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Supplemental Table 1 Genes Up-Regulated (>2.0) in Stat3

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Supplemental Table 1 Genes up-regulated (>2.0) in Stat3∆/∆ compared with Stat3flox/flox Probe ID Gene Symbol Gene Description Entrez gene ID 1460470_at Acoxl acyl-Coenzyme A oxidase-like 74121 1459876_at --- --- --- 1459875_x_at 5730494M16Rik RIKEN cDNA 5730494M16 gene 66648 1459841_x_at Laptm5 lysosomal-associated protein transmembrane 5 16792 1459118_at D230038C21 hypothetical protein D230038C21 328872 1459018_at D10Ertd447e DNA segment, Chr 10, ERATO Doi 447, expressed 52607 1458924_at D430013B06Rik RIKEN cDNA D430013B06 gene 399594 1458729_at --- --- --- 1458712_at --- --- --- 1458274_at Zfp69 zinc finger protein 69 381549 1457966_at --- --- --- 1457851_at --- --- --- 1457743_at --- --- --- 1457633_x_at Cox6a2 cytochrome c oxidase, subunit VI a, polypeptide 2 12862 1457589_at Fat3 FAT tumor suppressor homolog 3 (Drosophila) 270120 1457491_at Plekha1 Pleckstrin homology domain containing, family A (phosphoinositide binding 101476 specific) member 1 1457332_at Prmt3 protein arginine N-methyltransferase 3 71974 1457247_at Lmln leishmanolysin-like (metallopeptidase M8 family) 239833 1457129_at LOC100504796 hypothetical LOC100504796 100504796 1456854_at Neurl1a neuralized homolog 1A (Drosophila) 18011 1456794_at E230016M11Rik RIKEN cDNA E230016M11 gene 320172 1456793_at Cytl1 cytokine-like 1 231162 1456780_at --- --- --- 1456527_at Hecw1 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 94253 1456418_at Kcnj13 potassium inwardly-rectifying channel, subfamily J, member 13 100040591 1456404_at Adamts5 a disintegrin-like and metallopeptidase (reprolysin type) with thrombospondin 23794 type 1 motif, 5 (aggrecanase-2) 1456402_at A330076H08Rik RIKEN cDNA A330076H08 gene 320026 1455999_at Cphx cytoplasmic polyadenylated homeobox 105594 1455784_at Sec1 secretory blood group 1 56546 1455627_at Col8a1 collagen, type VIII, alpha 1 12837 1455521_at Klf12 Kruppel-like factor 12 16597 1455445_at Cbln3 cerebellin 3 precursor protein 56410 1455074_at Efcab1 EF hand calcium binding domain 1 66793 1454871_at Rbm15b RNA binding motif protein 15B 109095 1454303_at Epn2 epsin 2 13855 1454299_at 4833422B07Rik RIKEN cDNA 4833422B07 gene 74587 1454123_at 4933406K04Rik RIKEN cDNA 4933406K04 gene 71033 1453854_at Ptar1 protein prenyltransferase alpha subunit repeat containing 1 72351 1453593_at Vgll3 vestigial like 3 (Drosophila) 73569 1453523_at Krtap17-1 keratin associated protein 17-1 77914 1453487_at Dhdh dihydrodiol dehydrogenase (dimeric) 71755 1453215_at Rnase10 ribonuclease, RNase A family, 10 (non-active) 75019 1453152_at Mamdc2 MAM domain containing 2 71738 1453083_at Vmn2r29 vomeronasal 2, receptor 29 76229 1452968_at Cthrc1 collagen triple helix repeat containing 1 68588 1452855_at Ly6k lymphocyte antigen 6 complex, locus