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Clayton NS, Carter EP, Fearon AE, Heward JA, Rodríguez Fernández L, Boughetane L, Wilkes EH, Cutillas PR, Grose RP. HDAC Inhibition Restores Response to HER2-Targeted Therapy in Breast Cancer via PHLDA1 Induction. Int J Mol Sci 2023; 24:6228. [PMID: 37047202 PMCID: PMC10094256 DOI: 10.3390/ijms24076228] [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: 03/06/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
The downregulation of Pleckstrin Homology-Like Domain family A member 1 (PHLDA1) expression mediates resistance to targeted therapies in receptor tyrosine kinase-driven cancers. The restoration and maintenance of PHLDA1 levels in cancer cells thus constitutes a potential strategy to circumvent resistance to inhibitors of receptor tyrosine kinases. Through a pharmacological approach, we identify the inhibition of MAPK signalling as a crucial step in PHLDA1 downregulation. Further ChIP-qPCR analysis revealed that MEK1/2 inhibition produces significant epigenetic changes at the PHLDA1 locus, specifically a decrease in the activatory marks H3Kme3 and H3K27ac. In line with this, we show that treatment with the clinically relevant class I histone deacetylase (HDAC) inhibitor 4SC-202 restores PHLDA1 expression in lapatinib-resistant human epidermal growth factor receptor-2 (HER2)+ breast cancer cells. Critically, we show that when given in combination, 4SC-202 and lapatinib exert synergistic effects on 2D cell proliferation and colony formation capacity. We therefore propose that co-treatment with 4SC-202 may prolong the clinical efficacy of lapatinib in HER2+ breast cancer patients.
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Affiliation(s)
- Natasha S. Clayton
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Edward P. Carter
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Abbie E. Fearon
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - James A. Heward
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Lucía Rodríguez Fernández
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Lina Boughetane
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Edmund H. Wilkes
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Pedro R. Cutillas
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Richard P. Grose
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
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2
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Abstract
The human genome is widely transcribed outside of protein-coding genes, producing thousands of noncoding RNAs from different subfamilies including enhancer RNAs. Functional studies to determine the role of individual genes are challenging with noncoding RNAs appearing to be more difficult to knockdown than mRNAs. One factor that may have hindered progress is that the majority of noncoding RNAs are thought to be located within the nucleus, where the efficiency of traditional RNA interference techniques is debatable. Here we present an alternative RNA interference technique utilizing Locked Nucleic Acids, which is able to efficiently knockdown noncoding RNAs irrespective of intracellular location.
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Affiliation(s)
- Benoit T Roux
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Mark A Lindsay
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - James A Heward
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
- Centre for Haemato-Oncology, Barts Cancer Institute, Charterhouse Square, London, EC1M 6BQ, UK.
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Roux BT, Heward JA, Donnelly LE, Jones SW, Lindsay MA. Catalog of Differentially Expressed Long Non-Coding RNA following Activation of Human and Mouse Innate Immune Response. Front Immunol 2017; 8:1038. [PMID: 28900427 PMCID: PMC5581803 DOI: 10.3389/fimmu.2017.01038] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [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: 06/06/2017] [Accepted: 08/11/2017] [Indexed: 12/12/2022] Open
Abstract
Despite increasing evidence to indicate that long non-coding RNAs (lncRNAs) are novel regulators of immunity, there has been no systematic attempt to identify and characterize the lncRNAs whose expression is changed following the induction of the innate immune response. To address this issue, we have employed next-generation sequencing data to determine the changes in the lncRNA profile in four human (monocytes, macrophages, epithelium, and chondrocytes) and four mouse cell types (RAW 264.7 macrophages, bone marrow-derived macrophages, peritoneal macrophages, and splenic dendritic cells) following exposure to the pro-inflammatory mediators, lipopolysaccharides (LPS), or interleukin-1β. We show differential expression of 204 human and 210 mouse lncRNAs, with positional analysis demonstrating correlation with immune-related genes. These lncRNAs are predominantly cell-type specific, composed of large regions of repeat sequences, and show poor evolutionary conservation. Comparison within the human and mouse sequences showed less than 1% sequence conservation, although we identified multiple conserved motifs. Of the 204 human lncRNAs, 21 overlapped with syntenic mouse lncRNAs, of which five were differentially expressed in both species. Among these syntenic lncRNA was IL7-AS (antisense), which was induced in multiple cell types and shown to regulate the production of the pro-inflammatory mediator interleukin-6 in both human and mouse cells. In summary, we have identified and characterized those lncRNAs that are differentially expressed following activation of the human and mouse innate immune responses and believe that these catalogs will provide the foundation for the future analysis of the role of lncRNAs in immune and inflammatory responses.
