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Jesús Espinal-Enríquez, Daniel González-Terán, Enrique Hernández-Lemus
Understanding the general principles underlying genetic regulation in eukaryotes is an incomplete and challenging endeavor. The lack of experimental information regarding the regulation of the whole set of transcription factors and their targets in different cell types is one of the main reasons to this incompleteness. So far, there is a small set of curated known interactions between transcription factors and their downstream genes. Here, we built a transcription factor network for human monocytic THP-1 myeloid cells based on the experimentally curated FANTOM4 database where nodes are genes and the experimental interactions correspond to links...
2017: International Journal of Genomics
Rance Nault, Kelly A Fader, Jack R Harkema, Tim Zacharewski
The aryl hydrocarbon receptor (AhR) is a highly conserved transcription factor that mediates a broad spectrum of species-, strain-, sex-, age-, tissue-, and cell-specific responses elicited by structurally diverse ligands including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Dose-dependent effects on liver-specific and sexually dimorphic gene expression were examined in male and female mice gavaged with TCDD every 4 days for 28 or 92 days. RNA-seq data revealed the coordinated repression of 181 genes predominately expressed in the liver including albumin (3...
2017: PloS One
Shao-Jun Zhou, Yue-Ling Deng, Hui-Fang Liang, Jonathan C Jaoude, Fu-Yao Liu
Familiar clustering of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) has been frequently reported. However, limited information is available about the underlying molecular mechanisms in HBV-related HCC patients with family history of HCC. In our previous study, Agilent miRNA Base 16.0 microarray showed miRNA profiles of the plasma of HBV-related HCC patients who had a family history of HCC. This study aims to explore the expression, function, and mechanisms of miR-3188 in HCC that might provide novel insights into the role of family history on the risk of HCC...
September 2017: Cell Death and Differentiation
Jieyun Jiang, Kate Townsend Creasy, Justin Purnell, Martha L Peterson, Brett T Spear
The mouse major urinary proteins (Mups) are encoded by a large family of highly related genes clustered on chromosome 4. Mups, synthesized primarily and abundantly in the liver and secreted through the kidneys, exhibit male-biased expression. Mups bind a variety of volatile ligands; these ligands, and Mup proteins themselves, influence numerous behavioral traits. Although urinary Mup protein levels vary between inbred mouse strains, this difference is most pronounced in BALB/cJ mice, which have dramatically low urinary Mup levels; this BALB/cJ trait had been mapped to a locus on chromosome 15...
April 21, 2017: Journal of Biological Chemistry
Ryuk-Jun Kwon, Yun Hak Kim, Dae Cheon Jeong, Myoung-Eun Han, Ji-Young Kim, Liangwen Liu, Jin-Sup Jung, Sae-Ock Oh
Zinc fingers and homeoboxes (ZHX) is a transcription repressor family that contains three members; ZHX1, ZHX2, and ZHX3. Although ZHX family members have been associated with the progression of cancer, their values as prognostic factors in cancer patients have been poorly examined. Renal cell carcinoma (RCC) is a highly heterogeneous, aggressive cancer that responds variably to treatment. Thus, prognostic molecular markers are required to evaluate disease progression and to improve the survival. In clear cell RCC (ccRCC), ZHX1 and ZHX3 expression were found to be down-regulated but ZHX2 was up-regulated, and the expressions of ZHX1 and ZHX3 were significantly associated with pathological stage...
2017: PloS One
Raquel López-Mejías, Alfonso Corrales, Esther Vicente, Montserrat Robustillo-Villarino, Carlos González-Juanatey, Javier Llorca, Fernanda Genre, Sara Remuzgo-Martínez, Trinidad Dierssen-Sotos, José A Miranda-Filloy, Marco A Ramírez Huaranga, Trinitario Pina, Ricardo Blanco, Juan J Alegre-Sancho, Enrique Raya, Verónica Mijares, Begoña Ubilla, Iván Ferraz-Amaro, Carmen Gómez-Vaquero, Alejandro Balsa, Francisco J López-Longo, Patricia Carreira, Isidoro González-Álvaro, J Gonzalo Ocejo-Vinyals, Luis Rodríguez-Rodríguez, Benjamín Fernández-Gutiérrez, Santos Castañeda, Javier Martín, Miguel A González-Gay
A genetic component influences the development of atherosclerosis in the general population and also in rheumatoid arthritis (RA). However, genetic polymorphisms associated with atherosclerosis in the general population are not always involved in the development of cardiovascular disease (CVD) in RA. Accordingly, a study in North-American RA patients did not show the association reported in the general population of coronary artery disease with a series of relevant polymorphisms (TCF21, LPA, HHIPL1, RASD1-PEMT, MRPS6, CYP17A1-CNNM2-NT5C2, SMG6-SRR, PHACTR1, WDR12 and COL4A1-COL4A2)...
