Analysis of microbial changes in the tonsillar formalin-fixed paraffin-embedded tissue of Chinese patients with IgA nephropathy

Zhu, Anchao; Yang, Xinxin; Bai, Lijing; Hou, Yunjing; Guo, Chenxu; Zhao, Di; Wen, Meina; Jiang, Ping; Liu, Yuyan; Huang, Ying; Li, Chen; Meng, Hongxue

doi:10.1016/j.prp.2020.153174

Cited by 7 publications

(6 citation statements)

References 47 publications

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“…Thus, FFPE samples represent the largest collection of patient material and are currently recognized as a viable source material for bacterial analysis. ( 11 , 36 )…”

Section: Discussionmentioning

confidence: 99%

“…Thus, FFPE samples represent the largest collection of patient material and are currently recognized as a viable source material for bacterial analysis. (11,36) The microbiota can exert regulatory effects in other sites beyond the gut. In this study, we have characterized for the first time the tumor microbiome of FFPE samples from patients with PLC with different prognoses and different histopathological subtypes by using 16S rRNA MiSeq sequencing.…”

Section: Discussionmentioning

confidence: 99%

“…( 7 ) The technique of 16S ribosomal RNA (rRNA) sequencing was found to be more powerful and extensive for the detection of bacteria in FFPE tissue and also relatively economical and practical. ( 8 ) In addition, for 16S rRNA sequence analysis of FFPE tissue flora, reports have been published on gut, ( 9 ) endocarditis, ( 10 ) tonsillar tissue, ( 11 ) and cystic neutrophilic granulomatous mastitis. ( 12 ) To this end, we investigated the intratumoral microbiome on FFPE tissue samples of patients with PLC by 16S rRNA MiSeq sequencing.…”

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confidence: 99%

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Intratumoral Microbiome of Human Primary Liver Cancer

Wang

Xia

et al. 2022

Hepatol Commun

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Primary liver tumors (PLCs) and liver metastasis currently represent the leading cause of cancer‐related deaths worldwide due to poor outcomes, high incidence, and postsurgical recurrence. Hence, novel diagnostic markers and therapeutic strategies for PLCs are urgently needed. The human microbiome can directly or indirectly impact cancer initiation, progression, and response to therapy, including cancer immunotherapy; however, the roles of the microbiota in the tumor microenvironment are not clear and require more investigation. Here, we investigated intratumoral microbial community profiling on formalin‐fixed paraffin‐embedded tissue samples of patients with PLC by 16S ribosomal RNA using the MiSeq platform. We characterized the microbial communities in different histopathological subtypes and in the different prognoses of patients with PLC. The study revealed microbial population differences not only in carcinoma tissue and the matched adjacent nontumor tissue but in different histopathological subtypes, even in patients with PLC with different prognoses. Interestingly, the abundance of certain bacteria that have antitumor effects at family and genus level, such as Pseudomonadaceae , decreased in tumor tissue and was linearly associated with prognosis of patients with PLC. Conclusion: We provide a potential novel diagnostic biomarker and therapeutic strategy for early clinical diagnosis and treatment of PLC.

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“…Thus, FFPE samples represent the largest collection of patient material and are currently recognized as a viable source material for bacterial analysis. ( 11 , 36 )…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Intratumoral Microbiome of Human Primary Liver Cancer

Wang

Xia

et al. 2022

Hepatol Commun

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“…Paraffin samples can also be well used to conveniently detect the expression of specific proteins in disease states, such as p16 expression analysis by immunohistochemistry. Some researchers have studied the changes of microorganisms in tumors [ 11 , 19 ] or other diseases (e.g., IgA nephropathy [ 23 ]) by paraffin tissue.…”

Section: Introductionmentioning

confidence: 99%

Using formalin fixed paraffin embedded tissue to characterize the microbiota in p16-positive and p16-negative tongue squamous cell carcinoma: a pilot study

