Dissection of intratumor microbiome-host interactions at single-cell level in lung cancer

Human health is closely related with microbiome and their relationship is strongly intertwined. A large number of studies have shown that the human microbiome plays a critical role in tumorigenesis, tumor progression, and the efficacy of anticancer therapies such as radiotherapy through a variety of mechanisms. The microbiome can be used as a tumor marker and is expected to be a novel therapeutic target. However, as part of the tumor immune microenvironment, the intratumoral microbiome of lung cancer, which is the leading tumor in terms of new cases and deaths worldwide, is able to more directly influence and participate in the life activities of various cell types in lung cancer tumor tissues compared to the microbiota of other parts of the human body. Previous studies have revealed the molecular mechanism by which the immunosuppressive microenvironment induced by intratumoral fungi promotes the development of lung cancer, and confirmed that the enrichment of Aspergillus sydowii in tumors is positively correlated with adverse outcomes of lung cancer patients. However, the molecular mechanism of how the intratumoral microbiome interacts with host single cells during the development of lung cancer remains unclear.

They integrated six publicly published single-cell RNA sequencing datasets with 149 lung cancer patient tissue samples, including lung cancer, normal tissues adjacent to the cancer and brain metastases, and integrated the SAHMI tool for mining microbial sequence information and single-cell analysis, by removing potential microbial contamination and false-positive sequences and the batch effect during multi-datasets integration. They obtained the true microbial sequences associated with individual host cells and investigated the relationship between different host cells and specific microbiota within different tissue types at the single-cell resolution.

These findings suggest that host cell composition varies during lung cancer progression and metastasis. The proportions and numbers of bacterial- and fungal-associated host cells also differed in lung cancer-related tissues, with the number of bacterial-associated cells being higher than that of fungal-associated cells in all lung cancer and its paratumoral and brain metastatic tissue samples; with the proportion of fungal-associated cells being the highest in the primary lung cancer lesions compared to brain metastases and paratumoral normal tissues, whereas the proportion of bacterial-associated cells was highest abundant in brain metastatic tissues compared to primary lung tumor and paratumoral tissues. Meanwhile, there were differences in the proportions of cell types in samples of different tissue types, and there were significant differences in the distribution of fungi and bacteria in different cell types. The expression of host cell type-specific genes was associated with the presence of specific bacteria, and the presence of specific bacteria significantly and differentially affects the gene expression in their co-localized or resident host cells by modulating the activity of a variety of pathways related to rRNA processing, cellular responses to stimuli and stress, RNA and protein metabolism, etc. There was an effect of the presence or absence of bacteria on host cell communication and gene expression in different T cell subtypes. There is differential regulation of host macrophage by gene expression such as PLP1 by bacteria and fungi. It was upregulated in macrophages exposed to bacteria, but downregulated in fungus-associated macrophages. In addition, this study found that some microorganisms were associated with sample type and the smoking status of lung cancer patients. In terms of smoking frequency, various fungi such as Pichia, Saccharomyces, Pyricularia, and Sugiyamaella showed differential abundance in normal, primary lung cancer, and metastatic lung cancer tissues.

In summary, revealing the complex interaction between the host and microbiome at the single-cell level may be a new breakthrough to explore the factors affecting the occurrence, development, metastasis and prognosis of lung cancer, and provide new clues for the realization of personalized cancer treatment in clinical practice in the future.

They express their gratitude to all the enrolled participants who contributed data to this study. The funding from the MOST Key R&D Program of China (2022YFC2304703, 2020YFA0907200), the Natural Science Foundation of China (32270202, 62372286), Program of Shanghai Academic/Technology Research Leader (23XD1422300), Science and Technology Innovation Plan of Shanghai (23JC1403200), and Innovative research team of high-level local universities in Shanghai are greatly appreciated by all the authors.