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Lu S, Xu Y, Zhang H, Liu Z, Xu J, Zheng B, Shi D, Qiu F. Glycyrol Relieves Ulcerative Colitis by Promoting the Fusion of ZO-1 with the Cell Membrane through the Enteric Glial Cells GDNF/RET Pathway. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14653-14662. [PMID: 38860840 DOI: 10.1021/acs.jafc.4c00239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
The damage to the mechanical barrier of the intestinal mucosa is the initiating factor and the core link of the progression of ulcerative colitis (UC). Protecting the mechanical barrier of the intestinal mucosa is of great significance for improving the health status of UC patients. ZO-1 is a key scaffold protein of the mechanical barrier of the intestinal mucosa, and its fusion with the membrane of the intestinal epithelium is a necessary condition to maintain the integrity of the mechanical barrier of the intestinal mucosa. Enteric glial cells (EGCs) play an important role in the maintenance of intestinal homeostasis and have become a new target for regulating intestinal health in recent years. In this study, we found that glycyrol (GC), a representative coumarin compound isolated from Licorice (Glycyrrhiza uralensis Fisch, used for medicine and food), can alleviate UC by promoting the production of neurotrophic factor GDNF in mice EGCs. Specifically, we demonstrated that GC promotes the production of GDNF, then activates its receptor RET, promotes ZO-1 fusion with cell membranes, and protects the intestinal mucosal mechanical barrier. The results of this study can provide new ideas for the prevention and treatment of UC.
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Affiliation(s)
- Shangyun Lu
- Nutritional and Food Science Research Institute, Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
- Key Laboratory of Coal Environmental Pathogenicity and Prevention, Ministry of Education, Taiyuan 030001, China
- Center for Ecological Public Health Security of Yellow River Basin, Shanxi Medical University, Taiyuan 030001, China
| | - Yang Xu
- Nutritional and Food Science Research Institute, Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Huixia Zhang
- Nutritional and Food Science Research Institute, Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Ziling Liu
- Nutritional and Food Science Research Institute, Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Jiali Xu
- Nutritional and Food Science Research Institute, Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
| | - Bowen Zheng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Dongxing Shi
- Nutritional and Food Science Research Institute, Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
- Key Laboratory of Coal Environmental Pathogenicity and Prevention, Ministry of Education, Taiyuan 030001, China
- Center for Ecological Public Health Security of Yellow River Basin, Shanxi Medical University, Taiyuan 030001, China
| | - Fubin Qiu
- Nutritional and Food Science Research Institute, Department of Nutrition and Food Hygiene, School of Public Health, Shanxi Medical University, Taiyuan 030001, China
- Key Laboratory of Coal Environmental Pathogenicity and Prevention, Ministry of Education, Taiyuan 030001, China
- Center for Ecological Public Health Security of Yellow River Basin, Shanxi Medical University, Taiyuan 030001, China
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Chen Y, Li X, Sun R, Yang F, Tian W, Huang Q. Screening and experimental validation of diagnostic gene in ulcerative colitis with anti-TNF-α therapy. IUBMB Life 2024; 76:451-463. [PMID: 38269750 DOI: 10.1002/iub.2807] [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: 07/13/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024]
Abstract
In clinical practice, the diagnosis of ulcerative colitis (UC) mainly relies on a comprehensive analysis of a series of signs and symptoms of patients. The current biomarkers for diagnosis of UC and prognostic prediction of anti-TNF-α therapy are inaccurate. The present study aimed to perform an integrative analysis of gene expression profiles in patients with UC. A total of seven datasets from the GEO database that met our strict inclusion criteria were included. After identifying differentially expressed genes (DEGs) between UC patients and healthy individuals, the diagnostic and prognostic utility of the DEGs were then analyzed via least absolute shrinkage and selection operator and support-vector machine recursive feature elimination. Subgroup analyses of the treated and untreated groups, as well as the treatment-response group and non-response group, were also performed. Furthermore, the relationship between the expressions of UC-related genes and infiltration of immune cells in the course of treatment was also investigated. Immunohistochemical (IHC) assay was used to verify the gene expression in inflamed UC tissues. When considering all the applied methods, DUOX2, PI3, S100P, MMP7, and S100A8 had priority to be defined as the characteristic genes among DEGs. The area under curve (AUC) of the five genes, which were all consistently over-expressed, based on an external validation dataset, were all above 0.94 for UC diagnosis. Four of the five genes (DUOX2, PI3, MMP7, and S100A8) were down-regulated between treatment-responsive and nonresponsive patients. A significant difference was also observed concerning the infiltration of immune cells, including macrophage and neutrophil, between the two groups (treatment responsive and nonresponsive). The changes in the expression of DUOX2 and MMP7 based on the IHC assay were highly consistent with the results obtained in the current study. This confirmed the mild to moderate diagnostic and predictive value of DUOX2 and MMP7 in patients with UC. The conducted analyses showed that the expression profile of the five identified biomarkers accurately detects UC, whereas four of the five genes evidently predicted the response to anti-TNF-α therapy.
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Affiliation(s)
- Yuan Chen
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Xinfang Li
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Ran Sun
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Fan Yang
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Weiliang Tian
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
| | - Qian Huang
- Research Institute of General Surgery, Jinling Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, People's Republic of China
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Liu M, Zhong XS, Krishnachaitanya SS, Ou R, Dashwood RH, Powell DW, Li Q. Erlotinib suppresses tumorigenesis in a mouse model of colitis-associated cancer. Biomed Pharmacother 2024; 175:116580. [PMID: 38723513 DOI: 10.1016/j.biopha.2024.116580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/28/2024] [Accepted: 04/10/2024] [Indexed: 06/03/2024] Open
Abstract
Colitis-associated cancer (CAC) in inflammatory bowel diseases exhibits more aggressive behavior than sporadic colorectal cancer; however, the molecular mechanisms remain unclear. No definitive preventative agent against CAC is currently established in the clinical setting. We investigated the molecular mechanisms of CAC in the azoxymethane/dextran sulfate sodium (AOM/DSS) mouse model and assessed the antitumor efficacy of erlotinib, a small molecule inhibitor of the epidermal growth factor receptor (EGFR). Erlotinib premixed with AIN-93 G diet at 70 or 140 parts per million (ppm) inhibited tumor multiplicity significantly by 96%, with ∼60% of the treated mice exhibiting zero polyps at 12 weeks. Bulk RNA-sequencing revealed more than a thousand significant gene alterations in the colons of AOM/DSS-treated mice, with KEGG enrichment analysis highlighting 46 signaling pathways in CAC development. Erlotinib altered several signaling pathways and rescued 40 key genes dysregulated in CAC, including those involved in the Hippo and Wnt signaling. These findings suggest that the clinically-used antitumor agent erlotinib might be repurposed for suppression of CAC, and that further studies are warranted on the crosstalk between dysregulated Wnt and EGFR signaling in the corresponding patient population.
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Affiliation(s)
- Max Liu
- Division of Gastroenterology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Xiaoying S Zhong
- Division of Gastroenterology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Srikruthi S Krishnachaitanya
- Division of Gastroenterology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Rongliwen Ou
- Division of Gastroenterology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, USA; Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
| | - Roderick H Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M School of Medicine, Houston, TX, USA
| | - Don W Powell
- Division of Gastroenterology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Qingjie Li
- Division of Gastroenterology, Department of Internal Medicine, University of Texas Medical Branch at Galveston, Galveston, TX, USA.
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Chacon-Millan P, Lama S, Del Gaudio N, Gravina AG, Federico A, Pellegrino R, Luce A, Altucci L, Facchiano A, Caraglia M, Stiuso P. A Combination of Microarray-Based Profiling and Biocomputational Analysis Identified miR331-3p and hsa-let-7d-5p as Potential Biomarkers of Ulcerative Colitis Progression to Colorectal Cancer. Int J Mol Sci 2024; 25:5699. [PMID: 38891888 PMCID: PMC11171846 DOI: 10.3390/ijms25115699] [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: 03/22/2024] [Revised: 05/06/2024] [Accepted: 05/15/2024] [Indexed: 06/21/2024] Open
Abstract
Ulcerative colitis (UC), an inflammatory bowel disease (IBD), may increase the risk of colorectal cancer (CRC) by activating chronic proinflammatory pathways. The goal of this study was to find serum prediction biomarkers in UC to CRC development by combining low-density miRNA microarray and biocomputational approaches. The UC and CRC miRNA expression profiles were compared by low-density miRNA microarray, finding five upregulated miRNAs specific to UC progression to CRC (hsa-let-7d-5p, hsa-miR-16-5p, hsa-miR-145-5p, hsa-miR-223-5p, and hsa-miR-331-3p). The circRNA/miRNA/mRNA competitive endogenous RNA (ceRNA) network analysis showed that the candidate miRNAs were connected to well-known colitis-associated CRC ACVR2A, SOCS1, IGF2BP1, FAM126A, and CCDC85C mRNAs, and circ-SHPRH circRNA. SST and SCARA5 genes regulated by hsa-let-7d-5p, hsa-miR-145-5p, and hsa-miR-331-3p were linked to a poor survival prognosis in a CRC patient dataset from The Cancer Genome Atlas (TCGA). Lastly, our mRNA and miRNA candidates were validated by comparing their expression to differentially expressed mRNAs and miRNAs from colitis-associated CRC tissue databases. A high level of hsa-miR-331-3p and a parallel reduction in SOCS1 mRNA were found in tissue and serum. We propose hsa-miR-331-3p and possibly hsa-let-7d-5p as novel serum biomarkers for predicting UC progression to CRC. More clinical sample analysis is required for further validation.
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Affiliation(s)
- Pilar Chacon-Millan
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.C.-M.); (S.L.); (N.D.G.); (A.G.G.); (A.F.); (R.P.); (A.L.); (L.A.); (M.C.)
| | - Stefania Lama
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.C.-M.); (S.L.); (N.D.G.); (A.G.G.); (A.F.); (R.P.); (A.L.); (L.A.); (M.C.)
| | - Nunzio Del Gaudio
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.C.-M.); (S.L.); (N.D.G.); (A.G.G.); (A.F.); (R.P.); (A.L.); (L.A.); (M.C.)
| | - Antonietta Gerarda Gravina
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.C.-M.); (S.L.); (N.D.G.); (A.G.G.); (A.F.); (R.P.); (A.L.); (L.A.); (M.C.)
| | - Alessandro Federico
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.C.-M.); (S.L.); (N.D.G.); (A.G.G.); (A.F.); (R.P.); (A.L.); (L.A.); (M.C.)
| | - Raffaele Pellegrino
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.C.-M.); (S.L.); (N.D.G.); (A.G.G.); (A.F.); (R.P.); (A.L.); (L.A.); (M.C.)
| | - Amalia Luce
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.C.-M.); (S.L.); (N.D.G.); (A.G.G.); (A.F.); (R.P.); (A.L.); (L.A.); (M.C.)
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.C.-M.); (S.L.); (N.D.G.); (A.G.G.); (A.F.); (R.P.); (A.L.); (L.A.); (M.C.)
- Biogem Scarl, Institute of Genetic Research, Laboratory of Molecular and Precision Oncology, 83031 Ariano Irpino, Italy
- Institute of Experimental Endocrinology and Oncology “Gaetano Salvatore” (IEOS)-National Research Council (CNR), Via Sergio Pansini, 80131 Naples, Italy
- Programma di Epigenetica Medica, A.O.U. “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Angelo Facchiano
- Institute of Food Sciences, National Research Council, 83100 Avellino, Italy;
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.C.-M.); (S.L.); (N.D.G.); (A.G.G.); (A.F.); (R.P.); (A.L.); (L.A.); (M.C.)
- Biogem Scarl, Institute of Genetic Research, Laboratory of Molecular and Precision Oncology, 83031 Ariano Irpino, Italy
- Programma di Epigenetica Medica, A.O.U. “Luigi Vanvitelli”, 80138 Naples, Italy
| | - Paola Stiuso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (P.C.-M.); (S.L.); (N.D.G.); (A.G.G.); (A.F.); (R.P.); (A.L.); (L.A.); (M.C.)
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Yu H, Cui Y, Guo F, Zhu Y, Zhang X, Shang D, Dong D, Xiang H. Vanin1 (VNN1) in chronic diseases: Future directions for targeted therapy. Eur J Pharmacol 2024; 962:176220. [PMID: 38042463 DOI: 10.1016/j.ejphar.2023.176220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023]
Abstract
Vanin1 (VNN1) is an exogenous enzyme with pantetheinase activity that mainly exerts physiological functions through enzyme catalysis products, including pantothenic acid and cysteamine. In recent years, the crosstalk between VNN1 and metabolism and oxidative stress has attracted much attention. As a result of the ability of VNN1 to affect multiple metabolic pathways and oxidative stress to exacerbate or alleviate pathological processes, it has become a key component of disease progression. This review discusses the functions of VNN1 in glucolipid metabolism, cysteamine metabolism, and glutathione metabolism to provide perspectives on VNN1-targeted therapy for chronic diseases.
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Affiliation(s)
- Hao Yu
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, 116011, China; College of Pharmacy, Dalian Medical University, 116044, China
| | - Yuying Cui
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China; Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - Fangyue Guo
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China; Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - YuTong Zhu
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China; Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - Xiaonan Zhang
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China; Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, China
| | - Dong Shang
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China; Institute (College) of Integrative Medicine, Dalian Medical University, Dalian, 116044, China; Department of General Surgery, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Deshi Dong
- Department of Pharmacy, First Affiliated Hospital of Dalian Medical University, 116011, China.
| | - Hong Xiang
- Laboratory of Integrative Medicine, First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China.
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Yang Y, Hua Y, Zheng H, Jia R, Ye Z, Su G, Gu Y, Zhan K, Tang K, Qi S, Wu H, Qin S, Huang S. Biomarkers prediction and immune landscape in ulcerative colitis: Findings based on bioinformatics and machine learning. Comput Biol Med 2024; 168:107778. [PMID: 38070204 DOI: 10.1016/j.compbiomed.2023.107778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/02/2023] [Accepted: 11/28/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND Ulcerative colitis (UC) presents diagnostic and therapeutic difficulties. The primary objective of this study is to identify efficacious biomarkers for diagnosis and treatment, as well as acquire a deeper understanding of the immuneological characteristics associated with the disease. METHODS Datasets relating to UC were obtained from GEO database. Among these, three datasets were merged to create a metadata for bioinformatics analysis and machine learning. Additionally, one dataset specifically utilized for external validation. Least absolute shrinkage and selection operator (LASSO) and random forest (RF) were employed to screen signature genes. The artificial neural network (ANN) model and receiver operating characteristic (ROC) curve were used to assess the diagnostic performance of signature genes. The single sample gene set enrichment analysis (ssGSEA) was applied to reveal the immune landscape. Finally, the relationship between the signature genes, immune infiltration, and clinical characteristics was investigated through correlation analysis. RESULT By intersecting the result of LASSO, RF and WGCNA, 8 signature genes were identified, including S100A8, IL-1B, CXCL1, TCN1, MMP10, GREM1, DUOX2 and SLC6A14. The biological progress of this gene mostly encompasses acute inflammatory response, aggregation and chemotaxis of leukocyte, and response to lipopolysaccharide by mediating IL-17 signaling pathway, NF-kappa B signaling pathway, TNF signaling pathway, NOD-like receptor signaling pathway. Immune infiltration analysis shows 25 immune cells are significantly elevated in UC samples. Moreover, these signature genes exhibit a strong correlation with various immune cells and a mild to moderate correlation with the Mayo score. CONCLUSION S100A8, IL-1B, CXCL1, TCN1, MMP10, GREM1, DUOX2 and SLC6A14 have been identified as credible potential biomarkers for the diagnosis and therapy of UC. The immune response mediated by these signature biomarkers plays a crucial role in the occurrence and advancement of UC by means of the reciprocal interaction between the signature biomarkers and immune-infiltrated cells.
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Affiliation(s)
- Yuanming Yang
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Yiwei Hua
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Huan Zheng
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Rui Jia
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Zhining Ye
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Guifang Su
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Yueming Gu
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Kai Zhan
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Kairui Tang
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Shuhao Qi
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China
| | - Haomeng Wu
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, 510120, China; Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou 510120, China
| | - Shumin Qin
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, 510120, China; Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou 510120, China.
| | - Shaogang Huang
- Dongguan Hospital of Guangzhou University of Chinese Medicine, Dongguan, 523000, China; The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China; State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China; Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou, 510120, China; Guangdong Provincial Key Laboratory of Clinical Research on Traditional Chinese Medicine Syndrome, Guangzhou 510120, China; Yang Chunbo academic experience inheritance studio of Guangdong provincial hospital of Chinese Medicine, Guangzhou, 510006, China.
