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Somani J, Ramchandran S, Lähdesmäki H. A personalised approach for identifying disease-relevant pathways in heterogeneous diseases. NPJ Syst Biol Appl 2020; 6:17. [PMID: 32518234 PMCID: PMC7283216 DOI: 10.1038/s41540-020-0130-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 03/12/2020] [Indexed: 11/30/2022] Open
Abstract
Numerous time-course gene expression datasets have been generated for studying the biological dynamics that drive disease progression; and nearly as many methods have been proposed to analyse them. However, barely any method exists that can appropriately model time-course data while accounting for heterogeneity that entails many complex diseases. Most methods manage to fulfil either one of those qualities, but not both. The lack of appropriate methods hinders our capability of understanding the disease process and pursuing preventive treatments. We present a method that models time-course data in a personalised manner using Gaussian processes in order to identify differentially expressed genes (DEGs); and combines the DEG lists on a pathway-level using a permutation-based empirical hypothesis testing in order to overcome gene-level variability and inconsistencies prevalent to datasets from heterogenous diseases. Our method can be applied to study the time-course dynamics, as well as specific time-windows of heterogeneous diseases. We apply our personalised approach on three longitudinal type 1 diabetes (T1D) datasets, where the first two are used to determine perturbations taking place during early prognosis of the disease, as well as in time-windows before autoantibody positivity and T1D diagnosis; and the third is used to assess the generalisability of our method. By comparing to non-personalised methods, we demonstrate that our approach is biologically motivated and can reveal more insights into progression of heterogeneous diseases. With its robust capabilities of identifying disease-relevant pathways, our approach could be useful for predicting events in the progression of heterogeneous diseases and even for biomarker identification.
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Affiliation(s)
- Juhi Somani
- Department of Computer Science, Aalto University, 02150, Espoo, Finland
| | | | - Harri Lähdesmäki
- Department of Computer Science, Aalto University, 02150, Espoo, Finland.
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Marcovecchio ML, Wicker LS, Dunger DB, Dutton SJ, Kopijasz S, Scudder C, Todd JA, Johnson PRV. Interleukin-2 Therapy of Autoimmunity in Diabetes (ITAD): a phase 2, multicentre, double-blind, randomized, placebo-controlled trial. Wellcome Open Res 2020; 5:49. [PMID: 32399500 PMCID: PMC7194454 DOI: 10.12688/wellcomeopenres.15697.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/10/2020] [Indexed: 01/11/2023] Open
Abstract
Type 1 diabetes is a common autoimmune disease due to destruction of pancreatic β cells, resulting in lifelong need for insulin. Evidence suggest that maintaining residual β-cell function can improve glucose control and reduce risk of hypoglycaemia and vascular complications. Non-clinical, preclinical and some preliminary clinical data suggest that low-dose interleukin-2 (IL-2) therapy could block pancreatic β cells destruction by increasing the number of functional regulatory T cells (Tregs) that inhibit islet-specific autoreactive effector T cells (Teffs). However, there is lack of data on the effect of low-dose IL-2 in newly diagnosed children and adolescents with T1D as well as lack of specific data on its potential effect on β-cell function. The ' Interleukin-2 Therapy of Autoimmunity in Diabetes (ITAD)' is a phase 2, multicentre, double-blind, randomised, placebo-controlled trial in children and adolescents (6-18 years; having detectable C-peptide) initiated within 6 weeks of T1D diagnosis. A total of 45 participants will be randomised in a 2:1 ratio to receive either ultra-low dose IL-2 (aldesleukin), at a dose of 0.2 x 10 6 IU/m 2 twice-weekly, given subcutaneously, or placebo, for 6 months. The primary objective is to assess the effects of ultra-low dose aldesleukin administration on endogenous β-cell function as measured by frequent home dried blood spot (DBS) fasting and post-prandial C-peptide in children and adolescents with newly diagnosed T1D. The secondary objectives are: 1) to assess the efficacy of regular dosing of aldesleukin in increasing Treg levels; 2) to confirm the clinical safety and tolerability of ultra-low dose aldesleukin; 3) to assess changes in the immune system indicating benefit or potential risk for future gains/loss in β-cell function and immune function; 4) to assess treatment effect on glycaemic control. Trial registration: EudraCT 2017-002126-20 (06/02/2019).
