Canonical WNT Signalling Determines Lineage Specificity in Wilms Tumour
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Mechanism-Anchored Profiling Derived from Epigenetic Networks Predicts Outcome in Acute Lymphoblastic Leukemia Xinan Yang, PhD1, Yong Huang, MD1, James L Chen, MD1, Jianming Xie, MSc2, Xiao Sun, PhD2, Yves A Lussier, MD1,3,4§ 1Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637 USA 2State Key Laboratory of Bioelectronics, Southeast University, 210096 Nanjing, P.R.China 3The University of Chicago Cancer Research Center, and The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637 USA 4The Institute for Genomics and Systems Biology, and the Computational Institute, The University of Chicago, Chicago, IL 60637 USA §Corresponding author Email addresses: XY: [email protected] YH: [email protected] JC: [email protected] JX: [email protected] XS: [email protected] YL: [email protected] - 1 - Abstract Background Current outcome predictors based on “molecular profiling” rely on gene lists selected without consideration for their molecular mechanisms. This study was designed to demonstrate that we could learn about genes related to a specific mechanism and further use this knowledge to predict outcome in patients – a paradigm shift towards accurate “mechanism-anchored profiling”. We propose a novel algorithm, PGnet, which predicts a tripartite mechanism-anchored network associated to epigenetic regulation consisting of phenotypes, genes and mechanisms. Genes termed as GEMs in this network meet all of the following criteria: (i) they are co-expressed with genes known to be involved in the biological mechanism of interest, (ii) they are also differentially expressed between distinct phenotypes relevant to the study, and (iii) as a biomodule, genes correlate with both the mechanism and the phenotype. -
Variations in Microrna-25 Expression Influence the Severity of Diabetic
BASIC RESEARCH www.jasn.org Variations in MicroRNA-25 Expression Influence the Severity of Diabetic Kidney Disease † † † Yunshuang Liu,* Hongzhi Li,* Jieting Liu,* Pengfei Han, Xuefeng Li, He Bai,* Chunlei Zhang,* Xuelian Sun,* Yanjie Teng,* Yufei Zhang,* Xiaohuan Yuan,* Yanhui Chu,* and Binghai Zhao* *Heilongjiang Key Laboratory of Anti-Fibrosis Biotherapy, Medical Research Center, Heilongjiang, People’s Republic of China; and †Clinical Laboratory of Hong Qi Hospital, Mudanjiang Medical University, Heilongjiang, People’s Republic of China ABSTRACT Diabetic nephropathy is characterized by persistent albuminuria, progressive decline in GFR, and second- ary hypertension. MicroRNAs are dysregulated in diabetic nephropathy, but identification of the specific microRNAs involved remains incomplete. Here, we show that the peripheral blood from patients with diabetes and the kidneys of animals with type 1 or 2 diabetes have low levels of microRNA-25 (miR-25) compared with those of their nondiabetic counterparts. Furthermore, treatment with high glucose decreased the expression of miR-25 in cultured kidney cells. In db/db mice, systemic administration of an miR-25 agomir repressed glomerular fibrosis and reduced high BP. Notably, knockdown of miR-25 in normal mice by systemic administration of an miR-25 antagomir resulted in increased proteinuria, extracellular matrix accumulation, podocyte foot process effacement, and hypertension with renin-angiotensin system activation. However, excessive miR-25 did not cause kidney dysfunction in wild-type mice. RNA sequencing showed the alteration of miR-25 target genes in antagomir-treated mice, including the Ras-related gene CDC42. In vitro,cotrans- fection with the miR-25 antagomir repressed luciferase activity from a reporter construct containing the CDC42 39 untranslated region. -