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Wang L, Wang L, Cao C, Zhao J, Song C, Bao Z, Yan C, Song S. Chitosan and its oligosaccharide accelerate colonic motility and reverse serum metabolites in rats after excessive protein consumption. Int J Biol Macromol 2023; 253:127072. [PMID: 37774814 DOI: 10.1016/j.ijbiomac.2023.127072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023]
Abstract
Excessive protein consumption (EPC) could increase the gastrointestinal burden and impair gut motility. The present study was designed to explore the improvement of chitosan (CTS) and chitosan oligosaccharide (COS) on colonic motility and serum metabolites in rats after EPC. The results of in vivo experiments fully proved that CTS and COS could improve gut motility and reverse the serum metabolites in rats as indicated by LC-MS/MS analysis, and the COS group even showed a better effect than the CTS group. Furthermore, short-chain fatty acids (SCFAs), which could promote gut motility, were also increased to alleviate EPC-induced constipation after supplementation with CTS or COS. In addition, CTS and COS could decrease the concentration of ammonia in serum and down-regulate the levels of H2S and indole. In summary, the present study revealed that CTS and COS could produce SCFAs, improve the colonic motility in rats, reverse the levels of valine, adenosine, cysteine, 1-methyladenosine, indole, and uracil, and enhance aminoacyl-tRNA biosynthesis and valine, leucine and isoleucine degradation. The present study provides novel insights into the potential roles of CTS and COS in alleviating the adverse effects of EPC.
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Affiliation(s)
- Linlin Wang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China
| | - Lilong Wang
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China
| | - Cui Cao
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China; Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, PR China
| | - Jun Zhao
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China
| | - Chen Song
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China
| | - Zhijie Bao
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China
| | - Chunhong Yan
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China
| | - Shuang Song
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China.
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8
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Chew DCH, Khoo XH, Lee TS, Chin KY, Raja Ali RA, Muhammad Nawawi KN, Wan Ibrahim NR, Hilmi I. A Systematic Review on the Increasing Incidence of Inflammatory Bowel Disease in Southeast Asia: Looking Beyond the Urbanization Phenomenon. Inflamm Bowel Dis 2023:izad189. [PMID: 37935628 DOI: 10.1093/ibd/izad189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Indexed: 11/09/2023]
Abstract
The incidence of inflammatory bowel disease (IBD) has been increasing in Southeast Asia (SEA) in tandem with its economic growth and urbanization over the past 2 decades. Specific characteristics of IBD in SEA are similar to East Asia and the West, such as the declining ratio of ulcerative colitis to Crohn's disease. However, exceptionally low familial aggregation is seen. Smoking is also not a common risk factor in patients with Crohn's disease. The incidence of perianal disease is higher in SEA than in Australia and is comparable to the West. In a multiracial population, such as Singapore and Malaysia, Indians have the highest incidence and prevalence rates, which are likely to be due to important putative mutations. For instance, a higher frequency of the NOD2 predisposing mutation SNP5 and IBD risk allele IGR2198a and IGR2092a were found in Indians. Although differences in the genetic constitution play an important role in the epidemiology and prognosis of IBD in SEA, the emergence of this disease offers a unique opportunity to identify potential exposomes that contribute to its pathogenesis.
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Affiliation(s)
- Deborah Chia Hsin Chew
- Gastroenterology and hepatology Unit, Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Xin-Hui Khoo
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Tiong See Lee
- Department of Gastroenterology and Hepatology, Selayang Hospital, Kuala Lumpur, Malaysia
| | - Kok-Yong Chin
- Department of Pharmacology, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
| | - Raja Affendi Raja Ali
- Gastroenterology and hepatology Unit, Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Khairul Najmi Muhammad Nawawi
- Gastroenterology and hepatology Unit, Department of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Kuala Lumpur, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | | | - Ida Hilmi
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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Zou C, Zan X, Jia Z, Zheng L, Gu Y, Liu F, Han Y, Xu C, Wu A, Zhi Q. Crosstalk between alternative splicing and inflammatory bowel disease: Basic mechanisms, biotechnological progresses and future perspectives. Clin Transl Med 2023; 13:e1479. [PMID: 37983927 PMCID: PMC10659771 DOI: 10.1002/ctm2.1479] [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: 06/25/2023] [Revised: 10/07/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
BACKGROUND Alternative splicing (AS) is an omnipresent regulatory mechanism of gene expression that enables the generation of diverse splice isoforms from a single gene. Recently, AS events have gained considerable momentum in the pathogenesis of inflammatory bowel disease (IBD). METHODS Our review has summarized the complex process of RNA splicing, and firstly highlighted the potential involved molecules that target aberrant splicing events in IBD. The quantitative transcriptome analyses such as microarrays, next-generation sequencing (NGS) for AS events in IBD have been also discussed. RESULTS Available evidence suggests that some abnormal splicing RNAs can lead to multiple intestinal disorders during the onset of IBD as well as the progression to colitis-associated cancer (CAC), including gut microbiota perturbations, intestinal barrier dysfunctions, innate/adaptive immune dysregulations, pro-fibrosis activation and some other risk factors. Moreover, current data show that the advanced technologies, including microarrays and NGS, have been pioneeringly employed to screen the AS candidates and elucidate the potential regulatory mechanisms of IBD. Besides, other biotechnological progresses such as the applications of third-generation sequencing (TGS), single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), will be desired with great expectations. CONCLUSIONS To our knowledge, the current review is the first one to evaluate the potential regulatory mechanisms of AS events in IBD. The expanding list of aberrantly spliced genes in IBD along with the developed technologies provide us new clues to how IBD develops, and how these important AS events can be explored for future treatment.
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Affiliation(s)
- Chentao Zou
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Xinquan Zan
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Zhenyu Jia
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Lu Zheng
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Yijie Gu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Fei Liu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Ye Han
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Chunfang Xu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Airong Wu
- Department of GastroenterologyThe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Qiaoming Zhi
- Department of General SurgeryThe First Affiliated Hospital of Soochow UniversitySuzhouChina
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10
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Razali NN, Raja Ali RA, Muhammad Nawawi KN, Yahaya A, Mohd Rathi ND, Mokhtar NM. Roles of phosphatidylinositol-3-kinases signaling pathway in inflammation-related cancer: Impact of rs10889677 variant and buparlisib in colitis-associated cancer. World J Gastroenterol 2023; 29:5543-5556. [PMID: 37970476 PMCID: PMC10642440 DOI: 10.3748/wjg.v29.i40.5543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/05/2023] [Accepted: 10/11/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Phosphatidylinositol-3-kinases (PI3K) is a well-known route in inflammation-related cancer. Recent discovery on PI3K-related genes revealed a potential variant that links ulcerative colitis (UC) and colorectal cancer (CRC) with colitis-associated cancer (CAC). PI3K/AKT pathway has been recommended as a potential additional therapeutic option for CRC due to its substantial role in modifying cellular processes. Buparlisib is a pan-class I PI3K inhibitor previously shown to reduce tumor growth. AIM To investigate the regulation of rs10889677 and the role of buparlisib in the PI3K signaling pathway in CAC pathogenesis. METHODS Genomic DNA from 32 colonic samples, including CAC (n = 7), UC (n = 10) and CRC (n = 15), was sequenced for the rs10889677 mutation. The mutant and wildtype fragments were amplified and cloned in the pmirGLO vector. The luciferase activity of cloned vectors was assessed after transfection into the HT29 cell line. CAC mice were induced by a mixture of a single azoxymethane injection and three cycles of dextran sulphate sodium, then buparlisib was administered after 14 d. The excised colon was subjected to immunohistochemistry for Ki67 and Cleaved-caspase-3 markers and quantitative real-time polymerase chain reaction analysis for Pdk1 and Sgk2. RESULTS Luciferase activity decreased by 2.07-fold in the rs10889677 mutant, confirming the hypothesis that the variant disrupted miRNA binding sites, which led to an increase in IL23R expression and the activation of the PI3K signaling pathway. Furthermore, CAC-induced mice had a significantly higher disease activity index (P < 0.05). Buparlisib treatment significantly decreased mean weight loss in CAC-induced mice (P < 0.05), reduced the percentage of proliferating cells by 5%, and increased the number of apoptotic cells. The treatment also caused a downward trend of Pdk1 expression and significantly decreased Sgk2 expression. CONCLUSION Our findings suggested that the rs10889677 variant as a critical initiator of the PI3K signaling pathway, and buparlisib had the ability to prevent PI3K-non-AKT activation in the pathophysiology of CAC.
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Affiliation(s)
- Nurul Nadirah Razali
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras 56000, Kuala Lumpur, Malaysia
| | - Raja Affendi Raja Ali
- School of Medical and Life Sciences, Sunway University, Sunway City 47500, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras 56000, Kuala Lumpur, Malaysia
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras 56000, Kuala Lumpur, Malaysia
| | - Khairul Najmi Muhammad Nawawi
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras 56000, Kuala Lumpur, Malaysia
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras 56000, Kuala Lumpur, Malaysia
| | - Azyani Yahaya
- Department of Pathology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras 56000, Kuala Lumpur, Malaysia
| | - Norshafila Diana Mohd Rathi
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras 56000, Kuala Lumpur, Malaysia
| | - Norfilza Mohd Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras 56000, Kuala Lumpur, Malaysia
- GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras 56000, Kuala Lumpur, Malaysia
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11
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James JP, Nielsen BS, Christensen IJ, Langholz E, Malham M, Poulsen TS, Holmstrøm K, Riis LB, Høgdall E. Mucosal expression of PI3, ANXA1, and VDR discriminates Crohn's disease from ulcerative colitis. Sci Rep 2023; 13:18421. [PMID: 37891214 PMCID: PMC10611705 DOI: 10.1038/s41598-023-45569-3] [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: 05/27/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Differential diagnosis of inflammatory bowel disease (IBD) to Crohn's disease (CD) or ulcerative colitis (UC) is crucial for treatment decision making. With the aim of generating a clinically applicable molecular-based tool to classify IBD patients, we assessed whole transcriptome analysis on endoscopy samples. A total of 408 patient samples were included covering both internal and external samples cohorts. Whole transcriptome analysis was performed on an internal cohort of FFPE IBD samples (CD, n = 16 and UC, n = 17). The 100 most significantly differentially expressed genes (DEG) were tested in two external cohorts. Ten of the DEG were further processed by functional enrichment analysis from which seven were found to show consistent significant performance in discriminating CD from UC: PI3, ANXA1, VDR, MTCL1, SH3PXD2A-AS1, CLCF1, and CD180. Differential expression of PI3, ANXA1, and VDR was reproduced by RT-qPCR, which was performed on an independent sample cohort of 97 patient samples (CD, n = 44 and UC, n = 53). Gene expression levels of the three-gene profile, resulted in an area under the curve of 0.84 (P = 0.02) in discriminating CD from UC, and therefore appear as an attractive molecular-based diagnostic tool for clinicians to distinguish CD from UC.
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Affiliation(s)
| | | | - Ib Jarle Christensen
- Department of Pathology, Herlev University Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
| | - Ebbe Langholz
- Gastroenheden D, Herlev University Hospital, 2730, Herlev, Denmark
- Institute for Clinical Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Mikkel Malham
- The Department of Pediatric and Adolescence Medicine, Copenhagen University Hospital-Amager and Hvidovre, 2650, Hvidovre, Denmark
- Copenhagen Center for Inflammatory Bowel Disease in Children, Adolescents and Adults, Hvidovre Hospital, University of Copenhagen, 2650, Hvidovre, Denmark
| | - Tim Svenstrup Poulsen
- Department of Pathology, Herlev University Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
| | - Kim Holmstrøm
- Bioneer A/S, Hørsholm, Kogle Allé 2, 2970, Hørsholm, Denmark
| | - Lene Buhl Riis
- Department of Pathology, Herlev University Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
- Institute for Clinical Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Estrid Høgdall
- Department of Pathology, Herlev University Hospital, Borgmester Ib Juuls Vej 73, 2730, Herlev, Denmark
- Institute for Clinical Medicine, University of Copenhagen, 2200, Copenhagen, Denmark
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12
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Zhu D, Zhao D, Wang N, Cai F, Jiang M, Zheng Z. Current status and prospects of GREM1 research in cancer (Review). Mol Clin Oncol 2023; 19:69. [PMID: 37614374 PMCID: PMC10442762 DOI: 10.3892/mco.2023.2665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 03/21/2023] [Indexed: 08/25/2023] Open
Abstract
GREM1 is a secreted protein that antagonizes bone morphogenetic proteins (BMPs) and participates in critical biological processes, including embryonic development, organogenesis and tissue differentiation. Gremlin 1 (GREM1) is also an inhibitor of TGF-β and a ligand for vascular endothelial growth factor receptor 2. In addition, GREM1 can induce cells, participate in the process of epithelial-mesenchymal transition, and then participate in tumor development. GREM1 has a variety of biological functions and can participate in the malignant progression of a variety of tumors through the BMP signaling pathway. GREM1 also can inhibit TGF-β in some tumors, thereby inhibiting tumors, and its involvement in tumor development varies in different types of cancer. The present review examines the role and function of GREM1 in tumors. GREM1 is expressed in a variety of tumor types. GREM1 expression can affect the epithelial-mesenchymal transformation of tumor cells. GREM1 has been studied in breast and colon cancer, and its potential role is to promote cancer. However, in pancreatic cancer, which was found to act differently from other cancer types, overexpression of GREM1 inhibits tumor metastasis. The present review suggests that GREM1 can be a diagnostic and prognostic indicator. In future studies, the study of GREM1 based on single-cell sequencing technology will further clarify its role and function in tumors.
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Affiliation(s)
- Dantong Zhu
- Department of Medical Oncology, General Hospital of Northern Theater Command, Shenyang, Liaoning 110000, P.R. China
| | - Dong Zhao
- Department of Medical Oncology, General Hospital of Northern Theater Command, Shenyang, Liaoning 110000, P.R. China
| | - Naixue Wang
- Department of Oncology, General Hospital of Northern Theater Command, Jinzhou Medical University, Shenyang, Liaoning 121017, P.R. China
| | - Fei Cai
- Department of Oncology, General Hospital of Northern Theater Command, China Medical University, Shenyang, Liaoning 110000, P.R. China
| | - Mingzhe Jiang
- Department of Medical Oncology, General Hospital of Northern Theater Command, Shenyang, Liaoning 110000, P.R. China
| | - Zhendong Zheng
- Department of Medical Oncology, General Hospital of Northern Theater Command, Shenyang, Liaoning 110000, P.R. China
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13
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Zhang Y, Miao Y, Tan J, Chen F, Lei P, Zhang Q. Identification of mitochondrial related signature associated with immune microenvironment in Alzheimer's disease. J Transl Med 2023; 21:458. [PMID: 37434203 DOI: 10.1186/s12967-023-04254-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/07/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common neurodegenerative disease. Mitochondrial dysfunction and immune responses are important factors in the pathogenesis of AD, but their crosstalk in AD has not been studied. In this study, the independent role and interaction of mitochondria-related genes and immune cell infiltration in AD were investigated using bioinformatics methods. METHODS The datasets of AD were obtained from NCBI Gene Expression Omnibus (GEO), and the data of mitochondrial genes was from MitoCarta3.0 database. Subsequently, differential expression genes (DEGs) screening and GSEA functional enrichment analysis were performed. The intersection of DEGs and mitochondrial related genes was used to obtain MitoDEGs. The MitoDEGs most relevant to AD were determined by Least absolute shrinkage and selection operator and multiple support vector machine recursive feature elimination, as well as protein-protein interactions (PPI) network and random forest. The infiltration of 28 kinds of immune cells in AD was analyzed by ssGSEA, and the relationship between hub MitoDEGs and the proportion of immune infiltration was studied. The expression levels of hub MitoDEGs were verified in cell models and AD mice, and the role of OPA1 in mitochondrial damage and neuronal apoptosis was investigated. RESULTS The functions and pathways of DEGs were significantly enriched in AD, including immune response activation, IL1R pathway, mitochondrial metabolism, oxidative damage response and electron transport chain-oxphos system in mitochondria. Hub MitoDEGs closely related to AD were obtained based on PPI network, random forest and two machine learning algorithms. Five hub MitoDEGs associated with neurological disorders were identified by biological function examination. The hub MitoDEGs were found to be correlated with memory B cell, effector memory CD8 T cell, activated dendritic cell, natural killer T cell, type 17 T helper cell, Neutrophil, MDSC, plasmacytoid dendritic cell. These genes can also be used to predict the risk of AD and have good diagnostic efficacy. In addition, the mRNA expression levels of BDH1, TRAP1, OPA1, DLD in cell models and AD mice were consistent with the results of bioinformatics analysis, and expression levels of SPG7 showed a downward trend. Meanwhile, OPA1 overexpression alleviated mitochondrial damage and neuronal apoptosis induced by Aβ1-42. CONCLUSIONS Five potential hub MitoDEGs most associated with AD were identified. Their interaction with immune microenvironment may play a crucial role in the occurrence and prognosis of AD, which provides a new insight for studying the potential pathogenesis of AD and exploring new targets.
