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SOMATIC MUTATIONS Transcript Amino Acid Mutation Sample ID Gene Symbol Gene Description Nucleotide (genomic) Consequence Mut % Accession (protein) Type Nonsynonymous PGDX11T ACSBG2 acyl-CoA synthetase bubblegum family member 2 CCDS12159.1 chr19_6141628_6141628_C_A 654A>D Substitution 46% coding Nonsynonymous PGDX11T ATR ataxia telangiectasia and Rad3 related CCDS3124.1 chr3_143721232_143721232_G_A 1451R>W Substitution 32% coding Nonsynonymous PGDX11T C1orf183 chromosome 1 open reading frame 183 CCDS841.1 chr1_112071336_112071336_C_T 224R>Q Substitution 22% coding PGDX11T CMYA5 cardiomyopathy associated 5 NM_153610 chr5_79063455_79063455_C_A 1037C>X Substitution Nonsense 34% Nonsynonymous PGDX11T CNR1 cannabinoid receptor 1 (brain) CCDS5015.1 chr6_88911646_88911646_C_T 23V>M Substitution 35% coding Nonsynonymous PGDX11T COL4A4 collagen; type IV; alpha 4 CCDS42828.1 chr2_227681807_227681807_G_A 227R>C Substitution 20% coding Nonsynonymous PGDX11T CYBASC3 cytochrome b; ascorbate dependent 3 CCDS8004.1 chr11_60877136_60877136_G_A 149R>C Substitution 34% coding Nonsynonymous PGDX11T DYRK3 dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 3 CCDS30999.1 chr1_204888091_204888091_G_A 309V>I Substitution 44% coding Nonsynonymous PGDX11T ELMO1 engulfment and cell motility 1 CCDS5449.1 chr7_37239295_37239295_G_A 160T>M Substitution 24% coding Nonsynonymous PGDX11T FAM83H family with sequence similarity 83; member H CCDS6410.2 chr8_144884473_144884473_C_A 90G>C Substitution 53% coding Nonsynonymous PGDX11T KPTN kaptin (actin binding protein) CCDS42583.1 chr19_52675861_52675861_G_C 189N>K Substitution 28% coding Nonsynonymous PGDX11T KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog CCDS8703.1 chr12_25289551_25289551_C_A 12G>V Substitution 50% coding leucine rich transmembrane and O-methyltransferase domain Nonsynonymous PGDX11T LRTOMT NM_001145309 chr11_71496787_71496787_C_T 177R>C Substitution 30% containing coding Nonsynonymous PGDX11T NBEAL1 neurobeachin-like 1 NM_001114132 chr2_203699652_203699652_T_A 1009I>N Substitution 38% coding Nonsynonymous PGDX11T NCOA1 nuclear receptor coactivator 1 CCDS1712.1 chr2_24783137_24783137_A_T 432S>C Substitution 37% coding PGDX11T NDST4 N-deacetylase/N-sulfotransferase 4 CCDS3706.1 chr4_115993333_115993333__T NA Insertion Frameshift 27% Nonsynonymous PGDX11T OR5A1 olfactory receptor; family 5; subfamily A; member 1 CCDS31561.1 chr11_58967734_58967734_G_A 173G>R Substitution 29% coding Nonsynonymous PGDX11T OR5D13 olfactory receptor; family 5; subfamily D; member 13 CCDS31507.1 chr11_55298018_55298018_A_T 177N>Y Substitution 14% coding Nonsynonymous PGDX11T PCDHGA9 protocadherin gamma superfamily A, 9 NM_018921 chr5_140764301_140764301_C_T 533T>M Substitution 36% coding Nonsynonymous PGDX11T PIWIL3 piwi-like 3 CCDS33623.1 chr22_23454146_23454146_C_T 644D>N Substitution 46% coding Nonsynonymous PGDX11T PPP1R9B protein phosphatase 1; regulatory subunit 9B ENST00000316878 chr17_45577567_45577567_C_T 469E>K Substitution 18% coding Nonsynonymous PGDX11T PTCHD3 patched domain containing 3 NM_001034842 chr10_27742956_27742956_C_T 77R>Q Substitution 32% coding Nonsynonymous PGDX11T ROBO2 roundabout; axon guidance receptor; homolog 2 CCDS43109.1 chr3_77749499_77749499_C_A 1147Q>K Substitution 44% coding PGDX11T SLC15A2 solute carrier family 15; member 2 CCDS3007.1 chr3_123133274_123133274_T_G NA Substitution Splice site 29% Nonsynonymous PGDX11T SLC17A2 solute carrier family 17; member 2 CCDS4567.1 chr6_26029409_26029409_G_A 151R>W Substitution 52% coding Nonsynonymous PGDX11T SLC22A17 solute carrier family 22; member 17 CCDS9593.1 chr14_22888387_22888387_C_T 154V>I Substitution 45% coding solute carrier family 3 (activators of dibasic and neutral amino Nonsynonymous PGDX11T SLC3A2 CCDS31587.1 