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Supplementary file 1: Gene expression changes in the white matter of CD47 KO mice This table contains a list of all gene expression changes in the white matter of CD47 KO mice ( > 2-fold: |Log2 ratio| > 1) Expression of total 14,875 genes was detected in both or either of the genotypes. Genes (with different probe set ID#) found in both of the increased and decreased gene groups were excluded from the table. 594 and 548 genes were markedly (> 2-fold) increased and decreased, respectively, in CD47 KO compared with WT mice. column name description probe set ID# Affymetrix probe set ID number for Mouse 430 2.0 Genome Arrays gene gene description symbol gene symbol accession NCBI accession number Log2 ratio Gene expression fold change expressed as Log2 (KO/WT) probe set ID# gene symbol accession Log2 ratio 1449153_at matrix metallopeptidase 12 Mmp12 BC019135 7.2 1419534_at oxidized low density lipoprotein (lectin-like) receptor 1 Olr1 NM_138648 6.2 1444176_at ATPase, H+ transporting, lysosomal V0 subunit D2 Atp6v0d2 AV204216 5.7 1434798_at ATPase, H+ transporting, lysosomal V0 subunit D2 Atp6v0d2 BB769890 2.3 1420504_at solute carrier family 6 (neurotransmitter transporter), member 14 Slc6a14 AF320226 5.5 1459934_at ubiquitin specific peptidase 42 Usp42 AA516835 5.2 1431800_at von Willebrand factor A domain containing 8 Vwa8 AK004956 5.2 1431927_at RIKEN cDNA 5033417F24 gene 5033417F24Rik AK018199 4.9 1419202_at cystatin F (leukocystatin) Cst7 NM_009977 4.9 1439943_at vacuolar protein sorting 54 (yeast) Vps54 BB201271 4.6 1419966_at tubulin, beta 2a, pseudogene 2 Tubb2a-ps2 C79445 4.5 AV320801 /// expressed sequence AV320801 /// predicted gene 15023 /// predicted Gm15023 /// 1449962_at gene 5128 /// predicted gene 7903 /// preferentially expressed antigen in Gm5128 /// NM_031390 4.4 melanoma-like 3 Gm7903 /// Pramel3 1429682_at family with sequence similarity 46, member C Fam46c AK015259 4.4 1448021_at family with sequence similarity 46, member C Fam46c AA266723 1.2 1442367_at ATPase, class VI, type 11C Atp11c BB184010 4.3 cytochrome P450, family 4, subfamily a, polypeptide 10 /// cytochrome Cyp4a10 /// 1424853_s_at BC010747 4.3 P450, family 4, subfamily a, polypeptide 31 Cyp4a31 1423377_at insulin-like growth factor binding protein-like 1 Igfbpl1 BM935068 4.3 1435313_at CD200 receptor 4 Cd200r4 BB770873 4.2 1426286_at nucleolar complex associated 3 homolog (S. cerevisiae) Noc3l AB077991 4.2 1443600_at expressed sequence AA414992 AA414992 AA414992 4.1 1433930_at heparanase Hpse BG094050 3.9 1436262_x_at OTU domain containing 5 Otud5 BB112533 3.9 1427775_at defensin beta 10 Defb10 AJ437645 3.9 1420003_at NOL1/NOP2/Sun domain family, member 5 Nsun5 C80273 3.8 1442802_x_at proline-rich coiled-coil 2A Prrc2a BB409822 3.8 1453947_at kinesin family member 24 Kif24 BB091323 3.8 1425440_x_at solute carrier family 41, member 3 Slc41a3 BC011108 3.7 1453239_a_at ankyrin repeat domain 22 Ankrd22 AK012869 3.7 1440938_at triggering receptor expressed on myeloid cells-like 2 Treml2 BE457612 3.7 1459467_at expressed sequence AA986715 AA986715 BM249399 3.7 1458308_at strawberry notch homolog 2 (Drosophila) Sbno2 BF148215 3.6 1446952_at DNA segment, Chr 11, ERATO Doi 506, expressed D11Ertd506e BG068105 3.6 1416206_at signal-induced proliferation associated gene 1 Sipa1 D11374 3.5 1419561_at chemokine (C-C motif) ligand 3 Ccl3 NM_011337 3.5 1423719_at BPI fold containing family B, member 1 Bpifb1 U46068 3.5 1437831_at zinc finger, CCHC domain containing 4 Zcchc4 BB834670 3.5 1422864_at runt related transcription factor 1 Runx1 NM_009821 3.5 1449591_at caspase 4, apoptosis-related cysteine peptidase Casp4 NM_007609 3.5 1419372_at golgi SNAP receptor complex member 2 Gosr2 NM_019650 3.5 1440693_at palladin, cytoskeletal associated protein Palld BB424787 3.4 1422066_x_at killer cell lectin-like receptor subfamily B member 1B Klrb1b AF342896 3.4 1445399_at killer cell lectin-like receptor subfamily B member 1B Klrb1b AV294178 2.3 1420421_s_at killer cell lectin-like receptor subfamily B member 1B Klrb1b NM_008526 1.2 1456843_at Yamaguchi sarcoma viral (v-yes) oncogene homolog 1 Yes1 AV319407 3.4 1449500_at serine (or cysteine) peptidase inhibitor, clade B, member 7 Serpinb7 NM_027548 3.3 1434911_s_at Rho GTPase activating protein 19 Arhgap19 BG072763 3.3 1459045_at golgi integral membrane protein 4 Golim4 BM942873 3.3 1450104_at a disintegrin and metallopeptidase domain 10 Adam10 BG921598 3.3 1460606_at hydroxysteroid (17-beta) dehydrogenase 13 Hsd17b13 AV050442 3.3 1423813_at kinesin family member 22 Kif22 BC003427 3.3 1425910_at DnaJ (Hsp40) homolog, subfamily C, member 2 Dnajc2 BC004043 3.3 1426155_a_at odd-skipped related 2 Osr2 AY038074 3.2 1434204_x_at serine hydroxymethyltransferase 2 (mitochondrial) Shmt2 AV111300 3.2 1458867_at EGF-like repeats and discoidin I-like domains 3 Edil3 BG071949 3.2 1423190_at cytochrome c oxidase assembly protein 16 Cox16 BF166756 3.2 1427184_at T cell receptor beta, joining region Tcrb-J BF318536 3.2 probe set ID# gene symbol accession Log2 ratio 1453341_a_at transmembrane protein 202 Tmem202 AK008510 3.1 1433845_x_at dual specificity phosphatase 9 Dusp9 AV295798 3.1 1455980_a_at growth arrest-specific 2 like 3 Gas2l3 BB770972 3.1 1437244_at growth arrest-specific 2 like 3 Gas2l3 BB770972 1.7 1453416_at growth arrest-specific 2 like 3 Gas2l3 BE199211 1.3 1445298_at predicted gene 20667 Gm20667 AV323315 3.1 1418069_at apolipoprotein C-II Apoc2 NM_009695 3.1 1453265_at equatorin, sperm acrosome associated Eqtn BG066938 3.0 1458128_at KAT8 regulatory NSL complex subunit 1-like Kansl1l BB363084 3.0 1443584_at KAT8 regulatory NSL complex subunit 1-like Kansl1l AI595843 1.5 1422741_a_at bobby sox homolog (Drosophila) Bbx BF319769 3.0 1421905_at trimethylguanosine synthase homolog (S. cerevisiae) Tgs1 BM233196 3.0 seminal vesicle secretory protein 3A /// seminal vesicle secretory protein 1436782_at Svs3a /// Svs3b BB106990 2.9 3B 1420699_at C-type lectin domain family 7, member a Clec7a NM_020008 2.9 COP9 (constitutive photomorphogenic) homolog, subunit 5 (Arabidopsis 1439243_x_at Cops5 AI662452 2.9 thaliana) 1449911_at lymphocyte-activation gene 3 Lag3 NM_008479 2.9 1439092_at nuclear RNA export factor 1 Nxf1 BM220172 2.9 Gm10334 /// predicted gene 10334 /// predicted gene 5771 /// protease, serine, 1 1422682_s_at Gm5771 /// NM_053243 2.9 (trypsin 1) /// protease, serine, 3 Prss1 /// Prss3 1430173_x_at cytochrome P450, family 4, subfamily f, polypeptide 16 Cyp4f16 AK009445 2.8 1436480_at dipeptidylpeptidase 7 Dpp7 BB746075 2.8 1431427_at RIKEN cDNA 5430427M07 gene 5430427M07Rik AK017349 2.8 1444715_at ArfGAP with SH3 domain, ankyrin repeat and PH domain 3 Asap3 AW539049 2.8 1420243_at zinc finger