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Kiran NS, Chatterjee A, Yashaswini C, Deshmukh R, Alsaidan OA, Bhattacharya S, Prajapati BG. The gastrointestinal mycobiome in inflammation and cancer: unraveling fungal dysbiosis, pathogenesis, and therapeutic potential. Med Oncol 2025; 42:195. [PMID: 40323477 DOI: 10.1007/s12032-025-02761-x] [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: 03/09/2025] [Accepted: 04/28/2025] [Indexed: 06/01/2025]
Abstract
The gastrointestinal mycobiome, comprising diverse fungal species, plays a significant role in gastrointestinal carcinogenesis and inflammatory bowel disease (IBD) pathogenesis. Recent studies have demonstrated that dysbiosis of the gut mycobiome, characterized by an overrepresentation of pathogenic fungi such as Candida albicans and Aspergillus, correlates with increased inflammation and cancer risk. For instance, C. albicans has been shown to induce colonic inflammation through the activation of pattern recognition receptors and the release of pro-inflammatory cytokines, exacerbating IBD symptoms and potentially facilitating tumorigenesis. Additionally, metagenomic analyses have revealed distinct fungal signatures in colorectal cancer tissues compared to adjacent healthy tissues, highlighting the potential of fungi as biomarkers for disease progression. Mechanistically, gut fungi contribute to disease through biofilm formation, mycotoxin secretion (e.g., aflatoxins, candidalysin), pro-inflammatory cytokine induction (e.g., IL-1β, IL-17), and disruption of epithelial barriers-creating a tumor-promoting and inflammation-prone environment. Furthermore, the interplay between fungi and the bacterial microbiome can amplify inflammatory responses, contributing to chronic inflammation and cancer development. Fungal interactions with bacterial communities also play a synergistic role in shaping mucosal immune responses and enhancing disease severity in both cancer and IBD contexts. As research continues to elucidate these complex fungal-host and fungal-bacterial interactions, targeting the gut mycobiome may offer novel therapeutic avenues for managing IBD and gastrointestinal cancers, emphasizing the need for integrated, mechanistically informed approaches to microbiome research.
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Affiliation(s)
- Neelakanta Sarvashiva Kiran
- Department of Biotechnology, School of Applied Sciences, REVA University, Kattigenahalli, Yelahanka, Bengaluru, 560064, Karnataka, India
| | - Ankita Chatterjee
- Department of Biotechnology, School of Applied Sciences, REVA University, Kattigenahalli, Yelahanka, Bengaluru, 560064, Karnataka, India
| | - Chandrashekar Yashaswini
- Department of Biotechnology, School of Applied Sciences, REVA University, Kattigenahalli, Yelahanka, Bengaluru, 560064, Karnataka, India
| | - Rohitas Deshmukh
- Institute of Pharmaceutical Research, GLA University, Mathura, 281406, Uttar Pradesh, India
| | - Omar Awad Alsaidan
- Department of Pharmaceutics, College of Pharmacy, Jouf University, 72341, Sakaka, Saudi Arabia
| | - Sankha Bhattacharya
- School of Pharmacy and Technology Management, SVKM'S NMIMS Deemed-to-Be University, Shirpur, 425405, Maharashtra, India.
| | - Bhupendra G Prajapati
- Department of Pharmaceutics, Shree S K Patel College of Pharmaceutical Education and Research, Ganpat University, Kherva, 384012, Gujarat, India.
- Faculty of Pharmacy, Silpakorn University, Nakhon Pathom, 73000, Thailand.
- Centre for Research Impact & Outcome, Chitkara College of Pharmacy, Chitkara University, Rajpura, 140401, Punjab, India.
