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Sun J, Li P, Gui H, Rittié L, Lombard DB, Rietscher K, Magin TM, Xie Q, Liu L, Omary MB. Deacetylation via SIRT2 prevents keratin-mutation-associated injury and keratin aggregation. JCI Insight 2023; 8:e166314. [PMID: 37485877 PMCID: PMC10443796 DOI: 10.1172/jci.insight.166314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 06/02/2023] [Indexed: 07/25/2023] Open
Abstract
Keratin (K) and other intermediate filament (IF) protein mutations at conserved arginines disrupt keratin filaments into aggregates and cause human epidermolysis bullosa simplex (EBS; K14-R125C) or predispose to mouse liver injury (K18-R90C). The challenge for more than 70 IF-associated diseases is the lack of clinically utilized IF-targeted therapies. We used high-throughput drug screening to identify compounds that normalized mutation-triggered keratin filament disruption. Parthenolide, a plant sesquiterpene lactone, dramatically reversed keratin filament disruption and protected cells and mice expressing K18-R90C from apoptosis. K18-R90C became hyperacetylated compared with K18-WT and treatment with parthenolide normalized K18 acetylation. Parthenolide upregulated the NAD-dependent SIRT2, and increased SIRT2-keratin association. SIRT2 knockdown or pharmacologic inhibition blocked the parthenolide effect, while site-specific Lys-to-Arg mutation of keratin acetylation sites normalized K18-R90C filaments. Treatment of K18-R90C-expressing cells and mice with nicotinamide mononucleotide had a parthenolide-like protective effect. In 2 human K18 variants that associate with human fatal drug-induced liver injury, parthenolide protected K18-D89H- but not K8-K393R-induced filament disruption and cell death. Importantly, parthenolide normalized K14-R125C-mediated filament disruption in keratinocytes and inhibited dispase-triggered keratinocyte sheet fragmentation and Fas-mediated apoptosis. Therefore, keratin acetylation may provide a novel therapeutic target for some keratin-associated diseases.
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Affiliation(s)
- Jingyuan Sun
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - Pei Li
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
| | - Honglian Gui
- Department of Infectious Diseases, Ruijin Hospital, Jiaotong University School of Medicine, Shanghai, PR China
| | - Laure Rittié
- Department of Dermatology, University of Michigan, Ann Arbor, Michigan, USA
| | - David B. Lombard
- Sylvester Comprehensive Cancer Center, and Department of Pathology & Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Katrin Rietscher
- Division of Cell and Developmental Biology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Thomas M. Magin
- Division of Cell and Developmental Biology, Institute of Biology, Leipzig University, Leipzig, Germany
| | - Qing Xie
- Department of Infectious Diseases, Ruijin Hospital, Jiaotong University School of Medicine, Shanghai, PR China
| | - Li Liu
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, PR China
| | - M. Bishr Omary
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan, USA
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Kabir F, Atkinson R, Cook AL, Phipps AJ, King AE. The role of altered protein acetylation in neurodegenerative disease. Front Aging Neurosci 2023; 14:1025473. [PMID: 36688174 PMCID: PMC9845957 DOI: 10.3389/fnagi.2022.1025473] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/03/2022] [Indexed: 01/06/2023] Open
Abstract
Acetylation is a key post-translational modification (PTM) involved in the regulation of both histone and non-histone proteins. It controls cellular processes such as DNA transcription, RNA modifications, proteostasis, aging, autophagy, regulation of cytoskeletal structures, and metabolism. Acetylation is essential to maintain neuronal plasticity and therefore essential for memory and learning. Homeostasis of acetylation is maintained through the activities of histone acetyltransferases (HAT) and histone deacetylase (HDAC) enzymes, with alterations to these tightly regulated processes reported in several neurodegenerative diseases including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS). Both hyperacetylation and hypoacetylation can impair neuronal physiological homeostasis and increase the accumulation of pathophysiological proteins such as tau, α-synuclein, and Huntingtin protein implicated in AD, PD, and HD, respectively. Additionally, dysregulation of acetylation is linked to impaired axonal transport, a key pathological mechanism in ALS. This review article will discuss the physiological roles of protein acetylation and examine the current literature that describes altered protein acetylation in neurodegenerative disorders.
