Mouse Insm1 Conditional Knockout Project (CRISPR/Cas9)
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The Function of the Zinc Finger Transcription Factor Insm1 in Neuronal Progenitors Madeleine Julie Larrosa
The function of the zinc finger transcription factor Insm1 in neuronal progenitors Inaugural-Dissertation To obtain the academic degree Doctor rerum naturalium (Dr. rer. nat.) Submitted to the Department of Biology, Chemistry and Pharmacy of Freie Universität Berlin By Madeleine Julie Larrosa From Paris 2019 This work was carried out at the Max Delbrück Centrum for Molecular Medicine in Berlin from November 2015 to October 2019 under the supervision of Prof. Dr. Carmen Birchmeier and Prof. Dr. Holger Gerhardt. 1st Reviewer: Prof. Dr. Holger Gerhardt 2nd Reviewer: Prof. Dr. Stephan Sigrist Date of PhD Defense: This doctoral thesis is dedicated to my mother Juliette Ban, who offered unconditional love and endless devotion, and taught me to work hard for the things I aspire to achieve. I also dedicate this work to Mohammed Marine, who has been a constant source of support and encouragement, and without whom I would not have completed this doctoral thesis. In loving memory of my friend Lorelei Arbeille, who taught me to never give up through her incredible strength and perseverance. Statement of contribution I confirm that the work presented in this doctoral thesis is my own and that all information derived from other sources is indicated. Madlen Sohn, technician in the group of Prof. Dr. Wei Chen at the MDC, performed the sequencing of the immunoprecipitated chromatin and the transcriptome for the ChIP-seq and RNA-seq experiments, respectively. Dr. Mahmoud Ibrahim and Dr. Scott Lacadie, bioinformaticians in the group of Prof. Dr. Uwe Ohler at the MDC, analyzed the ChIP-seq data and Dr. -
Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights Into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle
animals Article Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle Masoumeh Naserkheil 1 , Abolfazl Bahrami 1 , Deukhwan Lee 2,* and Hossein Mehrban 3 1 Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; [email protected] (M.N.); [email protected] (A.B.) 2 Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si, Gyeonggi-do 17579, Korea 3 Department of Animal Science, Shahrekord University, Shahrekord 88186-34141, Iran; [email protected] * Correspondence: [email protected]; Tel.: +82-31-670-5091 Received: 25 August 2020; Accepted: 6 October 2020; Published: 9 October 2020 Simple Summary: Hanwoo is an indigenous cattle breed in Korea and popular for meat production owing to its rapid growth and high-quality meat. Its yearling weight and carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score) are economically important for the selection of young and proven bulls. In recent decades, the advent of high throughput genotyping technologies has made it possible to perform genome-wide association studies (GWAS) for the detection of genomic regions associated with traits of economic interest in different species. In this study, we conducted a weighted single-step genome-wide association study which combines all genotypes, phenotypes and pedigree data in one step (ssGBLUP). It allows for the use of all SNPs simultaneously along with all phenotypes from genotyped and ungenotyped animals. Our results revealed 33 relevant genomic regions related to the traits of interest. -
Integrative Epigenomic and Genomic Analysis of Malignant Pheochromocytoma
EXPERIMENTAL and MOLECULAR MEDICINE, Vol. 42, No. 7, 484-502, July 2010 Integrative epigenomic and genomic analysis of malignant pheochromocytoma Johanna Sandgren1,2* Robin Andersson3*, pression examination in a malignant pheochromocy- Alvaro Rada-Iglesias3, Stefan Enroth3, toma sample. The integrated analysis of the tumor ex- Goran̈ Akerstro̊ m̈ 1, Jan P. Dumanski2, pression levels, in relation to normal adrenal medulla, Jan Komorowski3,4, Gunnar Westin1 and indicated that either histone modifications or chromo- somal alterations, or both, have great impact on the ex- Claes Wadelius2,5 pression of a substantial fraction of the genes in the in- vestigated sample. Candidate tumor suppressor 1Department of Surgical Sciences genes