syndrome in female mice

AJP Endocrinology and Metabolism ◽

10.1152/ajpendo.00620.2012 ◽

2013 ◽

Vol 304 (12) ◽

pp. E1321-E1330 ◽

Cited By ~ 38

Author(s):

Kazunari Nohara ◽

Rizwana S. Waraich ◽

Suhuan Liu ◽

Mathieu Ferron ◽

Aurélie Waget ◽

...

Keyword(s):

Insulin Resistance ◽

Adipose Tissue ◽

Glucose Intolerance ◽

Adult Female ◽

Sympathetic Tone ◽

Visceral Adiposity ◽

Androgen Excess ◽

Altered Expression ◽

Female Mice ◽

The Impact

Among women, the polycystic ovarian syndrome (PCOS) is considered a form of metabolic syndrome with reproductive abnormalities. Women with PCOS show increased sympathetic tone, visceral adiposity with enlarged adipocytes, hypoadiponectinemia, insulin resistance, glucose intolerance, increased inactive osteocalcin, and hypertension. Excess fetal exposure to androgens has been hypothesized to play a role in the pathogenesis of PCOS. Previously, we showed that neonatal exposure to the androgen testosterone (NT) programs leptin resistance in adult female mice. Here, we studied the impact of NT on lean and adipose tissues, sympathetic tone in cardiometabolic tissues, and the development of metabolic dysfunction in mice. Neonatally androgenized adult female mice (NTF) displayed masculinization of lean tissues with increased cardiac and skeletal muscle as well as kidney masses. NTF mice showed increased and dysfunctional white adipose tissue with increased sympathetic tone in both visceral and subcutaneous fat as well as increased number of enlarged and insulin-resistant adipocytes that displayed altered expression of developmental genes and hypoadiponectinemia. NTF exhibited dysfunctional brown adipose tissue with increased mass and decreased energy expenditure. They also displayed decreased undercarboxylated and active osteocalcin and were predisposed to obesity during chronic androgen excess. NTF showed increased renal sympathetic tone associated with increased blood pressure, and they developed glucose intolerance and insulin resistance. Thus, developmental exposure to testosterone in female mice programs features of cardiometabolic dysfunction, as can be observed in women with PCOS, including increased sympathetic tone, visceral adiposity, insulin resistance, prediabetes, and hypertension.

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Integrated Physiological and Transcriptomic Analyses Responses to Altitude Stress in Oat (Avena sativa L.)

Frontiers in Genetics ◽

10.3389/fgene.2021.638683 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yu Jinqiu ◽

Li Bing ◽

Song Tingting ◽

He Jinglei ◽

KongLing Zelai ◽

...

Keyword(s):

High Altitude ◽

Avena Sativa ◽

Molecular Mechanisms ◽

Rna Seq ◽

High Altitudes ◽

Genome Wide ◽

New Findings ◽

Polymerase Chain ◽

Transcriptomic Changes ◽

Stressful Environments

Oat is an annual gramineous forage grass with the remarkable ability to survive under various stressful environments. However, understanding the effects of high altitude stresses on oats is poor. Therefore, the physiological and the transcriptomic changes were analyzed at two sites with different altitudes, low (ca. 2,080 m) or high (ca. 2,918 m), respectively. Higher levels of antioxidant enzyme activity, reactive oxygen and major reductions in photosynthesis-related markers were suggested for oats at high altitudes. Furthermore, oat yields were severely suppressed at the high altitude. RNA-seq results showed that 11,639 differentially expressed genes were detected at both the low and the high altitudes in which 5,203 up-regulated and 6,436 down-regulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment tests were conducted and a group of major high altitude-responsive pigment metabolism genes, photosynthesis, hormone signaling, and cutin, suberine and wax biosynthesis were excavated. Using quantitative real-time polymerase chain response, we also confirmed expression levels of 20 DEGs (qRT-PCR). In summary, our study generated genome-wide transcript profile and may be useful for understanding the molecular mechanisms of Avena sativa L. in response to high altitude stress. These new findings contribute to our deeper relevant researches on high altitude stresses and further exploring new candidategenes for adapting plateau environment oat molecular breeding.

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Transcriptomic Changes Induced by Deletion of Transcriptional Regulator GCR2 on Pentose Sugar Metabolism in Saccharomyces cerevisiae

Frontiers in Bioengineering and Biotechnology ◽

10.3389/fbioe.2021.654177 ◽

2021 ◽

Vol 9 ◽

Author(s):

Minhye Shin ◽

Heeyoung Park ◽

Sooah Kim ◽

Eun Joong Oh ◽

Deokyeol Jeong ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Xylose Fermentation ◽