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Metastasising Fibroblasts Show an HDAC6-Dependent Increase in Migration Speed and Loss of Directionality Linked to Major Changes in the Vimentin Interactome. Int J Mol Sci 2022; 23:ijms23041961. [PMID: 35216078 PMCID: PMC8880509 DOI: 10.3390/ijms23041961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 02/07/2023] Open
Abstract
Metastasising cells express the intermediate filament protein vimentin, which is used to diagnose invasive tumours in the clinic. We aimed to clarify how vimentin regulates the motility of metastasising fibroblasts. STED super-resolution microscopy, live-cell imaging and quantitative proteomics revealed that oncogene-expressing and metastasising fibroblasts show a less-elongated cell shape, reduced cell spreading, increased cell migration speed, reduced directionality, and stronger coupling between these migration parameters compared to normal control cells. In total, we identified and compared 555 proteins in the vimentin interactome. In metastasising cells, the levels of keratin 18 and Rab5C were increased, while those of actin and collagen were decreased. Inhibition of HDAC6 reversed the shape, spreading and migration phenotypes of metastasising cells back to normal. Inhibition of HDAC6 also decreased the levels of talin 1, tropomyosin, Rab GDI β, collagen and emilin 1 in the vimentin interactome, and partially reversed the nanoscale vimentin organisation in oncogene-expressing cells. These findings describe the changes in the vimentin interactome and nanoscale distribution that accompany the defective cell shape, spreading and migration of metastasising cells. These results support the hypothesis that oncogenes can act through HDAC6 to regulate the vimentin binding of the cytoskeletal and cell–extracellular matrix adhesion components that contribute to the defective motility of metastasising cells.
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Evans CA, Corfe BM. Colorectal keratins: Integrating nutrition, metabolism and colorectal health. Semin Cell Dev Biol 2021; 128:103-111. [PMID: 34481710 DOI: 10.1016/j.semcdb.2021.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/09/2021] [Accepted: 08/18/2021] [Indexed: 01/12/2023]
Abstract
The colon mucosa is lined with crypts of circa 300 cells, forming a continuous barrier whose roles include absorption of water, recovery of metabolic energy sources (notably short chain fatty acids), secretion of a protective mucus barrier, and physiological signalling. There is high turnover and replenishment of cells in the mucosa, disruption of this may lead to bowel pathologies including cancer and inflammatory bowel disease. Keratins have been implicated in the processes of cell death, epithelial integrity, response to inflammation and as a result are often described as guardians of the colonic epithelium. Keratin proteins carry extensive post-translational modifications, the cofactors for kinases, acetyl transferases and other modification-regulating enzymes are themselves products of metabolism. A cluster of studies has begun to reveal a bidirectional relationship between keratin form and function and metabolism. In this paper we hypothesise a mechanistic interaction between keratins and metabolism is governed through regulation of post-translational modifications and may contribute significantly to the normal functioning of the colon, placing keratins at the centre of a nutrition-metabolism-health triangle.
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Affiliation(s)
- Caroline A Evans
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin St, S1 3JD Sheffield, United Kingdom
| | - Bernard M Corfe
- Population Health Sciences Institute, Human Nutrition Research Centre, Faculty of Medical Sciences, Newcastle University, Newcastle NE2 4HH, United Kingdom.
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Yang T, Zhou R, Yu S, Yu S, Cui Z, Hu P, Liu J, Qiao Q, Zhang J. Cytoplasmic SIRT1 inhibits cell migration and invasion by impeding epithelial-mesenchymal transition in ovarian carcinoma. Mol Cell Biochem 2019; 459:157-169. [PMID: 31317367 PMCID: PMC6679836 DOI: 10.1007/s11010-019-03559-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/27/2019] [Indexed: 12/12/2022]
Abstract
Sirtuin1 (SIRT1) is a mammalian NAD+-dependent type III deacetylase that plays paramount roles in diverse cellular processes. The nucleocytoplasmic shuttling of SIRT1 was discovered more than a decade ago, but the roles of subcellular SIRT1 localization in tumor progression remain unclear. Here, we report that cytoplasmic SIRT1 acts as a tumor suppressor in ovarian carcinoma. By creating ovarian carcinoma cell lines overexpressing wild-type SIRT1 and nuclear localization signals (NLSs) mutated SIRT1 together with both unbiased proteomic and acetylomic approaches and Transwell assays, we identified that mutations in the NLS sequences prevented SIRT1 from entering the nucleus, resulting in the predominant cytoplasmic localization of SIRT1; the cytoplasmic localization of SIRT1 suppressed the mesenchymal program, activated the epithelial program, and inhibited the migration and invasion of tumor cells, thus providing experimental evidence that SIRT1 functions as a tumor suppressor or oncogene may depend on its subcellular localization. Altogether, our findings may highlight a novel role of cytoplasmic SIRT1 in ovarian carcinoma, providing new possible insights for studies investigating the role of SIRT1 in tumor progression.
