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Laklai H, Miroshnikova YA, Pickup MW, Collisson EA, Kim GE, Barrett AS, Hill RC, Lakins JN, Schlaepfer DD, Mouw JK, LeBleu VS, Roy N, Novitskiy SV, Johansen JS, Poli V, Kalluri R, Iacobuzio-Donahue CA, Wood LD, Hebrok M, Hansen K, Moses HL, Weaver VM. Author Correction: Genotype tunes pancreatic ductal adenocarcinoma tissue tension to induce matricellular fibrosis and tumor progression. Nat Med 2024; 30:908. [PMID: 38017076 DOI: 10.1038/s41591-023-02694-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Affiliation(s)
- Hanane Laklai
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Yekaterina A Miroshnikova
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Michael W Pickup
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Eric A Collisson
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Grace E Kim
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Alex S Barrett
- Department of Biochemistry and Molecular Genetics, University of Colorado, Denver, Aurora, Colorado, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado, Denver, Aurora, Colorado, USA
| | - Johnathon N Lakins
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, California, USA
| | - David D Schlaepfer
- Department of Reproductive Medicine, University of California, San Diego Moores Cancer Center, La Jolla, California, USA
| | - Janna K Mouw
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Valerie S LeBleu
- Department of Cancer Biology, Metastasis Research Center, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Nilotpal Roy
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Sergey V Novitskiy
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Julia S Johansen
- Department of Oncology, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Valeria Poli
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, Turin, Italy
| | - Raghu Kalluri
- Department of Cancer Biology, Metastasis Research Center, University of Texas M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, David Rubenstein Center for Pancreatic Cancer Research, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Laura D Wood
- Gastrointestinal and Liver Pathology Department, Johns Hopkins University, Baltimore, Maryland, USA
| | - Matthias Hebrok
- Diabetes Center, Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Kirk Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado, Denver, Aurora, Colorado, USA
| | - Harold L Moses
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, California, USA.
- Department of Anatomy, University of California, San Francisco, San Francisco, California, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, California, USA.
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA.
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Pascutti KM, O'Kell AL, Hill RC, Castro RA, Salute ME, Gilor C. The effect of capromorelin on glycemic control in healthy dogs. Domest Anim Endocrinol 2022; 81:106732. [PMID: 35689953 DOI: 10.1016/j.domaniend.2022.106732] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/27/2022] [Accepted: 05/04/2022] [Indexed: 11/23/2022]
Abstract
Capromorelin is a ghrelin-receptor agonist widely used as an appetite stimulant in dogs. Capromorelin disrupts glucose homeostasis in cats but information regarding its effects on canine glucose homeostasis is lacking. The study objective was to evaluate the effect of capromorelin on glucose homeostatic mechanisms in healthy dogs. Eight clinically healthy client-owned adult dogs were enrolled in this prospective, cross-over, placebo-controlled study. Dogs were randomized to receive capromorelin (Entyce, 3 mg/kg) or placebo, q24h for 3 d. A wk later, treatments were crossed over. Interstitial glucose (IG) concentrations were measured using a flash glucose monitoring system throughout. On d 1 of each treatment, blood glucose (BG), insulin, glucagon, glucose-dependent insulinotropic peptide (GIP), and glucagon-like peptide-1 (GLP-1) concentrations were measured before drug administration, then before and 30-120 min after feeding a glucose-rich diet (Ensure Plus, 21 kcal/kg). Data were analyzed as a 2-period crossover design using generalized least squares estimation. Capromorelin administration increased mean 48 h IG by10% and mean BG by 20% at 90 and 120 min post-prandially (P < 0.0001). Post-prandially, there was a time-by-treatment effect for insulin (P = 0.03) and GIP (P = 0.0002) because capromorelin doubled geometric mean insulin concentrations at 120 min and increased geometric mean GIP concentrations more rapidly than after placebo. There were no differences in glucagon or GLP-1 concentrations between treatment groups. The increase in post-prandial blood glucose was not the result of overt suppression of incretin hormone secretion. There was also no suppressive effect of capromorelin on insulin.
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Affiliation(s)
- K M Pascutti
- Department of Small Animal Clinical Sciences, University of Florida, College of Veterinary Medicine, 2015 SW 16th Ave, Gainesville, FL 32610, USA
| | - A L O'Kell
- Department of Small Animal Clinical Sciences, University of Florida, College of Veterinary Medicine, 2015 SW 16th Ave, Gainesville, FL 32610, USA
| | - R C Hill
- Department of Small Animal Clinical Sciences, University of Florida, College of Veterinary Medicine, 2015 SW 16th Ave, Gainesville, FL 32610, USA
| | - R A Castro
- Department of Small Animal Clinical Sciences, University of Florida, College of Veterinary Medicine, 2015 SW 16th Ave, Gainesville, FL 32610, USA
| | - M E Salute
- Department of Small Animal Clinical Sciences, University of Florida, College of Veterinary Medicine, 2015 SW 16th Ave, Gainesville, FL 32610, USA
| | - C Gilor
- Department of Small Animal Clinical Sciences, University of Florida, College of Veterinary Medicine, 2015 SW 16th Ave, Gainesville, FL 32610, USA.
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Wang RM, Mesfin JM, Hunter J, Cattaneo P, Guimarães-Camboa N, Braden RL, Luo C, Hill RC, Dzieciatkowska M, Hansen KC, Evans S, Christman KL. Myocardial matrix hydrogel acts as a reactive oxygen species scavenger and supports a proliferative microenvironment for cardiomyocytes. Acta Biomater 2022; 152:47-59. [PMID: 36041648 DOI: 10.1016/j.actbio.2022.08.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/10/2022] [Accepted: 08/23/2022] [Indexed: 11/20/2022]
Abstract
As the native regenerative potential of adult cardiac tissue is limited post-injury, stimulating endogenous repair mechanisms in the mammalian myocardium is a potential goal of regenerative medicine therapeutics. Injection of myocardial matrix hydrogels into the heart post-myocardial infarction (MI) has demonstrated increased cardiac muscle and promotion of pathways associated with cardiac development, suggesting potential promotion of cardiomyocyte turnover. In this study, the myocardial matrix hydrogel was shown to have native capability as an effective reactive oxygen species scavenger and protect against oxidative stress induced cell cycle inhibition in vitro. Encapsulation of cardiomyocytes demonstrated an enhanced turnover in in vitro studies, and in vivo assessments of myocardial matrix hydrogel treatment post-MI showed increased thymidine analog uptake in cardiomyocyte nuclei compared to saline controls. Overall, this study provides evidence that properties of the myocardial matrix material provide a microenvironment mitigating oxidative damage and supportive of cardiomyocytes undergoing DNA synthesis, toward possible DNA repair or cell cycle activation. STATEMENT OF SIGNIFICANCE: Loss of adult mammalian cardiomyocyte turnover is influenced by shifts in oxidative damage, which represents a potential mechanism for improving restoration of cardiac muscle after myocardial infarction (MI). Injection of a myocardial matrix hydrogel into the heart post-MI previously demonstrated increased cardiac muscle and promotion of pathways associated with cardiac development, suggesting potential in promoting proliferation of cardiomyocytes. In this study, the myocardial matrix hydrogel was shown to protect cells from oxidative stress and increase proliferation in vitro. In a rat MI model, greater presence of tissue free thiol content spared from oxidative damage, lesser mitochondrial superoxide content, and increased thymidine analog uptake in cardiomyocytes was found in matrix injected animals compared to saline controls. Overall, this study provides evidence that properties of the myocardial matrix material provide a microenvironment supportive of cardiomyocytes undergoing DNA synthesis, toward possible DNA repair or cell cycle activation.
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Affiliation(s)
- Raymond M Wang
- Department of Bioengineering and Sanford Consortium of Regenerative Medicine, University of California San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Joshua M Mesfin
- Department of Bioengineering and Sanford Consortium of Regenerative Medicine, University of California San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Jervaughn Hunter
- Department of Bioengineering and Sanford Consortium of Regenerative Medicine, University of California San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Paola Cattaneo
- Department of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; Institute of Genetics and Biomedical Research (Milan Unit), National Research Council of Italy, 20189 Rozzano, MI, Italy
| | - Nuno Guimarães-Camboa
- Department of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA; Institute of Cardiovascular Regeneration, Goethe University, Frankfurt 60590, Germany
| | - Rebecca L Braden
- Department of Bioengineering and Sanford Consortium of Regenerative Medicine, University of California San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Colin Luo
- Department of Bioengineering and Sanford Consortium of Regenerative Medicine, University of California San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Sylvia Evans
- Department of Medicine and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Karen L Christman
- Department of Bioengineering and Sanford Consortium of Regenerative Medicine, University of California San Diego, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA..
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4
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Murdock MH, Hussey GS, Chang JT, Hill RC, Nascari DG, Rao AV, Hansen KC, Foley LM, Hitchens TK, Amankulor NM, Badylak SF. A liquid fraction of extracellular matrix inhibits glioma cell viability in vitro and in vivo. Oncotarget 2022; 13:426-438. [PMID: 35198102 PMCID: PMC8860176 DOI: 10.18632/oncotarget.28203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 02/07/2022] [Indexed: 12/04/2022] Open
Abstract
Suppressive effects of extracellular matrix (ECM) upon various cancers have been reported. Glioblastoma multiforme has poor prognosis and new therapies are desired. This work investigated the effects of a saline-soluble fraction of urinary bladder ECM (ECM-SF) upon glioma cells. Viability at 24 hours in 1, 5, or 10 mg/mL ECM-SF-spiked media was evaluated in primary glioma cells (0319, 1015, 1119), glioma cell lines (A172, T98G, U87MG, C6), and brain cell lines (HCN-2, HMC3). Viability universally decreased at 5 and 10 mg/mL with U87MG, HCN-2, and HCM3 being least sensitive. Apoptosis in 0319 and 1119 cells was confirmed via NucView 488. Bi-weekly intravenous injection of ECM-SF (120 mg/kg) for 10 weeks in Sprague-Dawley rats did not affect weight, temperature, complete blood count, or multi-organ histology (N = 5). Intratumoral injection of ECM-SF (10 uL of 30 mg/mL) at weeks 2–4 post C6 inoculation in Wistar rats increased median survival from 24.5 to 51 days (hazard ratio for death 0.22) and decreased average tumor volume at time of death from 349 mm3 to 90 mm3 over 10 weeks (N = 6). Mass spectrometry identified 2,562 protein species in ECM-SF, parent ECM, and originating tissue. These results demonstrate the suppressive effects of ECM on glioma and warrant further study.
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Affiliation(s)
- Mark H. Murdock
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - George S. Hussey
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jordan T. Chang
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan C. Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, USA
| | - David G. Nascari
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aparna V. Rao
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, USA
| | - Lesley M. Foley
- Animal Imaging Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - T. Kevin Hitchens
- Animal Imaging Center, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nduka M. Amankulor
- Department of Neurological Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stephen F. Badylak
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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Guarino AL, Hill RC, Cardoso R, Donadeu X. Letter to the editor. Domest Anim Endocrinol 2021; 77:106629. [PMID: 34051470 DOI: 10.1016/j.domaniend.2021.106629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/01/2021] [Indexed: 11/16/2022]
Affiliation(s)
- A L Guarino
- University of Florida Small Animal Hospital, 2015 SW 16th Ave, Gainesville, FL 32610-0126, USA.
| | - R C Hill
- University of Florida Small Animal Hospital, 2015 SW 16th Ave, Gainesville, FL 32610-0126, USA
| | - R Cardoso
- University of Florida Small Animal Hospital, 2015 SW 16th Ave, Gainesville, FL 32610-0126, USA
| | - X Donadeu
- University of Florida Small Animal Hospital, 2015 SW 16th Ave, Gainesville, FL 32610-0126, USA
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Reed B, Crawford F, Hill RC, Jin N, White J, Krovi SH, Marrack P, Hansen K, Kappler JW. Lysosomal cathepsin creates chimeric epitopes for diabetogenic CD4 T cells via transpeptidation. J Exp Med 2021; 218:211485. [PMID: 33095259 PMCID: PMC7590512 DOI: 10.1084/jem.20192135] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 08/06/2020] [Accepted: 09/10/2020] [Indexed: 01/15/2023] Open
Abstract
The identification of the peptide epitopes presented by major histocompatibility complex class II (MHCII) molecules that drive the CD4 T cell component of autoimmune diseases has presented a formidable challenge over several decades. In type 1 diabetes (T1D), recent insight into this problem has come from the realization that several of the important epitopes are not directly processed from a protein source, but rather pieced together by fusion of different peptide fragments of secretory granule proteins to create new chimeric epitopes. We have proposed that this fusion is performed by a reverse proteolysis reaction called transpeptidation, occurring during the catabolic turnover of pancreatic proteins when secretory granules fuse with lysosomes (crinophagy). Here, we demonstrate several highly antigenic chimeric epitopes for diabetogenic CD4 T cells that are produced by digestion of the appropriate inactive fragments of the granule proteins with the lysosomal protease cathepsin L (Cat-L). This pathway has implications for how self-tolerance can be broken peripherally in T1D and other autoimmune diseases.