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Affiliation(s)
- Yaodan Zhang
- Department of Geriatrics, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China
- Tianjin Geriatrics Institute, Anshan Road No. 154, Tianjin, 300052, China
| | - Yuyang Miao
- Department of Geriatrics, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China
- Tianjin Geriatrics Institute, Anshan Road No. 154, Tianjin, 300052, China
| | - Jin Tan
- Department of Geriatrics, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China
- Tianjin Geriatrics Institute, Anshan Road No. 154, Tianjin, 300052, China
| | - Fanglian Chen
- Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Ping Lei
- Department of Geriatrics, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China.
- Tianjin Geriatrics Institute, Anshan Road No. 154, Tianjin, 300052, China.
- Haihe Laboratory of Cell Ecosystem, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China.
| | - Qiang Zhang
- Department of Geriatrics, Tianjin Medical University General Hospital, Anshan Road No. 154, Tianjin, 300052, China.
- Tianjin Geriatrics Institute, Anshan Road No. 154, Tianjin, 300052, China.
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14
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Xie Z, Zhou G, Zhang M, Han J, Wang Y, Li X, Wu Q, Li M, Zhang S. Recent developments on BMPs and their antagonists in inflammatory bowel diseases. Cell Death Discov 2023; 9:210. [PMID: 37391444 DOI: 10.1038/s41420-023-01520-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 07/02/2023] Open
Abstract
Inflammatory bowel diseases (IBDs), including ulcerative colitis, and Crohn's disease, are intestinal disorders characterized by chronic relapsing inflammation. A large proportion of patients with IBD will progress to develop colitis-associated colorectal cancer due to the chronic intestinal inflammation. Biologic agents that target tumour necrosis factor-α, integrin α4β7, and interleukin (IL)12/23p40 have been more successful than conventional therapies in treating IBD. However, drug intolerance and loss of response are serious drawbacks of current biologics, necessitating the development of novel drugs that target specific pathways in IBD pathogenesis. One promising group of candidate molecules are bone morphogenetic proteins (BMPs), members of the TGF-β family involved in regulating morphogenesis, homeostasis, stemness, and inflammatory responses in the gastrointestinal tract. Also worth examining are BMP antagonists, major regulators of these proteins. Evidence has shown that BMPs (especially BMP4/6/7) and BMP antagonists (especially Gremlin1 and follistatin-like protein 1) play essential roles in IBD pathogenesis. In this review, we provide an updated overview on the involvement of BMPs and BMP antagonists in IBD pathogenesis and in regulating the fate of intestinal stem cells. We also described the expression patterns of BMPs and BMP antagonists along the intestinal crypt-villus axis. Lastly, we synthesized available research on negative regulators of BMP signalling. This review summarizes recent developments on BMPs and BMP antagonists in IBD pathogenesis, which provides novel insights into future therapeutic strategies.
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Affiliation(s)
- Zhuo Xie
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P. R. China
| | - Gaoshi Zhou
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P. R. China
| | - Mudan Zhang
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P. R. China
| | - Jing Han
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P. R. China
| | - Ying Wang
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P. R. China
| | - Xiaoling Li
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P. R. China
| | - Qirui Wu
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P. R. China
| | - Manying Li
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P. R. China
| | - Shenghong Zhang
- Division of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, P. R. China.
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15
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Zhang RB, Dong LC, Huang Q, Shen Y, Li HY, Yu SG, Wu QF. Matrix metalloproteinases are key targets of acupuncture in the treatment of ulcerative colitis. Exp Biol Med (Maywood) 2023; 248:1229-1241. [PMID: 37438919 PMCID: PMC10621479 DOI: 10.1177/15353702231182205] [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: 09/15/2022] [Accepted: 04/10/2023] [Indexed: 07/14/2023] Open
Abstract
The aim of this study was to elucidate the key targets of acupuncture in the colon of ulcerative colitis (UC) mice model using full-length transcriptome sequencing. 2.5% dextran sodium sulfate (DSS)-induced colitis mice were treated with or without acupuncture. Intestinal pathology was observed, and full transcriptome sequencing and bioinformatic analysis were performed. The results demonstrated that acupuncture treatment reduced the UC symptoms, disease activity index score, and histological colitis score and increased body weight, colon length, and the number of intestinal goblet cells. In addition, acupuncture can also decrease the expression of necrotic biomarker phosphorylates mixed lineage kinase domain-like pseudo kinase (p-MLKL). Full-length transcriptome analysis indicated that acupuncture reversed the expression of 987 of the 1918 upregulated differentially expressed genes (DEGs), and 632 of the 1351 downregulated DEGs induced by DSS. DEGs regulated by acupuncture were mainly involved in inflammatory responses and intestinal barrier pathways. The protein-protein interaction network analysis revealed that matrix metalloproteinases (MMPs) are important genes regulated by acupuncture. Gene set enrichment analysis revealed that extracellular matrix (ECM)-receptor interaction was an important target of acupuncture. In addition, alternative splicing analysis suggested that acupuncture improved signaling pathways related to intestinal permeability, the biological processes of xenobiotics, sulfur compounds, and that monocarboxylic acids are closely associated with MMPs. Overall, our transcriptome analysis results indicate that acupuncture improves intestinal barrier function in UC through negative regulation of MMPs expression.
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Affiliation(s)
| | | | - Qin Huang
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Yuan Shen
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Hong-Ying Li
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Shu-Guang Yu
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
| | - Qiao-Feng Wu
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu 610075, China
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16
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Martín-Adrados B, Wculek SK, Fernández-Bravo S, Torres-Ruiz R, Valle-Noguera A, Gomez-Sánchez MJ, Hernández-Walias JC, Ferreira FM, Corraliza AM, Sancho D, Esteban V, Rodriguez-Perales S, Cruz-Adalia A, Nakaya HI, Salas A, Bernardo D, Campos-Martín Y, Martínez-Zamorano E, Muñoz-López D, Gómez del Moral M, Cubero FJ, Blumberg RS, Martínez-Naves E. Expression of HMGCS2 in intestinal epithelial cells is downregulated in inflammatory bowel disease associated with endoplasmic reticulum stress. Front Immunol 2023; 14:1185517. [PMID: 37457727 PMCID: PMC10348483 DOI: 10.3389/fimmu.2023.1185517] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction The Unfolded Protein Response, a mechanism triggered by the cell in response to Endoplasmic reticulum stress, is linked to inflammatory responses. Our aim was to identify novel Unfolded Protein Response-mechanisms that might be involved in triggering or perpetuating the inflammatory response carried out by the Intestinal Epithelial Cells in the context of Inflammatory Bowel Disease. Methods We analyzed the transcriptional profile of human Intestinal Epithelial Cell lines treated with an Endoplasmic Reticulum stress inducer (thapsigargin) and/or proinflammatory stimuli. Several genes were further analyzed in colonic biopsies from Ulcerative Colitis patients and healthy controls. Lastly, we generated Caco-2 cells lacking HMGCS2 by CRISPR Cas-9 and analyzed the functional implications of its absence in Intestinal Epithelial Cells. Results Exposure to a TLR ligand after thapsigargin treatment resulted in a powerful synergistic modulation of gene expression, which led us to identify new genes and pathways that could be involved in inflammatory responses linked to the Unfolded Protein Response. Key differentially expressed genes in the array also exhibited transcriptional alterations in colonic biopsies from active Ulcerative Colitis patients, including NKG2D ligands and the enzyme HMGCS2. Moreover, functional studies showed altered metabolic responses and epithelial barrier integrity in HMGCS2 deficient cell lines. Conclusion We have identified new genes and pathways that are regulated by the Unfolded Protein Response in the context of Inflammatory Bowel Disease including HMGCS2, a gene involved in the metabolism of Short Chain Fatty Acids that may have an important role in intestinal inflammation linked to Endoplasmic Reticulum stress and the resolution of the epithelial damage.
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Affiliation(s)
- Beatriz Martín-Adrados
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
| | - Stefanie K. Wculek
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Sergio Fernández-Bravo
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Universidad Autónoma of Madrid, Madrid, Spain
| | - Raúl Torres-Ruiz
- Molecular Cytogenetics & Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro, Madrid, Spain
- Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), Advanced Therapies Unit, Hematopoietic Innovative Therapies Division, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ana Valle-Noguera
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
| | - Maria José Gomez-Sánchez
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
| | - José Carlos Hernández-Walias
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
| | | | - Ana María Corraliza
- Department of Gastroenterology, Instituto de Investigaciones Biomédicas August Pi i Sunyer (IDIBAPS), Hospital Clinic of Barcelona, Centro de Investigación Biomédica en Red-Enfermedades Hepáticas y Digestivas (CIBER-EHD), Barcelona, Spain
| | - David Sancho
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Vanesa Esteban
- Department of Allergy and Immunology, IIS-Fundación Jiménez Díaz, Universidad Autónoma of Madrid, Madrid, Spain
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics & Genome Editing Unit, Human Cancer Genetics Program, Centro Nacional de Investigaciones Oncológicas (CNIO), Melchor Fernández Almagro, Madrid, Spain
| | - Aránzazu Cruz-Adalia
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
| | - Helder I. Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo (USP), Hospital Israelita Albert Einstein, São Paulo, SP, Brazil
| | - Azucena Salas
- Department of Gastroenterology, Instituto de Investigaciones Biomédicas August Pi i Sunyer (IDIBAPS), Hospital Clinic of Barcelona, Centro de Investigación Biomédica en Red-Enfermedades Hepáticas y Digestivas (CIBER-EHD), Barcelona, Spain
| | - David Bernardo
- Gut Immunology Research Group, Instituto de Investigación del Hospital Universitario de la Princesa, Madrid, Spain
- Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM, Universidad de Valladolid-Consejo Superior de Investigaciones Científicas (CSIC)), Valladolid, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Diego Muñoz-López
- Department of Pathology, Hospital Universitario de Toledo, Toledo, Spain
| | - Manuel Gómez del Moral
- Department of Cellular Biology, School of Medicine, Universidad Complutense of Madrid (UCM), Madrid, Spain
| | - Francisco Javier Cubero
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermeddes Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Richard S. Blumberg
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Eduardo Martínez-Naves
- Department of Immunology, Ophthalmology and ORL, School of Medicine, Universidad Complutense of Madrid (UCM), Instituto de Investigación Sanitaria Hospital 12 de octubre (imas12), Madrid, Spain
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17
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Zhao D, Qin D, Yin L, Yang Q. Integrated Bioinformatics Analysis and Experimental Verification of Immune Cell Infiltration and the Related Core Genes in Ulcerative Colitis. Pharmgenomics Pers Med 2023; 16:629-643. [PMID: 37383675 PMCID: PMC10296601 DOI: 10.2147/pgpm.s406644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/26/2023] [Indexed: 06/30/2023] Open
Abstract
Background Ulcerative colitis is a recurrent autoimmune disease. At present, the pathogenesis of UC is not completely clear. Hence, the etiology and underlying molecular mechanism need to be further investigated. Methods Three sets of microarray datasets were included from the Gene Expression Omnibus database. The differentially expressed genes in two sets of datasets were analyzed using the R software, and the core genes of UC were screened using machine learning. The sensitivity and specificity of the core genes were evaluated with the receiver operating characteristic curve in another microarray dataset. Subsequently, the CIBERSORT tool was used to analyze the relationship between UC and its core genes and immune cell infiltration. To verify the relationship between UC and core genes and the relationship between core genes and immune cell infiltration in vivo. Results A total of 36 DEGs were identified. AQP8, HMGCS2, and VNN1 were determined to be the core genes of UC. These genes had high sensitivity and specificity in receiver operating characteristic curve analysis. According to the analysis of immune cell infiltration, neutrophils, monocytes, and macrophages were positively correlated with UC. AQP8, HMGCS2, and VNN1 were also correlated with immune cell infiltration to varying degrees. In vivo experiments verified that the expressions of neutrophils, monocytes, and macrophages increased in the UC colon. Furthermore, the expressions of AQP8 and HMGCS2 decreased, whereas that of VNN1 increased. Azathioprine treatment improved all the indicators to different degrees. Conclusion AQP8, HMGCS2, and VNN1 are the core genes of UC and exhibit different degrees of correlation with immune cells. These genes are expected to become new therapeutic targets for UC. Moreover, the occurrence and development of UC are influenced by immune cell infiltration.
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Affiliation(s)
- Danya Zhao
- The First School of Clinical Medicine of Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
| | - Danping Qin
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
| | - Liming Yin
- Institute of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
| | - Qiang Yang
- Department of Gastroenterology, Hangzhou TCM Hospital Affiliated to Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
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18
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Jha D, Al-Taie Z, Krek A, Eshghi ST, Fantou A, Laurent T, Tankelevich M, Cao X, Meringer H, Livanos AE, Tokuyama M, Cossarini F, Bourreille A, Josien R, Hou R, Canales-Herrerias P, Ungaro RC, Kayal M, Marion J, Polydorides AD, Ko HM, D’souza D, Merand R, Kim-Schulze S, Hackney JA, Nguyen A, McBride JM, Yuan GC, Colombel JF, Martin JC, Argmann C, Suárez-Fariñas M, Petralia F, Mehandru S. Myeloid cell influx into the colonic epithelium is associated with disease severity and non-response to anti-Tumor Necrosis Factor Therapy in patients with Ulcerative Colitis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.542863. [PMID: 37333091 PMCID: PMC10274630 DOI: 10.1101/2023.06.02.542863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Ulcerative colitis (UC) is an idiopathic chronic inflammatory disease of the colon with sharply rising global prevalence. Dysfunctional epithelial compartment (EC) dynamics are implicated in UC pathogenesis although EC-specific studies are sparse. Applying orthogonal high-dimensional EC profiling to a Primary Cohort (PC; n=222), we detail major epithelial and immune cell perturbations in active UC. Prominently, reduced frequencies of mature BEST4+OTOP2+ absorptive and BEST2+WFDC2+ secretory epithelial enterocytes were associated with the replacement of homeostatic, resident TRDC+KLRD1+HOPX+ γδ+ T cells with RORA+CCL20+S100A4+ TH17 cells and the influx of inflammatory myeloid cells. The EC transcriptome (exemplified by S100A8, HIF1A, TREM1, CXCR1) correlated with clinical, endoscopic, and histological severity of UC in an independent validation cohort (n=649). Furthermore, therapeutic relevance of the observed cellular and transcriptomic changes was investigated in 3 additional published UC cohorts (n=23, 48 and 204 respectively) to reveal that non-response to anti-Tumor Necrosis Factor (anti-TNF) therapy was associated with EC related myeloid cell perturbations. Altogether, these data provide high resolution mapping of the EC to facilitate therapeutic decision-making and personalization of therapy in patients with UC.
