Bone Morphogenetic Protein-4 Affects Both Trophoblast and Non-Trophoblast Lineage-Associated Gene Expression in Human Embryonic Stem Cells

Total Page:16

File Type:pdf, Size:1020Kb

Bone Morphogenetic Protein-4 Affects Both Trophoblast and Non-Trophoblast Lineage-Associated Gene Expression in Human Embryonic Stem Cells Vol.2, No.4, 163-175 (2012) Stem Cell Discovery http://dx.doi.org/10.4236/scd.2012.24021 Bone morphogenetic protein-4 affects both trophoblast and non-trophoblast lineage-associated gene expression in human embryonic stem cells Margaret L. Shirley1,2*, Alison Venable1*, Raj R. Rao3, Nolan L. Boyd4, Steven L. Stice1,5,6, David Puett1#, Prema Narayan7# 1Department of Biochemistry and Molecular Biology, University of Georgia, Athens, USA; #Corresponding Author: [email protected] 2Department of Psychiatry, University of California, San Francisco, USA 3Department of Chemical and Life Science Engineering, School of Engineering, Virginia Commonwealth University, Richmond, USA 4Cardiovascular Innovation Institute, University of Louisville, Louisville, USA 5Regenerative Bioscience Center, University of Georgia, Athens, USA 6Department of Animal and Dairy Sciences, University of Georgia, Athens, USA 7Department of Physiology, Southern Illinois University School of Medicine, Carbondale, USA; #Corresponding Author: [email protected] Received 5 May 2012; revised 4 June 2012; accepted 1 July 2012 ABSTRACT cells were obtained. Gene expression by EB was characterized by an up-regulation of a num- Human embryonic stem cells (hESC) can be in- ber of genes associated with trophoblast, ecto- duced to differentiate to trophoblast by bone derm, endoderm, and mesoderm, and the pro- morphogenetic proteins (BMPs) and by aggre- duction of hCG and progesterone confirmed that gation to form embryoid bodies (EB), but there trophoblast-like cells were formed. These re- are many differences and controversies regard- sults suggest that, in the presence of FGF-2, ing the nature of the differentiated cells. Our BG02 cells respond to BMP4 to yield tropho- goals herein were to determine if BG02 cells form trophoblast-like cells (a) in the presence of blast-like cells, which are also obtained upon EB BMP4-plus-basic fibroblast growth factor (FGF-2) formation. Thus, BMP4-mediated differentiation and (b) upon EB formation, and (c) whether the of hESC represents a viable cell system for BMP4 antagonist noggin elicits direct effects on studying early developmental events post-im- gene expression and hormone production in the plantation; however, up-regulation of non-tro- cells. Transcriptome profiling of hESC incubated phoblast genes suggests a somewhat diverse with BMP4/FGF-2 showed a down-regulation of response to BMP4/FGF-2. Noggin altered the pluripotency-associated genes, an up-regulation transcription of a limited number of genes but, of trophoblast-associated genes, and either a not surprisingly, did not lead to secretion of down-regulation or no change in gene expres- hormones. sion for many markers of the three embryonic germ layers. Yet, there was up-regulation of Keywords: Human Embryonic Stem Cells; several genes associated with mesoderm, ec- Trophoblasts; Bone Morphogenetic Protein-4; toderm, and endoderm, strongly suggesting that Embryoid Bodies; Noggin differentiation to trophoblast-like cells under the conditions used does not yield a homogeneous 1. INTRODUCTION cell type. Several genes, heretofore unreported, were identified that are altered in hESC in re- In the human blastocyst, the first step of differentiation sponse to BMP4-mediated differentiation. The from the morula, composed of totipotent cells, yields the production of human chorionic gonadotropin inner cell mass and trophoblast. The former differentiates (hCG), progesterone, and estradiol in the dif- into the hypoblast, leading to the extraembryonic endo- ferentiated cells confirmed that trophoblast-like derm and the epiblast, that differentiates to give the am- niotic ectoderm and the primitive ectoderm. The primi- * These authors contributed equally to this work. tive ectoderm, in turn, differentiates into the embryonic Copyright © 2012 SciRes. OPEN ACCESS 164 M. L. Shirley et al. / Stem Cell Discovery 2 (2012) 163-175 ectoderm and the primitive streak, the latter giving rise to gene markers have been noted in BMP-treated hESCs extraembryonic mesoderm, primitive mesoderm, and em- [18,21]. Explanations for many of these controversial bryonic endoderm. The trophectoderm is composed of reports were recently provided by two groups. Yu et al. epithelial cells and differentiates into several lineages. [22] reported that