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Affiliation(s)
- Brendan Reed
- Department of Biomedical Research, National Jewish Health, Denver, CO.,Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, CO.,Research Division, Barbara Davis Center for Diabetes, Anschutz Medical Campus, University of Colorado, Aurora, CO
| | - Frances Crawford
- Department of Biomedical Research, National Jewish Health, Denver, CO
| | - Ryan C Hill
- Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado, Aurora, CO
| | - Niyun Jin
- Department of Biomedical Research, National Jewish Health, Denver, CO.,Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, CO.,Research Division, Barbara Davis Center for Diabetes, Anschutz Medical Campus, University of Colorado, Aurora, CO
| | - Janice White
- Department of Biomedical Research, National Jewish Health, Denver, CO
| | - S Harsha Krovi
- Department of Biomedical Research, National Jewish Health, Denver, CO.,Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, CO
| | - Philippa Marrack
- Department of Biomedical Research, National Jewish Health, Denver, CO.,Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, CO.,Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado, Aurora, CO
| | - Kirk Hansen
- Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado, Aurora, CO
| | - John W Kappler
- Department of Biomedical Research, National Jewish Health, Denver, CO.,Department of Immunology and Microbiology, Anschutz Medical Campus, University of Colorado, Aurora, CO.,Research Division, Barbara Davis Center for Diabetes, Anschutz Medical Campus, University of Colorado, Aurora, CO.,Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado, Aurora, CO
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Syedain ZH, Haynie B, Johnson SL, Lahti M, Berry J, Carney JP, Li J, Hill RC, Hansen KC, Thrivikraman G, Bianco R, Tranquillo RT. Pediatric tri-tube valved conduits made from fibroblast-produced extracellular matrix evaluated over 52 weeks in growing lambs. Sci Transl Med 2021; 13:13/585/eabb7225. [PMID: 33731437 DOI: 10.1126/scitranslmed.abb7225] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 12/07/2020] [Accepted: 02/26/2021] [Indexed: 12/18/2022]
Abstract
There is a need for replacement heart valves that can grow with children. We fabricated tubes of fibroblast-derived collagenous matrix that have been shown to regenerate and grow as a pulmonary artery replacement in lambs and implemented a design for a valved conduit consisting of three tubes sewn together. Seven lambs were implanted with tri-tube valved conduits in sequential cohorts and compared to bioprosthetic conduits. Valves implanted into the pulmonary artery of two lambs of the first cohort of four animals functioned with mild regurgitation and systolic pressure drops <10 mmHg up to 52 weeks after implantation, during which the valve diameter increased from 19 mm to a physiologically normal ~25 mm. In a second cohort, the valve design was modified to include an additional tube, creating a sleeve around the tri-tube valve to counteract faster root growth relative to the leaflets. Two valves exhibited trivial-to-mild regurgitation at 52 weeks with similar diameter increases to ~25 mm and systolic pressure drops of <5 mmHg, whereas the third valve showed similar findings until moderate regurgitation was observed at 52 weeks, correlating to hyperincrease in the valve diameter. In all explanted valves, the leaflets contained interstitial cells and an endothelium progressing from the base of the leaflets and remained thin and pliable with sparse, punctate microcalcifications. The tri-tube valves demonstrated reduced calcification and improved hemodynamic function compared to clinically used pediatric bioprosthetic valves tested in the same model. This tri-tube valved conduit has potential for long-term valve growth in children.
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Affiliation(s)
- Zeeshan H Syedain
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Sandra L Johnson
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Matthew Lahti
- Experimental Surgical Services, University of Minnesota, Minneapolis, MN 55455, USA
| | - James Berry
- Experimental Surgical Services, University of Minnesota, Minneapolis, MN 55455, USA
| | - John P Carney
- Experimental Surgical Services, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jirong Li
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado-Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado-Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Greeshma Thrivikraman
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Richard Bianco
- Experimental Surgical Services, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert T Tranquillo
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN 55455, USA. .,Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
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Percival SJ, Russo S, Priest C, Hill RC, Ohlhausen JA, Small LJ, Rempe SB, Spoerke ED. Bio-inspired incorporation of phenylalanine enhances ionic selectivity in layer-by-layer deposited polyelectrolyte films. Soft Matter 2021; 17:6315-6325. [PMID: 33982047 DOI: 10.1039/d1sm00134e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The addition of a common amino acid, phenylalanine, to a Layer-by-Layer (LbL) deposited polyelectrolyte (PE) film on a nanoporous membrane can increase its ionic selectivity over a PE film without the added amino acid. The addition of phenylalanine is inspired by detailed knowledge of the structure of the channelrhodopsins family of protein ion channels, where phenylalanine plays an instrumental role in facilitating sodium ion transport. The normally deposited and crosslinked PE films increase the cationic selectivity of a support membrane in a controllable manner where higher selectivity is achieved with thicker PE coatings, which in turn also increases the ionic resistance of the membrane. The increased ionic selectivity is desired while the increased resistance is not. We show that through incorporation of phenylalanine during the LbL deposition process, in solutions of NaCl with concentrations ranging from 0.1 to 100 mM, the ionic selectivity can be increased independently of the membrane resistance. Specifically, the addition is shown to increase the cationic transference of the PE films from 81.4% to 86.4%, an increase on par with PE films that are nearly triple the thickness while exhibiting much lower resistance compared to the thicker coatings, where the phenylalanine incorporated PE films display an area specific resistance of 1.81 Ω cm2 in 100 mM NaCl while much thicker PE membranes show a higher resistance of 2.75 Ω cm2 in the same 100 mM NaCl solution.
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Affiliation(s)
- Stephen J Percival
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Sara Russo
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Chad Priest
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Ryan C Hill
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - James A Ohlhausen
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Leo J Small
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Susan B Rempe
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
| | - Erik D Spoerke
- Sandia National Laboratories, PO Box 5800, MS 1411, Albuquerque, NM 87185, USA.
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9
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McCabe MC, Schmitt LR, Hill RC, Dzieciatkowska M, Maslanka M, Daamen WF, van Kuppevelt TH, Hof DJ, Hansen KC. Evaluation and Refinement of Sample Preparation Methods for Extracellular Matrix Proteome Coverage. Mol Cell Proteomics 2021; 20:100079. [PMID: 33845168 PMCID: PMC8188056 DOI: 10.1016/j.mcpro.2021.100079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 12/17/2022] Open
Abstract
The extracellular matrix is a key component of tissues, yet it is underrepresented in proteomic datasets. Identification and evaluation of proteins in the extracellular matrix (ECM) has proved challenging due to the insolubility of many ECM proteins in traditional protein extraction buffers. Here we separate the decellularization and ECM extraction steps of several prominent methods for evaluation under real-world conditions. The results are used to optimize a two-fraction ECM extraction method. Approximately one dozen additional parameters are tested, and recommendations for analysis based on overall ECM coverage or specific ECM classes are given. Compared with a standard in-solution digest, the optimized method yielded a fourfold improvement in unique ECM peptide identifications.
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Affiliation(s)
- Maxwell C McCabe
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Lauren R Schmitt
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA; Cancer Center Proteomics Core, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA; Cancer Center Proteomics Core, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Mark Maslanka
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA; Cancer Center Proteomics Core, School of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Willeke F Daamen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Toin H van Kuppevelt
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Danique J Hof
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, Colorado, USA; Cancer Center Proteomics Core, School of Medicine, University of Colorado, Aurora, Colorado, USA.
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10
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Diaz MD, Tran E, Spang M, Wang R, Gaetani R, Luo CG, Braden R, Hill RC, Hansen KC, DeMaria AN, Christman KL. Injectable Myocardial Matrix Hydrogel Mitigates Negative Left Ventricular Remodeling in a Chronic Myocardial Infarction Model. JACC Basic Transl Sci 2021; 6:350-361. [PMID: 33997521 PMCID: PMC8093531 DOI: 10.1016/j.jacbts.2021.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/04/2021] [Accepted: 01/04/2021] [Indexed: 12/12/2022]
Abstract
Myocardial matrix hydrogel preserves LV volumes and apical wall thickening in a chronic MI model. Myocardial matrix hydrogel trends toward reduced fibrosis. In vivo differential gene expression analysis shows the matrix modulates cardiac muscle contraction, metabolism, fibrosis, and the inflammatory/immune response in a chronic MI model.
A first-in-man clinical study on a myocardial-derived decellularized extracellular matrix hydrogel suggested the potential for efficacy in chronic myocardial infarction (MI) patients. However, little is understood about the mechanism of action in chronic MI. In this study, the authors investigated the efficacy and mechanism by which the myocardial matrix hydrogel can mitigate negative left ventricular (LV) remodeling in a rat chronic MI model. Assessment of cardiac function via magnetic resonance imaging demonstrated preservation of LV volumes and apical wall thickening. Differential gene expression analyses showed the matrix is able to prevent further negative LV remodeling in the chronic MI model through modulation of the immune response, down-regulation of pathways involved in heart failure progression and fibrosis, and up-regulation of genes important for cardiac muscle contraction.
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Key Words
- CMR, cardiac magnetic resonance
- ECM, extracellular matrix
- EDV, end-diastolic volume
- EF, ejection fraction
- ESV, end-systolic volume
- HF, heart failure
- IHC, immunohistochemistry
- KEGG, Kyoto Encyclopedia of Genes and Genomes
- LV, left ventricular
- MI, myocardial infarction
- MS, mass spectrometry
- QconCAT, quantitative concatamer
- biomaterials
- chronic inflammation
- chronic myocardial infarction
- gene expression
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Affiliation(s)
- Miranda D Diaz
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, California, USA
| | - Elaine Tran
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, California, USA
| | - Martin Spang
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, California, USA
| | - Raymond Wang
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, California, USA
| | - Roberto Gaetani
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, California, USA.,Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Colin G Luo
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, California, USA
| | - Rebecca Braden
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, California, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado, Aurora, Colorado, USA
| | - Anthony N DeMaria
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Karen L Christman
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.,Sanford Consortium for Regenerative Medicine, La Jolla, California, USA
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11
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Wang Y, Hu G, Hill RC, Dzieciatkowska M, Hansen KC, Zhang XB, Yan Z, Pei M. Matrix reverses immortalization-mediated stem cell fate determination. Biomaterials 2021; 265:120387. [PMID: 32987274 PMCID: PMC7944411 DOI: 10.1016/j.biomaterials.2020.120387] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/24/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022]
Abstract
Primary cell culture in vitro suffers from cellular senescence. We hypothesized that expansion on decellularized extracellular matrix (dECM) deposited by simian virus 40 large T antigen (SV40LT) transduced autologous infrapatellar fat pad stem cells (IPFSCs) could rejuvenate high-passage IPFSCs in both proliferation and chondrogenic differentiation. In the study, we found that SV40LT transduced IPFSCs exhibited increased proliferation and adipogenic potential but decreased chondrogenic potential. Expansion on dECMs deposited by passage 5 IPFSCs yielded IPFSCs with dramatically increased proliferation and chondrogenic differentiation capacity; however, this enhanced capacity diminished if IPFSCs were grown on dECM deposited by passage 15 IPFSCs. Interestingly, expansion on dECM deposited by SV40LT transduced IPFSCs yielded IPFSCs with enhanced proliferation and chondrogenic capacity but decreased adipogenic potential, particularly for the dECM group derived from SV40LT transduced passage 15 cells. Our immunofluorescence staining and proteomics data identify matrix components such as basement membrane proteins as top candidates for matrix mediated IPFSC rejuvenation. Both cell proliferation and differentiation were endorsed by transcripts measured by RNASeq during the process. This study provides a promising model for in-depth investigation of the matrix protein influence on surrounding stem cell differentiation.
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Affiliation(s)
- Yiming Wang
- Stem Cell and Tissue Engineering Laboratory, Department of Orthopaedics, West Virginia University, Morgantown, WV, USA; Department of Orthopaedics, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Gangqing Hu
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV, USA; Bioinformatics Core, West Virginia University, Morgantown, WV, USA
| | - Ryan C Hill
- Department of Biochemistry & Molecular Genetics, University of Colorado Denver, Aurora, CO, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry & Molecular Genetics, University of Colorado Denver, Aurora, CO, USA
| | - Kirk C Hansen
- Department of Biochemistry & Molecular Genetics, University of Colorado Denver, Aurora, CO, USA
| | - Xiao-Bing Zhang
- State Key Laboratory of Experimental Hematology, Tianjin, China; Department of Medicine, Loma Linda University, Loma Linda, CA, USA.
| | - Zuoqin Yan
- Department of Orthopaedics, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Ming Pei
- Stem Cell and Tissue Engineering Laboratory, Department of Orthopaedics, West Virginia University, Morgantown, WV, USA; WVU Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, USA.
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12
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D’Alessandro A, Thomas T, Dzieciatkowska M, Hill RC, O Francis R, Hudson KE, Zimring JC, Hod EA, Spitalnik SL, Hansen KC. Serum Proteomics in COVID-19 Patients: Altered Coagulation and Complement Status as a Function of IL-6 Level. J Proteome Res 2020; 19:4417-4427. [PMID: 32786691 PMCID: PMC7640953 DOI: 10.1021/acs.jproteome.0c00365] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 01/08/2023]
Abstract
Over 5 million people around the world have tested positive for the beta coronavirus SARS-CoV-2 as of May 29, 2020, a third of which are in the United States alone. These infections are associated with the development of a disease known as COVID-19, which is characterized by several symptoms, including persistent dry cough, shortness of breath, chills, muscle pain, headache, loss of taste or smell, and gastrointestinal distress. COVID-19 has been characterized by elevated mortality (over 100 thousand people have already died in the US alone), mostly due to thromboinflammatory complications that impair lung perfusion and systemic oxygenation in the most severe cases. While the levels of pro-inflammatory cytokines such as interleukin-6 (IL-6) have been associated with the severity of the disease, little is known about the impact of IL-6 levels on the proteome of COVID-19 patients. The present study provides the first proteomics analysis of sera from COVID-19 patients, stratified by circulating levels of IL-6, and correlated to markers of inflammation and renal function. As a function of IL-6 levels, we identified significant dysregulation in serum levels of various coagulation factors, accompanied by increased levels of antifibrinolytic components, including several serine protease inhibitors (SERPINs). These were accompanied by up-regulation of the complement cascade and antimicrobial enzymes, especially in subjects with the highest levels of IL-6, which is consistent with an exacerbation of the acute phase response in these subjects. Although our results are observational, they highlight a clear increase in the levels of inhibitory components of the fibrinolytic cascade in severe COVID-19 disease, providing potential clues related to the etiology of coagulopathic complications in COVID-19 and paving the way for potential therapeutic interventions, such as the use of pro-fibrinolytic agents. Raw data for this study are available through ProteomeXchange with identifier PXD020601.
