1
|
Schaschkow A, Pang L, Vandenbempt V, Elvira B, Litwak SA, Vekeriotaite B, Maillard E, Vermeersch M, Paula FMM, Pinget M, Perez-Morga D, Gough DJ, Gurzov EN. STAT3 Regulates Mitochondrial Gene Expression in Pancreatic β-Cells and Its Deficiency Induces Glucose Intolerance in Obesity. Diabetes 2021; 70:2026-2041. [PMID: 34183374 DOI: 10.2337/db20-1222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 06/20/2021] [Indexed: 11/13/2022]
Abstract
Most obese and insulin-resistant individuals do not develop diabetes. This is the result of the capacity of β-cells to adapt and produce enough insulin to cover the needs of the organism. The underlying mechanism of β-cell adaptation in obesity, however, remains unclear. Previous studies have suggested a role for STAT3 in mediating β-cell development and human glucose homeostasis, but little is known about STAT3 in β-cells in obesity. We observed enhanced cytoplasmic expression of STAT3 in severely obese subjects with diabetes. To address the functional role of STAT3 in adult β-cells, we generated mice with tamoxifen-inducible partial or full deletion of STAT3 in β-cells and fed them a high-fat diet before analysis. Interestingly, β-cell heterozygous and homozygous STAT3-deficient mice showed glucose intolerance when fed a high-fat diet. Gene expression analysis with RNA sequencing showed that reduced expression of mitochondrial genes in STAT3 knocked down human EndoC-β1H cells, confirmed in FACS-purified β-cells from obese STAT3-deficient mice. Moreover, silencing of STAT3 impaired mitochondria activity in EndoC-β1H cells and human islets, suggesting a mechanism for STAT3-modulated β-cell function. Our study postulates STAT3 as a novel regulator of β-cell function in obesity.
Collapse
Affiliation(s)
- Anaïs Schaschkow
- Signal Transduction and Metabolism Laboratory, Laboratoire de Gastroentérologie Expérimental et Endotools, Université libre de Bruxelles, Brussels, Belgium
| | - Lokman Pang
- Department of Medicine, The University of Melbourne, Parkville, Australia
- St Vincent's Institute of Medical Research, Fitzroy, Australia
| | - Valerie Vandenbempt
- Signal Transduction and Metabolism Laboratory, Laboratoire de Gastroentérologie Expérimental et Endotools, Université libre de Bruxelles, Brussels, Belgium
| | - Bernat Elvira
- Signal Transduction and Metabolism Laboratory, Laboratoire de Gastroentérologie Expérimental et Endotools, Université libre de Bruxelles, Brussels, Belgium
| | - Sara A Litwak
- St Vincent's Institute of Medical Research, Fitzroy, Australia
| | - Beata Vekeriotaite
- Signal Transduction and Metabolism Laboratory, Laboratoire de Gastroentérologie Expérimental et Endotools, Université libre de Bruxelles, Brussels, Belgium
| | - Elisa Maillard
- Université de Strasbourg, Strasbourg, France
- Centre Européen d'Etude du Diabéte, Strasbourg, France
| | - Marjorie Vermeersch
- Center for Microscopy and Molecular Imaging, Université libre de Bruxelles, Brussels, Belgium
| | - Flavia M M Paula
- ULB-Center for Diabetes Research, Université libre de Bruxelles, Brussels, Belgium
| | - Michel Pinget
- Université de Strasbourg, Strasbourg, France
- Centre Européen d'Etude du Diabéte, Strasbourg, France
| | - David Perez-Morga
- Center for Microscopy and Molecular Imaging, Université libre de Bruxelles, Brussels, Belgium
| | - Daniel J Gough
- Centre for Cancer Research, Hudson Institute of Medical Research, Melbourne, Australia
- Department of Science and Translational Medicine, Monash University, Melbourne, Australia
| | - Esteban N Gurzov
- Signal Transduction and Metabolism Laboratory, Laboratoire de Gastroentérologie Expérimental et Endotools, Université libre de Bruxelles, Brussels, Belgium
- Department of Medicine, The University of Melbourne, Parkville, Australia
| |
Collapse
|
2
|
Bamodu O, Chao TY. Dissecting the functional pleiotropism of lysine demethylase 5B in physiology and pathology. JOURNAL OF CANCER RESEARCH AND PRACTICE 2020. [DOI: 10.4103/jcrp.jcrp_5_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
3
|
Farahmand S, O’Connor C, Macoska JA, Zarringhalam K. Causal Inference Engine: a platform for directional gene set enrichment analysis and inference of active transcriptional regulators. Nucleic Acids Res 2019; 47:11563-11573. [PMID: 31701125 PMCID: PMC7145661 DOI: 10.1093/nar/gkz1046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/19/2019] [Accepted: 10/28/2019] [Indexed: 02/07/2023] Open
Abstract
