DOCSLIB.ORG

Long Noncoding RNA PROX1-AS1 Promoted Ovarian Cancer Cell Proliferation and Metastasis by Suppressing KLF6

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Long Noncoding RNA PROX1-AS1 Promoted Ovarian Cancer Cell Proliferation and Metastasis by Suppressing KLF6 European Review for Medical and Pharmacological Sciences 2020; 24: 6561-6568 Long noncoding RNA PROX1-AS1 promoted ovarian cancer cell proliferation and metastasis by suppressing KLF6 L. ZHAO1, J.-F. LI2, X.-J. TONG3 1Department of Gynecology Center, The First Affiliated Hospital of XinJiang Medical University, Urumqi, China 2Department of Ultrasound, WeiHai Municipal Hospital, WeiHai, China 3Department of Gynecology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China Abstract. – OBJECTIVE: Recently, the role of Introduction long noncoding RNAs (lncRNAs) in tumor pro- gression has attracted much attention world- Ovarian cancer remains one of the most fa- wide. Numerous studies have identified lncRNA tal and common tumors in women globally, PROX1-AS1 as an oncogene in cancers. There- accounting for 5-6% cancer-related deaths1,2. It fore, the aim of this research was to explore the function of PROX1-AS1 in the development of has been reported that 22,500 patients are newly ovarian cancer. diagnosed of ovarian cancer in America in 2017, PATIENTS AND METHODS: PROX1-AS1 ex- with 14,100 deaths3,4. Due to the vagueness pression in both ovarian cancer patients and of symptoms and the lack of early detection normal subjects was detected by quantitative tests, 70-75% of patients have already been in Real Time-Polymerase Chain Reaction (qRT- advanced stages when first diagnosed5. Where- PCR). Subsequently, PROX1-AS1 shRNA was constructed and transfected in vitro. 3-(4,5-di- as, almost 80% of the patients may develop methylthiazol-2-yl)-2,5-diphenyl tetrazolium bro- resistance to chemotherapy or recurrence after 6,7 mide (MTT) assay, colony formation assay, tran- surgery . Therefore, the severe situation un- swell assay, and Matrigel assay were utilized derscores the urgency of early detection and the to detect the function of PROX1-AS1 in ovari- establishment of new therapeutic interventions an cancer. In addition, the potential mechanism for ovarian cancer patients. was explored using qRT-PCR and Western blot Long non-coding RNAs (lncRNAs) are a sub- assay. RESULTS: PROX1-AS1 was highly expressed group of non-coding RNAs that do not encode in ovarian carcinoma samples and cell lines proteins. Currently, lncRNAs have emerged as an (p<0.05). The proliferation, migration, and inva- important role in tumorigenesis. Multiple studies sion of ovarian cells were significantly inhibit- have found that lncRNAs have the potential to ed after PROX1-AS1 was downregulated in vi- regulate gene expression. By regulating vasculo- tro (p<0.05). Besides, the mRNA and protein ex- genic angiogenesis, lncRNA MALAT1 promotes pressions of KLF6 were significantly promot- 8. ed after PROX1-AS1 knockdown in ovarian can- tumorigenicity and metastasis in gastric cancer cer cells (p<0.05). Further functional assays LncRNA AC132217.4 promotes the metastasis of showed that KLF6 expression was negatively oral squamous cell carcinoma by regulating IGF2 correlated with PROX1-AS1 expression in ovari- expression modulated by KLF89. By sponging an cancer samples. miR-124-3p, lncRNA OGFRP1 has been report- CONCLUSIONS: PROX1-AS1 enhances the ed to take part in the proliferation of non-small metastasis and proliferation of ovarian cancer cell lung cancer cells10. Upregulation of lncRNA cells via suppressing KLF6. Our findings sug- gest that PROX1-AS1 may be applied as a novel LINC01510 has been confirmed negatively as- target for therapy of ovarian cancer. sociated with the prognosis of colorectal cancer (CRC) patients. Meanwhile, lncRNA LINC01510 Key Words: may serve as a potential independent prognostic Long noncoding RNAs, PROX1-AS1, Ovarian can- biomarker for CRC11. LncRNA HCCL5 activated cer, KLF6. RETRACTEDby ZEB1 accelerates cell viability, cell migra- Corresponding Author: Xiaojing Tong, MD; e-mail: [email protected] 6561 L. Zhao, J.