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Affiliation(s)
- Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, Aurora, CO, USA
| | - Tiffany Thomas
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, Aurora, CO, USA
| | - Ryan C. Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, Aurora, CO, USA
| | - Richard O Francis
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Krystalyn E. Hudson
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - James C. Zimring
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Eldad A. Hod
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Steven L. Spitalnik
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, Aurora, CO, USA
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13
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Thomas T, Stefanoni D, Dzieciatkowska M, Issaian A, Nemkov T, Hill RC, Francis RO, Hudson KE, Buehler PW, Zimring JC, Hod EA, Hansen KC, Spitalnik SL, D’Alessandro A. Evidence of Structural Protein Damage and Membrane Lipid Remodeling in Red Blood Cells from COVID-19 Patients. J Proteome Res 2020; 19:4455-4469. [PMID: 33103907 PMCID: PMC7640979 DOI: 10.1021/acs.jproteome.0c00606] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Indexed: 12/13/2022]
Abstract
The SARS-CoV-2 beta coronavirus is the etiological driver of COVID-19 disease, which is primarily characterized by shortness of breath, persistent dry cough, and fever. Because they transport oxygen, red blood cells (RBCs) may play a role in the severity of hypoxemia in COVID-19 patients. The present study combines state-of-the-art metabolomics, proteomics, and lipidomics approaches to investigate the impact of COVID-19 on RBCs from 23 healthy subjects and 29 molecularly diagnosed COVID-19 patients. RBCs from COVID-19 patients had increased levels of glycolytic intermediates, accompanied by oxidation and fragmentation of ankyrin, spectrin beta, and the N-terminal cytosolic domain of band 3 (AE1). Significantly altered lipid metabolism was also observed, in particular, short- and medium-chain saturated fatty acids, acyl-carnitines, and sphingolipids. Nonetheless, there were no alterations of clinical hematological parameters, such as RBC count, hematocrit, or mean corpuscular hemoglobin concentration, with only minor increases in mean corpuscular volume. Taken together, these results suggest a significant impact of SARS-CoV-2 infection on RBC structural membrane homeostasis at the protein and lipid levels. Increases in RBC glycolytic metabolites are consistent with a theoretically improved capacity of hemoglobin to off-load oxygen as a function of allosteric modulation by high-energy phosphate compounds, perhaps to counteract COVID-19-induced hypoxia. Conversely, because the N-terminus of AE1 stabilizes deoxyhemoglobin and finely tunes oxygen off-loading and metabolic rewiring toward the hexose monophosphate shunt, RBCs from COVID-19 patients may be less capable of responding to environmental variations in hemoglobin oxygen saturation/oxidant stress when traveling from the lungs to peripheral capillaries and vice versa.
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Affiliation(s)
- Tiffany Thomas
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Davide Stefanoni
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, Aurora, CO, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, Aurora, CO, USA
| | - Aaron Issaian
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, Aurora, CO, USA
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, Aurora, CO, USA
| | - Ryan C. Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, Aurora, CO, USA
| | - Richard O Francis
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Krystalyn E. Hudson
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Paul W. Buehler
- Department of Pathology, University of Maryland, Baltimore, MD, USA
| | - James C. Zimring
- Department of Pathology, University of Virginia, Charlottesville, VA, USA
| | - Eldad A. Hod
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, Aurora, CO, USA
| | - Steven L. Spitalnik
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, Aurora, CO, USA
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14
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Naranjo JD, Saldin LT, Sobieski E, Quijano LM, Hill RC, Chan PG, Torres C, Dziki JL, Cramer MC, Lee YC, Das R, Bajwa AK, Nossair R, Klimak M, Marchal L, Patel S, Velankar SS, Hansen KC, McGrath K, Badylak SF. Esophageal extracellular matrix hydrogel mitigates metaplastic change in a dog model of Barrett's esophagus. Sci Adv 2020; 6:eaba4526. [PMID: 32656339 PMCID: PMC7329334 DOI: 10.1126/sciadv.aba4526] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/16/2020] [Indexed: 05/17/2023]
Abstract
Chronic inflammatory gastric reflux alters the esophageal microenvironment and induces metaplastic transformation of the epithelium, a precancerous condition termed Barrett's esophagus (BE). The microenvironmental niche, which includes the extracellular matrix (ECM), substantially influences cell phenotype. ECM harvested from normal porcine esophageal mucosa (eECM) was formulated as a mucoadhesive hydrogel, and shown to largely retain basement membrane and matrix-cell adhesion proteins. Dogs with BE were treated orally with eECM hydrogel and omeprazole (n = 6) or omeprazole alone (n = 2) for 30 days. eECM treatment resolved esophagitis, reverted metaplasia to a normal, squamous epithelium in four of six animals, and downregulated the pro-inflammatory tumor necrosis factor-α+ cell infiltrate compared to control animals. The metaplastic tissue in control animals (n = 2) did not regress. The results suggest that in vivo alteration of the microenvironment with a site-appropriate, mucoadhesive ECM hydrogel can mitigate the inflammatory and metaplastic response in a dog model of BE.
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Affiliation(s)
- Juan Diego Naranjo
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Lindsey T. Saldin
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Eric Sobieski
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Lina M. Quijano
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Ryan C. Hill
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Patrick G. Chan
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Cardiothoracic Surgery, UPMC, Pittsburgh, PA 15213, USA
| | - Crisanto Torres
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Cardiothoracic Surgery, UPMC, Pittsburgh, PA 15213, USA
| | - Jenna L. Dziki
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Madeline C. Cramer
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yoojin C. Lee
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Rohit Das
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, UPMC, Pittsburgh, PA 15213, USA
| | - Anant K. Bajwa
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Rania Nossair
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Molly Klimak
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Lucile Marchal
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Shil Patel
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Sachin S. Velankar
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Chemical Engineering, Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kevin McGrath
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, UPMC, Pittsburgh, PA 15213, USA
| | - Stephen F. Badylak
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
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15
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Thrivikraman G, Johnson SL, Syedain ZH, Hill RC, Hansen KC, Lee HS, Tranquillo RT. Biologically-engineered mechanical model of a calcified artery. Acta Biomater 2020; 110:164-174. [PMID: 32305446 DOI: 10.1016/j.actbio.2020.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 03/27/2020] [Accepted: 04/08/2020] [Indexed: 12/22/2022]
Abstract
Vascular calcification is a commonly occurring pathological process and is recognized as an independent prognostic marker for cardiovascular morbidity and mortality. Recent progress in developing novel therapies to modify vascular calcification is critically hampered due to the lack of reliable in vitro experimental models that recapitulate the structural and mechanical attributes of calcified arteries. In this study, we show the ability to model the behavior of diffuse vascular calcification in vitro using biologically-engineered grafts approximating the composition, structure, and mechanical properties of arteries. Transmural calcification was achieved by exposing the acellular grafts of collagenous ECM to complete medium containing elevated Calcium (Ca) and Phosphate (P) concentrations. It was found that increasing the serum concentration from 2% to 10% increased the extent and degree of calcification based on histochemical, ultrastructural, chemical and thermal analyses. The presence of variably-sized spherical calcific deposits within the matrix further confirmed its morphological similarity to pathologic calcification. Mechanical testing demonstrated up to a 16-fold decrease in compliance due to the calcification, consistent with prior reports for calcified arteries. The model developed thus has potential to improve the design and development of interventional devices and therapies for the diagnosis and treatment of arterial calcification. STATEMENT OF SIGNIFICANCE: The presence of extensive vascular calcification makes angiographic/interventional procedures difficult due to reduced arterial compliance. Current attempts to develop safe and effective non-surgical adjunctive techniques to treat calcified arteries are largely limited by the lack of a physiologically relevant testing platform that mimics the structural and mechanical features of vascular calcification. Herein, we developed an off-the-shelf calcified artery model, with the goal to accelerate the pre-clinical development of novel therapies for the management of arterial calcification. To the extent of our knowledge, this is the first report of an in vitro tissue-engineered model of diffuse arterial calcification.
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16
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Thomas T, Stefanoni D, Dzieciatkowska M, Issaian A, Nemkov T, Hill RC, Francis RO, Hudson KE, Buehler PW, Zimring JC, Hod EA, Hansen KC, Spitalnik SL, D'Alessandro A. Evidence for structural protein damage and membrane lipid remodeling in red blood cells from COVID-19 patients. medRxiv 2020. [PMID: 32637980 DOI: 10.1101/2020.06.29.20142703] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The SARS-CoV-2 beta coronavirus is the etiological driver of COVID-19 disease, which is primarily characterized by shortness of breath, persistent dry cough, and fever. Because they transport oxygen, red blood cells (RBCs) may play a role in the severity of hypoxemia in COVID-19 patients. The present study combines state-of-the-art metabolomics, proteomics, and lipidomics approaches to investigate the impact of COVID-19 on RBCs from 23 healthy subjects and 29 molecularly-diagnosed COVID-19 patients. RBCs from COVID-19 patients had increased levels of glycolytic intermediates, accompanied by oxidation and fragmentation of ankyrin, spectrin beta, and the N-terminal cytosolic domain of band 3 (AE1). Significantly altered lipid metabolism was also observed, especially short and medium chain saturated fatty acids, acyl-carnitines, and sphingolipids. Nonetheless, there were no alterations of clinical hematological parameters, such as RBC count, hematocrit, and mean corpuscular hemoglobin concentration, with only minor increases in mean corpuscular volume. Taken together, these results suggest a significant impact of SARS-CoV-2 infection on RBC structural membrane homeostasis at the protein and lipid levels. Increases in RBC glycolytic metabolites are consistent with a theoretically improved capacity of hemoglobin to off-load oxygen as a function of allosteric modulation by high-energy phosphate compounds, perhaps to counteract COVID-19-induced hypoxia. Conversely, because the N-terminus of AE1 stabilizes deoxyhemoglobin and finely tunes oxygen off-loading, RBCs from COVID-19 patients may be incapable of responding to environmental variations in hemoglobin oxygen saturation when traveling from the lungs to peripheral capillaries and, as such, may have a compromised capacity to transport and deliver oxygen.
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17
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Holditch SJ, Brown CN, Atwood DJ, Pokhrel D, Brown SE, Lombardi AM, Nguyen KN, Hill RC, Lanaspa M, Hopp K, Weiser-Evans MCM, Edelstein CL. The consequences of increased 4E-BP1 in polycystic kidney disease. Hum Mol Genet 2020; 28:4132-4147. [PMID: 31646342 DOI: 10.1093/hmg/ddz244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/28/2019] [Accepted: 09/25/2019] [Indexed: 01/02/2023] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common hereditary renal disease, characterized by cyst formation and growth. Hyperproliferation is a major contributor to cyst growth. At the nexus of regulating proliferation, is 4E-BP1. We demonstrate that ADPKD mouse and rat models, ADPKD patient renal biopsies and PKD1-/- cells exhibited hyperphosphorylated 4E-BP1, a biomarker of increased translation and proliferation. We hypothesized that expression of constitutively active 4E-BP1 constructs (4E-BP1F113A and 4E-BP1R13AF113A) would decrease proliferation and reduce cyst expansion. Utilizing the Pkd1RC/RC mouse, we determined the effect of 4E-BP1F113A on PKD. Unexpectedly, 4E-BP1F113A resulted in increased cyst burden and suppressed apoptosis markers, increased anti-apoptotic Bcl-2 protein and increased mitochondrial proteins. Exogenous 4E-BP1 enhanced proliferation, decreased apoptosis, increased anti-apoptotic Bcl-2 protein, impaired NADPH oxidoreductase activity, increased mitochondrial proteins and increased superoxide production in PKD patient-derived renal epithelial cells. Reduced 4E-BP1 expression suppressed proliferation, restored apoptosis and improved cellular metabolism. These findings provide insight into how cyst-lining cells respond to 4E-BP1.
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Affiliation(s)
- Sara J Holditch
- Division of Renal Diseases and Hypertension, University of Colorado at Denver, Denver, CO, USA
| | - Carolyn N Brown
- Division of Renal Diseases and Hypertension, University of Colorado at Denver, Denver, CO, USA
| | - Daniel J Atwood
- Division of Renal Diseases and Hypertension, University of Colorado at Denver, Denver, CO, USA
| | - Deepak Pokhrel
- Division of Renal Diseases and Hypertension, University of Colorado at Denver, Denver, CO, USA
| | - Sara E Brown
- Division of Renal Diseases and Hypertension, University of Colorado at Denver, Denver, CO, USA
| | - Andrew M Lombardi
- Division of Renal Diseases and Hypertension, University of Colorado at Denver, Denver, CO, USA
| | - Khoa N Nguyen
- Division of Renal Diseases and Hypertension, University of Colorado at Denver, Denver, CO, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Miguel Lanaspa
- Division of Renal Diseases and Hypertension, University of Colorado at Denver, Denver, CO, USA
| | - Katharina Hopp
- Division of Renal Diseases and Hypertension, University of Colorado at Denver, Denver, CO, USA
| | - Mary C M Weiser-Evans
- Division of Renal Diseases and Hypertension, University of Colorado at Denver, Denver, CO, USA
| | - Charles L Edelstein
- Division of Renal Diseases and Hypertension, University of Colorado at Denver, Denver, CO, USA
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18
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McCabe MC, Hill RC, Calderone K, Cui Y, Yan Y, Quan T, Fisher GJ, Hansen KC. Alterations in extracellular matrix composition during aging and photoaging of the skin. Matrix Biol Plus 2020; 8:100041. [PMID: 33543036 PMCID: PMC7852213 DOI: 10.1016/j.mbplus.2020.100041] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 04/02/2020] [Accepted: 06/05/2020] [Indexed: 02/07/2023] Open
Abstract
Human skin is composed of the cell-rich epidermis, the extracellular matrix (ECM) rich dermis, and the hypodermis. Within the dermis, a dense network of ECM proteins provides structural support to the skin and regulates a wide variety of signaling pathways which govern cell proliferation and other critical processes. Both intrinsic aging, which occurs steadily over time, and extrinsic aging (photoaging), which occurs as a result of external insults such as solar radiation, cause alterations to the dermal ECM. In this study, we utilized both quantitative and global proteomics, alongside single harmonic generation (SHG) and two-photon autofluorescence (TPAF) imaging, to assess changes in dermal composition during intrinsic and extrinsic aging. We find that both intrinsic and extrinsic aging result in significant decreases in ECM-supporting proteoglycans and structural ECM integrity, evidenced by decreasing collagen abundance and increasing fibril fragmentation. Intrinsic aging also produces changes distinct from those produced by photoaging, including reductions in elastic fiber and crosslinking enzyme abundance. In contrast, photoaging is primarily defined by increases in elastic fiber-associated protein and pro-inflammatory proteases. Changes associated with photoaging are evident even in young (mid 20s) sun-exposed forearm skin, indicating that proteomic evidence of photoaging is present decades prior to clinical signs of photoaging. GO term enrichment revealed that both intrinsic aging and photoaging share common features of chronic inflammation. The proteomic data has been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD015982. Intrinsic aging and photoaging both decrease ECM-supporting proteoglycans and structural ECM. Intrinsic aging produces reductions in elastic fiber and crosslinking enzyme abundance. Photoaging results in increases in pro-inflammatory proteases and elastic fiber abundance. Intrinsic aging and photoaging share common features associated with chronic inflammation. Proteomic changes associated with photoaging are evident decades prior to clinical aging signs.
