DOCSLIB.ORG

Supplementary Figure 1 1 2 Promoter Analysis for the Putative

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supplementary Figure 1 1 2 Promoter Analysis for the Putative 1 Supplementary Figure 1 2 3 Promoter analysis for the putative BRCA1 target genes. (A) A graph for luciferase reporter assay of 4 the CKS1B and MEIS2 promoter plasmids, in combination with wild type BRCA1 (wtBRCA1) or non- 5 functional mutant (C61G). (B) ChIP results for CKS1B and MEIS2 promoter with two different BRCA1 6 antibodies and HDAC2. IgG and Input was used as a negative or positive control, respectively. 7 8 9 Supplementary Table 1. The BRCA1 ChIP signal from ENCODE database and BRCA1 dependent expression change from two GEO datasets GSE22259 GSE30822 Gene Name ENCODE data (BRCA1 CHIP seq) Expression Expression data data ANPEP unnamed (-79179) #N/A 0.140046483 CENPE unnamed (-76) 0.463340941 0.155474015 ID1 unnamed (-32379), unnamed (+7707) 1.020982905 0.214958903 PNN unnamed (+161) 0.772059373 0.215856379 SUSD2 unnamed (-24295) #N/A 0.230809307 LEMD1 unnamed (-63610) #N/A 0.254516474 DLGAP5 unnamed (-79580) 0.914187251 0.281355563 DARS2 unnamed (-11) 0.9045215 0.289088038 SMC3 unnamed (-361) 1.021103204 0.309860113 TNNI3 unnamed (-3119) #N/A 0.318065991 FUT8 unnamed (+1870) 0.992421144 0.322867733 MOB1B unnamed (-154) #N/A 0.328830217 HMGCS1 unnamed (-283) 1.677479154 0.338263784 CTH unnamed (-163) 1.30602241 0.341207388 SEPT10 unnamed (+15) 1.04077455 0.345515568 SLC45A3 unnamed (-68696), unnamed (+49304) #N/A 0.346195509 TAF1B unnamed (-73) 0.797296768 0.348470135 OXCT1 unnamed (-33516) 0.996978985 0.353844424 KIF15 unnamed (+76) 0.678047851 0.356200772 FBP1 unnamed (-87049) #N/A 0.36391027 C4orf21 unnamed (-234) #N/A 0.367754534 HMGB2 unnamed (-1054) 1.137292779 0.368187682 PTGR2 unnamed (+147) #N/A 0.375853006 IDI1 unnamed (-58) 0.760898277 0.376427911 NSRP1 unnamed (-20) #N/A 0.378117286 FER unnamed (+1060) 0.8294352 0.37987163 KIF18A unnamed (-2078) 0.858023151 0.381624982 PHF3 unnamed (-73235) 0.589242724 0.385235959 CORO6 unnamed (-140127) #N/A 0.394731959 TTC18 unnamed (-3) #N/A 0.397570018 STAG1 unnamed (-149) 0.820095844 0.400692437 CUL4B unnamed (+14495) 0.826892 0.401545178 SFR1 unnamed (+109822) #N/A 0.404459958 CWC27 unnamed (+80) 0.91259454 0.405328964 FYTTD1 unnamed (-8) 0.566419036 0.410533966 FADS1 unnamed (+84) 1.113099392 0.410780339 CELSR3 unnamed (+8998) #N/A 0.413508261 MRPS18B unnamed (-1491) 0.859723503 0.415137504 AHSA2 unnamed (-352) 0.326957844 0.418477842 CREBZF unnamed (-28) 0.793315308 0.421151257 AGBL2 unnamed (-51902) #N/A 0.423998893 PCM1 unnamed (-54) 0.693233394 0.427891438 IER2 unnamed (+4941) 1.32968529 0.429742875 LGALS3 unnamed (-77469) 1.073609087 0.431220222 GJC1 unnamed (+55821) 0.765822073 0.431282472 PJA2 unnamed (+661092) 1.004277127 0.433109387 SMARCAD1 unnamed (+96) 0.830872651 0.433959047 STX16 unnamed (-124) 0.783611628 0.437318659 EIF5B unnamed (-959) 0.546961619 0.44208339 SPOCD1 unnamed (+26565) #N/A 0.44294245 ZBTB25 unnamed (-1052), unnamed (-23) 0.963847438 0.445669273 TMF1 unnamed (+2) 1.403000802 0.449739795 DARS unnamed (-101) 0.996569457 0.451375361 MYSM1 unnamed (+137) 1.338821339 0.455914991 TUBA1B unnamed (+1070) 1.035181245 0.456099714 EFHA1 unnamed (+123) 1.014915078 0.457187082 GNE unnamed (+18507) 1.178785378 0.460751632 MRPS9 unnamed (+295) 0.957214321 