E-box binding homeobox 1 Zeb1 AV292586 2.7 1441954_s_at H1 histone family, member N, testis-specific H1fnt AV265150 2.7 a disintegrin-like and metallopeptidase (reprolysin type) with 1418270_at Adamts8 NM_013906 2.7 thrombospondin type 1 motif, 8 1416645_a_at alpha fetoprotein Afp NM_007423 2.7 1445724_at IQ motif containing GTPase activating protein 1 Iqgap1 BB153562 2.7 1447160_at non-POU-domain-containing, octamer binding protein Nono BM235749 2.7 1421792_s_at triggering receptor expressed on myeloid cells 2 Trem2 NM_031254 2.7 BMP and activin membrane-bound inhibitor, pseudogene (Xenopus 1456178_at Bambi-ps1 BF730112 2.7 laevis) 1424457_at amyloid beta (A4) precursor protein-binding, family B, member 3 Apbb3 BC024809 2.7 1431783_at RIKEN cDNA 1700010L04 gene 1700010L04Rik AK005840 2.7 1417579_x_at GDP-mannose pyrophosphorylase A Gmppa NM_133708 2.7 TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated 1416450_at Taf8 NM_022015 2.7 factorq 1419128_at integrin alpha X Itgax NM_021334 2.6 1424975_at sialic acid binding Ig-like lectin 5 Siglec5 AF293371 2.6 1424963_at retinitis pigmentosa 1 (human) Rp1 AF155141 2.6 1443840_x_at RIKEN cDNA 1700010H22 gene 1700010H22Rik AV209320 2.6 A730046G19Ri 1457517_at RIKEN cDNA A730046G19 gene BB251424 2.6 k 1446914_at expressed sequence C80425 C80425 C80425 2.6 1429229_s_at centrosomal protein 128 Cep128 BE980134 2.6 1444327_at ubiquitin protein ligase E3 component n-recognin 5 Ubr5 BF224640 2.6 1448303_at glycoprotein (transmembrane) nmb Gpnmb NM_053110 2.6 1433760_a_at rhomboid domain containing 3 Rhbdd3 BG075392 2.5 1448891_at Fc receptor-like S, scavenger receptor Fcrls BC016551 2.5 1460715_x_at transcription factor CP2-like 1 Tfcp2l1 BF303285 2.5 1444699_at SURP and G patch domain containing 1 Sugp1 AW540332 2.5 1415904_at lipoprotein lipase Lpl BC003305 2.5 1431056_a_at lipoprotein lipase Lpl AK017272 2.5 1422148_at matrilin 3 Matn3 NM_010770 2.5 1452014_a_at insulin-like growth factor 1 Igf1 AF440694 2.5 1419519_at insulin-like growth factor 1 Igf1 NM_010512 1.5 1434413_at insulin-like growth factor 1 Igf1 BG092677 1.3 1430963_at glucosaminyl (N-acetyl) transferase 3, mucin type Gcnt3 AK008762 2.5 1453882_at RIKEN cDNA 1700034F02 gene 1700034F02Rik AK006591 2.4 1447250_a_at coiled-coil domain containing 141 Ccdc141 BB830098 2.4 1460125_at coiled-coil domain containing 141 Ccdc141 BB517076 2.2 1439353_x_at transmembrane protein 56 Tmem56 BB768133 2.4 1453732_at mitochondrial calcium uniporter regulator 1 Mcur1 BF533688 2.4 1424729_at adipogenin Adig AY092026 2.4 1422812_at chemokine (C-X-C motif) receptor 6 Cxcr6 NM_030712 2.4 1449164_at CD68 antigen Cd68 BC021637 2.4 1442456_at spermatogenesis associated 5 Spata5 BG066112 2.4 1430376_at leucine rich repeat containing 9 Lrrc9 AK019545 2.3 1458838_at RIKEN cDNA 4732468M13 gene 4732468M13Rik BB005885 2.3 1421578_at
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    Lindenboim et al. Cell Death Discovery (2020) 6:29 https://doi.org/10.1038/s41420-020-0256-5 Cell Death Discovery REVIEW ARTICLE Open Access The nuclear envelope: target and mediator of the apoptotic process Liora Lindenboim1, Hila Zohar1,HowardJ.Worman2 and Reuven Stein1 Abstract Apoptosis is characterized by the destruction of essential cell organelles, including the cell nucleus. The nuclear envelope (NE) separates the nuclear interior from the cytosol. During