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Cao Y, Wang J, Hou W, Ding Y, Zhu Y, Zheng J, Huang Q, Cao Z, Xie R, Wei Q, Qin H. Colorectal cancer-associated T cell receptor repertoire abnormalities are linked to gut microbiome shifts and somatic cell mutations. Gut Microbes 2023; 15:2263934. [PMID: 37795995 PMCID: PMC10557533 DOI: 10.1080/19490976.2023.2263934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/24/2023] [Indexed: 10/06/2023] Open
Abstract
As with many diseases, tumor formation in colorectal cancer (CRC) is multifactorial and involves immune, environmental factors and various genetics that contribute to disease development. Accumulating evidence suggests that the gut microbiome is linked to the occurrence and development of CRC, and these microorganisms are important for immune maturation. However, a systematic perspective integrating microbial profiling, T cell receptor (TCR) and somatic mutations in humans with CRC is lacking. Here, we report distinct features of the expressed TCRβ repertoires in the peripheral blood of and CRC patients (n = 107) and healthy donors (n = 30). CRC patients have elevated numbers of large TCRβ clones and they have very low TCR diversity. The metagenomic sequencing data showed that the relative abundance of Fusobacterium nucleatum (F. nucleatum), Escherichia coli and Dasheen mosaic virus were elevated consistently in CRC patients (n = 97) compared to HC individuals (n = 30). The abundance of Faecalibacterium prausnitzii and Roseburia intestinalis was reduced in CRC (n = 97) compared to HC (n = 30). The correlation between somatic mutations of target genes (16 genes, n = 79) and TCR clonality and microbial biomarkers in CRC had been investigated. Importantly, we constructed a random forest classifier (contains 15 features) based on microbiome and TCR repertoires, which can be used as a clinical detection method to screen patients for CRC. We also analysis of F. nucleatum-specific TCR repertoire characteristics. Collectively, our large-cohort multi-omics data aimed to identify novel biomarkers to inform clinical decision-making in the detection and diagnosis of CRC, which is of possible etiological and diagnostic significance.
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Affiliation(s)
- Yuan Cao
- Department of Pathology, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Jifeng Wang
- Department of Pathology, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Weiliang Hou
- Research Institute of Intestinal Diseases, Tongji University School of Medicine, Shanghai, China
| | - Yanqiang Ding
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yefei Zhu
- Research Institute of Intestinal Diseases, Tongji University School of Medicine, Shanghai, China
| | - Jiayi Zheng
- Department of Pathology, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Qiongyi Huang
- Department of Pathology, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Zhan Cao
- Shanghai Institution of Gut Microbiota Research and Engineering Development, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Ruting Xie
- Department of Pathology, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Qing Wei
- Department of Pathology, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
| | - Huanlong Qin
- Department of Gastrointestinal Surgery, Shanghai Tenth People’s Hospital Affiliated to Tongji University, Shanghai, China
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Kidanemariam DB, Sukal AC, Abraham AD, Njuguna JN, Stomeo F, Dale JL, James AP, Harding RM. Incidence of RNA viruses infecting taro and tannia in East Africa and molecular characterisation of dasheen mosaic virus isolates. THE ANNALS OF APPLIED BIOLOGY 2022; 180:211-223. [PMID: 35873878 PMCID: PMC9293211 DOI: 10.1111/aab.12725] [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: 09/18/2018] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 06/15/2023]
Abstract
Taro (Colocasia esculenta) and tannia (Xanthosoma sp.) plants growing in 25 districts across Ethiopia, Kenya, Tanzania and Uganda were surveyed for four RNA viruses. Leaf samples from 392 plants were tested for cucumber mosaic virus (CMV), dasheen mosaic virus (DsMV), taro vein chlorosis virus (TaVCV) and Colocasia bobone disease-associated virus (CBDaV) by RT-PCR. No samples tested positive for TaVCV or CBDaV, while CMV was only detected in three tannia samples with mosaic symptoms from Uganda. DsMV was detected in 40 samples, including 36 out of 171 from Ethiopia, one out of 94 from Uganda and three out of 41 from Tanzania, while none of the 86 samples from Kenya tested positive for any of the four viruses. The complete genomes of nine DsMV isolates from East Africa were cloned and sequenced. Phylogenetic analyses based on the amino acid sequence of the DsMV CP-coding region revealed two distinct clades. Isolates from Ethiopia were distributed in both clades, while samples from Uganda and Tanzania belong to different clades. Seven possible recombination events were identified from the analysis carried out on the available 15 full-length DsMV isolates. Nucleotide substitution ratio analysis revealed that all the DsMV genes are under strong negative selection pressure.
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Affiliation(s)
- Dawit B. Kidanemariam
- Centre for Agriculture and the BioeconomyQueensland University of TechnologyBrisbaneQueenslandAustralia
- National Agricultural Biotechnology Research CentreEthiopian Institute of Agricultural ResearchAddis AbabaEthiopia
| | - Amit C. Sukal
- Centre for Agriculture and the BioeconomyQueensland University of TechnologyBrisbaneQueenslandAustralia
- Centre for Pacific Crops and Trees (CePaCT), Land Resources Division (LRD), Pacific Community (SPC)SuvaFiji
| | - Adane D. Abraham
- Department of Biological Sciences and BiotechnologyBotswana International University of Science and TechnologyPalapyeBotswana
| | - Joyce N. Njuguna
- Biosciences Eastern and Central AfricaInternational Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - Francesca Stomeo
- Biosciences Eastern and Central AfricaInternational Livestock Research Institute (BecA‐ILRI) HubNairobiKenya
| | - James L. Dale
- Centre for Agriculture and the BioeconomyQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Anthony P. James
- Centre for Agriculture and the BioeconomyQueensland University of TechnologyBrisbaneQueenslandAustralia
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology ‐ HellasHeraklionGreece
| | - Robert M. Harding
- Centre for Agriculture and the BioeconomyQueensland University of TechnologyBrisbaneQueenslandAustralia
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