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Affiliation(s)
- Tong Yang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, The Fourth Military Medical University, No. 169, Changle West Road, Xi'an, 710032, Shaanxi, China
| | - Ru Zhou
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, The Fourth Military Medical University, No. 169, Changle West Road, Xi'an, 710032, Shaanxi, China
| | - Shentong Yu
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, The Fourth Military Medical University, No. 169, Changle West Road, Xi'an, 710032, Shaanxi, China
| | - Shuhong Yu
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, The Fourth Military Medical University, No. 169, Changle West Road, Xi'an, 710032, Shaanxi, China
| | - Zhuqing Cui
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, The Fourth Military Medical University, No. 169, Changle West Road, Xi'an, 710032, Shaanxi, China
| | - Peizhen Hu
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, The Fourth Military Medical University, No. 169, Changle West Road, Xi'an, 710032, Shaanxi, China
| | - Jinsong Liu
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Qing Qiao
- Department of General Surgery, Tangdu Hospital, The Fourth Military Medical University, No. 569 Xinsi Road, Xi'an, 710038, Shaanxi, China.
| | - Jing Zhang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, The Fourth Military Medical University, No. 169, Changle West Road, Xi'an, 710032, Shaanxi, China.
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Chicooree N, Unwin RD, Griffiths JR. The application of targeted mass spectrometry-based strategies to the detection and localization of post-translational modifications. MASS SPECTROMETRY REVIEWS 2015; 34:595-626. [PMID: 24737647 DOI: 10.1002/mas.21421] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/10/2013] [Indexed: 06/03/2023]
Abstract
This review describes some of the more interesting and imaginative ways in which mass spectrometry has been utilized to study a number of important post-translational modifications over the past two decades; from circa 1990 to 2013. A diverse range of modifications is covered, including citrullination, sulfation, hydroxylation and sumoylation. A summary of the biological role of each modification described, along with some brief mechanistic detail, is also included. Emphasis has been placed on strategies specifically aimed at detecting target modifications, as opposed to more serendipitous modification discovery approaches, which rely upon straightforward product ion scanning methods. The authors have intentionally excluded from this review both phosphorylation and glycosylation since these major modifications have been extensively reviewed elsewhere.
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Affiliation(s)
- Navin Chicooree
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
- School of Chemistry, University of Manchester, Brunswick Street, Manchester, M13 9SU, UK
| | - Richard D Unwin
- Centre for Advanced Discovery and Experimental Therapeutics (CADET), Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, M13 9WL, UK
- Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - John R Griffiths
- CRUK Manchester Institute, University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK
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Corfe BM, Majumdar D, Assadsangabi A, Marsh AMR, Cross SS, Connolly JB, Evans CA, Lobo AJ. Inflammation decreases keratin level in ulcerative colitis; inadequate restoration associates with increased risk of colitis-associated cancer. BMJ Open Gastroenterol 2015; 2:e000024. [PMID: 26462276 PMCID: PMC4599170 DOI: 10.1136/bmjgast-2014-000024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/21/2014] [Accepted: 01/04/2015] [Indexed: 01/08/2023] Open
Abstract
Background Keratins are intermediate filament (IF) proteins, which form part of the epithelial cytoskeleton and which have been implicated pathology of inflammatory bowel diseases (IBD). Methods In this study biopsies were obtained from IBD patients grouped by disease duration and subtype into eight categories based on cancer risk and inflammatory status: quiescent recent onset (<5 years) UC (ROUC); UC with primary sclerosing cholangitis; quiescent long-standing pancolitis (20–40 years) (LSPC); active colitis and non-inflamed proximal colonic mucosa; pancolitis with dysplasia-both dysplastic lesions (DT) and distal rectal mucosa (DR); control group without pathology. Alterations in IF protein composition across the groups were determined by quantitative proteomics. Key protein changes were validated by western immunoblotting and immunohistochemical analysis. Result Acute inflammation resulted in reduced K8, K18, K19 and VIM (all p<0.05) compared to controls and non inflamed mucosa; reduced levels of if– associated proteins were also seen in DT and DR. Increased levels of keratins in LSPC was noted relative to controls or ROUC (K8, K18, K19 and VIM, p<0.05). Multiple K8 forms were noted on immunoblotting, with K8 phosphorylation reduced in progressive disease along with an increase in VIM:K8 ratio. K8 levels and phosphorylation are reduced in acute inflammation but appear restored or elevated in subjects with clinical and endoscopic remission (LSPC) but not apparent in subjects with elevated risk of cancer. Conclusions These data suggest that keratin regulation in remission may influence subsequent cancer risk.
