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List of Genes De-Regulated Between Treatment (QD) and Vehicle at 1H

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List of genes de-regulated between treatment (QD) and vehicle at 1h 4080_vs_untreat Fold-change q.value Gene Acc Description 1,9 2,48E-02 Ogt AK076418 O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase) 1,66 2,48E-02 AK036420 AK036420 #N/D 1,64 2,48E-02 Rbm25 AK169022 RNA binding motif protein 25 1,48 2,48E-02 EG639396 NM_001039251 #N/D 2,27 3,04E-02 D830012I16Rik AK031521 RIKEN cDNA D830012I16 gene 1,83 3,04E-02 4833414E09Rik BC023710 RIKEN cDNA 4833414E09 gene 1,78 3,04E-02 Wnk1 AK044849 WNK lysine deficient protein kinase 1 1,78 3,04E-02 D530037H12Rik AK052577 RIKEN cDNA D530037H12 gene 1,58 3,04E-02 Mast2 AK048193 microtubule associated serine/threonine kinase 2 1,49 3,04E-02 Sfpq BC033603 splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated) 2,46 3,12E-02 BM114715 BM114715 #N/D 2,4 3,12E-02 Luc7l2 AK166155 LUC7-like 2 (S. cerevisiae) 2,33 3,12E-02 2310067E19Rik NM_172427 RIKEN cDNA 2310067E19 gene 2,09 3,12E-02 AK076574 AK076574 #N/D 2,02 3,12E-02 Tlk2 AK048492 tousled-like kinase 2 (Arabidopsis) 2 3,12E-02 Ccnt2 AK156621 cyclin T2 1,96 3,12E-02 AK037824 AK037824 #N/D 1,94 3,12E-02 D17Ertd165e BG066166 DNA segment, Chr 17, ERATO Doi 165, expressed 1,92 3,12E-02 BE995972 BE995972 #N/D 1,88 3,12E-02 Tead1 AK035595 TEA domain family member 1 1,83 3,12E-02 Thrap3 BC026580 thyroid hormone receptor associated protein 3 1,81 3,12E-02 2810017D21Rik AK012752 RIKEN cDNA 2810017D21 gene 1,8 3,12E-02 Rad23b AK084917 RAD23b homolog (S. cerevisiae) 1,78 3,12E-02 2610001A08Rik AK011250 RIKEN cDNA 2610001A08 gene 1,74 3,12E-02 A430081F14Rik AK084623 RIKEN cDNA A430081F14 gene 1,74 3,12E-02 2610319H10Rik AK012053 RIKEN cDNA 2610319H10 gene 1,73 3,12E-02 Phf21a AK083682 PHD finger protein 21A 1,73 3,12E-02 AI317158 BY732663 expressed sequence AI317158 1,71 3,12E-02 D5Ertd798e AK041660 DNA segment, Chr 5, ERATO Doi 798, expressed 1,71 3,12E-02 C76450 BG065672 expressed sequence C76450 1,69 3,12E-02 9930017N22Rik AK036847 RIKEN cDNA 9930017N22 gene 1,68 3,12E-02 Mll3 AK087368 myeloid/lymphoid or mixed-lineage leukemia 3 1,67 3,12E-02 Cltc AK049578 clathrin, heavy polypeptide (Hc) 1,66 3,12E-02 AK034548 AK034548 #N/D 1,65 3,12E-02 5830411K21Rik AY039009 #N/D 1,64 3,12E-02 AK156581 AK156581 #N/D 1,6 3,12E-02 D18Ertd693e BG083290 DNA segment, Chr 18, ERATO Doi 693, expressed 1,6 3,12E-02 2610011E03Rik AK011375 RIKEN cDNA 2610011E03 gene 1,54 3,12E-02 6330417A16Rik AK018186 RIKEN cDNA 6330417A16 gene 1,54 3,12E-02 AK041923 AK041923 #N/D 1,53 3,12E-02 C230096C10Rik BB591623 RIKEN cDNA C230096C10 gene 1,5 3,12E-02 C530036F05Rik AK083039 RIKEN cDNA C530036F05 gene 1,49 3,12E-02 