0.46081088 YIPF3 unnamed (-39) 0.974015333 0.462831691 CFL2 unnamed (-158742) 1.071882131 0.465198096 TBC1D5 unnamed (-102) 0.63021023 0.465575013 WNT7A unnamed (+229497) #N/A 0.467512187 RANBP2 unnamed (-49), unnamed (+67189) 0.985749145 0.468284624 NEMF unnamed (-10152) #N/A 0.470033855 SMARCAL1 unnamed (-243) 1.258806314 0.470929141 DNTTIP2 unnamed (-30) 0.950002933 0.474349306 RBBP8 unnamed (+62) 1.258783826 0.474576323 TTC32 unnamed (+153) 0.83599461 0.4756728 MTHFD1 unnamed (-108) 0.992885456 0.478477648 DALRD3 unnamed (-3517), unnamed (-2835) 0.780682291 0.479377527 MYL12A unnamed (+96) 0.715193136 0.482497558 DDX27 unnamed (+66) 1.066801662 0.482638644 WRN unnamed (+453) #N/A 0.482865316 FZD2 unnamed (+132439) 1.463979329 0.483434728 PIBF1 unnamed (-206) 0.837491244 0.483440865 MYL12B unnamed (-82) 1.158012413 0.485099694 RPL26 unnamed (+199) 0.942067041 0.488757831 C8orf45 unnamed (+54811) #N/A 0.489973284 ABHD15 unnamed (-1837) 1.35646249 0.490135984 PTCD2 unnamed (-103) 0.784423362 0.491987581 PIK3C2A unnamed (-38084) 0.866073062 0.492322837 IFT74 unnamed (+22) 0.980687007 0.493561426 ZNF33B unnamed (-125) 0.504812323 0.493840564 FKBP3 unnamed (+279) 0.928847661 0.494618435 USO1 unnamed (-431) 1.10033935 0.49992946 SREK1 unnamed (+180) 0.814338842 0.499997287 WDR6 unnamed (+136) 1.030953641 0.50139691 DZIP3 unnamed (+252) #N/A 0.501446168 TRMT61B unnamed (-17) 1.202193217 0.502075521 SIRT1 unnamed (-35136), unnamed (-182) 1.345268044 0.502874307 NCOR2 unnamed (-199732) 1.452910334 0.502914155 DHX29 unnamed (-336) 0.88383919 0.504268385 XPO1 unnamed (-108) 0.876640976 0.504425492 RPS6 unnamed (-13) 0.836769321 0.506523013 FANCM unnamed (-1406) #N/A 0.507235835 SKIV2L2 unnamed (+281) 0.82493928 0.507854399 MATR3 unnamed (-4) 0.648285837 0.50811514 MTIF2 unnamed (+151) 1.088390892 0.508573501 CCP110 unnamed (-1795) #N/A 0.508672443 FAM174B unnamed (-153470) #N/A 0.508703969 FYCO1 unnamed (-89) #N/A 0.508784893 ARL6IP6 unnamed (-370), unnamed (+611) 0.982441245 0.509097408 KIAA0196 unnamed (+10) 0.862717371 0.509895147 TMEM41B unnamed (-137) 1.126248035 0.510039241 CCDC99 unnamed (+231) 1.116666597 0.51345111 METTL4 unnamed (+108) 1.099489708 0.513785132 RPGRIP1L unnamed (-230) 0.829525311 0.516450805 MKRN2 unnamed (-125) 0.800701455 0.516583401 GCC2 unnamed (+17) 1.019550709 0.517152323 RAB42 unnamed (-10554) 1.34291915 0.518066868 CTR9 unnamed (-104) 0.954013154 0.518450282 DDIT4 unnamed (+61) 0.673959548 0.519209825 IPO11 unnamed (-6228) 0.823808048 0.519552137 TLE2 unnamed (-6539) 0.667176356 0.52176234 DBN1 unnamed (+19014) 0.939822984 0.522444304 NUF2 unnamed (-383) 0.772921169 0.523014843 TLCD2 unnamed (-6054) 0.657502608 0.523092656 ZDHHC3 unnamed (-68) 0.809660159 0.523816835 ARHGEF40 unnamed (+22309) #N/A 0.524061266 CALM2 unnamed (-118) 0.992701546 0.524316755 COPS2 unnamed (-105) 0.593330326 0.524386166 SENP7 unnamed (-236) #N/A 0.524436259 EIF1B unnamed (-150) 0.805460345 0.524645688 KNTC1 unnamed (-477) 0.776829935 0.527817073 TAF1D unnamed (+432) 0.897045176 0.528445346 COASY unnamed (-12) 0.865192992 0.529293947 CDNF unnamed (-204) #N/A 0.529850135 ZZZ3 unnamed (-834), unnamed (+85) 0.852681176 0.530594634 CBR4 unnamed (+302) 0.884638731 0.532001901 RAB5A unnamed (-287) 0.98126523 0.533440677 LIG4 unnamed (-2933) 0.997700723 0.533897573 DFNB59 unnamed (+194) #N/A 0.534070662 CETN3 unnamed (+63) 0.977189771 