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Antonatos C, Georgakilas GK, Evangelou E, Vasilopoulos Y. Transcriptomic meta-analysis characterizes molecular commonalities between psoriasis and obesity. Genes Immun 2024; 25:179-187. [PMID: 38580831 DOI: 10.1038/s41435-024-00271-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/07/2024]
Abstract
Despite the abundance of epidemiological evidence for the high comorbid rate between psoriasis and obesity, systematic approaches to common inflammatory mechanisms have not been adequately explored. We performed a meta-analysis of publicly available RNA-sequencing datasets to unveil putative mechanisms that are postulated to exacerbate both diseases, utilizing both late-stage, disease-specific meta-analyses and consensus gene co-expression network (cWGCNA). Single-gene meta-analyses reported several common inflammatory mechanisms fostered by the perturbed expression profile of inflammatory cells. Assessment of gene overlaps between both diseases revealed significant overlaps between up- (n = 170, P value = 6.07 × 10-65) and down-regulated (n = 49, P value = 7.1 × 10-7) genes, associated with increased T cell response and activated transcription factors. Our cWGCNA approach disentangled 48 consensus modules, associated with either the differentiation of leukocytes or metabolic pathways with similar correlation signals in both diseases. Notably, all our analyses confirmed the association of the perturbed T helper (Th)17 differentiation pathway in both diseases. Our novel findings through whole transcriptomic analyses characterize the inflammatory commonalities between psoriasis and obesity implying the assessment of several expression profiles that could serve as putative comorbid disease progression biomarkers and therapeutic interventions.
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Affiliation(s)
- Charalabos Antonatos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504, Patras, Greece
| | - Georgios K Georgakilas
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504, Patras, Greece
- Information Management Systems Institute (IMSI), ATHENA Research Center, 15125, Athens, Greece
| | - Evangelos Evangelou
- Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina, 45110, Greece
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, 45110, Ioannina, Greece
- Department of Epidemiology & Biostatistics, MRC Centre for Environment and Health, Imperial College London, London, W2 1PG, UK
| | - Yiannis Vasilopoulos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504, Patras, Greece.
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Long Y, Mao C, Liu S, Tao Y, Xiao D. Epigenetic modifications in obesity-associated diseases. MedComm (Beijing) 2024; 5:e496. [PMID: 38405061 PMCID: PMC10893559 DOI: 10.1002/mco2.496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
The global prevalence of obesity has reached epidemic levels, significantly elevating the susceptibility to various cardiometabolic conditions and certain types of cancer. In addition to causing metabolic abnormalities such as insulin resistance (IR), elevated blood glucose and lipids, and ectopic fat deposition, obesity can also damage pancreatic islet cells, endothelial cells, and cardiomyocytes through chronic inflammation, and even promote the development of a microenvironment conducive to cancer initiation. Improper dietary habits and lack of physical exercise are important behavioral factors that increase the risk of obesity, which can affect gene expression through epigenetic modifications. Epigenetic alterations can occur in early stage of obesity, some of which are reversible, while others persist over time and lead to obesity-related complications. Therefore, the dynamic adjustability of epigenetic modifications can be leveraged to reverse the development of obesity-associated diseases through behavioral interventions, drugs, and bariatric surgery. This review provides a comprehensive summary of the impact of epigenetic regulation on the initiation and development of obesity-associated cancers, type 2 diabetes, and cardiovascular diseases, establishing a theoretical basis for prevention, diagnosis, and treatment of these conditions.