apoptosis, the apoptotic machinery, in particular caspases, increases NE permeability by cleaving its proteins, such as those of the nuclear pore complex (NPC) and the nuclear lamina. This in turns leads to passive diffusion of cytosolic apoptogenic proteins, such as caspases and nucleases, through NPCs into the nucleus and the subsequent breakdown of the NE and destruction of the nucleus. However, NE leakiness at early stages of the apoptotic process can also occur in a caspase-independent manner, where Bax, by a non-canonical action, promotes transient and repetitive localized generation and subsequent rupture of nuclear protein-filled nuclear bubbles. This NE rupture leads to discharge of apoptogenic nuclear proteins from the nucleus to the cytosol, a process that can contribute to the death process. Therefore, the NE may play a role as mediator of cell death at early stages of apoptosis. The NE can also serve as a platform for assembly of complexes that regulate the death process. Thus, the NE should be viewed as both a mediator of the cell death process and a target. 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Facts redistribution of the nuclear proteins to the cytosol that might subsequently act as amplifiers of the ● The NE is an important target of the apoptotic apoptotic process.
  • 140503 IPF Signatures Supplement Withfigs Thorax

    140503 IPF Signatures Supplement Withfigs Thorax

    Supplementary material for Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis Daryle J. DePianto1*, Sanjay Chandriani1⌘*, Alexander R. Abbas1, Guiquan Jia1, Elsa N. N’Diaye1, Patrick Caplazi1, Steven E. Kauder1, Sabyasachi Biswas1, Satyajit K. Karnik1#, Connie Ha1, Zora Modrusan1, Michael A. Matthay2, Jasleen Kukreja3, Harold R. Collard2, Jackson G. Egen1, Paul J. Wolters2§, and Joseph R. Arron1§ 1Genentech Research and Early Development, South San Francisco, CA 2Department of Medicine, University of California, San Francisco, CA 3Department of Surgery, University of California, San Francisco, CA ⌘Current address: Novartis Institutes for Biomedical Research, Emeryville, CA. #Current address: Gilead Sciences, Foster City, CA. *DJD and SC contributed equally to this manuscript §PJW and JRA co-directed this project Address correspondence to Paul J. Wolters, MD University of California, San Francisco Department of Medicine Box 0111 San Francisco, CA 94143-0111 [email protected] or Joseph R. Arron, MD, PhD Genentech, Inc. MS 231C 1 DNA Way South San Francisco, CA 94080 [email protected] 1 METHODS Human lung tissue samples Tissues were obtained at UCSF from clinical samples from IPF patients at the time of biopsy or lung transplantation. All patients were seen at UCSF and the diagnosis of IPF was established through multidisciplinary review of clinical, radiological, and pathological data according to criteria established by the consensus classification of the American Thoracic Society (ATS) and European Respiratory Society (ERS), Japanese Respiratory Society (JRS), and the Latin American Thoracic Association (ALAT) (ref. 5 in main text). Non-diseased normal lung tissues were procured from lungs not used by the Northern California Transplant Donor Network.
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD

    Supplementary Table S4. FGA Co-Expressed Gene List in LUAD

    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase