IBCN 2023: An Holistic and Intergrated Approach for Investigating the Bacterial Microbiome, Gene Expression Profile and Immune Cell Profile in the Non-Muscle Invasive Bladder Cancer Tumour Microenvironment

(UroToday.com) Bladder cancer (BC) is the 10th most common cancer worldwide with an estimated 570,000+ people being diagnosed in 2020. Communities of bacteria exist in both normal and cancerous tissues and can impact treatment efficacy (e.g. metabolizing chemotherapeutics).

The researchers investigated the bacterial microbiome in formalin-fixed paraffin-embedded (FFPE) tumor tissue across different stages of Bladder Cancer compared to adjacent normal tissue to investigate differentially expressed (DE) bacteria between Bacillus-Calmette Guerin (BCG) treatment responders vs. non-responders. These findings were correlated to host gene expression, infiltrating immune cell profiles, and urinary cytokine within the tumor microenvironment (TME).

They described the methods for the analysis of the bacterial signatures within the urine (n=56) and FFPE tissues (n=66), (matching patients n=44), derived from the Royal Surrey County Hospital, Guildford, UK, were determined using 16s rRNA sequencing (V3-V4). Sequencing data were processed through QIIME2 and clustered into amplicon sequence variants (ASVs).  Alpha (Shannon and observed) and Beta (Bray-Curtis, weighted/unweighted uniFrac) diversity analysis was performed. RNA extracted from FFPE BC tissues generated gene expression data using the Nanostring IO360 panel (770 gene CodeSet) and was correlated to the tumor microbiome. 9- color multiplex immunohistochemistry (mIHC) using Phenoimager HT (Akoya Biosciences) was performed to investigate and spatially define immune cell types (CD4, CD8, CD68, CD57, FOXP3, GRZB, PD-L1, PANCK, DAPI), within the TME (n=71), which were correlated to gene expression, bacterial signatures, and clinical patient information.

Bladder cancer bacterial microbiome showed decreased diversity with disease progression (P<0.01). The bacterial profiles between urine and FFPE cancer tissues revealed independent groups (P<0.01), showing urine is not an accurate proxy. DE bacteria were found between BCG responders vs non-responders. Immune cell counts and spatial relationships determined via mIHC showed differences between disease staging. Analysis has also shown links between bacteria, immune gene expression, and immune cell populations.

In summary, bacteria may influence patient BCG treatment responses and pose as an interesting target for modulation to improve therapeutic outcomes.

Presented by: Tyler Wooldridge, University of Surrey, Guildford, UK

Written by: Stephen B. Williams, MD, MBA, MS @SWilliams_MD on Twitter during the International Bladder Cancer Network (IBCN) Annual Meeting, September 29-30, 2023, Montreal, Canada