0.534319884 ZBTB11 unnamed (-200) 0.870179964 0.534561207 GIN1 unnamed (+89) 0.711356152 0.534617816 ATG16L2 unnamed (+189) #N/A 0.534757444 TGDS unnamed (+151), unnamed (+46416) 1.225683706 0.534941987 MRPS31 unnamed (-47) 1.083926731 0.535181668 PRPF40A unnamed (-1043), unnamed (-62) 0.957916058 0.537013979 PPIG unnamed (+40) 0.966641871 0.537016537 RBBP7 unnamed (-960) 1.088827692 0.537933296 USP8 unnamed (-31) 0.419457672 0.539868384 DUSP13 unnamed (-2151) #N/A 0.54056628 KIF18B unnamed (-202) 1.259865988 0.541004972 C15orf23 unnamed (+161) 0.777861394 0.542959881 NCAPG unnamed (+1) 0.787987203 0.543743932 PIM1 unnamed (-445) 1.359836913 0.544021585 THAP9 unnamed (+45) 1.535761887 0.545715611 RPL14 unnamed (-4366), unnamed (-57) 0.617296484 0.546698833 THUMPD3 unnamed (+113), unnamed (+33517) 0.976501203 0.546705312 TMEM55A unnamed (-29186) #N/A 0.547022319 SRSF2 unnamed (-145) 0.76059065 0.547461291 EIF3A unnamed (+708) 0.85585189 0.550391746 APPL1 unnamed (-149) 0.727878269 0.550765559 KBTBD6 unnamed (-144) 1.010497121 0.552237117 CCNH unnamed (+295) 0.853542732 0.552630847 NKRF unnamed (-578) 0.861622649 0.552718387 HEXIM1 unnamed (+987) 1.043847281 0.553962082 OXNAD1 unnamed (-218) 1.323607751 0.554477506 ENOPH1 unnamed (-979), unnamed (-97) 0.903774006 0.555059749 HELLS unnamed (-327) 0.572755837 0.556497987 PLCD3 unnamed (-663) #N/A 0.55655551 ZMYM1 unnamed (+75) 0.839394238 0.558220882 DDX5 unnamed (-498) 0.976638597 0.559204873 ZNF518A unnamed (+228) 1.324832806 0.559989713 RRAGA unnamed (-103) 1.094485198 0.560586474 MRPS25 unnamed (-24) 0.634050069 0.561591513 C1D unnamed (-1) 0.792077747 0.561828919 TTC7B unnamed (+57801) #N/A 0.563396662 ZC3H15 unnamed (-216) 1.03897568 0.563441268 GPBP1 unnamed (-39982) 0.738343719 0.56373824 MAK16 unnamed (-21) 0.903259655 0.565240025 C3orf23 unnamed (+137) 0.828773823 0.566276787 MNS1 unnamed (+99762) #N/A 0.566494584 FAM110A unnamed (+61) #N/A 0.570633266 CCNJ unnamed (-13) 1.230814738 0.570978648 CNOT7 unnamed (+1) 0.797735205 0.57499947 OAZ1 unnamed (+4281) 1.29717828 0.575054782 DLG1 unnamed (-211723) 0.670474221 0.575687737 RPL23A unnamed (+124) 0.973659717 0.577102396 NKAP unnamed (+43) 0.526640578 0.577392153 CCDC88A unnamed (-43) 0.433928126 0.57853153 COX15 unnamed (+501) 1.448195544 0.57918922 GTPBP2 unnamed (-604) 1.312319649 0.580047729 RPL36AL unnamed (-95) 0.983460761 0.581601462 DHX36 unnamed (+75) 0.805997171 0.581972825 PNPLA2 unnamed (+783) #N/A 0.582135848 KDM1A unnamed (-124) 0.988486644 0.582883237 H2AFX unnamed (-101) 1.009357569 0.583110866 DNAAF2 unnamed (+789), unnamed (+1617) #N/A 0.583373584 DNAJC28 unnamed (+11275) #N/A 0.586136243 CD2AP unnamed (-56) 0.955885708 0.586969339 NDUFAF3 unnamed (-222), unnamed (+460) 0.582777657 0.587688474 PARP2 unnamed (-34) 0.663952077 0.589039911 FANCD2 unnamed (-24) 0.705909016 0.589303745 SMC1B unnamed (+40) #N/A 0.589367358 CCNE1 unnamed (+33391) 0.829094241 0.590069121 BAZ1A unnamed (+2082) 1.096976654 0.590344082 TSC22D2 unnamed (-909) 0.928908126
Load more

Recommended publications
  • De Novo MEIS2 Mutation Causes Syndromic Developmental Delay with Persistent Gastro-Esophageal Reflux