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Affiliation(s)
- Divya Jha
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zainab Al-Taie
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Shadi Toghi Eshghi
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Aurelie Fantou
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Thomas Laurent
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Michael Tankelevich
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xuan Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Hadar Meringer
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexandra E Livanos
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Minami Tokuyama
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Francesca Cossarini
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Arnaud Bourreille
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Regis Josien
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Ruixue Hou
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Pablo Canales-Herrerias
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ryan C. Ungaro
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maia Kayal
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Marion
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Huaibin M. Ko
- Department of Pathology and Cell Biology, Columbia University Medical Center-New York Presbyterian Hospital, New York, New York
| | - Darwin D’souza
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raphael Merand
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Core, Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jason A. Hackney
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Allen Nguyen
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Jacqueline M. McBride
- Biomarker Discovery, OMNI, Genentech Inc. South SanFrancisco, CA, USA
- OMNI Biomarker Development, Genentech Inc. South SanFrancisco, CA, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Jean Frederic Colombel
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jerome C. Martin
- Université de Nantes, Inserm, CHU Nantes, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, F-44000 Nantes, France
| | - Carmen Argmann
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, New York City, NY, USA
| | - Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, NY, USA
| | - Saurabh Mehandru
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Institute of Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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19
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Zhai L, Yang W, Li D, Zhou W, Cui M, Yao P. Network pharmacology and molecular docking reveal the immunomodulatory mechanism of rhubarb peony decoction for the treatment of ulcerative colitis and irritable bowel syndrome. JOURNAL OF PHARMACY & PHARMACEUTICAL SCIENCES : A PUBLICATION OF THE CANADIAN SOCIETY FOR PHARMACEUTICAL SCIENCES, SOCIETE CANADIENNE DES SCIENCES PHARMACEUTIQUES 2023; 26:11225. [PMID: 37305432 PMCID: PMC10248730 DOI: 10.3389/jpps.2023.11225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/28/2023] [Indexed: 06/13/2023]
Abstract
Background: Ulcerative colitis (UC) and irritable bowel syndrome (IBS) share various similarities in clinical symptoms, pathogenesis, and treatment. UC concurrent IBS tends toward more severe symptoms and worse prognosis, and promising feasible therapies for the overlapping symptoms remains a challenge. Rhubarb peony decoction (RPD) is a well-known traditional Chinese medicine that has been widely applied in treating UC. RPD may exert extensive therapeutic effects on both IBS and UC. However, the common mechanism of its treatment remains unclear. We aimed to assess the potential pharmacological mechanism of RPD in the treatment of overlapping IBS and UC. Methods: The active components and targets of RPD were retrieved from ETCM, TCMSP, BATMAN-TCM, and TCM databases. The disease targets were screened by searching the DrugBank, OMIM, TTD, and PharmGKB databases. PPI network analysis was performed and visualized via the STRING platform and Cytoscape software. GO and KEGG enrichment analyses of the hub genes of RPD were predicted to elucidate the potential molecular mechanism. Subsequently, molecular docking was carried out to verify the combination of active compounds with core targets. Results: By integrating all targets of RPD and disease, a total of 31 bioactive ingredients were identified including quercetin, kaempferol, aloe-emodin, beta-sitosterol, and (+)-catechin, etc. JUN, TP53, MAPK1, RELA, MYC, and ESR1 were explored as potential therapeutic targets among 126 common drug-disease-related targets. They were enriched in the AGE-RAGE signaling pathway in diabetic complications, as well as the NF-kappa B signaling pathway and MAPK signaling pathway. Additionally, some active ingredients were identified as candidates for binding to the hub targets via molecular docking, further suggesting their anti-inflammatory and antioxidative properties. Conclusion: RPD may exert the overall treatment effect for UC and IBS overlap syndrome via the biological mechanism of "multi-ingredients, multi-targets, and multi-pathways" on inflammation, oxidative stress, immune, oncogenicity, and gut microbiota dysbiosis.
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Affiliation(s)
- Leilei Zhai
- Graduate School, Xinjiang Medical University, Urumqi, China
- Department of Gastroenterology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Weiming Yang
- Graduate School, Xinjiang Medical University, Urumqi, China
- Department of Gastroenterology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Dianrong Li
- Graduate School, Xinjiang Medical University, Urumqi, China
| | - Wei Zhou
- Department of Nephrology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Min Cui
- Department of Gastroenterology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Ping Yao
- Department of Gastroenterology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
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20
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Meng W, Johnsen KM, Fenton CG, Florholmen J, Paulssen RH. Anti-apoptotic genes and non-coding RNAs are potential outcome predictors for ulcerative colitis. Funct Integr Genomics 2023; 23:165. [PMID: 37199828 DOI: 10.1007/s10142-023-01099-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Due to the lack of clinical, immunologic, genetic, and laboratory markers to predict remission in ulcerative colitis (UC) without relapse, there is no clear recommendation regarding withdrawal of therapy. Therefore, this study was to investigate if transcriptional analysis together with Cox survival analysis might be able to reveal molecular markers that are specific for remission duration and outcome. Mucosal biopsies from patients in remission with active treatment-naïve UC and healthy control subjects underwent whole-transcriptome RNA-seq. Principal component analysis (PCA) and Cox proportional hazards regression analysis were applied to the remission data concerning duration and status of patients. A randomly chosen remission sample set was used for validation of the applied methods and results. The analyses distinguished two different UC remission patient groups with respect to remission duration and outcome (relapse). Both groups showed that altered states of UC with quiescent microscopic disease activity are still present. The patient group with the longest remission duration and no relapse revealed specific and increased expression of antiapoptotic factors belonging to the MTRNR2-like gene family and non-coding RNAs. In summary, the expression of anti-apoptotic factors and non-coding RNAs may contribute to personalized medicine approaches in UC by improving patient stratification for different treatment regimens.
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Affiliation(s)
- Wei Meng
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Kay-Martin Johnsen
- Gastroenterology and Nutrition Research Group, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
- Department of Medical Gastroenterology, University Hospital of North Norway, Tromsø, Norway
| | - Christopher G Fenton
- Genomics Support Centre Tromsø, UiT- The Arctic University of Norway, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Sykehusveien 44, N-9037, Tromsø, Norway
| | - Jon Florholmen
- Gastroenterology and Nutrition Research Group, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway
| | - Ruth H Paulssen
- Clinical Bioinformatics Research Group, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Tromsø, Norway.
- Genomics Support Centre Tromsø, UiT- The Arctic University of Norway, Department of Clinical Medicine, Faculty of Health Sciences, UiT- The Arctic University of Norway, Sykehusveien 44, N-9037, Tromsø, Norway.
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21
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Hu X, Liu W, He M, Qiu Q, Zhou B, Liu R, Wu F, Huang Z. Comparison of the molecular mechanisms of Fuzi Lizhong Pill and Huangqin decoction in the treatment of the cold and heat syndromes of ulcerative colitis based on network pharmacology. Comput Biol Med 2023; 159:106870. [PMID: 37084637 DOI: 10.1016/j.compbiomed.2023.106870] [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: 08/18/2022] [Revised: 02/21/2023] [Accepted: 03/30/2023] [Indexed: 04/23/2023]
Abstract
OBJECTIVE The aim of this study was to illuminate the similarities and differences of two prescriptions as "cold" and "heat" drugs for treating ulcerative colitis (UC) with the simultaneous occurrence of heat and cold syndrome via network pharmacology. METHODS (1) Active compounds of Fuzi-Lizhong Pill (FLP) and Huangqin Decoction (HQT) were retrieved from the TCMSP database, and their common active compounds were compared using the Venn diagram. (2) Potential proteins targeted to three sets of compounds either (i) shared by FLP and HQT, (ii) unique to FLP or (iii) unique to HQT were screened from the STP, STITCH and TCMSP databases, and three corresponding core compound sets were identified in Herb-Compound-Target (H-C-T) networks. (3) Targets related to UC were identified from the DisGeNET and GeneCards databases and compared with the FLP-HQT common targets to identify potential targets of FLP-HQT compounds related to UC. (4) Three potential target sets were imported into the STRING database for protein‒protein interaction (PPI) analysis, and three core target sets were defined. (5) The binding capabilities and interacting modes between core compounds and key targets were verified by molecular docking via Discovery Studio 2019 and molecular dynamics (MD) simulations via Amber 2018. (6) The target sets were enriched for KEGG pathways using the DAVID database. RESULTS (1) FLP and HQT included 95 and 113 active compounds, respectively, with 46 common compounds, 49 FLP-specific compounds and 67 HQT-specific compounds. (2) 174 targets of FLP-HQT common compounds, 168 targets of FLP-specific compounds, and 369 targets of HQT-specific compounds were predicted from the STP, STITCH and TCMSP databases; six core compounds specific to FLP and HQT were screened in the FLP-specific and HQT-specific H-C-T networks, respectively. (3) 103 targets overlapped from the 174 predicted targets and the 4749 UC-related targets; two core compounds for FLP-HQT were identified from the FLP-HQT H-C-T network. (4) 103 FLP-HQT-UC common targets, 168 of FLP-specific targets and 369 of HQT-specific targets had shared core targets (AKT1, MAPK3, TNF, JUN and CASP3) based on the PPI network analysis. (5) Molecular docking demonstrated that naringenin, formononetin, luteolin, glycitein, quercetin, kaempferol and baicalein of FLP and HQT play a critical role in treating UC; meanwhile, MD simulations revealed the stability of protein‒ligand interactions. (6) The enriched pathways indicated that most targets were related to anti-inflammatory, immunomodulatory and other pathways. Compared with the pathways identified using traditional methods, FLP-specific pathways included the PPAR signaling pathway and the bile secretion pathway, and HQT-specific pathways included the vascular smooth muscle contraction pathway and the natural killer cell-mediated cytotoxicity pathway etc. CONCLUSION: In this study, we clarified the common mechanisms of FLP and HQT in treating UC and their specific mechanisms in treating cold and heat syndrome in UC through compound, target and pathway distinction and a literature comparison based on network pharmacology; these results provide a new perspective on the detailed mechanism of "multidrugs and single-disease" thought in traditional Chinese medicine.
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Affiliation(s)
- Xiyun Hu
- Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523710, China; Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Dongguan, 523808, China
| | - Weidong Liu
- Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523710, China; Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Dongguan, 523808, China
| | - Meiqi He
- Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523710, China; Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Dongguan, 523808, China
| | - Qimiao Qiu
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Dongguan, 523808, China
| | - Bingjie Zhou
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Dongguan, 523808, China
| | - Ruining Liu
- Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Dongguan, 523808, China
| | - Fengxu Wu
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, School of Pharmaceutical Sciences, Hubei University of Medicine, Shiyan, 442000, China.
| | - Zunnan Huang
- Key Laboratory of Computer-Aided Drug Design of Dongguan City, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523710, China; Key Laboratory of Big Data Mining and Precision Drug Design of Guangdong Medical University, Key Laboratory for Research and Development of Natural Drugs of Guangdong Province, School of Pharmacy, Dongguan, 523808, China; Marine Biomedical Research Institute of Guangdong Zhanjiang, Zhanjiang, 524023, China.
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22
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Hong L, Zang X, Hu Q, He Y, Xu Z, Xie Y, Gu T, Yang H, Yang J, Shi J, Zheng E, Huang S, Xu Z, Liu D, Cai G, Li Z, Wu Z. Uterine luminal-derived extracellular vesicles: potential nanomaterials to improve embryo implantation. J Nanobiotechnology 2023; 21:79. [PMID: 36882792 PMCID: PMC9990359 DOI: 10.1186/s12951-023-01834-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Most pregnancy losses worldwide are caused by implantation failure for which there is a lack of effective therapeutics. Extracellular vesicles are considered potential endogenous nanomedicines because of their unique biological functions. However, the limited supply of ULF-EVs prevents their development and application in infertility diseases such as implantation failure. In this study, pigs were used as a human biomedical model, and ULF-EVs were isolated from the uterine luminal. We comprehensively characterized the proteins enriched in ULF-EVs and revealed their biological functions in promoting embryo implantation. By exogenously supplying ULF-EVs, we demonstrated that ULF-EVs improve embryo implantation, suggesting that ULF-EVs are a potential nanomaterial to treat implantation failure. Furthermore, we identified that MEP1B is important in improving embryo implantation by promoting trophoblast cell proliferation and migration. These results indicated that ULF-EVs can be a potential nanomaterial to improve embryo implantation.
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Affiliation(s)
- Linjun Hong
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China. .,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China.
| | - Xupeng Zang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Qun Hu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Yanjuan He
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Zhiqian Xu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Yanshe Xie
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Ting Gu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Huaqiang Yang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Jie Yang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Junsong Shi
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Yunfu Subcenter of Guangdong Laboratory for Lingnan Modern Agriculture, Yunfu, 527300, People's Republic of China
| | - Enqin Zheng
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Sixiu Huang
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Zheng Xu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Dewu Liu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Gengyuan Cai
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China
| | - Zicong Li
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China. .,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China. .,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, 510642, People's Republic of China.
| | - Zhenfang Wu
- National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China. .,Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China. .,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, People's Republic of China. .,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou, 510642, People's Republic of China.
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Yousef M, Ozdemir F, Jaber A, Allmer J, Bakir-Gungor B. PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach. BMC Bioinformatics 2023; 24:60. [PMID: 36823571 PMCID: PMC9947447 DOI: 10.1186/s12859-023-05187-2] [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: 03/25/2022] [Accepted: 02/14/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Cell homeostasis relies on the concerted actions of genes, and dysregulated genes can lead to diseases. In living organisms, genes or their products do not act alone but within networks. Subsets of these networks can be viewed as modules that provide specific functionality to an organism. The Kyoto encyclopedia of genes and genomes (KEGG) systematically analyzes gene functions, proteins, and molecules and combines them into pathways. Measurements of gene expression (e.g., RNA-seq data) can be mapped to KEGG pathways to determine which modules are affected or dysregulated in the disease. However, genes acting in multiple pathways and other inherent issues complicate such analyses. Many current approaches may only employ gene expression data and need to pay more attention to some of the existing knowledge stored in KEGG pathways for detecting dysregulated pathways. New methods that consider more precompiled information are required for a more holistic association between gene expression and diseases. RESULTS PriPath is a novel approach that transfers the generic process of grouping and scoring, followed by modeling to analyze gene expression with KEGG pathways. In PriPath, KEGG pathways are utilized as the grouping function as part of a machine learning algorithm for selecting the most significant KEGG pathways. A machine learning model is trained to differentiate between diseases and controls using those groups. We have tested PriPath on 13 gene expression datasets of various cancers and other diseases. Our proposed approach successfully assigned biologically and clinically relevant KEGG terms to the samples based on the differentially expressed genes. We have comparatively evaluated the performance of PriPath against other tools, which are similar in their merit. For each dataset, we manually confirmed the top results of PriPath in the literature and found that most predictions can be supported by previous experimental research. CONCLUSIONS PriPath can thus aid in determining dysregulated pathways, which applies to medical diagnostics. In the future, we aim to advance this approach so that it can perform patient stratification based on gene expression and identify druggable targets. Thereby, we cover two aspects of precision medicine.
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Affiliation(s)
- Malik Yousef
- Department of Information Systems, Zefat Academic College, 13206, Zefat, Israel. .,Galilee Digital Health Research Center (GDH), Zefat Academic College, Zefat, Israel.
| | - Fatma Ozdemir
- grid.440414.10000 0004 0558 2628Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Turkey ,grid.5570.70000 0004 0490 981XUniversity Institute of Digital Communication Systems, Ruhr-University, Bochum, Germany
| | - Amhar Jaber
- grid.440414.10000 0004 0558 2628Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Turkey
| | - Jens Allmer
- grid.454318.f0000 0004 0431 5034Medical Informatics and Bioinformatics, Institute for Measurement Engineering and Sensor Technology, Hochschule Ruhr West, University of Applied Sciences, Mülheim an der Ruhr, Germany
| | - Burcu Bakir-Gungor
- grid.440414.10000 0004 0558 2628Department of Computer Engineering, Faculty of Engineering, Abdullah Gul University, Kayseri, Turkey
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24
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Duca M, Malagolini N, Dall'Olio F. The story of the Sd a antigen and of its cognate enzyme B4GALNT2: What is new? Glycoconj J 2023; 40:123-133. [PMID: 36287346 DOI: 10.1007/s10719-022-10089-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/25/2022]
Abstract
The structure Siaα2,3(GalNAcβ1,4)Gal- is the epitope of the Sda antigen, which is expressed on the erythrocytes and secretions of the vast majority of Caucasians, carried by N- and O-linked chains of glycoproteins, as well as by glycolipids. Sda is very similar, but not identical, to ganglioside GM2 [Siaα2,3(GalNAcβ1,4)Galβ1,4Glc-Cer]. The Sda synthase β1,4 N-acetylgalactosaminyl transferase 2 (B4GALNT2) exists in a short and a long form, diverging in the aminoterminal domain. The latter has a very long cytoplasmic tail and displays a Golgi- as well as a post-Golgi localization. The biosynthesis of Sda is mutually exclusive with that of the cancer-associated sialyl Lewis antigens, whose structure is Siaα2,3Galβ1,3/4(Fucα1,4/3)GlcNAc-. B4GALNT2 is down-regulated in colon cancer but patients with higher expression survive longer. In experimental systems, B4GALNT2 inhibits colon cancer progression,not only through inhibition of sialyl Lewis antigen biosynthesis. By contrast, in breast cancer B4GALNT2 is associated with malignancy. In colon cancer, the B4GALNT2 gene is regulated by multiple mechanisms, which include miRNA and transcription factor expression, as well as CpG methylation. In addition, Sda/B4GALNT2 regulates the susceptibility to infectious agents, the protection from muscle dystrophy, the activity of immune system in pregnancy and the immune rejection in xenotransplantation.