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Pawlak M, Kałuzińska-Kołat Ż, Pasieka ZW, Kołat D, Płuciennik E. The critical role of COL1A1 revealed by integrated bioinformatics analysis of differentially-expressed genes in colorectal cancer and inflammatory bowel disease. Comput Biol Med 2025; 190:110116. [PMID: 40179807 DOI: 10.1016/j.compbiomed.2025.110116] [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: 10/07/2024] [Revised: 03/27/2025] [Accepted: 03/28/2025] [Indexed: 04/05/2025]
Abstract
PURPOSE There is an urgent need to identify biomarkers of tumorigenesis for colitis-associated cancer (CAC) as early cancer detection remains crucial for patients with inflammatory bowel disease (IBD). This in silico study examines the relationship between IBD and CAC, with particular regard to differentially-expressed genes (DEGs). METHODS Integrated bioinformatics tools and public databases were employed. Data from GEO (GSE102133, GSE48958, GSE9348, GSE83687, GSE138202) were processed using GEOexplorer. DEGs were then functionally annotated with DAVID, SRplot, and integrated analysis via Metascape. Validation used Oncopression and Human Protein Atlas. Survival analysis employed GEPIA2. miRNA interactions were studied via miRTargetLink 2.0. Immune infiltration was analyzed with TIMER 2.0. COL1A1 expression and mutations were examined using cBioPortal, Kaplan-Meier plotter, and DNA methylation was analyzed using MethSurv. Correlation of COL1A1 gene promoter methylation with tissue type and clinical data was performed using the UALCAN database. The ROC analysis of COL1A1 was conducted in the R environment. RESULTS Our analysis identified three potential hub genes (ICAM1, LAMC1, and COL1A1), which are overexpressed in IBD and cancer tissues compared to normal tissue, and hence may play a role in CAC. Furthermore, patients with lower COL1A1 expression had longer disease-free survival (p = 0.01) than those with higher expression. Therefore, this gene was chosen for further analysis and identified as the most crucial. CONCLUSION COL1A1 reveals significant immunohistochemistry, mutations, and methylation data. Further studies involving machine learning and clinical data are required to validate the results.
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Affiliation(s)
- Martyna Pawlak
- Department of Biomedical Sciences, Faculty of Medicine, Medical University of Lodz, Poland
| | - Żaneta Kałuzińska-Kołat
- Department of Functional Genomics, Medical University of Lodz, Poland; Department of Biomedicine and Experimental Surgery, Faculty of Medicine, Medical University of Lodz, Poland
| | - Zbigniew W Pasieka
- Department of Biomedicine and Experimental Surgery, Faculty of Medicine, Medical University of Lodz, Poland
| | - Damian Kołat
- Department of Functional Genomics, Medical University of Lodz, Poland; Department of Biomedicine and Experimental Surgery, Faculty of Medicine, Medical University of Lodz, Poland
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Zhou Y, Zhang X, Yin S, Yao Y, Chen T, Huang L, Liu Z. Shared genetic association between inflammatory bowel disease and acute myeloid leukemia: insights from mendelian randomization and transcriptomic analyses. Inflamm Res 2025; 74:77. [PMID: 40304766 DOI: 10.1007/s00011-025-02038-z] [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: 01/09/2025] [Revised: 03/10/2025] [Accepted: 04/11/2025] [Indexed: 05/02/2025] Open
Abstract
BACKGROUND Observational studies suggest that a history of inflammatory bowel disease (IBD) is associated with the onset of acute myeloid leukemia (AML), often attributed to drug use. However, these findings are inconsistent. This study aimed to assess the causal relationship between IBD and AML, identify shared pathogenesis, and discover diagnostic and prognostic markers and potential therapeutic drugs. METHODS Two-sample Mendelian randomization (MR) was employed to analyze genetic associations between IBD [ulcerative colitis (UC) and Crohn's disease (CD)] and AML. Transcriptomic data from gene expression omnibus (GEO) identified differentially expressed genes (DEGs) in UC, AML, and controls. Weighted Gene Co-expression Network Analysis (WGCNA) and enrichment analyses [Gene Multiple Association Network Integration Algorithm (GeneMANIA), Kyoto Encyclopedia of Genes and Genomes (KEGG), Ractom pathway] and Gene Ontology (GO) explored shared genetic pathways. Receiver Operating Characteristic (ROC) curve and survival analyses screened diagnostic and prognostic markers. Cibersort and GSVA were employed to analyze the proportion of immune cells in UC and AML datasets, as well as to assess the association of specific genes with immune infiltration. The Drug Signatures Database (DSigDB) and Autodock molecular docking identified potential therapeutic small molecules. RESULTS MR analysis revealed a causal association between UC and the onset of AML. Differential expression and WGCNA analyses identified 23 co-driver genes regulated by Signal Transducer and Activator of Transcription 3 (STAT3) and Activating Transcription Factor 4 (AFT4), enriched in immune, inflammatory, and cell proliferation pathways. Tissue Inhibitor of Metalloproteinases 1 (TIMP1) and F2R-Like Trypsin Receptor 1 (F2RL1) were identified as practical diagnostic and prognostic markers for AML, with high TIMP1 and low F2RL1 expression promoting an immunosuppressive and inflammatory tumor microenvironment. Quercetin was identified as a promising candidate for UC-associated AML. CONCLUSIONS UC is a risk factor for AML pathogenesis. TIMP1 and F2RL1 are diagnostic and prognostic markers for UC-associated AML, potentially facilitating AML development through sustained inflammation and an immunosuppressive tumor microenvironment. Quercetin, a potential TIMP1 and F2RL1 inhibitor, may mitigate UC-AML transformation, providing insights into UC management, AML monitoring, and preventive therapy development.
