PRSS2) Variant Protects Against Chronic Pancreatitis
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PARSANA-DISSERTATION-2020.Pdf
DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks. -
Newly Developed Serine Protease Inhibitors Decrease Visceral Hypersensitivity in a Post-Inflammatory Rat Model for Irritable Bowel Syndrome
This item is the archived peer-reviewed author-version of: Newly developed serine protease inhibitors decrease visceral hypersensitivity in a post-inflammatory rat model for irritable bowel syndrome Reference: Ceuleers Hannah, Hanning Nikita, Heirbaut Leen, Van Remoortel Samuel, Joossens Jurgen, van der Veken Pieter, Francque Sven, De Bruyn Michelle, Lambeir Anne-Marie, de Man Joris, ....- New ly developed serine protease inhibitors decrease visceral hypersensitivity in a post-inflammatory rat model for irritable bow el syndrome British journal of pharmacology - ISSN 0007-1188 - 175:17(2018), p. 3516-3533 Full text (Publisher's DOI): https://doi.org/10.1111/BPH.14396 To cite this reference: https://hdl.handle.net/10067/1530780151162165141 Institutional repository IRUA NEWLY DEVELOPED SERINE PROTEASE INHIBITORS DECREASE VISCERAL HYPERSENSITIVITY IN A POST-INFLAMMATORY RAT MODEL FOR IRRITABLE BOWEL SYNDROME. Running title: Serine proteases in visceral hypersensitivity Hannah Ceuleers, Nikita Hanning, Jelena Heirbaut, Samuel Van Remoortel, Michelle De bruyn, Jurgen Joossens, Pieter van der Veken, Anne-Marie Lambeir, Sven M Francque, Joris G De Man, Jean-Pierre Timmermans, Koen Augustyns, Ingrid De Meester, Benedicte Y De Winter Hannah Ceuleers, Nikita Hanning, Jelena Heirbaut, Sven Francque, Joris G De Man, Benedicte Y De Winter, Laboratory of Experimental Medicine and Pediatrics, Division of Gastroenterology, University of Antwerp, Antwerp, Belgium. Samuel Van Remoortel, Jean-Pierre Timmermans, Laboratory of Cell Biology and Histology, University of Antwerp, Antwerp, Belgium. Jurgen Joossens, Pieter van der Veken, Koen Augustyns, Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, Belgium. Sven Francque, Antwerp University Hospital, Antwerp, Belgium. Michelle De bruyn, Anne-Marie Lambeir, Ingrid De Meester, Laboratory of Medical Biochemistry, University of Antwerp, Antwerp, Belgium. -
PRSS3 Monoclonal Antibody (419911) Catalog Number MA5-24156 Product Data Sheet
Lot Number: TC2545731D Website: thermofisher.com Customer Service (US): 1 800 955 6288 ext. 1 Technical Support (US): 1 800 955 6288 ext. 441 thermofisher.com/contactus PRSS3 Monoclonal Antibody (419911) Catalog Number MA5-24156 Product Data Sheet Details Species Reactivity Size 100 µg Tested species reactivity Mouse Host / Isotype Rat IgG1 Tested Applications Dilution * Class Monoclonal Immunohistochemistry (Frozen) 8-25 µg/ml Type Antibody (IHC (F)) Clone 419911 * Suggested working dilutions are given as a guide only. It is recommended that the user titrate the product for use in their own experiment using appropriate negative and positive controls. Mouse myeloma cell line Immunogen NS0-derived recombinant mouse Trypsin 3/PRSS3 Phe16-Asn246 Conjugate Unconjugated Form Lyophilized Concentration 0.5mg/ml Purification Protein A/G Storage Buffer PBS with 5% trehalose Contains No Preservative Storage Conditions -20° C, Avoid Freeze/Thaw Cycles Product Specific Information Reconstitute at 0.5 mg/mL in sterile PBS. Background/Target Information PRSS3 encodes a trypsinogen, which is a member of the trypsin family of serine proteases. This enzyme is expressed in the brain and pancreas and is resistant to common trypsin inhibitors. It is active on peptide linkages involving the carboxyl group of lysine or arginine. PRSS3 is localized to the locus of T cell receptor beta variable orphans on chromosome 9. Four transcript variants encoding different isoforms have been described for this gene. For Research Use Only. Not for use in diagnostic procedures. Not for resale without express authorization. For Research Use Only. Not for use in diagnostic procedures. Not for resale without express authorization. -