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Affiliation(s)
- Martina Duca
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), General Pathology Building, University of Bologna, Via San Giacomo 14, 40126, Bologna, Italy
| | - Nadia Malagolini
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), General Pathology Building, University of Bologna, Via San Giacomo 14, 40126, Bologna, Italy
| | - Fabio Dall'Olio
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), General Pathology Building, University of Bologna, Via San Giacomo 14, 40126, Bologna, Italy.
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25
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He Q, Wu J, Ke J, Zhang Q, Zeng W, Luo Z, Gong J, Chen Y, He Z, Lan P. Therapeutic role of ursodeoxycholic acid in colitis-associated cancer via gut microbiota modulation. Mol Ther 2023; 31:585-598. [PMID: 38556635 PMCID: PMC9931610 DOI: 10.1016/j.ymthe.2022.10.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 09/21/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a predisposing factor for colitis-associated cancer (CAC). The association between bile acids and the gut microbiota has been demonstrated in colon neoplasia; however, the effect of ursodeoxycholic acid (UDCA) on gut microbiota alteration in development of colitis and CAC is unknown. Our analysis of publicly available datasets demonstrated the association of UDCA treatment and accumulation of Akkermansia. UDCA-mediated alleviation of DSS-induced colitis was microbially dependent. UDCA treatment significantly upregulated Akkermansia colonization in a mouse model. Colonization of Akkermansia was associated with enhancement of the mucus layer upon UDCA treatment as well as activation of bile acid receptors in macrophages. UDCA played a role in CAC prevention and treatment in the AOM-DSS and ApcMin/+-DSS models through downregulation of inflammation and accumulation of Akkermansia. This study suggests that UDCA intervention could reshape intestinal gut homeostasis, facilitating colonization of Akkermansia and preventing and treating colitis and CAC.
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Affiliation(s)
- Qilang He
- The Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, 510655 Guangdong, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655 Guangdong, China
| | - Jinjie Wu
- The Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, 510655 Guangdong, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655 Guangdong, China
| | - Jia Ke
- The Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, 510655 Guangdong, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655 Guangdong, China
| | - Qiang Zhang
- The Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, 510655 Guangdong, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655 Guangdong, China
| | - Wanyi Zeng
- The Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, 510655 Guangdong, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655 Guangdong, China
| | - Zhanhao Luo
- The Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, 510655 Guangdong, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655 Guangdong, China
| | - Junli Gong
- The Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, 510655 Guangdong, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655 Guangdong, China
| | - Yuan Chen
- The Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, 510655 Guangdong, China
| | - Zhen He
- The Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, 510655 Guangdong, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655 Guangdong, China.
| | - Ping Lan
- The Sixth Affiliated Hospital, School of Medicine, Sun Yat-sen University, Guangzhou, 510655 Guangdong, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou, 510655 Guangdong, China.
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26
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Zhou J, Zhang Q, Zhao Y, Song Y, Leng Y, Chen M, Zhou S, Wang Z. The regulatory role of alternative splicing in inflammatory bowel disease. Front Immunol 2023; 14:1095267. [PMID: 37153612 PMCID: PMC10160418 DOI: 10.3389/fimmu.2023.1095267] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
Inflammatory bowel disease (IBD) mainly includes Crohn's disease and ulcerative colitis. These diseases have a progressive course of chronic relapse and remission and affect a large number of children and adults worldwide. The burden of IBD is rising worldwide, with levels and trends varying greatly in countries and regions. Like most chronic diseases, the costs associated with IBD are high, including hospitalizations, outpatient and emergency visits, surgeries, and pharmacotherapies. However, there is no radical cure for it yet, and its therapeutic targets still need further study. Currently, the pathogenesis of IBD remains unclear. It is generally assumed that the occurrence and development of IBD are related to the environmental factors, gut microbiota, immune imbalance, and genetic susceptibility. Alternative splicing contributes to a various diseases, such as spinal muscular atrophy, liver diseases, and cancers. In the past, it has been reported that alternative splicing events, splicing factors, and splicing mutations were associated with IBD, but there were no reports on the practical application for clinical diagnosis and treatment of IBD using splicing-related methods. Therefore, this article reviews research progress on alternative splicing events, splicing factors, and splicing mutations associated with IBD.
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Affiliation(s)
- Jianli Zhou
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Qiao Zhang
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yuzhen Zhao
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yuchen Song
- Co-Innovation Center for Sustainable Forestry in Southern China and Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Yanan Leng
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
| | - Moxian Chen
- Clinical Laboratory, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
| | - Shaoming Zhou
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
| | - Zhaoxia Wang
- Department of Gastroenterology, Shenzhen Children’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Zhaoxia Wang, ; Shaoming Zhou, ; Moxian Chen,
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27
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Lu L, Liu Y, Zhang G, Xu Y, Hu D, Ji G, Xu H. The circRNA expression profile of colorectal inflammatory cancer transformation revealed potential predictive biomarkers. Aging (Albany NY) 2022; 14:9280-9299. [PMID: 36446351 PMCID: PMC9740358 DOI: 10.18632/aging.204406] [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: 03/22/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022]
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumors in the world, and most colorectal cancer is transformed from colorectal adenoma (CRA). Identifying biomarkers for the early prediction of colorectal cancer would be an important finding. Circular RNA (circRNA) plays a key role in the occurrence and development of tumors, and its biological characteristics make it a potential biomarker for the early diagnosis of diseases. Therefore, we explored the relationship between circRNA and the malignant transformation from colorectal adenoma to colorectal cancer. We constructed inflammation-based tumorigenesis mouse models and performed high-throughput RNA sequencing to determine the expression profile of circRNAs in tissues at different stages of disease. Subsequent STEM analysis showed that with the development of the disease, 30 circRNAs were significantly downregulated, and 10 circRNAs were significantly upregulated. After qRT-PCR and Fish analysis verification, it was clear that mmu_circ_0008035 and mmu_circ_0000420 were significantly and continuously overexpressed in the development of colorectal cancer in our mouse model. Next, through homology analysis of circRNA in human and mouse and validation of clinical normal tissues, adenoma tissues and CRC tissues, we found biomarkers of has_circ0101338 ahashsa_circ0022426 that could predict the malignant transformation of human colorectal inflammation into CRC and have certain diagnostic value. In conclusion, our results may shed light on the mechanism of progression from precancerous adenoma to cancer and provide biomarkers that may be used in the early diagnosis of CRC.
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Affiliation(s)
- Lu Lu
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Yujing Liu
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Guangtao Zhang
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Yangxian Xu
- Department of General Surgery, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Dan Hu
- Department of Internal Medicine, Shanghai Pudong New Area Hospital of Traditional Chinese Medicine, Shanghai 200032, China
| | - Guang Ji
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
| | - Hanchen Xu
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 200032, China
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28
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Li Y, Tang M, Zhang FJ, Huang Y, Zhang J, Li J, Wang Y, Yang J, Zhu S. Screening of ulcerative colitis biomarkers and potential pathways based on weighted gene co-expression network, machine learning and ceRNA hypothesis. Hereditas 2022; 159:42. [PMID: 36419192 PMCID: PMC9685902 DOI: 10.1186/s41065-022-00259-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/12/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Ulcerative colitis (UC) refers to an intractable intestinal inflammatory disease. Its increasing incidence rate imposes a huge burden on patients and society. The UC etiology has not been determined, so screening potential biomarkers is critical to preventing disease progression and selecting optimal therapeutic strategies more effectively. METHODS The microarray datasets of intestinal mucosal biopsy of UC patients were selected from the GEO database, and integrated with R language to screen differentially expressed genes and draw proteins interaction network diagrams. GO, KEGG, DO and GSEA enrichment analyses were performed to explore their biological functions. Through machine learning and WGCNA analysis, targets that can be used as UC potential biomarkers are screened out. ROC curves were drawn to verify the reliability of the results and predicted the mechanism of marker genes from the aspects of immune cell infiltration, co-expression analysis, and competitive endogenous network (ceRNA). RESULTS Two datasets GSE75214 and GSE87466 were integrated for screening, and a total of 107 differentially expressed genes were obtained. They were mainly related to biological functions such as humoral immune response and inflammatory response. Further screened out five marker genes, and found that they were associated with M0 macrophages, quiescent mast cells, M2 macrophages, and activated NK cells in terms of immune cell infiltration. The co-expression network found significant co-expression relationships between 54 miRNAs and 5 marker genes. According to the ceRNA hypothesis, NEAT1-miR-342-3p/miR-650-SLC6A14, NEAT1-miR-650-IRAK3, and XIST-miR-342-3p-IRAK3 axes were found as potential regulatory pathways in UC. CONCLUSION This study screened out five biomarkers that can be used for the diagnosis and treatment of UC, namely SLC6A14, TIMP1, IRAK3, HMGCS2, and APOBEC3B. Confirmed that they play a role in the occurrence and development of UC at the level of immune infiltration, and proposed a potential RNA regulatory pathway that controls the progression of UC.
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Affiliation(s)
- Ying Li
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China ,grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, The First College for Clinical Medicine, Jinan, China
| | - Mengyao Tang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Innovation and Research of Traditional Chinese Medicine, Jinan, 250000 China
| | - Feng Jun Zhang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China ,grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, The First College for Clinical Medicine, Jinan, China
| | - Yihan Huang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China
| | - Jing Zhang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China
| | - Junqi Li
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China
| | - Yunpeng Wang
- grid.479672.9Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Department of Gastroenterology, Jinan, China
| | - Jinguang Yang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, The First College for Clinical Medicine, Jinan, China
| | - Shu Zhu
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Innovation and Research of Traditional Chinese Medicine, Jinan, 250000 China
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29
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Reconstruction and Differential Expression Profiling Core Target Analyses of the circRNA-miRNA-mRNA Network Based on Competitive Endogenous RNAs in Ulcerative Colitis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4572181. [PMID: 36310619 PMCID: PMC9616663 DOI: 10.1155/2022/4572181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/08/2022] [Indexed: 11/24/2022]
Abstract
Ulcerative colitis (UC) is a common autoimmune disease worldwide. Circular RNA (circRNA) is a type of noncoding ribonucleic acids (ncRNAs). In addition to their roles in numerous biological processes, circRNAs are also linked to a vast range of diseases including UC. Although previous studies have examined many circRNAs, the physiological and pathological roles of the circRNA-associated competing endogenous RNA (ceRNA) network in UC remain unclear. Thus, we constructed a circRNA-miRNA-mRNA network based on the ceRNA hypothesis by analyzing data from the National Center for Biotechnology Information Gene Expression Omnibus (NCBI-GEO) database. Genes with higher degree values than others in the ceRNA network were selected as central nodes when constructing the corresponding core subnetworks. To fully understand the biological function of the ceRNA network, we entered all differentially expressed mRNAs (DEmRNAs) from the ceRNA network into the Database for Annotation and Integrated Discovery (DAVID), which was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. We further entered DEmRNAs into the STRING database for protein-protein interaction (PPI) network analysis. The results elucidated that the ceRNA network comprised 403 circRNA nodes, 5 miRNA nodes, 138 mRNA nodes, and 559 edges. Three core ceRNA subnetworks centered on hsa-miR-342-3p, hsa-miR-199a-5p, and hsa-miR-142-3p were reconstructed in this study. GO and KEGG enrichment analyses identified 167 enriched GO categories and 14 enriched KEGG pathway terms. The core PPI network was composed of 15 core targets, of which CD44, HIF1A, and MMP2 were the most significant. In summary, 3 hub miRNAs (hsa-miR-342-3p, hsa-miR-199a-5p, hsa-miR-142-3p) and 3 hub genes (CD44, HIF1A, and MMP2) might play an important role in the development of UC. These hub nodes, first proposed here, might also be used as potential diagnostic markers and therapeutic targets.
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30
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Targeted Sequencing of Cytokine-Induced PI3K-Related Genes in Ulcerative Colitis, Colorectal Cancer and Colitis-Associated Cancer. Int J Mol Sci 2022; 23:ijms231911472. [PMID: 36232773 PMCID: PMC9569582 DOI: 10.3390/ijms231911472] [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: 08/16/2022] [Revised: 09/15/2022] [Accepted: 09/20/2022] [Indexed: 11/17/2022] Open
Abstract
Chronic relapsing inflammatory bowel disease is strongly linked to an increased risk of colitis-associated cancer (CAC). One of the well-known inflammatory carcinogenesis pathways, phosphatidylinositol 3-kinase (PI3K), was identified to be a crucial mechanism in long-standing ulcerative colitis (UC). The goal of this study was to identify somatic variants in the cytokine-induced PI3K-related genes in UC, colorectal cancer (CRC) and CAC. Thirty biopsies (n = 8 long-standing UC, n = 11 CRC, n = 8 paired normal colorectal mucosa and n = 3 CAC) were subjected to targeted sequencing on 13 PI3K-related genes using Illumina sequencing and the SureSelectXT Target Enrichment System. The Genome Analysis Toolkit was used to analyze variants, while ANNOVAR was employed to detect annotations. There were 5116 intronic, 355 exonic, 172 untranslated region (UTR) and 59 noncoding intronic variations detected across all samples. Apart from a very small number of frameshifts, the distribution of missense and synonymous variants was almost equal. We discovered changed levels of IL23R, IL12Rß1, IL12Rß2, TYK2, JAK2 and OSMR in more than 50% of the samples. The IL23R variant in the UTR region, rs10889677, was identified to be a possible variant that might potentially connect CAC with UC and CRC. Additional secondary structure prediction using RNAfold revealed that mutant structures were more unstable than wildtype structures. Further functional research on the potential variants is, therefore, highly recommended since it may provide insight on the relationship between inflammation and cancer risk in the cytokine-induced PI3K pathway.
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31
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Akiyama S, Hamdeh S, Sakamoto T, Suzuki H, Tsuchiya K. The Feasibility, Safety, and Long-term Outcomes of Endoscopic Submucosal Dissection for Colorectal Neoplasia in Patients With Inflammatory Bowel Disease: A Systematic Review and Meta-analysis. J Clin Gastroenterol 2022:00004836-990000000-00042. [PMID: 35943418 DOI: 10.1097/mcg.0000000000001740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 06/21/2022] [Indexed: 12/10/2022]
Abstract
BACKGROUND Evidence regarding the utility of endoscopic submucosal dissection (ESD) for neoplasia in patients with inflammatory bowel disease (IBD) is limited. This meta-analysis aims to understand the feasibility, safety, and long-term outcomes of ESD in IBD patients. METHODS Electronic databases were searched for observational and case-controlled studies. Primary endpoints were en bloc resection and margin-negative resection of neoplastic lesions. Secondary endpoints included procedure-related bleeding and perforation, local recurrence, and metachronous neoplasia. RESULTS We analyzed 25 studies with a total of 585 neoplastic lesions in 552 patients. The rates of en bloc resection and margin-negative resection were 0.88 [95% confidence interval (CI) 0.82-0.92] and 0.78 (95% CI 0.72-0.83), respectively. Meta-regression analysis showed longer disease duration was significantly associated with the higher rate of en bloc resection. The rates of procedure-related bleeding and perforation were 0.080 (95% CI 0.057-0.11) and 0.055 (95% CI 0.038-0.081), respectively. The rates of local recurrence and metachronous neoplasia were 0.008 events/person-year (95% CI 0.002-0.013) and 0.031 event/person-year (95% CI 0.016-0.046), respectively. Meta-analysis of case-controlled studies found no significant differences in the endpoints between IBD patients treated by ESD and those treated by endoscopic mucosal resection, or non-IBD patients treated by ESD. CONCLUSIONS ESD is a feasible and safe procedure to remove neoplastic lesions in IBD patients. Given there is a considerable risk of metachronous neoplasia development, postoperative surveillance colonoscopy with an appropriate consultation with surgeons is essential to monitor not only local recurrence but also neoplastic changes in the remaining colon.