AK164390 AK164390 #N/D 1,43 3,12E-02 Ubap2l AK014274 ubiquitin associated protein 2-like 1,38 3,12E-02 Slc26a11 NM_178743 solute carrier family 26, member 11 1,35 3,12E-02 Tagap NM_145968 T-cell activation Rho GTPase-activating protein 1,35 3,12E-02 Pten AK164302 phosphatase and tensin homolog 1,34 3,12E-02 Fcho2 BC053718 FCH domain only 2 1,23 3,12E-02 Slc4a3 NM_009208 solute carrier family 4 (anion exchanger), member 3 2,11 3,17E-02 Rbm26 NM_134077 RNA binding motif protein 26 2,07 3,17E-02 AK141643 AK141643 #N/D 1,96 3,17E-02 AI790442 AK039096 expressed sequence AI790442 1,92 3,17E-02 B430203M17Rik CA882616 #N/D 1,89 3,17E-02 Tcf4 AK033220 transcription factor 4 1,84 3,17E-02 E230020A03Rik AK084995 RIKEN cDNA E230020A03 gene 1,82 3,17E-02 Trpc2 ENSMUST00000094130 transient receptor potential cation channel, subfamily C, member 2 1,81 3,17E-02 2900018N21Rik AK013552 RIKEN cDNA 2900018N21 gene 1,79 3,17E-02 AK143436 AK143436 #N/D 1,75 3,17E-02 Man2b1 AK169830 mannosidase 2, alpha B1 1,75 3,17E-02 AK038224 AK038224 #N/D 1,7 3,17E-02 AI843755 AK132333 #N/D 1,68 3,17E-02 Rnf130 AK220529 ring finger protein 130 1,64 3,17E-02 AK134193 AK134193 #N/D 1,61 3,17E-02 AA589532 AK079655 expressed sequence AA589532 1,61 3,17E-02 AI324963 CA526845 expressed sequence AI324963 1,58 3,17E-02 Fbxw11 AK135210 F-box and WD-40 domain protein 11 1,54 3,17E-02 Ddef1 DV047853 #N/D 1,51 3,17E-02 B930096F20Rik AK081173 RIKEN cDNA B930096F20 gene 1,5 3,17E-02 1500012F01Rik LIT1141 RIKEN cDNA 1500012F01 gene 1,49 3,17E-02 Hrbl NM_145566 #N/D 1,47 3,17E-02 5930405F01Rik AK037374 RIKEN cDNA 5930405F01 gene 1,43 3,17E-02 5830443J22Rik AK017987 RIKEN cDNA 5830443J22 gene 1,38 3,17E-02 B3gnt3 BC047217 UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3 1,37 3,17E-02 Mta3 BC050134 metastasis associated 3 1,34 3,17E-02 2610202C22Rik AK011859 RIKEN cDNA 2610202C22 gene 1,34 3,17E-02 Tspyl2 NM_029836 TSPY-like 2 1,32 3,17E-02 Acrbp BC011079 proacrosin binding protein 1,31 3,17E-02 CD544507 CD544507 #N/D 1,29 3,17E-02 D14Ertd581e NM_029454 #N/D 1,24 3,17E-02 Zdhhc2 NM_178395 zinc finger, DHHC domain containing 2 1,87 3,18E-02 5930436O19Rik AK020044 RIKEN cDNA 5930436O19 gene List of genes de-regulated between treatment (QD) and vehicle at 6h Fold-change q.value Fold-change q.value Fold-change q.value 4080_vs_untreat 40_vs_untreat 80_vs_untreat Gene Acc Description -11,39 8,55E-03 -9,35 0,02 -15,97 0,02 Gli1 NM_010296 GLI-Kruppel family member GLI1 -3,73 8,55E-03 -3,51 0,02 -4,15 0,02 Sox18 NM_009236 SRY-box containing gene 18 -3,62 8,55E-03 -3,26 0,02 -4,29 0,02 Pdgfa NM_008808 platelet derived growth factor, alpha -3,14 8,55E-03 -2,71 0,02 -4,02 0,02 Clic6 NM_172469 chloride intracellular channel 6 -3,14 8,55E-03 -3,12 0,02 -3,18 0,02 Rgma NM_177740 RGM domain