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Affiliation(s)
- Bernard M Corfe
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology , University of Sheffield, The Medical School , Sheffield , UK ; Insigneo Institute for in silico Medicine, University of Sheffield , Sheffield , UK
| | - Debabrata Majumdar
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology , University of Sheffield, The Medical School , Sheffield , UK ; Gastroenterology Unit , Royal Hallamshire Hospital , Sheffield , UK
| | - Arash Assadsangabi
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology , University of Sheffield, The Medical School , Sheffield , UK ; Gastroenterology Unit , Royal Hallamshire Hospital , Sheffield , UK
| | - Alexandra M R Marsh
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology , University of Sheffield, The Medical School , Sheffield , UK ; Gastroenterology Unit , Royal Hallamshire Hospital , Sheffield , UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, Faculty of Medicine, Dentistry & Health , University of Sheffield , Sheffield , UK
| | | | - Caroline A Evans
- Biological and Systems Engineering Group, Department of Chemical and Biological Engineering , ChELSI Institute, University of Sheffield , Sheffield , UK
| | - Alan J Lobo
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology , University of Sheffield, The Medical School , Sheffield , UK ; Gastroenterology Unit , Royal Hallamshire Hospital , Sheffield , UK
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Evans CA, Rosser R, Waby JS, Noirel J, Lai D, Wright PC, Williams EA, Riley SA, Bury JP, Corfe BM. Reduced keratin expression in colorectal neoplasia and associated fields is reversible by diet and resection. BMJ Open Gastroenterol 2015; 2:e000022. [PMID: 26462274 PMCID: PMC4599164 DOI: 10.1136/bmjgast-2014-000022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Patients with adenomatous colonic polyps are at increased risk of developing further polyps suggesting field-wide alterations in cancer predisposition. The current study aimed to identify molecular alterations in the normal mucosa in the proximity of adenomatous polyps and to assess the modulating effect of butyrate, a chemopreventive compound produced by fermentation of dietary residues. METHODS A cross-sectional study was undertaken in patients with adenomatous polyps: biopsy samples were taken from the adenoma, and from macroscopically normal mucosa on the contralateral wall to the adenoma and from the mid-sigmoid colon. In normal subjects biopsies were taken from the mid-sigmoid colon. Biopsies were frozen for proteomic analysis or formalin-fixed for immunohistochemistry. Proteomic analysis was undertaken using iTRAQ workflows followed by bioinformatics analyses. A second dietary fibre intervention study arm used the same endpoints and sampling strategy at the beginning and end of a high-fibre intervention. RESULTS Key findings were that keratins 8, 18 and 19 were reduced in expression level with progressive proximity to the lesion. Lesional tissue exhibited multiple K8 immunoreactive bands and overall reduced levels of keratin. Biopsies from normal subjects with low faecal butyrate also showed depressed keratin expression. Resection of the lesion and elevation of dietary fibre intake both appeared to restore keratin expression level. CONCLUSION Changes in keratin expression associate with progression towards neoplasia, but remain modifiable risk factors. Dietary strategies may improve secondary chemoprevention. TRIAL REGISTRATION NUMBER ISRCTN90852168.
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Affiliation(s)
- Caroline A Evans
- Department of Chemical and Biological Engineering , ChELSI Institute, University of Sheffield , Sheffield , UK
| | - Ria Rosser
- Molecular Gastroenterology Research Group, Department of Oncology , University of Sheffield, The Medical School , Sheffield , UK
| | - Jennifer S Waby
- Molecular Gastroenterology Research Group, Department of Oncology , University of Sheffield, The Medical School , Sheffield , UK ; Department of Biological Sciences , The University of Hull , Hull , UK
| | - Josselin Noirel
- Department of Chemical and Biological Engineering , ChELSI Institute, University of Sheffield , Sheffield , UK ; Conservatoire National des Arts et Mmétiers , Paris , France
| | - Daphne Lai
- Molecular Gastroenterology Research Group, Department of Oncology , University of Sheffield, The Medical School , Sheffield , UK ; Department of Geography , University of Sheffield , Sheffield , UK
| | - Phillip C Wright
- Department of Chemical and Biological Engineering , ChELSI Institute, University of Sheffield , Sheffield , UK
| | - Elizabeth A Williams
- Human Nutrition Unit, Department of Oncology , University of Sheffield, The Medical School , Sheffield , UK
| | - Stuart A Riley
- Department of Gastroenterology , Northern General Hospital , Sheffield , UK
| | - Jonathan P Bury
- Department of Pathology , Royal Hallamshire Hospital , Sheffield , UK
| | - Bernard M Corfe
- Molecular Gastroenterology Research Group, Department of Oncology , University of Sheffield, The Medical School , Sheffield , UK ; Insigneo Institute for in Silico Medicine, The University of Sheffield , Sheffield , UK
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10
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Schatten H, Sun QY. Posttranslationally modified tubulins and other cytoskeletal proteins: their role in gametogenesis, oocyte maturation, fertilization and Pre-implantation embryo development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 759:57-87. [PMID: 25030760 DOI: 10.1007/978-1-4939-0817-2_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The cytoskeleton, mainly consisting of microtubules, intermediate filaments and microfilaments, along with cytoskeleton associated and interconnecting proteins as well as the centrosome, plays enormously important roles in all stages of embryogenesis and undergoes significant changes to accommodate a diversity of cellular functions during gametogenesis, oocyte maturation, fertilization and pre-implantation embryo development. The varied functions of the cytoskeleton can be accomplished on many different levels, among which are a diversity of different posttranslational modifications (PTMs), chemical modifications that regulate activity, localization and interactions with other cellular molecules. PTMs of the cytoskeleton, including phosphorylation, glycosylation, ubiquitination, detyrosination/tyrosination, (poly)glutamylation and (poly)glycylation, acetylation, sumoylation, and palmitoylation, will be addressed in this chapter. Focus will be on (1) Microtubules, microtubule organizing centers (centrosomes), intermediate filaments, microfilaments and their PTMs; (2) Cytoskeletal functions and cytoskeletal PTMs during gametogenesis and oocyte maturation; and (3) Cytoskeletal functions and cytoskeletal PTMs during fertilization and pre-implantation embryo development.
