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https://www.readbyqxmd.com/read/28700586/systematic-identification-and-characterization-of-regulatory-elements-derived-from-human-endogenous-retroviruses
#1
Jumpei Ito, Ryota Sugimoto, Hirofumi Nakaoka, Shiro Yamada, Tetsuaki Kimura, Takahide Hayano, Ituro Inoue
Human endogenous retroviruses (HERVs) and other long terminal repeat (LTR)-type retrotransposons (HERV/LTRs) have regulatory elements that possibly influence the transcription of host genes. We systematically identified and characterized these regulatory elements based on publicly available datasets of ChIP-Seq of 97 transcription factors (TFs) provided by ENCODE and Roadmap Epigenomics projects. We determined transcription factor-binding sites (TFBSs) using the ChIP-Seq datasets and identified TFBSs observed on HERV/LTR sequences (HERV-TFBSs)...
July 12, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28673244/a-comprehensive-genomic-pan-cancer-classification-using-the-cancer-genome-atlas-gene-expression-data
#2
Yuanyuan Li, Kai Kang, Juno M Krahn, Nicole Croutwater, Kevin Lee, David M Umbach, Leping Li
BACKGROUND: The Cancer Genome Atlas (TCGA) has generated comprehensive molecular profiles. We aim to identify a set of genes whose expression patterns can distinguish diverse tumor types. Those features may serve as biomarkers for tumor diagnosis and drug development. METHODS: Using RNA-seq expression data, we undertook a pan-cancer classification of 9,096 TCGA tumor samples representing 31 tumor types. We randomly assigned 75% of samples into training and 25% into testing, proportionally allocating samples from each tumor type...
July 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28662305/degranulation-and-shrinkage-of-dark-cells-in-eccrine-glands-and-elevated-serum-carcinoembryonic-antigen-in-patients-with-acquired-idiopathic-generalized-anhidrosis
#3
K Sano, M Asahina, T Uehara, K Matsumoto, N Araki, R Okuyama
BACKGROUND: Acquired idiopathic generalized anhidrosis (AIGA) is characterized by anhidrosis/hypohidrosis without other autonomic and neurological dysfunctions. Pathologically, AIGA is considered to usually present no significant morphological alterations in eccrine glands, the secretory portion of which consists of clear cells, dark cells, and myoepithelial cells. AIGA patients recently have been reported to show high serum concentrations of carcinoembryonic antigen (CEA). OBJECTIVE: Our aim is to reveal morphological abnormalities of dark cells and investigate their relationship with serum CEA...
June 29, 2017: Journal of the European Academy of Dermatology and Venereology: JEADV
https://www.readbyqxmd.com/read/28659719/somatic-mutation-analyses-in-studies-of-the-clonal-evolution-and-diagnostic-targets-of-prostate-cancer
#4
REVIEW
Dmitry S Mikhaylenko, Gennady D Efremov, Vladimir V Strelnikov, Dmitry V Zaletaev, Boris Y Alekseev
Prostate cancer (PC) is the most common uro-oncological disease in the global population and still requires a more efficient laboratory diagnosis. Point mutations of oncogenes and tumor sup-pressor genes are the most frequent molecular genetic events in carcinogenesis. The mutations are re-sponsible, to a great extent, for the clonal evolution of cancer and can be considered as primary candi-date molecular markers of PC. Using next-generation sequencing to analyze the mutations in PC, the main molecular PC subtypes were identified, which depended on the presence of fusion genes and FOXA1, CHD1, and SPOP point mutations; other driver mutations responsible for the progression of PC subclones were also characterized...
June 2017: Current Genomics
https://www.readbyqxmd.com/read/28658208/recurrent-and-functional-regulatory-mutations-in-breast-cancer
#5
Esther Rheinbay, Prasanna Parasuraman, Jonna Grimsby, Grace Tiao, Jesse M Engreitz, Jaegil Kim, Michael S Lawrence, Amaro Taylor-Weiner, Sergio Rodriguez-Cuevas, Mara Rosenberg, Julian Hess, Chip Stewart, Yosef E Maruvka, Petar Stojanov, Maria L Cortes, Sara Seepo, Carrie Cibulskis, Adam Tracy, Trevor J Pugh, Jesse Lee, Zongli Zheng, Leif W Ellisen, A John Iafrate, Jesse S Boehm, Stacey B Gabriel, Matthew Meyerson, Todd R Golub, Jose Baselga, Alfredo Hidalgo-Miranda, Toshi Shioda, Andre Bernards, Eric S Lander, Gad Getz
Genomic analysis of tumours has led to the identification of hundreds of cancer genes on the basis of the presence of mutations in protein-coding regions. By contrast, much less is known about cancer-causing mutations in non-coding regions. Here we perform deep sequencing in 360 primary breast cancers and develop computational methods to identify significantly mutated promoters. Clear signals are found in the promoters of three genes. FOXA1, a known driver of hormone-receptor positive breast cancer, harbours a mutational hotspot in its promoter leading to overexpression through increased E2F binding...