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Key Words
- AUC, area under the curve
- Aging
- CE, cornified envelope
- CNBr, cyanogen bromide
- Collagen
- ECM, extracellular matrix
- Extracellular matrix
- GO, gene ontology
- Photoaging
- Proteomics
- QconCATs, quantitative concatemers
- SHG, single harmonic generation
- Skin
- TPAF, two-photon autofluorescence
- UV, ultraviolet
- iECM, insoluble ECM
- sECM, soluble ECM
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Affiliation(s)
- Maxwell C. McCabe
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Ryan C. Hill
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, 12801 E 17th Ave., Aurora, CO 80045, USA
| | - Kenneth Calderone
- Department of Dermatology, University of Michigan, 1150 W. Medical Center Drive, Medical Science I R6447, Ann Arbor, MI 48109, USA
| | - Yilei Cui
- Department of Dermatology, University of Michigan, 1150 W. Medical Center Drive, Medical Science I R6447, Ann Arbor, MI 48109, USA
| | - Yan Yan
- Department of Dermatology, University of Michigan, 1150 W. Medical Center Drive, Medical Science I R6447, Ann Arbor, MI 48109, USA
| | - Taihao Quan
- Department of Dermatology, University of Michigan, 1150 W. Medical Center Drive, Medical Science I R6447, Ann Arbor, MI 48109, USA
| | - Gary J. Fisher
- Department of Dermatology, University of Michigan, 1150 W. Medical Center Drive, Medical Science I R6447, Ann Arbor, MI 48109, USA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, 12801 E 17th Ave., Aurora, CO 80045, USA
- Corresponding author.
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19
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Wang T, Hill RC, Dzieciatkowska M, Zhu L, Infante AM, Hu G, Hansen KC, Pei M. Site-Dependent Lineage Preference of Adipose Stem Cells. Front Cell Dev Biol 2020; 8:237. [PMID: 32351957 PMCID: PMC7174673 DOI: 10.3389/fcell.2020.00237] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/20/2020] [Indexed: 12/15/2022] Open
Abstract
Adult stem cells have unique properties in both proliferation and differentiation preference. In this study, we hypothesized that adipose stem cells have a depot-dependent lineage preference. Four rabbits were used to provide donor-matched adipose stem cells from either subcutaneous adipose tissue (ScAT) or infrapatellar fat pad (IPFP). Proliferation and multi-lineage differentiation were evaluated in adipose stem cells from donor-matched ScAT and IPFP. RNA sequencing (RNA-seq) and proteomics were conducted to uncover potential molecular discrepancy in adipose stem cells and their corresponding matrix microenvironments. We found that stem cells from ScAT exhibited significantly higher proliferation and adipogenic capacity compared to those from donor-matched IPFP while stem cells from IPFP displayed significantly higher chondrogenic potential compared to those from donor-matched ScAT. Our findings are strongly endorsed by supportive data from transcriptome and proteomics analyses, indicating a site-dependent lineage preference of adipose stem cells.
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Affiliation(s)
- Tingliang Wang
- Stem Cell and Tissue Engineering Laboratory, Department of Orthopedics, West Virginia University, Morgantown, WV, United States
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital Affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ryan C. Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, United States
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, United States
| | - Lian Zhu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People’s Hospital Affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aniello M. Infante
- Bioinformatics Core Facility, West Virginia University, Morgantown, WV, United States
| | - Gangqing Hu
- Bioinformatics Core Facility, West Virginia University, Morgantown, WV, United States
- Department of Microbiology, Immunology and Cell Biology, School of Medicine, West Virginia University, Morgantown, WV, United States
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, United States
| | - Ming Pei
- Stem Cell and Tissue Engineering Laboratory, Department of Orthopedics, West Virginia University, Morgantown, WV, United States
- WVU Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, United States
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20
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Tarullo SE, Hill RC, Hansen KC, Behbod F, Borges VF, Nelson AC, Lyons TR. Postpartum breast cancer progression is driven by semaphorin 7a-mediated invasion and survival. Oncogene 2020; 39:2772-2785. [PMID: 32020054 PMCID: PMC7103487 DOI: 10.1038/s41388-020-1192-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/13/2020] [Accepted: 01/24/2020] [Indexed: 11/09/2022]
Abstract
Young women diagnosed with breast cancer (BC) have poor prognosis due to increased rates of metastasis. In addition, women diagnosed within 10 years of most recent childbirth are approximately three times more likely to develop metastasis than age- and stage-matched nulliparous women. We define these cases as postpartum BC (PPBC) and propose that the unique biology of the postpartum mammary gland drives tumor progression. Our published results revealed roles for SEMA7A in breast tumor cell growth, motility, invasion, and tumor-associated lymphangiogenesis, all of which are also increased in preclinical models of PPBC. However, whether SEMA7A drives progression in PPBC remains largely unexplored. Our results presented herein show that silencing of SEMA7A decreases tumor growth in a model of PPBC, while overexpression is sufficient to increase growth in nulliparous hosts. Further, we show that SEMA7A promotes multiple known drivers of PPBC progression including tumor-associated COX-2 expression and fibroblast-mediated collagen deposition in the tumor microenvironment. In addition, we show for the first time that SEMA7A-expressing cells deposit fibronectin to promote tumor cell survival. Finally, we show that co-expression of SEMA7A/COX-2/FN predicts for poor prognosis in breast cancer patient cohorts. These studies suggest SEMA7A as a key mediator of BC progression, and that targeting SEMA7A may open avenues for novel therapeutic strategies.
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Affiliation(s)
- Sarah E Tarullo
- Division of Medical Oncology, Department of Medicine, CU Anschutz Medical Campus, Aurora, CO, 80045, USA
- Young Women's BC Translational Program, CU Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, CU Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, CU Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Fariba Behbod
- Division of Cancer and Developmental Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Virginia F Borges
- Division of Medical Oncology, Department of Medicine, CU Anschutz Medical Campus, Aurora, CO, 80045, USA
- Young Women's BC Translational Program, CU Anschutz Medical Campus, Aurora, CO, 80045, USA
- University of Colorado Cancer Center, Aurora, CO, 80045, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Traci R Lyons
- Division of Medical Oncology, Department of Medicine, CU Anschutz Medical Campus, Aurora, CO, 80045, USA.
- Young Women's BC Translational Program, CU Anschutz Medical Campus, Aurora, CO, 80045, USA.
- University of Colorado Cancer Center, Aurora, CO, 80045, USA.
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21
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Li J, Narayanan K, Zhang Y, Hill RC, He F, Hansen KC, Pei M. Role of lineage-specific matrix in stem cell chondrogenesis. Biomaterials 2019; 231:119681. [PMID: 31864016 DOI: 10.1016/j.biomaterials.2019.119681] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/06/2019] [Accepted: 12/11/2019] [Indexed: 12/12/2022]
Abstract
Cartilage repair in clinics is a challenge owing to the limited regenerative capacities of cartilage. Synovium-derived stem cells (SDSCs) are suggested as tissue-specific stem cells for chondrogenesis. In this study, we hypothesize that decellularized extracellular matrix (dECM) deposited by SDSCs could provide a superior tissue-specific matrix microenvironment for optimal rejuvenation of adult SDSCs for cartilage regeneration. dECMs were deposited by adult stem cells with varying chondrogenic capacities; SDSCs (strong) (SECM), adipose-derived stem cells (weak) (AECM) and dermal fibroblasts (weak) (DECM), and urine-derived stem cells (none) (UECM). Plastic flasks (Plastic) were used as a control substrate. Human SDSCs were expanded on the above substrates for one passage and examined for chondrogenic capacities. We found that each dECM consisted of unique matrix proteins and exhibited varied stiffnesses, which affected cell morphology and elasticity. Human SDSCs grown on dECMs displayed a significant increase in cell proliferation and unique surface phenotypes. Under induction media, dECM expanded cells yielded pellets with a dramatically increased number of chondrogenic markers. Interestingly, SECM expanded cells had less potential for hypertrophy compared to those grown on other dECMs, indicating that a tissue-specific matrix might provide a superior microenvironment for stem cell chondrogenic differentiation.
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Affiliation(s)
- Jingting Li
- Stem Cell and Tissue Engineering Laboratory, Department of Orthopaedics, West Virginia University, Morgantown, WV, 26506, USA; Department of Dermatology, Department of Cellular and Molecular Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Karthikeyan Narayanan
- Stem Cell and Tissue Engineering Laboratory, Department of Orthopaedics, West Virginia University, Morgantown, WV, 26506, USA; Department of Biochemistry, West Virginia University, Morgantown, WV, 26506, USA
| | - Ying Zhang
- Stem Cell and Tissue Engineering Laboratory, Department of Orthopaedics, West Virginia University, Morgantown, WV, 26506, USA; Key Laboratory of Precision Oncology of Shandong Higher Education, Institute of Precision Medicine, Jining Medical University, Jining, Shandong, 272067, China
| | - Ryan C Hill
- Department of Biochemistry & Molecular Genetics, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Fan He
- Orthopaedic Institute, Medical College, Soochow University, Suzhou, 215007, China
| | - Kirk C Hansen
- Department of Biochemistry & Molecular Genetics, University of Colorado Denver, Aurora, CO, 80045, USA
| | - Ming Pei
- Stem Cell and Tissue Engineering Laboratory, Department of Orthopaedics, West Virginia University, Morgantown, WV, 26506, USA; WVU Cancer Institute, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, WV, 26506, USA.
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22
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Agrawal K, Hill RC, Wilkinson BL, Allison PB, Thomas CE. Quantification of the anti-murine PD-1 monoclonal antibody RMP1-14 in BALB/c mouse plasma by liquid chromatography-tandem mass spectrometry and application to a pharmacokinetic study. Anal Bioanal Chem 2019; 412:739-752. [PMID: 31832706 DOI: 10.1007/s00216-019-02292-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 11/18/2019] [Indexed: 11/26/2022]
Abstract
RMP1-14 is a monoclonal antibody that targets the murine PD-1 protein, and has been used extensively to probe the effects of PD-1 inhibition in preclinical murine models. However, to date, no quantitative analytical methods have been published for RMP1-14. To evaluate its anti-tumor activity in BALB/c mice inoculated with CT26.WT murine colon cancer cells, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method to quantify RMP1-14 in BALB/c mouse K3EDTA plasma was developed and validated. The methodology used a signature peptide (GFYPPDIYTEWK) as a surrogate for RMP1-14 quantitation and an isotopically labeled analog of the signature peptide as the internal standard. Initial method development focused on a hybrid LC-MS/MS assay involving Protein G immunoprecipitation, but this strategy was abandoned due to lack of selectivity. The final validated method consisted of dilution with Tris-buffered saline, trypsin digestion, and desalting using micro solid-phase extraction. Analytical run time was 3.50 min, and the method demonstrated linearity between 0.500 and 50.0 μg/mL of intact RMP1-14. Accuracy, precision, and robustness were all acceptable, and the method was demonstrated to be comparable to a commercially available fit-for-purpose enzyme-linked immunosorbent assay (ELISA) capable of measuring RMP1-14. The validated method was used to generate pharmacokinetic parameters from tumor-bearing BALB/c mice dosed with RMP1-14 at either 2.50 or 7.50 mg/kg. Overall, the validated method represents a novel tool that can be used to evaluate RMP1-14 activity in future immuno-oncology studies.
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Affiliation(s)
- Karan Agrawal
- Covance Laboratories, Inc., 8211 SciCor Drive, Indianapolis, IN, 46214, USA.
| | - Ryan C Hill
- Covance Laboratories, Inc., 8211 SciCor Drive, Indianapolis, IN, 46214, USA
- Eli Lilly and Company, 893 Delaware Street, Indianapolis, IN, 46225, USA
| | - Brandy L Wilkinson
- Covance Laboratories, Inc., 671 South Meridian Road, Greenfield, IN, 46140, USA
- Explora BioLabs, 11175 Flintkote Avenue, Suite B, San Diego, CA, 92121, USA
| | - Patrick B Allison
- Covance Laboratories, Inc., 671 South Meridian Road, Greenfield, IN, 46140, USA
- MI Bioresearch, 800 Technology Drive, Ann Arbor, MI, 48108, USA
| | - C Eric Thomas
- Covance Laboratories, Inc., 8211 SciCor Drive, Indianapolis, IN, 46214, USA
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23
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Hernandez MJ, Yakutis GE, Zelus EI, Hill RC, Dzieciatkowska M, Hansen KC, Christman KL. Manufacturing considerations for producing and assessing decellularized extracellular matrix hydrogels. Methods 2019; 171:20-27. [PMID: 31546012 DOI: 10.1016/j.ymeth.2019.09.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 01/26/2023] Open
Abstract
Although several decellularized extracellular matrix (ECM) sheets or patches have been commercialized for use in the clinic, only one injectable decellularized ECM hydrogel, a decellularized myocardial matrix, has reached clinical trials. Consequently, very little information is available for established manufacturing standards or assessments of these materials. Here we present detailed methodology for investigating three parameters related to manufacturing optimization for a porcine derived skeletal muscle ECM hydrogel - animal-to-animal variability, bioburden reduction, and harvesting conditions. Results from characterization assays, including residual dsDNA content and sulfated glycosaminoglycan content, did not yield noteworthy differences amongst individual animals or following the addition of a bioburden reducing agent. However, the tissue collected under different harvesting conditions contained varying amounts of fat, and the protein compositions of the decellularized products differed, which could ultimately impact subsequent efficacy in vitro or in vivo. As decellularized ECM hydrogels continue to be evaluated for various applications, the differences between laboratory-scale and manufacturing-scale material batches should be thoroughly considered to avoid costly and timely optimization during scale-up.