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Affiliation(s)
- Heide Schatten
- Department of Veterinary Pathobiology, University of Missouri, 1600 E Rollins Street, Columbia, MO, 65211, USA,
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Snider NT, Leonard JM, Kwan R, Griggs NW, Rui L, Omary MB. Glucose and SIRT2 reciprocally mediate the regulation of keratin 8 by lysine acetylation. ACTA ACUST UNITED AC 2013; 200:241-7. [PMID: 23358244 PMCID: PMC3563689 DOI: 10.1083/jcb.201209028] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Keratin 8 lysine acetylation, which is enhanced by hyperglycemia and reduced by SIRT2, alters filament organization and reduces solubility. Lysine acetylation is an important posttranslational modification that regulates microtubules and microfilaments, but its effects on intermediate filament proteins (IFs) are unknown. We investigated the regulation of keratin 8 (K8), a type II simple epithelial IF, by lysine acetylation. K8 was basally acetylated and the highly conserved Lys-207 was a major acetylation site. K8 acetylation regulated filament organization and decreased keratin solubility. Acetylation of K8 was rapidly responsive to changes in glucose levels and was up-regulated in response to nicotinamide adenine dinucleotide (NAD) depletion and in diabetic mouse and human livers. The NAD-dependent deacetylase sirtuin 2 (SIRT2) associated with and deacetylated K8. Pharmacologic or genetic inhibition of SIRT2 decreased K8 solubility and affected filament organization. Inhibition of K8 Lys-207 acetylation resulted in site-specific phosphorylation changes of K8. Therefore, K8 acetylation at Lys-207, a highly conserved residue among type II keratins and other IFs, is up-regulated upon hyperglycemia and down-regulated by SIRT2. Keratin acetylation provides a new mechanism to regulate keratin filaments, possibly via modulating keratin phosphorylation.
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Affiliation(s)
- Natasha T Snider
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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Application of the CIRAD mass spectrometry approach for lysine acetylation site discovery. Methods Mol Biol 2013; 981:13-23. [PMID: 23381850 DOI: 10.1007/978-1-62703-305-3_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Mass spectrometry (MS)-based methods typically assess acetylation by detection of a diagnostic ion at 126.1 m/z, corresponding to the immonium ion of acetyl-lysine -NH(3), which is generated by collisionally induced dissociation. A novel implementation of this approach, based on the accurate mass and retention time technique, couples high mass resolution measurement with rapid cycling between low and elevated collision energies to generate intact and fragment high-resolution mass spectra. This allows acetyl lysine diagnostic ions at 126.1 m/z to be monitored and aligned to the precursor m/z based on retention time profile. The technique is termed Collisionally Induced Release of Acetyl Diagnostic. Sequence information is also obtained for acetylation site assignment. This technique to identify acetylation species is information independent as it does not require the sequence of the protein/peptides to identify acetylation, and thus complementary to data-dependent methods. It is suitable for analysis of acetylated peptides, or proteins enriched by immunoprecipitation with acetyl lysine-specific antibodies.
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Evans CA, Griffiths JR, Unwin RD, Whetton AD, Corfe BM. Application of the MIDAS approach for analysis of lysine acetylation sites. Methods Mol Biol 2013; 981:25-36. [PMID: 23381851 DOI: 10.1007/978-1-62703-305-3_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Multiple Reaction Monitoring Initiated Detection and Sequencing (MIDAS™) is a mass spectrometry-based technique for the detection and characterization of specific post-translational modifications (Unwin et al. 4:1134-1144, 2005), for example acetylated lysine residues (Griffiths et al. 18:1423-1428, 2007). The MIDAS™ technique has application for discovery and analysis of acetylation sites. It is a hypothesis-driven approach that requires a priori knowledge of the primary sequence of the target protein and a proteolytic digest of this protein. MIDAS essentially performs a targeted search for the presence of modified, for example acetylated, peptides. The detection is based on the combination of the predicted molecular weight (measured as mass-charge ratio) of the acetylated proteolytic peptide and a diagnostic fragment (product ion of m/z 126.1), which is generated by specific fragmentation of acetylated peptides during collision induced dissociation performed in tandem mass spectrometry (MS) analysis. Sequence information is subsequently obtained which enables acetylation site assignment. The technique of MIDAS was later trademarked by ABSciex for targeted protein analysis where an MRM scan is combined with full MS/MS product ion scan to enable sequence confirmation.
