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Fetal transcriptome

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https://www.readbyqxmd.com/read/28060419/a-molecular-roadmap-of-definitive-erythropoiesis-from-human-induced-pluripotent-stem-cells
#1
Muhammad A Razaq, Stephen Taylor, David J Roberts, Lee Carpenter
Human induced pluripotent stem cells (hiPSCs) are being considered for use in understanding haematopoietic disorders and as a potential source of in vitro manufactured red cells. Here, we show that hiPSCs are able to recapitulate various stages of developmental erythropoiesis. We show that primitive erythroblasts arise first, express CD31(+) with CD235a(+) , embryonic globins and red cell markers, but fail to express the hallmark red cell transcripts of adult erythropoiesis. When hiPSC-derived CD45(+) CD235a(-) haematopoietic progenitors are isolated on day 12 and further differentiated on OP9 stroma, they selectively express CD36(+) and CD235a(+) , adult erythroid transcripts for transcription factors (e...
January 6, 2017: British Journal of Haematology
https://www.readbyqxmd.com/read/28046103/transcriptome-profiling-identifies-ribosome-biogenesis-as-a-target-of-alcohol-teratogenicity-and-vulnerability-during-early-embryogenesis
#2
Mark E Berres, Ana Garic, George R Flentke, Susan M Smith
Fetal alcohol spectrum disorder (FASD) is a leading cause of neurodevelopmental disability. Individuals with FASD may exhibit a characteristic facial appearance that has diagnostic utility. The mechanism by which alcohol disrupts craniofacial development is incompletely understood, as are the genetic factors that can modify individual alcohol vulnerability. Using an established avian model, we characterized the cranial transcriptome in response to alcohol to inform the mechanism underlying these cells' vulnerability...
2017: PloS One
https://www.readbyqxmd.com/read/28031337/immune-modifications-in-fetal-membranes-overlying-the-cervix-precede-parturition-in-humans
#3
Louis Marcellin, Thomas Schmitz, Meriem Messaoudene, Driss Chader, Christophe Parizot, Sébastien Jacques, Jérémy Delaire, Jean Gogusev, Alain Schmitt, Corinne Lesaffre, Michelle Breuiller-Fouché, Anne Caignard, Daniel Vaiman, François Goffinet, Dominique Cabrol, Guy Gorochov, Céline Méhats
In humans, parturition is currently viewed as an intrauterine outbreak of inflammation, accompanied by a massive release of proinflammatory cytokines at the maternal-fetal interface that comprises the maternal decidua, placenta, and fetal membranes. At term, fetal membranes overlying the cervix, the future site of rupture, show altered morphology and are termed the zone of altered morphology (ZAM). These alterations occur in normal fetal membranes during late pregnancy, in preparation for labor. In this study, transcriptome, flow cytometry, electron microscopy, and immunohistochemistry analyses collectively highlight a local shift in gene expression and lymphocyte activation in the ZAM...
December 28, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28011779/cerebroviz-an-r-package-for-anatomical-visu-alization-of-spatiotemporal-brain-data
#4
Ethan Bahl, Tanner Koomar, Jacob J Michaelson
: Spatiotemporal transcriptomic profiling has provided valuable insight into the patterning of gene expression throughout the human brain from early fetal development to adulthood. When combined with prior knowledge of a disease's age at onset and region-specificity, these expression profiles have provided the necessary context to both strengthen putative gene-disease associations and infer new associations. While a wealth of spatiotemporal expression data exists, there are currently no tools available to visualize this data within the anatomical context of the brain, thus limiting the intuitive interpretation of many such findings...
December 22, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28009303/cerebral-organoids-recapitulate-epigenomic-signatures-of-the-human-fetal-brain
#5
Chongyuan Luo, Madeline A Lancaster, Rosa Castanon, Joseph R Nery, Juergen A Knoblich, Joseph R Ecker
Organoids derived from human pluripotent stem cells recapitulate the early three-dimensional organization of the human brain, but whether they establish the epigenomic and transcriptional programs essential for brain development is unknown. We compared epigenomic and regulatory features in cerebral organoids and human fetal brain, using genome-wide, base resolution DNA methylome and transcriptome sequencing. Transcriptomic dynamics in organoids faithfully modeled gene expression trajectories in early-to-mid human fetal brains...