K 76486 1452815_at P2ry10 purinergic receptor P2Y, G-protein coupled 10 78826 1447948_at A430107O13Rik RIKEN cDNA A430107O13 gene 214642 1447891_at --- --- --- 1447708_x_at Pde2a phosphodiesterase 2A, cGMP-stimulated 207728 1447683_x_at Mettl1 methyltransferase like 1 17299 1447643_x_at Snai2 snail homolog 2 (Drosophila) 20583 1447341_at --- --- --- 1447252_s_at Mep1a meprin 1 alpha 17287 1447240_at --- --- --- 1447046_at Ucp2 Uncoupling protein 2 (mitochondrial, proton carrier) 22228 1446968_at Picalm phosphatidylinositol binding clathrin assembly protein 233489 1446846_at --- --- --- 1446331_at Ptgfr prostaglandin F receptor 19220 1446291_at Vipar VPS33B interacting protein, apical-basolateral polarity regulator 104799 1446129_at --- --- --- 1446102_at D9Ertd292e DNA segment, Chr 9, ERATO Doi 292, expressed 52208 1445918_at Tmem2 Transmembrane protein 2 83921 1445562_at --- --- --- 1445531_at Csmd1 CUB and Sushi multiple domains 1 94109 1445421_at --- --- --- 1445097_at --- --- --- 1444644_x_at Tatdn1 TatD DNase domain containing 1 69694 1444518_at Acox1 Acyl-Coenzyme A oxidase 1, palmitoyl 11430 1444465_at Ube4b Ubiquitination factor E4B, UFD2 homolog (S. cerevisiae) 63958 1444288_at Pnpt1 polyribonucleotide nucleotidyltransferase 1 71701 1444256_at Rae1 RAE1 RNA export 1 homolog (S. pombe) 66679 1444152_at Celf2 CUGBP, Elav-like family member 2 14007 1444057_at --- --- --- 1443988_at Rbm39 RNA binding motif protein 39 170791 1443984_at Lin9 lin-9 homolog (C. elegans) 72568 1443931_at Zfp882 zinc finger protein 882 382019 1443832_s_at Sdpr serum deprivation response 20324 1443782_x_at Cyp20a1 cytochrome P450, family 20, subfamily A, polypeptide 1 77951 1443768_at Rhoa Ras homolog gene family, member A 11848 1443657_at Fhdc1 FH2 domain containing 1 229474 1443539_at Arhgef11 Rho guanine nucleotide exchange factor (GEF) 11 213498 1443467_at Dock11 dedicator of cytokinesis 11 75974 1443302_at 6720403M19Rik RIKEN cDNA 6720403M19 gene 320619 1443262_at Mrps14 mitochondrial ribosomal protein S14 64659 1443249_at --- --- --- 1443230_at --- --- --- 1443137_at --- --- --- 1443087_at Cdc23 CDC23 (cell division cycle 23, yeast, homolog) 52563 1443007_at --- --- --- 1442880_at --- --- --- 1442629_at --- --- --- 1442556_at --- --- --- 1442351_a_at BC029214 cDNA sequence BC029214 227622 1442305_at Gtpbp2 GTP binding protein 2 56055 1442292_at Arhgef6 Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 73341 1442175_at C030027H14Rik /// Srgap1 RIKEN cDNA C030027H14 gene /// SLIT-ROBO Rho GTPase activating protein 1 117600 /// 77465 1442115_at Fam38b family with sequence similarity 38, member B 667742 1442041_at LOC552876 hypothetical LOC552876 552876 1441954_s_at H1fnt H1 histone family, member N, testis-specific 70069 1441899_x_at Bcan brevican 12032 1441857_x_at Seh1l SEH1-like (S. cerevisiae 72124 1441799_at 6030422H21Rik RIKEN cDNA 6030422H21 gene 402765 1441416_at Inpp4b inositol