Yuanbo,

Tianyi,

Xuejing

et al. 2024

BMC Oral Health

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Background Tongue squamous cell carcinoma (TSCC) is the most common oral cavity cancer, and p16 immunohistochemistry is an exact and available tool in the prognostic and predictive characterization of squamous cell cancers in the head and neck. Microorganisms have a close relationship with the development of TSCC. However, the association between oral bacteria and p16 status has not been well defined in the case of TSCC. Compared with traditional clinical microbial collection methods, formalin-fixed paraffin-embedded (FFPE) tissue samples have several advantages. Methods To compare the microbiota compositions between p16-positive and p16-negative patients with TSCC, we performed a small pilot study of microbiological studies of TSCC by paraffin tissue. DNA from FFPE tissue blocks were extracted and microbiomes were profiled by sequencing the 16 S-rRNA-encoding gene (V1–V2/V3-V4/V4 regions). Alterations in the functional potential of the microbiome were predicted using PICRUSt, Tax4Fun, and BugBase. Results A total of 60 patients with TSCC were enrolled in the study, however, some challenges associated with DNA damage in FFPE tissues existed, and only 27 (15 p16-positive and 12 p16-negative) passed DNA quality control. Nevertheless, we have tentatively found some meaningful results. The p16 status is associated with microbiota diversity, which is significantly increased in p16-positive patients compared with p16-negative patients. Desulfobacteria, Limnochordia, Phycisphaerae, Anaerolineae, Saccharimonadia and Kapabacteria had higher abundances among participants with p16-positive. Moreover, functional prediction revealed that the increase of these bacteria may enhance viral carcinogenesis in p16-positive TSCC. Conclusions Bacterial profiles showed a significant difference between p16-positive TSCC and p16-negative TSCC. These findings may provide insights into the relationship between p16 status and the microbial taxa in TSCC, and these bacteria may provide new clues for developing therapeutic targets for TSCC.

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“…It is well known that upper respiratory tract infections often worsen IgAN, particularly acute tonsils. IgAN is thought to be a tonsillion-related disease caused by a breakdown in the immune tolerance of the resident bacteria in the tonsil ( 7 ), and several bacterial species have been reported as antigens in the pathogenesis of IgAN ( 8 – 10 ). Bacteria involved in chronic oral infections may be pathogenic candidates.…”

Section: Introductionmentioning

confidence: 99%

Transcriptomic analysis reveals the potential crosstalk genes and immune relationship between IgA nephropathy and periodontitis

et al. 2023

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BackgroundIt is well known that periodontitis has an important impact on systemic diseases. The aim of this study was to investigate potential crosstalk genes, pathways and immune cells between periodontitis and IgA nephropathy (IgAN).MethodsWe downloaded periodontitis and IgAN data from the Gene Expression Omnibus (GEO) database. Differential expression analysis and weighted gene co-expression network analysis (WGCNA) were used to identify shared genes. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on the shared genes. Hub genes were further screened using least absolute shrinkage and selection operator (LASSO) regression, and a receiver operating characteristic (ROC) curve was drawn according to the screening results. Finally, single-sample GSEA (ssGSEA) was used to analyze the infiltration level of 28 immune cells in the expression profile and its relationship with shared hub genes.ResultsBy taking the intersection of WGCNA important module genes and DEGs, we found that the SPAG4, CCDC69, KRT10, CXCL12, HPGD, CLDN20 and CCL187 genes were the most important cross-talk genes between periodontitis and IgAN. GO analysis showed that the shard genes were most significantly enriched in kinase regulator activity. The LASSO analysis results showed that two overlapping genes (CCDC69 and CXCL12) were the optimal shared diagnostic biomarkers for periodontitis and IgAN. The immune infiltration results revealed that T cells and B cells play an important role in the pathogenesis of periodontitis and IgAN.ConclusionThis study is the first to use bioinformatics tools to explore the close genetic relationship between periodontitis and IgAN. The SPAG4, CCDC69, KRT10, CXCL12, HPGD, CLDN20 and CCL187 genes were the most important cross-talk genes between periodontitis and IgAN. T-cell and B-cell-driven immune responses may play an important role in the association between periodontitis and IgAN.

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Analysis of microbial changes in the tonsillar formalin-fixed paraffin-embedded tissue of Chinese patients with IgA nephropathy

Cited by 7 publications

References 47 publications

Intratumoral Microbiome of Human Primary Liver Cancer

Intratumoral Microbiome of Human Primary Liver Cancer

Using formalin fixed paraffin embedded tissue to characterize the microbiota in p16-positive and p16-negative tongue squamous cell carcinoma: a pilot study

Transcriptomic analysis reveals the potential crosstalk genes and immune relationship between IgA nephropathy and periodontitis

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