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Affiliation(s)
- Yanqun Zhou
- The Second Clinical Medical School of Guizhou University of Chinese Medicine, No. 83, Feishan Street, Yunyan District, Guiyang, 550003, Guizhou Province, People's Republic of China
- Department of Hematology, The Second Affiliated Hospital of Guizhou University of Chinese Medicine, Guiyang, People's Republic of China
| | - Xiongfeng Zhang
- The Second Clinical Medical School of Guizhou University of Chinese Medicine, No. 83, Feishan Street, Yunyan District, Guiyang, 550003, Guizhou Province, People's Republic of China
- Department of Nephrology, The Second Affiliated Hospital of Guizhou University of Chinese Medicine, Guiyang, People's Republic of China
| | - Shangjin Yin
- The Second Clinical Medical School of Guizhou University of Chinese Medicine, No. 83, Feishan Street, Yunyan District, Guiyang, 550003, Guizhou Province, People's Republic of China
- Department of Hematology, The Second Affiliated Hospital of Guizhou University of Chinese Medicine, Guiyang, People's Republic of China
| | - Yuhong Yao
- The Second Clinical Medical School of Guizhou University of Chinese Medicine, No. 83, Feishan Street, Yunyan District, Guiyang, 550003, Guizhou Province, People's Republic of China
- Department of Hematology, The Second Affiliated Hospital of Guizhou University of Chinese Medicine, Guiyang, People's Republic of China
| | - Tao Chen
- The Second Clinical Medical School of Guizhou University of Chinese Medicine, No. 83, Feishan Street, Yunyan District, Guiyang, 550003, Guizhou Province, People's Republic of China
- Department of Hematology, The Second Affiliated Hospital of Guizhou University of Chinese Medicine, Guiyang, People's Republic of China
| | - Liming Huang
- The Second Clinical Medical School of Guizhou University of Chinese Medicine, No. 83, Feishan Street, Yunyan District, Guiyang, 550003, Guizhou Province, People's Republic of China.
- Department of Hematology, The Second Affiliated Hospital of Guizhou University of Chinese Medicine, Guiyang, People's Republic of China.
| | - Zenghui Liu
- Department of Hematology, The First Affiliated Hospital of Guangzhou University of Traditional Chinese Medicine, No. 16 Jichang Road, Guangzhou, 510405, Guangdong Province, People's Republic of China.
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Kaur G, Tiwari P, Singla S, Panghal A, Jena G. The intervention of NLRP3 inflammasome inhibitor: oridonin against azoxymethane and dextran sulfate sodium-induced colitis-associated colorectal cancer in male BALB/c mice. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025:10.1007/s00210-025-03871-z. [PMID: 40035821 DOI: 10.1007/s00210-025-03871-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 01/31/2025] [Indexed: 03/06/2025]
Abstract
Colorectal cancer (CRC) ranks third globally in cancer diagnoses. The dysregulation of the NLRP3 inflammasome is prominently linked to several types of cancers. Oridonin, a principal component of Rabdosia rubescens, exhibits inhibitory activity against NLRP3 and is well-recognized for its diverse pharmacological benefits. However, its role in an animal model of colitis-associated colorectal cancer (CACC) remains unexplored. In the present study, the effectiveness of oridonin was investigated against CACC, developed using azoxymethane (AOM), a tumour initiator, and dextran sulphate sodium (DSS), a tumour promoter, in male BALB/c mice. The two-stage murine model of inflammation-associated cancer was established by administering AOM (10 mg/kg b.w.; i.p., once) followed by DSS (2% w/v) in drinking water (3 cycles, 7 days/cycle). Over a span of 10 weeks, the dose-dependent (2.5, 5, and 10 mg/kg, b.w.; i.p.) effects of oridonin were investigated in BALB/c mice. Oridonin significantly alleviated CACC severity, as evidenced by reduced DAI scores and restored body weight. Moreover, it attenuated surrogate markers of inflammation, including myeloperoxidase, nitrite, plasma LPS, TNF-α, IL-1β, and DNA damage. Histopathological examination revealed diminished tumorigenesis and apoptotic cells, corroborated by reduced Ki-67 and TNF-α, along with increased p53 expression in the colon. Following oridonin treatment, IHC/immunofluorescence analyses demonstrated a significantly reduced expression of the components of NLRP3 inflammasome including NLRP3, ASC-1, and caspase-1. Notably, the high dose of oridonin (10 mg/kg) consistently exhibited significant protective effects against CACC by modulating various molecular targets. Present findings confirmed the potential of oridonin in the protection of colitis-associated colorectal cancer, providing valuable insights into its mechanism of action and clinical significance.