polyphosphate-4-phosphatase, type II 234515 1441150_x_at Samsn1 SAM domain, SH3 domain and nuclear localization signals, 1 67742 1441101_at Hecw1 HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 94253 1440919_at Mobkl2c MOB1, Mps One Binder kinase activator-like 2C (yeast) 100465 1440685_at --- --- --- 1440441_at Fbxl7 F-box and leucine-rich repeat protein 7 448987 1440286_at Fbxl16 F-box and leucine-rich repeat protein 16 214931 1440205_at Zmynd19 zinc finger, MYND domain containing 19 67187 1440156_s_at Tox2 TOX high mobility group box family member 2 269389 1440087_at --- --- --- 1439950_at Dync1h1 dynein cytoplasmic 1 heavy chain 1 13424 1439794_at Ntn4 netrin 4 57764 1439768_x_at Sema4f sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic 20355 domain 1439665_at Lpar4 lysophosphatidic acid receptor 4 78134 1439478_at Acot2 acyl-CoA thioesterase 2 171210 1439265_at --- --- --- 1439131_at Txlng taxilin gamma 353170 1439127_at AI314180 expressed sequence AI314180 230249 1439053_at D10Bwg1070e DNA segment, Chr 10, Brigham & Women's Genetics 1070 expressed 52902 1438614_x_at Osbpl9 oxysterol binding protein-like 9 100273 1438576_x_at --- --- --- 1438301_at --- --- --- 1438239_at Mid1 midline 1 17318 1438081_at Mcc mutated in colorectal cancers 328949 1437759_at Pfkp Phosphofructokinase, platelet 56421 1437559_at Rgs7bp regulator of G-protein signalling 7 binding protein 52882 1437482_at Tecrl trans-2,3-enoyl-CoA reductase-like 243078 1437479_x_at Tbx3 T-box 3 21386 1437260_at Mmrn1 multimerin 1 70945 1436830_at Marveld1 MARVEL (membrane-associating) domain containing 1 277010 1436786_at 1110069O07Rik RIKEN cDNA 1110069O07 gene 71798 -> 380683 1436659_at Dclk1 doublecortin-like kinase 1 13175 1436614_at --- --- --- 1436503_at BC048546 cDNA sequence BC048546 232400 1436502_at Mtus1 mitochondrial tumor suppressor 1 102103 1436218_at Lgr6 leucine-rich repeat-containing G protein-coupled receptor 6 329252 1436155_at Nmnat2 nicotinamide nucleotide adenylyltransferase 2 226518 1436044_at Scn7a sodium channel, voltage-gated, type VII, alpha 20272 1436043_at Scn7a sodium channel, voltage-gated, type VII, alpha 20272 1435701_at Cyyr1 cysteine and tyrosine-rich protein 1 224405 1435640_x_at A130040M12Rik RIKEN cDNA A130040M12 gene 319269 1435471_at Zfp708 zinc finger protein 708 432769 1435354_at Kcnj15 potassium inwardly-rectifying channel, subfamily J, member 15 16516 1435351_at Bend5 BEN domain containing 5 67621 1435261_at Tmtc1 transmembrane and tetratricopeptide repeat containing 1 387314 1435204_at Prmt8 protein arginine N-methyltransferase 8 381813 1434639_at Klhl29 kelch-like 29 (Drosophila) 208439 1434458_at Fst follistatin 14313 1434186_at Lpar4 lysophosphatidic acid receptor 4 78134 1434141_at Gucy1a3 guanylate cyclase 1, soluble, alpha 3 60596 1433914_at Lipo1 lipase, member O1 381236 1433716_x_at Gfra2 glial cell line derived neurotrophic factor family