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Affiliation(s)
- Shintaro Akiyama
- Department of Gastroenterology, University of Tsukuba, Ibaraki, Japan
| | - Shadi Hamdeh
- Department of Internal Medicine, Division of Gastroenterology, Hepatology and Motility, University of Kansas, Lawrence, KS
| | - Taku Sakamoto
- Department of Gastroenterology, University of Tsukuba, Ibaraki, Japan
| | - Hideo Suzuki
- Department of Gastroenterology, University of Tsukuba, Ibaraki, Japan
| | - Kiichiro Tsuchiya
- Department of Gastroenterology, University of Tsukuba, Ibaraki, Japan
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Identification of Potential Biomarkers and Immune Infiltration Characteristics in Ulcerative Colitis by Combining Results from Two Machine Learning Algorithms. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5412627. [PMID: 35959356 PMCID: PMC9359832 DOI: 10.1155/2022/5412627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 06/30/2022] [Accepted: 07/07/2022] [Indexed: 12/03/2022]
Abstract
Objective This study was designed to identify potential biomarkers for ulcerative colitis (UC) and analyze the immune infiltration characteristics in UC. Methods Datasets containing human UC and normal control tissues (GSE87466, GSE107597, and GSE13367) were downloaded from the GEO database. Then, the GSE87466 and GSE107597 datasets were merged, and the differentially expressed genes (DEGs) between UC and normal control tissues were screened out by the “limma R” package. The LASSO regression model and support vector machine recursive feature elimination (SVM-RFE) were performed to screen out the best biomarkers. The GSE13367 dataset was used as a validation cohort, and the receiver operating characteristic curve (ROC) was used to evaluate the diagnostic performance. Finally, the immune infiltration characteristics in UC were explored by CIBERSORT, and we further analyzed the correlation between potential biomarkers and different immune cells. Results A total of 76 DEGs were screened out, among which 56 genes were upregulated and 20 genes were downregulated. Functional enrichment analysis revealed that these DEGs were mainly involved in immune response, chemokine signaling, IL−17 signaling, cytokine receptor interactions, inflammatory bowel disease, etc. ABCG2, HSPB3, SLC6A14, and VNN1 were identified as potential biomarkers for UC and validated in the GSE13367 dataset (AUC = 0.889, 95% CI: 0.797~0.961). Immune infiltration analysis by CIBERSORT revealed that there were significant differences in immune infiltration characteristics between UC and normal control tissues. A high level of memory B cells, γδ T cells, activated mast cells, M1 macrophages, neutrophils, etc. were found in the UC group, while a high level of M2 type macrophages, resting mast cells, eosinophils, CD8+ T cells, etc. were found in the normal control group. Conclusion ABCG2, HSPB3, SLC6A14, and VNN 1 were identified as potential biomarkers for UC. There was an obvious difference in immune infiltration between UC and normal control tissues, which may provide help to guide individualized treatment and develop new research directions.
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Li X, Yang W, Shen Y, Liu F, Xiong X, Wu Q, Xiao Z, Yang X, Dang R, Manaenko A, Xie P, Li Q. Analysis of Age-Dependent Transcriptomic Changes in Response to Intracerebral Hemorrhage in Mice. Front Mol Neurosci 2022; 15:908683. [PMID: 35677585 PMCID: PMC9169040 DOI: 10.3389/fnmol.2022.908683] [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: 03/30/2022] [Accepted: 04/21/2022] [Indexed: 11/18/2022] Open
Abstract
Age is a well-known risk factor that is independently associated with poor outcomes after intracerebral hemorrhage (ICH). However, the interrelationship between age and poor outcomes after ICH is not well defined. In this study, we aimed to investigate this relationship based on collagenase-induced ICH mice models. After being assessed neurological deficit 24 h after ICH, mice were euthanized and brain perihematomal tissues were used for RNA-sequencing (RNA-seq). And then the functions of differentially expressed genes (DEGs) identified by RNA-seq were analyzed using Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, Ingenuity Pathway Analysis (IPA) and protein-protein interaction (PPI) analysis. In addition, we performed real-time quantitative polymerase chain reaction (RT-qPCR) for validation of candidate DEGs. In the behavioral tests, aged mice presented significantly worse neurological function than young mice and greater weight loss than aged sham controls 24 h after ICH. In DEGs analysis, ICH affected the expression of more genes in young mice (2,337 DEGs) compared with aged mice (2,005 DEGs). We found aged mice exhibited increased brain inflammatory responses compared with young animals and ICH induced significant activation of the interferon-β (IFN-β) and IFN signaling pathways exclusively in aged mice. Moreover, further analysis demonstrated that ICH resulted in the activation of cytosolic DNA-sensing pathway with the production of downstream molecule type I IFN, and the response to type I IFN was more significant in aged mice than in young mice. In agreement with the results of RNA-seq, RT-qPCR indicated that the expression of candidate genes of cyclic GMP-AMP synthase (cGAS), Z-DNA-binding protein 1 (ZBP1), and IFN-β was significantly altered in aged mice after ICH. Taken together, our study indicated that compared to young animals, aged mice exhibit increased vulnerability to ICH and that the differences in transcriptional response patterns to ICH between young and aged mice. We believe that these findings will facilitate our understanding of ICH pathology and help to translate the results of preclinical studies into a clinical setting.
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Affiliation(s)
- Xinhui Li
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wensong Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yiqing Shen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Fangyu Liu
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin Xiong
- Department of Neurology, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Qingyuan Wu
- Department of Neurology, Chongqing University Three Gorges Hospital, Chongqing, China
| | - Zhongsong Xiao
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xun Yang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ruozhi Dang
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Anatol Manaenko
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peng Xie
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Qi Li,
| | - Qi Li
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Qi Li,
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Lu C, Wei F, He X, Yao X, Yu C. LncRNA expression in idiopathic achalasia: New insight and preliminary exploration into pathogenesis. Open Med (Wars) 2022; 17:732-740. [PMID: 35509690 PMCID: PMC9007103 DOI: 10.1515/med-2022-0473] [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: 04/27/2021] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 11/15/2022] Open
Abstract
Idiopathic achalasia is a primary esophageal motility disorder characterized by the absence of esophageal peristalsis and impaired relaxation of the lower esophageal sphincter (LES). However, the pathogenesis of idiopathic achalasia remains unclear. To further understand the pathogenesis, we conducted lncRNA and mRNA microarray analyses. LES specimens from 5 patients and 4 controls were used for microarray. Potential target genes with significantly changed lncRNA and mRNA were predicted using cis/trans-regulatory algorithms, followed by the Gene Ontology and KEGG pathway enrichment analysis to understand the biophysical effect. Finally, 7,133 significantly dysregulated mRNAs (3,136 increased and 3,997 decreased), along with 6,892 significantly dysregulated lncRNAs (4,900 increased and 1,992 decreased). Biophysical function analysis revealed that the cell adhesion molecule (CAM) pathway was a common pathway. The predicted lncRNA targets of NRXN1 (Down FC: 9.07), NTNG2 (UP FC: 2.75), CADM1 (Down FC: 2.26), NLGN1 (Down FC: 4.60), NEGR1 (Down FC: 2.335), CD22 (Down FC: 5.62), HLA-DQB1 (Down FC: 5.06), and HLA-DOA (Down FC: 2.31) were inputted in this pathway, which was mainly located in the synapse part of the neural system and immune system. Our study demonstrates the lncRNAs and corresponding mRNAs that may play important roles in idiopathic achalasia.
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Affiliation(s)
- Chao Lu
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , 310003 , China
| | - Furong Wei
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , 310003 , China
| | - Xinjue He
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , 310003 , China
| | - Xin Yao
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , 310003 , China
| | - Chaohui Yu
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou , 310003 , China
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Yan S, Wei H, Jia R, Zhen M, Bao S, Wang W, Liu F, Li J. Wu-Mei-Wan Ameliorates Murine Ulcerative Colitis by Regulating Macrophage Polarization. Front Pharmacol 2022; 13:859167. [PMID: 35387334 PMCID: PMC8978603 DOI: 10.3389/fphar.2022.859167] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/02/2022] [Indexed: 12/24/2022] Open
Abstract
An increasing body of evidence shows that macrophages play an important role in the pathogenesis of ulcerative colitis (UC). Macrophage polarization and changes in related signaling pathways are reported to have a protective effect on intestinal inflammation. The well-known Chinese medicine Wumeiwan (WMW) has been used to treat diarrhea, one of the main symptoms of colitis, for more than 2,000 years. Increasing evidence shows that WMW can inhibit intestinal inflammation and repair damaged intestinal mucosa, but its effector mechanisms are unknown. Therefore, we studied the prophylactic effects of WMW in dextran sulfate sodium (DSS)-induced UC and its effects on macrophage mechanisms and polarization. The results show that colitis was significantly alleviated in mice in the WMW group, and the secretion and expression of pro-inflammatory factors TNF-α, IL-1, and IL-6 were inhibited in the serum and colonic tissues of mice with WMW-treated colitis, whereas anti-inflammatory factors IL-10, Arg-1, and TGF-β1 were increased. Subsequent studies found that WMW could inhibit M1 polarization and promote M2 polarization in colonic macrophages in DSS-induced colitis mice. Network pharmacology was used to predict potential targets and pathways, and further studies confirmed the related targets The results showed that WMW gradually inhibits the activation of the P38MAPK and NF-κB signaling pathways and further activates the STAT6 signaling pathway. In summary, WMW interferes with the p38MAPK, NF-κB and STAT6 signaling pathways to regulate M1/M2 polarization in macrophages, thereby protecting mice against DSS-induced colitis.
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Affiliation(s)
- Shuguang Yan
- College of Basic Medicine, Shaanxi University of Chinese Medicine, Xianyang, China.,Key Laboratory of Gastrointestinal Diseases and Prescriptions in Shaanxi Province, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Hailiang Wei
- Key Laboratory of Gastrointestinal Diseases and Prescriptions in Shaanxi Province, Shaanxi University of Chinese Medicine, Xianyang, China.,Department of General Surgery, The Affliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
| | - Rui Jia
- College of Basic Medicine, Shaanxi University of Chinese Medicine, Xianyang, China.,Key Laboratory of Gastrointestinal Diseases and Prescriptions in Shaanxi Province, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Meijia Zhen
- College of Basic Medicine, Shaanxi University of Chinese Medicine, Xianyang, China.,Key Laboratory of Gastrointestinal Diseases and Prescriptions in Shaanxi Province, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Shengchuan Bao
- College of Basic Medicine, Shaanxi University of Chinese Medicine, Xianyang, China.,Key Laboratory of Gastrointestinal Diseases and Prescriptions in Shaanxi Province, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Wenba Wang
- College of Basic Medicine, Shaanxi University of Chinese Medicine, Xianyang, China.,Key Laboratory of Gastrointestinal Diseases and Prescriptions in Shaanxi Province, Shaanxi University of Chinese Medicine, Xianyang, China
| | - Fanrong Liu
- Department of Gastroenterology, Yulin Hospital of Traditional Chinese Medicine in Shaanxi Province, Yulin, China
| | - Jingtao Li
- Key Laboratory of Gastrointestinal Diseases and Prescriptions in Shaanxi Province, Shaanxi University of Chinese Medicine, Xianyang, China.,Departments of Infectious Disease, The Affliated Hospital of Shaanxi University of Chinese Medicine, Xianyang, China
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Wang S, Zhen L, Li X, Fu X, Li P, Zhang D. Search for Key Genes and Functional Pathways of Ulcerative Colitis to Colon Cancer Based on Bioinformatics. Front Oncol 2022; 12:857148. [PMID: 35372018 PMCID: PMC8965385 DOI: 10.3389/fonc.2022.857148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/16/2022] [Indexed: 12/30/2022] Open
Abstract
Ulcerative colitis (UC) is a persistent and diffuse inflammatory disease of the intestine. It is widely prevalent in developed countries. Approximately 30% of patients with UC suffer from widespread and aggressive colitis and are at increased risk of colon cancer. In this study, the genetic features and potential molecular mechanisms shared between UC and colorectal cancer were investigated. The datasets from GEO and TCGA were analyzed to obtain differentially expressed genes, of which there were 116 overlapping genes. A module containing 15 genes was obtained using String and Cytoscape to analyze the module and identify hub genes. Weighted gene co-expression network analysis (WGCNA) was used to identify co-expression modules associated with UC and colon cancer, with 52 overlapping genes. Functional clustering of the two gene cohorts was performed using the Metascape online tool, with three significant functions or pathways associated with both gene cohorts. A total of 19 key genes were included, and CCT2 was identified after expression and survival analyses. CCT2 is highly expressed in colon cancer and lowly expressed in UC, and its low expression is associated with a poor prognostic ratio. This study reveals, for the first time, that CCT2 may be a promoter of UC transformation into colon cancer and identifies new gene candidates that could be used as biomarkers or potential therapeutic targets.
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Affiliation(s)
- Shengbao Wang
- Emergency Center, Gansu Emergency Medicine Clinical Research Center,Lanzhou University Second Hospital, Lanzhou, China
| | - Lingling Zhen
- Infectious Department, Lanzhou University Second Hospital, Lanzhou, China
| | - Xiaoli Li
- Digestive Department, Lanzhou University Second Hospital, Lanzhou, China
| | - Xu Fu
- Key Laboratory of Emergency Medicine, Lanzhou University Second Hospital, Lanzhou, China
| | - Peiwu Li
- Emergency Center, Gansu Emergency Medicine Clinical Research Center,Lanzhou University Second Hospital, Lanzhou, China
| | - Dekui Zhang
- Department of Gastroenterology, Key Laboratory of Digestive Diseases Lanzhou University Second Hospital, Lanzhou, China
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Guo S, Sun Y. OTOP2, Inversely Modulated by miR-3148, Inhibits CRC Cell Migration, Proliferation and Epithelial–Mesenchymal Transition: Evidence from Bioinformatics Data Mining and Experimental Verification. Cancer Manag Res 2022; 14:1371-1384. [PMID: 35418782 PMCID: PMC9000554 DOI: 10.2147/cmar.s345299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 03/04/2022] [Indexed: 01/22/2023] Open
Abstract
Introduction Colorectal cancer (CRC) represents one of the most frequent human malignancies with its underlying pathogenesis still unclear. The prevalence of multi-omics in screening biomarkers associated with CRC has largely accelerated our understanding into the pathophysiology of CRC. The present work aimed to mine the Gene Expression Omnibus (GEO) datasets associated with CRC studies and identify potential targets correlated with CRC pathogenesis. Methods We screened the DEGs in GSE50760 and GSE104178 and performed functional Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Furthermore, the overlapped DEGs were subjected to functional GO enrichment and KEGG pathway enrichment analysis. The protein–protein interaction (PPI) network and miRNA-mRNA network were constructed based on the overlapped DEGs. The in vitro functional assays including qRT-PCR, caspase-3 and -9 activity assay, wound healing assay, CCK-8 assay and luciferase reporter assay were performed to determine the role of OTOP2/miR-3148 axis in regulating CRC cell progression. Results Fifty-three overlapped genes were screened over GSE50760 and GSE104178 and ten hub genes were identified by PPI network analysis. Expression levels of GCG, SST, NPY, GUCA2B, PYY, UCN3, GUCA2A, TMEM82 and BEST4 were not correlated with the overall survival of patients with CRC. However, the high expression of otopetrin 2 (OTOP2) in the CRC tissues was significantly correlated with better overall survival of patients with CRC. The expression of OTOP2 in CRC tissues was significantly lowever than that in normal ones. The in vitro functional assays demonstrated that OTOP2 silence reduced caspase-3/-9 activities, promoted cell migration, proliferation and epithelial–mesenchymal transition in HT29 and SW620 cells. Furthermore, miR-3148 could inversely regulate OTOP2 expression in CRC cell lines. Conclusion Collectively, the work suggested the potential role of the OTOP2/miR-3148 axis in the pathophysiology of CRC by mining the GEO database.
