Abstract P5-06-04: A multi-omics approach to study the host-microbiota interaction in breast cancer tissue
Authors: Francesca Pirini, Tania Rossi, Soulaimane Aboulouard, Bruno Fosso, Maurizio Puccetti, Sara Ravaioli, Maria Maddalena Tumedei, Michela Cortesi, Michele Zanoni, Luca Magnani, Giovanni Martinelli, Michel Salzet, Sara Bravaccini
Journal: Cancer Research (2022)

Abstract The microbiota is considered a component of the tumor microenvironment (TME) but its functional role is still not completely clear. In this study, we use both meta-proteomic/transcriptomic and metabarcoding approaches to investigate the composition and the role of microbiota-derived proteins in breast cancer (BC) and microbial diversity, respectively. Three tumoral regions (peripheral tumor, tumor core, in situ carcinoma) and 2 healthy regions (intra-tumoral fibrosis, healthy tissue) were selected on 12 formalin-fixed, paraffin-embedded (FFPE) BC samples. Ten µm tissue slides were used for DNA/RNA extraction and proteomics. The proteomic analysis was performed by nanoLC-MS/MS analysis and data analysis by Perseus and Maxquant, transcriptomic by NEBNext Ultra II Library Prep kit for Illumina and analyzed by Kraken2. Metabarcoding was performed by Ion 16S metagenomics kit for Ion s5 and analyzed by extracting the reads covering the V4 hypervariable region, denoising them with DADA2 and finally taxonomically annotating the obtained ASVs in BioMaS. The proteomic analysis of the 5 areas identified 29 bacterial proteins: 13 chaperonins, 7 ATP synthase subunits, 7 metabolic enzymes, 2 elongation factors. Most of the proteins (16) were located in the intra-tumoral fibrosis. A Glyceraldehyde-3-phosphate dehydrogenase (gapA) and three Chaperone proteins DnaK were overexpressed in the tumor compared to the healthy tissue. Only one of the 4 proteins (DnaK ID:B8IHL3) was associated with a single species: Methylobacterium nodulans. In order to narrow the number of possible species to which the other 3 proteins belong, we have compared the proteomic results with the taxonomic results obtained by metatranscriptomic. The remaining two DnaKs possibly belong to Methylobacterium sp4-46 and Clavibacter michiganensis, while the gapA to Escherichia coli. Overall the investigation based on the V4 hypervariable region of the 16S rRNA gene allowed to highlight a higher alpha diversity in tumor samples than in the healthy ones. In conclusion, the meta-proteomic investigation highlighted the overexpression in tumor tissues of DnaKs, bacterial chaperones able to interfere with important pathways related to DNA damage control/repair and cell-cycle/apoptosis and supposed to promote cancer, and gapA, which plays an important role in multiple cellular functions including metabolism and gene transcription. The most recurrent genera is Methylobacterium which had previously been found as more abundant in BC tissues than healthy tissues. We hypothesize that bacteria supply the tumor cells with proteins that potentially promote cancer progression, and that Methylobacterium could have a key role in breast cancer, but more studies are needed to confirm the hypothesis. Citation Format: Francesca Pirini, Tania Rossi, Soulaimane Aboulouard, Bruno Fosso, Maurizio Puccetti, Sara Ravaioli, Maria Maddalena Tumedei, Michela Cortesi, Michele Zanoni, Luca Magnani, Giovanni Martinelli, Michel Salzet, Sara Bravaccini. A multi-omics approach to study the host-microbiota interaction in breast cancer tissue [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-06-04.