Identification of Pancreatic Juice Proteins As Biomarkers of Pancreatic Cancer
1683-1692.qxd 23/4/2010 10:57 Ì ™ÂÏ›‰·1683 ONCOLOGY REPORTS 23: 1683-1692, 2010 Identification of pancreatic juice proteins as biomarkers of pancreatic cancer JUN GAO1*, FENG ZHU1*, SHUNLI LV1*, ZHAOSHEN LI1, ZHANG LING1, YANFANG GONG1, CHEN JIE1 and LIE MA2 1Department of Gastroenterology, Changhai Hospital, 2Department of Biochemistry, Basic Medicine, Second Military Medical University, Shanghai 200433, P.R. China Received December 17, 2009; Accepted February 4, 2010 DOI: 10.3892/or_00000812 Abstract. Pancreatic juice is a potential source of proteins analysis of pancreatic juice from PC patients is a powerful associated with pancreatic cancer (PC) due to the proximity of method to find new PC biomarkers. Hyperexpression of the ducts to tumor tissue. Therefore, screening of proteins in PRSS2 gene and hypermethylation of ELA3B gene promoter pancreatic juice from PC patients may identify new PC were associated with PC, raising the possibility of their biomarkers. We analyzed pancreatic juice from patients with application as new biomarkers in PC diagnosis and screening. pancreatic diseases including PC, chronic pancreatitis (CP) and simple choledocholithiasis (CDS) by 2-DE. Protein spots Introduction from PC patients that changed >2-fold compared with both CP and CDS were selected and identified by mass spectro- Pancreatic cancer (PC) is an almost uniformly fatal disease, metry (MS). mRNA levels were measured by QRT-PCR in with a 5-year survival rate of less than 4%. In the United PC cell lines, PC tissues and adjacent pancreatic normal (PN) States, PC is the 4th leading cause of cancer death, while in tissues. Relationships between mRNA levels in PC tissues Europe it is the 6th (1). -
B Inhibition in a Mouse Model of Chronic Colitis1
The Journal of Immunology Differential Expression of Inflammatory and Fibrogenic Genes and Their Regulation by NF-B Inhibition in a Mouse Model of Chronic Colitis1 Feng Wu and Shukti Chakravarti2 Fibrosis is a major complication of chronic inflammation, as seen in Crohn’s disease and ulcerative colitis, two forms of inflam- matory bowel diseases. To elucidate inflammatory signals that regulate fibrosis, we investigated gene expression changes under- lying chronic inflammation and fibrosis in trinitrobenzene sulfonic acid-induced murine colitis. Six weekly 2,4,6-trinitrobenzene sulfonic acid enemas were given to establish colitis and temporal gene expression patterns were obtained at 6-, 8-, 10-, and 12-wk time points. The 6-wk point, TNBS-w6, was the active, chronic inflammatory stage of the model marked by macrophage, neu- trophil, and CD3؉ and CD4؉ T cell infiltrates in the colon, consistent with the idea that this model is T cell immune response driven. Proinflammatory genes Cxcl1, Ccl2, Il1b, Lcn2, Pla2g2a, Saa3, S100a9, Nos2, Reg2, and Reg3g, and profibrogenic extra- cellular matrix genes Col1a1, Col1a2, Col3a1, and Lum (lumican), encoding a collagen-associated proteoglycan, were up-regulated at the active/chronic inflammatory stages. Rectal administration of the NF-B p65 antisense oligonucleotide reduced but did not abrogate inflammation and fibrosis completely. The antisense oligonucleotide treatment reduced total NF-B by 60% and down- regulated most proinflammatory genes. However, Ccl2, a proinflammatory chemokine known to promote fibrosis, was not down- regulated. Among extracellular matrix gene expressions Lum was suppressed while Col1a1 and Col3a1 were not. Thus, effective treatment of fibrosis in inflammatory bowel disease may require early and complete blockade of NF-B with particular attention to specific proinflammatory and profibrogenic genes that remain active at low levels of NF-B. -
PRSS2 Polyclonal Antibody