December 20, 2016: Cell Reports
https://www.readbyqxmd.com/read/27974560/zika-virus-infects-early-and-mid-gestation-human-maternal-decidual-tissues-inducing-distinct-innate-tissue-responses-in-the-maternal-fetal-interface
#6
Yiska Weisblum, Esther Oiknine-Djian, Olesya M Vorontsov, Ronit Haimov-Kochman, Zichria Zakay-Rones, Karen Meir, David Shveiky, Sharona Elgavish, Yuval Nevo, Moshe Roseman, Michal Bronstein, David Stockheim, Ido From, Iris Eisenberg, Aya A Lewkowicz, Simcha Yagel, Amos Panet, Dana G Wolf
: Zika virus (ZIKV) has emerged as a cause of congenital brain anomalies and a range of placental-related abnormalities, highlighting the need to unveil the modes of maternal-to-fetal transmission. The most likely route of vertical ZIKV transmission is via the placenta. The earliest events of ZIKV transmission in the maternal decidua, representing the maternal-uterine aspect of the chimeric placenta, have remained unexplored. Here we show that ZIKV replicates in first-trimester human maternal-decidual tissues grown ex-vivo as 3D organ cultures...
December 14, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27960177/alterations-in-fetal-leydig-cell-gene-expression-during-fetal-and-adult-development
#7
Kanako Miyabayashi, Yuichi Shima, Miki Inoue, Tetsuya Sato, Takashi Baba, Yasuyuki Ohkawa, Mikita Suyama, Ken-Ichirou Morohashi
Fetal Leydig cells (FLCs) and adult Leydig cells (ALCs) develop in the mammalian prenatal and postnatal testes, respectively. In mice, FLCs emerge in the interstitial space of the testis as early as embryonic day 12.5 and thereafter increase in number during the fetal stage. We previously established a transgenic mouse line in which FLCs are labeled with EGFP and demonstrated that the EGFP-labeled FLCs were present even in adult testes. However, the characteristics of FLCs during postnatal stages remained unclear...
December 14, 2016: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/27914989/transcriptome-analysis-of-adult-and-fetal-trabecular-meshwork-cornea-and-ciliary-body-tissues-by-rna-sequencing
#8
Megan Ulmer Carnes, R Rand Allingham, Allison Ashley-Koch, Michael A Hauser
PURPOSE: To characterize the transcriptional landscape of human adult and fetal trabecular meshwork (TM), cornea, and ciliary body (CB) tissues, and to evaluate the expression level of candidate genes selected from genetic association studies of primary-open angle glaucoma, central corneal thickness, intraocular pressure, vertical cup to disc ratio, and optic nerve parameters. METHODS: Deep RNA sequencing was performed on the selected human tissues. Transcriptome analyses were performed to 1) characterize the total number of expressed genes, 2) identify the most highly expressed genes, 3) estimate the number of novel transcripts, and 4) evaluate the expression of candidate genes in each tissue...
November 30, 2016: Experimental Eye Research
https://www.readbyqxmd.com/read/27910913/loss-of-egfr-asap1-signaling-in-metastatic-and-unresectable-hepatoblastoma
#9
Sarangarajan Ranganathan, Mylarappa Ningappa, Chethan Ashokkumar, Brandon W Higgs, Jun Min, Qing Sun, Lori Schmitt, Shankar Subramaniam, Hakon Hakonarson, Rakesh Sindhi
Hepatoblastoma (HBL), the most common childhood liver cancer is cured with surgical resection after chemotherapy or with liver transplantation if local invasion and multifocality preclude resection. However, variable survival rates of 60-80% and debilitating chemotherapy sequelae argue for more informed treatment selection, which is not possible by grading the Wnt-β-catenin over activity present in most HBL tumors. A hypothesis-generating whole transcriptome analysis shows that HBL tumors removed at transplantation are enriched most for cancer signaling pathways which depend predominantly on epidermal growth factor (EGF) signaling, and to a lesser extent, on aberrant Wnt-β-catenin signaling...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27897008/tracing-co-regulatory-network-dynamics-in-noisy-single-cell-transcriptome-trajectories
#10
Pablo Cordero, Joshua M Stuart
The availability of gene expression data at the single cell level makes it possible to probe the molecular underpinnings of complex biological processes such as differentiation and oncogenesis. Promising new methods have emerged for reconstructing a progression 'trajectory' from static single-cell transcriptome measurements. However, it remains unclear how to adequately model the appreciable level of noise in these data to elucidate gene regulatory network rewiring. Here, we present a framework called Single Cell Inference of MorphIng Trajectories and their Associated Regulation (SCIMITAR) that infers progressions from static single-cell transcriptomes by employing a continuous parametrization of Gaussian mixtures in high-dimensional curves...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27893464/the-h3k9-dimethyltransferases-ehmt1-2-protect-against-pathological-cardiac-hypertrophy