identified with decreased expression, a Uppsala University, Uppsala University Hospital H3K27me3 mark and/or in regions of deletion were for SE-75185 Uppsala, Sweden 2 instance TGIF1, DSC3, TNFRSF10B, RASSF2, HOXA9, Department of Genetics and Pathology Rudbeck Laboratory, Uppsala University PTPRE and CDH11. More genes were found with in- SE-75185 Uppsala, Sweden creased expression, a H3K4me3 mark, and/or in re- 3The Linnaeus Centre for Bioinformatics gions of gain. Potential oncogenes detected among Uppsala University those were GNAS, INSM1, DOK5, ETV1, RET, NTRK1, SE-751 24 Uppsala, Sweden IGF2, and the H3K27 trimethylase gene EZH2. Our ap- 4Interdisciplinary Centre for Mathematical and proach to associate histone methylations and DNA Computational Modelling copy number changes to gene expression revealed ap- Warsaw University parent impact on global gene transcription, and en- PL-02-106 Warszawa, Poland abled the identification of candidate tumor genes for 5Corresponding author: Tel, 46-18-471-40-76; further exploration. -
Comparative Transcriptomics Reveals Similarities and Differences
Seifert et al. BMC Cancer (2015) 15:952 DOI 10.1186/s12885-015-1939-9 RESEARCH ARTICLE Open Access Comparative transcriptomics reveals similarities and differences between astrocytoma grades Michael Seifert1,2,5*, Martin Garbe1, Betty Friedrich1,3, Michel Mittelbronn4 and Barbara Klink5,6,7 Abstract Background: Astrocytomas are the most common primary brain tumors distinguished into four histological grades. Molecular analyses of individual astrocytoma grades have revealed detailed insights into genetic, transcriptomic and epigenetic alterations. This provides an excellent basis to identify similarities and differences between astrocytoma grades. Methods: We utilized public omics data of all four astrocytoma grades focusing on pilocytic astrocytomas (PA I), diffuse astrocytomas (AS II), anaplastic astrocytomas (AS III) and glioblastomas (GBM IV) to identify similarities and differences using well-established bioinformatics and systems biology approaches. We further validated the expression and localization of Ang2 involved in angiogenesis using immunohistochemistry. Results: Our analyses show similarities and differences between astrocytoma grades at the level of individual genes, signaling pathways and regulatory networks. We identified many differentially expressed genes that were either exclusively observed in a specific astrocytoma grade or commonly affected in specific subsets of astrocytoma grades in comparison to normal brain. Further, the number of differentially expressed genes generally increased with the astrocytoma grade with one major exception. The cytokine receptor pathway showed nearly the same number of differentially expressed genes in PA I and GBM IV and was further characterized by a significant overlap of commonly altered genes and an exclusive enrichment of overexpressed cancer genes in GBM IV. Additional analyses revealed a strong exclusive overexpression of CX3CL1 (fractalkine) and its receptor CX3CR1 in PA I possibly contributing to the absence of invasive growth. -
(INSM1) Is a Sensitive and Highly Specific Marker Of
Modern Pathology (2019) 32:100–109 https://doi.org/10.1038/s41379-018-0122-7 ARTICLE Insulinoma-associated protein 1 (INSM1) is a sensitive and highly specific marker of neuroendocrine differentiation in primary lung neoplasms: an immunohistochemical study of 345 cases, including 292 whole-tissue sections 1 1 1 1 Sanjay Mukhopadhyay ● Josephine K. Dermawan ● Christopher P. Lanigan ● Carol F. Farver Received: 20 May 2018 / Revised: 24 July 2018 / Accepted: 28 July 2018 / Published online: 28 August 2018 © United States & Canadian Academy of Pathology 2018 Abstract Recent evidence suggests a role for the nuclear marker INSM1 in the diagnosis of neuroendocrine lung neoplasms. The aim of this study was to determine the utility of INSM1 as a marker of neuroendocrine differentiation using a large series of whole-tissue sections of primary lung neoplasms. We stained 345 primary lung neoplasms with INSM1, including 292 whole-tissue sections. Most cases were also stained with synaptophysin, chromogranin, and CD56. The tumors included 64 small cell lung carcinomas, 