January 6, 2017: Scientific Reports
Martin I Sigurdsson, Louis Saddic, Mahyar Heydarpour, Tzuu-Wang Chang, Prem Shekar, Sary Aranki, Gregory S Couper, Stanton K Shernan, Jon G Seidman, Simon C Body, Jochen D Muehlschlegel
BACKGROUND: Allele-specific expression (ASE) is differential expression of each of the two chromosomal alleles of an autosomal gene. We assessed ASE patterns in the human left atrium (LA, n = 62) and paired samples from the left ventricle (LV, n = 76) before and after ischemia, and tested the utility of differential ASE to identify genes associated with postoperative atrial fibrillation (poAF) and myocardial ischemia. METHODS: Following genotyping from whole blood and whole-genome sequencing of LA and LV samples, we called ASE using sequences overlapping heterozygous SNPs using rigorous quality control to minimize false ASE calling...
December 6, 2016: Genome Medicine
Hans-Juergen Schulten, Deema Hussein, Fatima Al-Adwani, Sajjad Karim, Jaudah Al-Maghrabi, Mona Al-Sharif, Awatif Jamal, Sherin Bakhashab, Jolanta Weaver, Fahad Al-Ghamdi, Saleh S Baeesa, Mohammed Bangash, Adeel Chaudhary, Mohammed Al-Qahtani
Brain metastatic papillary thyroid carcinomas (PTCs) are afflicted with unfavorable prognosis; however, the underlying molecular genetics of these rare metastases are virtually unknown. In this study, we compared whole transcript microarray expression profiles of a BRAF mutant, brain metastasis from a PTC, including its technical replicate (TR), with eight non-brain metastatic PTCs and eight primary brain tumors. The top 95 probe sets (false discovery rate (FDR) p-value < 0.05 and fold change (FC) > 2) that were differentially expressed between the brain metastatic PTC, including the TR, and both, non-brain metastatic PTCs and primary brain tumors were in the vast majority upregulated and comprise, e...
2016: American Journal of Cancer Research
Isabelle Chang, Marta Parrilla
Homeodomain proteins are encoded by homeobox genes and regulate development and differentiation in many neuronal systems. The mouse vomeronasal organ (VNO) generates in situ mature chemosensory neurons from stem cells. The roles of homeodomain proteins in neuronal differentiation in the VNO are poorly understood. Here we have characterized the expression patterns of 28 homeobox genes in the VNO of C57BL/6 mice at postnatal stages using multicolor fluorescent in situ hybridization. We identified 11 homeobox genes (Dlx3, Dlx4, Emx2, Lhx2, Meis1, Pbx3, Pknox2, Pou6f1, Tshz2, Zhx1, Zhx3) that were expressed exclusively in neurons; 4 homeobox genes (Pax6, Six1, Tgif1, Zfhx3) that were expressed in all non-neuronal cell populations, with Pax6, Six1 and Tgif1 also expressed in some neuronal progenitors and precursors; 12 homeobox genes (Adnp, Cux1, Dlx5, Dlx6, Meis2, Pbx2, Pknox1, Pou2f1, Satb1, Tshz1, Tshz3, Zhx2) with expression in both neuronal and non-neuronal cell populations; and one homeobox gene (Hopx) that was exclusively expressed in the non-sensory epithelium...