#11
Bernard Thienpont, Jan Magnus Aronsen, Emma Louise Robinson, Hanneke Okkenhaug, Elena Loche, Arianna Ferrini, Patrick Brien, Kanar Alkass, Antonio Tomasso, Asmita Agrawal, Olaf Bergmann, Ivar Sjaastad, Wolf Reik, Hywel Llewelyn Roderick
Cardiac hypertrophic growth in response to pathological cues is associated with reexpression of fetal genes and decreased cardiac function and is often a precursor to heart failure. In contrast, physiologically induced hypertrophy is adaptive, resulting in improved cardiac function. The processes that selectively induce these hypertrophic states are poorly understood. Here, we have profiled 2 repressive epigenetic marks, H3K9me2 and H3K27me3, which are involved in stable cellular differentiation, specifically in cardiomyocytes from physiologically and pathologically hypertrophied rat hearts, and correlated these marks with their associated transcriptomes...
January 3, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/27856275/rnaseq-profiling-of-primary-microglia-and-astrocyte-cultures-in-near-term-ovine-fetus-a-glial-in-vivo-in-vitro-multi-hit-paradigm-in-large-mammalian-brain
#12
M Cortes, M Cao, H L Liu, P Burns, C Moore, G Fecteau, A Desrochers, L B Barreiro, J P Antel, M G Frasch
BACKGROUND: The chronically instrumented fetal sheep is a widely used animal model to study fetal brain development in health and disease, but no methods exist yet to interrogate dedicated brain cell populations to identify their molecular and genomic phenotype. For example, the molecular mechanisms whereby microglia or astrocytes contribute to inflammation in the brain remain incompletely understood. NEW METHOD: Here we present a protocol to derive primary pure microglial or astrocyte cultures from near-term fetal sheep brain, after the animals have been chronically instrumented and studied in vivo...
January 30, 2017: Journal of Neuroscience Methods
https://www.readbyqxmd.com/read/27852726/thyroid-hormone-regulated-genes-in-cerebral-cortex-development
#13
REVIEW
Juan Bernal
The physiological and developmental effects of thyroid hormones are mainly due to the control of gene expression after interaction of T3 with the nuclear receptors. To understand the role of thyroid hormones on cerebral cortex development, knowledge of the genes regulated by T3 during specific stages of development is required. In our laboratory, we previously identified genes regulated by T3 in primary cerebrocortical cells in culture. By comparing these data with transcriptomics of purified cell types from the developing cortex, the cellular targets of T3 can be identified...
February 2017: Journal of Endocrinology
https://www.readbyqxmd.com/read/27846835/equine-dendritic-cells-generated-with-horse-serum-have-enhanced-functionality-in-comparison-to-dendritic-cells-generated-with-fetal-bovine-serum
#14
Anja Ziegler, Helen Everett, Eman Hamza, Mattia Garbani, Vinzenz Gerber, Eliane Marti, Falko Steinbach
BACKGROUND: Dendritic cells are professional antigen-presenting cells that play an essential role in the initiation and modulation of T cell responses. They have been studied widely for their potential clinical applications, but for clinical use to be successful, alternatives to xenogeneic substances like fetal bovine serum (FBS) in cell culture need to be found. Protocols for the generation of dendritic cells ex vivo from monocytes are well established for several species, including horses...
November 15, 2016: BMC Veterinary Research
https://www.readbyqxmd.com/read/27821074/a-quantitative-transcriptomic-analysis-of-the-physiological-significance-of-mtor-signaling-in-goat-fetal-fibroblasts
#15
Yuting Fu, Xu Zheng, Xiaoyang Jia, Uyanga Binderiya, Yanfeng Wang, Wenlei Bao, Lili Bao, Keyu Zhao, Yu Fu, Huifang Hao, Zhigang Wang
BACKGROUND: Mammalian target of rapamycin (mTOR) is an evolutionarily conserved serine/threonine kinase that is a central regulator of cell growth and metabolism. CCI-779 is a specific inhibitor of the mTORC1 signaling pathway. RESULTS: We performed comparative transcriptome profiling on Inner Mongolia Cashmere goat fetal fibroblasts (GFbs) that were treated with CCI-779 and untreated cells. A total of 365 differentially expressed genes (DEGs) appeared between untreated and CCI-779-treated GFbs, with an FDR ≤0...