bFGF (FGF-2), which acts via the The trophoblast precursor cells begin rapid proliferation MEK-ERK pathway, redirects BMP4-mediated differen- into cytotrophoblasts, with some fusing to form multinu- tiation from trophectoderm to mesendoderm as judged by cleate syncytiotrophoblasts, a terminally differentiated the expression of brachyury. The activated MEK-ERK trophoblast cell; in addition, villous and extravillous cy- pathway sustains NANOG expression leading to a totrophoblasts are formed [1-3]. One of the hallmarks of bFGF-independent induction of mesendoderm by BMP4. trophoblast differentiation is the production of the hete- Another recent paper concluded that in the cooperative rodimeric glycoprotein hormone, human chorionic gona- presence of FGF2, BMP4 (that acts through brachyury dotropin (hCG), that is secreted throughout gestation, and CDX2) leads to the induction of mesoderm, not tro- being essential for progesterone production by the corpus phoblast [39]. luteum in the first trimester of human pregnancy [4,5]. The present study was undertaken with the goals of: 1) There is a paucity of adequate cell models for studying extending the previous reports that were based on a va- early trophoblast development, and a reliable system will riety of cell lines, different culture conditions, and at greatly facilitate progress in the area of human reproduc- times conflicting results, and 2) to critically examine the tion. trophoblast and non-trophoblast BMP-regulated genes, Recent studies have shown that human embryonic particularly since a number of the non-trophoblast BMP- stem cells (hESCs) can undergo differentiation into tro- regulated genes have been noted in the earlier studies. phoblast-like cells spontaneously from colonies [6], We chose to use the hESC line, BG02 (karyotype 46, growth of the cells beyond confluence [7], or embryoid XY), that has not been thoroughly studied in hESC dif- bodies (EBs) [3,8-12]. Similarly, trophoblast-like cells ferentiation to trophoblast. This cell line was established can be obtained from hESCs via induced differentiation from a 6-day embryo with an embryo grade of 3CC [7]. from the bone morphogenetic proteins (BMPs) 2, 4, and Herein, BMP4, in the presence of FGF2, was incubated 7 [13-24]. Fortunately, timely reviews are available [25- with adherent colonies of BG02 cells to initiate tro- 28]. Others have reported that RNAi-mediated knock- phoblast differentiation. Identical studies were also done down of Oct4 in hESCs can also lead to trophoblast-like in the presence of the BMP4 antagonist noggin, since it cells [29,30]. The BMPs, members of the transforming has been shown that noggin alters hESC gene expression growth factor-b (TGFb) superfamily, function to regulate and morphology, perhaps leading to differentiation to- many aspects of development which act by binding to ward early neuroectoderm [18]. In addition, trophoblast cell surface serine/threonine kinase receptors that, in turn, differentiation was initiated by formation of EBs. Parti- phosphorylate particular Smads, thus enabling them to cular emphasis was placed on quantitative profiling of a enter the nucleus and act as transcriptional regulators variety of genes via qRT-PCR, and measurements were [31-34]. made to determine hCG and steroid hormone production These cellular models for trophectoderm differentia- by the cells and EBs. Our results have many similarities tion begin to fill a long-awaited need for new systems to with the findings of others, including for example the study early development, particularly in view of the ma- down-regulation of pluripotency genes, the up-regulation jor differences between human and mouse trophoblast of trophoblast genes, and placental hormone production, [35-37]. Yet, the characteristics of the human trophoblast but there are also notable differences, particularly with cells obtained by BMP-mediated differentiation vary, the up-regulation of certain genes associated with the three sometimes quite significantly, depending upon the cell primary germ layers. type, culture conditions (including the presence or ab- sence of growth factors, particularly FGF2), and mode of 2. MATERIALS AND METHODS differentiation [10,18,38]. Moreover, in a number of in- stances there are considerable differences and controver- 2.1. Maintenance of Undifferentiated Cells sies regarding the product(s) of differentiation obtained In order to ensure pluripotency, the BG02 cells, ob- with BMP. For example, BMP4-mediated differentiation tained with proper authorization from Bresagen, Athens, was found to yield little evidence of trophoblast-like GA, were manually passaged every 2 - 3 days onto mito- cells under standard culture conditions [38]. Another stu- tically-inactivated mouse embryonic feeder (MEF) layers dy found that 14 genes were highly up-regulated as de- derived from E13.5 mouse fetuses. The MEF layer was termined by microarrays, in addition to many others [21], removed from the hESC colony, which was then gently while another report did not identify six of these particu- dispersed with the colony pieces being transferred to lar genes [17]. Also, differences in cell morphology and another 10 cm MEF-containing plate and treated with Copyright