chr11_62405382_62405382_T_C 236V>A Substitution 89% acid transport); member 2 coding PGDX11T SMAD4 SMAD family member 4 CCDS11950.1 chr18_46857146_46857146_T_G NA Substitution Splice site 71% PGDX11T SNURF SNRPN upstream reading frame CCDS10016.1 chr15_22751286_22751286_G_A NA Substitution UTR 29% TAF2 RNA polymerase II; TATA box binding protein (TBP)- Nonsynonymous PGDX11T TAF2 CCDS34937.1 chr8_120913139_120913139_C_T 33V>I Substitution 50% associated factor coding Nonsynonymous PGDX11T TOMM70A translocase of outer mitochondrial membrane 70 homolog A CCDS33807.1 chr3_101602176_101602176_C_A 103G>V Substitution 28% coding Nonsynonymous PGDX11T TP53 tumor protein p53 CCDS11118.1 chr17_7519182_7519182_C_A 158R>L Substitution 42% coding Nonsynonymous PGDX11T TSR1 TSR1; 20S rRNA accumulation; homolog CCDS32525.1 chr17_2174753_2174753_C_T 714R>H Substitution 61% coding Nonsynonymous PGDX11T UBA1 ubiquitin-like modifier activating enzyme 1 CCDS14275.1 chrX_46957165_46957165_C_T 869R>W Substitution 12% coding Nonsynonymous PGDX11T UMPS uridine monophosphate synthetase CCDS3029.1 chr3_125941683_125941683_G_A 369A>T Substitution 35% coding Nonsynonymous PGDX11T XPNPEP2 X-prolyl aminopeptidase (aminopeptidase P) 2; membrane-bound CCDS14613.1 chrX_128718172_128718172_T_C 443S>P Substitution 60% coding Nonsynonymous PGDX11T ZCCHC16 zinc finger; CCHC domain containing 16 CCDS35369.1 chrX_111585520_111585520_C_T 303T>M Substitution 39% coding Nonsynonymous PGDX11T ZNF684 zinc finger protein 684 CCDS454.1 chr1_40785045_40785045_G_T 155V>L Substitution 21% coding Nonsynonymous PGDX135T ABCC1 ATP-binding cassette; sub-family C (CFTR/MRP); member 1 CCDS42122.1 chr16_16047253_16047253_C_G 367T>S Substitution 50% coding Nonsynonymous PGDX135T AK1 adenylate kinase 1 CCDS6881.1 chr9_129670554_129670554_C_T 128R>Q Substitution 25% coding Nonsynonymous PGDX135T AKD1 adenylate kinase domain containing 1 CCDS5077.1 chr6_110102099_110102099_A_G 59V>A Substitution 23% coding Nonsynonymous PGDX135T APITD1 apoptosis-inducing; TAF9-like domain 1 CCDS114.1 chr1_10416570_10416570_A_G 46T>A Substitution 28% coding Nonsynonymous PGDX135T BAI3 brain-specific angiogenesis inhibitor 3 CCDS4968.1 chr6_70155472_70155472_G_A 1513V>M Substitution 27% coding Nonsynonymous PGDX135T CHRNB3 cholinergic receptor; nicotinic; beta 3 CCDS6134.1 chr8_42706289_42706289_G_A 228V>I Substitution 22% coding Nonsynonymous PGDX135T COG7 component of oligomeric golgi complex 7 CCDS10610.1 chr16_23316930_23316930_C_G 609G>R Substitution 30% coding Nonsynonymous PGDX135T DNAH5 dynein; axonemal; heavy chain 5 CCDS3882.1 chr5_13815932_13815932_C_T 3394E>K Substitution 25% coding Nonsynonymous PGDX135T EFR3A EFR3 homolog A (S. cerevisiae) NM_015137 chr8_133027986_133027986_T_C 97V>A Substitution 22% coding Nonsynonymous PGDX135T FBN1 fibrillin 1 CCDS32232.1 chr15_46593070_46593070_T_A 519Y>F Substitution 45% coding Nonsynonymous PGDX135T HK3 hexokinase 3 (white cell) CCDS4407.1 chr5_176250507_176250507_A_C 152D>E Substitution 26% coding Nonsynonymous PGDX135T LMTK2 lemur tyrosine kinase 2 CCDS5654.1 chr7_97638916_97638916_T_G 262L>R Substitution 44% coding PGDX135T MDN1 MDN1; midasin homolog (yeast) CCDS5024.1 chr6_90524772_90524772__AGG NA Insertion In-frame insertion 24% Nonsynonymous PGDX135T MUC16 mucin 16, cell surface associated NM_024690 chr19_8921495_8921495_G_A 8984P>L Substitution 31% coding Nonsynonymous PGDX135T MYO16 myosin XVI CCDS32008.1 chr13_108575470_108575470_G_A 1160G>E Substitution 23% coding Nonsynonymous PGDX135T MYOM1 myomesin 1 NM_003803 chr18_3092484_3092484_C_T 1188S>N Substitution 26% coding Nonsynonymous PGDX135T NADSYN1 NAD synthetase 1 CCDS8201.1 chr11_70852154_70852154_A_T 98N>Y Substitution 21% coding Nonsynonymous PGDX135T NRAS neuroblastoma RAS viral (v-ras) oncogene homolog CCDS877.1 chr1_115060268_115060268_C_G 13G>R