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Zhu X, Xu P, Zhu R, Gao W, Yin W, Lan P, Zhu L, Jiao N. Multi-kingdom microbial signatures in excess body weight colorectal cancer based on global metagenomic analysis. Commun Biol 2024; 7:24. [PMID: 38182885 PMCID: PMC10770074 DOI: 10.1038/s42003-023-05714-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/15/2023] [Indexed: 01/07/2024] Open
Abstract
Excess body weight (EBW) increases the risk of colorectal cancer (CRC) and is linked to lower colonoscopy compliance. Here, we extensively analyzed 981 metagenome samples from multiple cohorts to pinpoint the specific microbial signatures and their potential capability distinguishing EBW patients with CRC. The gut microbiome displayed considerable variations between EBW and lean CRC. We identify 44 and 37 distinct multi-kingdom microbial species differentiating CRC and controls in EBW and lean populations, respectively. Unique bacterial-fungal associations are also observed between EBW-CRC and lean-CRC. Our analysis revealed specific microbial functions in EBW-CRC, including D-Arginine and D-ornithine metabolism, and lipopolysaccharide biosynthesis. The best-performing classifier for EBW-CRC, comprising 12 bacterial and three fungal species, achieved an AUROC of 0.90, which was robustly validated across three independent cohorts (AUROC = 0.96, 0.94, and 0.80). Pathogenic microbial species, Anaerobutyricum hallii, Clostridioides difficile and Fusobacterium nucleatum, are EBW-CRC specific signatures. This work unearths the specific multi-kingdom microbial signatures for EBW-CRC and lean CRC, which may contribute to precision diagnosis and treatment of CRC.
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Affiliation(s)
- Xinyue Zhu
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, PR China
| | - Pingping Xu
- Department of Colorectal Surgery, Zhongshan Hospital, Fudan University, Shanghai, PR China
| | - Ruixin Zhu
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, PR China.
| | - Wenxing Gao
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, PR China
| | - Wenjing Yin
- Putuo People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, PR China
| | - Ping Lan
- Guangdong Institute of Gastroenterology; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases; Biomedical Innovation Center, Sun Yat-Sen University, Guangzhou, PR China
- Department of General Surgery, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, PR China
| | - Lixin Zhu
- Guangdong Institute of Gastroenterology; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases; Biomedical Innovation Center, Sun Yat-Sen University, Guangzhou, PR China.
- Department of General Surgery, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, PR China.
| | - Na Jiao
- National Clinical Research Center for Child Health, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, PR China.
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Gao W, Gao X, Zhu L, Gao S, Sun R, Feng Z, Wu D, Liu Z, Zhu R, Jiao N. Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer. Gut Microbes 2023; 15:2245562. [PMID: 37635357 PMCID: PMC10464540 DOI: 10.1080/19490976.2023.2245562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
Microbial signatures show remarkable potentials in predicting colorectal cancer (CRC). This study aimed to evaluate the diagnostic powers of multimodal microbial signatures, multi-kingdom species, genes, and single-nucleotide variants (SNVs) for detecting precancerous adenomas. We performed cross-cohort analyses on whole metagenome sequencing data of 750 samples via xMarkerFinder to identify adenoma-associated microbial multimodal signatures. Our data revealed that fungal species outperformed species from other kingdoms with an area under the ROC curve (AUC) of 0.71 in distinguishing adenomas from controls. The microbial SNVs, including dark SNVs with synonymous mutations, displayed the strongest diagnostic capability with an AUC value of 0.89, sensitivity of 0.79, specificity of 0.85, and Matthews correlation coefficient (MCC) of 0.74. SNV biomarkers also exhibited outstanding performances in three independent validation cohorts (AUCs = 0.83, 0.82, 0.76; sensitivity = 1.0, 0.72, 0.93; specificity = 0.67, 0.81, 0.67, MCCs = 0.69, 0.83, 0.72) with high disease specificity for adenoma. In further support of the above results, functional analyses revealed more frequent inter-kingdom associations between bacteria and fungi, and abnormalities in quorum sensing, purine and butanoate metabolism in adenoma, which were validated in a newly recruited cohort via qRT-PCR. Therefore, these data extend our understanding of adenoma-associated multimodal alterations in the gut microbiome and provide a rationale of microbial SNVs for the early detection of CRC.