    Journal of Human Genetics (2016) 61, 835–838 & 2016 The Japan Society of Human Genetics All rights reserved 1434-5161/16 www.nature.com/jhg SHORT COMMUNICATION De novo MEIS2 mutation causes syndromic developmental delay with persistent gastro-esophageal reflux Atsushi Fujita1, Bertrand Isidor2,3, Hugues Piloquet4, Pierre Corre5, Nobuhiko Okamoto6, Mitsuko Nakashima1, Yoshinori Tsurusaki1, Hirotomo Saitsu1, Noriko Miyake1 and Naomichi Matsumoto1 MEIS2 aberrations are considered to be the cause of intellectual disability, cleft palate and cardiac septal defect, as MEIS2 copy number variation is often observed with these phenotypes. To our knowledge, only one nucleotide-level change— specifically, an in-frame MEIS2 deletion—has so far been reported. Here, we report a female patient with a de novo nonsense mutation (c.611C4G, p.Ser204*) in MEIS2. She showed severe intellectual disability, moderate motor/verbal developmental delay, cleft palate, cardiac septal defect, hypermetropia, severe feeding difficulties with gastro-esophageal reflux and constipation. By reviewing this patient and previous patients with MEIS2 point mutations, we found that feeding difficulty with gastro-esophageal reflux appears to be one of the core clinical features of MEIS2 haploinsufficiency, in addition to intellectual disability, cleft palate and cardiac septal defect. Journal of Human Genetics (2016) 61, 835–838; doi:10.1038/jhg.2016.54; published online 26 May 2016 INTRODUCTION at the homeodomain may interfere with DNA binding. Moreover, Meis homeobox 2 (MEIS2;alsoknownasMRG1, NM_170677.4) this female patient also presented with various anomalous features encodes a homeobox (HOX) protein belonging to the three amino and developmental abnormalities. Here, we report on another acid loop extension (TALE) superfamily.
    [Show full text]
  • Genetic Variation Across the Human Olfactory Receptor Repertoire Alters Odor Perception
    bioRxiv preprint doi: https://doi.org/10.1101/212431; this version posted November 1, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Genetic variation across the human olfactory receptor repertoire alters odor perception Casey Trimmer1,*, Andreas Keller2, Nicolle R. Murphy1, Lindsey L. Snyder1, Jason R. Willer3, Maira Nagai4,5, Nicholas Katsanis3, Leslie B. Vosshall2,6,7, Hiroaki Matsunami4,8, and Joel D. Mainland1,9 1Monell Chemical Senses Center, Philadelphia, Pennsylvania, USA 2Laboratory of Neurogenetics and Behavior, The Rockefeller University, New York, New York, USA 3Center for Human Disease Modeling, Duke University Medical Center, Durham, North Carolina, USA 4Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA 5Department of Biochemistry, University of Sao Paulo, Sao Paulo, Brazil 6Howard Hughes Medical Institute, New York, New York, USA 7Kavli Neural Systems Institute, New York, New York, USA 8Department of Neurobiology and Duke Institute for Brain Sciences, Duke University Medical Center, Durham, North Carolina, USA 9Department of Neuroscience, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, USA *[email protected] ABSTRACT The human olfactory receptor repertoire is characterized by an abundance of genetic variation that affects receptor response, but the perceptual effects of this variation are unclear. To address this issue, we sequenced the OR repertoire in 332 individuals and examined the relationship between genetic variation and 276 olfactory phenotypes, including the perceived intensity and pleasantness of 68 odorants at two concentrations, detection thresholds of three odorants, and general olfactory acuity.