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Affiliation(s)
- Gurpreet Kaur
- Facility of Risk Assessment and Intervention Studies, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, 160062, India
| | - Priyanka Tiwari
- Facility of Risk Assessment and Intervention Studies, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, 160062, India
| | - Shivani Singla
- Facility of Risk Assessment and Intervention Studies, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, 160062, India
| | - Archna Panghal
- Facility of Risk Assessment and Intervention Studies, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, 160062, India
| | - Gopabandhu Jena
- Facility of Risk Assessment and Intervention Studies, Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, 160062, India.
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Dzhalilova D, Silina M, Kosyreva A, Fokichev N, Makarova O. Morphofunctional changes in the immune system in colitis-associated colorectal cancer in tolerant and susceptible to hypoxia mice. PeerJ 2025; 13:e19024. [PMID: 40028198 PMCID: PMC11869898 DOI: 10.7717/peerj.19024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 01/29/2025] [Indexed: 03/05/2025] Open
Abstract
Background One of the effective strategies for the treatment of tumor diseases, including colitis-associated colorectal cancer (CAC), is immunotherapy. During inflammation, NF-κB is activated, which is connected with the hypoxia-inducible factor-HIF, regulating the immune cells functioning and influences the CAC development. Organisms differ according to their hypoxia resistance and HIF expression. Therefore, the aim of the study was to characterize the thymus, spleen and mesenteric lymph nodes morphofunctional features, as well as changes in the subpopulation composition of peripheral blood cells and mesenteric lymph nodes in tolerant and susceptible to hypoxia C57Bl/6 mice in CAC. Methods Hypoxia tolerance was assessed by gasping time measurement in hypobaric decompression chamber. Based on the outcome, the mice were assigned to three groups characterized as 'tolerant to hypoxia', 'normal', and 'susceptible to hypoxia'. A month after determining hypoxia resistance CAC was modeled by intraperitoneal azoxymethane (AOM) administration and three cycles of dextran sulfate sodium consumption. Mice were sacrificed on the 141st day after the AOM administration, a morphological, morphometric and immunohistochemical study of tumors, morphological and morphometric study of thymus and spleen, and subpopulation composition of peripheral blood cells and mesenteric lymph nodes assessment were carried out. Results Tumors in tolerant and susceptible to hypoxia mice were represented by glandular intraepithelial neoplasia and adenocarcinomas, the area of which was larger in susceptible mice. Immunohistochemical study revealed a more pronounced Ki-67+ staining in tumors of susceptible mice. In CAC, only in tolerant mice, expansion of the thymic cortex was observed relative to the control group, while in susceptible ones, no changes were detected. Only in susceptible to hypoxia mice, spleen germinal centers of lymphoid follicles enlargement were observed. Only in susceptible mice during CAC, in comparison to the control group, the relative and absolute number of B-lymphocytes and relative-cytotoxic T-lymphocytes in blood increased. The relative cytotoxic T-lymphocytes and NK cells number in peripheral blood during CAC was higher in susceptible to hypoxia mice compared to tolerant ones. In susceptible to hypoxia mice, more pronounced changes in the mesenteric lymph nodes subpopulation composition of cells were revealed-only in them the absolute and relative number of B-lymphocytes and NK cells, the absolute number of cytotoxic T-lymphocytes increased, and the relative number of macrophages decreased. Conclusions Morphofunctional differences in the thymus, spleen, mesenteric lymph nodes and blood immune cells reactions indicated the more pronounced immune response to the CAC development in susceptible to hypoxia mice, which should be taken into account in experimental studies.