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Affiliation(s)
| | - Linda S. Wicker
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, OX3 7BN, UK
| | - David B. Dunger
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Susan J. Dutton
- Oxford Clinical Trials Research Unit, Centre for Statistics in Medicine, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, OX3 7LD, UK
| | - Sylwia Kopijasz
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, OX3 7BN, UK
| | - Claire Scudder
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, OX3 7BN, UK
| | - John A. Todd
- JDRF/Wellcome Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Wellcome Centre for Human Genetics, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, OX3 7BN, UK
| | - Paul R. V. Johnson
- Islet Transplant Research Group, Nuffield Department of Surgical Sciences, Centre for Diabetes, Endocrinology and Metabolism (OCDEM), University of Oxford, Oxford, OX3 9DU, UK
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Sochett E, Noone D, Grattan M, Slorach C, Moineddin R, Elia Y, Mahmud FH, Dunger DB, Dalton N, Cherney D, Scholey J, Reich H, Deanfield J. Relationship between serum inflammatory markers and vascular function in a cohort of adolescents with type 1 diabetes. Cytokine 2017; 99:233-239. [PMID: 28760408 DOI: 10.1016/j.cyto.2017.07.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 06/27/2017] [Accepted: 07/17/2017] [Indexed: 12/20/2022]
Abstract
OBJECTIVE The contribution of inflammation to endothelial/vascular dysfunction in early Type I Diabetes (T1D) is not well understood. The objective of this study was to examine the interaction between systemic inflammation and vascular function in adolescent's with and without-T1D. METHODS 51 subjects from our observational cohort of adolescents with T1D (JDRF-CCTN), and 59 healthy controls (HC) were studied. Serum cytokines-chemokines were quantified using Human 41-Plex Array, and vascular function was measured by Flow Mediated Dilatation (FMD), Pulse Wave Velocity (PWV) and Blood Pressure (BP). Factor Analysis was used to identify pro- and anti-inflammatory cytokine-chemokine factors, which were then correlated with vascular outcomes. RESULTS Three pro-inflammatory factors were identified in HC and three in TID, and a single anti-inflammatory factor in both groups. In HC there was a positive correlation (r=0.33; p=0.01) between control proinflammatory Factor 1 and systolic BP and a negative correlation between control proinflammatory Factor 3(r=-0.29; p=0.02) and diastolic BP. Control proinflammatory Factor 2 correlated positively with PWV. In TID subjects, no correlations were found between any of the pro-inflammatory factors and the vascular measurements. No correlations were found between the anti-inflammatory factors and BP, FMD and PWV in either HC or T1D. Levels of pro-inflammatory analytes, EGF, GRO, PDGF-BB, PDGF-AA and sCD40L were significantly higher in T1D. CONCLUSIONS The cytokine-chemokine signature in early T1D, prior to the development of arterial disease, is significantly different from that seen in healthy controls. This may be relevant to pathophysiology, determining risk and identifying target cytokines-chemokines for intervention in T1D.
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Affiliation(s)
- Etienne Sochett
- Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, Canada; Division of Endocrinology, Hospital for Sick Children, Toronto, Canada.