    [Show full text]
  • Binnenwerk Cindy Postma.Indd
    CHAPTER 6 Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression Gut 2009, 58: 79-89 Beatriz Carvalho Cindy Postma Sandra Mongera Erik Hopmans Sharon Diskin Mark A. van de Wiel Wim van Criekinge Olivier Thas Anja Matthäi Miguel A. Cuesta Jochim S. Terhaar sive Droste Mike Craanen Evelin Schröck Bauke Ylstra Gerrit A. Meijer 104 | Chapter 6 Abstract Objective: This study aimed to identify the oncogenes at 20q involved in colorectal adenoma to carcinoma progression by measuring the effect of 20q gain on mRNA expression of genes in this amplicon. Methods: Segmentation of DNA copy number changes on 20q was performed by array CGH in 34 non-progressed colorectal adenomas, 41 progressed adenomas (i.e. adenomas that present a focus of cancer) and 33 adenocarcinomas. Moreover, a robust analysis of altered expression of genes in these segments was performed by microarray analysis in 37 adenomas and 31 adenocarcinomas. Protein expression was evaluated by immunohistochemistry on tissue microarrays. Results: The genes C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5, mapping at 20q were signifi cantly overexpressed in carcinomas compared to adenomas as consequence of copy number gain of 20q. Conclusion: This approach revealed C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5 genes to be important in chromosomal instability-related adenoma to carcinoma progression. These genes therefore may serve as highly specifi c biomarkers for colorectal cancer with potential clinical applications. Putative oncogenes at chromosome 20q in colorectal carcinogenesis | 105 Introduction The majority of cancers are epithelial in origin and arise through a stepwise progression from normal cells, through dysplasia, into malignant cells that invade surrounding tissues and have metastatic potential.
    [Show full text]
  • Detailed Review Paper on Retinoid Pathway Signalling
    1 1 Detailed Review Paper on Retinoid Pathway Signalling 2 December 2020 3 2 4 Foreword 5 1. Project 4.97 to develop a Detailed Review Paper (DRP) on the Retinoid System 6 was added to the Test Guidelines Programme work plan in 2015. The project was 7 originally proposed by Sweden and the European Commission later joined the project as 8 a co-lead. In 2019, the OECD Secretariat was added to coordinate input from expert 9 consultants. The initial objectives of the project were to: 10 draft a review of the biology of retinoid signalling pathway, 11 describe retinoid-mediated effects on various organ systems, 12 identify relevant retinoid in vitro and ex vivo assays that measure mechanistic 13 effects of chemicals for development, and 14 Identify in vivo endpoints that could be added to existing test guidelines to 15 identify chemical effects on retinoid pathway signalling. 16 2. This DRP is intended to expand the recommendations for the retinoid pathway 17 included in the OECD Detailed Review Paper on the State of the Science on Novel In 18 vitro and In vivo Screening and Testing Methods and Endpoints for Evaluating 19 Endocrine Disruptors (DRP No 178). The retinoid signalling pathway was one of seven 20 endocrine pathways considered to be susceptible to environmental endocrine disruption 21 and for which relevant endpoints could be measured in new or existing OECD Test 22 Guidelines for evaluating endocrine disruption. Due to the complexity of retinoid 23 signalling across multiple organ systems, this effort was foreseen as a multi-step process.
