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Sun HW, Zhang X, Shen CC. The shared circulating diagnostic biomarkers and molecular mechanisms of systemic lupus erythematosus and inflammatory bowel disease. Front Immunol 2024; 15:1354348. [PMID: 38774864 PMCID: PMC11106441 DOI: 10.3389/fimmu.2024.1354348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
Background Systemic lupus erythematosus (SLE) is a multi-organ chronic autoimmune disease. Inflammatory bowel disease (IBD) is a common chronic inflammatory disease of the gastrointestinal tract. Previous studies have shown that SLE and IBD share common pathogenic pathways and genetic susceptibility, but the specific pathogenic mechanisms remain unclear. Methods The datasets of SLE and IBD were downloaded from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were identified using the Limma package. Weighted gene coexpression network analysis (WGCNA) was used to determine co-expression modules related to SLE and IBD. Pathway enrichment was performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis for co-driver genes. Using the Least AbsoluteShrinkage and Selection Operator (Lasso) regressionand Support Vector Machine-Recursive Feature Elimination (SVM-RFE), common diagnostic markers for both diseases were further evaluated. Then, we utilizedthe CIBERSORT method to assess the abundance of immune cell infiltration. Finally,we used the single-cell analysis to obtain the location of common diagnostic markers. Results 71 common driver genes were identified in the SLE and IBD cohorts based on the DEGs and module genes. KEGG and GO enrichment results showed that these genes were closely associated with positive regulation of programmed cell death and inflammatory responses. By using LASSO regression and SVM, five hub genes (KLRF1, GZMK, KLRB1, CD40LG, and IL-7R) were ultimately determined as common diagnostic markers for SLE and IBD. ROC curve analysis also showed good diagnostic performance. The outcomes of immune cell infiltration demonstrated that SLE and IBD shared almost identical immune infiltration patterns. Furthermore, the majority of the hub genes were commonly expressed in NK cells by single-cell analysis. Conclusion This study demonstrates that SLE and IBD share common diagnostic markers and pathogenic pathways. In addition, SLE and IBD show similar immune cellinfiltration microenvironments which provides newperspectives for future treatment.
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Affiliation(s)
- Hao-Wen Sun
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Xin Zhang
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Cong-Cong Shen
- Department of Dermatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
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Li H, Huang S, Jing J, Yu H, Gu T, Ou X, Pan S, Zhu Y, Su X. Dietary intake and gastrointestinal symptoms are altered in children with Autism Spectrum Disorder: the relative contribution of autism-linked traits. Nutr J 2024; 23:27. [PMID: 38419087 PMCID: PMC10900601 DOI: 10.1186/s12937-024-00930-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/23/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Dietary and gastrointestinal (GI) problems have been frequently reported in autism spectrum disorder (ASD). However, the relative contributions of autism-linked traits to dietary and GI problems in children with ASD are poorly understood. This study firstly compared the dietary intake and GI symptoms between children with ASD and typically developing children (TDC), and then quantified the relative contributions of autism-linked traits to dietary intake, and relative contributions of autism-linked traits and dietary intake to GI symptoms within the ASD group. METHODS A sample of 121 children with ASD and 121 age-matched TDC were eligible for this study. The dietary intake indicators included food groups intakes, food variety, and diet quality. The autism-linked traits included ASD symptom severity, restricted repetitive behaviors (RRBs), sensory profiles, mealtime behaviors, and their subtypes. Linear mixed-effects models and mixed-effects logistic regression models were used to estimate the relative contributions. RESULTS Children with ASD had poorer diets with fewer vegetables/fruits, less variety of food, a higher degree of inadequate/unbalanced dietary intake, and more severe constipation/total GI symptoms than age-matched TDC. Within the ASD group, compulsive behavior (a subtype of RRBs) and taste/smell sensitivity were the only traits associated with lower vegetables and fruit consumption, respectively. Self-injurious behavior (a subtype of RRBs) was the only contributing trait to less variety of food. Limited variety (a subtype of mealtime behavior problems) and ASD symptom severity were the primary and secondary contributors to inadequate dietary intake, respectively. ASD symptom severity and limited variety were the primary and secondary contributors to unbalanced dietary intake, respectively. Notably, unbalanced dietary intake was a significant independent factor associated with constipation/total GI symptoms, and autism-linked traits manifested no contributions. CONCLUSIONS ASD symptom severity and unbalanced diets were the most important contributors to unbalanced dietary intake and GI symptoms, respectively. Our findings highlight that ASD symptom severity and unbalanced diets could provide the largest benefits for the dietary and GI problems of ASD if they were targeted for early detection and optimal treatment.