family, member A -3,08 8,55E-03 -2,94 0,02 -3,33 0,02 Bcl11b NM_021399 B-cell leukemia/lymphoma 11B -2,63 8,55E-03 -2,51 0,02 -2,85 0,02 9430069J07Rik NM_213727 #N/D -2,49 8,55E-03 -2,39 0,02 -2,65 0,02 Hk2 NM_013820 hexokinase 2 -4,94 8,55E-03 -5,18 0,02 -4,57 0,02 Gdf10 NM_145741 growth differentiation factor 10 -3,18 8,55E-03 -3,03 0,02 -3,45 0,02 4631405J19Rik NM_001002794 RIKEN cDNA 4631405J19 gene -2,29 8,55E-03 -2,15 0,02 -2,54 0,02 Ptch1 AK147626 patched homolog 1 -3,26 8,55E-03 -2,93 0,02 -3,90 0,02 Wif1 NM_011915 Wnt inhibitory factor 1 -2,91 8,55E-03 -2,79 0,02 -3,11 0,02 Tmem28 NM_173446 transmembrane protein 28 -2,89 8,55E-03 -2,65 0,02 -3,33 0,02 Bcl11b AK020296 B-cell leukemia/lymphoma 11B -2,72 8,55E-03 -2,65 0,02 -2,85 0,02 Tmem28 AK162130 transmembrane protein 28 -2,51 8,55E-03 -2,51 0,02 -2,51 0,02 AU022229 AK046833 expressed sequence AU022229 -1,97 8,55E-03 -1,81 0,02 -2,25 0,02 Col27a1 NM_025685 collagen, type XXVII, alpha 1 -2,07 8,55E-03 -1,87 0,02 -2,45 0,02 Hs3st3b1 AK171996 heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1 -2,42 8,55E-03 -2,19 0,02 -2,85 0,02 9130211I03Rik NM_030060 #N/D -2,17 8,55E-03 -2,57 0,02 Pgf NM_008827 placental growth factor -3,18 8,55E-03 -2,99 0,02 -3,50 0,02 Bcl11b ENSMUST00000066060 B-cell leukemia/lymphoma 11B -2,11 8,55E-03 -2,00 0,02 -2,32 0,02 Phldb1 NM_153537 pleckstrin homology-like domain, family B, member 1 2,26 8,55E-03 2,25 0,02 2,30 0,02 Igfbp5 NM_010518 insulin-like growth factor binding protein 5 -2,15 8,55E-03 -2,07 0,02 -2,31 0,02 Sez6l ENSMUST00000075387 seizure related 6 homolog like -2,77 8,55E-03 -2,47 0,02 -3,38 0,02 Angptl2 NM_011923 angiopoietin-like 2 -2,49 8,55E-03 -2,48 0,02 -2,52 0,02 Wnt4 NM_009523 wingless-related MMTV integration site 4 -2,40 8,55E-03 -2,33 0,02 -2,54 0,02 Hk2 AK009328 hexokinase 2 -2,30 8,55E-03 -2,27 0,02 -2,37 0,02 Ngfr NM_033217 nerve growth factor receptor (TNFR superfamily, member 16) -2,42 8,55E-03 -2,43 0,02 -2,40 0,02 Cfc1 NM_007685 cripto, FRL-1, cryptic family 1 -2,38 8,55E-03 -2,27 0,02 -2,60 0,02 Angptl2 AK155464 angiopoietin-like 2 -2,32 8,55E-03 -2,26 0,02 -2,41 0,02 Tiam1 NM_009384 T-cell lymphoma invasion and metastasis 1 -2,23 8,55E-03 -2,10 0,02 -2,47 0,02 Col27a1 AK003879 collagen, type XXVII, alpha 1 -2,17 8,55E-03 -2,18 0,02 -2,16 0,02 Wnt4 AK135561 wingless-related MMTV integration site 4 -2,15 8,55E-03 -2,26 0,02 -1,99 0,02 Ptch1 NM_008957 patched homolog 1 -2,12 8,55E-03 -2,21 0,02 -1,99 0,02 Smad3 NM_016769 MAD homolog 3 (Drosophila) -1,87 8,55E-03 -1,75 0,02 -2,09 0,02 Gpr153 NM_178406 G protein-coupled receptor 153 1,85 8,55E-03 1,87 0,02 1,81 0,02 Barhl1 AF264026 BarH-like 1 (Drosophila) -2,42 8,55E-03 -2,28 0,02 -2,68 0,02 Tiam1 AK161477 T-cell lymphoma invasion and metastasis 1 1,99 8,55E-03 1,98 0,02 2,01 0,02 