-F. Li, X.-J. Tong tion, epithelial-mesenchymal transition, and the using quantitative Real Time-Polymerase Chain malignancy of hepatocellular carcinoma12. How- Reaction (RT-qPCR). ever, few studies have uncovered the exact role of PROX1-AS1 in ovarian cancer, as well as the RNA Extraction and RT-qPCR underlying mechanism. Total RNA in tissues and cells was extracted In our study, we found that PROX1-AS1 was by using TRIzol reagent (Invitrogen, Carlsbad, remarkably upregulated in ovarian cancer tis- CA, USA). Subsequently, extracted total RNA sues. PROX1-AS1 enhanced the proliferation and was reverse-transcribed to complementary de- metastasis of ovarian cancer in vitro. Moreover, oxyribose nucleic acids (cDNAs) through Reverse KLF6, a tumor suppressor gene, was associated Transcription Kit (TaKaRa Biotechnology Co., with the function of PROX1-AS1 in ovarian can- Ltd., Dalian, China). Thermo-cycling conditions cer. were as follows: 30s at 95°C, 5s for 40 cycles at 95°C, and 35 s at 60°C. 2-ΔΔCt method was utilized for calculating relative expression of genes. The Patients and Methods primer sequences used in this study were as fol- lows: PROX1-AS1 forward 5′-CTAGTTAGCAG- Tissue Specimens GGGCAGCAC-3′, PROX1-AS1 reverse 5′-AA- Paired ovarian carcinoma tissues and adjacent CAGAGAGGCGTGGAAGAA-3′; β-actin, for- normal tissues were sequentially collected from ward 5′-GATGGAAATCGTCAGAGGCT-3′ and 50 ovarian carcinoma patients undergoing sur- reverse 5′-TGGCACTTAGTTGGAAATGC-3′. gery from December 2017 to December 2019 in The First Affiliated Hospital of XinJiang Med- Western Blot Analysis ical University. The selection of patients was Total proteins were collected from cells via ra- based on the guideline proposed by the Union dioimmunoprecipitation assay (RIPA) buffer and for International Cancer Control (UICC). This quantified by using a protein assay (bicinchoninic study was approved by The Ethics Committee of acid method; Beyotime, Shanghai, China). Tar- The First Affiliated Hospital of XinJiang Med- get proteins were separated by sodium dodecyl ical University. The protocol of the study was sulphate-polyacrylamide gel electrophoresis performed as Declaration of Helsinki Principles (SDS-PAGE) and transferred onto polyvinylidene required. difluoride (PVDF) membranes. Then, the mem- branes were incubated with primary antibodies Cell Culture overnight. On the next day, the membranes were Human ovarian cancer cell lines (A2780, TO- incubated with rabbit anti-β-actin (Cell Signal- V112D, HO-8910, and SKOV3) and normal ovar- ing Technology, Danvers, MA, USA) and rabbit ian cell line (ISOE80) were cultured in Dulbec- anti-KLF6 (Cell Signaling Technology, Danvers, co’s Modified Eagle’s Medium (DMEM; Thermo MA, USA). The Pierce enhanced chemilumines- Fisher Scientific, Inc., Waltham, MA, USA) con- cence (ECL) was utilized for visualizing Western sisting of 10% fetal bovine serum (FBS; Thermo Blotting Substrate Immunoreactive bands (Santa Fisher Scientific, Inc., Waltham, MA, USA) and Cruz Biotechnology, Inc., Santa Cruz, CA, USA). penicillin, and maintained in a humidified atmo- sphere with 5% CO2 at 37°C. MTT (3-(4,5-Dimethylthiazol-2-yl)- 2,5-Diphenyl Tetrazolium Bromide) Assay Lentivirus Expressing Short-Hairpin RNA MTT (Roche, Basel, Switzerland) assay was and Cell Transfection used to detect cell proliferation. 200 μL of trans- Lentivirus expressing short-hairpin RNA fected cells were first seeded into 96-well plates (shRNA) directed against PROX1-AS1 were pro- at a density of 2×103 cells per well. Following the vided by GenePharma (Shanghai, China). The manufacturer’s protocol, cell proliferation was complementary DNA encoding PROX1-AS1 was assessed every 24 h. amplified and inserted into pcDNA3.1 (Gene- Pharma, Shanghai, China). Subsequently, they Colony Formation Assay were transfected into ovarian cancer cells, ac- To detect the long-term effect of PROX1-AS1 cording to the instructions of Lipofectamine 3000 on cell proliferation, colony formation assay was (Invitrogen, Carlsbad, CA, USA). PROX1-AS1 conducted. 