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Affiliation(s)
- Dzhuliia Dzhalilova
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Centre of Surgery, Moscow, Russia
| | - Maria Silina
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Centre of Surgery, Moscow, Russia
| | - Anna Kosyreva
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Centre of Surgery, Moscow, Russia
- Research Institute of Molecular and Cellular Medicine, People’s Friendship University of Russia (RUDN University), Moscow, Russia
| | - Nikolai Fokichev
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Centre of Surgery, Moscow, Russia
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Olga Makarova
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Centre of Surgery, Moscow, Russia
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Liu YQ, Li ZZ, Han YL, Wang QB. The role of efferocytosis in inflammatory bowel disease. Front Immunol 2025; 16:1524058. [PMID: 40040696 PMCID: PMC11876057 DOI: 10.3389/fimmu.2025.1524058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Accepted: 01/16/2025] [Indexed: 03/06/2025] Open
Abstract
Efferocytosis is the process by which various phagocytes clear apoptotic cells. In recent years, an increasing body of evidence has emphasized the importance of efferocytosis in maintaining internal homeostasis. Intestinal macrophages play a crucial role in modulating intestinal inflammation and promoting tissue repair. Inflammatory bowel disease (IBD) is a chronic, progressive, and relapsing condition, primarily marked by the presence of ulcers in the digestive tract. The exact mechanisms underlying IBD are not yet fully understood, and current treatment approaches mainly aim at repairing the damaged intestinal mucosa and reducing inflammatory responses to ease symptoms.This article provides new perspectives on IBD treatment and clinical management by examining the expression of macrophage efferocytosis-related molecules, the effects of efferocytosis on IBD development, the various roles of macrophage efferocytosis in IBD, and treatment strategies for IBD that focus on efferocytosis.
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Affiliation(s)
- Yi-Qian Liu
- Institute of Acupuncture and Moxibustion, Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Zhan-Zhan Li
- Academy of Traditional Chinese Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yong-Li Han
- Acupuncture Department, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Qing-Bo Wang
- Acupuncture Department, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
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Calcaterra V, Penagini F, Rossi V, Abbattista L, Bianchi A, Turzi M, Cococcioni L, Zuccotti G. Thyroid disorders and inflammatory bowel disease: an association present in adults but also in children and adolescents. Front Endocrinol (Lausanne) 2025; 16:1425241. [PMID: 39968296 PMCID: PMC11832402 DOI: 10.3389/fendo.2025.1425241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 01/13/2025] [Indexed: 02/20/2025] Open
Abstract
Inflammatory bowel diseases (IBD) represent chronic inflammatory multisystemic disorders that primarily involve the gastrointestinal tract. Patients with ulcerative colitis (UC) and Crohn's disease (CD) exhibit a higher prevalence of thyroid disorders compared to the general population. The aim of this review is to summarize the literature on concomitant IBD and thyroid disorders, specifically autoimmune thyroid diseases such as Graves' disease (GD) and Hashimoto's thyroiditis (HT), as well as thyroid cancer, with a focus on children and adolescents. We provide an overview of the age-related differences between children and adults in the prevalence of this association. Literature shows that relatively few studies have been conducted on this subject in pediatric populations. The etiopathogenetic similarities between IBD and autoimmune thyroiditis are undeniable. Nevertheless, current data does not indicate a unanimous association between GD and HT and chronic IBD (both CD and UC). Although evidence suggests a potential association between IBD and thyroid cancer, particularly papillary thyroid cancer, the precise nature of this relationship varies across studies and is influenced by multiple factors. The limited information regarding the relationship between IBD and thyroid disorders in children highlights a significant knowledge gap. Since the thyroid plays a critical role in the pediatric population's development, it is essential to promptly recognize and treat thyroid diseases. A thyroid function monitoring and future research exploring the genetic and immunologic connections are essential to enhance our understanding of the interrelation between IBD and thyroid disorders.
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Affiliation(s)
- Valeria Calcaterra
- Pediatric and Adolescent Unit, Department of Internal Medicine, University of Pavia, Pavia, Italy
- Pediatric Department, Buzzi Children’s Hospital, Milano, Italy
| | | | - Virginia Rossi
- Pediatric Department, Buzzi Children’s Hospital, Milano, Italy
| | | | - Alice Bianchi
- Pediatric Department, Buzzi Children’s Hospital, Milano, Italy
| | | | | | - Gianvincenzo Zuccotti
- Pediatric Department, Buzzi Children’s Hospital, Milano, Italy
- Department of Biomedical and Clinical Science, University of Milan, Milano, Italy
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8
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Lv C, Abdullah M, Su CL, Chen W, Zhou N, Cheng Z, Chen Y, Li M, Simpson KW, Elsaadi A, Zhu Y, Lipkin SM, Chang YF. Genomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients. BMC Genomics 2025; 26:19. [PMID: 39780077 PMCID: PMC11707995 DOI: 10.1186/s12864-024-11198-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 12/30/2024] [Indexed: 01/30/2025] Open
Abstract
The E. coli strains harboring the polyketide synthase (pks) island encode the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involves whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organisms. Fifteen E. coli strains isolated from patients with ulcerative colitis (UC) were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks-positive (pks+) isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158 + 13) pks+ isolates belonged to phylogroup B2, and most of the isolates belong to sequence types ST73 and ST95. One isolate from a UC patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks+ isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the0020preponderance of virulence genes and a reduced number of antimicrobial genes in pks+ isolates. This study significantly contributes to understanding the evolution of pks islands in E. coli.