    [Show full text]
  • Neurons That Regulate Mouse Torpor
    Article Neurons that regulate mouse torpor https://doi.org/10.1038/s41586-020-2387-5 Sinisa Hrvatin1,6 ✉, Senmiao Sun1,2,6, Oren F. Wilcox1, Hanqi Yao1, Aurora J. Lavin-Peter1, Marcelo Cicconet3, Elena G. Assad1, Michaela E. Palmer1, Sage Aronson4, Received: 22 January 2020 Alexander S. Banks5, Eric C. Griffith1 & Michael E. Greenberg1 ✉ Accepted: 7 May 2020 Published online: xx xx xxxx The advent of endothermy, which is achieved through the continuous homeostatic Check for updates regulation of body temperature and metabolism1,2, is a defning feature of mammalian and avian evolution. However, when challenged by food deprivation or harsh environmental conditions, many mammalian species initiate adaptive energy-conserving survival strategies—including torpor and hibernation—during which their body temperature decreases far below its homeostatic set-point3–5. How homeothermic mammals initiate and regulate these hypothermic states remains largely unknown. Here we show that entry into mouse torpor, a fasting-induced state with a greatly decreased metabolic rate and a body temperature as low as 20 °C6, is regulated by neurons in the medial and lateral preoptic area of the hypothalamus. We show that restimulation of neurons that were activated during a previous bout of torpor is sufcient to initiate the key features of torpor, even in mice that are not calorically restricted. Among these neurons we identify a population of glutamatergic Adcyap1-positive cells, the activity of which accurately determines when mice naturally initiate and exit torpor, and the inhibition of which disrupts the natural process of torpor entry, maintenance and arousal. Taken together, our results reveal a specifc neuronal population in the mouse hypothalamus that serves as a core regulator of torpor.
    [Show full text]
  • Tumor Elastography and Its Association with Cell-Free Tumor DNA in the Plasma of Breast Tumor Patients: a Pilot Study
    3534 Original Article Tumor elastography and its association with cell-free tumor DNA in the plasma of breast tumor patients: a pilot study Yi Hao1#, Wei Yang2#, Wenyi Zheng2,3#, Xiaona Chen3,4, Hui Wang1,5, Liang Zhao1,5, Jinfeng Xu6,7, Xia Guo4 1Department of Ultrasound, South China Hospital of Shenzhen University, Shenzhen, China; 2Department of Ultrasound, Shenzhen Hospital, Southern Medical University, Shenzhen, China; 3The Third School of Clinical Medicine, Southern Medical University, Guangzhou, China; 4Shenzhen Key Laboratory of Viral Oncology, Center for Clinical Research and Innovation (CCRI), Shenzhen Hospital, Southern Medical University, Shenzhen, China; 5Department of Ultrasound, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, China; 6Department of Ultrasound, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, Shenzhen, China; 7The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China #These authors contributed equally to this work. Correspondence to: Xia Guo. Shenzhen Key Laboratory of Viral Oncology, Center for Clinical Research and Innovation (CCRI), Shenzhen Hospital, Southern Medical University, Shenzhen 518000, China. Email: [email protected]; Jinfeng Xu. Department of Ultrasound, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, Shenzhen 518020, China; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, China. Email: [email protected]. Background: Breast tumor stiffness, which can be objectively and noninvasively evaluated by ultrasound elastography (UE), has been useful for the differentiation of benign and malignant breast lesions and the prediction of clinical outcomes. Liquid biopsy analyses, including cell-free tumor DNA (ctDNA), exhibit great potential for personalized treatment. This study aimed to investigate the correlations between the UE and ctDNA for early breast cancer diagnosis.
    [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]
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation
    Methods Mice: 4-6 weeks old female C57BL/6 mice obtained from Jackson labs were used for cell isolation. Female Foxp3-IRES-GFP reporter mice (1), backcrossed to B6/C57 background for 10 generations, were used for the isolation of naïve CD4 and naïve CD8 cells for the RNAseq experiments. The mice were housed in pathogen-free animal facility in the La Jolla Institute for Allergy and Immunology and were used according to protocols approved by the Institutional Animal Care and use Committee. Preparation of cells: Subsets of thymocytes were isolated by cell sorting as previously described (2), after cell surface staining using CD4 (GK1.5), CD8 (53-6.7), CD3ε (145- 2C11), CD24 (M1/69) (all from Biolegend). DP cells: CD4+CD8 int/hi; CD4 SP cells: CD4CD3 hi, CD24 int/lo; CD8 SP cells: CD8 int/hi CD4 CD3 hi, CD24 int/lo (Fig S2). Peripheral subsets were isolated after pooling spleen and lymph nodes. T cells were enriched by negative isolation using Dynabeads (Dynabeads untouched mouse T cells, 11413D, Invitrogen). After surface staining for CD4 (GK1.5), CD8 (53-6.7), CD62L (MEL-14), CD25 (PC61) and CD44 (IM7), naïve CD4+CD62L hiCD25-CD44lo and naïve CD8+CD62L hiCD25-CD44lo were obtained by sorting (BD FACS Aria). Additionally, for the RNAseq experiments, CD4 and CD8 naïve cells were isolated by sorting T cells from the Foxp3- IRES-GFP mice: CD4+CD62LhiCD25–CD44lo GFP(FOXP3)– and CD8+CD62LhiCD25– CD44lo GFP(FOXP3)– (antibodies were from Biolegend). In some cases, naïve CD4 cells were cultured in vitro under Th1 or Th2 polarizing conditions (3, 4).