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Affiliation(s)
- Hailin Li
- Research Center of Children and Adolescent Psychological and Behavioral Development, Department of Maternal and Child Health, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P.R. China
| | - Saijun Huang
- Department of Child Healthcare, Foshan Women and Children Hospital, Foshan, Guangdong, 528000, P.R. China
| | - Jin Jing
- Research Center of Children and Adolescent Psychological and Behavioral Development, Department of Maternal and Child Health, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P.R. China
| | - Hong Yu
- Department of Child Healthcare, Foshan Women and Children Hospital, Foshan, Guangdong, 528000, P.R. China
| | - Tingfeng Gu
- Research Center of Children and Adolescent Psychological and Behavioral Development, Department of Maternal and Child Health, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P.R. China
| | - Xiaoxuan Ou
- Research Center of Children and Adolescent Psychological and Behavioral Development, Department of Maternal and Child Health, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P.R. China
| | - Shuolin Pan
- Research Center of Children and Adolescent Psychological and Behavioral Development, Department of Maternal and Child Health, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P.R. China
| | - Yanna Zhu
- Research Center of Children and Adolescent Psychological and Behavioral Development, Department of Maternal and Child Health, School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P.R. China.
- Department of Maternal and Child Health, School of Public Health, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou, Guangdong, 510080, P.R. China.
| | - Xi Su
- Department of Child Healthcare, Foshan Women and Children Hospital, Foshan, Guangdong, 528000, P.R. China.
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Bai X, Zhang F, Zhou C, Yan J, Liang H, Zhu R, Gong M, Song H, Niu J, Miao Y. Identification of cuproptosis-related molecular classification and characteristic genes in ulcerative colitis. Heliyon 2024; 10:e24875. [PMID: 38312708 PMCID: PMC10835364 DOI: 10.1016/j.heliyon.2024.e24875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 02/06/2024] Open
Abstract
Ulcerative colitis (UC) is a refractory inflammatory disease with imbalances in intestinal mucosal homeostasis. Cuproptosis serves as newly identified programmed cell death (PCD) form involved in UC. In the study, UC-related datasets were extracted from the Gene Expression Omnibus (GEO) database. A comparison of UC patients and healthy controls identified 11 differentially expressed cuproptosis-related genes (DE-CRGs), where FDX1, LIAS, and DLAT were differentially expressed in UC groups from the mouse models and clinical samples, with their expression correlating with disease severity. By comprehending weighted gene co-expression network analysis (WGCNA) and differential expression analysis, the key genes common to the module genes relevant to different cuproptosis-related clusters and differentially expressed genes (DEGs) both in different clusters and patients with and without UC were identified using several bioinformatic analysis. Furthermore, the mRNA levels of four characteristic genes with diagnostic potential demonstrated significant decrease in both mouse models and clinical UC samples. Our discoveries offer a theoretical foundation for cuproptosis effect in UC.
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Affiliation(s)
- Xinyu Bai
- Kunming Medical University, Kunming, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Fengrui Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Chan Zhou
- Kunming Medical University, Kunming, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Jingxian Yan
- Kunming Medical University, Kunming, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Hao Liang
- Kunming Medical University, Kunming, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Rui Zhu
- Kunming Medical University, Kunming, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Min Gong
- Kunming Medical University, Kunming, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Huixian Song
- Kunming Medical University, Kunming, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Junkun Niu
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
| | - Yinglei Miao
- Department of Gastroenterology, The First Affiliated Hospital of Kunming Medical University, Kunming, China
- Yunnan Province Clinical Research Center for Digestive Diseases, Kunming, China
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Xiao YP, Cheng YC, Chen C, Xue HM, Yang M, Lin C. Identification of the Shared Gene Signatures of HCK, NOG, RNF125 and Biological Mechanism in Pediatric Acute Lymphoblastic Leukaemia and Pediatric Sepsis. Mol Biotechnol 2023:10.1007/s12033-023-00979-6. [PMID: 38123749 DOI: 10.1007/s12033-023-00979-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 11/02/2023] [Indexed: 12/23/2023]
Abstract
The shared mechanisms between pediatric acute lymphoblastic leukaemia (ALL) and pediatric sepsis are currently unclear. This study was aimed to explore the shared key genes of pediatric ALL and pediatric sepsis. The datasets involved were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) between disease and control samples in GSE13904 and GSE79533 were intersected. The least absolute shrinkage and selection operator (LASSO) and the boruta analyses were performed in GSE13904 and GSE79533 separately based on shared DEGs, and shared key genes were obtained by taking the intersection of sepsis-related key genes and ALL-related key genes. Three shared key genes (HCK, NOG, RNF125) were obtained, that have a good diagnostic value for both sepsis and ALL. The correlation between shared key genes and differentially expressed immune cells was higher in GSE13904 and conversely, the correlation of which was lower in GSE79533. Suggesting that the sharing key genes had a different impact on the immune environment in pediatric ALL and pediatric sepsis. We make the case that this study provides a new perspective to study the relationship between pediatric ALL and pediatric sepsis.