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Affiliation(s)
- Caroline A Evans
- Department of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield, UK
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Majumdar D, Tiernan JP, Lobo AJ, Evans CA, Corfe BM. Keratins in colorectal epithelial function and disease. Int J Exp Pathol 2012; 93:305-18. [PMID: 22974212 DOI: 10.1111/j.1365-2613.2012.00830.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Keratins are the largest subgroup of intermediate filament proteins, which are an important constituent of the cellular cytoskeleton. The principally expressed keratins (K) of the intestinal epithelium are K8, K18 and K19. The specific keratin profile of a particular epithelium provides it with strength and integrity. In the colon, keratins have been shown to regulate electrolyte transport, likely by targeting ion transporters to their correct location in the colonocytes. Keratins are highly dynamic and are subject to post-translational modifications including phosphorylation, acetylation and glycosylation. These affect the filament dynamics and hence solubility of keratins and may contribute to protection against degradation. Keratin null mice (K8(-/-) ) develop colitis, and abnormal keratin mutations have been shown to be associated with inflammatory bowel disease (IBD). Abnormal expression of K7 and K20 has been noted in colitis-associated dysplasia and cancers. In sporadic colorectal cancers (CRCs) may be useful in predicting tumour prognosis; a low K20 expression is noted in CRCs with high microsatellite instability; and keratins have been noted as dysregulated in peri-adenomatous fields. Caspase-cleaved fragment of K18 (M30) in the serum of patients with CRC has been used as a marker of cancer load and to assess response to therapy. These data suggest an emerging importance of keratins in maintaining normal function of the gastrointestinal epithelium as well as being a marker of various colorectal diseases. This review will primarily focus on the biology of these proteins, physiological functions and alterations in IBD and CRCs.
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Affiliation(s)
- Debabrata Majumdar
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology, The Medical School, University of Sheffield, Sheffield, UK
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Majumdar D, Rosser R, Havard S, Lobo AJ, Wright PC, Evans CA, Corfe BM. An integrated workflow for extraction and solubilization of intermediate filaments from colorectal biopsies for proteomic analysis. Electrophoresis 2012; 33:1967-74. [PMID: 22806461 DOI: 10.1002/elps.201100662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report a technique for isolation and solubilization of intermediate filament (IF) proteins from colonic biopsies compatible with both gel electrophoresis and liquid chromatography "shotgun" proteomics using mass spectrometry (MS). This is important because changes in the IF proteome, particularly in keratin expression and modification, are noted in colonic mucosa of patients with colorectal cancer. Though keratins have traditionally been dissolved in high concentration of urea, the latter solvent precludes efficient proteolytic digestion by trypsin prior to gel-free LC-MS/MS approaches. The extraction of cytoskeletal proteins was initially evaluated using MCF-7 cancer cell lines using a published, differential detergent solubilization protocol. IF proteins were extracted from colonic biopsies using a combination of homogenization and sonication. Since comparable efficiency of solubilization was noted on the extracted IF from cell lines between urea and guanidine hydrochloride (GuHCl) in triethylammonium bicarbonate buffer, isolated proteins from endoscopic biopsies were solubilized in GuHCl. Using immunoblotting techniques, we successfully demonstrated isolation of keratins and preservation of posttranslational modifications (phosphorylation, acetylation). Dissolved proteins were tryptically digested and peptides analyzed by MS, showing the functionality of the workflow in shotgun proteomic applications, specifically compatibility of the workflow for isobaric tagging relative and absolute quantification based quantitation approaches.
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Affiliation(s)
- Debabrata Majumdar
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology, The Medical School, University of Sheffield, Sheffield, UK
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Abstract
PTMs (post-translational modifications) of lysine residues have proven to be major regulators of gene expression, protein-protein interactions, and protein processing and degradation. This is of particular importance in regulating the cytoskeleton, an enormously complex system of proteins responsible for cell motility, intracellular trafficking, and maintenance of cell form and structure. The cytoskeleton is present in all cells, including eukaryotes and prokaryotes, and comprises structures such as flagella, cilia and lamellipodia which play critical roles in intracellular transport and cellular division. Cytoskeletal regulation relies on numerous multi-component assemblies. In this chapter, we focus on the regulation of the cytoskeleton by means of PTMs of lysine residues on the cytoskeletal subunits and their accessory proteins. We specifically address the three main classes of cytoskeletal proteins in eukaryotes that polymerize into filaments, including microfilaments (actin filaments), intermediate filaments and microtubules. We discuss the identification and biological importance of lysine acetylation, a regulator of all three filament types. We also review additional lysine modifications, such as ubiquitination and SUMOylation, and their role in protein regulation and processing.