receptor alpha 2 14586 1433600_at Adra2a adrenergic receptor, alpha 2a 11551 1432631_at Prrc1 proline-rich coiled-coil 1 73137 1432356_at 1700056N10Rik RIKEN cDNA 1700056N10 gene 73392 1432217_a_at Wdr16 WD repeat domain 16 71860 1431970_at Tm7sf4 transmembrane 7 superfamily member 4 75766 1431788_at Fabp12 fatty acid binding protein 12 75497 1430852_at 1600029I14Rik RIKEN cDNA 1600029I14 gene 69797 1430557_at 4930434J08Rik RIKEN cDNA 4930434J08 gene 73979 1430498_at 9130009I01Rik RIKEN cDNA 9130009I01 gene 71594 1430367_at Stambpl1 STAM binding protein like 1 76630 1430296_at Krtap31-1 keratin associated protein 31-1 70831 1429767_at 2810013P06Rik RIKEN cDNA 2810013P06 gene 67206 1429751_at Zswim2 zinc finger, SWIM domain containing 2 71861 1428909_at A130040M12Rik RIKEN cDNA A130040M12 gene 319269 1420294_at --- --- --- 1420154_at --- --- --- 1460699_at Rps27 ribosomal protein S27 57294 1460407_at Spib Spi-B transcription factor (Spi-1/PU.1 related)
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    molecules Article Proteomic and Bioinformatic Investigation of Altered Pathways in Neuroglobin-Deficient Breast Cancer Cells Michele Costanzo 1,2 , Marco Fiocchetti 3 , Paolo Ascenzi 3, Maria Marino 3 , Marianna Caterino 1,2,* and Margherita Ruoppolo 1,2,* 1 Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, 80131 Naples, Italy; [email protected] 2 CEINGE—Biotecnologie Avanzate S.C.Ar.L., 80145 Naples, Italy 3 Department of Science, University Roma Tre, 00146 Rome, Italy; marco.fi[email protected] (M.F.); [email protected] (P.A.); [email protected] (M.M.) * Correspondence: [email protected] (M.C.); [email protected] (M.R.) Abstract: Neuroglobin (NGB) is a myoglobin-like monomeric globin that is involved in several processes, displaying a pivotal redox-dependent protective role in neuronal and extra-neuronal cells. NGB remarkably exerts its function upon upregulation by NGB inducers, such as 17β-estradiol (E2) and H2O2. However, the molecular bases of NGB’s functions remain undefined, mainly in non- neuronal cancer cells. Human MCF-7 breast cancer cells with a knocked-out (KO) NGB gene obtained using CRISPR/Cas9 technology were analyzed using shotgun label-free quantitative proteomics in comparison with control cells. The differential proteomics experiments were also performed after treatment with E2, H2O2, and E2 + H2O2. All the runs acquired using liquid chromatography–tandem mass spectrometry were elaborated within the same MaxQuant analysis, leading to the quantification Citation: Costanzo, M.; Fiocchetti, of 1872 proteins in the global proteomic dataset. Then, a differentially regulated protein dataset was M.; Ascenzi, P.; Marino, M.; Caterino, M.; Ruoppolo, M.
  • Supplementary Table 1. Pain and PTSS Associated Genes (N = 604

    Supplementary Table 1. Pain and PTSS Associated Genes (N = 604