Recommended publications
  • Activated Peripheral-Blood-Derived Mononuclear Cells
    Transcription factor expression in lipopolysaccharide- activated peripheral-blood-derived mononuclear cells Jared C. Roach*†, Kelly D. Smith*‡, Katie L. Strobe*, Stephanie M. Nissen*, Christian D. Haudenschild§, Daixing Zhou§, Thomas J. Vasicek¶, G. A. Heldʈ, Gustavo A. Stolovitzkyʈ, Leroy E. Hood*†, and Alan Aderem* *Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103; ‡Department of Pathology, University of Washington, Seattle, WA 98195; §Illumina, 25861 Industrial Boulevard, Hayward, CA 94545; ¶Medtronic, 710 Medtronic Parkway, Minneapolis, MN 55432; and ʈIBM Computational Biology Center, P.O. Box 218, Yorktown Heights, NY 10598 Contributed by Leroy E. Hood, August 21, 2007 (sent for review January 7, 2007) Transcription factors play a key role in integrating and modulating system. In this model system, we activated peripheral-blood-derived biological information. In this study, we comprehensively measured mononuclear cells, which can be loosely termed ‘‘macrophages,’’ the changing abundances of mRNAs over a time course of activation with lipopolysaccharide (LPS). We focused on the precise mea- of human peripheral-blood-derived mononuclear cells (‘‘macro- surement of mRNA concentrations. There is currently no high- phages’’) with lipopolysaccharide. Global and dynamic analysis of throughput technology that can precisely and sensitively measure all transcription factors in response to a physiological stimulus has yet to mRNAs in a system, although such technologies are likely to be be achieved in a human system, and our efforts significantly available in the near future. To demonstrate the potential utility of advanced this goal. We used multiple global high-throughput tech- such technologies, and to motivate their development and encour- nologies for measuring mRNA levels, including massively parallel age their use, we produced data from a combination of two distinct signature sequencing and GeneChip microarrays.
    [Show full text]
  • Correct Setup of the Substantia Nigra Requires Reelin-Mediated Fast, Laterally- Directed Migration of Dopaminergic Neurons
    RESEARCH ARTICLE Correct setup of the substantia nigra requires Reelin-mediated fast, laterally- directed migration of dopaminergic neurons Ankita Ravi Vaswani1, Beatrice Weykopf2†, Cathleen Hagemann1, Hans-Ulrich Fried3, Oliver Bru¨ stle2, Sandra Blaess1* 1Neurodevelopmental Genetics, Institute of Reconstructive Neurobiology, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany; 2Institute of Reconstructive Neurobiology, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany; 3Light Microscope Facility, German Center for Neurodegenerative Diseases, Bonn, Germany Abstract Midbrain dopaminergic (mDA) neurons migrate to form the laterally-located substantia nigra pars compacta (SN) and medially-located ventral tegmental area (VTA), but little is known about the underlying cellular and molecular processes. Here we visualize the dynamic cell morphologies of tangentially migrating SN-mDA neurons in 3D and identify two distinct migration modes. Slow migration is the default mode in SN-mDA neurons, while fast, laterally-directed *For correspondence: migration occurs infrequently and is strongly associated with bipolar cell morphology. Tangential [email protected] migration of SN-mDA neurons is altered in absence of Reelin signaling, but it is unclear whether Reelin acts directly on migrating SN-mDA neurons and how it affects their cell morphology and † Present address: Precision migratory behavior. By specifically inactivating Reelin signaling in mDA neurons we demonstrate its Neurology Program & Advanced direct role in SN-mDA tangential migration. Reelin promotes laterally-biased movements in mDA Center for Parkinson’s Disease neurons during their slow migration mode, stabilizes leading process morphology and increases the Research, Harvard Medical School and Brigham & Women’s probability of fast, laterally-directed migration.
    [Show full text]
  • Watsonjn2018.Pdf (1.780Mb)
    UNIVERSITY OF CENTRAL OKLAHOMA Edmond, Oklahoma Department of Biology Investigating Differential Gene Expression in vivo of Cardiac Birth Defects in an Avian Model of Maternal Phenylketonuria A THESIS SUBMITTED TO THE GRADUATE FACULTY In partial fulfillment of the requirements For the degree of MASTER OF SCIENCE IN BIOLOGY By Jamie N. Watson Edmond, OK June 5, 2018 J. Watson/Dr. Nikki Seagraves ii J. Watson/Dr. Nikki Seagraves Acknowledgements It is difficult to articulate the amount of gratitude I have for the support and encouragement I have received throughout my master’s thesis. Many people have added value and support to my life during this time. I am thankful for the education, experience, and friendships I have gained at the University of Central Oklahoma. First, I would like to thank Dr. Nikki Seagraves for her mentorship and friendship. I lucked out when I met her. I have enjoyed working on this project and I am very thankful for her support. I would like thank Thomas Crane for his support and patience throughout my master’s degree. I would like to thank Dr. Shannon Conley for her continued mentorship and support. I would like to thank Liz Bullen and Dr. Eric Howard for their training and help on this project. I would like to thank Kristy Meyer for her friendship and help throughout graduate school. I would like to thank my committee members Dr. Robert Brennan and Dr. Lilian Chooback for their advisement on this project. Also, I would like to thank the biology faculty and staff. I would like to thank the Seagraves lab members: Jailene Canales, Kayley Pate, Mckayla Muse, Grace Thetford, Kody Harvey, Jordan Guffey, and Kayle Patatanian for their hard work and support.
    [Show full text]
  • Supplemental Materials ZNF281 Enhances Cardiac Reprogramming
    Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7
    [Show full text]
  • Long Noncoding Rnas in Vascular Smooth Muscle Cells Regulate
    www.nature.com/scientificreports OPEN Long noncoding RNAs in vascular smooth muscle cells regulate vascular calcifcation Received: 21 November 2018 Geon Jeong1,2,3, Duk-Hwa Kwon1,4, Sera Shin1,4, Nakwon Choe1,4, Juhee Ryu1,2,3,4, Accepted: 27 March 2019 Yeong-Hwan Lim1,2,3, Jaetaek Kim1,5, Woo Jin Park1,6, Hyun Kook1,3,4 & Young-Kook Kim 1,2,3 Published: xx xx xxxx Vascular calcifcation is characterized by the accumulation of hydroxyapatite crystals, which is a result of aberrant mineral metabolism. Although many clinical studies have reported its adverse efects on cardiovascular morbidity, the molecular mechanism of vascular calcifcation, especially the involvement of long noncoding RNAs (lncRNAs), is not yet reported. From the transcriptomic analysis, we discovered hundreds of lncRNAs diferentially expressed in rat vascular smooth muscle cells (VSMCs) treated with inorganic phosphate, which mimics vascular calcifcation. We focused on Lrrc75a-as1 and elucidated its transcript structure and confrmed its cytoplasmic localization. Our results showed that calcium deposition was elevated after knockdown of Lrrc75a-as1, while its overexpression inhibited calcium accumulation in A10 cells. In addition, Lrrc75a-as1 attenuated VSMCs calcifcation by decreasing the expression of osteoblast-related factors. These fndings suggest that Lrrc75a-as1 acts as a negative regulator of vascular calcifcation, and may serve as a possible therapeutic target in vascular calcifcation. Vascular calcifcation is caused by an imbalance of mineral metabolism, especially calcium phosphate metabo- lism1. It decreases vessel wall tension and increases vascular stifness, thereby increasing the risk of myocardial ischemia, heart failure, arrhythmias, and other cardiovascular diseases2. Vascular calcifcation includes several major types including medial arterial calcifcation, intimal atherosclerosis, and arterial calcifcation of chronic kidney diseases3.