Inference of active regulatory mechanisms underlying specific molecular and environmental perturbations is essential for understanding cellular response. The success of inference algorithms relies on the quality and coverage of the underlying network of regulator-gene interactions. Several commercial platforms provide large and manually curated regulatory networks and functionality to perform inference on these networks. Adaptation of such platforms for open-source academic applications has been hindered by the lack of availability of accurate, high-coverage networks of regulatory interactions and integration of efficient causal inference algorithms. In this work, we present CIE, an integrated platform for causal inference of active regulatory mechanisms form differential gene expression data. Using a regularized Gaussian Graphical Model, we construct a transcriptional regulatory network by integrating publicly available ChIP-seq experiments with gene-expression data from tissue-specific RNA-seq experiments. Our GGM approach identifies high confidence transcription factor (TF)-gene interactions and annotates the interactions with information on mode of regulation (activation vs. repression). Benchmarks against manually curated databases of TF-gene interactions show that our method can accurately detect mode of regulation. We demonstrate the ability of our platform to identify active transcriptional regulators by using controlled in vitro overexpression and stem-cell differentiation studies and utilize our method to investigate transcriptional mechanisms of fibroblast phenotypic plasticity.
Collapse
Affiliation(s)
- Saman Farahmand
- Computational Sciences PhD program, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Corey O’Connor
- Department of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Jill A Macoska
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kourosh Zarringhalam
- Computational Sciences PhD program, University of Massachusetts Boston, Boston, MA 02125, USA
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
| |
Collapse
|
4
|
An Activating STAT3 Mutation Causes Neonatal Diabetes through Premature Induction of Pancreatic Differentiation. Cell Rep 2017; 19:281-294. [DOI: 10.1016/j.celrep.2017.03.055] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 02/10/2017] [Accepted: 03/17/2017] [Indexed: 02/06/2023] Open
|
5
|
Fakhry CT, Choudhary P, Gutteridge A, Sidders B, Chen P, Ziemek D, Zarringhalam K. Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks. BMC Bioinformatics 2016; 17:318. [PMID: 27553489 PMCID: PMC4995651 DOI: 10.1186/s12859-016-1181-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/11/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inference of active regulatory cascades under specific molecular and environmental perturbations is a recurring task in transcriptional data analysis. Commercial tools based on large, manually curated networks of causal relationships offering such functionality have been used in thousands of articles in the biomedical literature. The adoption and extension of such methods in the academic community has been hampered by the lack of freely available, efficient algorithms and an accompanying demonstration of their applicability using current public networks. RESULTS In this article, we propose a new statistical method that will infer likely upstream regulators based on observed patterns of up- and down-regulated transcripts. The method is suitable for use with public interaction networks with a mix of signed and unsigned causal edges. It subsumes and extends two previously published approaches and we provide a novel algorithmic method for efficient statistical inference. Notably, we demonstrate the feasibility of using the approach to generate biological insights given current public networks in the context of controlled in-vitro overexpression experiments, stem-cell differentiation data and animal disease models. We also provide an efficient implementation of our method in the R package QuaternaryProd available to download from Bioconductor. CONCLUSIONS In this work, we have closed an important gap in utilizing causal networks to analyze differentially expressed genes. Our proposed Quaternary test statistic incorporates all available evidence on the potential relevance of an upstream regulator. The new approach broadens the use of these types of statistics for highly curated signed networks in which ambiguities arise but also enables the use of networks with unsigned edges. We design and implement a novel computational method that can efficiently estimate p-values for upstream regulators in current biological settings. We demonstrate the ready applicability of the implemented method to analyze differentially expressed genes using the publicly available networks.