PRODUCT DATA SHEET Bioworld Technology,Inc. PRSS2 polyclonal antibody Catalog: BS61619 Host: Rabbit Reactivity: Human,Mouse,Rat BackGround: Applications: This gene belongs to the trypsin family of serine proteas- WB: 1:500~1:1000 es and encodes anionic trypsinogen. It is part of a cluster Storage&Stability: of trypsinogen genes that are located within the T cell re- Store at 4°C short term. Aliquot and store at -20°C long ceptor beta locus. Enzymes of this family cleave peptide term. Avoid freeze-thaw cycles. bonds that follow lysine or arginine residues. This protein Specificity: is found at high levels in pancreatic juice and its upregu- PRSS2 polyclonal antibody detects endogenous levels of lation is a characteristic feature of pancreatitis. This pro- PRSS2 protein. tein has also been found to activate pro-urokinase in DATA: ovarian tumors, suggesting a function in tumor invasion. In addition, this enzyme is able to cleave across the type II collagen triple helix in rheumatoid arthritis synovitis tissue, potentially participating in the degradation of type II collagen-rich cartilage matrix. Alternative splicing re- sults in multiple transcript variants. Product: Western blot (WB) analysis of PRSS2 polyclonal antibody at 1:500 Rabbit IgG, 1mg/ml in PBS with 0.02% sodium azide, dilution 50% glycerol, pH7.2 Lane1:HT102 whole cell lysate(40ug) Molecular Weight: Lane2:SW620 whole cell lysate(40ug) ~ 26 kDa Lane3:CT26 whole cell lysate(40ug) Swiss-Prot: Lane4:PC12 whole cell lysate(40ug) P07478 Note: Purification&Purity: For research use only, not for use in diagnostic procedure. The antibody was affinity-purified from rabbit antiserum by affinity-chromatography using epitope-specific im- munogen and the purity is > 95% (by SDS-PAGE). -
Trypsin-Encoding PRSS1-PRSS2 Variations
ARTICLE Acute Lymphoblastic Leukemia Ferrata Storti Foundation Trypsin-encoding PRSS1-PRSS2 variations influence the risk of asparaginase-associated pancreatitis in children with acute lymphoblastic leukemia: a Ponte di Legno toxicity working group report Haematologica 2019 Benjamin O. Wolthers,1 Thomas L. Frandsen,1 Chirag J. Patel,2 Rachid Abaji,3 Volume 104(3):556-563 Andishe Attarbaschi,4 Shlomit Barzilai,5 Antonella Colombini,6 Gabriele Escherich,7 Marie Grosjean,8 Maja Krajinovic,3,9 Eric Larsen,10 Der-Cherng Liang,11 Anja Möricke,12 Kirsten K. Rasmussen,1 Sujith Samarasinghe,13 Lewis B. Silverman,14 Inge M. van der Sluis,15 Martin Stanulla,16 Morten Tulstrup,1 Rachita Yadav,8,17 Wenjian Yang,18 Ester Zapotocka,19 Ramneek Gupta8 and Kjeld Schmiegelow1,20 on behalf of the Ponte di Legno toxicity working group 1Department of Pediatrics and Adolescent Medicine, University Hospital Rigshospitalet, Copenhagen, Denmark; 2Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; 3CHU Sainte-Justine Research Center and Department of Pharmacology, University of Montreal, QC, Canada; 4Department of Pediatric Hematology and Oncology, St Anna Children's Hospital and Department of Pediatric and Adolescent Medicine, Medical University of Vienna, Austria; 5Pediatric Hematology and Oncology, Schneider Children's Medical Center of Israel, Petah-Tikva, Israel and Sackler Faculty of Medicine, Tel Aviv University, Israel; 6Department of Pediatrics, Ospedale San Gerardo, University of Milano-Bicocca, Fondazione MBBM, Monza, Italy; -
Irf2)Intrypsinogen5 Gene Transcription
Characterization of dsRNA-induced pancreatitis model reveals the regulatory role of IFN regulatory factor 2 (Irf2)intrypsinogen5 gene transcription Hideki Hayashia, Tomoko Kohnoa, Kiyoshi Yasuia, Hiroyuki Murotab, Tohru Kimurac, Gordon S. Duncand, Tomoki Nakashimae, Kazuo Yamamotod, Ichiro Katayamab, Yuhua Maa, Koon Jiew Chuaa, Takashi Suematsua, Isao Shimokawaf, Shizuo Akirag, Yoshinao Kuboa, Tak Wah Makd,1, and Toshifumi Matsuyamaa,h,1 aDivision of Cytokine Signaling, Department of Molecular Biology and Immunology and fDepartment of Investigative Pathology, Nagasaki University Graduate School of Biomedical Science, Nagasaki 852-8523, Japan; Departments of bDermatology and cPathology, Graduate School of Medicine and gDepartment of Host Defense, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; dCampbell Family Cancer Research Institute, Princess Margaret Hospital, Toronto, ON, Canada M5G 2M9; eDepartment of Cell