    [Show full text]
  • SUPPLEMENTARY MATERIAL Bone Morphogenetic Protein 4 Promotes
    www.intjdevbiol.com doi: 10.1387/ijdb.160040mk SUPPLEMENTARY MATERIAL corresponding to: Bone morphogenetic protein 4 promotes craniofacial neural crest induction from human pluripotent stem cells SUMIYO MIMURA, MIKA SUGA, KAORI OKADA, MASAKI KINEHARA, HIROKI NIKAWA and MIHO K. FURUE* *Address correspondence to: Miho Kusuda Furue. Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan. Tel: 81-72-641-9819. Fax: 81-72-641-9812. E-mail: [email protected] Full text for this paper is available at: http://dx.doi.org/10.1387/ijdb.160040mk TABLE S1 PRIMER LIST FOR QRT-PCR Gene forward reverse AP2α AATTTCTCAACCGACAACATT ATCTGTTTTGTAGCCAGGAGC CDX2 CTGGAGCTGGAGAAGGAGTTTC ATTTTAACCTGCCTCTCAGAGAGC DLX1 AGTTTGCAGTTGCAGGCTTT CCCTGCTTCATCAGCTTCTT FOXD3 CAGCGGTTCGGCGGGAGG TGAGTGAGAGGTTGTGGCGGATG GAPDH CAAAGTTGTCATGGATGACC CCATGGAGAAGGCTGGGG MSX1 GGATCAGACTTCGGAGAGTGAACT GCCTTCCCTTTAACCCTCACA NANOG TGAACCTCAGCTACAAACAG TGGTGGTAGGAAGAGTAAAG OCT4 GACAGGGGGAGGGGAGGAGCTAGG CTTCCCTCCAACCAGTTGCCCCAAA PAX3 TTGCAATGGCCTCTCAC AGGGGAGAGCGCGTAATC PAX6 GTCCATCTTTGCTTGGGAAA TAGCCAGGTTGCGAAGAACT p75 TCATCCCTGTCTATTGCTCCA TGTTCTGCTTGCAGCTGTTC SOX9 AATGGAGCAGCGAAATCAAC CAGAGAGATTTAGCACACTGATC SOX10 GACCAGTACCCGCACCTG CGCTTGTCACTTTCGTTCAG Suppl. Fig. S1. Comparison of the gene expression profiles of the ES cells and the cells induced by NC and NC-B condition. Scatter plots compares the normalized expression of every gene on the array (refer to Table S3). The central line
    [Show full text]
  • Combinatorial Bzip Dimers Display Complex DNA-Binding Specificity Landscapes
    Combinatorial bZIP dimers display complex DNA-binding specificity landscapes The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Rodriguez-Martinez, Jose A et al. “Combinatorial bZIP Dimers Display Complex DNA-Binding Specificity Landscapes.” eLife 6 (2017): n. pag. As Published http://dx.doi.org/10.7554/eLife.19272 Publisher eLife Sciences Publications, Ltd. Version Final published version Citable link http://hdl.handle.net/1721.1/110147 Terms of Use Creative Commons Attribution 4.0 International License Detailed Terms http://creativecommons.org/licenses/by-nc/4.0/ RESEARCH ARTICLE Combinatorial bZIP dimers display complex DNA-binding specificity landscapes Jose´ A Rodrı´guez-Martı´nez1†, Aaron W Reinke2†, Devesh Bhimsaria1,3†, Amy E Keating2,4, Aseem Z Ansari1,5* 1Department of Biochemistry, University of Wisconsin-Madison, Madison, United States; 2Department of Biology, Massachusetts Institute of Technology, Cambridge, United States; 3Department of Electrical and Computer Engineering, University of Wisconsin-Madison, Madison, Unites States; 4Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States; 5The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, United States Abstract How transcription factor dimerization impacts DNA-binding specificity is poorly understood. Guided by protein dimerization properties, we examined DNA binding specificities of 270 human bZIP pairs. DNA interactomes of 80 heterodimers and 22 homodimers revealed that 72% of heterodimer motifs correspond to conjoined half-sites preferred by partnering monomers. Remarkably, the remaining motifs are composed of variably-spaced half-sites (12%) or ‘emergent’ sites (16%) that cannot be readily inferred from half-site preferences of partnering monomers.