5×10 2 cells/well cells were seeded into expression in transfectedRETRACTED cells was conducted 6-well plate, and culture medium was replaced 6562 Role of PROX1-AS1 in ovarian cancer every day. 7 day later, formed colonies were fixed two groups were compared by Student t-test. with 75% ethanol for 30 min and stained with p<0.05 was considered statistically significant. 0.2% crystal violet. Finally, colonies were photo- graphed and counted. Results Wound Healing Assay After transfection, the cells were seeded into PROX1-AS1 Was Highly Expressed in 6-well plates and incubated in DMEM medi- Ovarian Cancer Tissues and Cells um overnight. On the next day, the cells were PROX1-AS1 expression in 50 pairs of ovarian scratched with a plastic tip and cultured in se- cancer tissues and adjacent normal tissues was de- rum-free DMEM. Each assay was repeated in tected via qRT-PCR. PROX1-AS1 was highly ex- triplicate independently. Relate distance was pressed in ovarian cancer tissues when compared viewed under a light microscope (Olympus Corp., with adjacent normal tissues (p<0.05, Figure 1A). Tokyo, Japan) at 48 h. Moreover, PROX1-AS1 level in ovarian cancer cells was significantly higher than that of normal Transwell Assay and Matrigel Assay ovarian cell line ISOE80 (p<0.05, Figure 1B). After transfection, 1 ×105 cells in 200 µL serum-free DMEM were replanted in top cham- Cell Proliferation Was Repressed Via ber (Corning, Inc., Corning, NY, USA) with Silence of PROX1-AS1 in Ovarian Cancer or without 50 µg Matrigel (BD, Bedford, MA, In our study, HO-8910 cells were chosen for USA). Meanwhile, DMEM and FBS were added the knockdown of PROX1-AS1 in vitro. qRT- to the lower chamber. These chambers were then PCR was utilized for detecting PROX1-AS1 ex- cultured overnight in an incubator supplemented pression (Figure 2A). MTT assay indicated that with 5% CO2 at 37°C. The top surface of cham- the growth ability of HO-8910 cells was signifi- bers was fixed with methanol for 30 min after cantly repressed after PROX1-AS1 was knocked wiped by cotton swab, followed by staining with down (p<0.05, Figure 2B). Colony formation crystal violet for 20 min. Five fields were ran- assay demonstrated that the number of colonies domly selected for each sample.
Load more

Recommended publications
  • The Prognostic Utility and Clinical Outcomes of MNX1-AS1 Expression in Cancers: a Systematic Review and Meta-Analysis
    The prognostic utility and clinical outcomes of MNX1-AS1 expression in cancers: a systematic review and meta-analysis Juan Li The rst aliated hospital, college of medicine, zhejiang university https://orcid.org/0000-0002-0121-7098 Wen Jin The rst aliated hospital, college of medicine, zhejiang university Zhengyu Zhang The rst aliated hospital, college of medicine, zhejiang university Jingjing Chu The rst aliated hospital, college of medicine, zhejiang university Hui Yang The rst aliated hospital, college of meicine, zhejiang university Chang Li the rst aliated hospital, college of medicine, zhejiang university Ruiyin Dong The rst aliated hospital, college of medicine, zhejiang university Cailian Zhao ( [email protected] ) https://orcid.org/0000-0001-8337-0610 Primary research Keywords: Long non-coding RNA, MNX1-AS1, Cancer, Prognosis Posted Date: March 25th, 2020 DOI: https://doi.org/10.21203/rs.3.rs-19089/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/9 Abstract Background: Recently, emerging studies have identied that MNX1-AS1 highly expressed among variety of cancers and related with worse prognosis of cancer patients. The purpose of this study was to evaluate the relationship between MNX1-AS1 expression with clinical features and prognosis in different cancers. Methods: In this study, we searched the Web of Science, PubMed, CNKI, and Wanfang databases to nd relevant studies of MNX1-AS1. Pooled hazard ratios (HRs) and odds ratios (ORs) with 95% condence intervals (CIs) were applied to explore the prognostic and clinical signicance of MNX1-AS1. Results: A total of 9 literatures were included in this study, including 882 cancer patients.