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Affiliation(s)
- Benoit T Roux
- Department of Pharmacy and Pharmacology, University of Bath, Bath, United Kingdom
| | - James A Heward
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Louise E Donnelly
- Airway Disease, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Simon W Jones
- Institute of Inflammation and Ageing, MRC-ARUK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, United Kingdom
| | - Mark A Lindsay
- Department of Pharmacy and Pharmacology, University of Bath, Bath, United Kingdom.,Airway Disease, National Heart and Lung Institute, Imperial College, London, United Kingdom
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Hamann PD, Roux BT, Heward JA, Love S, McHugh NJ, Jones SW, Lindsay MA. Transcriptional profiling identifies differential expression of long non-coding RNAs in Jo-1 associated and inclusion body myositis. Sci Rep 2017; 7:8024. [PMID: 28808260 PMCID: PMC5556005 DOI: 10.1038/s41598-017-08603-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 05/11/2017] [Accepted: 07/14/2017] [Indexed: 12/22/2022] Open
Abstract
Myositis is characterised by muscle inflammation and weakness. Although generally thought to be driven by a systemic autoimmune response, increasing evidence suggests that intrinsic changes in the muscle might also contribute to the pathogenesis. Long non-coding RNAs (lncRNAs) are a family of novel genes that regulate gene transcription and translation. To determine the potential role of lncRNAs, we employed next generation sequencing to examine the transcriptome in muscle biopsies obtained from two histologically distinct patient populations, inclusion body myositis (IBM) and anti-Jo-1-associated myositis (Jo-1). 1287 mRNAs and 1068 mRNAs were differentially expressed in the muscle from Jo-1 and IBM patients, respectively. Pathway analysis showed the top canonical pathway in both Jo-1 and IBM was oxidative phosphorylation and mitochondrial dysfunction. We identified 731 known and 325 novel lncRNAs in the muscles biopsies. Comparison with controls showed 55 and 46 lncRNAs were differentially expressed in IBM and Jo-1 myositis, respectively. Of these, 16 lncRNAs were differentially expressed in both IBM and Jo-1 myositis and included upregulated H19, lncMyoD and MALAT1. Given that these are known to regulate muscle proliferation and differentiation, we speculate that changes in lncRNAs might contribute to the phenotypic changes in Jo-1 and IBM myositis.
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Affiliation(s)
- Philip D Hamann
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK.,Royal National Hospital for Rheumatic Diseases, Upper Borough Walls, Bath, BA1 1RL, UK
| | - Benoit T Roux
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - James A Heward
- Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Seth Love
- Dementia Research Group, Institute of Clinical Neurosciences, School of Clinical Sciences, University of Bristol, Bristol, BS16 1LE, UK
| | - Neil J McHugh
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK.,Royal National Hospital for Rheumatic Diseases, Upper Borough Walls, Bath, BA1 1RL, UK
| | - Simon W Jones
- MRC ARK Centre for Musculoskeletal Aging Research, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Mark A Lindsay
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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Korfi K, Ali S, Heward JA, Fitzgibbon J. Follicular lymphoma, a B cell malignancy addicted to epigenetic mutations. Epigenetics 2017; 12:370-377. [PMID: 28106467 PMCID: PMC5453190 DOI: 10.1080/15592294.2017.1282587] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 10/31/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 01/07/2023] Open
Abstract
While follicular lymphoma (FL) is exquisitely responsive to immuno-chemotherapy, many patients follow a relapsing remitting clinical course driven in part by a common precursor cell (CPC) population. Advances in next generation sequencing have provided valuable insights into the genetic landscape of FL and its clonal evolution in response to therapy, implicating perturbations of epigenetic regulators as a hallmark of the disease. Recurrent mutations of histone modifiers KMT2D, CREBBP, EP300, EZH2, ARIDIA, and linker histones are likely early events arising in the CPC pool, rendering epigenetic based therapies conceptually attractive for treatment of indolent and transformed FL. This review provides a synopsis of the main epigenetic aberrations and the current efforts in development and testing of epigenetic therapies in this B cell malignancy.