24 large cell neuroendocrine carcinomas, 64 carcinoid tumors (48 typical, 16 atypical), 130 1234567890();,: 1234567890();,: adenocarcinomas, and 33 squamous cell carcinomas. For small cell lung carcinoma, the sensitivity of INSM1 (98%) was similar to synaptophysin (100%) and CD56 (95%) but considerably higher than chromogranin (83%). For large cell neuroendocrine carcinoma, CD56 (92%) and synaptophysin (88%) were more sensitive than INSM1 (75%), while chromogranin was less sensitive (46%). All markers stained 100% of carcinoid tumors, except one atypical carcinoid tumor, which was negative for INSM1. The sensitivity of INSM1 for neuroendocrine lung neoplasms as a group (95%) was similar to synaptophysin (98%) and CD56 (97%), but higher than chromogranin (84%). -
393LN V 393P 344SQ V 393P Probe Set Entrez Gene
393LN v 393P 344SQ v 393P Entrez fold fold probe set Gene Gene Symbol Gene cluster Gene Title p-value change p-value change chemokine (C-C motif) ligand 21b /// chemokine (C-C motif) ligand 21a /// chemokine (C-C motif) ligand 21c 1419426_s_at 18829 /// Ccl21b /// Ccl2 1 - up 393 LN only (leucine) 0.0047 9.199837 0.45212 6.847887 nuclear factor of activated T-cells, cytoplasmic, calcineurin- 1447085_s_at 18018 Nfatc1 1 - up 393 LN only dependent 1 0.009048 12.065 0.13718 4.81 RIKEN cDNA 1453647_at 78668 9530059J11Rik1 - up 393 LN only 9530059J11 gene 0.002208 5.482897 0.27642 3.45171 transient receptor potential cation channel, subfamily 1457164_at 277328 Trpa1 1 - up 393 LN only A, member 1 0.000111 9.180344 0.01771 3.048114 regulating synaptic membrane 1422809_at 116838 Rims2 1 - up 393 LN only exocytosis 2 0.001891 8.560424 0.13159 2.980501 glial cell line derived neurotrophic factor family receptor alpha 1433716_x_at 14586 Gfra2 1 - up 393 LN only 2 0.006868 30.88736 0.01066 2.811211 1446936_at --- --- 1 - up 393 LN only --- 0.007695 6.373955 0.11733 2.480287 zinc finger protein 1438742_at 320683 Zfp629 1 - up 393 LN only 629 0.002644 5.231855 0.38124 2.377016 phospholipase A2, 1426019_at 18786 Plaa 1 - up 393 LN only activating protein 0.008657 6.2364 0.12336 2.262117 1445314_at 14009 Etv1 1 - up 393 LN only ets variant gene 1 0.007224 3.643646 0.36434 2.01989 ciliary rootlet coiled- 1427338_at 230872 Crocc 1 - up 393 LN only coil, rootletin 0.002482 7.783242 0.49977 1.794171 expressed sequence 1436585_at 99463 BB182297 1 - up 393 -
Insulinoma-Associated Protein 1 (INSM1) Is a Sensitive and Highly
Modern Pathology https://doi.org/10.1038/s41379-018-0122-7 ARTICLE Insulinoma-associated protein 1 (INSM1) is a sensitive and highly specific marker of neuroendocrine differentiation in primary lung neoplasms: an immunohistochemical study of 345 cases, including 292 whole-tissue sections 1 1 1 1 Sanjay Mukhopadhyay ● Josephine K. Dermawan ● Christopher P. Lanigan ● Carol F. Farver Received: 20 May 2018 / Revised: 24 July 2018 / Accepted: 28 July 2018 © United States & Canadian Academy of Pathology 2018 Abstract Recent evidence suggests a role for the nuclear marker INSM1 in the diagnosis of neuroendocrine lung neoplasms. The aim of this study was to determine the utility of INSM1 as a marker of neuroendocrine differentiation using a large series of whole-tissue sections of primary lung neoplasms. We stained 345 primary lung neoplasms with INSM1, including 292 whole-tissue sections. Most cases were also stained with synaptophysin, chromogranin, and CD56. The tumors included 64 small cell lung carcinomas, 24 large cell neuroendocrine carcinomas, 64 carcinoid tumors (48 typical, 16 atypical), 130 1234567890();,: 1234567890();,: adenocarcinomas, and 33 squamous cell carcinomas. For small cell lung carcinoma, the sensitivity of INSM1 (98%) was similar to synaptophysin (100%) and CD56 (95%) but considerably higher than chromogranin (83%). For large cell neuroendocrine carcinoma, CD56 (92%) and synaptophysin (88%) were more sensitive than INSM1 (75%), while chromogranin was less sensitive (46%). All markers stained 100% of carcinoid tumors, except one atypical carcinoid tumor, which was negative for INSM1. The sensitivity of INSM1 for neuroendocrine lung neoplasms as a group (95%) was similar to synaptophysin (98%) and CD56 (97%), but higher than chromogranin (84%). -