November 7, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27802351/an-integrative-analysis-of-preeclampsia-based-on-the-construction-of-an-extended-composite-network-featuring-protein-protein-physical-interactions-and-transcriptional-relationships
#16
Daniel Vaiman, Francisco Miralles
Preeclampsia (PE) is a pregnancy disorder defined by hypertension and proteinuria. This disease remains a major cause of maternal and fetal morbidity and mortality. Defective placentation is generally described as being at the root of the disease. The characterization of the transcriptome signature of the preeclamptic placenta has allowed to identify differentially expressed genes (DEGs). However, we still lack a detailed knowledge on how these DEGs impact the function of the placenta. The tools of network biology offer a methodology to explore complex diseases at a systems level...
2016: PloS One
https://www.readbyqxmd.com/read/27800478/making-the-switch-alternatives-to-fetal-bovine-serum-for-adipose-derived-stromal-cell-expansion
#17
REVIEW
Carla Dessels, Marnie Potgieter, Michael S Pepper
Adipose-derived stromal cells (ASCs) are being used extensively in clinical trials. These trials require that ASCs are prepared using good manufacturing practices (GMPs) and are safe for use in humans. The majority of clinical trials in which ASCs are expanded make use of fetal bovine serum (FBS). While FBS is used traditionally in the research setting for in vitro expansion, it does carry the risk of xenoimmunization and zoonotic transmission when used for expanding cells destined for therapeutic purposes...
2016: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/27785155/improper-hydration-induces-global-gene-expression-changes-associated-with-renal-development-in-infant-mice
#18
Chong-Su Kim, Dong-Mi Shin
BACKGROUND: The kidney is a major organ in which fluid balance and waste excretion is regulated. For the kidney to achieve maturity with functions, normal renal developmental processes need to occur. Comprehensive genetic programs underlying renal development during the prenatal period have been widely studied. However, postnatal renal development, from infancy to the juvenile period, has not been studied yet. Here, we investigated whether structural and functional kidney development was still ongoing in early life by analyzing the renal transcriptional networks of infant (4 weeks old) and juvenile (7 weeks old) mice...
2016: Genes & Nutrition
https://www.readbyqxmd.com/read/27777632/the-effect-of-maternal-undernutrition-on-the-rat-placental-transcriptome-protein-restriction-up-regulates-cholesterol-transport
#19
Zoe Daniel, Angelina Swali, Richard Emes, Simon C Langley-Evans
BACKGROUND: Fetal exposure to a maternal low protein diet during rat pregnancy is associated with hypertension, renal dysfunction and metabolic disturbance in adult life. These effects are present when dietary manipulations target only the first half of pregnancy. It was hypothesised that early gestation protein restriction would impact upon placental gene expression and that this may give clues to the mechanism which links maternal diet to later consequences. METHODS: Pregnant rats were fed control or a low protein diet from conception to day 13 gestation...
2016: Genes & Nutrition
https://www.readbyqxmd.com/read/27769742/all-trans-retinoic-acid-promotes-wound-healing-of-primary-amniocytes-through-the-induction-of-loxl4-a-member-of-the-lysyl-oxidase-family
#20
Marion Rouzaire, Aurélie Comptour, Corinne Belville, Damien Bouvier, Gaël Clairefond, Flora Ponelle, Vincent Sapin, Denis Gallot, Loïc Blanchon
Thirty percent of preterm births directly result from preterm premature rupture of fetal membranes (PPROM). Clinical management currently proposes using a collagen plug to mechanically stop loss of amniotic fluid. Vitamin A and its active metabolite (retinoic acid) have well-known pro-healing properties and could thus make good candidates as a proposable adjuvant to this mechanical approach. Here we investigate the molecular mechanisms involved in the pro-healing properties of all-trans retinoic acid (atRA) in fetal membranes via an approach using an in vitro primary amniocyte wound model and transcriptomics...
December 2016: International Journal of Biochemistry & Cell Biology
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