Sugar Metabolism ◽

Pentose Phosphate ◽

Biofuel Production ◽

Rna Seq ◽

Loss Of Function ◽

Lignocellulosic Biofuel ◽

Pentose Sugar ◽

Transcriptomic Changes

Being a microbial host for lignocellulosic biofuel production, Saccharomyces cerevisiae needs to be engineered to express a heterologous xylose pathway; however, it has been challenging to optimize the engineered strain for efficient and rapid fermentation of xylose. Deletion of PHO13 (Δpho13) has been reported to be a crucial genetic perturbation in improving xylose fermentation. A confirmed mechanism of the Δpho13 effect on xylose fermentation is that the Δpho13 transcriptionally activates the genes in the non-oxidative pentose phosphate pathway (PPP). In the current study, we found a couple of engineered strains, of which phenotypes were not affected by Δpho13 (Δpho13-negative), among many others we examined. Genome resequencing of the Δpho13-negative strains revealed that a loss-of-function mutation in GCR2 was responsible for the phenotype. Gcr2 is a global transcriptional factor involved in glucose metabolism. The results of RNA-seq confirmed that the deletion of GCR2 (Δgcr2) led to the upregulation of PPP genes as well as downregulation of glycolytic genes, and changes were more significant under xylose conditions than those under glucose conditions. Although there was no synergistic effect between Δpho13 and Δgcr2 in improving xylose fermentation, these results suggested that GCR2 is a novel knockout target in improving lignocellulosic ethanol production.

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Androgen excess in pancreatic β cells and neurons predisposes female mice to type 2 diabetes

JCI Insight ◽

10.1172/jci.insight.98607 ◽

2018 ◽

Vol 3 (12) ◽

Cited By ~ 13

Author(s):

Guadalupe Navarro ◽

Camille Allard ◽

Jamie J. Morford ◽

Weiwei Xu ◽

Suhuan Liu ◽

...

Keyword(s):

Type 2 Diabetes ◽

Β Cells ◽

Pancreatic Β Cells ◽

Androgen Excess ◽

Female Mice

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f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq

Genome Biology ◽

10.1186/s13059-017-1334-8 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 47

Author(s):

Florian Buettner ◽

Naruemon Pratanwanich ◽

Davis J. McCarthy ◽

John C. Marioni ◽

Oliver Stegle

Keyword(s):

Factor Analysis ◽

Single Cell ◽

Rna Seq

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Assessment of Embryo-Induced Transcriptomic Changes in Hamster Uterus Using RNA-Seq

Cellular Physiology and Biochemistry ◽

10.1159/000489371 ◽

2018 ◽

Vol 46 (5) ◽

pp. 1868-1878 ◽

Cited By ~ 6

Author(s):

Ming-Yu Huang ◽

Wen-Qian Zhang ◽

Miao Zhao ◽

Can Zhu ◽

Jia-Peng He ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Embryo Implantation ◽

Bioinformatic Analysis ◽

Differentially Expressed ◽

Implantation Site ◽

Rna Seq ◽

Promoter Regions ◽

Functional Clustering ◽

Gene Network Analysis ◽

Transcriptomic Changes

Background/Aims: The mouse is widely used as an animal model for studying human embryo implantation. However, the mouse is unique in that both ovarian progesterone and estrogen are critical to implantation, whereas in the majority of species (e.g. human and hamster) implantation can occur in the presence of progesterone alone. Methods: In this study, we analyzed embryo-induced transcriptomic changes in the hamster uterus during embryo implantation by using RNA-seq. Differentially expressed genes were characterized by bioinformatic analysis. Results: We identified a total of 781 differentially expressed genes, of which 367 genes were up-regulated and 414 genes were down-regulated at the implantation site compared to the inter-implantation site. Functional clustering and gene network analysis highlighted the cell cycle process in uterus upon embryo implantation. By examining of the promoter regions of differentially expressed genes, we identified 7 causal transcription factors. Additionally, through connectivity map (CMap) analysis, multiple compounds were identified to have potential anti-implantation effects due to their ability to reverse embryo-induced transcriptomic changes. Conclusion: Our study provides a valuable resource for in-depth understanding of the mechanism underlying embryo implantation.

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scMerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1820006116 ◽

2019 ◽

Vol 116 (20) ◽

pp. 9775-9784 ◽

Cited By ~ 38

Author(s):

Yingxin Lin ◽

Shila Ghazanfar ◽

Kevin Y. X. Wang ◽

Johann A. Gagnon-Bartsch ◽

Kitty K. Lo ◽

...

Keyword(s):

Factor Analysis ◽

Data Integration ◽

Single Cell ◽

Rna Seq ◽

Cell Type ◽

Large Collection ◽

Single Cell Rna Sequencing ◽

Development Trajectory ◽

Biological Discovery ◽

Public Datasets

Concerted examination of multiple collections of single-cell RNA sequencing (RNA-seq) data promises further biological insights that cannot be uncovered with individual datasets. Here we present scMerge, an algorithm that integrates multiple single-cell RNA-seq datasets using factor analysis of stably expressed genes and pseudoreplicates across datasets. Using a large collection of public datasets, we benchmark scMerge against published methods and demonstrate that it consistently provides improved cell type separation by removing unwanted factors; scMerge can also enhance biological discovery through robust data integration, which we show through the inference of development trajectory in a liver dataset collection.

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