    [Show full text]
  • Appendix 2. Significantly Differentially Regulated Genes in Term Compared with Second Trimester Amniotic Fluid Supernatant
    Appendix 2. Significantly Differentially Regulated Genes in Term Compared With Second Trimester Amniotic Fluid Supernatant Fold Change in term vs second trimester Amniotic Affymetrix Duplicate Fluid Probe ID probes Symbol Entrez Gene Name 1019.9 217059_at D MUC7 mucin 7, secreted 424.5 211735_x_at D SFTPC surfactant protein C 416.2 206835_at STATH statherin 363.4 214387_x_at D SFTPC surfactant protein C 295.5 205982_x_at D SFTPC surfactant protein C 288.7 1553454_at RPTN repetin solute carrier family 34 (sodium 251.3 204124_at SLC34A2 phosphate), member 2 238.9 206786_at HTN3 histatin 3 161.5 220191_at GKN1 gastrokine 1 152.7 223678_s_at D SFTPA2 surfactant protein A2 130.9 207430_s_at D MSMB microseminoprotein, beta- 99.0 214199_at SFTPD surfactant protein D major histocompatibility complex, class II, 96.5 210982_s_at D HLA-DRA DR alpha 96.5 221133_s_at D CLDN18 claudin 18 94.4 238222_at GKN2 gastrokine 2 93.7 1557961_s_at D LOC100127983 uncharacterized LOC100127983 93.1 229584_at LRRK2 leucine-rich repeat kinase 2 HOXD cluster antisense RNA 1 (non- 88.6 242042_s_at D HOXD-AS1 protein coding) 86.0 205569_at LAMP3 lysosomal-associated membrane protein 3 85.4 232698_at BPIFB2 BPI fold containing family B, member 2 84.4 205979_at SCGB2A1 secretoglobin, family 2A, member 1 84.3 230469_at RTKN2 rhotekin 2 82.2 204130_at HSD11B2 hydroxysteroid (11-beta) dehydrogenase 2 81.9 222242_s_at KLK5 kallikrein-related peptidase 5 77.0 237281_at AKAP14 A kinase (PRKA) anchor protein 14 76.7 1553602_at MUCL1 mucin-like 1 76.3 216359_at D MUC7 mucin 7,
    [Show full text]
  • Atf5 As a Regulator of a Mammalian Mitochondrial Unfolded
    ATF5 AS A REGULATOR OF A MAMMALIAN MITOCHONDRIAL UNFOLDED PROTEIN RESPONSE A Dissertation Presented to the Faculty of the Weill Cornell Graduate School of Medical Sciences in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy By Christopher Fiorese January 2017 © 2017 Christopher Fiorese ATF5 AS A REGULATOR OF A MAMMALIAN MITOCHONDRIAL UNFOLDED PROTEIN RESPONSE Christopher J. Fiorese, Ph.D. Cornell University 2017 Mitochondrial dysfunction is pervasive in human pathologies such as neurodegeneration, diabetes, cancer and pathogen infections as well as during normal aging. Cells sense and respond to mitochondrial stress or dysfunction by activating a protective transcriptional program known as the mitochondrial unfolded protein response (UPR mt ), which includes genes that promote mitochondrial protein homeostasis and the regeneration of metabolically defective organelles (Nargund, Pellegrino et al. 2012, Nargund, Fiorese et al. 2015). Work in C. elegans has shown that the UPR mt is regulated by the transcription factor ATFS-1, which is regulated by organelle partitioning. Normally, ATFS-1 accumulates within mitochondria, but during respiratory chain dysfunction, high levels of ROS or mitochondrial protein folding stress, a percentage of ATFS-1 accumulates in the cytosol and traffics to the nucleus where it activates the UPR mt (Nargund, Pellegrino et al. 2012). While similar transcriptional responses have been described in mammals (Zhao, Wang et al. 2002, Wu, Williams et al. 2014), how the UPR mt is regulated remains unclear. Here, we describe a mammalian transcription factor, ATF5, which is regulated similarly to ATFS-1 and induces a similar transcriptional response. ATF5 expression can rescue UPR mt signaling in atfs-1-deficient worms requiring the same UPR mt promoter element identified in C.