July 2016: Gene Expression Patterns: GEP
Kate T Creasy, Jieyun Jiang, Hui Ren, Martha L Peterson, Brett T Spear
The mammalian cytochrome P450 (Cyp) gene family encodes a large number of structurally related enzymes that catalyze a variety of metabolic and detoxification reactions. The liver is the primary site of Cyp expression in terms of expression levels and number of expressed genes, consistent with this organ's essential role in metabolism of endogenous and xenobiotic compounds. Many Cyp genes exhibit sexually dimorphic expression. For example, Cyp2a4 is expressed significantly higher in the adult liver of female mice compared to male mice...
2016: Gene Expression
Marie H Geisel, Stefan Coassin, Nicole Heßler, Marcus Bauer, Lewin Eisele, Raimund Erbel, Margot Haun, Frauke Hennig, Susanna Moskau-Hartmann, Barbara Hoffmann, Karl-Heinz Jöckel, Lyudmyla Kedenko, Stefan Kiechl, Barbara Kollerits, Amir-Abbas Mahabadi, Susanne Moebus, Gudrun Nürnberg, Peter Nürnberg, Bernhard Paulweber, Maren Vens, Johann Willeit, Karin Willeit, Thomas Klockgether, Andreas Ziegler, André Scherag, Florian Kronenberg
Carotid intima media thickness (cIMT) is a marker for subclinical atherosclerosis. The most recent genome-wide association meta-analysis (GWAMA) from the CHARGE consortium identified four genomic regions showing either significant (ZHX2, APOC1, PINX1) or suggestive evidence (SLC17A4) for an association. Here we assess these four cIMT loci in a pooled analysis of four independent studies including 5446 individuals by providing updated unbiased effect estimates of the cIMT association signals. The pooled estimates of our four independent samples pointed in the same direction and were similar to those of the GWAMA...
June 2016: Atherosclerosis
Oscar Alvarez-Garcia, Kathleen M Fisch, Nathan E Wineinger, Ryuichiro Akagi, Masahiko Saito, Takahisa Sasho, Andrew I Su, Martin K Lotz
OBJECTIVE: To analyze the methylome of normal and osteoarthritic (OA) knee articular cartilage and to determine the role of DNA methylation in the regulation of gene expression in vitro. METHODS: DNA was isolated from human normal (n = 11) and OA (n = 12) knee articular cartilage and analyzed using the Infinium HumanMethylation450 BeadChip array. To integrate methylation and transcription, RNA sequencing was performed on normal and OA cartilage and validated by quantitative polymerase chain reaction...
August 2016: Arthritis & Rheumatology
Fang Wan, Lifen Gao, Yating Lu, Hongxin Ma, Hongxing Wang, Xiaohong Liang, Yan Wang, Chunhong Ma
In the process of tooth root development, stem cells from the apical papilla (SCAPs) can differentiate into odontoblasts and form root dentin, however, molecules regulating SCAPs differentiation have not been elucidated. Zinc fingers and homeoboxes 2 (ZHX2) is a novel transcriptional inhibitor. It is reported to modulate the development of nerve cells, liver cells, B cells, red blood cells, and so on. However, the role of ZHX2 in tooth root development remains unclear. In this study, we explored the potential role of ZHX2 in the process of SCAPs differentiation...
January 15, 2016: Biochemical and Biophysical Research Communications
Chih-Ping Chen, Ming-Huei Lin, Yi-Yung Chen, Schu-Rern Chern, Yen-Ni Chen, Peih-Shan Wu, Chen-Wen Pan, Meng-Shan Lee, Wayseen Wang
OBJECTIVE: The aim of this research was to present prenatal diagnosis of Langer-Giedion syndrome (LGS/TRPS type II) and Cornelia de Lange syndrome-4 (CDLS4). MATERIALS AND METHODS: A 36-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Conventional cytogenetic analysis of amniocentesis revealed an interstitial deletion of chromosome 8q or del(8)(q23.3q24.13). Level II prenatal ultrasound examination revealed craniofacial dysmorphism...
October 2015: Taiwanese Journal of Obstetrics & Gynecology
Stefan Nagel, Stefan Ehrentraut, Corinna Meyer, Maren Kaufmann, Hans G Drexler, Roderick A F MacLeod
In Hodgkin lymphoma (HL) we recently reported that deregulated homeobox gene MSX1 mediates repression of the B-cell specific transcription factor ZHX2. In this study we investigated regulation of MSX1 in this B-cell malignancy. Accordingly, we analyzed expression and function of OTX homeobox genes which activate MSX1 transcription during embryonal development in the neural plate border region. Our data demonstrate that OTX1 and OTX2 are aberrantly expressed in both HL patients and cell lines. Moreover, both OTX loci are targeted by genomic gains in overexpressing cell lines...