    [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]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Spatial and Temporal Specification of Neural Fates by Transcription Factor Codes François Guillemot
    REVIEW 3771 Development 134, 3771-3780 (2007) doi:10.1242/dev.006379 Spatial and temporal specification of neural fates by transcription factor codes François Guillemot The vertebrate central nervous system contains a great diversity Box 1. Neurons and glial cells of neurons and glial cells, which are generated in the embryonic neural tube at specific times and positions. Several classes of transcription factors have been shown to control various steps in the differentiation of progenitor cells in the neural tube and to determine the identity of the cells produced. Recent evidence indicates that combinations of transcription factors of the homeodomain and basic helix-loop-helix families establish molecular codes that determine both where and when the different kinds of neurons and glial cells are generated. Introduction Neuron Oligodendrocyte Astrocyte A multitude of neurons of different types, as well as oligodendrocytes and astrocytes (see Box 1), are generated as the vertebrate central The vertebrate central nervous system comprises three primary cell nervous system develops. These different neural cells are generated types, including neurons and two types of glial cells. Neurons are at defined times and positions by multipotent progenitors located in electrically excitable cells that process and transmit information via the walls of the embryonic neural tube. Progenitors located in the the release of neurotransmitters at synapses. Different subtypes of ventral neural tube at spinal cord level first produce motor neurons, neurons can be distinguished by the morphology of their cell body which innervate skeletal muscles and later produce oligodendrocytes and dendritic tree, the type of cells they connect with via their axon, the type of neurotransmitter used, etc.
    [Show full text]
  • Aberrant Development of Pancreatic Beta Cells Derived from Human Ipscs with FOXA2 Deficiency Ahmed K
    Elsayed et al. Cell Death and Disease (2021) 12:103 https://doi.org/10.1038/s41419-021-03390-8 Cell Death & Disease ARTICLE Open Access Aberrant development of pancreatic beta cells derived from human iPSCs with FOXA2 deficiency Ahmed K. Elsayed1, Ihab Younis2, Gowher Ali1, Khalid Hussain3 and Essam M. Abdelalim 1,4 Abstract FOXA2 has been identified as an essential factor for pancreas development and emerging evidence supports an association between FOXA2 and diabetes. Although the role of FOXA2 during pancreatic development is well-studied in animal models, its role during human islet cell development remains unclear. Here, we generated induced pluripotent stem cells (iPSCs) from a patient with FOXA2 haploinsufficiency (FOXA2+/− iPSCs) followed by beta-cell differentiation to understand the role of FOXA2 during pancreatic beta-cell development. Our results showed that FOXA2 haploinsufficiency resulted in aberrant expression of genes essential for the differentiation and proper functioning of beta cells. At pancreatic progenitor (PP2) and endocrine progenitor (EPs) stages, transcriptome analysis showed downregulation in genes associated with pancreatic development and diabetes and upregulation in genes associated with nervous system development and WNT signaling pathway. Knockout of FOXA2 in control iPSCs (FOXA2−/− iPSCs) led to severe phenotypes in EPs and beta-cell stages. The expression of NGN3 and its downstream targets at EPs as well as INSUILIN and GLUCAGON at the beta-cell stage, were almost absent in the cells derived from FOXA2−/− iPSCs. These findings indicate that FOXA2 is crucial for human pancreatic endocrine development and its defect may lead to diabetes based on FOXA2 dosage. 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Introduction TFs lead to neonatal diabetes, which can be associated During human development, early endodermal tissue with pancreatic hypoplasia/agenesis in some mutations4.
    [Show full text]
  • (HLXB9) in Infant Acute Myeloid Leukemia
    EDITORIALS Novel insights into the role of aberrantly expressed MNX1 (HLXB9) in infant acute myeloid leukemia Juerg Schwaller University Children’s Hospital beider Basel (UKBB), Department of Biomedicine, University of Basel Childhood Leukemia Group ZLF, Switzerland. E-mail: [email protected] doi:10.3324/haematol.2018.205971 lmost two decades ago, the molecular characteriza- TP53 and its target the cyclin-dependent kinase inhibitor 1A tion of a t(7;12)(q36;p13) chromosomal translocation (CDKN1A, aka p21WAF1/CIP1). As oncogene-induced senescence Ain very young children with acute myeloid leukemia is a hallmark of early malignant transformation of solid (AML) and poor outcome identified a fusion mRNA poten- tumors, this finding suggests that MNX1 overexpression may tially encoding for a chimeric protein that contains the point- result in a pre-cancerous state.16 However, one has to keep in ed (PNT) and ETS domains of the ETS variant 6 (ETV6) gene, mind that both of the models used are immortalized solid also known as TEL1 (Translocating E26 transforming-specific cancer cell lines that may carry potent oncogenes such as leukemia 1) on 12p13, joined to the regulatory sequences and mutated NRASQ61K present in HT-1080 (https://portals.broadinsti- first exons of the HLXB9 homeobox gene.1 Previous work tute.org/ccle/page?cell_line= HT1080_SOFT_TISSUE). reported a series of infant AML patients with t(7;12)(q36;p13) Nevertheless, previous work has shown that overexpression with blasts carrying a potential ETV6 translocation (revealed of well-characterized AML-associated fusion oncogenes (e.g. by a split FISH signal).2,3 In fact, the entire HLBX9 gene seems PML-RARA, RUNX1-ETO, CBFB-MYH11) induces DNA to be transferred onto the der(12) without disruption of the damage, and activates a CDKN1A-dependent cell cycle arrest gene itself.