    Supplementary Table 1. Pain and PTSS associated genes (n = 604) compiled from three established pain gene databases (PainNetworks,[61] Algynomics,[52] and PainGenes[42]) and one PTSS gene database (PTSDgene[88]). These genes were used in in silico analyses aimed at identifying miRNA that are predicted to preferentially target this list genes vs. a random set of genes (of the same length). ABCC4 ACE2 ACHE ACPP ACSL1 ADAM11 ADAMTS5 ADCY5 ADCYAP1 ADCYAP1R1 ADM ADORA2A ADORA2B ADRA1A ADRA1B ADRA1D ADRA2A ADRA2C ADRB1 ADRB2 ADRB3 ADRBK1 ADRBK2 AGTR2 ALOX12 ANO1 ANO3 APOE APP AQP1 AQP4 ARL5B ARRB1 ARRB2 ASIC1 ASIC2 ATF1 ATF3 ATF6B ATP1A1 ATP1B3 ATP2B1 ATP6V1A ATP6V1B2 ATP6V1G2 AVPR1A AVPR2 BACE1 BAMBI BDKRB2 BDNF BHLHE22 BTG2 CA8 CACNA1A CACNA1B CACNA1C CACNA1E CACNA1G CACNA1H CACNA2D1 CACNA2D2 CACNA2D3 CACNB3 CACNG2 CALB1 CALCRL CALM2 CAMK2A CAMK2B CAMK4 CAT CCK CCKAR CCKBR CCL2 CCL3 CCL4 CCR1 CCR7 CD274 CD38 CD4 CD40 CDH11 CDK5 CDK5R1 CDKN1A CHRM1 CHRM2 CHRM3 CHRM5 CHRNA5 CHRNA7 CHRNB2 CHRNB4 CHUK CLCN6 CLOCK CNGA3 CNR1 COL11A2 COL9A1 COMT COQ10A CPN1 CPS1 CREB1 CRH CRHBP CRHR1 CRHR2 CRIP2 CRYAA CSF2 CSF2RB CSK CSMD1 CSNK1A1 CSNK1E CTSB CTSS CX3CL1 CXCL5 CXCR3 CXCR4 CYBB CYP19A1 CYP2D6 CYP3A4 DAB1 DAO DBH DBI DICER1 DISC1 DLG2 DLG4 DPCR1 DPP4 DRD1 DRD2 DRD3 DRD4 DRGX DTNBP1 DUSP6 ECE2 EDN1 EDNRA EDNRB EFNB1 EFNB2 EGF EGFR EGR1 EGR3 ENPP2 EPB41L2 EPHB1 EPHB2 EPHB3 EPHB4 EPHB6 EPHX2 ERBB2 ERBB4 EREG ESR1 ESR2 ETV1 EZR F2R F2RL1 F2RL2 FAAH FAM19A4 FGF2 FKBP5 FLOT1 FMR1 FOS FOSB FOSL2 FOXN1 FRMPD4 FSTL1 FYN GABARAPL1 GABBR1 GABBR2 GABRA2 GABRA4
  • Supplementary Table S1. Correlation Between the Mutant P53-Interacting Partners and PTTG3P, PTTG1 and PTTG2, Based on Data from Starbase V3.0 Database

    Supplementary Table S1. Correlation Between the Mutant P53-Interacting Partners and PTTG3P, PTTG1 and PTTG2, Based on Data from Starbase V3.0 Database

    Supplementary Table S1. Correlation between the mutant p53-interacting partners and PTTG3P, PTTG1 and PTTG2, based on data from StarBase v3.0 database. PTTG3P PTTG1 PTTG2 Gene ID Coefficient-R p-value Coefficient-R p-value Coefficient-R p-value NF-YA ENSG00000001167 −0.077 8.59e-2 −0.210 2.09e-6 −0.122 6.23e-3 NF-YB ENSG00000120837 0.176 7.12e-5 0.227 2.82e-7 0.094 3.59e-2 NF-YC ENSG00000066136 0.124 5.45e-3 0.124 5.40e-3 0.051 2.51e-1 Sp1 ENSG00000185591 −0.014 7.50e-1 −0.201 5.82e-6 −0.072 1.07e-1 Ets-1 ENSG00000134954 −0.096 3.14e-2 −0.257 4.83e-9 0.034 4.46e-1 VDR ENSG00000111424 −0.091 4.10e-2 −0.216 1.03e-6 0.014 7.48e-1 SREBP-2 ENSG00000198911 −0.064 1.53e-1 −0.147 9.27e-4 −0.073 1.01e-1 TopBP1 ENSG00000163781 0.067 1.36e-1 0.051 2.57e-1 −0.020 6.57e-1 Pin1 ENSG00000127445 0.250 1.40e-8 0.571 9.56e-45 0.187 2.52e-5 MRE11 ENSG00000020922 0.063 1.56e-1 −0.007 8.81e-1 −0.024 5.93e-1 PML ENSG00000140464 0.072 1.05e-1 0.217 9.36e-7 0.166 1.85e-4 p63 ENSG00000073282 −0.120 7.04e-3 −0.283 1.08e-10 −0.198 7.71e-6 p73 ENSG00000078900 0.104 2.03e-2 0.258 4.67e-9 0.097 3.02e-2 Supplementary Table S2.