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Affiliation(s)
- Melissa J Hernandez
- Department of Bioengineering, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Grace E Yakutis
- Department of Bioengineering, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Emma I Zelus
- Department of Bioengineering, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Karen L Christman
- Department of Bioengineering, Sanford Consortium for Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA.
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24
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Li X, Liu S, Zhang L, Issaian A, Hill RC, Espinosa S, Shi S, Cui Y, Kappel K, Das R, Hansen KC, Zhou ZH, Zhao R. A unified mechanism for intron and exon definition and back-splicing. Nature 2019; 573:375-380. [PMID: 31485080 PMCID: PMC6939996 DOI: 10.1038/s41586-019-1523-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 08/01/2019] [Indexed: 01/07/2023]
Abstract
The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E complex assembled on introns, providing a view of the earliest event in the splicing cycle that commits pre-mRNAs to splicing. The E complex architecture suggests that the same spliceosome can assemble across an exon, and that it either remodels to span an intron for canonical linear splicing (typically on short exons) or catalyses back-splicing to generate circular RNA (on long exons). The model is supported by our experiments, which show that an E complex assembled on the middle exon of yeast EFM5 or HMRA1 can be chased into circular RNA when the exon is sufficiently long. This simple model unifies intron definition, exon definition, and back-splicing through the same spliceosome in all eukaryotes and should inspire experiments in many other systems to understand the mechanism and regulation of these processes.
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Affiliation(s)
- Xueni Li
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Shiheng Liu
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA
- Electron Imaging Center for Nanomachines, UCLA, Los Angeles, CA, USA
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Aaron Issaian
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sara Espinosa
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Shasha Shi
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yanxiang Cui
- Electron Imaging Center for Nanomachines, UCLA, Los Angeles, CA, USA
| | - Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
- Department of Physics, Stanford University, Stanford, CA, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA, USA.
- Electron Imaging Center for Nanomachines, UCLA, Los Angeles, CA, USA.
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
- RNA Bioscience Initiative, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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25
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Small LJ, Hill RC, Krumhansl JL, Schindelholz ME, Chen Z, Chapman KW, Zhang X, Yang S, Schröder M, Nenoff TM. Reversible MOF-Based Sensors for the Electrical Detection of Iodine Gas. ACS Appl Mater Interfaces 2019; 11:27982-27988. [PMID: 31313899 PMCID: PMC6814244 DOI: 10.1021/acsami.9b09938] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 07/17/2019] [Indexed: 05/23/2023]
Abstract
Iodine detection is crucial for nuclear waste clean-up and first responder activities. For ease of use and durability of response, robust active materials that enable the direct electrical detection of I2 are needed. Herein, a large reversible electrical response is demonstrated as I2 is controllably and repeatedly adsorbed and desorbed from a series of metal-organic frameworks (MOFs) MFM-300(X), each possessing a different metal center (X = Al, Fe, In, or Sc) bridged by biphenyl-3,3',5,5'-tetracarboxylate linkers. Impedance spectroscopy is used to evaluate how the different metal centers influence the electrical response upon cycling of I2 gas, ranging from 10× to 106× decrease in resistance upon I2 adsorption in air. This large variation in electrical response is attributed not only to the differing structural characteristics of the MOFs but also to the differing MOF morphologies and how this influences the degree of reversibility of I2 adsorption. Interestingly, MFM-300(Al) and MFM-300(In) displayed the largest changes in resistance (up to 106×) yet lost much of their adsorption capacity after five I2 adsorption cycles in air. On the other hand, MFM-300(Fe) and MFM-300(Sc) revealed more moderate changes in resistance (10-100×), maintaining most of their original adsorption capacity after five cycles. This work demonstrates how changes in MOFs can profoundly affect the magnitude and reversibility of the electrical response of sensor materials. Tuning both the intrinsic (resistivity and adsorption capacity) and extrinsic (surface area and particle morphology) properties is necessary to develop highly reversible, large signal-generating MOF materials for direct electrical readout for I2 sensing.
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Affiliation(s)
- Leo J. Small
- Sandia
National Laboratories, Albuquerque 87185, New Mexico, United States
| | - Ryan C. Hill
- Sandia
National Laboratories, Albuquerque 87185, New Mexico, United States
| | - James L. Krumhansl
- Sandia
National Laboratories, Albuquerque 87185, New Mexico, United States
| | | | - Zhihengyu Chen
- Department
of Chemistry, Stony Brook University, 100 Nicolls Road, New York 11794, United States
| | - Karena W. Chapman
- Department
of Chemistry, Stony Brook University, 100 Nicolls Road, New York 11794, United States
| | - Xinran Zhang
- School
of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Sihai Yang
- School
of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Martin Schröder
- School
of Chemistry, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Tina M. Nenoff
- Sandia
National Laboratories, Albuquerque 87185, New Mexico, United States
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26
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Affiliation(s)
- Sandi G. Dempsey
- Aroa Biosurgery Limited, Airport Oaks, Auckland 2022, New Zealand
| | | | - Ryan C. Hill
- Omix Technologies LLC, Bioscience 1, 12635 E. Montview Blvd. Suite 100, Aurora, Colorado 80045, United States
| | - Kirk C. Hansen
- Omix Technologies LLC, Bioscience 1, 12635 E. Montview Blvd. Suite 100, Aurora, Colorado 80045, United States
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27
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Li X, Liu S, Jiang J, Zhang L, Espinosa S, Hill RC, Hansen KC, Zhou ZH, Zhao R. Author Correction: CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing. Nat Commun 2018; 9:1495. [PMID: 29643343 PMCID: PMC5895711 DOI: 10.1038/s41467-018-03708-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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28
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Reisz JA, Nemkov T, Dzieciatkowska M, Culp-Hill R, Stefanoni D, Hill RC, Yoshida T, Dunham A, Kanias T, Dumont LJ, Busch M, Eisenmesser EZ, Zimring JC, Hansen KC, D'Alessandro A. Methylation of protein aspartates and deamidated asparagines as a function of blood bank storage and oxidative stress in human red blood cells. Transfusion 2018; 58:2978-2991. [PMID: 30312994 DOI: 10.1111/trf.14936] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/30/2018] [Accepted: 08/15/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND Being devoid of de novo protein synthesis capacity, red blood cells (RBCs) have evolved to recycle oxidatively damaged proteins via mechanisms that involve methylation of dehydrated and deamidated aspartate and asparagine residues. Here we hypothesize that such mechanisms are relevant to routine storage in the blood bank. STUDY DESIGN AND METHODS Within the framework of the REDS-III RBC-Omics (Recipient Epidemiology Donor Evaluation Study III Red Blood Cell-Omics) study, packed RBC units (n = 599) were stored under blood bank conditions for 10, 23, and 42 days and profiled for oxidative hemolysis and time-dependent metabolic dysregulation of the trans-sulfuration pathway. RESULTS In these units, methionine consumption positively correlated with storage age and oxidative hemolysis. Mechanistic studies show that this phenomenon is favored by oxidative stress or hyperoxic storage (sulfur dioxide >95%), and prevented by hypoxia or methyltransferase inhibition. Through a combination of proteomics approaches and 13 C-methionine tracing, we observed oxidation-induced increases in both Asn deamidation to Asp and formation of methyl-Asp on key structural proteins and enzymes, including Band 3, hemoglobin, ankyrin, 4.1, spectrin beta, aldolase, glyceraldehyde 3-phosphate dehydrogenase, biphosphoglycerate mutase, lactate dehydrogenase and catalase. Methylated regions tended to map proximal to the active site (e.g., N316 of glyceraldehyde 3-phosphate dehydrogenase) and/or residues interacting with the N-terminal cytosolic domain of Band 3. CONCLUSION While methylation of basic amino acid residues serves as an epigenetic modification in nucleated cells, protein methylation at carboxylate side chains and deamidated asparagines is a nonepigenetic posttranslational sensor of oxidative stress and refrigerated storage in anucleated human RBCs.
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Affiliation(s)
- Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado
| | - Rachel Culp-Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado
| | - Davide Stefanoni
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado
| | | | | | - Tamir Kanias
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Michael Busch
- Blood Systems Research Institute, San Francisco, California
| | - Elan Z Eisenmesser
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado
| | | | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado.,Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
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Tomko LA, Hill RC, Barrett A, Szulczewski JM, Conklin MW, Eliceiri KW, Keely PJ, Hansen KC, Ponik SM. Targeted matrisome analysis identifies thrombospondin-2 and tenascin-C in aligned collagen stroma from invasive breast carcinoma. Sci Rep 2018; 8:12941. [PMID: 30154546 PMCID: PMC6113240 DOI: 10.1038/s41598-018-31126-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/12/2018] [Indexed: 01/05/2023] Open
Abstract
Increasing evidence demonstrates an important role for the extracellular matrix (ECM) in breast cancer progression. Collagen type I, a core constituent of the fibrous ECM, undergoes a significant set of changes that accompany tumor progression, termed Tumor Associated Collagen Signatures (TACS). Late stages of this progression are characterized by the presence of bundled, straight collagen (TACS-2) that become oriented perpendicular to the tumor-stromal boundary (TACS-3). Importantly, the presence of TACS-3 collagen is an independent predictor of poor patient outcome. At present, it remains unclear whether reorganization of the collagen matrix is the consequence of mechanical or compositional tissue remodeling. Here, we identify compositional changes in ECM correlating to collagen fiber reorganization from nineteen normal and invasive ductal carcinoma (IDC) patient biopsies using matrisome-targeted proteomics. Twenty-seven ECM proteins were significantly altered in IDC samples compared to normal tissue. Further, a set of nineteen matrisome proteins positively correlate and five proteins inversely correlate with IDC tissues containing straightened collagen fibers. Tenascin-C and thrombospondin-2 significantly co-localized with aligned collagen fibers in IDC tissues. This study highlights the compositional change in matrisome proteins accompanying collagen re-organization during breast cancer progression and provides candidate proteins for investigation into cellular and structural influences on collagen alignment.
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Affiliation(s)
- Lucas A Tomko
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., WIMR II Rm. 4528, Madison, WI, 53705, United States
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado-Denver, 12801 E. 17th Avenue, Bldg. RC-1 South, Aurora, CO, 80045, United States
| | - Alexander Barrett
- Department of Biochemistry and Molecular Genetics, University of Colorado-Denver, 12801 E. 17th Avenue, Bldg. RC-1 South, Aurora, CO, 80045, United States
| | - Joseph M Szulczewski
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., WIMR II Rm. 4528, Madison, WI, 53705, United States
| | - Matthew W Conklin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., WIMR II Rm. 4528, Madison, WI, 53705, United States
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin at Madison, 1675 Observatory Dr., Madison, WI, 53706, United States
| | - Patricia J Keely
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., WIMR II Rm. 4528, Madison, WI, 53705, United States
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado-Denver, 12801 E. 17th Avenue, Bldg. RC-1 South, Aurora, CO, 80045, United States.
| | - Suzanne M Ponik
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., WIMR II Rm. 4528, Madison, WI, 53705, United States.
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30
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Zhao R, Li X, Liu S, Jiang J, Zhang L, Espinosa S, Hill RC, Hansen KC, Zhou ZH. Cryo-EM structure of yeast U1 snRNP offers insight into alternative splicing. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318095843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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31
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Liu S, Li X, Zhang L, Jiang J, Hill RC, Cui Y, Hansen KC, Zhou ZH, Zhao R. Structure of the yeast spliceosomal postcatalytic P complex. Science 2017; 358:1278-1283. [PMID: 29146870 PMCID: PMC5828012 DOI: 10.1126/science.aar3462] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 11/09/2017] [Indexed: 12/20/2022]
Abstract
The spliceosome undergoes dramatic changes in a splicing cycle. Structures of B, Bact, C, C*, and intron lariat spliceosome complexes revealed mechanisms of 5'-splice site (ss) recognition, branching, and intron release, but lacked information on 3'-ss recognition, exon ligation, and exon release. Here we report a cryo-electron microscopy structure of the postcatalytic P complex at 3.3-angstrom resolution, revealing that the 3' ss is mainly recognized through non-Watson-Crick base pairing with the 5' ss and branch point. Furthermore, one or more unidentified proteins become stably associated with the P complex, securing the 3' exon and potentially regulating activity of the helicase Prp22. Prp22 binds nucleotides 15 to 21 in the 3' exon, enabling it to pull the intron-exon or ligated exons in a 3' to 5' direction to achieve 3'-ss proofreading or exon release, respectively.
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Affiliation(s)
- Shiheng Liu
- Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Xueni Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jiansen Jiang
- Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Yanxiang Cui
- Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Z Hong Zhou
- Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA.
