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Li Z, Pan X, Cai YD. Identification of Type 2 Diabetes Biomarkers From Mixed Single-Cell Sequencing Data With Feature Selection Methods. Front Bioeng Biotechnol 2022; 10:890901. [PMID: 35721855 PMCID: PMC9201257 DOI: 10.3389/fbioe.2022.890901] [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: 03/07/2022] [Accepted: 04/04/2022] [Indexed: 11/18/2022] Open
Abstract
Diabetes is the most common disease and a major threat to human health. Type 2 diabetes (T2D) makes up about 90% of all cases. With the development of high-throughput sequencing technologies, more and more fundamental pathogenesis of T2D at genetic and transcriptomic levels has been revealed. The recent single-cell sequencing can further reveal the cellular heterogenicity of complex diseases in an unprecedented way. With the expectation on the molecular essence of T2D across multiple cell types, we investigated the expression profiling of more than 1,600 single cells (949 cells from T2D patients and 651 cells from normal controls) and identified the differential expression profiling and characteristics at the transcriptomics level that can distinguish such two groups of cells at the single-cell level. The expression profile was analyzed by several machine learning algorithms, including Monte Carlo feature selection, support vector machine, and repeated incremental pruning to produce error reduction (RIPPER). On one hand, some T2D-associated genes (MTND4P24, MTND2P28, and LOC100128906) were discovered. On the other hand, we revealed novel potential pathogenic mechanisms in a rule manner. They are induced by newly recognized genes and neglected by traditional bulk sequencing techniques. Particularly, the newly identified T2D genes were shown to follow specific quantitative rules with diabetes prediction potentials, and such rules further indicated several potential functional crosstalks involved in T2D.
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Affiliation(s)
- Zhandong Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Xiaoyong Pan
- Key Laboratory of System Control and Information Processing, Institute of Image Processing and Pattern Recognition, Ministry of Education of China, Shanghai Jiao Tong University, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
- *Correspondence: Yu-Dong Cai,
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Xiaohong L, Zhenting Z, Yunjie Y, Wei C, Xiangjin X, Kun X, Xin L, Lu L, Jun L, Pin C. Activation of the STING-IRF3 pathway involved in psoriasis with diabetes mellitus. J Cell Mol Med 2022; 26:2139-2151. [PMID: 35174638 PMCID: PMC8995451 DOI: 10.1111/jcmm.17236] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/30/2022] [Accepted: 02/02/2022] [Indexed: 12/22/2022] Open
Abstract
Psoriasis and type 2 diabetes mellitus (T2DM) share similar inflammatory pathways in their pathogenesis. The stimulator of interferon genes (STING)‐interferon regulatory factor 3 (IRF3) pathway has recently been shown to play an important role in immune and metabolic diseases. In this study, we investigated the activation of the STING‐IRF3 pathway in human immortalized keratinocytes (HaCaT) cells treated with palmitic acid (PA) and imiquimod (IMQ). Additionally, we detected the STING‐IRF3 pathway in diabetic mice with imiquimod (IMQ)‐induced psoriasis and assessed the potential of STING inhibitor C‐176. Furthermore, skin samples from patients with psoriasis and diabetes were collected for immunohistochemical analysis. The results indicated that the STING‐IRF3 pathway was activated in HaCaT cells. Moreover, the STING pathway was also found to be induced in the skin tissue of diabetic mice with psoriasis; the inflammatory responses were ameliorated by treatment with C‐176. In the skin tissue samples of patients with psoriasis and diabetes, immunohistochemistry showed that the expression levels of STING and phosphorylated IRF3 were also significantly increased. Thus, we conclude that the STING‐IRF3 pathway is involved in the inflammatory response in the manifestation of psoriasis with T2DM. Inhibition of the activation of the STING pathway can ameliorate the development of psoriasis in diabetes and could be targeted for the development of therapeutic agents for these conditions.