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 -
Association of Gene Ontology Categories with Decay Rate for Hepg2 Experiments These Tables Show Details for All Gene Ontology Categories
Supplementary Table 1: Association of Gene Ontology Categories with Decay Rate for HepG2 Experiments These tables show details for all Gene Ontology categories. Inferences for manual classification scheme shown at the bottom. Those categories used in Figure 1A are highlighted in bold. Standard Deviations are shown in parentheses. P-values less than 1E-20 are indicated with a "0". Rate r (hour^-1) Half-life < 2hr. Decay % GO Number Category Name Probe Sets Group Non-Group Distribution p-value In-Group Non-Group Representation p-value GO:0006350 transcription 1523 0.221 (0.009) 0.127 (0.002) FASTER 0 13.1 (0.4) 4.5 (0.1) OVER 0 GO:0006351 transcription, DNA-dependent 1498 0.220 (0.009) 0.127 (0.002) FASTER 0 13.0 (0.4) 4.5 (0.1) OVER 0 GO:0006355 regulation of transcription, DNA-dependent 1163 0.230 (0.011) 0.128 (0.002) FASTER 5.00E-21 14.2 (0.5) 4.6 (0.1) OVER 0 GO:0006366 transcription from Pol II promoter 845 0.225 (0.012) 0.130 (0.002) FASTER 1.88E-14 13.0 (0.5) 4.8 (0.1) OVER 0 GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism3004 0.173 (0.006) 0.127 (0.002) FASTER 1.28E-12 8.4 (0.2) 4.5 (0.1) OVER 0 GO:0006357 regulation of transcription from Pol II promoter 487 0.231 (0.016) 0.132 (0.002) FASTER 6.05E-10 13.5 (0.6) 4.9 (0.1) OVER 0 GO:0008283 cell proliferation 625 0.189 (0.014) 0.132 (0.002) FASTER 1.95E-05 10.1 (0.6) 5.0 (0.1) OVER 1.50E-20 GO:0006513 monoubiquitination 36 0.305 (0.049) 0.134 (0.002) FASTER 2.69E-04 25.4 (4.4) 5.1 (0.1) OVER 2.04E-06 GO:0007050 cell cycle arrest 57 0.311 (0.054) 0.133 (0.002) -
Alveolar Rhabdomyosarcoma-Associated Proteins PAX3/FOXO1A and PAX7/FOXO1A Suppress the Transcriptional Activity of Myod-Target Genes in Muscle Stem Cells
Oncogene (2013) 32, 651 --662 & 2013 Macmillan Publishers Limited All rights reserved 0950-9232/13 www.nature.com/onc ORIGINAL ARTICLE Alveolar rhabdomyosarcoma-associated proteins PAX3/FOXO1A and PAX7/FOXO1A suppress the transcriptional activity of MyoD-target genes in muscle stem cells F Calhabeu1, S Hayashi2, JE Morgan3, F Relaix2 and PS Zammit1 Rhabdomyosarcoma (RMS) is the commonest soft-tissue sarcoma in childhood and is characterized by expression of myogenic proteins, including the transcription factors MyoD and myogenin. There are two main subgroups, embryonal RMS and alveolar RMS (ARMS). Most ARMS are associated with chromosomal translocations that have breakpoints in introns of either PAX3 or PAX7, and FOXO1A. These translocations create chimeric transcription factors termed PAX3/FOXO1A and PAX7/FOXO1A respectively. Upon ectopic PAX3/FOXO1A expression, together with other genetic manipulation in mice, both differentiating myoblasts and satellite cells (the resident stem cells of postnatal muscle) can give rise to tumours with ARMS characteristics. As PAX3 and PAX7 are part of transcriptional networks that regulate muscle stem cell function in utero and during early postnatal life, PAX3/FOXO1A and PAX7/FOXO1A may subvert normal PAX3 and PAX7 functions. Here we examined how PAX3/FOXO1A and PAX7/FOXO1A affect myogenesis in satellite cells. PAX3/FOXO1A or PAX7/FOXO1A inhibited myogenin expression and prevented terminal differentiation in murine satellite cells: the same effect as dominant-negative (DN) Pax3 or Pax7 constructs. The transcription of MyoD-target genes myogenin and muscle creatine kinase were suppressed by PAX3/FOXO1A or PAX7/ FOXO1A in C2C12 myogenic cells again as seen with Pax3/7DN. PAX3/FOXO1A or PAX7/FOXO1A did not inhibit the transcriptional activity of MyoD by perturbing MyoD expression, localization, phosphorylation or interaction with E-proteins. -