Collapse
Affiliation(s)
- Carl Tony Fakhry
- Department of Computer Science, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, 02125, USA
| | - Parul Choudhary
- Computational Sciences, Pfizer Worldwide Research & Development, Cambridge, USA
| | - Alex Gutteridge
- Computational Sciences, Pfizer Worldwide Research & Development, Cambridge, USA
| | - Ben Sidders
- Computational Sciences, Pfizer Worldwide Research & Development, Cambridge, USA
| | - Ping Chen
- Department of Engineering, University of Massachusetts Boston, Boston, 100 Morrissey Boulevard02125, USA
| | - Daniel Ziemek
- Computational Sciences, Pfizer Worldwide Research & Development, Berlin, USA
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, 02125, USA.
| |
Collapse
|
6
|
Dauriz M, Trombetta M, Boselli L, Santi L, Brangani C, Pichiri I, Bonora E, Bonadonna RC. Interleukin-6 as a potential positive modulator of human beta-cell function: an exploratory analysis-the Verona Newly Diagnosed Type 2 Diabetes Study (VNDS) 6. Acta Diabetol 2016; 53:393-402. [PMID: 26538364 DOI: 10.1007/s00592-015-0807-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 08/28/2015] [Indexed: 12/15/2022]
Abstract
AIMS Recent studies in mouse models of T2D showed that interleukin-6 (IL-6), released from skeletal muscle, is associated with increased glucose-dependent insulin secretion. Few data currently exist exploring the relationship between IL-6 and beta-cell function in humans. We investigated whether IL-6 is positively associated with beta-cell function in newly diagnosed T2D. We extended the same analyses to IL-10, because it regulated similarly to IL-6 in skeletal muscle, and TNF-α and C-reactive protein (CRP), as general biomarkers of inflammation. METHODS In 330 VNDS participants, we assessed (1) basal plasma concentrations of IL-6, IL-10, TNF-α, and CRP; (2) beta-cell function, estimated by OGTT minimal modeling and expressed as derivative (DC) and proportional control (PC); (3) insulin sensitivity, by euglycemic insulin clamp. RESULTS IL-6 was positively associated with PC in both univariate analysis (p = 0.04) and after adjustment for age, sex, BMI, HbA1c, and M-clamp (p = 0.01). HbA1c was the major independent contributor to the overall variance of PC (16 %), followed by BMI and IL-6 (~2 % each). Similar results were obtained for IL-10 (p = 0.048, univariate; p = 0.04, fully adjusted). TNF-α and CRP were not significantly associated with any component of beta-cell function. CONCLUSIONS Our data are the first evidence in human subjects that an endocrine loop involving IL-6 may act as positive modulator of glucose-dependent insulin secretion. Further functional studies are needed to corroborate IL-6 system as a potential druggable target in diabetes. CLINICAL TRIAL REGISTRATION NUMBER NCT01526720 ( http://www.clinicaltrial.gov ).
Collapse
Affiliation(s)
- Marco Dauriz
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University and Hospital Trust of Verona - Ospedale Civile Maggiore, Piazzale Stefani, 1, 37126, Verona, Italy
| | - Maddalena Trombetta
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University and Hospital Trust of Verona - Ospedale Civile Maggiore, Piazzale Stefani, 1, 37126, Verona, Italy
| | - Linda Boselli
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University and Hospital Trust of Verona - Ospedale Civile Maggiore, Piazzale Stefani, 1, 37126, Verona, Italy
| | - Lorenza Santi
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University and Hospital Trust of Verona - Ospedale Civile Maggiore, Piazzale Stefani, 1, 37126, Verona, Italy
| | - Corinna Brangani
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University and Hospital Trust of Verona - Ospedale Civile Maggiore, Piazzale Stefani, 1, 37126, Verona, Italy
| | - Isabella Pichiri
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University and Hospital Trust of Verona - Ospedale Civile Maggiore, Piazzale Stefani, 1, 37126, Verona, Italy
| | - Enzo Bonora
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University and Hospital Trust of Verona - Ospedale Civile Maggiore, Piazzale Stefani, 1, 37126, Verona, Italy
| | - Riccardo C Bonadonna
- Division of Endocrinology, Department of Clinical and Experimental Medicine, University of Parma School of Medicine and Azienda Ospedaliera Universitaria - Ospedale Maggiore, Via Gramsci 14, 43126, Parma, Italy.