July 6, 2017: Nature
https://www.readbyqxmd.com/read/28632777/immunohistochemiocal-subtyping-using-ck20-and-ck5-can-identify-urothelial-carcinomas-of-the-upper-urinary-tract-with-a-poor-prognosis
#6
Danijel Sikic, Bastian Keck, Sven Wach, Helge Taubert, Bernd Wullich, Peter J Goebell, Andreas Kahlmeyer, Peter Olbert, Philipp Isfort, Wilhelm Nimphius, Arndt Hartmann, Johannes Giedl
PURPOSE: Genome-wide analyses revealed basal and luminal subtypes of urothelial carcinomas of the bladder. It is unknown if this subtyping can also be applied to upper tract urothelial carcinomas. MATERIALS AND METHODS: Tumor samples from 222 patients with upper tract urothelial carcinomas who were treated with radical nephroureterectomy were analyzed for the expression of seven basal/luminal immunohistochemical markers (CK5, EGFR, CD44, CK20, p63, GATA3, FOXA1)...
2017: PloS One
https://www.readbyqxmd.com/read/28608964/hbx-elevated-msl2-modulates-hbv-cccdna-through-inducing-degradation-of-apobec3b-to-enhance-hepatocarcinogenesis
#7
Yuen Gao, Jinyan Feng, Guang Yang, Shuqin Zhang, Yunxia Liu, Yanan Bu, Mingming Sun, Man Zhao, Fuquan Chen, Weiying Zhang, Lihong Ye, Xiaodong Zhang
Chronic hepatitis B virus (HBV) infection is a leading cause in the occurrence of hepatitis B, liver cirrhosis and liver cancer, in which nuclear HBV covalently closed circular DNA (cccDNA), the genomic form that templates viral transcription and sustains viral persistence, plays crucial roles. In the present study, we explored the hypothesis that HBV X protein (HBx)-elevated male-specific lethal 2 (MSL2) activated HBV replication via modulating cccDNA in hepatoma cells, leading to hepatocarcinogenesis. Immunohistochemical analysis revealed that the expression of MSL2 was positively associated with that of HBV and was increased in the liver tissues of HBV-transgenic mice and clinical HCC patients...
June 13, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28565816/microrna-212-targets-foxa1-and-suppresses-the-proliferation-and-invasion-of-intrahepatic-cholangiocarcinoma-cells
#8
Lei Zhu, Feizhou Huang, Gang Deng, Wanpin Nie, Wei Huang, Hongbo Xu, Shaopeng Zheng, Zhongjie Yi, Tao Wan
[This retracts the article DOI: 10.3892/etm.2016.3824.].
May 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28546130/a-study-of-foxa1-expression-in-thyroid-tumors
#9
Daisuke Nonaka
FoxA1 regulates a variety of tissues during embryogenesis and early life. In thyroid, FoxA1 expression has recently been shown in C cells and medullary thyroid carcinomas but not in follicular cells. FoxA1 has also been proposed as potential oncogene in anaplastic thyroid carcinomas. However, FoxA1 expression has not been extensively investigated in a spectrum of thyroid non-neoplastic lesions and tumors. A variety of thyroid tumors and lesions and their morphologic mimics were stained with monoclonal anti-FoxA1 antibody...
May 22, 2017: Human Pathology
https://www.readbyqxmd.com/read/28534958/mir-204-regulates-the-biological-behavior-of-breast-cancer-mcf-7-cells-by-directly-targeting-foxa1
#10
Si-Qiao Shen, Lan-Shan Huang, Xiao-Ling Xiao, Xiao-Fei Zhu, Dan-Dan Xiong, Xue-Mei Cao, Kang-Lai Wei, Gang Chen, Zhen-Bo Feng
MicroRNAs (miRNAs) are short, non-protein-coding RNAs and transcripts that are 18-24 nt in length. miR-204 was first identified as an anti-oncogene and is reported to be downregulated in non-small cell lung cancer, glioma, gastric and thyroid cancer. Recent studies have proposed that a low level of miR-204 expression is associated with tumor progression and disease outcome in breast cancer. Forkhead box A1 (FOXA1), a transcription factor, plays a crucial role in breast cancer and has been predicted as a target of miR-204...
May 16, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28530243/corrigendum-neuronal-ifn-beta-induced-pi3k-akt-foxa1-signalling-is-essential-for-generation-of-foxa1-treg-cells
#11
Yawei Liu, Andrea Marin, Patrick Ejlerskov, Louise Munk Rasmussen, Marco Prinz, Shohreh Issazadeh-Navikas
This corrects the article DOI: 10.1038/ncomms14709.