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Affiliation(s)
- Yiqian Long
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - Chao Mao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaChina
| | - Shuang Liu
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Yongguang Tao
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaChina
- Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Department of Thoracic SurgerySecond Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Desheng Xiao
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
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Berardo C, Calcaterra V, Mauri A, Carelli S, Messa L, Destro F, Rey F, Cordaro E, Pelizzo G, Zuccotti G, Cereda C. Subcutaneous Adipose Tissue Transcriptome Highlights Specific Expression Profiles in Severe Pediatric Obesity: A Pilot Study. Cells 2023; 12:cells12081105. [PMID: 37190014 DOI: 10.3390/cells12081105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/05/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
The prevalence of pediatric obesity is rising rapidly worldwide, and "omic" approaches are helpful in investigating the molecular pathophysiology of obesity. This work aims to identify transcriptional differences in the subcutaneous adipose tissue (scAT) of children with overweight (OW), obesity (OB), or severe obesity (SV) compared with those of normal weight (NW). Periumbilical scAT biopsies were collected from 20 male children aged 1-12 years. The children were stratified into the following four groups according to their BMI z-scores: SV, OB, OW, and NW. scAT RNA-Seq analyses were performed, and a differential expression analysis was conducted using the DESeq2 R package. A pathways analysis was performed to gain biological insights into gene expression. Our data highlight the significant deregulation in both coding and non-coding transcripts in the SV group when compared with the NW, OW, and OB groups. A KEGG pathway analysis showed that coding transcripts were mainly involved in lipid metabolism. A GSEA analysis revealed the upregulation of lipid degradation and metabolism in SV vs. OB and SV vs. OW. Bioenergetic processes and the catabolism of branched-chain amino acids were upregulated in SV compared with OB, OW, and NW. In conclusion, we report for the first time that a significant transcriptional deregulation occurs in the periumbilical scAT of children with severe obesity compared with those of normal weight or those with overweight or mild obesity.
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Affiliation(s)
- Clarissa Berardo
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Science, University of Milan, 20157 Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Valeria Calcaterra
- Pediatric and Adolescent Unit, Department of Internal Medicine, University of Pavia, 27100 Pavia, Italy
- Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Alessia Mauri
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Science, University of Milan, 20157 Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Stephana Carelli
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Science, University of Milan, 20157 Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Letizia Messa
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milan, Italy
| | - Francesca Destro
- Surgery Department, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Federica Rey
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Science, University of Milan, 20157 Milan, Italy
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Erika Cordaro
- Pediatric and Adolescent Unit, Department of Internal Medicine, University of Pavia, 27100 Pavia, Italy
| | - Gloria Pelizzo
- Surgery Department, Buzzi Children's Hospital, 20154 Milan, Italy
- Department of Biomedical and Clinical Science, University of Milan, 20157 Milan, Italy
| | - Gianvincenzo Zuccotti
- Pediatric Clinical Research Center "Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Science, University of Milan, 20157 Milan, Italy
- Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
| | - Cristina Cereda
- Center of Functional Genomics and Rare Diseases, Department of Pediatrics, Buzzi Children's Hospital, 20154 Milan, Italy
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Rey F, Messa L, Pandini C, Barzaghini B, Micheletto G, Raimondi MT, Bertoli S, Cereda C, Zuccotti GV, Cancello R, Carelli S. Transcriptional characterization of subcutaneous adipose tissue in obesity affected women highlights metabolic dysfunction and implications for lncRNAs. Genomics 2021; 113:3919-3934. [PMID: 34555498 DOI: 10.1016/j.ygeno.2021.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/03/2021] [Accepted: 09/17/2021] [Indexed: 10/20/2022]
Abstract
Obesity is a complex disease with multifactorial causes, and its prevalence is becoming a serious health crisis. For this reason, there is a crucial need to identify novel targets and players. With this aim in mind, we analyzed via RNA-sequencing the subcutaneous adipose tissue of normal weight and obesity-affected women, highlighting the differential expression in the two tissues. We specifically focused on long non-coding RNAs, as 6 of these emerged as dysregulated in the diseased-tissue (COL4A2-AS2, RPS21-AS, PELATON, ITGB2-AS1, ACER2-AS and CTEPHA1). For each of them, we performed both a thorough in silico dissection and in vitro validation, to predict their function during adipogenesis. We report the lncRNAs expression during adipose derived stem cells differentiation to adipocytes as model of adipogenesis and their potential modulation by adipogenesis-related transcription factors (C/EBPs and PPARγ). Moreover, inhibiting CTEPHA1 expression we investigated its impact on adipogenesis-related transcription factors, showing its significative dysregulation of C/EBPα expression. Lastly, we dissected the subcellular localization, pathway involvement and disease-correlation for coding differentially expressed genes. Together, these findings highlight a transcriptional deregulation at the basis of obesity, impacted by both coding and long non-coding RNAs.