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Affiliation(s)
- Koorosh Korfi
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Sara Ali
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - James A. Heward
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jude Fitzgibbon
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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Dawkins JBN, Wang J, Maniati E, Heward JA, Koniali L, Kocher HM, Martin SA, Chelala C, Balkwill FR, Fitzgibbon J, Grose RP. Reduced Expression of Histone Methyltransferases KMT2C and KMT2D Correlates with Improved Outcome in Pancreatic Ductal Adenocarcinoma. Cancer Res 2016; 76:4861-71. [PMID: 27280393 PMCID: PMC5321534 DOI: 10.1158/0008-5472.can-16-0481] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [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: 02/18/2016] [Accepted: 05/30/2016] [Indexed: 12/21/2022]
Abstract
Genes encoding the histone H3 lysine 4 methyltransferases KMT2C and KMT2D are subject to deletion and mutation in pancreatic ductal adenocarcinoma (PDAC), where these lesions identify a group of patients with a more favorable prognosis. In this study, we demonstrate that low KMT2C and KMT2D expression in biopsies also defines better outcome groups, with median survivals of 15.9 versus 9.2 months (P = 0.029) and 19.9 versus 11.8 months (P = 0.001), respectively. Experiments with eight human pancreatic cell lines showed attenuated cell proliferation when these methyltransferases were depleted, suggesting that this improved outcome may reflect a cell-cycle block with diminished progression from G0-G1 RNA-seq analysis of PDAC cell lines following KMT2C or KMT2D knockdown identified 31 and 124 differentially expressed genes, respectively, with 19 genes in common. Gene-set enrichment analysis revealed significant downregulation of genes related to cell-cycle and growth. These data were corroborated independently by examining KMT2C/D signatures extracted from the International Cancer Genome Consortium and The Cancer Genome Atlas datasets. Furthermore, these experiments highlighted a potential role for NCAPD3, a condensin II complex subunit, as an outcome predictor in PDAC using existing gene expression series. Kmt2d depletion in KC/KPC cell lines also led to an increased response to the nucleoside analogue 5-fluorouracil, suggesting that lower levels of this methyltransferase may mediate the sensitivity of PDAC to particular treatments. Therefore, it may also be therapeutically beneficial to target these methyltransferases in PDAC, especially in those patients demonstrating higher KTM2C/D expression. Cancer Res; 76(16); 4861-71. ©2016 AACR.
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Affiliation(s)
- Joshua B N Dawkins
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jun Wang
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Eleni Maniati
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - James A Heward
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Lola Koniali
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Hemant M Kocher
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Sarah A Martin
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Claude Chelala
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Frances R Balkwill
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jude Fitzgibbon
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Richard P Grose
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.
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Pearson MJ, Philp AM, Heward JA, Roux BT, Walsh DA, Davis ET, Lindsay MA, Jones SW. Long Intergenic Noncoding RNAs Mediate the Human Chondrocyte Inflammatory Response and Are Differentially Expressed in Osteoarthritis Cartilage. Arthritis Rheumatol 2016; 68:845-56. [PMID: 27023358 PMCID: PMC4950001 DOI: 10.1002/art.39520] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [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: 07/01/2015] [Accepted: 11/12/2015] [Indexed: 01/07/2023]
Abstract
OBJECTIVE To identify long noncoding RNAs (lncRNAs), including long intergenic noncoding RNAs (lincRNAs), antisense RNAs, and pseudogenes, associated with the inflammatory response in human primary osteoarthritis (OA) chondrocytes and to explore their expression and function in OA. METHODS OA cartilage was obtained from patients with hip or knee OA following joint replacement surgery. Non-OA cartilage was obtained from postmortem donors and patients with fracture of the neck of the femur. Primary OA chondrocytes were isolated by collagenase digestion. LncRNA expression analysis was performed by RNA sequencing (RNAseq) and quantitative reverse transcriptase-polymerase chain reaction. Modulation of lncRNA chondrocyte expression was achieved using LNA longRNA GapmeRs (Exiqon). Cytokine production was measured with Luminex. RESULTS RNAseq identified 983 lncRNAs in primary human hip OA chondrocytes, 183 of which had not previously been identified. Following interleukin-1β (IL-1β) stimulation, we identified 125 lincRNAs that were differentially expressed. The lincRNA p50-associated cyclooxygenase 2-extragenic RNA (PACER) and 2 novel chondrocyte inflammation-associated lincRNAs (CILinc01 and CILinc02) were differentially expressed in both knee and hip OA cartilage compared to non-OA cartilage. In primary OA chondrocytes, these lincRNAs were rapidly and transiently induced in response to multiple proinflammatory cytokines. Knockdown of CILinc01 and CILinc02 expression in human chondrocytes significantly enhanced the IL-1-stimulated secretion of proinflammatory cytokines. CONCLUSION The inflammatory response in human OA chondrocytes is associated with widespread changes in the profile of lncRNAs, including PACER, CILinc01, and CILinc02. Differential expression of CILinc01 and CIinc02 in hip and knee OA cartilage, and their role in modulating cytokine production during the chondrocyte inflammatory response, suggest that they may play an important role in mediating inflammation-driven cartilage degeneration in OA.