The Oestrogen Receptor Alpha-Regulated Lncrna NEAT1 Is a Critical Modulator of Prostate Cancer
ARTICLE Received 5 Dec 2013 | Accepted 26 Sep 2014 | Published 21 Nov 2014 DOI: 10.1038/ncomms6383 OPEN The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer Dimple Chakravarty1,2, Andrea Sboner1,2,3, Sujit S. Nair4, Eugenia Giannopoulou5,6, Ruohan Li7, Sven Hennig8, Juan Miguel Mosquera1,2, Jonathan Pauwels1, Kyung Park1, Myriam Kossai1,2, Theresa Y. MacDonald1, Jacqueline Fontugne1,2, Nicholas Erho9, Ismael A. Vergara9, Mercedeh Ghadessi9, Elai Davicioni9, Robert B. Jenkins10, Nallasivam Palanisamy11,12, Zhengming Chen13, Shinichi Nakagawa14, Tetsuro Hirose15, Neil H. Bander16, Himisha Beltran1,2, Archa H. Fox7, Olivier Elemento2,3 & Mark A. Rubin1,2 The androgen receptor (AR) plays a central role in establishing an oncogenic cascade that drives prostate cancer progression. Some prostate cancers escape androgen dependence and are often associated with an aggressive phenotype. The oestrogen receptor alpha (ERa)is expressed in prostate cancers, independent of AR status. However, the role of ERa remains elusive. Using a combination of chromatin immunoprecipitation (ChIP) and RNA-sequencing data, we identified an ERa-specific non-coding transcriptome signature. Among putatively ERa-regulated intergenic long non-coding RNAs (lncRNAs), we identified nuclear enriched abundant transcript 1 (NEAT1) as the most significantly overexpressed lncRNA in prostate cancer. Analysis of two large clinical cohorts also revealed that NEAT1 expression is asso- ciated with prostate cancer progression. Prostate cancer cells expressing high levels of NEAT1 were recalcitrant to androgen or AR antagonists. Finally, we provide evidence that NEAT1 drives oncogenic growth by altering the epigenetic landscape of target gene promoters to favour transcription. 1 Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, 413 East 69th Street, Room 1402, New York, New York 10021, USA. -
Inhibition of Single Minded 2 Gene Expression Mediates Tumor-Selective Apoptosis and Differentiation in Human Colon Cancer Cells
Inhibition of Single Minded 2 gene expression mediates tumor-selective apoptosis and differentiation in human colon cancer cells Mireille J. Aleman*†‡§, Maurice Phil DeYoung*†§¶, Matthew Tress*†, Patricia Keating*†, Gary W. Perryʈ, and Ramaswamy Narayanan*†** *Center for Molecular Biology and Biotechnology, Departments of †Biology and ‡Chemistry, and ¶Center for Complex System and Brain Sciences, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431 Communicated by Herbert Weissbach, Florida Atlantic University, Boca Raton, FL, July 21, 2005 (received for review April 4, 2005) A Down’s syndrome associated gene, Single Minded 2 gene short bound AhR͞ARNT complex (12) and hence prevent carcinogen form (SIM2-s), is specifically expressed in colon tumors but not in metabolism, leading to cumulative DNA damage and cancer. the normal colon. Antisense inhibition of SIM2-s in a RKO-derived The growth arrest and DNA damage (GADD) family of genes colon carcinoma cell line causes growth inhibition, apoptosis, and was originally isolated from UV radiation-treated cells and subse- inhibition of tumor growth in a nude mouse tumoriginicity model. quently grouped according to their coordinate regulation by growth The mechanism of cell death in tumor cells is unclear. In the present arrest and DNA damage (13). The GADD family members include study, we investigated the pathways underlying apoptosis. Apo- GADD34,-45␣,-45,-45␥, and -153 (14, 15). These are stress- ptosis was seen in a tumor cell-specific manner in RKO cells but not response genes induced by both genotoxic and nongenotoxic in normal renal epithelial cells, despite inhibition of SIM2-s expres- stresses (16–18). GADD45␣ is the most extensively studied mem- sion in both of these cells by the antisense. -