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Effect of different long-chain fatty acids on cholecystokinin release in vitro and energy intake in free-living healthy males. Br J Nutr 2012; 108:755-8. [PMID: 22313587 DOI: 10.1017/s0007114511006003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Long-chain fatty acids have been shown to suppress appetite and reduce energy intake (EI) by stimulating the release of gastrointestinal hormones such as cholecystokinin (CCK). The effect of NEFA acyl chain length on these parameters is not comprehensively understood. An in vitro screen tested the capacity of individual NEFA (C12 to C22) to trigger CCK release. There was a gradient in CCK release with increasing chain length. DHA (C22) stimulated significantly (P < 0.01) more CCK release than all other NEFA tested. Subsequently, we conducted a randomised, controlled, crossover intervention study using healthy males (n 18). The effects of no treatment (NT) and oral doses of emulsified DHA-rich (DHA) and oleic acid (OA)-rich oils were compared using 24 h EI as the primary endpoint. Participants reported significantly (P = 0.039) lower total daily EI (29 % reduction) with DHA compared to NT. There were no differences between DHA compared to OA and OA compared to NT. There was no between-treatment difference in the time to, or EI of, the first post-intervention eating occasion. It is concluded that NEFA stimulate CCK release in a chain length-dependent manner up to C22. These effects may be extended to the in vivo setting, as a DHA-based emulsion significantly reduced short-term EI.
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Kilner J, Waby JS, Chowdry J, Khan AQ, Noirel J, Wright PC, Corfe BM, Evans CA. A proteomic analysis of differential cellular responses to the short-chain fatty acids butyrate, valerate and propionate in colon epithelial cancer cells. MOLECULAR BIOSYSTEMS 2011; 8:1146-56. [PMID: 22075547 DOI: 10.1039/c1mb05219e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The short chain fatty acids (SCFAs) are inhibitors of histone deacetylases (HDACi); they are produced naturally in the colon by fermentation. They affect cellular processes at a molecular and transcriptional level, the mechanisms of which may involve large numbers of proteins and integrated pathways. Butyrate is the most biologically potent of the SCFAs in colon epithelial cells, inhibiting human colon carcinoma cell proliferation and inducing apoptosis in vitro. In order to investigate the hypothesis that propionate and valerate possess unique and independent actions from butyrate, we combined proteomic and cellomic approaches for large-scale comparative analysis. Proteomic evaluation was undertaken using an iTRAQ tandem mass-spectrometry workflow and high-throughput High-content Analysis microscopy (HCA) was applied to generate cellomic information on the cell cycle and the cytoskeletal structure. Our results show that these SCFAs possess specific effects. Butyrate was shown to have more pronounced effects on the keratins and intermediate filaments (IFs); while valerate altered the β-tubulin isotypes' expression and the microtubules (MTs); propionate was involved in both mechanisms, displaying intermediate effects. These data suggest distinct physiological roles for SCFAs in colon epithelial function, offering new possibilities for cancer therapeutics.
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Affiliation(s)
- Josephine Kilner
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, United Kingdom
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Fung KYC, Cursaro C, Lewanowitsch T, Brierley GV, McColl SR, Lockett T, Head R, Hoffmann P, Cosgrove L. A combined free-flow electrophoresis and DIGE approach to identify proteins regulated by butyrate in HT29 cells. Proteomics 2011; 11:964-971. [DOI: 10.1002/pmic.201000429] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Sadoul K, Wang J, Diagouraga B, Khochbin S. The tale of protein lysine acetylation in the cytoplasm. J Biomed Biotechnol 2011; 2011:970382. [PMID: 21151618 PMCID: PMC2997609 DOI: 10.1155/2011/970382] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Accepted: 09/29/2010] [Indexed: 12/21/2022] Open
Abstract
Reversible posttranslational modification of internal lysines in many cellular or viral proteins is now emerging as part of critical signalling processes controlling a variety of cellular functions beyond chromatin and transcription. This paper aims at demonstrating the role of lysine acetylation in the cytoplasm driving and coordinating key events such as cytoskeleton dynamics, intracellular trafficking, vesicle fusion, metabolism, and stress response.