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32
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Barrett AS, Wither MJ, Hill RC, Dzieciatkowska M, D’Alessandro A, Reisz JA, Hansen KC. Hydroxylamine Chemical Digestion for Insoluble Extracellular Matrix Characterization. J Proteome Res 2017; 16:4177-4184. [PMID: 28971683 PMCID: PMC5802359 DOI: 10.1021/acs.jproteome.7b00527] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The extracellular matrix (ECM) is readily enriched by decellularizing tissues with nondenaturing detergents to solubilize and deplete the vast majority of cellular components. This approach has been used extensively to generate ECM scaffolds for regenerative medicine technologies and in 3D cell culture to model how the ECM contributes to disease progression. A highly enriched ECM fraction can then be generated using a strong chaotrope buffer that is compatible with downstream bottom-up proteomic analysis or 3D cell culture experiments after extensive dialysis. With most tissues, an insoluble pellet remains after chaotrope extraction that is rich in structural ECM components. Previously, we showed that this understudied fraction represented approximately 80% of total fibrillar collagen from the lung and other ECM fiber components that are known to be covalently cross-linked. Here, we present a hydroxylamine digestion approach for chaotrope-insoluble ECM analysis with comparison to an established CNBr method for matrisome characterization. Because ECM characteristics vary widely among tissues, we chose five tissues that represent unique and diverse ECM abundances, composition, and biomechanical properties. Hydroxylamine digestion is compatible with downstream proteomic workflows, yields high levels of ECM peptides from the insoluble ECM fraction, and reduces analytical variability when compared to CNBr digestion. Data are available via ProteomeXchange with identifier PXD006428.
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Affiliation(s)
- Alexander S. Barrett
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
| | - Matthew J. Wither
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
- Biological Mass Spectrometry Facility, University of Colorado Denver, Aurora, Colorado, USA
| | - Ryan C. Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
- Biological Mass Spectrometry Facility, University of Colorado Denver, Aurora, Colorado, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
- Biological Mass Spectrometry Facility, University of Colorado Denver, Aurora, Colorado, USA
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
- Biological Mass Spectrometry Facility, University of Colorado Denver, Aurora, Colorado, USA
| | - Julie A. Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
- Biological Mass Spectrometry Facility, University of Colorado Denver, Aurora, Colorado, USA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado, USA
- Biological Mass Spectrometry Facility, University of Colorado Denver, Aurora, Colorado, USA
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Li X, Liu S, Jiang J, Zhang L, Espinosa S, Hill RC, Hansen KC, Zhou ZH, Zhao R. CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing. Nat Commun 2017; 8:1035. [PMID: 29051543 PMCID: PMC5648754 DOI: 10.1038/s41467-017-01241-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/29/2017] [Indexed: 12/23/2022] Open
Abstract
U1 snRNP plays a critical role in 5'-splice site recognition and is a frequent target of alternative splicing factors. These factors transiently associate with human U1 snRNP and are not amenable for structural studies, while their Saccharomyces cerevisiae (yeast) homologs are stable components of U1 snRNP. Here, we report the cryoEM structure of yeast U1 snRNP at 3.6 Å resolution with atomic models for ten core proteins, nearly all essential domains of its RNA, and five stably associated auxiliary proteins. The foot-shaped yeast U1 snRNP contains a core in the "ball-and-toes" region architecturally similar to the human U1 snRNP. All auxiliary proteins are in the "arch-and-heel" region and connected to the core through the Prp42/Prp39 paralogs. Our demonstration that homodimeric human PrpF39 directly interacts with U1C-CTD, mirroring yeast Prp42/Prp39, supports yeast U1 snRNP as a model for understanding how transiently associated auxiliary proteins recruit human U1 snRNP in alternative splicing.
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Affiliation(s)
- Xueni Li
- 0000 0001 0703 675Xgrid.430503.1Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Shiheng Liu
- 0000 0000 9632 6718grid.19006.3eElectron Imaging Center for Nanomachines University of California, Los Angeles (UCLA), Los Angeles, CA 90095 USA ,0000 0000 9632 6718grid.19006.3eDepartment of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095 USA
| | - Jiansen Jiang
- 0000 0000 9632 6718grid.19006.3eElectron Imaging Center for Nanomachines University of California, Los Angeles (UCLA), Los Angeles, CA 90095 USA ,0000 0000 9632 6718grid.19006.3eDepartment of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095 USA
| | - Lingdi Zhang
- 0000 0001 0703 675Xgrid.430503.1Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Sara Espinosa
- 0000 0001 0703 675Xgrid.430503.1Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Ryan C. Hill
- 0000 0001 0703 675Xgrid.430503.1Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Kirk C. Hansen
- 0000 0001 0703 675Xgrid.430503.1Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO 80045 USA
| | - Z. Hong Zhou
- 0000 0000 9632 6718grid.19006.3eElectron Imaging Center for Nanomachines University of California, Los Angeles (UCLA), Los Angeles, CA 90095 USA ,0000 0000 9632 6718grid.19006.3eDepartment of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095 USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, 80045, USA.
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Ardente AJ, Wells RS, Smith CR, Walsh MT, Jensen ED, Schmitt TL, Colee J, Vagt BJ, Hill RC. Dietary cation-anion difference may explain why ammonium urate nephrolithiasis occurs more frequently in common bottlenose dolphins () under human care than in free-ranging common bottlenose dolphins. J Anim Sci 2017; 95:1396-1406. [PMID: 28380506 DOI: 10.2527/jas.2016.1113] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ammonium urate nephrolithiasis frequently develops in common bottlenose dolphins () managed under human care but is rare in free-ranging common bottlenose dolphins. In other species, the dietary cation-anion difference (DCAD) can affect ammonium urate urolith formation by increasing proton excretion as ammonium ions. Therefore, differences in diet between the 2 dolphin populations could affect urolith formation, but the DCAD of most species consumed by free-ranging and managed dolphins is unknown. To compare the nutrient composition of diets consumed by free-ranging and managed bottlenose dolphins, samples ( = 5) of the 8 species of fish commonly consumed by free-ranging bottlenose dolphins in Sarasota Bay, FL, and the 7 species of fish and squid commonly fed to managed bottlenose dolphins were analyzed for nutrient content. Metabolizable energy was calculated using Atwater factors; the DCAD was calculated using 4 equations commonly used in people and animals that use different absorption coefficients. The nutrient composition of individual species was used to predict the DCAD of 2 model diets typically fed to managed common bottlenose dolphins and a model diet typically consumed by common bottlenose dolphins in Sarasota Bay. To mimic differences in postmortem handling of fish for the 2 populations of bottlenose dolphins, "free-ranging" samples were immediately frozen at -80°C and minimally thawed before analysis, whereas "managed" samples were frozen for 6 to 9 mo at -18°C and completely thawed. "Free-ranging" species contained more Ca and P and less Na and Cl than "managed" fish and squid species. As a consequence, the DCAD of both model managed dolphin diets obtained using 3 of the 4 equations was much more negative than the DCAD of the model free-ranging bottlenose dolphin diet ( < 0.05). The results imply that managed bottlenose dolphins must excrete more protons in urine than free-ranging bottlenose dolphins, which will promote nephrolith formation. The nutrient composition of the free-ranging bottlenose dolphin diet, determined for the first time here, can be used as a guide for feeding managed bottlenose dolphins, but research in vivo is warranted to determine whether adding more cations to the diet will prevent urolith formation in managed dolphins.
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Hill RC, Fast BJ, Herman RA. Transgenesis affects endogenous soybean allergen levels less than traditional breeding. Regul Toxicol Pharmacol 2017; 89:70-73. [PMID: 28720347 DOI: 10.1016/j.yrtph.2017.07.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 07/13/2017] [Accepted: 07/14/2017] [Indexed: 11/22/2022]
Abstract
The regulatory body that oversees the safety assessment of genetically modified (GM) crops in the European Union, the European Food Safety Authority (EFSA), uniquely requires that endogenous allergen levels be quantified as part of the compositional characterization of GM versions of crops, such as soybean, that are considered to be major allergenic foods. The value of this requirement for assessing food safety has been challenged for multiple reasons including negligible risk of altering allergen levels compared with traditional non-GM breeding. Scatter plots comparing the mean endogenous allergen levels in non-GM soybean isoline grain with the respective levels in GM grain or concurrently grown non-GM commercial reference varieties clearly show that transgenesis causes less change compared with traditional breeding. This visual assessment is confirmed by the quantitative fit of the line of identity (y = x) to the datasets. The current science on allergy does not support the requirement for quantifying allergen levels in GM crops to support safety assessment.
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Affiliation(s)
- Ryan C Hill
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, United States.
| | - Brandon J Fast
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, United States
| | - Rod A Herman
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, United States
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36
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Hill RC, Wang X, Schafer BW, Gampala SS, Herman RA. Measurement of lipid transfer proteins in genetically engineered maize using liquid chromatography with tandem mass spectrometry (LC-MS/MS). GM Crops Food 2017; 8:239-252. [PMID: 28758829 DOI: 10.1080/21645698.2017.1349602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Endogenous allergenicity evaluation is a required part of the risk assessment for genetically engineered (GE) crops. Although maize is not considered a major allergenic food, a lipid transfer protein (Zea m 14) in maize grain has been identified as a potential IgE-mediated food allergen. Currently, the relationship between allergen exposure and risk of sensitization is not well understood. Hence, reliable quantitative methods are useful for determining the natural range and variability of allergen levels across multiple geographies and genetic backgrounds. A LC-MS/MS analytical method was developed and validated in our laboratory to quantify Zea m 14 in grain from 2 GE maize hybrids and 20 non-GE maize hybrids. The measured Zea m 14 levels in GE maize grain and conventional non-GE maize grain ranged from 146.87 to 574.93 ng/mg across 16 field sites located in the United States and Argentina. The method accurately quantified endogenous Zea m 14 from maize grain and results show Zea m 14 levels in the GE maize varieties were within the natural variation observed in traditionally bred non-GE maize.
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Affiliation(s)
- Ryan C Hill
- a Dow AgroSciences LLC , Indianapolis , IN , USA
| | - Xiujuan Wang
- a Dow AgroSciences LLC , Indianapolis , IN , USA
| | | | | | - Rod A Herman
- a Dow AgroSciences LLC , Indianapolis , IN , USA
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Hill RC, Oman TJ, Wang X, Shan G, Schafer B, Herman RA, Tobias R, Shippar J, Malayappan B, Sheng L, Xu A, Bradshaw J. Development, Validation, and Interlaboratory Evaluation of a Quantitative Multiplexing Method To Assess Levels of Ten Endogenous Allergens in Soybean Seed and Its Application to Field Trials Spanning Three Growing Seasons. J Agric Food Chem 2017; 65:5531-5544. [PMID: 28635260 DOI: 10.1021/acs.jafc.7b01018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
As part of the regulatory approval process in Europe, comparison of endogenous soybean allergen levels between genetically engineered (GE) and non-GE plants has been requested. A quantitative multiplex analytical method using tandem mass spectrometry was developed and validated to measure 10 potential soybean allergens from soybean seed. The analytical method was implemented at six laboratories to demonstrate the robustness of the method and further applied to three soybean field studies across multiple growing seasons (including 21 non-GE soybean varieties) to assess the natural variation of allergen levels. The results show environmental factors contribute more than genetic factors to the large variation in allergen abundance (2- to 50-fold between environmental replicates) as well as a large contribution of Gly m 5 and Gly m 6 to the total allergen profile, calling into question the scientific rational for measurement of endogenous allergen levels between GE and non-GE varieties in the safety assessment.
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Affiliation(s)
- Ryan C Hill
- Dow AgroSciences LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Trent J Oman
- Dow AgroSciences LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Xiujuan Wang
- Dow AgroSciences LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Guomin Shan
- Dow AgroSciences LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Barry Schafer
- Dow AgroSciences LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Rod A Herman
- Dow AgroSciences LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Rowel Tobias
- EAG Laboratories , 4780 Discovery Drive, Columbia, Missouri 65201, United States
| | - Jeff Shippar
- Covance Laboratories , 3301 Kinsman Blvd., Madison, Wisconsin 53704, United States
| | - Bhaskar Malayappan
- Critical Path Services LLC , 3070 McCann Farm Drive, Garnet Valley, Pennsylvania 19060, United States
| | - Li Sheng
- EPL Bioanalytical Services , 9095 W. Harristown Blvd, Niantic, Illinois 62551, United States
| | - Austin Xu
- Primera Analytical Solutions , 259 Wall Street, Princeton, New Jersey 08540, United States
| | - Jason Bradshaw
- Pyxant Laboratories , 4720 Forge Road #106, Colorado Springs, Colorado 80907, United States
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Goddard ET, Hill RC, Nemkov T, D'Alessandro A, Hansen KC, Maller O, Mongoue-Tchokote S, Mori M, Partridge AH, Borges VF, Schedin P. The Rodent Liver Undergoes Weaning-Induced Involution and Supports Breast Cancer Metastasis. Cancer Discov 2017; 7:177-187. [PMID: 27974414 PMCID: PMC5459606 DOI: 10.1158/2159-8290.cd-16-0822] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/08/2016] [Accepted: 12/08/2016] [Indexed: 01/01/2023]
Abstract
Patients with postpartum breast cancer are at increased risk for metastasis compared with age-matched nulliparous or pregnant patients. Here, we address whether circulating tumor cells have a metastatic advantage in the postpartum host and find the postlactation rodent liver preferentially supports metastasis. Upon weaning, we observed liver weight loss, hepatocyte apoptosis, extracellular matrix remodeling including deposition of collagen and tenascin-C, and myeloid cell influx, data consistent with weaning-induced liver involution and establishment of a prometastatic microenvironment. Using intracardiac and intraportal metastasis models, we observed increased liver metastasis in post-weaning BALB/c mice compared with nulliparous controls. Human relevance is suggested by a ∼3-fold increase in liver metastasis in patients with postpartum breast cancer (n = 564) and by liver-specific tropism (n = 117). In sum, our data reveal a previously unknown biology of the rodent liver, weaning-induced liver involution, which may provide insight into the increased liver metastasis and poor prognosis of women diagnosed with postpartum breast cancer. SIGNIFICANCE We find that patients with postpartum breast cancer are at elevated risk for liver metastasis. We identify a previously unrecognized biology, namely weaning-induced liver involution, that establishes a prometastatic microenvironment, and which may account in part for the poor prognosis of patients with postpartum breast cancer. Cancer Discov; 7(2); 177-87. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 115.