2015: PloS One
Christina M Duzyj, Michael J Paidas, Lellean Jebailey, Jing Shun Huang, Eytan R Barnea
BACKGROUND: Intimate embryo-maternal interaction is paramount for pregnancy success post-implantation. The embryo follows a specific developmental timeline starting with neural system, dependent on endogenous and decidual factors. Beyond altered genetics/epigenetics, post-natal diseases may initiate at prenatal/neonatal, post-natal period, or through a continuum. Preimplantation factor (PIF) secreted by viable embryos promotes implantation and trophoblast invasion. Synthetic PIF reverses neuroinflammation in non-pregnant models...
2014: Journal of Neurodevelopmental Disorders
Changwei Li, Wei Chen, Fan Jiang, Jeannette Simino, Sathanur R Srinivasan, Gerald S Berenson, Hao Mei
OBJECTIVES: To examine the associations of five GWAS-identified genes with carotid intima-media thickness (IMT) in a biracial sample from the Bogalusa Heart Study, and evaluate their participation in gene-smoking interactions. METHODS: Far wall IMTs of common carotid arteries were measured using high-resolution B-mode ultrasound. Both the gene-smoking interactions and single-marker associations were evaluated by linear models of carotid IMT levels, while the gene-based analyses were assessed through the truncated product method...
May 15, 2015: Gene
Martina Kluth, Rami Galal, Antje Krohn, Joachim Weischenfeldt, Christina Tsourlakis, Lisa Paustian, Ramin Ahrary, Malik Ahmed, Sekander Scherzai, Anne Meyer, Hüseyin Sirma, Jan Korbel, Guido Sauter, Thorsten Schlomm, Ronald Simon, Sarah Minner
Prostate cancer is characterized by structural rearrangements, most frequently including translocations between androgen-dependent genes and members of the ETS family of transcription factor like TMPRSS2:ERG. In a recent whole genome sequencing study we identified 140 gene fusions that were unrelated to ETS genes in 11 prostate cancers. The aim of the present study was to estimate the prevalence of non-ETS gene fusions. We randomly selected 27 of these rearrangements and analyzed them by fluorescence in situ hybridization (FISH) in a tissue microarray format containing 500 prostate cancers...
April 2015: International Journal of Oncology
Hongxin Ma, Xuetian Yue, Lifen Gao, Xiaohong Liang, Wenjiang Yan, Zhenyu Zhang, Haixia Shan, Hualin Zhang, Brett T Spear, Chunhong Ma
We previously reported the tumor suppressor function of Zinc-fingers and homeoboxes 2 (ZHX2) in hepatocellular carcinoma (HCC). Other studies indicate the association of increased ZHX2 expression with improved response to high dose chemotherapy in multiple myeloma. Here, we aim to test whether increased ZHX2 levels in HCC cells repress multidrug resistance 1(MDR1) expression resulting in increased sensitivity to chemotherapeutic drugs. We showed evidence that increased ZHX2 levels correlated with reduced MDR1 expression and enhanced the cytotoxicity of CDDP and ADM in different HCC cell lines...
January 20, 2015: Oncotarget
Fang Luan, Peng Liu, Hongxin Ma, Xuetian Yue, Jun Liu, Lifen Gao, Xiaohong Liang, Chunhong Ma
Glypican 3 (GPC3) has been paid particular attention owing to its potential as diagnosis marker for hepatocellular carcinoma (HCC). Identifying the mechanisms regulating the reactivation of GPC3 in HCC appears to be clinically meaningful. Previous study identified zinc-fingers and homeoboxes 2 (ZHX2) as transcriptional factor responsible for postnatal repression of GPC3 in mice. Here, in this study, we provided the first evidence that down regulated ZHX2 is responsible for GPC3 reactivation in HCC. First, inverse correlation of ZHX2 with GPC3 expression was shown in cultured liver cell lines...
October 2014: International Journal of Biochemistry & Cell Biology
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