Signaling, Tokyo Medical and Dental University, Tokyo 113-8549, Japan; and hGlobal Center of Excellence Program, Nagasaki University, Nagasaki 852-8523, Japan Contributed by Tak Wah Mak, October 5, 2011 (sent for review September 8, 2011) − − Mice deficient for interferon regulatory factor (Irf)2 (Irf2 / mice) transcriptional activation of dsRNA-sensing PRRs were critical for exhibit immunological abnormalities and cannot survive lympho- the pIC-induced death. cytic choriomeningitis virus infection. The pancreas of these ani- mals is highly inflamed, a phenotype replicated by treatment with Results and Discussion − − poly(I:C), a synthetic double-stranded RNA. Trypsinogen5 mRNA Irf2 / Mice Show IFN-Dependent Poly(I:C)-Induced Pancreatitis and −/− IFN-Independent Secretory Dysfunction in Pancreatic Acinar Cells. was constitutively up-regulated about 1,000-fold in Irf2 mice − − LCMV-infected Irf2 / mice die within 4 wk postinfection (3), compared with controls as assessed by quantitative RT-PCR. -
PRSS3 Is a Prognostic Marker in Invasive Ductal Carcinoma of the Breast
www.impactjournals.com/oncotarget/ Oncotarget, 2017, Vol. 8, (No. 13), pp: 21444-21453 Research Paper PRSS3 is a prognostic marker in invasive ductal carcinoma of the breast Li Qian1,*, Xiangxiang Gao2,*, Hua Huang1, Shumin Lu3, Yin Cai3, Yu Hua3, Yifei Liu1, Jianguo Zhang1 1Department of Clinical Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China 2Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong Tumor Hospital, Nantong, Jiangsu, China 3Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China *These authors contributed equally to this work Correspondence to: Jianguo Zhang, email: [email protected] Yifei Liu, email: [email protected] Keywords: invasive ductal carcinoma, immunohistochemistry, PRSS3, prognosis Received: November 08, 2016 Accepted: January 27, 2017 Published: February 21, 2017 ABSTRACT Objective: Serine protease 3 (PRSS3) is an isoform of trypsinogen, and plays an important role in the development of many malignancies. The objective of this study was to determine PRSS3 mRNA and protein expression levels in invasive ductal carcinoma of the breast and normal surrounding tissue samples. Results: Both PRSS3 mRNA and protein levels were significantly higher in invasive ductal carcinoma of the breast tissues than in normal or benign tissues (all P < 0.05). High PRSS3 protein levels were associated with patients’ age, histological grade, Her-2 expression level, ki-67 expression, and the 5.0-year survival rate. These high protein levels are independent prognostic markers in invasive ductal carcinoma of the breast. Materials and Methods: We used real-time quantitative polymerase chain reactions (N = 40) and tissue microarray immunohistochemistry analysis (N = 286) to determine PRSS3 mRNA and protein expression, respectively. -
Human Trypsin-3 / PRSS3 Protein (His Tag)
Human Trypsin-3 / PRSS3 Protein (His Tag) Catalog Number: 11866-H08H General Information SDS-PAGE: Gene Name Synonym: MTG; PRSS4; RP11-176F3.3; T9; TRY3; TRY4 Protein Construction: A DNA sequence encoding the human PRSS3 isoform c (P35030-3) (Met 1- Ser 247) was expressed, with a polyhistidine tag at the C-terminus. Source: Human Expression Host: HEK293 Cells QC Testing Purity: > 95 % as determined by SDS-PAGE Bio Activity: Protein Description Measured by its ability to cleave the fluorogenic peptide substrate, Mca- RPKPVE-Nval-WRK(Dnp)-NH2 (AnaSpec, Catalog#27114) . The specific Trypsin-3, also known as Trypsin III, brain trypsinogen, Serine protease 3 activity is >4,000 pmoles/min/μg. (Activation description: The proenzyme and PRSS3, is a secreted protein which belongs to thepeptidase S1 family. needs to be activated by enteropeptidase for an activated form) Trypsin-3 / PRSS3 is expressed is in pancreas and brain. It contains onepeptidase S1 domain. Trypsin-3 / PRSS3 can degrade intrapancreatic Endotoxin: trypsin inhibitors that protect against CP. Genetic variants that cause higher mesotrypsin activity might increase the risk for chronic