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Affiliation(s)
- Shuai Guo
- Division of No.2 Gastrointestinal Surgery, Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, People’s Republic of China
| | - Yang Sun
- Division of No.2 Gastrointestinal Surgery, Department of General Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian, People’s Republic of China
- Correspondence: Yang Sun, Tel +86-17709872003, Email
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Li M, Liu Z, Song J, Wang T, Wang H, Wang Y, Guo J. Identification of Down-Regulated ADH1C is Associated With Poor Prognosis in Colorectal Cancer Using Bioinformatics Analysis. Front Mol Biosci 2022; 9:791249. [PMID: 35300114 PMCID: PMC8921497 DOI: 10.3389/fmolb.2022.791249] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 02/08/2022] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is the second most deadly cancer in the whole world, with the underlying mechanisms largely indistinct. Therefore, we aimed to identify significant pathways and genes involved in the initiation, formation and poor prognosis of CRC using bioinformatics methods. In this study, we compared gene expression profiles of CRC cases with those from normal colorectal tissues from three chip datasets (GSE33113, GSE23878 and GSE41328) to identify 105 differentially expressed genes (DEGs) that were common to the three datasets. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that the highest proportion of up-regulated DEGs was involved in extracellular region and cytokine-cytokine receptor interaction pathways. Integral components of membrane and bile secretion pathways were identified as containing down-regulated DEGs. 13 hub DEGs were chosen and their expression were further validated by GEPIA. Only four DEGs (ADH1C, CLCA4, CXCL8 and GUCA2A) were associated with a significantly lower overall survival after the prognosis analysis. Lower ADH1C protein level and higher CXCL8 protein level were verified by immunohistochemical staining and western blot in clinical CRC and normal colorectal tissues. In conclusion, our study indicated that the extracellular tumor microenvironment and bile metabolism pathways play critical roles in the formation and progression of CRC. Furthermore, we confirmed ADH1C being down-regulated in CRC and reported ADH1C as a prognostic predictor for the first time.
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Affiliation(s)
- Ming Li
- School of Basic Medical Sciences, Hebei University, Baoding, China
| | - Ziming Liu
- College of Clinical Medicine, Hebei University, Baoding, China
| | - Jia Song
- School of Basic Medical Sciences, Hebei University, Baoding, China
| | - Tian Wang
- College of Clinical Medicine, Hebei University, Baoding, China
| | - Hongjie Wang
- School of Basic Medical Sciences, Hebei University, Baoding, China
- Affiliated Hospital of Hebei University, Baoding, China
| | - Yanan Wang
- Department of Pathology, Affiliated Hospital of Hebei University, Baoding, China
- *Correspondence: Yanan Wang, ; Jiguang Guo,
| | - Jiguang Guo
- School of Basic Medical Sciences, Hebei University, Baoding, China
- *Correspondence: Yanan Wang, ; Jiguang Guo,
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Kou F, Cheng Y, Shi L, Liu J, Liu Y, Shi R, Peng G, Li J. LCN2 as a Potential Diagnostic Biomarker for Ulcerative Colitis-Associated Carcinogenesis Related to Disease Duration. Front Oncol 2022; 11:793760. [PMID: 35111677 PMCID: PMC8801604 DOI: 10.3389/fonc.2021.793760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/20/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Patients with long-duration ulcerative colitis (UC) had a higher risk of developing ulcerative colitis-associated carcinogenesis (UCAC) when compared to those with short-duration UC. This study aimed to discover the biomarker for cancer surveillance related to disease duration. METHODS The microarrays were divided into short-duration (<10 years) UC, long-duration (≥10 years) UC, UCAC, and normal groups in the Gene Expression Omnibus (GEO) datasets. Differentially expressed genes (DEGs) of GEO and the hub genes of the selected weighted gene co-expression network analysis (WGCNA) were intersected to obtain the overlapping genes. Among these genes, the key gene was identified by using the protein-protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the cytoHubba of Cytoscape, and the expression levels. Also, immunofluorescence of human colonic mucosa and animal experiment were used to validate the expression trend of the key gene in the progress of UC developing into UCAC. RESULTS Lipocalin-2 (LCN2) was more relevant with disease duration of UC and significantly negatively correlated with the risk of UCAC. The expression level of LCN2 in short-duration UC was higher than that of long-duration UC (P < 0.01), long-duration UC was higher than that of UCAC (P = 0.001), and UC and UCAC were all higher than that of the normal (P < 0.001). We then discovered that the expression trend of LCN2 in blood and stool samples was consistent with that in colorectal mucosa. CONCLUSION The research indicates that LCN2 could be a novel biomarker to evaluate cancer surveillance related to disease duration of developing UC into UCAC. Compared with that of blood samples, stool detection of LCN2 may have more advantages for diagnosis value of early stage of UCAC as a complement to colonoscopy surveillance.
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Affiliation(s)
- Fushun Kou
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yuan Cheng
- Graduate School, Beijing University of Chinese Medicine, Beijing, China
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Lei Shi
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Jiajing Liu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Yuyue Liu
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Rui Shi
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Guiying Peng
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Junxiang Li
- Gastroenterology Department, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing, China
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Ahmad Kendong SM, Raja Ali RA, Nawawi KNM, Ahmad HF, Mokhtar NM. Gut Dysbiosis and Intestinal Barrier Dysfunction: Potential Explanation for Early-Onset Colorectal Cancer. Front Cell Infect Microbiol 2021; 11:744606. [PMID: 34966694 PMCID: PMC8710575 DOI: 10.3389/fcimb.2021.744606] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is a heterogeneous disease that commonly affects individuals aged more than 50 years old globally. Regular colorectal screening, which is recommended for individuals aged 50 and above, has decreased the number of cancer death toll over the years. However, CRC incidence has increased among younger population (below 50 years old). Environmental factors, such as smoking, dietary factor, urbanization, sedentary lifestyle, and obesity, may contribute to the rising trend of early-onset colorectal cancer (EOCRC) because of the lack of genetic susceptibility. Research has focused on the role of gut microbiota and its interaction with epithelial barrier genes in sporadic CRC. Population with increased consumption of grain and vegetables showed high abundance of Prevotella, which reduces the risk of CRC. Microbes, such as Fusobacterium nucleatum, Bacteroides fragilis and Escherichia coli deteriorate in the intestinal barrier, which leads to the infiltration of inflammatory mediators and chemokines. Gut dysbiosis may also occur following inflammation as clearly observed in animal model. Both gut dysbiosis pre- or post-inflammatory process may cause major alteration in the morphology and functional properties of the gut tissue and explain the pathological outcome of EOCRC. The precise mechanism of disease progression from an early stage until cancer establishment is not fully understood. We hypothesized that gut dysbiosis, which may be influenced by environmental factors, may induce changes in the genome, metabolome, and immunome that could destruct the intestinal barrier function. Also, the possible underlying inflammation may give impact microbial community leading to disruption of physical and functional role of intestinal barrier. This review explains the potential role of the interaction among host factors, gut microenvironment, and gut microbiota, which may provide an answer to EOCRC.
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Affiliation(s)
- Siti Maryam Ahmad Kendong
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.,Department of Basic Medical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, Sarawak, Malaysia
| | - Raja Affendi Raja Ali
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.,GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Khairul Najmi Muhammad Nawawi
- Gastroenterology Unit, Department of Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.,GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
| | - Hajar Fauzan Ahmad
- Department of Industrial Biotechnology, Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Gambang, Malaysia.,Center for Research in Advanced Tropical Bioscience, Universiti Malaysia Pahang, Gambang, Malaysia
| | - Norfilza Mohd Mokhtar
- Department of Physiology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.,GUT Research Group, Faculty of Medicine, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia
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Niu M, Li H, Li X, Yan X, Ma A, Pan X, Zhu X. Circulating Exosomal miRNAs as Novel Biomarkers Perform Superior Diagnostic Efficiency Compared With Plasma miRNAs for Large-Artery Atherosclerosis Stroke. Front Pharmacol 2021; 12:791644. [PMID: 34899352 PMCID: PMC8661454 DOI: 10.3389/fphar.2021.791644] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Recently, exosomal miRNAs have been reported to be associated with some diseases, and these miRNAs can be used for diagnosis and treatment. However, diagnostic biomarkers of exosomal miRNAs for ischemic stroke have rarely been studied. In the present study, we aimed to identify exosomal miRNAs that are associated with large-artery atherosclerosis (LAA) stroke, the most common subtype of ischemic stroke; to further verify their diagnostic efficiency; and to obtain promising biomarkers. High-throughput sequencing was performed on samples from 10 subjects. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed on exosomes and plasma in the discovery phase (66 subjects in total) and the validation phase (520 subjects in total). We identified 5 candidate differentially expressed miRNAs (miR-369-3p, miR-493-3p, miR-379-5p, miR-1296-5p, and miR-1277-5p) in the discovery phase according to their biological functions, 4 of which (miR-369-3p, miR-493-3p, miR-379-5p, and miR-1296-5p) were confirmed in the validation phase. These four exosomal miRNAs could be used to distinguish LAA samples from small artery occlusion (SAO) samples, LAA samples from atherosclerosis (AS) samples, and LAA samples from control samples and were superior to plasma miRNAs. In addition, composite biomarkers achieved higher area under the curve (AUC) values than single biomarkers. According to our analysis, the expression levels of exosomal miR-493-3p and miR-1296-5p were negatively correlated with the National Institutes of Health Stroke Scale (NIHSS) score. The four identified exosomal miRNAs are promising biomarkers for the diagnosis of LAA stroke, and their diagnostic efficiency is superior to that of their counterparts in plasma.
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Affiliation(s)
- Mengying Niu
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hong Li
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xu Li
- Institute of Cerebrovascular Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaoqian Yan
- Department of Critical Care Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Aijun Ma
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xudong Pan
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China.,Institute of Cerebrovascular Diseases, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaoyan Zhu
- Department of Critical Care Medicine, The Affiliated Hospital of Qingdao University, Qingdao, China
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Li D, Tan Y. Dysregulation of alternative splicing is associated with the pathogenesis of ulcerative colitis. Biomed Eng Online 2021; 20:121. [PMID: 34838026 PMCID: PMC8627048 DOI: 10.1186/s12938-021-00959-4] [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: 08/19/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
Background Although numerous risk loci for ulcerative colitis (UC) have been identified in the human genome, the pathogenesis of UC remains unclear. Recently, multiple transcriptomic analyses have shown that aberrant gene expression in the colon tissues of UC patients is associated with disease progression. A pioneering study also demonstrated that altered post-transcriptional regulation is involved in the progression of UC. Here, we provide a genome-wide analysis of alternative splicing (AS) signatures in UC patients. We analyzed three datasets containing 74 tissue samples from UC patients and identified over 2000 significant AS events. Results Skipped exon and alternative first exon were the two most significantly altered AS events in UC patients. The immune response-related pathways were remarkably enriched in the UC-related AS events. Genes with significant AS events were more likely to be dysregulated at the expression level. Conclusions We present a genomic landscape of AS events in UC patients based on a combined analysis of two cohorts. Our results indicate that dysregulation of AS may have a pivotal role in determining the pathogenesis of UC. In addition, our study uncovers genes with potential therapeutic implications for UC treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12938-021-00959-4.
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Affiliation(s)
- Daowei Li
- Department of Radiology, The People's Hospital of China Medical University & The People's Hospital of Liaoning Province, No. 33, Wenyi Road, Shenhe District, Shenyang, 110016, China
| | - Yue Tan
- Department of Gastroenterology, Shengjing Hospital of China Medical University, Tiexi District, 39 Huaxiang Road, Shenyang, 110022, China.
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Abstract
Sour taste, the taste of acids, is one of the most enigmatic of the five basic taste qualities; its function is unclear and its receptor was until recently unknown. Sour tastes are transduced in taste buds on the tongue and palate epithelium by a subset of taste receptor cells, known as type III cells. Type III cells express a number of unique markers, including the PKD2L1 gene, which allow for their identification and manipulation. These cells respond to acid stimuli with action potentials and release neurotransmitters onto afferent nerve fibers, with cell bodies in geniculate and petrosal ganglia. Here, we review classical studies of sour taste leading up to the identification of the sour receptor as the proton channel, OTOP1. Expected final online publication date for the Annual Review of Physiology, Volume 84 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Heather N Turner
- Department of Biological Sciences, Section of Neurobiology, University of Southern California, Los Angeles, California, USA; ,
| | - Emily R Liman
- Department of Biological Sciences, Section of Neurobiology, University of Southern California, Los Angeles, California, USA; ,
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The Cancer-Associated Antigens Sialyl Lewis a/x and Sd a: Two Opposite Faces of Terminal Glycosylation. Cancers (Basel) 2021; 13:cancers13215273. [PMID: 34771437 PMCID: PMC8582462 DOI: 10.3390/cancers13215273] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/11/2021] [Accepted: 10/19/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The glycosyltransferase β1,4-N-acetylgalactosaminyltransferae 2 (B4GALNT2), product of the B4GALNT2 gene is responsible for the biosynthesis of the carbohydrate antigen Sda. Both the enzyme and its cognate antigen display a restricted pattern of tissue expression and modulation in colorectal, gastric, and mammary cancers. In colorectal cancer, B4GALNT2 is generally downregulated, but patients displaying higher expression survive longer. The sialyl Lewisa and sialyl Lewisx antigens are associated with malignancy. Their biosynthesis and that of Sda are mutually exclusive. Forced expression of B4GALNT2 in colorectal cancer cell lines modulates the transcriptome towards lower malignancy, reducing stemness. These effects are independent of B4GALNT2-induced sLea/sLex inhibition. Thus, B4GALNT2 is a marker of better prognosis and a cancer-restraining enzyme in colorectal cancer, with a therapeutic potential. Abstract Terminal carbohydrate structures are particularly relevant in oncology because they can serve as cancer markers and alter the phenotype of cancer cells. The Sda antigen and the sialyl Lewisx and sialyl Lewisa (sLex and sLea) antigens are terminal structures whose biosynthesis is mutually exclusive. In this review, we describe the main features of the Sda antigen in cancer and its relationship with sLex/a antigens. Information was obtained from an extensive literature search and from The Cancer Genome Atlas (TCGA) public database. The Sda biosynthetic enzyme B4GALNT2 undergoes downregulation in colorectal (CRC) and stomach cancer, while it is ectopically expressed by a minority of breast cancer (BRCA) patients. High expression of B4GALNT2 is associated with better prognosis and a less malignant gene expression profile in CRC, while the opposite occurs in BRCA. The regulation of B4GALNT2 expression in CRC is multifactorial, involving gene methylation and miRNA expression. Forced expression of B4GALNT2 inhibited sLea/sLex and reduced malignancy and stemness in cells constitutively expressing sLex/a antigens. However, consistent effects were observed upon B4GALNT2 forced expression and in cells not expressing sLex/a antigens. Thus, B4GALNT2 and the Sda antigen exert a tumor-restraining activity in CRC and probably other gastrointestinal cancers, independently of sLex/a antigens.
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Gao J, Wang Y, Lyu B, Chen J, Chen G. Component Identification of Phenolic Acids in Cell Suspension Cultures of Saussureainvolucrata and Its Mechanism of Anti-Hepatoma Revealed by TMT Quantitative Proteomics. Foods 2021; 10:foods10102466. [PMID: 34681515 PMCID: PMC8535732 DOI: 10.3390/foods10102466] [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: 09/02/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
Saussurea involucrata (S. involucrata) had been reported to have anti-hepatoma function. However, the mechanism is complex and unclear. To evaluate the anti-hepatoma mechanism of S. involucrata comprehensively and make a theoretical basis for the mechanical verification of later research, we carried out this work. In this study, the total phenolic acids from S. involucrata determined by a cell suspension culture (ESPI) was mainly composed of 4,5-dicaffeoylquinic acid, according to the LC-MS analysis. BALB/c nude female mice were injected with HepG2 cells to establish an animal model of liver tumor before being divided into a control group, a low-dose group, a middle-dose group, a high-dose group, and a DDP group. Subsequently, EPSI was used as the intervention drug for mice. Biochemical indicators and differences in protein expression determined by TMT quantitative proteomics were used to resolve the mechanism after the low- (100 mg/kg), middle- (200 mg/kg), and high-dose (400 mg/kg) interventions for 24 days. The results showed that EPSI can not only limit the growth of HepG2 cells in vitro, but also can inhibit liver tumors significantly with no toxicity at high doses in vivo. Proteomics analysis revealed that the upregulated differentially expressed proteins (DE proteins) in the high-dose group were over three times that in the control group. ESPI affected the pathways significantly associated with the protein metabolic process, metabolic process, catalytic activity, hydrolase activity, proteolysis, endopeptidase activity, serine-type endopeptidase activity, etc. The treatment group showed significant differences in the pathways associated with the renin-angiotensin system, hematopoietic cell lineage, etc. In conclusion, ESPI has a significant anti-hepatoma effect and the potential mechanism was revealed.