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Affiliation(s)
- Karin Sadoul
- 1INSERM, U823, Institut Albert Bonniot, Université Joseph Fourier Grenoble 1, 38700 Grenoble, France
- *Karin Sadoul:
| | - Jin Wang
- 1INSERM, U823, Institut Albert Bonniot, Université Joseph Fourier Grenoble 1, 38700 Grenoble, France
- 2State Key Laboratory of Medical Genomics, Department of Hematology, Ruijin Hospital, Shanghai Institute of Hematology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Boubou Diagouraga
- 1INSERM, U823, Institut Albert Bonniot, Université Joseph Fourier Grenoble 1, 38700 Grenoble, France
| | - Saadi Khochbin
- 1INSERM, U823, Institut Albert Bonniot, Université Joseph Fourier Grenoble 1, 38700 Grenoble, France
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Kilner J, Corfe BM, Wilkinson SJ. Modelling the microtubule: towards a better understanding of short-chain fatty acid molecular pharmacology. MOLECULAR BIOSYSTEMS 2011; 7:975-83. [DOI: 10.1039/c0mb00281j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Development of a high throughput, quantitative assay of the effects of fungal-derived griseofulvin and cordycepin, and butyrate on the cytoskeleton. Proc Nutr Soc 2011. [DOI: 10.1017/s0029665111000966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ikonomou G, Samiotaki M, Panayotou G. Proteomic methodologies and their application in colorectal cancer research. Crit Rev Clin Lab Sci 2009; 46:319-42. [DOI: 10.3109/10408360903375277] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Corfe BM, Williams EA, Bury JP, Riley SA, Croucher LJ, Lai DYL, Evans CA. A study protocol to investigate the relationship between dietary fibre intake and fermentation, colon cell turnover, global protein acetylation and early carcinogenesis: the FACT study. BMC Cancer 2009; 9:332. [PMID: 19765278 PMCID: PMC2751778 DOI: 10.1186/1471-2407-9-332] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Accepted: 09/18/2009] [Indexed: 12/17/2022] Open
Abstract
Background A number of studies, notably EPIC, have shown a descrease in colorectal cancer risk associated with increased fibre consumption. Whilst the underlying mechanisms are likely to be multifactorial, production of the short-chain fatty-acid butyrate fro butyratye is frequently cited as a major potential contributor to the effect. Butyrate inhibits histone deacetylases, which work on a wide range of proteins over and above histones. We therefore hypothesized that alterations in the acetylated proteome may be associated with a cancer risk phenotype in the colorectal mucosa, and that such alterations are candidate biomarkers for effectiveness of fibre interventions in cancer prevention. Methods an design There are two principal arms to this study: (i) a cross-sectional study (FACT OBS) of 90 subjects recruited from gastroenterology clinics and; (ii) an intervention trial in 40 subjects with an 8 week high fibre intervention. In both studies the principal goal is to investigate a link between fibre intake, SCFA production and global protein acetylation. The primary measure is level of faecal butyrate, which it is hoped will be elevated by moving subjects to a high fibre diet. Fibre intakes will be estimated in the cross-sectional group using the EPIC Food Frequency Questionnaire. Subsidiary measures of the effect of butyrate on colon mucosal function and pre-cancerous phenotype will include measures of apoptosis, apoptotic regulators cell cycle and cell division. Discussion This study will provide a new level of mechanistic data on alterations in the functional proteome in response to the colon microenvironment which may underwrite the observed cancer preventive effect of fibre. The study may yield novel candidate biomarkers of fibre fermentation and colon mucosal function. Trial Registration Trial Registration Number: ISRCTN90852168
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Affiliation(s)
- Bernard M Corfe
- Department of Oncology, University of Sheffield, The Medical School, Beech Hill Road, Sheffield, S10 2RX, UK.
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Drake PJM, Griffiths GJ, Shaw L, Benson RP, Corfe BM. Application of High-Content Analysis to the Study of Post-Translational Modifications of the Cytoskeleton. J Proteome Res 2008; 8:28-34. [DOI: 10.1021/pr8006396] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Peter J. M. Drake
- Human Nutrition Unit, School of Medicine, University of Sheffield, Royal Hallamshire Hospital, Sheffield S10 2JF, United Kingdom, and Imagen Biotechnology Ltd., Grafton Street, Manchester M13 9NT, United Kingdom
| | - Gareth J. Griffiths
- Human Nutrition Unit, School of Medicine, University of Sheffield, Royal Hallamshire Hospital, Sheffield S10 2JF, United Kingdom, and Imagen Biotechnology Ltd., Grafton Street, Manchester M13 9NT, United Kingdom
| | - Leila Shaw
- Human Nutrition Unit, School of Medicine, University of Sheffield, Royal Hallamshire Hospital, Sheffield S10 2JF, United Kingdom, and Imagen Biotechnology Ltd., Grafton Street, Manchester M13 9NT, United Kingdom
| | - Rod P. Benson
- Human Nutrition Unit, School of Medicine, University of Sheffield, Royal Hallamshire Hospital, Sheffield S10 2JF, United Kingdom, and Imagen Biotechnology Ltd., Grafton Street, Manchester M13 9NT, United Kingdom
| | - Bernard M. Corfe
- Human Nutrition Unit, School of Medicine, University of Sheffield, Royal Hallamshire Hospital, Sheffield S10 2JF, United Kingdom, and Imagen Biotechnology Ltd., Grafton Street, Manchester M13 9NT, United Kingdom
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