Tumor Tissue-Specific Bacterial Biomarker Panel for Colorectal Cancer: Bacteroides Massiliensis, Alistipes Species, Alistipes Onderdonkii, Bifidobacterium Pseudocatenulatum, Corynebacterium Appendicis

Abstract Human microbiome studies have shown diversity to exist among different ethnic populations. However, studies pertaining to the microbial composition of CRC among the Indian population have not been well explored. We aimed to decipher the microbial signature in tumor tissues from North Indian CRC patients. Next-generation sequencing of tumor and adjacent tissue derived bacterial 16s rRNA V3-V4 hypevariable regions was performed to investigate the abundance of specific microbes. The expression profile analysis deciphered a decreased diversity among the tumor-associated microbial communities, and at the phyla level, Proteobacteria was differentially expressed in CRC tissues than adjacent normal. Further, DESeq2 normalization identified 4 out of 79 distinct species (p<0.005) only in CRC, Bacteroides massiliensis, Alistipes onderdonkii, Bifidobacterium pseudocatenulatum, and Corynebacterium appendicis. Thus, our findings suggest the use of these microbial signatures as putative biomarkers that can distinguish CRC tissues from their adjacent normal, which may shed light on the pathogenesis of CRC.

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Circulating 16S RNA in Biofluids: Extracellular Vesicles as Mirrors of Human Microbiome?

International Journal of Molecular Sciences ◽

10.3390/ijms21238959 ◽

2020 ◽

Vol 21 (23) ◽

pp. 8959

Author(s):

Veronica Ricci ◽

Davide Carcione ◽

Simone Messina ◽

Gualtiero I. Colombo ◽

Yuri D’Alessandra

Keyword(s):

Extracellular Vesicles ◽

Human Body ◽

Human Microbiome ◽

Microbial Composition ◽

Gold Standard Method ◽

Rna Molecules ◽

Detection And Identification ◽

16S Rna ◽

Principal Tool ◽

Generation Sequencing

The human body is inhabited by around 1013 microbes composing a multicomplex system, termed microbiota, which is strongly involved in the regulation and maintenance of homeostasis. Perturbations in microbiota composition can lead to dysbiosis, which has been associated with several human pathologies. The gold-standard method to explore microbial composition is next-generation sequencing, which involves the analysis of 16S rRNA, an indicator of the presence of specific microorganisms and the principal tool used in bacterial taxonomic classification. Indeed, the development of 16S RNA sequencing allows us to explore microbial composition in several environments and human body districts and fluids, since it has been detected in “germ-free” environments such as blood, plasma, and urine of diseased and healthy subjects. Recently, prokaryotes showed to generate extracellular vesicles, which are known to be responsible for shuttling different intracellular components such as proteins and nucleic acids (including 16S molecules) by protecting their cargo from degradation. These vesicles can be found in several human biofluids and can be exploited as tools for bacterial detection and identification. In this review, we examine the complex link between circulating 16S RNA molecules and bacteria-derived vesicles.

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Expression profile analysis of long noncoding RNA in HER-2-enriched subtype breast cancer by next-generation sequencing and bioinformatics

OncoTargets and Therapy ◽

10.2147/ott.s97664 ◽

2016 ◽

pp. 761 ◽

Cited By ~ 42

Author(s):

Fan Yang ◽

Shixu Lyu ◽

Siyang Dong ◽

Yehuan Liu ◽

Ouchen Wang ◽

...

Keyword(s):

Breast Cancer ◽

Next Generation Sequencing ◽

Expression Profile ◽

Long Noncoding Rna ◽

Noncoding Rna ◽

Profile Analysis ◽

Next Generation ◽

Expression Profile Analysis ◽

Her 2 ◽

Generation Sequencing

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Expression profile analysis of long non-coding RNA associated with vincristine resistance in colon cancer cells by next-generation sequencing

Gene ◽

10.1016/j.gene.2015.06.087 ◽

2015 ◽

Vol 572 (1) ◽

pp. 79-86 ◽

Cited By ~ 26

Author(s):

Qiu-Li Sun ◽

Chun-Peng Zhao ◽

Tian-Yun Wang ◽

Xiao-Bo Hao ◽

Xiao-Yin Wang ◽

...

Keyword(s):

Colon Cancer ◽

Next Generation Sequencing ◽

Cancer Cells ◽

Expression Profile ◽

Profile Analysis ◽

Colon Cancer Cells ◽

Expression Profile Analysis ◽

Non Coding Rna ◽

Long Non Coding Rna ◽

Generation Sequencing

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DEPDC1/ EEF1A1 complex promotes the progression of human osteosarcoma via downregulation of FOXO3a

10.1101/2021.04.14.439766 ◽

2021 ◽

Author(s):

Lin Shen ◽

Han Li ◽

Aijun Zhang ◽

Ronghan Liu ◽

Chendan Zhou ◽

...

Keyword(s):

Tumor Metastasis ◽

Profile Analysis ◽

Osteosarcoma Cell ◽

Osteosarcoma Cells ◽

Critical Pathway ◽

Human Osteosarcoma ◽

Expression Profile Analysis ◽

Tumor Tissues ◽

Human Osteosarcoma Cells ◽

Patient Survival Rate

This study deciphers a potentially critical interplay of DEPDC1-EEF1A1-FOXO3a axis during the osteosarcoma progression. Bioinformatics analysis of documented 25,035 genes for differentially expressed genes were accompanied by transcriptional and translational examinations of clinical osteosarcoma specimens and osteosarcoma cell lines to assess the roles and interactions of DEPDC1, EEF1A1, and FOXO3a in the tumor cells proliferation and prognosis. Gene expression profile analysis and clinical tests revealed highly expressed DEPDC1 in human osteosarcoma cells and tumor tissues. Vector-mediated silence of DEPDC1 resulted in halted osteosarcoma cell proliferation, promoted apoptosis, and ceased tumor metastasis. Immunoprecipitation assay confirmed that EEF1A1 directly bind to DEPDC1 protein through three binding regions. Further, DEPDC1/EEF1A1 complex significantly decreased the expression of FOXO3a at transcription and translation levels, which subsequently promoted the proliferation of osteosarcoma cells and tumor metastasis. Correlation studies exhibited that overexpression of DEPDC1/EEF1A1 complex in the clinical specimens negatively correlated with the patient survival rate. In conclusion, DEPDC1-EEF1A1-FOXO3a axis plays as a critical pathway that regulates the progression and prognosis of osteosarcoma.

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