May 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28514748/a-transcriptional-complex-composed-of-er-%C3%AE-gata3-foxa1-and-ell3-regulates-il-20-expression-in-breast-cancer-cells
#12
Jae Yong Lee, Young Joon Park, Nuri Oh, Kyu Bum Kwack, Kyung-Soon Park
Interleukin-20 (IL-20) is a member of the IL-10 family. IL-20 expression is regulated by a transcription elongation factor, Ell3, in estrogen receptor-positive (ER(+)) breast cancer cells. In this study, we demonstrated that ER(α), GATA3 and FOXA1 form a transcriptional complex with Ell3 to regulate IL-20 expression in ER(+) breast cancer cells. We also determined that GATA3 and FOXA1 share a binding site with ER(α) in the interleukin-20 promoter. Furthermore, we found that FOXA1 represses IL-20 expression, whereas GATA3 and ER(α) activate it...
June 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28488543/the-transcription-factor-foxa1-induces-epithelial-ovarian-cancer-tumorigenesis-and-progression
#13
Li-Li Wang, Yin-Ling Xiu, Xi Chen, Kai-Xuan Sun, Shuo Chen, Dan-Dan Wu, Bo-Liang Liu, Yang Zhao
FOXA1 (forkhead box A1), a member of the FOXA transcription factor superfamily, plays an important role in tumor occurrence and development. However, the relationship between FOXA1 and ovarian cancer has not been reported. We examined normal ovarian tissue and ovarian cancer tissue and found increased FOXA1 expression in the cancer tissue. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and flow cytometry assays demonstrated that transfection with small interfering RNA to silence FOXA1 (si-FOXA1) in ovarian cancer cell lines decreased cell proliferation and induced apoptosis and S-phase arrest...
May 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28456685/association-of-regulatory-tph2-polymorphisms-with-higher-reduction-in-depressive-symptoms-in-children-and-adolescents-treated-with-fluoxetine
#14
Patricia Gassó, Natalia Rodríguez, Daniel Boloc, Ana Blázquez, Teresa Torres, Ana Gortat, Maria Teresa Plana, Amalia Lafuente, Sergi Mas, Joan Albert Arnaiz, Luisa Lázaro
Genetic variability related to the brain serotonergic system has a significant impact on both the susceptibility to psychiatric disorders, such as major depressive disorder (MDD), and the response to antidepressant drugs, such as fluoxetine. TPH2 is one of the most important serotonergic candidate genes in selective serotonin reuptake inhibitors (SSRIs) pharmacogenetic studies. The aim of the present study was to evaluate the influence of regulatory polymorphisms that are specifically located in human TPH2 transcription factor binding sites (TFBSs), and therefore could be functional by altering gene expression, on clinical improvement in children and adolescents treated with fluoxetine...
April 26, 2017: Progress in Neuro-psychopharmacology & Biological Psychiatry
https://www.readbyqxmd.com/read/28455227/suppression-of-ogt-by-microrna24-reduces-foxa1-stability-and-prevents-breast-cancer-cells-invasion
#15
Yubo Liu, Huang Huang, Yu Cao, Qiong Wu, Wenli Li, Jianing Zhang
O-GlcNAc transferase (OGT) catalyzes the addition of O-GlcNAc to certain serine or threonine residue on a wide variety of cytosolic and nuclear proteins and regulates cellular activities such as signaling and transcription. Although there are emerging evidences that OGT plays important roles in breast cancer metastasis, the underlying mechanism is not fully understood. In this study, we demonstrated that up-regulation of OGT correlates with breast cancer cells invasion. Over-expression of OGT stimulates cells invasion, while OGT silence exhibits the opposite effects...