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Affiliation(s)
- Federica Rey
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Via Grassi 74, 20157 Milan, Italy; Pediatric Clinical Research Centre Fondazione "Romeo ed Enrica Invernizzi", University of Milano, Milano, Italy
| | - Letizia Messa
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milano, Italy
| | - Cecilia Pandini
- Genomic and post-Genomic Centre, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Bianca Barzaghini
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milano, Italy
| | - Giancarlo Micheletto
- Department of Pathophysiology and Transplantation, INCO, Department of General Surgery, Istituto Clinico Sant'Ambrogio, University of Milan, Milan, Italy
| | - Manuela Teresa Raimondi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milano, Italy
| | - Simona Bertoli
- Obesity Unit, Laboratory of Nutrition and Obesity Research, Department of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan, Italy; International Center for the Assessment of Nutritional Status (ICANS), Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Milan, Italy
| | - Cristina Cereda
- Genomic and post-Genomic Centre, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Gian Vincenzo Zuccotti
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Via Grassi 74, 20157 Milan, Italy; Pediatric Clinical Research Centre Fondazione "Romeo ed Enrica Invernizzi", University of Milano, Milano, Italy; Department of Pediatrics, Children's Hospital "V. Buzzi", Milan, Italy
| | - Raffaella Cancello
- Obesity Unit, Laboratory of Nutrition and Obesity Research, Department of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Milan, Italy
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Via Grassi 74, 20157 Milan, Italy; Pediatric Clinical Research Centre Fondazione "Romeo ed Enrica Invernizzi", University of Milano, Milano, Italy.
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Neural Precursor Cells Expanded Inside the 3D Micro-Scaffold Nichoid Present Different Non-Coding RNAs Profiles and Transcript Isoforms Expression: Possible Epigenetic Modulation by 3D Growth. Biomedicines 2021; 9:biomedicines9091120. [PMID: 34572306 PMCID: PMC8472193 DOI: 10.3390/biomedicines9091120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/24/2022] Open
Abstract
Non-coding RNAs show relevant implications in various biological and pathological processes. Thus, understanding the biological implications of these molecules in stem cell biology still represents a major challenge. The aim of this work is to study the transcriptional dysregulation of 357 non-coding genes, found through RNA-Seq approach, in murine neural precursor cells expanded inside the 3D micro-scaffold Nichoid versus standard culture conditions. Through weighted co-expression network analysis and functional enrichment, we highlight the role of non-coding RNAs in altering the expression of coding genes involved in mechanotransduction, stemness, and neural differentiation. Moreover, as non-coding RNAs are poorly conserved between species, we focus on those with human homologue sequences, performing further computational characterization. Lastly, we looked for isoform switching as possible mechanism in altering coding and non-coding gene expression. Our results provide a comprehensive dissection of the 3D scaffold Nichoid's influence on the biological and genetic response of neural precursor cells. These findings shed light on the possible role of non-coding RNAs in 3D cell growth, indicating that also non-coding RNAs are implicated in cellular response to mechanical stimuli.