Barhl1 NM_019446 BarH-like 1 (Drosophila) 2,20 8,55E-03 2,30 0,02 2,05 0,02 Dmrta1 NM_175647 doublesex and mab-3 related transcription factor like family A1 -2,02 8,55E-03 -2,01 0,02 -2,04 0,02 Lhx3 NM_001039653 LIM homeobox protein 3 -1,89 8,55E-03 -1,89 0,02 -1,88 0,02 1700021K02Rik NM_001017433 #N/D -1,83 8,55E-03 -1,76 0,02 -1,96 0,02 Lrig3 NM_177152 leucine-rich repeats and immunoglobulin-like domains 3 -2,11 8,55E-03 -1,98 0,02 -2,33 0,02 Hes3 NM_008237 hairy and enhancer of split 3 (Drosophila) -1,91 8,55E-03 -1,90 0,02 -1,94 0,02 Ung NM_001040691 uracil DNA glycosylase -1,88 8,55E-03 -1,81 0,02 -2,02 0,02 Gli2 AK078489 GLI-Kruppel family member GLI2 -1,68 8,55E-03 -1,66 0,02 -1,71 0,02 Gpsm1 NM_153410 G-protein signalling modulator 1 (AGS3-like, C.
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    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.
  • Protein Identities in Evs Isolated from U87-MG GBM Cells As Determined by NG LC-MS/MS

    Protein Identities in Evs Isolated from U87-MG GBM Cells As Determined by NG LC-MS/MS

    Protein identities in EVs isolated from U87-MG GBM cells as determined by NG LC-MS/MS. No. Accession Description Σ Coverage Σ# Proteins Σ# Unique Peptides Σ# Peptides Σ# PSMs # AAs MW [kDa] calc. pI 1 A8MS94 Putative golgin subfamily A member 2-like protein 5 OS=Homo sapiens PE=5 SV=2 - [GG2L5_HUMAN] 100 1 1 7 88 110 12,03704523 5,681152344 2 P60660 Myosin light polypeptide 6 OS=Homo sapiens GN=MYL6 PE=1 SV=2 - [MYL6_HUMAN] 100 3 5 17 173 151 16,91913397 4,652832031 3 Q6ZYL4 General transcription factor IIH subunit 5 OS=Homo sapiens GN=GTF2H5 PE=1 SV=1 - [TF2H5_HUMAN] 98,59 1 1 4 13 71 8,048185945 4,652832031 4 P60709 Actin, cytoplasmic 1 OS=Homo sapiens GN=ACTB PE=1 SV=1 - [ACTB_HUMAN] 97,6 5 5 35 917 375 41,70973209 5,478027344 5 P13489 Ribonuclease inhibitor OS=Homo sapiens GN=RNH1 PE=1 SV=2 - [RINI_HUMAN] 96,75 1 12 37 173 461 49,94108966 4,817871094 6 P09382 Galectin-1 OS=Homo sapiens GN=LGALS1 PE=1 SV=2 - [LEG1_HUMAN] 96,3 1 7 14 283 135 14,70620005 5,503417969 7 P60174 Triosephosphate isomerase OS=Homo sapiens GN=TPI1 PE=1 SV=3 - [TPIS_HUMAN] 95,1 3 16 25 375 286 30,77169764 5,922363281 8 P04406 Glyceraldehyde-3-phosphate dehydrogenase OS=Homo sapiens GN=GAPDH PE=1 SV=3 - [G3P_HUMAN] 94,63 2 13 31 509 335 36,03039959 8,455566406 9 Q15185 Prostaglandin E synthase 3 OS=Homo sapiens GN=PTGES3 PE=1 SV=1 - [TEBP_HUMAN] 93,13 1 5 12 74 160 18,68541938 4,538574219 10 P09417 Dihydropteridine reductase OS=Homo sapiens GN=QDPR PE=1 SV=2 - [DHPR_HUMAN] 93,03 1 1 17 69 244 25,77302971 7,371582031 11 P01911 HLA class II histocompatibility antigen,
  • 4-6 Weeks Old Female C57BL/6 Mice Obtained from Jackson Labs Were Used for Cell Isolation

    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).