    [Show full text]
  • Figure S1. Basic Information of RNA-Seq Results. (A) Bar Plot of Reads Component for Each Sample
    Figure S1. Basic information of RNA-seq results. (A) Bar plot of reads component for each sample. (B) Dot plot shows the principal component analysis (PCA) of each sample. (C) Venn diagram of DEGs for three time points, the overlap part of the circles represents common differentially expressed genes between combinations. Figure S2. Scatter plot of DEGs for each time point. The X and Y axes represent the logarithmic value of gene expression. Red represents up-regulated DEG, blue represents down-regulated DEG, and gray represents non-DEG. Table S1. Primers used for quantitative real-time PCR analysis of DEGs. Gene Primer Sequence Forward 5’-CTACGAGTGGATGGTCAAGAGC-3’ FOXO1 Reverse 5’-CCAGTTCCTTCATTCTGCACACG-3’ Forward 5’-GACGTCCGGCATCAGAGAAA-3’ IRS2 Reverse 5’-TCCACGGCTAATCGTCACAG-3’ Forward 5’-CACAACCAGGACCTCACACC-3’ IRS1 Reverse 5’-CTTGGCACGATAGAGAGCGT-3’ Forward 5’-AGGATACCACTCCCAACAGACCT-3’ IL6 Reverse 5’-CAAGTGCATCATCGTTGTTCATAC-3’ Forward 5’-TCACGTTGTACGCAGCTACC-3’ CCL5 Reverse 5’-CAGTCCTCTTACAGCCTTTGG-3’ Forward 5’-CTGTGCAGCCGCAGTGCCTACC-3’ BMP7 Reverse 5’-ATCCCTCCCCACCCCACCATCT-3’ Forward 5’-CTCTCCCCCTCGACTTCTGA-3’ BCL2 Reverse 5’-AGTCACGCGGAACACTTGAT-3’ Forward 5’-CTGTCGAACACAGTGGTACCTG-3’ FGF7 Reverse 5’-CCAACTGCCACTGTCCTGATTTC-3’ Forward 5’-GGGAGCCAAAAGGGTCATCA-3’ GAPDH Reverse 5’-CGTGGACTGTGGTCATGAGT-3’ Supplementary material: Differentially expressed genes log2(SADS-CoV_12h/ Qvalue (SADS-CoV _12h/ Gene Symbol Control_12h) Control_12h) PTGER4 -1.03693 6.79E-04 TMEM72 -3.08132 3.66E-04 IFIT2 -1.02918 2.11E-07 FRAT2 -1.09282 4.66E-05
    [Show full text]
  • Transdifferentiation to Pancreatic Progenitors
    UNIVERSITY OF MANCHESTER Transdifferentiation to pancreatic progenitors A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Biology, Medicine and Health 2019 Stephen John Wearne School of Medical Sciences Division of Diabetes Endocrinology and Gastroenterology Contents Contents..................................................................................................................................................................................... 1 List of tables ............................................................................................................................................................................... 3 List of figures.............................................................................................................................................................................. 4 List of abbreviations ................................................................................................................................................................... 5 List of publications ..................................................................................................................................................................... 8 Abstract ...................................................................................................................................................................................... 9 Declaration ..............................................................................................................................................................................