    [Show full text]
  • Copy Number Variation in Fetal Alcohol Spectrum Disorder
    Biochemistry and Cell Biology Copy number variation in fetal alcohol spectrum disorder Journal: Biochemistry and Cell Biology Manuscript ID bcb-2017-0241.R1 Manuscript Type: Article Date Submitted by the Author: 09-Nov-2017 Complete List of Authors: Zarrei, Mehdi; The Centre for Applied Genomics Hicks, Geoffrey G.; University of Manitoba College of Medicine, Regenerative Medicine Reynolds, James N.; Queen's University School of Medicine, Biomedical and Molecular SciencesDraft Thiruvahindrapuram, Bhooma; The Centre for Applied Genomics Engchuan, Worrawat; Hospital for Sick Children SickKids Learning Institute Pind, Molly; University of Manitoba College of Medicine, Regenerative Medicine Lamoureux, Sylvia; The Centre for Applied Genomics Wei, John; The Centre for Applied Genomics Wang, Zhouzhi; The Centre for Applied Genomics Marshall, Christian R.; The Centre for Applied Genomics Wintle, Richard; The Centre for Applied Genomics Chudley, Albert; University of Manitoba Scherer, Stephen W.; The Centre for Applied Genomics Is the invited manuscript for consideration in a Special Fetal Alcohol Spectrum Disorder Issue? : Keyword: Fetal alcohol spectrum disorder, FASD, copy number variations, CNV https://mc06.manuscriptcentral.com/bcb-pubs Page 1 of 354 Biochemistry and Cell Biology 1 Copy number variation in fetal alcohol spectrum disorder 2 Mehdi Zarrei,a Geoffrey G. Hicks,b James N. Reynolds,c,d Bhooma Thiruvahindrapuram,a 3 Worrawat Engchuan,a Molly Pind,b Sylvia Lamoureux,a John Wei,a Zhouzhi Wang,a Christian R. 4 Marshall,a Richard F. Wintle,a Albert E. Chudleye,f and Stephen W. Scherer,a,g 5 aThe Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital 6 for Sick Children, Toronto, Ontario, Canada 7 bRegenerative Medicine Program, University of Manitoba, Winnipeg, Canada 8 cCentre for Neuroscience Studies, Queen's University, Kingston, Ontario, Canada.
    [Show full text]
  • OR4F16 Antibody Cat
    OR4F16 Antibody Cat. No.: 57-758 OR4F16 Antibody Specifications HOST SPECIES: Rabbit SPECIES REACTIVITY: Human This OR4F16 antibody is generated from rabbits immunized with a KLH conjugated IMMUNOGEN: synthetic peptide between 68-96 amino acids from the N-terminal region of human OR4F16. TESTED APPLICATIONS: WB APPLICATIONS: For WB starting dilution is: 1:1000 PREDICTED MOLECULAR 35 kDa WEIGHT: Properties This antibody is purified through a protein A column, followed by peptide affinity PURIFICATION: purification. CLONALITY: Polyclonal ISOTYPE: Rabbit Ig CONJUGATE: Unconjugated September 27, 2021 1 https://www.prosci-inc.com/or4f16-antibody-57-758.html PHYSICAL STATE: Liquid BUFFER: Supplied in PBS with 0.09% (W/V) sodium azide. CONCENTRATION: batch dependent Store at 4˚C for three months and -20˚C, stable for up to one year. As with all antibodies STORAGE CONDITIONS: care should be taken to avoid repeated freeze thaw cycles. Antibodies should not be exposed to prolonged high temperatures. Additional Info OFFICIAL SYMBOL: OR4F3 ALTERNATE NAMES: Olfactory receptor 4F3/4F16/4F29, Olfactory receptor OR1-1, OR4F3 ACCESSION NO.: Q6IEY1 PROTEIN GI NO.: 74762307 GENE ID: 26683, 729759, 81399 USER NOTE: Optimal dilutions for each application to be determined by the researcher. Background and References Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with BACKGROUND: many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals.