  • Figure S1. Representative Report Generated by the Ion Torrent System Server for Each of the KCC71 Panel Analysis and Pcafusion Analysis

    Figure S1. Representative Report Generated by the Ion Torrent System Server for Each of the KCC71 Panel Analysis and Pcafusion Analysis

    Figure S1. Representative report generated by the Ion Torrent system server for each of the KCC71 panel analysis and PCaFusion analysis. (A) Details of the run summary report followed by the alignment summary report for the KCC71 panel analysis sequencing. (B) Details of the run summary report for the PCaFusion panel analysis. A Figure S1. Continued. Representative report generated by the Ion Torrent system server for each of the KCC71 panel analysis and PCaFusion analysis. (A) Details of the run summary report followed by the alignment summary report for the KCC71 panel analysis sequencing. (B) Details of the run summary report for the PCaFusion panel analysis. B Figure S2. Comparative analysis of the variant frequency found by the KCC71 panel and calculated from publicly available cBioPortal datasets. For each of the 71 genes in the KCC71 panel, the frequency of variants was calculated as the variant number found in the examined cases. Datasets marked with different colors and sample numbers of prostate cancer are presented in the upper right. *Significantly high in the present study. Figure S3. Seven subnetworks extracted from each of seven public prostate cancer gene networks in TCNG (Table SVI). Blue dots represent genes that include initial seed genes (parent nodes), and parent‑child and child‑grandchild genes in the network. Graphical representation of node‑to‑node associations and subnetwork structures that differed among and were unique to each of the seven subnetworks. TCNG, The Cancer Network Galaxy. Figure S4. REVIGO tree map showing the predicted biological processes of prostate cancer in the Japanese. Each rectangle represents a biological function in terms of a Gene Ontology (GO) term, with the size adjusted to represent the P‑value of the GO term in the underlying GO term database.
  • Molecular and Cellular Mechanisms of the Angiogenic Effect of Poly(Methacrylic Acid-Co-Methyl Methacrylate) Beads

    Molecular and Cellular Mechanisms of the Angiogenic Effect of Poly(Methacrylic Acid-Co-Methyl Methacrylate) Beads

    Molecular and Cellular Mechanisms of the Angiogenic Effect of Poly(methacrylic acid-co-methyl methacrylate) Beads by Lindsay Elizabeth Fitzpatrick A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Institute of Biomaterials and Biomedical Engineering University of Toronto © Copyright by Lindsay Elizabeth Fitzpatrick 2012 Molecular and Cellular Mechanisms of the Angiogenic Effect of Poly(methacrylic acid-co-methyl methacrylate) Beads Lindsay Elizabeth Fitzpatrick Doctorate of Philosophy Institute of Biomaterials and Biomedical Engineering University of Toronto 2012 Abstract Poly(methacrylic acid -co- methyl methacrylate) beads were previously shown to have a therapeutic effect on wound closure through the promotion of angiogenesis. However, it was unclear how this polymer elicited its beneficial properties. The goal of this thesis was to characterize the host response to MAA beads by identifying molecules of interest involved in MAA-mediated angiogenesis (in comparison to poly(methyl methacrylate) beads, PMMA). Using a model of diabetic wound healing and a macrophage-like cell line (dTHP-1), eight molecules of interest were identified in the host response to MAA beads. Gene and/or protein expression analysis showed that MAA beads increased the expression of Shh, IL-1β, IL-6, TNF- α and Spry2, but decreased the expression of CXCL10 and CXCL12, compared to PMMA and no beads. MAA beads also appeared to modulate the expression of OPN. In vivo, the global gene expression of OPN was increased in wounds treated with MAA beads, compared to PMMA and no beads. In contrast, dTHP-1 decreased OPN gene expression compared to PMMA and no beads, but expressed the same amount of secreted OPN, suggesting that the cells decreased the expression of the intracellular isoform of OPN.