    [Show full text]
  • Transcription Factor Gene Expression Profiling and Analysis of SOX Gene Family Transcription Factors in Human Limbal Epithelial
    Transcription factor gene expression profiling and analysis of SOX gene family transcription factors in human limbal epithelial progenitor cells Der Naturwissenschaftlichen Fakultät der Friedrich-Alexander-Universität Erlangen-Nürnberg zur Erlangung des Doktorgrades Dr. rer. nat. vorgelegt von Dr. med. Johannes Menzel-Severing aus Bonn Als Dissertation genehmigt von der Naturwissenschaftlichen Fakultät der Friedrich-Alexander-Universität Erlangen-Nürnberg Tag der mündlichen Prüfung: 7. Februar 2018 Vorsitzender des Promotionsorgans: Prof. Dr. Georg Kreimer Gutachter: Prof. Dr. Andreas Feigenspan Prof. Dr. Ursula Schlötzer-Schrehardt 1 INDEX 1. ABSTRACTS Page 1.1. Abstract in English 4 1.2. Zusammenfassung auf Deutsch 7 2. INTRODUCTION 2.1. Anatomy and histology of the cornea and the corneal surface 11 2.2. Homeostasis of corneal epithelium and the limbal stem cell paradigm 13 2.3. The limbal stem cell niche 15 2.4. Cell therapeutic strategies in ocular surface disease 17 2.5. Alternative cell sources for transplantation to the corneal surface 18 2.6. Transcription factors in cell differentiation and reprogramming 21 2.7. Transcription factors in limbal epithelial cells 22 2.8. Research question 25 3. MATERIALS AND METHODS 3.1. Human donor corneas 27 3.2. Laser Capture Microdissection (LCM) 28 3.3. RNA amplification and RT2 profiler PCR arrays 29 3.4. Real-time PCR analysis 33 3.5. Immunohistochemistry 34 3.6. Limbal epithelial cell culture 38 3.7. Transcription-factor knockdown/overexpression in vitro 39 3.8. Proliferation assay 40 3.9. Western blot 40 3.10. Statistical analysis 41 2 4. RESULTS 4.1. Quality control of LCM-isolated and amplified RNA 42 4.2.
    [Show full text]
  • SPEN Protein Expression and Interactions with Chromatin in Mouse Testicular Cells
    156 3 REPRODUCTIONRESEARCH SPEN protein expression and interactions with chromatin in mouse testicular cells Joanna Korfanty1, Tomasz Stokowy2, Marek Chadalski1, Agnieszka Toma-Jonik1, Natalia Vydra1, Piotr Widłak1, Bartosz Wojtaś3, Bartłomiej Gielniewski3 and Wieslawa Widlak1 1Maria Sklodowska-Curie Institute – Oncology Center, Gliwice Branch, Gliwice, Poland, 2Department of Clinical Science, University of Bergen, Bergen, Norway and 3Laboratory of Molecular Neurobiology, Neurobiology Center, Nencki Institute of Experimental Biology, PAS, Warsaw, Poland Correspondence should be addressed to W Widlak; Email: [email protected] Abstract SPEN (spen family transcription repressor) is a nucleic acid-binding protein putatively involved in repression of gene expression. We hypothesized that SPEN could be involved in general downregulation of the transcription during the heat shock response in mouse spermatogenic cells through its interactions with chromatin. We documented predominant nuclear localization of the SPEN protein in spermatocytes and round spermatids, which was retained after heat shock. Moreover, the protein was excluded from the highly condensed chromatin. Chromatin immunoprecipitation experiments clearly indicated interactions of SPEN with chromatin in vivo. However, ChIP-Seq analyses did not reveal any strong specific peaks both in untreated and heat shocked cells, which might suggest dispersed localization of SPEN and/or its indirect binding to DNA. Using in situ proximity ligation assay we found close in vivo associations of SPEN with MTA1 (metastasis-associated 1), a member of the nucleosome remodeling complex with histone deacetylase activity, which might contribute to interactions of SPEN with chromatin. Reproduction (2018) 156 195–206 Introduction However, regulation of osteocalcin expression by SPEN depends on its interactions with other proteins.