    [Show full text]
  • Supplementary Methods
    Heterogeneous Contribution of Microdeletions in the Development of Common Generalized and Focal epilepsies. SUPPLEMENTARY METHODS Epilepsy subtype extended description. Genetic Gereralized Epilepsy (GGE): Features unprovoked tonic and/or clonic seizures, originated inconsistently at some focal point within the brain that rapidly generalizes engaging bilateral distributed spikes and waves discharges on the electroencephalogram. This generalization can include cortical and sub cortical structures but not necessarily the entire cortex[1]. GGE is the most common group of epilepsies accounting for 20% of all cases[2]. It is characterized by an age-related onset and a strong familial aggregation and heritability which allows the assumption of a genetic cause. Although genetic associations have been identified, a broad spectrum of causes is acknowledged and remains largely unsolved [3]. Rolandic Epilepsy (RE): Commonly known also as Benign Epilepsy with Centrotemporal Spikes (BECTS), hallmarks early onset diagnosis (mean onset = 7 years old) with brief, focal hemifacial or oropharyngeal sensorimotor seizures alongside speech arrest and secondarily generalized tonic– clonic seizures, which mainly occur during sleep[4]. Rolandic epilepsy features a broad spectrum of less benign related syndromes called atypical Rolandic epilepsy (ARE), including benign partial epilepsy (ABPE), Landau–Kleffner syndrome(LKS) and epileptic encephalopathy with continuous spike-and-waves during sleep (CSWSS)[5]. Together they are the most common childhood epilepsy with a prevalence of 0.2–0.73/1000 (i.e. _1/2500)[6]. Adult Focal Epilepsy (AFE). Focal epilepsy is characterized by sporadic events of seizures originated within a specific brain region and restricted to one hemisphere. Although they can exhibit more than one network of wave discharges on the electroencephalogram, and different degrees of spreading, they feature a consistent site of origin.
    [Show full text]
  • (12) United States Patent (10) Patent No.: US 8.440,393 B2 Birrer Et Al
    USOO8440393B2 (12) United States Patent (10) Patent No.: US 8.440,393 B2 Birrer et al. (45) Date of Patent: May 14, 2013 (54) PRO-ANGIOGENIC GENES IN OVARIAN OTHER PUBLICATIONS TUMORENDOTHELIAL CELL, SOLATES Boyd (The Basic Science of Oncology, 1992, McGraw-Hill, Inc., p. (75) Inventors: Michael J. Birrer, Mt. Airy, MD (US); 379). Tomas A. Bonome, Washington, DC Tockman et al. (Cancer Res., 1992, 52:2711s-2718s).* (US); Anil Sood, Pearland, TX (US); Pritzker (Clinical Chemistry, 2002, 48: 1147-1150).* Chunhua Lu, Missouri City, TX (US) Benedict et al. (J. Exp. Medicine, 2001, 193(1) 89-99).* Jiang et al. (J. Biol. Chem., 2003, 278(7) 4763-4769).* (73) Assignees: The United States of America as Matsushita et al. (FEBS Letters, 1999, vol. 443, pp. 348-352).* Represented by the Secretary of the Singh et al. (Glycobiology, 2001, vol. 11, pp. 587-592).* Department of Health and Human Abbosh et al. (Cancer Res. Jun. 1, 2006 66:5582-55.91 and Supple Services, Washington, DC (US); The mental Figs. S1-S7).* University of MD Anderson Cancer Zhai et al. (Chinese General Practice Aug. 2008, 11(8A): 1366 Center, Houston, TX (US) 1367).* Lu et al. (Cancer Res. Feb. 15, 2007, 64(4): 1757-1768).* (*) Notice: Subject to any disclaimer, the term of this Bagnato et al., “Activation of Mitogenic Signaling by Endothelin 1 in patent is extended or adjusted under 35 Ovarian Carcinoma Cells', Cancer Research, vol. 57, pp. 1306-1311, U.S.C. 154(b) by 194 days. 1997. Bouras et al., “Stanniocalcin 2 is an Estrogen-responsive Gene (21) Appl.
    [Show full text]