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Affiliation(s)
- Erica T Goddard
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado
| | - Ori Maller
- Department of Surgery, Center for Bioengineering and Tissue Regeneration, University of California, San Francisco, San Francisco, California
| | | | - Motomi Mori
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- School of Public Health, Oregon Health & Science University, Portland, Oregon
| | - Ann H Partridge
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Virginia F Borges
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
- University of Colorado Cancer Center, Aurora, Colorado
- Young Women's Breast Cancer Translational Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Pepper Schedin
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, Oregon.
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Young Women's Breast Cancer Translational Program, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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Ardente AJ, Garrett TJ, Wells RS, Walsh M, Smith CR, Colee J, Hill RC. A Targeted Metabolomics Assay to Measure Eight Purines in the Diet of Common Bottlenose Dolphins, Tursiops truncatus. J Chromatogr Sep Tech 2016. [PMID: 27904786 DOI: 10.4172/2157-7064.1000334.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bottlenose dolphins managed under human care, human beings and Dalmatian dogs are prone to forming urate uroliths. Limiting dietary purine intake limits urate urolith formation in people and dogs because purines are metabolized to uric acid, which is excreted in urine. Managed dolphins develop ammonium urate nephroliths, whereas free-ranging dolphins do not. Free-ranging dolphins consume live fish, whereas managed dolphins consume different species that have been stored frozen and thawed. Differences in the purine content of fish consumed by dolphins under human care versus in the wild may be responsible for the difference in urolith prevalence. Commercially available purine assays measure only four purines, but reported changes in purines during frozen storage suggest that a wider range of metabolites should be measured when comparing fresh and stored fish. A method using high performance liquid chromatography with tandem mass spectrometry was developed to quantify eight purine metabolites in whole fish and squid commonly consumed by dolphins. The coefficient of variation within and among days was sometimes high for purines present in small amounts but was acceptable (≤ 25%) for guanine, hypoxanthine, and inosine, which were present in high concentrations. This expanded assay identified a total purine content up to 2.5 times greater than the total that would be quantified if only four purines were measured. Assuming additional purines are absorbed, these results suggest that additional purine metabolites should be measured to better understand the associated risk when fish or other purine-rich foods are consumed by people or animals prone to developing uroliths.
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Affiliation(s)
- A J Ardente
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - T J Garrett
- Southeast Center for Integrated Metabolomics, Mass Spectrometry Core Laboratory, University of Florida, Gainesville, FL, USA
| | - R S Wells
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA; Chicago Zoological Society's Sarasota Dolphin Research Program, C/O Mote Marine Laboratory, Sarasota, FL, USA
| | - M Walsh
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - C R Smith
- National Marine Mammal Foundation, San Diego, CA, USA
| | - J Colee
- Department of Statistics, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - R C Hill
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
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Calle EA, Hill RC, Leiby KL, Le AV, Gard AL, Madri JA, Hansen KC, Niklason LE. Targeted proteomics effectively quantifies differences between native lung and detergent-decellularized lung extracellular matrices. Acta Biomater 2016; 46:91-100. [PMID: 27693690 DOI: 10.1016/j.actbio.2016.09.043] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 08/25/2016] [Accepted: 09/28/2016] [Indexed: 12/16/2022]
Abstract
Extracellular matrix is a key component of many products in regenerative medicine. Multiple regenerative medicine products currently in the clinic are comprised of human or xenogeneic extracellular matrix. In addition, whole-organ regeneration exploits decellularized native organs as scaffolds for organotypic cell culture. However, precise understanding of the constituents of such extracellular matrix-based implants and scaffolds has sorely lagged behind their use. We present here an advanced protein extraction method using known quantities of proteotypic 13C-labeled peptides to quantify matrix proteins in native and decellularized lung tissues. Using quantitative proteomics that produce picomole-level measurements of a large number of matrix proteins, we show that a mild decellularization technique ("Triton/SDC") results in near-native retention of laminins, proteoglycans, and other basement membrane and ECM-associated proteins. Retention of these biologically important glycoproteins and proteoglycans is quantified to be up to 27-fold higher in gently-decellularized lung scaffolds compared to scaffolds generated using a previously published decellularization regimen. Cells seeded onto this new decellularized matrix also proliferate robustly, showing positive staining for proliferating cell nuclear antigen (PCNA). The high fidelity of the gently decellularized scaffold as compared to the original lung extracellular matrix represents an important step forward in the ultimate recapitulation of whole organs using tissue-engineering techniques. This method of ECM and scaffold protein analysis allows for better understanding, and ultimately quality control, of matrices that are used for tissue engineering and human implantation. These results should advance regenerative medicine in general, and whole organ regeneration in particular. STATEMENT OF SIGNIFICANCE The extracellular matrix (ECM) in large part defines the biochemical and mechanical properties of tissues and organs; these inherent cues make acellular ECM scaffolds potent substrates for tissue regeneration. As such, they are increasingly prevalent in the clinic and the laboratory. However, the exact composition of these scaffolds has been difficult to ascertain. This paper uses targeted proteomics to definitively quantify 71 proteins present in acellular lung ECM scaffolds. We use this technique to compare two decellularization methods and demonstrate superior retention of ECM proteins important for cell adhesion, migration, proliferation, and differentiation in scaffolds treated with low-concentration detergent solutions. In the long term, the ability to acquire quantitative biochemical data about biological substrates will facilitate the rational design of engineered tissues and organs based on precise cell-matrix interactions.
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Goddard ET, Hill RC, Barrett A, Betts C, Guo Q, Maller O, Borges VF, Hansen KC, Schedin P. Quantitative extracellular matrix proteomics to study mammary and liver tissue microenvironments. Int J Biochem Cell Biol 2016; 81:223-232. [PMID: 27771439 DOI: 10.1016/j.biocel.2016.10.014] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 01/22/2023]
Abstract
Normal epithelium exists within a dynamic extracellular matrix (ECM) that is tuned to regulate tissue specific epithelial cell function. As such, ECM contributes to tissue homeostasis, differentiation, and disease, including cancer. Though it is now recognized that the functional unit of normal and transformed epithelium is the epithelial cell and its adjacent ECM, we lack a basic understanding of tissue-specific ECM composition and abundance, as well as how physiologic changes in ECM impact cancer risk and outcomes. While traditional proteomic techniques have advanced to robustly identify ECM proteins within tissues, methods to determine absolute abundance have lagged. Here, with a focus on tissues relevant to breast cancer, we utilize mass spectrometry methods optimized for absolute quantitative ECM analysis. Employing an extensive protein extraction and digestion method, combined with stable isotope labeled Quantitative conCATamer (QconCAT) peptides that serve as internal standards for absolute quantification of protein, we quantify 98 ECM, ECM-associated, and cellular proteins in a single analytical run. In rodent models, we applied this approach to the primary site of breast cancer, the normal mammary gland, as well as a common and particularly deadly site of breast cancer metastasis, the liver. We find that mammary gland and liver have distinct ECM abundance and relative composition. Further, we show mammary gland ECM abundance and relative compositions differ across the reproductive cycle, with the most dramatic changes occurring during the pro-tumorigenic window of weaning-induced involution. Combined, this work suggests ECM candidates for investigation of breast cancer progression and metastasis, particularly in postpartum breast cancers that are characterized by high metastatic rates. Finally, we suggest that with use of absolute quantitative ECM proteomics to characterize tissues of interest, it will be possible to reconstruct more relevant in vitro models to investigate tumor-ECM dynamics at higher resolution.
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Affiliation(s)
- Erica T Goddard
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alexander Barrett
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Courtney Betts
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Qiuchen Guo
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
| | - Ori Maller
- Department of Surgery, Center for Bioengineering and Tissue Regeneration, University of California San Francisco, San Francisco, CA, USA
| | - Virginia F Borges
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; University of Colorado Cancer Center, Aurora, CO, USA; Young Women's Breast Cancer Translational Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Pepper Schedin
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, Portland, OR, USA; Young Women's Breast Cancer Translational Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.
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Ardente AJ, Garrett TJ, Wells RS, Walsh M, Smith CR, Colee J, Hill RC. A Targeted Metabolomics Assay to Measure Eight Purines in the Diet of Common Bottlenose Dolphins, Tursiops truncatus. J Chromatogr Sep Tech 2016; 7:334. [PMID: 27904786 PMCID: PMC5125776 DOI: 10.4172/2157-7064.1000334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bottlenose dolphins managed under human care, human beings and Dalmatian dogs are prone to forming urate uroliths. Limiting dietary purine intake limits urate urolith formation in people and dogs because purines are metabolized to uric acid, which is excreted in urine. Managed dolphins develop ammonium urate nephroliths, whereas free-ranging dolphins do not. Free-ranging dolphins consume live fish, whereas managed dolphins consume different species that have been stored frozen and thawed. Differences in the purine content of fish consumed by dolphins under human care versus in the wild may be responsible for the difference in urolith prevalence. Commercially available purine assays measure only four purines, but reported changes in purines during frozen storage suggest that a wider range of metabolites should be measured when comparing fresh and stored fish. A method using high performance liquid chromatography with tandem mass spectrometry was developed to quantify eight purine metabolites in whole fish and squid commonly consumed by dolphins. The coefficient of variation within and among days was sometimes high for purines present in small amounts but was acceptable (≤ 25%) for guanine, hypoxanthine, and inosine, which were present in high concentrations. This expanded assay identified a total purine content up to 2.5 times greater than the total that would be quantified if only four purines were measured. Assuming additional purines are absorbed, these results suggest that additional purine metabolites should be measured to better understand the associated risk when fish or other purine-rich foods are consumed by people or animals prone to developing uroliths.
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Affiliation(s)
- AJ Ardente
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - TJ Garrett
- Southeast Center for Integrated Metabolomics, Mass Spectrometry Core Laboratory, University of Florida, Gainesville, FL, USA
| | - RS Wells
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
- Chicago Zoological Society's Sarasota Dolphin Research Program, C/O Mote Marine Laboratory, Sarasota, FL, USA
| | - M Walsh
- College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - CR Smith
- National Marine Mammal Foundation, San Diego, CA, USA
| | - J Colee
- Department of Statistics, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - RC Hill
- Corresponding author: Hill RC, Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, 2015 SW 16th Ave., Gainesville, FL 32608, USA, Tel: +13523922235;
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Laklai H, Miroshnikova YA, Pickup MW, Collisson EA, Kim GE, Barrett AS, Hill RC, Lakins JN, Schlaepfer DD, Mouw JK, LeBleu VS, Roy N, Novitskiy SV, Johansen JS, Poli V, Kalluri R, Iacobuzio-Donahue CA, Wood LD, Hebrok M, Hansen K, Moses HL, Weaver VM. Genotype tunes pancreatic ductal adenocarcinoma tissue tension to induce matricellular fibrosis and tumor progression. Nat Med 2016; 22:497-505. [PMID: 27089513 PMCID: PMC4860133 DOI: 10.1038/nm.4082] [Citation(s) in RCA: 408] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/11/2016] [Indexed: 12/13/2022]
Abstract
Fibrosis compromises pancreatic ductal carcinoma (PDAC) treatment and contributes to patient mortality, yet antistromal therapies are controversial. We found that human PDACs with impaired epithelial transforming growth factor-β (TGF-β) signaling have high epithelial STAT3 activity and develop stiff, matricellular-enriched fibrosis associated with high epithelial tension and shorter patient survival. In several KRAS-driven mouse models, both the loss of TGF-β signaling and elevated β1-integrin mechanosignaling engaged a positive feedback loop whereby STAT3 signaling promotes tumor progression by increasing matricellular fibrosis and tissue tension. In contrast, epithelial STAT3 ablation attenuated tumor progression by reducing the stromal stiffening and epithelial contractility induced by loss of TGF-β signaling. In PDAC patient biopsies, higher matricellular protein and activated STAT3 were associated with SMAD4 mutation and shorter survival. The findings implicate epithelial tension and matricellular fibrosis in the aggressiveness of SMAD4 mutant pancreatic tumors and highlight STAT3 and mechanics as key drivers of this phenotype.
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Affiliation(s)
- Hanane Laklai
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Yekaterina A. Miroshnikova
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Michael W. Pickup
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Eric A. Collisson
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Grace E. Kim
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Alex S. Barrett
- Department of Biochemistry and Molecular Genetics, University of Colorado, Denver, Aurora, CO, USA
| | - Ryan C. Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado, Denver, Aurora, CO, USA
| | - Johnathon N. Lakins
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - David D. Schlaepfer
- Department of Reproductive Medicine, University of California, San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Janna K. Mouw
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Valerie S. LeBleu
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston–Medical School, Houston, TX, USA
| | - Nilotpal Roy
- Diabetes Center, Department of Medicine, University of California, San Francisco, CA USA
| | - Sergey V. Novitskiy
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Julia S. Johansen
- Department of Oncology, Herlev Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Valeria Poli
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center, University of Turin, Turin, Italy
| | - Raghu Kalluri
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston–Medical School, Houston, TX, USA
| | - Christine A. Iacobuzio-Donahue
- Department of Pathology, David Rubenstein Center for Pancreatic Cancer Research, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Laura D. Wood
- Gastrointestinal and Liver Pathology Department, Johns Hopkins University, Baltimore, MD, USA
| | - Matthias Hebrok
- Diabetes Center, Department of Medicine, University of California, San Francisco, CA USA
| | - Kirk Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado, Denver, Aurora, CO, USA
| | - Harold L. Moses
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Valerie M. Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
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D'Alessandro A, Dzieciatkowska M, Hill RC, Hansen KC. Supernatant protein biomarkers of red blood cell storage hemolysis as determined through an absolute quantification proteomics technology. Transfusion 2016; 56:1329-39. [PMID: 26813021 DOI: 10.1111/trf.13483] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 12/09/2015] [Accepted: 12/09/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Laboratory technologies have highlighted the progressive accumulation of the so-called "storage lesion," a wide series of alterations to stored red blood cells (RBCs) that may affect the safety and effectiveness of the transfusion therapy. New improvements in the field are awaited to ameliorate this lesion, such as the introduction of washing technologies in the cell processing pipeline. Laboratory studies that have tested such technologies so far rely on observational qualitative or semiquantitative techniques. STUDY DESIGN AND METHODS A state-of-the-art quantitative proteomics approach utilizing quantitative concatamers (QconCAT) was used to simultaneously monitor fluctuations in the abundance of 114 proteins in AS-3 RBC supernatants (n = 5; 11 time points, including before and after leukoreduction, at 3 hours, on Days 1 and 2, and weekly sampling from Day 7 through Day 42). RESULTS Leukoreduction-dependent depletion of plasma proteins was observed at the earliest time points. A subset of proteins showed very high linear correlation (r(2) > 0.9) not only with storage time, but also with absolute levels of hemoglobin α1 and β, a proxy for RBC hemolysis and vesiculation. Linear regression was performed to describe the temporal relationship between these proteins. Our findings suggest a role for supernatant glyceraldehyde-3-phosphate dehydrogenase; peroxiredoxin-1, -2, and -6; carbonic anhydrase-1 and -2; selenium binding protein-1; biliverdin reductase; aminolevulinate dehydratase; and catalase as potential biomarkers of RBC quality during storage. CONCLUSION A targeted proteomics technology revealed novel biomarkers of the RBC storage lesion and promises to become a key analytical readout for the development and testing of alternative cell processing strategies.