    [Show full text]
  • Xo GENE PANEL
    xO GENE PANEL Targeted panel of 1714 genes | Tumor DNA Coverage: 500x | RNA reads: 50 million Onco-seq panel includes clinically relevant genes and a wide array of biologically relevant genes Genes A-C Genes D-F Genes G-I Genes J-L AATK ATAD2B BTG1 CDH7 CREM DACH1 EPHA1 FES G6PC3 HGF IL18RAP JADE1 LMO1 ABCA1 ATF1 BTG2 CDK1 CRHR1 DACH2 EPHA2 FEV G6PD HIF1A IL1R1 JAK1 LMO2 ABCB1 ATM BTG3 CDK10 CRK DAXX EPHA3 FGF1 GAB1 HIF1AN IL1R2 JAK2 LMO7 ABCB11 ATR BTK CDK11A CRKL DBH EPHA4 FGF10 GAB2 HIST1H1E IL1RAP JAK3 LMTK2 ABCB4 ATRX BTRC CDK11B CRLF2 DCC EPHA5 FGF11 GABPA HIST1H3B IL20RA JARID2 LMTK3 ABCC1 AURKA BUB1 CDK12 CRTC1 DCUN1D1 EPHA6 FGF12 GALNT12 HIST1H4E IL20RB JAZF1 LPHN2 ABCC2 AURKB BUB1B CDK13 CRTC2 DCUN1D2 EPHA7 FGF13 GATA1 HLA-A IL21R JMJD1C LPHN3 ABCG1 AURKC BUB3 CDK14 CRTC3 DDB2 EPHA8 FGF14 GATA2 HLA-B IL22RA1 JMJD4 LPP ABCG2 AXIN1 C11orf30 CDK15 CSF1 DDIT3 EPHB1 FGF16 GATA3 HLF IL22RA2 JMJD6 LRP1B ABI1 AXIN2 CACNA1C CDK16 CSF1R DDR1 EPHB2 FGF17 GATA5 HLTF IL23R JMJD7 LRP5 ABL1 AXL CACNA1S CDK17 CSF2RA DDR2 EPHB3 FGF18 GATA6 HMGA1 IL2RA JMJD8 LRP6 ABL2 B2M CACNB2 CDK18 CSF2RB DDX3X EPHB4 FGF19 GDNF HMGA2 IL2RB JUN LRRK2 ACE BABAM1 CADM2 CDK19 CSF3R DDX5 EPHB6 FGF2 GFI1 HMGCR IL2RG JUNB LSM1 ACSL6 BACH1 CALR CDK2 CSK DDX6 EPOR FGF20 GFI1B HNF1A IL3 JUND LTK ACTA2 BACH2 CAMTA1 CDK20 CSNK1D DEK ERBB2 FGF21 GFRA4 HNF1B IL3RA JUP LYL1 ACTC1 BAG4 CAPRIN2 CDK3 CSNK1E DHFR ERBB3 FGF22 GGCX HNRNPA3 IL4R KAT2A LYN ACVR1 BAI3 CARD10 CDK4 CTCF DHH ERBB4 FGF23 GHR HOXA10 IL5RA KAT2B LZTR1 ACVR1B BAP1 CARD11 CDK5 CTCFL DIAPH1 ERCC1 FGF3 GID4
    [Show full text]