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Affiliation(s)
- Li Xiaohong
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Zhang Zhenting
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Yu Yunjie
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Cai Wei
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Xu Xiangjin
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China.,Department of Endocrinology, 900th Hospital of the Joint Logistics Team, Fuzhou, China
| | - Xie Kun
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Lin Xin
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Lin Lu
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Lu Jun
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China.,Fujian Provincial Key Laboratory of Transplant Biology, Laboratory of Basic Medicine, Dongfang Hospital, Xiamen University, Fuzhou, China
| | - Chen Pin
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, China.,Department of Endocrinology, 900th Hospital of the Joint Logistics Team, Fuzhou, China
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Cinti F, Mezza T, Severi I, Suleiman M, Cefalo CMA, Sorice GP, Moffa S, Impronta F, Quero G, Alfieri S, Mari A, Pontecorvi A, Marselli L, Cinti S, Marchetti P, Giaccari A. Noradrenergic fibers are associated with beta-cell dedifferentiation and impaired beta-cell function in humans. Metabolism 2021; 114:154414. [PMID: 33129839 DOI: 10.1016/j.metabol.2020.154414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/20/2020] [Accepted: 10/21/2020] [Indexed: 12/19/2022]
Abstract
AIMS/HYPOTHESIS Type 2 diabetes (T2D) is characterized by a progressive loss of beta-cell function, and the "disappearance" of beta-cells in T2D may also be caused by the process of beta -cell dedifferentiation. Since noradrenergic innervation inhibits insulin secretion and density of noradrenergic fibers is increased in type 2 diabetes mouse models, we aimed to study the relation between islet innervation, dedifferentiation and beta-cell function in humans. METHODS Using immunohistochemistry and electron microscopy, we analyzed pancreata from organ donors and from patients undergoing pancreatic surgery. In the latter, a pre-surgical detailed metabolic characterization by oral glucose tolerance test (OGTT) and hyperglycemic clamp was performed before surgery, thus obtaining in vivo functional parameters of beta-cell function and insulin secretion. RESULTS The islets of diabetic subjects were 3 times more innervated than controls (0.91 ± 0.21 vs 0.32 ± 0.10, n.fibers/islet; p = 0.01), and directly correlated with the dedifferentiation score (r = 0.39; p = 0.03). In vivo functional parameters of insulin secretion, assessed by hyperglycemic clamp, negatively correlated with the increase in fibers [beta-cell Glucose Sensitivity (r = -0.84; p = 0.01), incremental second-phase insulin secretion (r = -0.84, p = 0.03) and arginine-stimulated insulin secretion (r = -0.76, p = 0.04)]. Moreover, we observed a progressive increase in fibers, paralleling worsening glucose tolerance (from NGT through IGT to T2D). CONCLUSIONS/INTERPRETATION Noradrenergic fibers are significantly increased in the islets of diabetic subjects and this positively correlates with beta-cell dedifferentiation score. The correlation between in vivo insulin secretion parameters and the density of pancreatic noradrenergic fibers suggests a significant involvement of these fibers in the pathogenesis of the disease, and indirectly, in the islet dedifferentiation process.
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Affiliation(s)
- F Cinti
- Centro per le Malattie Endocrine e Metaboliche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy; Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - T Mezza
- Centro per le Malattie Endocrine e Metaboliche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy; Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - I Severi
- Department of Clinical and Experimental Medicine, Center of Obesity, Università Politecnica delle Marche, Ancona, Italy
| | - M Suleiman
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - C M A Cefalo
- Centro per le Malattie Endocrine e Metaboliche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy; Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - G P Sorice
- Centro per le Malattie Endocrine e Metaboliche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy; Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - S Moffa
- Centro per le Malattie Endocrine e Metaboliche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy; Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - F Impronta
- Centro per le Malattie Endocrine e Metaboliche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy; Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - G Quero
- Chirurgia Digestiva, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy; Istituto di Semeiotica Chirurgica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - S Alfieri
- Chirurgia Digestiva, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy; Istituto di Semeiotica Chirurgica, Università Cattolica del Sacro Cuore, Roma, Italy
| | - A Mari
- Institute of Neuroscience, National Research Council, Padua, Italy
| | - A Pontecorvi
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - L Marselli
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - S Cinti
- Department of Clinical and Experimental Medicine, Center of Obesity, Università Politecnica delle Marche, Ancona, Italy
| | - P Marchetti
- Department of Clinical and Experimental Medicine, Islet Cell Laboratory, University of Pisa, Pisa, Italy
| | - A Giaccari
- Centro per le Malattie Endocrine e Metaboliche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Roma, Italy; Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy.
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