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Affiliation(s)
- Chao Lv
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mohd Abdullah
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Chun-Li Su
- Graduate Program of Nutrition Science, School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Weiye Chen
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China
| | - Nan Zhou
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China
| | - Zile Cheng
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China
| | - Yiwen Chen
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China
| | - Min Li
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China
| | - Kenneth W Simpson
- Graduate Program of Nutrition Science, School of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Ahmed Elsaadi
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Yongzhang Zhu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention (Chinese Center for Tropical Diseases Research), National Health Commission Key Laboratory of Parasite and Vector Biology, WHO Collaborating Centre for Tropical Diseases, National Center for International Research on Tropical Diseases, Shanghai, 200025, China.
- Sanford and Joan Weill Department of Medicine, Weill Cornell Medical School, Cornell University, New York City, USA.
| | - Steven M Lipkin
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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Cifuentes M, Verdejo HE, Castro PF, Corvalan AH, Ferreccio C, Quest AFG, Kogan MJ, Lavandero S. Low-Grade Chronic Inflammation: a Shared Mechanism for Chronic Diseases. Physiology (Bethesda) 2025; 40:0. [PMID: 39078396 DOI: 10.1152/physiol.00021.2024] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/25/2024] [Accepted: 07/17/2024] [Indexed: 07/31/2024] Open
Abstract
Inflammation is an important physiological response of the organism to restore homeostasis upon pathogenic or damaging stimuli. However, the persistence of the harmful trigger or a deficient resolution of the process can evolve into a state of low-grade, chronic inflammation. This condition is strongly associated with the development of several increasingly prevalent and serious chronic conditions, such as obesity, cancer, and cardiovascular diseases, elevating overall morbidity and mortality worldwide. The current pandemic of chronic diseases underscores the need to address chronic inflammation, its pathogenic mechanisms, and potential preventive measures to limit its current widespread impact. The present review discusses the current knowledge and research gaps regarding the association between low-grade chronic inflammation and chronic diseases, focusing on obesity, cardiovascular diseases, digestive diseases, and cancer. We examine the state of the art in selected aspects of the topic and propose future directions and approaches for the field.
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Affiliation(s)
- Mariana Cifuentes
- Advanced Center for Chronic Diseases (ACCDiS), Facultad Ciencias Quimicas y Farmaceuticas, Facultad Medicina & Instituto de Nutricion y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
- OMEGA Laboratory, Instituto de Nutricion y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Hugo E Verdejo
- Advanced Center for Chronic Diseases (ACCDiS), Facultad Medicina, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Division of Cardiovascular Diseases, Facultad Medicina, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Pablo F Castro
- Advanced Center for Chronic Diseases (ACCDiS), Facultad Medicina, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Division of Cardiovascular Diseases, Facultad Medicina, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Alejandro H Corvalan
- Advanced Center for Chronic Diseases (ACCDiS), Facultad Medicina, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Department of Hematology and Oncology, Facultad Medicina, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Catterina Ferreccio
- Advanced Center for Chronic Diseases (ACCDiS), Facultad Medicina, Pontificia Universidad Catolica de Chile, Santiago, Chile
- Department of Public Health, Facultad Medicina, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Andrew F G Quest
- Advanced Center for Chronic Diseases (ACCDiS), Facultad Ciencias Quimicas y Farmaceuticas, Facultad Medicina & Instituto de Nutricion y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
- Center for Studies on Exercise, Metabolism and Cancer (CEMC), Instituto de Ciencias Biomedicas (ICBM), Facultad Medicina, Universidad de Chile, Santiago, Chile
| | - Marcelo J Kogan
- Advanced Center for Chronic Diseases (ACCDiS), Facultad Ciencias Quimicas y Farmaceuticas, Facultad Medicina & Instituto de Nutricion y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
- Department of Pharmacological & Toxicological Chemistry, Facultad Ciencias Quimicas y Farmaceuticas, Universidad de Chile, Santiago, Chile
| | - Sergio Lavandero
- Advanced Center for Chronic Diseases (ACCDiS), Facultad Ciencias Quimicas y Farmaceuticas, Facultad Medicina & Instituto de Nutricion y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
- Center for Studies on Exercise, Metabolism and Cancer (CEMC), Instituto de Ciencias Biomedicas (ICBM), Facultad Medicina, Universidad de Chile, Santiago, Chile