Dual Functions for Insulinoma-Associated 1 in Retinal Development
University of Kentucky UKnowledge Theses and Dissertations--Biology Biology 2015 DUAL FUNCTIONS FOR INSULINOMA-ASSOCIATED 1 IN RETINAL DEVELOPMENT Marie A. Forbes-Osborne University of Kentucky, [email protected] Right click to open a feedback form in a new tab to let us know how this document benefits ou.y Recommended Citation Forbes-Osborne, Marie A., "DUAL FUNCTIONS FOR INSULINOMA-ASSOCIATED 1 IN RETINAL DEVELOPMENT" (2015). Theses and Dissertations--Biology. 31. https://uknowledge.uky.edu/biology_etds/31 This Doctoral Dissertation is brought to you for free and open access by the Biology at UKnowledge. It has been accepted for inclusion in Theses and Dissertations--Biology by an authorized administrator of UKnowledge. For more information, please contact [email protected]. STUDENT AGREEMENT: I represent that my thesis or dissertation and abstract are my original work. Proper attribution has been given to all outside sources. I understand that I am solely responsible for obtaining any needed copyright permissions. I have obtained needed written permission statement(s) from the owner(s) of each third-party copyrighted matter to be included in my work, allowing electronic distribution (if such use is not permitted by the fair use doctrine) which will be submitted to UKnowledge as Additional File. I hereby grant to The University of Kentucky and its agents the irrevocable, non-exclusive, and royalty-free license to archive and make accessible my work in whole or in part in all forms of media, now or hereafter known. I agree that the document mentioned above may be made available immediately for worldwide access unless an embargo applies. -
Sheet1 Page 1 Gene Symbol Gene Description Entrez Gene ID
Sheet1 RefSeq ID ProbeSets Gene Symbol Gene Description Entrez Gene ID Sequence annotation Seed matches location(s) Ago-2 binding specific enrichment (replicate 1) Ago-2 binding specific enrichment (replicate 2) OE lysate log2 fold change (replicate 1) OE lysate log2 fold change (replicate 2) Probability Pulled down in Karginov? NM_005646 202813_at TARBP1 Homo sapiens TAR (HIV-1) RNA binding protein 1 (TARBP1), mRNA. 6894 TR(1..5130)CDS(1..4866) 4868..4874,5006..5013 3.73 2.53 -1.54 -0.44 1 Yes NM_001665 203175_at RHOG Homo sapiens ras homolog gene family, member G (rho G) (RHOG), mRNA. 391 TR(1..1332)CDS(159..734) 810..817,782..788,790..796,873..879 3.56 2.78 -1.62 -1 1 Yes NM_002742 205880_at PRKD1 Homo sapiens protein kinase D1 (PRKD1), mRNA. 5587 TR(1..3679)CDS(182..2920) 3538..3544,3202..3208 4.15 1.83 -2.55 -0.42 1 Yes NM_003068 213139_at SNAI2 Homo sapiens snail homolog 2 (Drosophila) (SNAI2), mRNA. 6591 TR(1..2101)CDS(165..971) 1410..1417,1814..1820,1610..1616 3.5 2.79 -1.38 -0.31 1 Yes NM_006270 212647_at RRAS Homo sapiens related RAS viral (r-ras) oncogene homolog (RRAS), mRNA. 6237 TR(1..1013)CDS(46..702) 871..877 3.82 2.27 -1.54 -0.55 1 Yes NM_025188 219923_at,242056_at TRIM45 Homo sapiens tripartite motif-containing 45 (TRIM45), mRNA. 80263 TR(1..3584)CDS(589..2331) 3408..3414,2437..2444,3425..3431,2781..2787 3.87 1.89 -0.62 -0.09 1 Yes NM_024684 221600_s_at,221599_at C11orf67 Homo sapiens chromosome 11 open reading frame 67 (C11orf67), mRNA. -
An Integrated Approach Identifies Nhlh1 and Insm1 As Sonic
Volume 10 Number 1 January 2008 pp. 89–98 89 www.neoplasia.com\ RESEARCH ARTICLE An Integrated Approach Identifies Enrico De Smaele*, Caterina Fragomeli*,3, Elisabetta Ferretti*,3, Marianna Pelloni*,3, Nhlh1 and Insm1 as Sonic Agnese Po*, Gianluca Canettieri*, Sonia Coni*, Lucia Di Marcotullio*, Azzura Greco*, – † Hedgehog regulated Genes Marta Moretti*, Concezio Di Rocco , ‡ in Developing Cerebellum Simona Pazzaglia , Marella Maroder*, 1,2 Isabella Screpanti*, Giuseppe Giannini* and Medulloblastoma and Alberto Gulino*,§ *Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy; †Neurosurgery Institute, Catholic University, Rome, Italy; ‡Biotechnology Unit, Ente Per Le Nuove Technologie, l'Energia e l'Ambiente (ENEA), Centro Ricerche Casaccia, Casaccia, Rome, Italy; §Neuromed Institute, Pozzilli (Isernia), Italy Abstract Medulloblastoma (MB) is the most common malignant brain tumor of childhood arising from deregulated