Microarray-Based Analysis of Genes, Transcription Factors, and Epigenetic Modifications in Lung Cancer Exposed to Nitric Oxide
CANCER GENOMICS & PROTEOMICS 17 : 401-415 (2020) doi:10.21873/cgp.20199 Microarray-based Analysis of Genes, Transcription Factors, and Epigenetic Modifications in Lung Cancer Exposed to Nitric Oxide ARNATCHAI MAIUTHED 1, ORNJIRA PRAKHONGCHEEP 2,3 and PITHI CHANVORACHOTE 2,3 1Department of Pharmacology, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand; 2Cell-based Drug and Health Product Development Research Unit, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand; 3Department of Pharmacology and Physiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand Abstract. Background/Aim: Nitric oxide (NO) is recognized NO exposure of lung cancer cells resulted in a change in as an important biological mediator that exerts several transcription factors (TFs) and epigenetic modifications human physiological functions. As its nature is an aqueous (histone modification and miRNA). Interestingly, NO soluble gas that can diffuse through cells and tissues, NO treatment was shown to potentiate cancer stem cell-related can affect cell signaling, the phenotype of cancer and modify genes and transcription factors Oct4, Klf4, and Myc. surrounding cells. The variety of effects of NO on cancer cell Conclusion: Through this comprehensive approach, the biology has convinced researchers to determine the defined present study illustrated the scheme of how NO affects mechanisms of these effects and how to control this mediator molecular events in lung cancer cells. for a better understanding as well as for therapeutic gain. Materials and Methods: We used bioinformatics and Lung cancer is one of the leading causes of cancer-related pharmacological experiments to elucidate the potential deaths worldwide (1, 2). Since the aggressive phenotypes regulation and underlying mechanisms of NO in non-small and treatment failures have been frequently observed in lung a lung cancer cell model. -
Pig Antibodies
Pig Antibodies gene_name sku Entry_Name Protein_Names Organism Length Identity CDX‐2 ARP31476_P050 D0V4H7_PIG Caudal type homeobox 2 (Fragment) Sus scrofa (Pig) 147 100.00% CDX‐2 ARP31476_P050 A7MAE3_PIG Caudal type homeobox transcription factor 2 (Fragment) Sus scrofa (Pig) 75 100.00% Tnnt3 ARP51286_P050 Q75NH3_PIG Troponin T fast skeletal muscle type Sus scrofa (Pig) 271 85.00% Tnnt3 ARP51286_P050 Q75NH2_PIG Troponin T fast skeletal muscle type Sus scrofa (Pig) 266 85.00% Tnnt3 ARP51286_P050 Q75NH1_PIG Troponin T fast skeletal muscle type Sus scrofa (Pig) 260 85.00% Tnnt3 ARP51286_P050 Q75NH0_PIG Troponin T fast skeletal muscle type Sus scrofa (Pig) 250 85.00% Tnnt3 ARP51286_P050 Q75NG8_PIG Troponin T fast skeletal muscle type Sus scrofa (Pig) 266 85.00% Tnnt3 ARP51286_P050 Q75NG7_PIG Troponin T fast skeletal muscle type Sus scrofa (Pig) 260 85.00% Tnnt3 ARP51286_P050 Q75NG6_PIG Troponin T fast skeletal muscle type Sus scrofa (Pig) 250 85.00% Tnnt3 ARP51286_P050 TNNT3_PIG Troponin T, fast skeletal muscle (TnTf) Sus scrofa (Pig) 271 85.00% ORF Names:PANDA_000462 EMBL EFB13877.1OrganismAiluropod High mobility group protein B2 (High mobility group protein a melanoleuca (Giant panda) ARP31939_P050 HMGB2_PIG 2) (HMG‐2) Sus scrofa (Pig) 210 100.00% Agpat5 ARP47429_P050 B8XTR3_PIG 1‐acylglycerol‐3‐phosphate O‐acyltransferase 5 Sus scrofa (Pig) 365 85.00% irf9 ARP31200_P050 Q29390_PIG Transcriptional regulator ISGF3 gamma subunit (Fragment) Sus scrofa (Pig) 57 100.00% irf9 ARP31200_P050 Q0GFA1_PIG Interferon regulatory factor 9 Sus scrofa (Pig) -