| | - Damien Noone
- Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, Canada; Division of Nephrology, Hospital for Sick Children, Toronto, Canada
| | - Michael Grattan
- Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, Canada; London Health Sciences Centre, Children's Hospital, University of Western Ontario, London, Ontario, Canada
| | - Cameron Slorach
- Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Rahim Moineddin
- Department of Family and Community Medicine, University of Toronto, Toronto, Canada
| | - Yesmino Elia
- Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Farid H Mahmud
- Department of Paediatrics, Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - David B Dunger
- Department of Paediatrics, University of Cambridge, Cambridge, UK Department of Medicine, UK
| | - Neil Dalton
- WellChild Laboratory, Evelina Children's Hospital, St Thomas' Hospital, London, UK
| | - David Cherney
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Canada
| | - James Scholey
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Canada
| | - Heather Reich
- Division of Nephrology, University Health Network, University of Toronto, Toronto, Canada
| | - John Deanfield
- Institute of Child Health, University College London, London, UK
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Gelaleti RB, Damasceno DC, Salvadori DMF, Calderon IMP, Costa RAA, Piculo F, Martins DC, Rudge MVC. Gene expression profile of whole blood cells differs in pregnant women with positive screening and negative diagnosis for gestational diabetes. BMJ Open Diabetes Res Care 2016; 4:e000273. [PMID: 27843554 PMCID: PMC5073650 DOI: 10.1136/bmjdrc-2016-000273] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/02/2016] [Accepted: 09/05/2016] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVE To evaluate the gene expression profile of whole blood cells in pregnant women without diabetes (with positive screening and negative diagnosis for gestational diabetes mellitus (GDM)) compared with pregnant women with negative screening for GDM. RESEARCH DESIGN AND METHODS Pregnant women were recruited in the Diabetes Perinatal Research Centre-Botucatu Medical School-UNESP and Botucatuense Mercy Hospital (UNIMED). Distributed into 2 groups: control (n=8), women with negative screening and non-diabetic (ND, n=13), with positive screening and negative diagnosis of GDM. A peripheral blood sample was collected for glucose, glycated hemoglobin, and microarray gene expression analyses. RESULTS The evaluation of gene expression profiles showed significant differences between the control group and the ND group, with 22 differentially expressed gene sequences. Gene networks and interaction tables were generated to evaluate the biological processes associated with differentially expressed genes of interest. CONCLUSIONS In the group with positive screening, there is an apparent regulatory balance between the functions of the differentially expressed genes related to the pathogenesis of diabetes and a compensatory attempt to mitigate the possible etiology. These results support the 'two-step Carpenter-Coustan' strategy because pregnant women with negative screening do not need to continue on diagnostic investigation of gestational diabetes, thus reducing the cost of healthcare and the medicalization of pregnancy. Although not diabetic, they do have risk factors, and thus attention to these genes is important when considering disease evolution because this pregnant women are a step toward developing diabetes compared with women without these risk factors.
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Affiliation(s)
- Rafael B Gelaleti
- Department of Gynecology and Obstetrics, Botucatu Medical School, UNESP_Univ Estadual Paulista, Laboratory of Experimental Research in Gynecology and Obstetrics, Botucatu, Brazil
| | - Débora C Damasceno
- Department of Gynecology and Obstetrics, Botucatu Medical School, UNESP_Univ Estadual Paulista, Laboratory of Experimental Research in Gynecology and Obstetrics, Botucatu, Brazil
| | - Daisy M F Salvadori
- Department of Pathology, Botucatu Medical School, UNESP_Univ Estadual Paulista, Laboratory of Toxicogenomics and Nutrigenomics, Botucatu, Brazil
| | - Iracema M P Calderon
- Department of Gynecology and Obstetrics, Botucatu Medical School, UNESP_Univ Estadual Paulista, Laboratory of Experimental Research in Gynecology and Obstetrics, Botucatu, Brazil
| | - Roberto A A Costa