cerebel- lar development. Sonic Hedgehog (Shh) pathway plays a critical role in cerebellar development and its aberrant expression has been identified in MB. Gene expression profiling of cerebella from 1- to 14-day-old mice unveiled a cluster of genes whose expression correlates with the levels of Hedgehog (HH) activity. From this cluster, we identified Insm1 and Nhlh1/NSCL1 as novel HH targets induced by Shh treatment in cultured cerebellar granule cell progenitors. Nhlh1 promoter was found to be bound and activated by Gli1 transcription factor. Remarkably, the expression of these genes is also upregulated in mouse and human HH–dependent MBs, suggesting that they may be either a part of the HH-induced tumorigenic process or a specific trait of HH-dependent tumor cells. Neoplasia (2008) 10, 89–98 Introduction A major regulator of this process is the Hedgehog (HH) pathway Medulloblastoma (MB) is the most common malignant pediatric brain [7]. -
Identifying Mechanisms of Initiation and Maintenance of Neuroendocrine Prostate Cancer Alexandra N. Corella a Dissertation Subm
Identifying mechanisms of initiation and maintenance of neuroendocrine prostate cancer Alexandra N. Corella A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2020 Reading Committee: Peter S. Nelson, Chair Colm Morrissey David MacPherson Program Authorized to Offer Degree: Molecular and Cellular Biology © Copyright 2020 Alexandra N. Corella University of Washington Abstract Identifying mechanisms of initiation and maintenance of neuroendocrine prostate cancer Alexandra N. Corella Chair of the Supervisory Committee: Peter S. Nelson Professor, Department of Medicine, University of Washington Small cell or neuroendocrine prostate cancer (SCNPC) is a rare but aggressive subtype of prostate cancer with no FDA-approved targeted therapies. SCNPC is an androgen-receptor independent subtype that often emerges as foci within conventional androgen-receptor dependent prostate cancers (ARPCs) that have undergone androgen-deprivation therapy (ADT). SCNPC and ARPC have highly similar mutational landscapes (including fusions in AR-regulated genes) but display distinct transcriptional programs. Investigations into the molecular mechanisms that are responsible for the development and maintenance of the neuroendocrine phenotype in prostate cancer have been hindered due to the scarcity of tumors and a lack of model systems with which to study the subtype. Small cell or neuroendocrine tumors (SCNTs) arise in many organ sites throughout the body and have similar expression patterns of marker genes used to identify and diagnose this class of tumors, including chromogranins and synaptophysins. In the following thesis, I conducted a transcriptome-wide comparison of SCNTs from different organ sites in order to identify related features. I found similar expression in thousands of genes among SCNTs, including transcription factors that may orchestrate the development of neuroendocrine gene expression programs and their downstream effectors, some of which may present as attractive therapeutic targets. -
SARS-Cov-2 Exploits Sexually Dimorphic and Adaptive IFN and Tnfa
bioRxiv preprint doi: https://doi.org/10.1101/2021.07.23.453505; this version posted July 23, 2021. 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. 1 2 3 SARS-CoV-2 Exploits Sexually Dimorphic and Adaptive IFN and TNFa 4 Signaling to Gain Entry into Alveolar Epithelium 5 6 7 Authors: Yan Wang1†, Sreeharsha Gurrapu1†, Hong Chen1†, Sara Laudato1†, Emily 8 Caggiano1,2, Yan Jiang1, Hsiang-Hsi Ling1,2, and Filippo G. Giancotti1,3* 9 Affiliations: 10 1 Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Unit 11 1906, PO Box 301429, Houston, TX 77054/77030-1429, USA. 12 2 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical 13 Sciences, Houston, TX 77030, USA. 14 3 Department of Genitournary Oncology, The University of Texas MD Anderson Cancer Center, 15 Houston, TX 77054, USA. 16 † These authors contributed equally to this work. 17 * Corresponding author. Email: [email protected] 18 19 20 21 22 23 24 25 26 27 28 29 30 1 bioRxiv preprint doi: https://doi.org/10.1101/2021.07.23.453505; this version posted July 23, 2021. 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.