- Department of Biochemistry & Molecular Biology, Facultad Ciencias Quimicas y Farmaceuticas, Universidad de Chile, Santiago, Chile
- Department of Internal Medicine (Cardiology), University of Texas Southwestern Medical Center, Dallas, Texas, United States
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10
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Ziegler AR, Anderson BM, Latorre R, McQuade RM, Dufour A, Schmidt BL, Bunnett NW, Scott NE, Edgington‐Mitchell LE. N-terminomics profiling of naïve and inflamed murine colon reveals proteolytic signatures of legumain. J Cell Physiol 2025; 240:e31466. [PMID: 39392222 PMCID: PMC11735880 DOI: 10.1002/jcp.31466] [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: 05/23/2024] [Revised: 08/27/2024] [Accepted: 09/30/2024] [Indexed: 10/12/2024]
Abstract
Legumain is a cysteine protease broadly associated with inflammation. It has been reported to cleave and activate protease-activated receptor 2 to provoke pain associated with oral cancer. Outside of gastric and colon cancer, little has been reported on the roles of legumain within the gastrointestinal tract. Using a legumain-selective activity-based probe, LE28, we report that legumain is activated within colonocytes and macrophages of the murine colon, and that it is upregulated in models of acute experimental colitis. We demonstrated that loss of legumain activity in colonocytes, either through pharmacological inhibition or gene deletion, had no impact on epithelial permeability in vitro. Moreover, legumain inhibition or deletion had no obvious impacts on symptoms or histological features associated with dextran sulfate sodium-induced colitis, suggesting its proteolytic activity is dispensable for colitis initiation. To gain insight into potential functions of legumain within the colon, we performed field asymmetric waveform ion mobility spectrometry-facilitated quantitative proteomics and N-terminomics analyses on naïve and inflamed colon tissue from wild-type and legumain-deficient mice. We identified 16 altered cleavage sites with an asparaginyl endopeptidase signature that may be direct substrates of legumain and a further 16 cleavage sites that may be indirectly mediated by legumain. We also analyzed changes in protein abundance and proteolytic events broadly associated with colitis in the gut, which permitted comparison to recent analyses on mucosal biopsies from patients with inflammatory bowel disease. Collectively, these results shed light on potential functions of legumain and highlight its potential roles in the transition from inflammation to colorectal cancer.
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Affiliation(s)
- Alexander R. Ziegler
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - Bethany M. Anderson
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - Rocco Latorre
- Department of Molecular PathobiologyNew York University College of DentistryNew YorkNew YorkUSA
| | - Rachel M. McQuade
- Department of Anatomy and PhysiologyThe University of MelbourneParkvilleVictoriaAustralia
| | - Antoine Dufour
- Department of Physiology and PharmacologyUniversity of CalgaryCalgaryAlbertaCanada
| | - Brian L. Schmidt
- Department of Oral and Maxillofacial SurgeryNew York University College of Dentistry, Bluestone Center for Clinical ResearchNew YorkNew YorkUSA
| | - Nigel W. Bunnett
- Department of Molecular PathobiologyNew York University College of DentistryNew YorkNew YorkUSA
| | - Nichollas E. Scott
- Department of Microbiology and Immunology, Peter Doherty InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - Laura E. Edgington‐Mitchell
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVictoriaAustralia
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11
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Asikaer A, Sun C, Shen Y. Thiostrepton: multifaceted biological activities and its applications in treatment of inflammatory diseases. Inflammopharmacology 2025; 33:183-194. [PMID: 39487942 DOI: 10.1007/s10787-024-01587-9] [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: 08/02/2024] [Accepted: 10/14/2024] [Indexed: 11/04/2024]
Abstract
Thiostrepton (TST) is a naturally occurring oligopeptide antibiotic with a demonstrated capacity to antagonize a broad spectrum of Gram-positive bacteria. It has been utilized as a safe antimicrobial agent in veterinary medicine. Despite its therapeutic potential, the clinical application of TST has been constrained by its poor solubility and bioavailability. However, an increasing number of studies indicate that TST possesses diverse pharmacological activities, including its significant role in microbe resistance and cancer countering. Notably, recent studies have pointed out that TST also possesses anti-inflammatory potential. It has exhibited promising therapeutic efficacy across various in vivo and in vitro disease models, including non-alcoholic fatty liver disease, inflammatory bowel disease, sepsis, psoriasis-like inflammation, and periodontitis. In this review, we describe the various pharmacological activities of TST, particularly its anti-inflammatory activity demonstrated in a variety of inflammatory diseases and the underlying mechanisms. These effects highlight the potential of TST as an anti-inflammatory agent for the treatment of inflammation diseases and for enhancing cellular therapies.