| |
Collapse
|
7
|
Konorov SO, Schulze HG, Gage BK, Kieffer TJ, Piret JM, Blades MW, Turner RFB. Process Analytical Utility of Raman Microspectroscopy in the Directed Differentiation of Human Pancreatic Insulin-Positive Cells. Anal Chem 2015; 87:10762-9. [DOI: 10.1021/acs.analchem.5b03295] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Stanislav O. Konorov
- Michael
Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, BC Canada, V6T 1Z4
- Department
of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, BC Canada, V6T 1Z1
| | - H. Georg Schulze
- Michael
Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, BC Canada, V6T 1Z4
| | - Blair K. Gage
- Department
of Cellular and Physiological Sciences, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC Canada, V6T 1Z3
| | - Timothy J. Kieffer
- Department
of Cellular and Physiological Sciences, The University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC Canada, V6T 1Z3
- Department
of Surgery, The University of British Columbia, 910 West 10th Avenue, Vancouver, BC Canada, V5Z 4E3
| | - James M. Piret
- Michael
Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, BC Canada, V6T 1Z4
- Department
of Chemical and Biological Engineering, The University of British Columbia, 2360 East Mall, Vancouver, BC Canada, V6T 1Z3
| | - Michael W. Blades
- Department
of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, BC Canada, V6T 1Z1
| | - Robin F. B. Turner
- Michael
Smith Laboratories, The University of British Columbia, 2185 East Mall, Vancouver, BC Canada, V6T 1Z4
- Department
of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, BC Canada, V6T 1Z1
- Department
of Electrical and Computer Engineering, The University of British Columbia, 2332 Main Mall, Vancouver, BC Canada, V6T 1Z4
| |
Collapse
|
8
|
Jaramillo M, Mathew S, Mamiya H, Goh SK, Banerjee I. Endothelial cells mediate islet-specific maturation of human embryonic stem cell-derived pancreatic progenitor cells. Tissue Eng Part A 2014; 21:14-25. [PMID: 24943736 DOI: 10.1089/ten.tea.2014.0013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
It is well recognized that in vitro differentiation of embryonic stem cells (ESC) can be best achieved by closely recapitulating the in vivo developmental niche. Thus, implementation of directed differentiation strategies has yielded encouraging results in the area of pancreatic islet differentiation. These strategies have concentrated on direct addition of chemical signals, however, other aspect of the developmental niche are yet to be explored. During development, pancreatic progenitor (PP) cells grow as an epithelial sheet, which aggregates with endothelial cells (ECs) during the final stages of maturation. Several findings suggest that the interactions with EC play a role in pancreatic development. In this study, we recapitulated this phenomenon in an in vitro environment by maturing the human ESC (hESC)-derived PP cells in close contact with ECs. We find that co-culture with different ECs (but not fibroblast) alone results in pancreatic islet-specific differentiation of hESC-derived PP cells even in the absence of additional chemical induction. The differentiated cells responded to exogenous glucose levels by enhanced C-peptide synthesis. The co-culture system aligned well with endocrine development as determined by comprehensive analysis of involved signaling pathways. By recapitulating cell-cell interaction aspects of the developmental niche we achieved a differentiation model that aligns closely with islet organogenesis.