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NEUROSCIENCE RESEARCH NOTES OPEN ACCESS | RESEARCH NOTES ISSN: 2576-828X Transcriptomic profiling of skeletal muscle from the Ts1Cje mouse model of Down syndrome suggests dysregulation of trisomic genes associated with neuromuscular junction signaling, oxidative stress and chronic inflammation Melody Pui Yee Leong 1,2, Usman Bala 2,3, Chai Ling Lim 2,3, Rozita Rosli 1,2, Pike-See Cheah 2,3 and King-Hwa Ling 1,2,* 1 Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. 2 Genetics and Regenerative Medicine Research Centre (GRMRC), Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. 3 Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia. * Correspondence: [email protected]; Tel.: +603-8947 2564 Received: 10 May 2018; Accepted: 21 August 2018; Published: 27 August 2018 Edited by: Azlina Ahmad Annuar (University of Malaya, Malaysia) Reviewed by: Ruth Chia (National Institute on Aging, National Institutes of Health, USA); Shelisa Tey (Institute of Neuropathology, RWTH University Hospital Aachen, Germany) DOI: https://doi.org/10.31117/neuroscirn.v1i1.12 Abstract: Ts1Cje is a mouse model of Down syndrome (DS) with partial triplication of chromosome 16, which encompasses a high number of human chromosome 21 (HSA21) orthologous genes. The mouse model exhibits muscle weakness resembling hypotonia in DS individuals. The effect of extra gene dosages on muscle weakness or hypotonia in Ts1Cje and DS individuals remains unknown. To identify molecular dysregulation of the skeletal muscle, we compared the transcriptomic signatures of soleus and extensor digitorum longus (EDL) muscles between the adult Ts1Cje and disomic littermates. -
The Nuclear Hormone Receptor Coactivator SRC-1 Is a Specific Target of P300 TSO-PANG YAO, GREGORY Ku, NAIDONG ZHOU, RALPH SCULLY, and DAVID M
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 10626-10631, October 1996 Biochemistry The nuclear hormone receptor coactivator SRC-1 is a specific target of p300 TSO-PANG YAO, GREGORY Ku, NAIDONG ZHOU, RALPH SCULLY, AND DAVID M. LIvINGSTON* Dana-Farber Cancer Institute and Harvard Medical School, 44 Binney Street, Boston, MA 02115 Contributed by David M. Livingston, June 17, 1996 ABSTRACT p300 and its family member, CREB-binding derlying ligand activation of nuclear receptor transcription protein (CBP), function as key transcriptional coactivators by activity. virtue of their interaction with the activated forms of certain Specifically, it has been shown that, upon ligand binding, a transcription factors. In a search for additional cellular specific set of proteins are recruited to the hormone bound targets of p300/CBP, a protein-protein cloning strategy, (i.e., activated) receptor (11-13). It was hypothesized that surprisingly identified SRC-1, a coactivator involved in nu- these multiprotein complexes assemble and become transcrip- clear hormone receptor transcriptional activity, as a p300/ tionally active in response to hormone binding. Identifying and CBP interactive protein. p300 and SRC-1 interact, specifically, understanding how individual components of these complexes in vitro and they also form complexes in vivo. Moreover, we function are part of the key to understand how nuclear show that SRC-1 encodes a new member of the basic helix- receptors modulate transcription. Recently, one of the nuclear loop-helix-PAS domain family and that it physically interacts receptor-binding proteins, steroid receptor coactivator-1 with the retinoic acid receptor in response to hormone bind- (SRC-1), was identified and cloned. -
The Role of Npas4 in Neuroprotection and Neurogenesis
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