Spatial transcriptomic analysis reveals local effects of intratumoral fusobacterial infection on DNA damage and immune signaling in rectal cancer

ABSTRACT

Mucinous colorectal cancer (CRC) is a common histological subtype of colorectal adenocarcinoma, associated with a poor response to chemoradiotherapy. The commensal facultative anaerobes fusobacteria, have been associated with poor prognosis specifically in mesenchymal CRC. Interestingly, fusobacterial infection is especially prevalent in mucinous CRC. The objective of this study was therefore to increase our understanding of beneficial and detrimental effects of fusobacterial infection, by contrasting host cell signaling and immune responses in areas of high vs. low infection, using mucinous rectal cancer as a clinically relevant example. We employed spatial transcriptomic profiling of 106 regions of interest from 8 mucinous rectal cancer samples to study gene expression in the epithelial and immune segments across regions of high versus low fusobacterial infection. Fusobacteria high regions were associated with increased oxidative stress, DNA damage, and P53 signaling. Meanwhile regions of low fusobacterial prevalence were characterized by elevated JAK-STAT, Il-17, Il-1, chemokine and TNF signaling. Immune masks within fusobacterial high regions were characterized by elevated proportions of cytotoxic (CD8+) T cells (p = 0.037), natural killer (NK) cells (p < 0.001), B-cells (p < 0.001), and gamma delta T cells (p = 0.003). Meanwhile, fusobacteria low regions were associated with significantly greater M2 macrophage (p < 0.001), fibroblast (p < 0.001), pericyte (p = 0.002), and endothelial (p < 0.001) counts.

KEYWORDS:

• Rectal cancer
• digital spatial profiling
• immunogenicity
• microsatellite stability
• mucinous cancer
• chemoresistance

Acknowledgments

We acknowledge the technical support provided by Carmen Jeanette Stepek, Éanna B. Ryan, Albert Sanfeliu and Karen Conboy. We would also like to thank Mathias Holpert of Nanostring for his support throughout the project and Annelien Verfaillie from the Leuven Genomics Core for her assistance.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data that support the findings of this study are available on request from the corresponding author, JHMP. The data are not publicly available due to their containing information that could compromise the privacy of research participants.

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/19490976.2024.2350149

Additional information

Funding

WPD and BM were supported by an RCSI/Bon Secours Hospital MD StAR fellowship. BK is supported by Science Foundation Ireland through the SFI Centre for Research Training in Genomics Data Science under Grant number 18/CRT/6214, EU’s Horizon 2020 research, and innovation programme under the Marie Sklodowska-Curie grant H2020-MSCA-COFUND-2019–945385. JHMP is supported by the HEA North-South Program Strand 3 (AICRI-Start), and a US-Northern Ireland-Ireland Tripartite grant from Science Foundation Ireland and the Health Research Board (16/US/3301).