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Affiliation(s)
- Ying-Ping Xiao
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Yu-Cai Cheng
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Chun Chen
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Hong-Man Xue
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China
| | - Mo Yang
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
| | - Chao Lin
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, Guangdong, China.
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Zhu XC, Tang BF, Zhu MZ, Lu J, Lin HX, Tang JM, Li R, Ma T. Analysis of complement system and its related factors in Alzheimer's disease. BMC Neurol 2023; 23:446. [PMID: 38114984 PMCID: PMC10729410 DOI: 10.1186/s12883-023-03503-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023] Open
Abstract
Alzheimer's disease (AD) is a primary cause of dementia. The complement system is closely related to AD pathology and may be a potential target for the prevention and treatment of AD. In our study, we conducted a bioinformatics analysis to analyze the role of the complement system and its related factors in AD using Gene Expression Omnibus (GEO) data. We also conducted a functional analysis. Our study verified that 23 genes were closely related to differentially expressed complement system genes in diseases after intersecting the disease-related complement system module genes and differentially expressed genes. The STRING database was used to predict the interactions between the modular gene proteins of the differential complement system. A total of 21 gene proteins and 44 interaction pairs showed close interactions. We screened key genes and created a diagnostic model. The predictive effect of the model was constructed using GSE5281 and our study indicated that the predictive effect of the model was good. Our study also showed enriched negative regulation of Notch signaling, cytokine secretion involved in the immune response pathway, and cytokine secretion involved in immune response hormone-mediated apoptotic signaling pathway. We hope that our study provides a promising target to prevent and delay the onset, diagnosis, and treatment of AD.
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Affiliation(s)
- Xi-Chen Zhu
- Department of Neurology, The Wuxi No. 2 People's Hospital, Jiangnan University Medical Center, Wuxi, Jiangsu Province, China.
- Brain Institue, Jiangnan University, Wuxi, Jiangsu Province, China.
- Department of Neurology, The Wuxi No. 2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu Province, China.
- Department of Neurology, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, No. 68 Zhongshan Road, Wuxi, Jiangsu, 214000, China.
| | - Bin-Feng Tang
- Department of Neurology, The Wuxi No. 2 People's Hospital, Jiangnan University Medical Center, Wuxi, Jiangsu Province, China
| | - Meng-Zhuo Zhu
- Department of Neurology, The Wuxi No. 2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu Province, China
| | - Jing Lu
- Department of Neurology, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, No. 68 Zhongshan Road, Wuxi, Jiangsu, 214000, China
| | - Han-Xiao Lin
- Department of Neurology, The Wuxi No. 2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu Province, China
| | - Jia-Ming Tang
- Department of Neurology, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, No. 68 Zhongshan Road, Wuxi, Jiangsu, 214000, China
| | - Rong Li
- Department of Pharmacy, The Affiliated Wuxi No. 2 People's Hospital, Jiangnan University Medical Center, Wuxi, Jiangsu Province, China.
| | - Tao Ma
- Department of Neurology, The Wuxi No. 2 People's Hospital, Jiangnan University Medical Center, Wuxi, Jiangsu Province, China.
- Brain Institue, Jiangnan University, Wuxi, Jiangsu Province, China.
- Department of Neurology, The Wuxi No. 2 People's Hospital, Affiliated Wuxi Clinical College of Nantong University, Wuxi, Jiangsu Province, China.
- Department of Neurology, The Affiliated Wuxi No. 2 People's Hospital of Nanjing Medical University, No. 68 Zhongshan Road, Wuxi, Jiangsu, 214000, China.
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