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Ilott NE, Heward JA, Roux B, Tsitsiou E, Fenwick PS, Lenzi L, Goodhead I, Hertz-Fowler C, Heger A, Hall N, Donnelly LE, Sims D, Lindsay MA. Corrigendum: Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes. Nat Commun 2015; 6:6814. [PMID: 25855049 PMCID: PMC5784311 DOI: 10.1038/ncomms7814] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Heward JA, Roux BT, Lindsay MA. Divergent signalling pathways regulate lipopolysaccharide-induced eRNA expression in human monocytic THP1 cells. FEBS Lett 2014; 589:396-406. [PMID: 25554418 PMCID: PMC4306547 DOI: 10.1016/j.febslet.2014.12.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/08/2014] [Accepted: 12/19/2014] [Indexed: 11/24/2022]
Abstract
eRNAs are expressed from enhancers and have been shown to regulate gene expression. Expression of eRNAs is widespread upon activation of the innate immune response. We show that the NF-κB signalling pathway regulates LPS-induced eRNAs. Expression of individual eRNAs is also dependent on ERK-1/2 and p38.
Recent studies have indicated that non-coding RNAs transcribed from enhancer regions are important regulators of enhancer function and gene expression. In this report, we have characterised the expression of six enhancer RNAs (eRNAs) induced in human monocytic THP1 cells following activation of the innate immune response by lipopolysaccharide (LPS). Specifically, we have demonstrated that LPS-induced expression of individual eRNAs is mediated through divergent intracellular signalling pathways that includes NF-κB and the mitogen activated protein kinases, extracellular regulated kinase-1/2 and p38.
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Affiliation(s)
- James A Heward
- Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, United Kingdom
| | - Benoit T Roux
- Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, United Kingdom
| | - Mark A Lindsay
- Department of Pharmacy and Pharmacology, University of Bath, Bath BA2 7AY, United Kingdom.
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Heward JA, Lindsay MA. Long non-coding RNAs in the regulation of the immune response. Trends Immunol 2014; 35:408-19. [PMID: 25113636 PMCID: PMC7106471 DOI: 10.1016/j.it.2014.07.005] [Citation(s) in RCA: 326] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 07/13/2014] [Accepted: 07/16/2014] [Indexed: 11/23/2022]
Abstract
Widespread changes in lncRNA expresssion are associated with the immune response. lncRNAs regulate the inflammatory response following activation of innate immunity. lncRNAs regulate T cell differentiation and migration. The action of long non-coding RNAs is mediated via diverse mechanisms.
It is increasingly clear that long non-coding RNAs (lncRNAs) regulate a variety biological responses, and that they do so by a diverse range of mechanisms. In the field of immunology, recent publications have shown widespread changes in the expression of lncRNAs during the activation of the innate immune response and T cell development, differentiation, and activation. These lncRNAs control important aspects of immunity such as production of inflammatory mediators, differentiation, and cell migration through regulating protein–protein interactions or via their ability to basepair with RNA and DNA. We review the current understanding of the mechanism of action of these immune-related lncRNAs, discuss their impact on physiological and pathological processes, and highlight important areas of inquiry at the intersection between immunology and lncRNA biology.
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Affiliation(s)
- James A Heward
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Mark A Lindsay
- Department of Pharmacy and Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, UK.
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Abstract
When referring pregnant women to an antenatal clinic many general practitioners and midwives presented details of their care in an incomplete and inconsistent manner. As a result, hospital staff often had insufficient basic data from which to work. We recommend that those providing care decide what information they need and make the rationale of collecting this information the subject of a well-evaluated local education programme.
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Affiliation(s)
- E A Cooper
- The Command Hygienic Laboratory, School of Army Sanitation, Aldershot
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