April 26, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28445112/tracking-the-evolution-of-non-small-cell-lung-cancer
#16
Mariam Jamal-Hanjani, Gareth A Wilson, Nicholas McGranahan, Nicolai J Birkbak, Thomas B K Watkins, Selvaraju Veeriah, Seema Shafi, Diana H Johnson, Richard Mitter, Rachel Rosenthal, Max Salm, Stuart Horswell, Mickael Escudero, Nik Matthews, Andrew Rowan, Tim Chambers, David A Moore, Samra Turajlic, Hang Xu, Siow-Ming Lee, Martin D Forster, Tanya Ahmad, Crispin T Hiley, Christopher Abbosh, Mary Falzon, Elaine Borg, Teresa Marafioti, David Lawrence, Martin Hayward, Shyam Kolvekar, Nikolaos Panagiotopoulos, Sam M Janes, Ricky Thakrar, Asia Ahmed, Fiona Blackhall, Yvonne Summers, Rajesh Shah, Leena Joseph, Anne M Quinn, Phil A Crosbie, Babu Naidu, Gary Middleton, Gerald Langman, Simon Trotter, Marianne Nicolson, Hardy Remmen, Keith Kerr, Mahendran Chetty, Lesley Gomersall, Dean A Fennell, Apostolos Nakas, Sridhar Rathinam, Girija Anand, Sajid Khan, Peter Russell, Veni Ezhil, Babikir Ismail, Melanie Irvin-Sellers, Vineet Prakash, Jason F Lester, Malgorzata Kornaszewska, Richard Attanoos, Haydn Adams, Helen Davies, Stefan Dentro, Philippe Taniere, Brendan O'Sullivan, Helen L Lowe, John A Hartley, Natasha Iles, Harriet Bell, Yenting Ngai, Jacqui A Shaw, Javier Herrero, Zoltan Szallasi, Roland F Schwarz, Aengus Stewart, Sergio A Quezada, John Le Quesne, Peter Van Loo, Caroline Dive, Allan Hackshaw, Charles Swanton
BACKGROUND: Among patients with non-small-cell lung cancer (NSCLC), data on intratumor heterogeneity and cancer genome evolution have been limited to small retrospective cohorts. We wanted to prospectively investigate intratumor heterogeneity in relation to clinical outcome and to determine the clonal nature of driver events and evolutionary processes in early-stage NSCLC. METHODS: In this prospective cohort study, we performed multiregion whole-exome sequencing on 100 early-stage NSCLC tumors that had been resected before systemic therapy...
June 1, 2017: New England Journal of Medicine
https://www.readbyqxmd.com/read/28436428/neuronal-ifn-beta-induced-pi3k-akt-foxa1-signalling-is-essential-for-generation-of-foxa1-treg-cells
#17
Yawei Liu, Andrea Marin, Patrick Ejlerskov, Louise Munk Rasmussen, Marco Prinz, Shohreh Issazadeh-Navikas
Neurons reprogramme encephalitogenic T cells (Tenc) to regulatory T cells (Tregs), either FoxP3(+)Tregs or FoxA1(+)Tregs. We reported previously that neuronal ability to generate FoxA1(+)Tregs was central to preventing neuroinflammation in experimental autoimmune encephalomyelitis (EAE). Mice lacking interferon (IFN)-β were defective in generating FoxA1(+)Tregs in the brain. Here we show that lack of neuronal IFNβ signalling is associated with the absence of programme death ligand-1 (PDL1), which prevents their ability to reprogramme Tenc cells to FoxA1(+)Tregs...
April 24, 2017: Nature Communications
https://www.readbyqxmd.com/read/28429718/a-computational-systems-approach-identifies-synergistic-specification-genes-that-facilitate-lineage-conversion-to-prostate-tissue
#18
Flaminia Talos, Antonina Mitrofanova, Sarah K Bergren, Andrea Califano, Michael M Shen
To date, reprogramming strategies for generating cell types of interest have been facilitated by detailed understanding of relevant developmental regulatory factors. However, identification of such regulatory drivers often represents a major challenge, as specific gene combinations may be required for reprogramming. Here we show that a computational systems approach can identify cell type specification genes (master regulators) that act synergistically, and demonstrate its application for reprogramming of fibroblasts to prostate tissue...
April 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28419831/molecular-phenotyping-of-transient-postnatal-tyrosine-hydroxylase-neurons-in-the-rat-bed-nucleus-of-the-stria-terminalis
#19
David A Carter
The bed nucleus of the stria terminalis (BNST) is a complex integrative centre in the forebrain, composed of multiple sub-nuclei, each with discrete populations of neurons. Progress in understanding BNST function, both in the adult and during postnatal maturation, is dependent upon a more complete characterization of neuronal phenotypes in the BNST. The aim of the current study was to define the molecular phenotype of one postnatal BNST neuronal population, in order to identify molecular factors that may underlie both (protein marker-related) immaturity, and secondly, the transience of this phenotype...
April 15, 2017: Journal of Chemical Neuroanatomy
https://www.readbyqxmd.com/read/28419278/integrative-analysis-identifies-targetable-creb1-foxa1-transcriptional-co-regulation-as-a-predictor-of-prostate-cancer-recurrence
#20
Benjamin Sunkel, Dayong Wu, Zhong Chen, Chiou-Miin Wang, Xiangtao Liu, Zhenqing Ye, Aaron M Horning, Joseph Liu, Devalingam Mahalingam, Horacio Lopez-Nicora, Chun-Lin Lin, Paul J Goodfellow, Steven K Clinton, Victor X Jin, Chun-Liang Chen, Tim H-M Huang, Qianben Wang
No abstract text is available yet for this article.
April 17, 2017: Nucleic Acids Research
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