- Department of Gynecology and Obstetrics, Botucatu Medical School, UNESP_Univ Estadual Paulista, Laboratory of Experimental Research in Gynecology and Obstetrics, Botucatu, Brazil
| | - Fernanda Piculo
- Department of Gynecology and Obstetrics, Botucatu Medical School, UNESP_Univ Estadual Paulista, Laboratory of Experimental Research in Gynecology and Obstetrics, Botucatu, Brazil
| | - David C Martins
- Center for Mathematics, Computation and Cognition, Federal University of ABC, Santo André, Brazil
| | - Marilza V C Rudge
- Department of Gynecology and Obstetrics, Botucatu Medical School, UNESP_Univ Estadual Paulista, Laboratory of Experimental Research in Gynecology and Obstetrics, Botucatu, Brazil
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Differential expression of dicer, miRNAs, and inflammatory markers in diabetic Ins2+/- Akita hearts. Cell Biochem Biophys 2014; 68:25-35. [PMID: 23797610 DOI: 10.1007/s12013-013-9679-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Diabetic cardiomyopathy is a leading cause of morbidity and mortality, and Insulin2 mutant (Ins2+/-) Akita is a genetic mice model of diabetes relevant to humans. Dicer, miRNAs, and inflammatory cytokines are associated with heart failure. However, the differential expression of miRNAs, dicer, and inflammatory molecules are not clear in diabetic cardiomyopathy of Akita. We measured the levels of miRNAs, dicer, pro-inflammatory tumor necrosis factor alpha (TNFα), and anti-inflammatory interleukin 10 (IL-10) in C57BL/6J (WT) and Akita hearts. The results revealed increased heart to body weight ratio and robust expression of brain natriuretic peptide (BNP: a hypertrophy marker) suggesting cardiac hypertrophy in Akita. The multiplex RT-PCR, qPCR, and immunoblotting showed up regulation of dicer, whereas miRNA array elicited spread down regulation of miRNAs in Akita including dramatic down regulation of let-7a, miR-130, miR-142-3p, miR-148, miR-338, miR-345-3p, miR-384-3p, miR-433, miR-450, miR-451, miR-455, miR-494, miR-499, miR-500, miR-542-3p, miR-744, and miR-872. Conversely, miR-295 is induced in Akita. Cardiac TNFα is upregulated at mRNA (RT-PCR and qPCR), protein (immunoblotting), and cellular (immunohistochemistry and confocal microscopy) levels, and is robust in hypertrophic cardiomyocytes suggesting direct association of TNFα with hypertrophy. Contrary to TNFα, cardiac IL-10 is downregulated in Akita. In conclusion, induction of dicer and TNFα, and attenuation of IL-10 and majority of miRNA are associated with cardiomyopathy in Akita and could be used for putative therapeutic target for heart failure in diabetics.
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Expression, Identification and Characterize of CD25-Binding Epitope Modified Human IL-2 in Pichia pastoris. Indian J Microbiol 2014; 53:283-7. [PMID: 24426123 DOI: 10.1007/s12088-013-0366-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 01/29/2013] [Indexed: 02/04/2023] Open
Abstract
Interleukin-2 (IL-2) plays important roles in variety of immune functions and it is widely used in the medication. But in recent years it was reported that vascular leak syndrome (VLS) was induced by IL-2. Evidences showed that the interaction of IL-2 and IL-2Rαβγ (CD25) caused VLS. Thus, this experiment modified the CD25-binding epitope in human IL-2 (hIL-2) to minimize the side effect of IL-2 in the medication. In this study, a recombinant human interleukin 2 (rhIL-2) was expressed in Pichia (P.) pastoris. An effective strategy was established to express rhIL-2 protein in 120 L scale and the optimal purification procedure was investigated. The purity of rhIL-2 in final product was about 98 % and the concentration of the rhIL-2 was 0.45 mg/mL. Bioactivity analysis showed that the purified rhIL-2 protein displayed high activity on proliferation of CTLL-2 cells and increased the ratio of CD4(+)/CD8(+). It indicates that the target protein is expressed and the character of the rhIL-2 has high activity. This study provides a strategy for large-scale production of bioactive rhIL-2 protein using P. pastoris as an expression host.
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Boitard C, Timsit J. Towards an aetiological treatment of type 1 diabetes? New tools, new strategies. DIABETES & METABOLISM 2012; 38:375-7. [PMID: 23122483 DOI: 10.1016/j.diabet.2012.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 09/14/2012] [Indexed: 11/25/2022]
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