Abstract 3043: Exploring the microbial landscape of NSCLC through TRACERx
Authors: Thakkar Krupa , Fu Hongchang , Veeriah Selvaraju , Litchfield Kevin , Swanton Charles ,   TRACERx Consortium
Published: June 2022

Bacterial and viral species present in the human lung are associated with COPD (chronic obstructive pulmonary disease) exacerbations, lung cancer initiation and response to immunotherapy by impacting immune cell recruitment. Recent studies have identified microbiomes present in normal and tumour low-biomass samples. These microbes, potentially present within cancer and immune cells, exist in niches specific to tumour types. These studies are often single-region and single-timepoint biopsy studies which promotes the question as to whether heterogeneity of the microbiome can exist within a tumour as well as progression of the microbiome from primary tumours to metastasis. Exploring microbial heterogeneity by leveraging the multi-region and longitudinal data from TRACERx, we aimed to identify microbes present clonally as well as studying enrichment of microbes in metastatic regions or associations with genotypes.

We conducted 16S (V3V4) sequencing of over 600 TRACERx samples including primary, adjacent normal and metastatic tissues. Stringent decontamination was applied using computational methods as well as completed at sequencing centre and extraction level sites. The 16S data was aligned to the SILVA-138 reference genome using the QIIME2 pipeline. We also performed analysis on matched RNA-sequencing data through tools such as KRAKEN2 and SHOGUN.

Diversity metrics across histological subtypes, COPD status or gender did not yield significant differences or show an enrichment of genus with patient characteristics. However, a trend of decreasing microbial diversity was associated with smoking which demonstrates that the effects of smoking can lead to dysbiosis of a healthy lung microbiome. Within primary tumours, increased tumour sampling improved the detection of microbial diversity and presence of microbes found at a lower abundance, revealing a heterogenous microbial landscape. Furthermore, matched primary and metastatic tumours are highly similar compared to tumours from unmatched patients (P = 0.017) This suggests that primary and metastatic tissues share a similar community within patients, however an enrichment of opportunistic microbes was found in metastatic tissue. Finally, we also measured the association of specific microbes with different driver genotypes and several significant associations were discovered such as NOTCH1+ LUSC (lung squamous cell carcinoma) patients were enriched for Firmicutes.

Studying the microbial landscape of NSCLC through an evolutionary lens provides insight into microbial dissemination from primary tumours to metastases and co-occurrence with genotypes. The multi-region and longitudinal approach to studying the microbiome has exposed levels of microbial intratumor heterogeneity. Moreover, recognising that metastatic tumours have an overlapping microbiome to the primary site offers potential for durable therapeutic utility, via targeting clonally present species.

Citation Format: Krupa Thakkar, Hongchang Fu, Selvaraju Veeriah, Kevin Litchfield, Charles Swanton, TRACERx Consortium. Exploring the microbial landscape of NSCLC through TRACERx [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3043.