Collapse
Affiliation(s)
- Maria Jaramillo
- 1 Department of Bioengineering, University of Pittsburgh, Pittsburgh , Pennsylvania
| | | | | | | | | |
Collapse
|
9
|
Abstract
Embryonic stem (ES) cells have been shown to recapitulate normal developmental stages. They are therefore a highly useful tool in the study of developmental biology. Profiling of ES cell-derived cells has yielded important information about the characteristics of differentiated cells, and allowed the identification of novel marker genes and pathways of differentiation. In this review, we focus on recent results from profiling studies of mouse embryos, human islets, and human ES cell-derived differentiated cells from several research groups. Global gene expression data from mouse embryos have been used to identify novel genes or pathways involved in the developmental process, and to search for transcription factors that regulate direct reprogramming. We introduce gene expression databases of human pancreas cells (Beta Cell Gene Atlas, EuroDia database), and summarize profiling studies of islet- or human ES cell-derived pancreatic cells, with a focus on gene expression, microRNAs, epigenetics, and protein expression. Then, we describe our gene expression profile analyses and our search for novel endoderm, or pancreatic, progenitor marker genes. We differentiated mouse ES cells into mesendoderm, definitive endoderm (DE), mesoderm, ectoderm, and Pdx1-expressing pancreatic lineages, and performed DNA microarray analyses. Genes specifically expressed in DE, and/or in Pdx1-expressing cells, were extracted and their expression patterns in normal embryonic development were studied by in situ hybridization. Out of 54 genes examined, 27 were expressed in the DE of E8.5 mouse embryos, and 15 genes were expressed in distinct domains in the pancreatic buds of E14.5 mouse embryos. Akr1c19, Aebp2, Pbxip1, and Creb3l1 were all novel, and none has been described as being expressed, either in the DE, or in the pancreas. By introducing the profiling results of ES cell-derived cells, the benefits of using ES cells to study early embryonic development will be discussed.
Collapse
Affiliation(s)
- Nobuaki Shiraki
- Department of Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Honjo 2-2-1, Kumamoto 860-0811, Japan
| | - Soichiro Ogaki
- Department of Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Honjo 2-2-1, Kumamoto 860-0811, Japan
| | - Shoen Kume
- Department of Stem Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Honjo 2-2-1, Kumamoto 860-0811, Japan
| |
Collapse
|
10
|
Zarringhalam K, Enayetallah A, Gutteridge A, Sidders B, Ziemek D. Molecular causes of transcriptional response: a Bayesian prior knowledge approach. ACTA ACUST UNITED AC 2013; 29:3167-73. [PMID: 24078682 DOI: 10.1093/bioinformatics/btt557] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
MOTIVATION The abundance of many transcripts changes significantly in response to a variety of molecular and environmental perturbations. A key question in this setting is as follows: what intermediate molecular perturbations gave rise to the observed transcriptional changes? Regulatory programs are not exclusively governed by transcriptional changes but also by protein abundance and post-translational modifications making direct causal inference from data difficult. However, biomedical research over the last decades has uncovered a plethora of causal signaling cascades that can be used to identify good candidates explaining a specific set of transcriptional changes. METHODS We take a Bayesian approach to integrate gene expression profiling with a causal graph of molecular interactions constructed from prior biological knowledge. In addition, we define the biological context of a specific interaction by the corresponding Medical Subject Headings terms. The Bayesian network can be queried to suggest upstream regulators that can be causally linked to the altered expression profile. RESULTS Our approach will treat candidate regulators in the right biological context preferentially, enables hierarchical exploration of resulting hypotheses and takes the complete network of causal relationships into account to arrive at the best set of upstream regulators. We demonstrate the power of our method on distinct biological datasets, namely response to dexamethasone treatment, stem cell differentiation and a neuropathic pain model. In all cases relevant biological insights could be validated. AVAILABILITY AND IMPLEMENTATION Source code for the method is available upon request.
Collapse
Affiliation(s)
- Kourosh Zarringhalam
- Computational Sciences Center of Emphasis, Pfizer Worldwide Research & Development, Cambridge, MA 02140, USA, Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA, Drug Safety Research & Development, Pfizer, Groton, CT 06340, USA and Neusentis, Pfizer Worldwide Research & Development, Cambridge CB21 6GS, UK
| | | | | | | | | |
Collapse
|