pancreatitis < 1.0 EU per μg of the protein as determined by the LAL method (CP). A sustained imbalance of pancreatic proteases and their inhibitors seems to be important for the development of CP. The trypsin inhibitor- Stability: degrading activity qualified PRSS3 as a candidate for a novel CP Samples are stable for up to twelve months from date of receipt at -70 ℃ susceptibility gene. Trypsin-3 / PRSS3 has been implicated as a putative tumor suppressor gene due to its loss of expression, which is correlated Predicted N terminal: Val 16 with promoter hypermethylation, in esophageal squamous cell carcinoma and gastric adenocarcinoma. -
Mouse Trypsin 2 / PRSS2 Protein (His Tag)
Mouse Trypsin 2 / PRSS2 Protein (His Tag) Catalog Number: 50383-M08H General Information SDS-PAGE: Gene Name Synonym: Prss2; Ta; Tesp4; Try2; TRY8; TRYP Protein Construction: A DNA sequence encoding the mouse PRSS2 (NP_033456.1) precursor (Met 1-Asn 246) was expressed, with a C-terminal polyhistidine tag. Source: Mouse Expression Host: HEK293 Cells QC Testing Purity: > 92 % as determined by SDS-PAGE Bio Activity: Protein Description Measured by its ability to cleave the fluorogenic peptide substrate, Mca- RPKPVE-Nval-WRK(Dnp)-NH2 (Anaspec, Catalog #27096) . The specific Trypsin-2, also known as Trypsin II, Anionic trypsinogen, Serine protease 2, activity is >1500 pmoles/min/μg . (Activation description: The proenzyme PRSS2 and TRY2, is a secreted protein which belongs to the trypsin serine needs to be activated by enteropeptidase for an activated form) protease family including Trypsin, PRSS1, PRSS2 and PRSS3. It consists of a signal peptide (residues 1-15), a pro region (residues 16-23), and a Endotoxin: proteolytically active mature chain (residues 24-247). PRSS2 contains onepeptidase S1 domain. It is secreted into theduodenum,hydrolysing < 1.0 EU per μg of the protein as determined by the LAL method peptides into their smaller building blocks, which is necessary for the uptake of protein in the food. It is secreted by the pancreas in the form of Stability: inactivezymogen,trypsinogen and cleaved to its active form in the small Samples are stable for up to twelve months from date of receipt at -70 ℃ intestine when the pancreas is stimulated bycholecystokinin through the common activation mechanism. Predicted N terminal: Phe 16 References Molecular Mass: 1.Rawlings, N.D. -
Supplementary Table 1: Gene List of 44 Upregulated Enzymes in Transformed Mesenchymal Stem Cell Cancer Model
Supplementary Table 1: Gene list of 44 upregulated enzymes in transformed mesenchymal stem cell cancer model. Gene expression values for parental MSC (MSC 0) and transformed MSC (MSC5) are an average of three replicate log-2 transformed expression values from affymetrix U133 plus 2 genechip experiments with the log-fold change (LFC) indicating the difference (MSC5-MSC0). Supplementary Table 1 HGNC Symbol Alias Enzyme ID U133 plus2 probe set MSC0 MSC5 LFC Ttest pval # Gene rifs # Pubmed cites from Genecards (Sep 2007) Pathway / Function PharmGKB Drugs? Drug pathways? Therapeutic Target Database Thomson Pharma RNASEH2A AGS4; JUNB; RNHL; RNHIA; RNASEHI 3.1.26.- 203022_at 8.56 9.87 1.31 1.56E-05 0 11 RNA degradation none none none PPAP2C LPP2; PAP-2c; PAP2-g 3.1.3.4 209529_at 6.48 8.63 2.16 5.74E-03 2 13 Glycerolipid synthesis none none none ADARB1 ADAR2, ADAR2a, ADAR2a-L1, ADAR2a-L2, ADAR2a-L3, ADAR2b, ADAR2c 3.5.-.- 234799_at 6.36 8.15 1.79 2.03E-04 10 58 RNA pre-mRNA editing none none none ADARB1 3.5.-.- 203865_s_at 6.99 8.42 1.43 6.94E-03 10 58 RNA pre-mRNA editing none none none UAP1 AgX; AGX1; SPAG2 2.7.7.23 209340_at 11.17 12.45 1.28 2.46E-07 0 37 polysaccharide synthesis none none RNMT MET; RG7MT1; hCMT1c; KIAA0398; DKFZp686H1252 2.1.1.56 202684_s_at 5.70 6.78 1.08 8.15E-03 1 24 RNA (mRNA) capping none none GPD2 GDH2, mGPDH 1.1.1.8 211613_s_at 5.71 6.73 1.02 7.02E-03 2 37 glycolysis none none GCDH ACAD5, GCD 1.3.99.7 237304_at 5.38 6.39 1.01 2.44E-02 4 63 lys, hydroxy-lys, and trp metabolism none none ESPL1 3.4.22.49 38158_at 8.03