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Affiliation(s)
- Wenxing Gao
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Xiang Gao
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Lixin Zhu
- Guangdong Institute of Gastroenterology; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases; Biomedical Innovation Center, Sun Yat-Sen University, Guangzhou, P. R. China
- Department of General Surgery, The Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, P. R. China
| | - Sheng Gao
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Ruicong Sun
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Zhongsheng Feng
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
| | - Dingfeng Wu
- National Clinical Research Center for Child Health, the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China
| | - Zhanju Liu
- Center for IBD Research, Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, P. R. China
| | - Ruixin Zhu
- Department of Gastroenterology, the Shanghai Tenth People’s Hospital, School of Medicine, School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
- Research Institute, GloriousMed Clinical Laboratory Co, Ltd, Shanghai, P. R. China
| | - Na Jiao
- National Clinical Research Center for Child Health, the Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, P. R. China
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Fu W, Xu L, Chen Z, Kan L, Ma Y, Qian H, Wang W. Recent advances on emerging nanomaterials for diagnosis and treatment of inflammatory bowel disease. J Control Release 2023; 363:149-179. [PMID: 37741461 DOI: 10.1016/j.jconrel.2023.09.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
Inflammatory bowel disease (IBD) is a chronic idiopathic inflammatory disorder that affects the entire gastrointestinal tract and is associated with an increased risk of colorectal cancer. Mainstream clinical testing methods are time-consuming, painful for patients, and insufficiently sensitive to detect early symptoms. Currently, there is no definitive cure for IBD, and frequent doses of medications with potentially severe side effects may affect patient response. In recent years, nanomaterials have demonstrated considerable potential for IBD management due to their diverse structures, composition, and physical and chemical properties. In this review, we provide an overview of the advances in nanomaterial-based diagnosis and treatment of IBD in recent five years. Multi-functional bio-nano platforms, including contrast agents, near-infrared (NIR) fluorescent probes, and bioactive substance detection agents have been developed for IBD diagnosis. Based on a series of pathogenic characteristics of IBD, the therapeutic strategies of antioxidant, anti-inflammatory, and intestinal microbiome regulation of IBD based on nanomaterials are systematically introduced. Finally, the future challenges and prospects in this field are presented to facilitate the development of diagnosis and treatment of IBD.
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Affiliation(s)
- Wanyue Fu
- School of Biomedical Engineering, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei 230032, PR China; Anhui Engineering Research Center for Medical Micro-Nano Devices, Hefei, Anhui 230012, China
| | - Lingling Xu
- School of Biomedical Engineering, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei 230032, PR China; Anhui Engineering Research Center for Medical Micro-Nano Devices, Hefei, Anhui 230012, China
| | - Zetong Chen
- School of Stomatology, Anhui Medical University, Hefei, Anhui 230032, PR China
| | - Lingling Kan
- School of Biomedical Engineering, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei 230032, PR China; Anhui Engineering Research Center for Medical Micro-Nano Devices, Hefei, Anhui 230012, China
| | - Yan Ma
- School of Biomedical Engineering, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei 230032, PR China; Anhui Engineering Research Center for Medical Micro-Nano Devices, Hefei, Anhui 230012, China.
| | - Haisheng Qian
- School of Biomedical Engineering, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei 230032, PR China; Anhui Engineering Research Center for Medical Micro-Nano Devices, Hefei, Anhui 230012, China.
| | - Wanni Wang
- School of Biomedical Engineering, Anhui Provincial Institute of Translational Medicine, Anhui Medical University, Hefei 230032, PR China; Anhui Engineering Research Center for Medical Micro-Nano Devices, Hefei, Anhui 230012, China.
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Jiao N, Ke X, Zhu L, Zhu R. Evidence challenging the causal role of gut microbiota in inflammatory bowel diseases. Gastroenterol Rep (Oxf) 2023; 11:goad064. [PMID: 37842202 PMCID: PMC10568522 DOI: 10.1093/gastro/goad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 09/21/2023] [Indexed: 10/17/2023] Open
Affiliation(s)
- Na Jiao
- Department of Nephrology, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang, P. R. China
| | - Xiao Ke
- The Second People's Hospital Affiliated to Fujian University of Chinese Medicine; Fujian Clinical Medical Research Centre of Chinese Medicine for Spleen and Stomach, Fuzhou, Fujian, P.R. China
| | - Lixin Zhu
- Department of General Surgery (Colorectal Surgery), Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology; Biomedical Innovation Center; The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P. R. China
| | - Ruixin Zhu
- Department of Gastroenterology, the Shanghai Tenth People's Hospital, School of Medicine; School of Life Sciences and Technology, Tongji University, Shanghai, P. R. China
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