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Affiliation(s)
- Junpeng Gao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China;
| | - Yi Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China; (Y.W.); (B.L.); (J.C.)
| | - Bo Lyu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China; (Y.W.); (B.L.); (J.C.)
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Jian Chen
- College of Food Science and Engineering, Jilin Agricultural University, Changchun 130118, China; (Y.W.); (B.L.); (J.C.)
| | - Guang Chen
- College of Life Science, Jilin Agricultural University, Changchun 130118, China;
- Correspondence:
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Song F, Zhang Y, Pan Z, Hu X, Zhang Q, Huang F, Ye X, Huang P. The role of alcohol dehydrogenase 1C in regulating inflammatory responses in ulcerative colitis. Biochem Pharmacol 2021; 192:114691. [PMID: 34293286 DOI: 10.1016/j.bcp.2021.114691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/19/2022]
Abstract
Ulcerative colitis (UC) is a chronic relapsing inflammatory bowel disease caused by an interaction of genetics, immune responses, and environmental factors. However, the precise pathogenesis of UC remains poorly understood. The aim of the present study was to explore the potential target genes implicated in UC and to elucidate its underlying pathogenic mechanism. Firstly, three UC-associated microarray datasets (GSE75214, GSE87466, and GSE92517) were obtained to screen the differentially expressed genes (DEGs). As a result, alcohol dehydrogenase 1C (ADH1C) was the most significantly downregulated DEG in UC. We confirmed that ADH1C was downregulated in colonic tissue taken from patients with UC and colitis mice. Moreover, ADH1C expression was also decreased in colonic cell lines (NCM460 and HT29) treated with mixed proinflammatory cytokines (TNF-α, IFN-γ, IL-1β). Interestingly, we found that overexpression of ADH1C could distinctly decrease the production of IL-6 and IL-8. To elucidate the molecular mechanism of ADH1C in UC, gene set enrichment analysis (GSEA) was performed and demonstrated that immune-related pathways were mainly enriched in the low ADH1C group. Further studies displayed that STAT1/NF-κB pathway was activated in colitis mice and inflammatory cell model. Importantly, overexpression of ADH1C could suppress the phosphorylation of STAT1 and IκB. Therefore, ADH1C might regulate inflammatory responses through STAT1/NF-κB pathway. In conclusion, ADH1C was downregulated during inflammation, and its increased expression could inhibit the activation of STAT1/NF-κB pathway, thereby alleviating the secretion of IL-6 and IL-8. These findings indicate that ADH1C may be a potential therapeutic target for UC therapy.
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Affiliation(s)
- Feifeng Song
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou 310014, Zhejiang, China
| | - Yiwen Zhang
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou 310014, Zhejiang, China
| | - Zongfu Pan
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou 310014, Zhejiang, China
| | - Xiaoping Hu
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou 310014, Zhejiang, China
| | - Qi Zhang
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Fang Huang
- Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou 310014, Zhejiang, China; Department of Pathology, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Xiaolan Ye
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China
| | - Ping Huang
- Clinical Pharmacy Center, Department of Pharmacy, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou 310014, Zhejiang, China; Key Laboratory of Endocrine Gland Diseases of Zhejiang Province, Hangzhou 310014, Zhejiang, China.
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Kim JT, Napier DL, Kim J, Li C, Lee EY, Weiss HL, Wang Q, Evers BM. Ketogenesis alleviates TNFα-induced apoptosis and inflammatory responses in intestinal cells. Free Radic Biol Med 2021; 172:90-100. [PMID: 34087430 PMCID: PMC8355065 DOI: 10.1016/j.freeradbiomed.2021.05.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/20/2022]
Abstract
The disturbance of strictly regulated self-regeneration in mammalian intestinal epithelium is associated with various intestinal disorders, particularly inflammatory bowel diseases (IBDs). TNFα, which plays a critical role in the pathogenesis of IBDs, has been reported to inhibit production of ketone bodies such as β-hydroxybutyrate (βHB). However, the role of ketogenesis in the TNFα-mediated pathological process is not entirely known. Here, we showed the regulation and role of HMGCS2, the rate-limiting enzyme of ketogenesis, in TNFα-induced apoptotic and inflammatory responses in intestinal epithelial cells. Treatment with TNFα dose-dependently decreased protein and mRNA expression of HMGCS2 and its product, βHB production in human colon cancer cell lines HT29 and Caco2 cells and mouse small intestinal organoids. Moreover, the repressed level of HMGCS2 protein was found in intestinal epithelium of IBD patients with Crohn's disease and ulcerative colitis as compared with normal tissues. Furthermore, knockdown of HMGCS2 enhanced and in contrast, HMGCS2 overexpression attenuated, the TNFα-induced apoptosis and expression of pro-inflammatory chemokines (CXCL1-3) in HT29, Caco2 cells and DLD1 cells, respectively. Treatment with βHB or rosiglitazone, an agonist of PPARγ, which increases ketogenesis, attenuated TNFα-induced apoptosis in the intestinal epithelial cells. Finally, HMGCS2 knockdown enhanced TNFα-induced reactive oxygen species (ROS) generation. In addition, hydrogen peroxide, the major ROS contributing to intestine injury, decreased HMGCS2 expression and βHB production in the intestinal cells and mouse organoids. Our findings demonstrate that increased ketogenesis attenuates TNFα-induced apoptosis and inflammation in intestinal cells, suggesting a protective role for ketogenesis in TNFα-induced intestinal pathologies.
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Affiliation(s)
- Ji Tae Kim
- Markey Cancer Center, Lexington, KY, 40536, USA
| | | | - Jinhwan Kim
- Markey Cancer Center, Lexington, KY, 40536, USA
| | - Chang Li
- Markey Cancer Center, Lexington, KY, 40536, USA
| | - Eun Y Lee
- Department of Pathology and Laboratory Medicine, Department of Surgery, Lexington, KY, 40536, USA
| | | | - Qingding Wang
- Markey Cancer Center, Lexington, KY, 40536, USA; Department of Surgery, University of Kentucky, Lexington, KY, 40536, USA.
| | - B Mark Evers
- Markey Cancer Center, Lexington, KY, 40536, USA; Department of Surgery, University of Kentucky, Lexington, KY, 40536, USA.
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Wen S, Zhong Z, He L, Zhao D, Chen X, Mi H, Liu F. Network pharmacology dissection of multiscale mechanisms for jiaoqi powder in treating ulcerative colitis. JOURNAL OF ETHNOPHARMACOLOGY 2021; 275:114109. [PMID: 33845143 DOI: 10.1016/j.jep.2021.114109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/28/2021] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The incidence of ulcerative colitis (UC) is increasing worldwide, making it a serious public health challenge. Currently, there are no accepted curative treatments for UC. As such, the exploration of new therapeutic strategies for UC treatment is of considerable clinical importance. Jiaoqi powder (JQP) is a classic Chinese medicinal formula commonly used as a complementary and alternative medicine for treating gastrointestinal bleeding. JQP is thus a potential alternative medicine for UC treatment. However, the protective mechanism underlying the action of JQP has not been elucidated, thereby, necessitating further studies to decipher the mechanisms involved in the complex interplay among its components. AIM OF THE STUDY To explore the protective effect of JQP against UC and to further investigate its mechanism in silico and in vivo using a systems pharmacology approach. MATERIALS AND METHODS A systems pharmacology approach was used to predict the active components of JQP. Putative targets and the potential mechanism of JQP on UC were obtained through target fishing, network construction, and enrichment analyses. An animal-based model of dextran sodium sulfate (DSS)-induced colitis in C57BL/6 mice was further used to validate the treatment mechanisms of JQP. The underlying pharmacological mechanisms of JQP in UC were determined using polymerase chain reaction tests, histological staining, immunohistochemistry, enzyme-linked immunoassays, and flow cytometry analysis. RESULTS In this study, 17 effective components and 941 potential targets of JQP were identified. Similarly, 2104 UC-related targets were also identified. Construction of PPI networks led to the identification of 184 putative therapeutic targets of JQP. Sixty-nine core targets among these 184 were further screened based on their DC values. Gene ontology (GO) functional and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the core targets were primarily enriched in immune response and inflammatory signalling pathways. Subsequent animal-based in vivo experiments revealed that JQP ameliorated symptoms and histological changes in DSS colitis by significantly impairing DSS's ability to induce high expression levels of NF-κB/p65, IL-1β, IL-6, and TNF-α. JQP also reduced the levels of COX-2, CCL2, CXCL2, HIF-1α, MMP3 and MMP9 and regulated the Th17/Treg cell balance in DSS-induced mice. CONCLUSIONS This study demonstrated that JQP could treat UC by improving the mucosal inflammatory response, repairing the intestinal barrier, and modulating the Th17/Treg immune balance. The results of this study provide new insights into UC treatment and further elucidate the theoretical and practical implications of the pharmaceutical development of TCMs.
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MESH Headings
- Animals
- Colitis, Ulcerative/chemically induced
- Colitis, Ulcerative/drug therapy
- Colitis, Ulcerative/immunology
- Colitis, Ulcerative/pathology
- Cytokines/metabolism
- Dextran Sulfate/toxicity
- Disease Models, Animal
- Drugs, Chinese Herbal/isolation & purification
- Drugs, Chinese Herbal/pharmacology
- Drugs, Chinese Herbal/therapeutic use
- Inflammation/chemically induced
- Inflammation/drug therapy
- Inflammation/immunology
- Lymph Nodes/immunology
- Male
- Metabolic Networks and Pathways/drug effects
- Mice, Inbred C57BL
- Powders
- Protein Interaction Maps
- Spleen/immunology
- T-Lymphocytes, Regulatory/metabolism
- Th17 Cells/metabolism
- Mice
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Affiliation(s)
- Shuting Wen
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Zhuotai Zhong
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Long He
- The First Clinical College, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Dike Zhao
- Basic Medical College, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Xu Chen
- Department of Gastroenterology,The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Hong Mi
- Department of Gastroenterology,The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China.
| | - Fengbin Liu
- Department of Gastroenterology,The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, China; Baiyun Hospital of the First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510000, China.
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Molecular Targets and Mechanisms of Scutellariae radix- Coptidis rhizoma Drug Pair for the Treatment of Ulcerative Colitis Based on Network Pharmacology and Molecular Docking. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:9929093. [PMID: 34149863 PMCID: PMC8195671 DOI: 10.1155/2021/9929093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022]
Abstract
This study aims to analyze the targets of the effective active ingredients of Scutellariae radix-Coptidis rhizoma drug pair (SCDP) in ulcerative colitis (UC) by network pharmacology and molecular docking and to explore the associated therapeutic mechanism. The effective active ingredients and targets of SCDP were determined from the TCMSP database, and the drug ingredient-target network was constructed using the Cytoscape software. The disease targets related to UC were searched in GeneCards, DisGeNET, OMIM, and DrugBank databases. Then, the drug ingredient and disease targets were intersected to construct a protein-protein interaction network through the STRING database. The Metascape database was used for the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses of the predicted targets of SCDP for UC. The Autodock software was used for molecular docking between the main active ingredient and the core target to evaluate the binding ability. SCDP has 43 effective active ingredients and 134 intersection targets. Core targets included AKT1, TP53, IL-6, VEGFA, CASP3, JUN, TNF, MYC, EGFR, and PTGS2. GO functional enrichment analysis showed that biological process was mainly associated with a cytokine-mediated signaling pathway, response to an inorganic substance, response to a toxic substance, response to lipopolysaccharide, reactive oxygen species metabolic process, positive regulation of cell death, apoptotic signaling pathway, and response to wounding. KEGG enrichment analysis showed main pathway concentrations were related to pathways in cancer, AGE-RAGE signaling pathway in diabetic complications, bladder cancer, IL-17 signaling pathway, apoptosis, p53 signaling pathway, and PI3K-Akt signaling pathway. The drug active ingredient-core target-key pathway network contains 41 nodes and 108 edges, of which quercetin, wogonin, baicalein, acacetin, oroxylin A, and beta-sitosterol are important active ingredients; PTGS2, CASP3, TP53, IL-6, TNF, and AKT1 are important targets; and the pathways involved in UC treatment include pathways in cancer, PI3K-Akt signaling pathway, AGE-RAGE signaling pathway in diabetic, apoptosis, IL-17 signaling pathway and herpes simplex infection. The active ingredient has a good binding capacity to the core target. SCDP key active ingredients are mainly quercetin, wogonin, baicalein, acacetin, oroxylin A, and beta-sitosterol, which function mainly by regulating targets, such as PTGS2, CASP3, TP53, IL-6, TNF, and AKT1, and are associated with multiple signaling pathways as pathways in cancer, PI3K-Akt signaling pathway, apoptosis, IL-17 signaling pathways.
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Mazzio E, Badisa R, Mack N, Cassim S, Zdralevic M, Pouyssegur J, Soliman KFA. Whole-transcriptome Analysis of Fully Viable Energy Efficient Glycolytic-null Cancer Cells Established by Double Genetic Knockout of Lactate Dehydrogenase A/B or Glucose-6-Phosphate Isomerase. Cancer Genomics Proteomics 2021; 17:469-497. [PMID: 32859627 DOI: 10.21873/cgp.20205] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/14/2020] [Accepted: 06/26/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND/AIM Nearly all mammalian tumors of diverse tissues are believed to be dependent on fermentative glycolysis, marked by elevated production of lactic acid and expression of glycolytic enzymes, most notably lactic acid dehydrogenase (LDH). Therefore, there has been significant interest in developing chemotherapy drugs that selectively target various isoforms of the LDH enzyme. However, considerable questions remain as to the consequences of biological ablation of LDH or upstream targeting of the glycolytic pathway. MATERIALS AND METHODS In this study, we explore the biochemical and whole transcriptomic effects of CRISPR-Cas9 gene knockout (KO) of lactate dehydrogenases A and B [LDHA/B double KO (DKO)] and glucose-6-phosphate isomerase (GPI KO) in the human colon cancer cell line LS174T, using Affymetrix 2.1 ST arrays. RESULTS The metabolic biochemical profiles corroborate that relative to wild type (WT), LDHA/B DKO produced no lactic acid, (GPI KO) produced minimal lactic acid and both KOs displayed higher mitochondrial respiration, and minimal use of glucose with no loss of cell viability. These findings show a high biochemical energy efficiency as measured by ATP in glycolysis-null cells. Next, transcriptomic analysis conducted on 48,226 mRNA transcripts reflect 273 differentially expressed genes (DEGS) in the GPI KO clone set, 193 DEGS in the LDHA/B DKO clone set with 47 DEGs common to both KO clones. Glycolytic-null cells reflect up-regulation in gene transcripts typically associated with nutrient deprivation / fasting and possible use of fats for energy: thioredoxin interacting protein (TXNIP), mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), PPARγ coactivator 1α (PGC-1α), and acetyl-CoA acyltransferase 2 (ACAA2). Other changes in non-ergometric transcripts in both KOs show losses in "stemness", WNT signaling pathway, chemo/radiation resistance, retinoic acid synthesis, drug detoxification, androgen/estrogen activation, and extracellular matrix reprogramming genes. CONCLUSION These findings demonstrate that: 1) The "Warburg effect" is dispensable, 2) loss of the LDHAB gene is not only inconsequential to viability but fosters greater mitochondrial energy, and 3) drugs that target LDHA/B are likely to be ineffective without a plausible combination second drug target.
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Affiliation(s)
- Elizabeth Mazzio
- College of Pharmacy & Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, U.S.A
| | - Ramesh Badisa
- College of Pharmacy & Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, U.S.A
| | - Nzinga Mack
- College of Pharmacy & Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, U.S.A
| | - Shamir Cassim
- Department of Medical Biology, Centre Scientifique de Monaco, Monaco, Monaco
| | - Masa Zdralevic
- University Côte d'Azur, IRCAN, CNRS, Centre A. Lacassagne, Nice, France
| | - Jacques Pouyssegur
- Department of Medical Biology, Centre Scientifique de Monaco, Monaco, Monaco .,University Côte d'Azur, IRCAN, CNRS, Centre A. Lacassagne, Nice, France
| | - Karam F A Soliman
- College of Pharmacy & Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL, U.S.A.
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