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Affiliation(s)
- Aiminuer Asikaer
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, PR, China
| | - Cai Sun
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, PR, China
| | - Yan Shen
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 405400, PR, China.
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12
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Cui G, Yuan A, Sørbye SW, Florholmen J. Th9 and Th17 Cells in Human Ulcerative Colitis-Associated Dysplastic Lesions. Clin Med Insights Oncol 2024; 18:11795549241301358. [PMID: 39651422 PMCID: PMC11624539 DOI: 10.1177/11795549241301358] [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: 04/11/2024] [Accepted: 11/04/2024] [Indexed: 12/11/2024] Open
Abstract
Background Inflammation is the most important deriving force for the development of colitis-associated colorectal cancer (CAC) through the Inflammation-Pretumor dysplasia-CAC sequence. T helper (Th) subsets Th9 and Th17 cells can potentially stimulate inflammation in the ulcerative colitis (UC). Therefore, Th9 and Th17 cells may play a promoting role in the colitis-associated dysplasia (CAD). Methods Using immunohistochemistry (IHC), we evaluated the presentation patterns and densities of T lymphocytes, Th9 and Th17 cells in human UC and CAD tissues. Results A general increasing trend of CD3-positive T lymphocytes, P.U.1-positive Th9 and interleukin (IL)-17A-positive Th17 cells was illustrated throughout the normal-UC-CAD sequence, IHC images showed that these cells were very prominent in the lamina propria, and some cells were also observed in the epithelium in the CAD tissues. Density analysis revealed that numbers of Th9 and Th17 cells were progressively increased in the CAD tissues as compared with the UC and control tissues. In general, densities of Th9 and Th17 cells in the lamina propria were slightly higher in the non-adenoma-like dysplasia (NALD) tissues than that in the adenoma-like dysplasia (ALD) tissues. However, densities of neither Th9 nor Th17 cells in both the ALD and NALD subgroups were associated with the degree of dysplasia in CAD lesions. Conclusion Accumulated Th9 and Th17 cells contribute to the immune cellular composition in the CAD tissues and may represent the early conditional change for the Dysplasia-CAC transition.
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Affiliation(s)
- Guanglin Cui
- Research Group of Gastrointestinal Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Faculty of Health Science, Nord University, Campus Levanger, Norway
| | - Aping Yuan
- Research Group of Gastrointestinal Diseases, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sveinung W Sørbye
- Department of Pathology, University Hospital of North Norway, University of Tromsø, Tromsø, Norway
| | - Jon Florholmen
- Department of Gastroenterology & Nutrition, University Hospital of North Norway, University of Tromsø, Tromsø, Norway
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13
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Feng Y, Lu J, Jiang J, Wang M, Guo K, Lin S. Berberine: Potential preventive and therapeutic strategies for human colorectal cancer. Cell Biochem Funct 2024; 42:e4033. [PMID: 38742849 DOI: 10.1002/cbf.4033] [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: 02/02/2024] [Revised: 03/28/2024] [Accepted: 04/28/2024] [Indexed: 05/16/2024]
Abstract
Colorectal cancer (CRC) is a common digestive tract tumor, with incidences continuing to rise. Although modern medicine has extended the survival time of CRC patients, its adverse effects and the financial burden cannot be ignored. CRC is a multi-step process and can be caused by the disturbance of gut microbiome and chronic inflammation's stimulation. Additionally, the presence of precancerous lesions is also a risk factor for CRC. Consequently, scientists are increasingly interested in identifying multi-target, safe, and economical herbal medicine and natural products. This paper summarizes berberine's (BBR) regulatory mechanisms in the occurrence and development of CRC. The findings indicate that BBR regulates gut microbiome homeostasis and controls mucosal inflammation to prevent CRC. In the CRC stage, BBR inhibits cell proliferation, invasion, and metastasis, blocks the cell cycle, induces cell apoptosis, regulates cell metabolism, inhibits angiogenesis, and enhances chemosensitivity. BBR plays a role in the overall management of CRC. Therefore, using BBR as an adjunct to CRC prevention and treatment could become a future trend in oncology.
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Affiliation(s)
- Yuqian Feng
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jiamin Lu
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Jing Jiang
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Menglei Wang
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China
| | - Kaibo Guo
- Department of Oncology, Hangzhou First People's Hospital, Hangzhou, Zhejiang, China
| | - Shengyou Lin
- Department of Oncology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang, China
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