Substitution 38% coding Nonsynonymous PGDX135T OTOF otoferlin CCDS1725.1 chr2_26551024_26551024_C_T 1050R>Q Substitution 26% coding Nonsynonymous PGDX135T RHAG Rh-associated glycoprotein CCDS4927.1 chr6_49688148_49688148_A_G 289M>T Substitution 44% coding Nonsynonymous PGDX135T SLC43A3 solute carrier family 43; member 3 CCDS7956.1 chr11_56945049_56945049_G_A 168S>F Substitution 19% coding Nonsynonymous PGDX135T SPTA1 spectrin; alpha; erythrocytic 1 (elliptocytosis 2) CCDS41423.1 chr1_156871014_156871014_A_C 1836N>K Substitution 43% coding Nonsynonymous PGDX135T STEAP4 STEAP family member 4 CCDS43611.1 chr7_87750032_87750032_A_C 282W>G Substitution 28% coding Nonsynonymous PGDX135T TCF20 transcription factor 20 (AR1) CCDS14033.1 chr22_40935876_40935876_C_G 1794D>H Substitution 11% coding PGDX135T TRAPPC6B trafficking protein particle complex 6B CCDS41947.1 chr14_38689339_38689339_A_ NA Deletion Splice site 11% Nonsynonymous PGDX135T TRO trophinin CCDS43959.1 chrX_54968828_54968828_G_A 522G>S Substitution 19% coding X-ray repair complementing defective repair in Chinese hamster Nonsynonymous PGDX135T XRCC5 CCDS2402.1 chr2_216721236_216721236_C_G 554F>L Substitution 28% cells 5 (double-strand-break rejoining) coding PGDX135T ZNF292 zinc finger protein 292 NM_015021 chr6_88012085_88012085_A_G NA Substitution Splice site 23% Nonsynonymous PGDX135T ZSCAN4 zinc finger and SCAN domain containing 4 CCDS12958.1 chr19_62879522_62879522_A_G 66Y>C Substitution 27% coding PGDX140 A2BP1 Fox-1 homolog CCDS10531.1 chr16_7699135_7699135_G_T NA Substitution Splice site 59% Nonsynonymous PGDX140 ABCB1 ATP-binding cassette; sub-family B (MDR/TAP); member 1 CCDS5608.1 chr7_87033489_87033489_C_T 179V>I Substitution 30% coding Nonsynonymous PGDX140 ABHD10 abhydrolase domain containing 10 CCDS2963.1 chr3_113193085_113193085_G_A 250D>N Substitution 86% coding PGDX140 ABI3BP target of Nesh-SH3 precursor NM_015429 chr3_102053478_102053478_A_
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    ONCOLOGY LETTERS 21: 58, 2021 Circular RNA hsa_circ_0005114‑miR‑142‑3p/miR‑590‑5p‑ adenomatous polyposis coli protein axis as a potential target for treatment of glioma BO WEI1*, LE WANG2* and JINGWEI ZHAO1 1Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033; 2Department of Ophthalmology, The First Hospital of Jilin University, Jilin University, Changchun, Jilin 130021, P.R. China Received September 12, 2019; Accepted October 22, 2020 DOI: 10.3892/ol.2020.12320 Abstract. Glioma is the most common type of brain tumor APC expression with a good overall survival rate. UALCAN and is associated with a high mortality rate. Despite recent analysis using TCGA data of glioblastoma multiforme and the advances in treatment options, the overall prognosis in patients GSE25632 and GSE103229 microarray datasets showed that with glioma remains poor. Studies have suggested that circular hsa‑miR‑142‑3p/hsa‑miR‑590‑5p was upregulated and APC (circ)RNAs serve important roles in the development and was downregulated. Thus, hsa‑miR‑142‑3p/hsa‑miR‑590‑5p‑ progression of glioma and may have potential as therapeutic APC‑related circ/ceRNA axes may be important in glioma, targets. However, the expression profiles of circRNAs and their and hsa_circ_0005114 interacted with both of these miRNAs. functions in glioma have rarely been studied. The present study Functional analysis showed that hsa_circ_0005114 was aimed to screen differentially expressed circRNAs (DECs) involved in insulin secretion, while APC was associated with between glioma and normal brain tissues using sequencing the Wnt signaling pathway. In conclusion, hsa_circ_0005114‑ data collected from the Gene Expression Omnibus database miR‑142‑3p/miR‑590‑5p‑APC ceRNA axes may be potential (GSE86202 and GSE92322 datasets) and explain their mecha‑ targets for the treatment of glioma.