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Rey F, Messa L, Pandini C, Maghraby E, Barzaghini B, Garofalo M, Micheletto G, Raimondi MT, Bertoli S, Cereda C, Zuccotti GV, Cancello R, Carelli S. RNA-seq Characterization of Sex-Differences in Adipose Tissue of Obesity Affected Patients: Computational Analysis of Differentially Expressed Coding and Non-Coding RNAs. J Pers Med 2021; 11:352. [PMID: 33924951 PMCID: PMC8145808 DOI: 10.3390/jpm11050352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
Obesity is a multifactorial disease presenting sex-related differences including adipocyte functions, sex hormone effects, genetics, and metabolic inflammation. These can influence individuals' risk for metabolic dysfunctions, with an urgent need to perform sex-based analysis to improve prevention, treatment, and rehabilitation programs. This research work is aimed at characterizing the transcriptional differences present in subcutaneous adipose tissue (SAT) of five obesity affected men versus five obesity affected women, with an additional focus on the role of long non-coding RNAs. Through RNA-sequencing, we highlighted the presence of both coding and non-coding differentially expressed RNAs, and with numerous computational analyses we identified the processes in which these genes are implicated, along with their role in co-morbidities development. We report 51 differentially expressed transcripts, 32 of which were coding genes and 19 were non-coding. Using the WGCNA R package (Weighted Correlation Network Analysis, version 1.70-3), we describe the interactions between coding and non-coding RNAs, and the non-coding RNAs association with the insurgence of specific diseases, such as cancer development, neurodegenerative diseases, and schizophrenia. In conclusion, our work highlights a specific gender sex-related transcriptional signature in the SAT of obesity affected patients.
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Affiliation(s)
- Federica Rey
- Department of Biomedical and Clinical Sciences “L. Sacco”, School of Medicine, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy; (F.R.); (E.M.); (G.V.Z.)
- Paediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy
| | - Letizia Messa
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy; (L.M.); (B.B.); (M.T.R.)
| | - Cecilia Pandini
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Via Mondino 2, 27100 Pavia, Italy; (C.P.); (M.G.); (C.C.)
| | - Erika Maghraby
- Department of Biomedical and Clinical Sciences “L. Sacco”, School of Medicine, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy; (F.R.); (E.M.); (G.V.Z.)
- Paediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy
| | - Bianca Barzaghini
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy; (L.M.); (B.B.); (M.T.R.)
| | - Maria Garofalo
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Via Mondino 2, 27100 Pavia, Italy; (C.P.); (M.G.); (C.C.)
| | - Giancarlo Micheletto
- Department of Pathophysiology and Transplantation, INCO and Department of General Surgery, Istituto Clinico Sant’Ambrogio, University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy;
| | - Manuela Teresa Raimondi
- Department of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy; (L.M.); (B.B.); (M.T.R.)
| | - Simona Bertoli
- Obesity Unit—Laboratory of Nutrition and Obesity Research, Department of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Via Ariosto 9, 20145 Milan, Italy; (S.B.); (R.C.)
- International Center for the Assessment of Nutritional Status (ICANS), Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milan, Italy
| | - Cristina Cereda
- Genomic and Post-Genomic Center, IRCCS Mondino Foundation, Via Mondino 2, 27100 Pavia, Italy; (C.P.); (M.G.); (C.C.)
| | - Gian Vincenzo Zuccotti
- Department of Biomedical and Clinical Sciences “L. Sacco”, School of Medicine, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy; (F.R.); (E.M.); (G.V.Z.)
- Paediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy
- Department of Pediatrics, Children’s Hospital “V. Buzzi”, Via Lodovico Castelvetro 32, 20154 Milano, Italy
| | - Raffaella Cancello
- Obesity Unit—Laboratory of Nutrition and Obesity Research, Department of Endocrine and Metabolic Diseases, IRCCS Istituto Auxologico Italiano, Via Ariosto 9, 20145 Milan, Italy; (S.B.); (R.C.)
| | - Stephana Carelli
- Department of Biomedical and Clinical Sciences “L. Sacco”, School of Medicine, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy; (F.R.); (E.M.); (G.V.Z.)
- Paediatric Clinical Research Center Fondazione “Romeo ed Enrica Invernizzi”, University of Milan, Via G.B. Grassi 74, 20157 Milan, Italy
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