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Affiliation(s)
- Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver-Anschutz Medical Campus, Aurora, Colorado
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Johnson TD, Hill RC, Dzieciatkowska M, Nigam V, Behfar A, Christman KL, Hansen KC. Quantification of decellularized human myocardial matrix: A comparison of six patients. Proteomics Clin Appl 2015; 10:75-83. [PMID: 26172914 DOI: 10.1002/prca.201500048] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/15/2015] [Accepted: 07/07/2015] [Indexed: 11/06/2022]
Abstract
PURPOSE The purpose of this study was to characterize and quantitatively analyze human cardiac extracellular matrix (ECM) isolated from six different cadaveric donor hearts. EXPERIMENTAL DESIGN ECM was isolated by decellularization of six human cadaveric donor hearts and characterized by quantifying sulfated glycosaminoglycan content (sGAG) and via PAGE. The protein content was then quantified using ECM-targeted Quantitative conCATamers (QconCAT) by LC-SRM analysis using 83 stable isotope labeled (SIL) peptides representing 48 different proteins. Nontargeted global analysis was also implemented using LC-MS/MS. RESULTS The sGAG content, PAGE, and QconCAT proteomics analysis showed significant variation between each of the six patient samples. The quantitative proteomics indicated that the majority of the protein content was composed of various fibrillar collagen components. Also, quantification of difficult to remove cellular proteins represented less than 1% of total protein content, which is very low for a decellularized biomaterial. Global proteomics identified over 200 distinct proteins present in the human cardiac ECM. CONCLUSION AND CLINICAL RELEVANCE In conclusion, quantification and characterization of human myocardial ECM showed significant patient-to-patient variability between the six investigated patients. This is an important outcome for the development of allogeneic derived biomaterials and for increasing our understanding of human myocardial ECM composition.
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Affiliation(s)
- Todd D Johnson
- Department of Bioengineering, Sanford Consortium for Regenerative Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ryan C Hill
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO, USA
| | - Vishal Nigam
- Department of Pediatrics (Cardiology), University of California San Diego and Rady Children's Hospital, San Diego, La Jolla, CA, USA
| | - Atta Behfar
- Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA
| | - Karen L Christman
- Department of Bioengineering, Sanford Consortium for Regenerative Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO, USA
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Hill RC, Oman TJ, Shan G, Schafer B, Eble J, Chen C. Development and Validation of a Multiplexed Protein Quantitation Assay for the Determination of Three Recombinant Proteins in Soybean Tissues by Liquid Chromatography with Tandem Mass Spectrometry. J Agric Food Chem 2015; 63:7450-61. [PMID: 26237374 DOI: 10.1021/acs.jafc.5b03083] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Currently, traditional immunochemistry technologies such as enzyme-linked immunosorbent assays (ELISA) are the predominant analytical tool used to measure levels of recombinant proteins expressed in genetically engineered (GE) plants. Recent advances in agricultural biotechnology have created a need to develop methods capable of selectively detecting and quantifying multiple proteins in complex matrices because of increasing numbers of transgenic proteins being coexpressed or "stacked" to achieve tolerance to multiple herbicides or to provide multiple modes of action for insect control. A multiplexing analytical method utilizing liquid chromatography with tandem mass spectrometry (LC-MS/MS) has been developed and validated to quantify three herbicide-tolerant proteins in soybean tissues: aryloxyalkanoate dioxygenase (AAD-12), 5-enol-pyruvylshikimate-3-phosphate synthase (2mEPSPS), and phosphinothricin acetyltransferase (PAT). Results from the validation showed high recovery and precision over multiple analysts and laboratories. Results from this method were comparable to those obtained with ELISA with respect to protein quantitation, and the described method was demonstrated to be suitable for multiplex quantitation of transgenic proteins in GE crops.
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Affiliation(s)
- Ryan C Hill
- Dow AgroSciences, LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Trent J Oman
- Dow AgroSciences, LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Guomin Shan
- Dow AgroSciences, LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Barry Schafer
- Dow AgroSciences, LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Julie Eble
- Critical Path Services, LLC , 3070 McCann Farm Drive, Garnet Valley, Pennsylvania 19060, United States
| | - Cynthia Chen
- Critical Path Services, LLC , 3070 McCann Farm Drive, Garnet Valley, Pennsylvania 19060, United States
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Duffy ME, Specht A, Hill RC. Comparison between Urine Protein: Creatinine Ratios of Samples Obtained from Dogs in Home and Hospital Settings. J Vet Intern Med 2015; 29:1029-35. [PMID: 26059431 PMCID: PMC4895355 DOI: 10.1111/jvim.12836] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/25/2015] [Accepted: 04/22/2015] [Indexed: 12/17/2022] Open
Abstract
Background The urine protein:creatinine ratio (UPC) is used to quantify urine protein excretion and guide recommendations for monitoring and treatment of proteinuria. Hypothesis/Objectives Home urine samples will have lower UPCs than hospital samples. The objectives were to compare UPCs of samples collected in each setting and to determine whether environment of sample collection might affect staging, monitoring or treatment recommendations. Animals Twenty‐four client‐owned dogs. Methods Prospective, nonmasked study. Clients collected a urine sample from their dog at home and a second sample was collected at the hospital. Dogs receiving corticosteroids or angiotensin‐converting enzyme inhibitors were excluded, as were those with urine samples of inadequate volume, no protein on dipstick analysis, or active urine sediment. Samples were refrigerated after collection, dipstick and sediment evaluations were completed and each sample was frozen at −80°C within 12 hours. UPCs were performed on frozen samples within 2 months. Results From 81 paired samples, 57 were excluded. Of the remaining 24, 12/24 (50%) had higher hospital sample UPCs, 9/24 (38%) had identical UPCs, and 3/24 (12%) had lower hospital UPCs. The UPCs of hospital samples were higher than home samples for the total population (P = .005) and the subset with UPC > 0.5 (P = .001). Conclusions Setting and related circumstances of urine collection in dogs is associated with UPC differences; results are usually higher in hospital than in home samples. This difference has the potential to affect clinical interpretation.
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Affiliation(s)
- M E Duffy
- Department of Small Animal Clinical Sciences, University of Florida College of Veterinary Medicine, Gainesville, FL
| | - A Specht
- Department of Small Animal Clinical Sciences, University of Florida College of Veterinary Medicine, Gainesville, FL
| | - R C Hill
- Department of Small Animal Clinical Sciences, University of Florida College of Veterinary Medicine, Gainesville, FL
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Hill RC, Wither MJ, Nemkov T, Barrett A, D'Alessandro A, Dzieciatkowska M, Hansen KC. Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen. Mol Cell Proteomics 2015; 14:1946-58. [PMID: 25948757 DOI: 10.1074/mcp.m114.047787] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Indexed: 11/06/2022] Open
Abstract
Bone samples from several vertebrates were collected from the Ziegler Reservoir fossil site, in Snowmass Village, Colorado, and processed for proteomics analysis. The specimens come from Pleistocene megafauna Bison latifrons, dating back ∼ 120,000 years. Proteomics analysis using a simplified sample preparation procedure and tandem mass spectrometry (MS/MS) was applied to obtain protein identifications. Several bioinformatics resources were used to obtain peptide identifications based on sequence homology to extant species with annotated genomes. With the exception of soil sample controls, all samples resulted in confident peptide identifications that mapped to type I collagen. In addition, we analyzed a specimen from the extinct B. latifrons that yielded peptide identifications mapping to over 33 bovine proteins. Our analysis resulted in extensive fibrillar collagen sequence coverage, including the identification of posttranslational modifications. Hydroxylysine glucosylgalactosylation, a modification thought to be involved in collagen fiber formation and bone mineralization, was identified for the first time in an ancient protein dataset. Meta-analysis of data from other studies indicates that this modification may be common in well-preserved prehistoric samples. Additional peptide sequences from extracellular matrix (ECM) and non-ECM proteins have also been identified for the first time in ancient tissue samples. These data provide a framework for analyzing ancient protein signatures in well-preserved fossil specimens, while also contributing novel insights into the molecular basis of organic matter preservation. As such, this analysis has unearthed common posttranslational modifications of collagen that may assist in its preservation over time. The data are available via ProteomeXchange with identifier PXD001827.
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Affiliation(s)
- Ryan C Hill
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Matthew J Wither
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Travis Nemkov
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Alexander Barrett
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Angelo D'Alessandro
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Monika Dzieciatkowska
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
| | - Kirk C Hansen
- From the ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, Colorado 80045, USA
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Hill RC, Calle EA, Dzieciatkowska M, Niklason LE, Hansen KC. Quantification of extracellular matrix proteins from a rat lung scaffold to provide a molecular readout for tissue engineering. Mol Cell Proteomics 2015; 14:961-73. [PMID: 25660013 PMCID: PMC4390273 DOI: 10.1074/mcp.m114.045260] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/06/2015] [Indexed: 01/20/2023] Open
Abstract
The use of extracellular matrix (ECM) scaffolds, derived from decellularized tissues for engineered organ generation, holds enormous potential in the field of regenerative medicine. To support organ engineering efforts, we developed a targeted proteomics method to extract and quantify extracellular matrix components from tissues. Our method provides more complete and accurate protein characterization than traditional approaches. This is accomplished through the analysis of both the chaotrope-soluble and -insoluble protein fractions and using recombinantly generated stable isotope labeled peptides for endogenous protein quantification. Using this approach, we have generated 74 peptides, representing 56 proteins to quantify protein in native (nondecellularized) and decellularized lung matrices. We have focused on proteins of the ECM and additional intracellular proteins that are challenging to remove during the decellularization procedure. Results indicate that the acellular lung scaffold is predominantly composed of structural collagens, with the majority of these proteins found in the insoluble ECM, a fraction that is often discarded using widely accepted proteomic methods. The decellularization procedure removes over 98% of intracellular proteins evaluated and retains, to varying degrees, proteoglycans and glycoproteins of the ECM. Accurate characterization of ECM proteins from tissue samples will help advance organ engineering efforts by generating a molecular readout that can be correlated with functional outcome to drive the next generation of engineered organs.
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Affiliation(s)
- Ryan C Hill
- ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045
| | | | - Monika Dzieciatkowska
- ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045
| | - Laura E Niklason
- §Department of Biomedical Engineering and Anesthesiology, ¶Yale University, New Haven, CT 06519
| | - Kirk C Hansen
- ‡Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80045,
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Dzieciatkowska M, D'Alessandro A, Hill RC, Hansen KC. Plasma QconCATs reveal a gender-specific proteomic signature in apheresis platelet plasma supernatants. J Proteomics 2015; 120:1-6. [PMID: 25743772 DOI: 10.1016/j.jprot.2015.02.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/20/2015] [Accepted: 02/21/2015] [Indexed: 11/29/2022]
Abstract
UNLABELLED Clinical translation of proteomic technologies is often hampered by technical limitations, including inter-laboratory inconsistencies of label-free derived relative quantification, time-consuming analytical approaches and the subsequent challenge of performing proteomic analyses on large cohorts of subjects. Here we introduce plasma QconCAT-based targeted proteomics, an approach that allows the simultaneous absolute quantitation down to the picogram level of hundreds of proteins in a single liquid chromatography-selected reaction monitoring mass spectrometry run. We demonstrate the robustness of the approach by analyzing apheresis platelet concentrate supernatants at storage day 1 and the end of the shelf life for this blood-derived therapeutic, day 5. The targeted approach was repeatable and robust revealing potential gender-specific signatures across a set of three male and female donors. This technical note represents a proof-of-principle of the application of QconCAT-based MRM strategies to transfusion-medicine relevant issues, such as storage and gender-dependent proteomic signatures in blood-derived therapeutics. BIOLOGICAL SIGNIFICANCE Gender differences in the proteome composition of apheresis platelet supernatants have always been postulated, and might underlie a higher risk of adverse reactions when transfusing apheresis products from female donors. Preliminary proteomic studies provided an overview of gender-dependent relative compositional differences in the proteome of apheresis platelet supernatants during routine storage in the blood bank. Here we apply a proteomics approach for absolute quantitation of approximately 100 proteins in apheresis platelet supernatants from male and female donors at storage days 1 and 5. Absolute quantitative proteomic analyses allowed us to confirm and expand on previous observations about gender and storage-dependency of platelet supernatant protein profiles.
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Affiliation(s)
- Monika Dzieciatkowska
- University of Colorado Denver School of Medicine, Biochemistry and Molecular Genetics, School of Medicine University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Angelo D'Alessandro
- University of Colorado Denver School of Medicine, Biochemistry and Molecular Genetics, School of Medicine University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Ryan C Hill
- University of Colorado Denver School of Medicine, Biochemistry and Molecular Genetics, School of Medicine University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - Kirk C Hansen
- University of Colorado Denver School of Medicine, Biochemistry and Molecular Genetics, School of Medicine University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.
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