  • ADAM10 Site-Dependent Biology: Keeping Control of a Pervasive Protease

    ADAM10 Site-Dependent Biology: Keeping Control of a Pervasive Protease

    International Journal of Molecular Sciences Review ADAM10 Site-Dependent Biology: Keeping Control of a Pervasive Protease Francesca Tosetti 1,* , Massimo Alessio 2, Alessandro Poggi 1,† and Maria Raffaella Zocchi 3,† 1 Molecular Oncology and Angiogenesis Unit, IRCCS Ospedale Policlinico S. Martino Largo R. Benzi 10, 16132 Genoa, Italy; [email protected] 2 Proteome Biochemistry, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; [email protected] 3 Division of Immunology, Transplants and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; [email protected] * Correspondence: [email protected] † These authors contributed equally to this work as last author. Abstract: Enzymes, once considered static molecular machines acting in defined spatial patterns and sites of action, move to different intra- and extracellular locations, changing their function. This topological regulation revealed a close cross-talk between proteases and signaling events involving post-translational modifications, membrane tyrosine kinase receptors and G-protein coupled recep- tors, motor proteins shuttling cargos in intracellular vesicles, and small-molecule messengers. Here, we highlight recent advances in our knowledge of regulation and function of A Disintegrin And Metalloproteinase (ADAM) endopeptidases at specific subcellular sites, or in multimolecular com- plexes, with a special focus on ADAM10, and tumor necrosis factor-α convertase (TACE/ADAM17), since these two enzymes belong to the same family, share selected substrates and bioactivity. We will discuss some examples of ADAM10 activity modulated by changing partners and subcellular compartmentalization, with the underlying hypothesis that restraining protease activity by spatial Citation: Tosetti, F.; Alessio, M.; segregation is a complex and powerful regulatory tool.
  • Patient-Based Cross-Platform Comparison of Oligonucleotide Microarray Expression Profiles

    Patient-Based Cross-Platform Comparison of Oligonucleotide Microarray Expression Profiles

    Laboratory Investigation (2005) 85, 1024–1039 & 2005 USCAP, Inc All rights reserved 0023-6837/05 $30.00 www.laboratoryinvestigation.org Patient-based cross-platform comparison of oligonucleotide microarray expression profiles Joerg Schlingemann1,*, Negusse Habtemichael2,*, Carina Ittrich3, Grischa Toedt1, Heidi Kramer1, Markus Hambek4, Rainald Knecht4, Peter Lichter1, Roland Stauber2 and Meinhard Hahn1 1Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Heidelberg, Germany; 2Chemotherapeutisches Forschungsinstitut Georg-Speyer-Haus, Frankfurt am Main, Germany; 3Central Unit Biostatistics, Deutsches Krebsforschungszentrum, Heidelberg, Germany and 4Department of Otorhinolaryngology, Universita¨tsklinik, Johann-Wolfgang-Goethe-Universita¨t Frankfurt, Frankfurt, Germany The comparison of gene expression measurements obtained with different technical approaches is of substantial interest in order to clarify whether interplatform differences may conceal biologically significant information. To address this concern, we analyzed gene expression in a set of head and neck squamous cell carcinoma patients, using both spotted oligonucleotide microarrays made from a large collection of 70-mer probes and commercial arrays produced by in situ synthesis of sets of multiple 25-mer oligonucleotides per gene. Expression measurements were compared for 4425 genes represented on both platforms, which revealed strong correlations between the corresponding data sets. Of note, a global tendency towards smaller absolute ratios was observed when
  • Supplementary Table 1: Adhesion Genes Data Set

    Supplementary Table 1: Adhesion Genes Data Set

    Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like,