Uncovering Microbial Composition in Human Breast Cancer Primary Tumour Tissue Using Transcriptomic RNA-seq.

Dominik Hadzega,Juraj Benca,Gabriel Minarik,Tatiana Sedlackova,Daniel Pindak,Martin Bohac,Marian Karaba,Sona Ciernikova,Sona Ciernikova,Michal Mego,Petra Nemcova,Katarina Kalavska,Lubos Klucar

doi:10.3390/ijms22169058

Abstract

Recent research studies are showing breast tissues as a place where various species of microorganisms can thrive and cannot be considered sterile, as previously thought. We analysed the microbial composition of primary tumour tissue and normal breast tissue and found differences between them and between multiple breast cancer phenotypes. We sequenced the transcriptome of breast tumours and normal tissues (from cancer-free women) of 23 individuals from Slovakia and used bioinformatics tools to uncover differences in the microbial composition of tissues. To analyse our RNA-seq data (rRNA depleted), we used and tested Kraken2 and Metaphlan3 tools. Kraken2 has shown higher reliability for our data. Additionally, we analysed 91 samples obtained from SRA database, originated in China and submitted by Sichuan University. In breast tissue, the most enriched group were Proteobacteria, then Firmicutes and Actinobacteria for both datasets, in Slovak samples also Bacteroides, while in Chinese samples Cyanobacteria were more frequent. We have observed changes in the microbiome between cancerous and healthy tissues and also different phenotypes of diseases, based on the presence of circulating tumour cells and few other markers.

Highlights

Data were acquired from primary breast tumours and normal breast tissue, which were collected from donors from Slovakia
The second dataset, that we used, RNA-seq data originated from primary breast tumour and normal breast tissue collected from donors in China, was acquired from SRA database (SRA study PRJNA553096)
In contrast to many taxa abundant in normal tissue, we identified just a few candioverrepresented in breast cancer (BC)

Summary

Introduction

In recent years it was found that various organisms are inhabiting different parts of the human body. Other forms of life and viruses [1]. It has been estimated that our body harbours 10 times more microbes than our own cells [2]. It was predicted, that 500–1000 species of bacteria possibly thrive in our body at any one time [3]. Bacteria, fungi and viruses have been found in many different places, in breast tissue or breast tumour tissue [4,5]

Methods

Results

Discussion

Conclusion