    [Show full text]
  • Related to Figure 1
    Figure S1. Temporal and spatial documentation of Olig2Cre-mediated recombination (related to Figure 1). (A-I) Serial transverse spinal cord sections from E8.5-E9.5 Control (Olig2Cre; R26RGFP) embryos. Tissue was immunostained with Nkx2.2, Olig2, Cre, and GFP antibodies to assess where and when recombination occurred. Scale bars = 50 µm. (J-Q) Analysis of E10.5 Olig2Cre; R26RGFP Control mice shows that Cre recombination takes place in both the pMN (Nkx6.1+/Olig2+) and p3 (Nkx6.1+/Nxk2.2+) domains, but not in the floor plate (FoxA2+ or Shh+). At this time point, Cre recombination had occurred in nearly all MNs (Isl1/2+), including both LMC (FoxP1+) and MMC (Lhx3+) subgroups. Inset in (P) reveals a small population of non-recombined MNs. Note that Lhx3 is also prominently expressed by newborn V2 interneurons that form above the motor columns. (R-W) Notch-Off embryos display an absence of Rbpj protein from pMN, p3 progenitors, and differentiated (Islet+/Hb9+) MNs starting around E9.5. Note that Sox2 is maintained in pMN/p3 cells despite the loss of Rbpj. Scale bars = 50 µm. Figure S2. Notch signaling is activated in Notch-On embryos and reduced in Notch-Off embryos without any major disruptions to the neuroepithelial organization (related to Figures 1 and 2). (A-U) Analysis of Notch signaling activity in Control (A-G), Notch-On (H-N), and Notch-Off (O-U) E11.5 embryos. (A, H, O) Green brackets demarcate the dorsoventral extent of the GFP+ region of recombination and white brackets indicate the thickness of the Sox2+ ventricular zone (VZ) within this same region.
    [Show full text]
  • Xo PANEL DNA GENE LIST
    xO PANEL DNA GENE LIST ~1700 gene comprehensive cancer panel enriched for clinically actionable genes with additional biologically relevant genes (at 400 -500x average coverage on tumor) 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 HOXA11
    [Show full text]
  • BMC Biology Biomed Central
    BMC Biology BioMed Central Research article Open Access Classification and nomenclature of all human homeobox genes PeterWHHolland*†1, H Anne F Booth†1 and Elspeth A Bruford2 Address: 1Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK and 2HUGO Gene Nomenclature Committee, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK Email: Peter WH Holland* - [email protected]; H Anne F Booth - [email protected]; Elspeth A Bruford - [email protected] * Corresponding author †Equal contributors Published: 26 October 2007 Received: 30 March 2007 Accepted: 26 October 2007 BMC Biology 2007, 5:47 doi:10.1186/1741-7007-5-47 This article is available from: http://www.biomedcentral.com/1741-7007/5/47 © 2007 Holland et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The homeobox genes are a large and diverse group of genes, many of which play important roles in the embryonic development of animals. Increasingly, homeobox genes are being compared between genomes in an attempt to understand the evolution of animal development. Despite their importance, the full diversity of human homeobox genes has not previously been described. Results: We have identified all homeobox genes and pseudogenes in the euchromatic regions of the human genome, finding many unannotated, incorrectly annotated, unnamed, misnamed or misclassified genes and pseudogenes.
    [Show full text]
  • Notch Controls Multiple Pancreatic Cell Fate Regulators Through Direct Hes1-Mediated Repression
    bioRxiv preprint doi: https://doi.org/10.1101/336305; this version posted June 1, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Notch Controls Multiple Pancreatic Cell Fate Regulators Through Direct Hes1-mediated Repression by Kristian H. de Lichtenberg1, Philip A. Seymour1, Mette C. Jørgensen1, Yung-Hae Kim1, Anne Grapin-Botton1, Mark A. Magnuson2, Nikolina Nakic3,4, Jorge Ferrer3, Palle Serup1* 1 Novo Nordisk Foundation Center for Stem Cell Biology (Danstem), University of Copenhagen, Denmark. 2 Center for Stem Cell Biology, Vanderbilt University, Tennessee, USA. 3 Section on Epigenetics and Disease, Imperial College London, UK. 4 Current Address: GSK, Stevenage, UK. *Corresponding Author: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/336305; this version posted June 1, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract Notch signaling and its effector Hes1 regulate multiple cell fate choices in the developing pancreas, but few direct target genes are known. Here we use transcriptome analyses combined with chromatin immunoprecipitation with next-generation sequencing (ChIP-seq) to identify direct target genes of Hes1. ChIP-seq analysis of endogenous Hes1 in 266-6 cells, a model of multipotent pancreatic progenitor cells, revealed high-confidence peaks associated with 354 genes. Among these were genes important for tip/trunk segregation such as Ptf1a and Nkx6-1, genes involved in endocrine differentiation such as Insm1 and Dll4, and genes encoding non-pancreatic basic-Helic-Loop-Helix (bHLH) factors such as Neurog2 and Ascl1.
    [Show full text]