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Comparative analysis of the tumor microbiome, molecular profiles, and immune cell abundances by HPV status in mucosal head and neck cancers and their impact on survival.
- Source :
-
Cancer biology & therapy [Cancer Biol Ther] 2024 Dec 31; Vol. 25 (1), pp. 2350249. Date of Electronic Publication: 2024 May 09. - Publication Year :
- 2024
-
Abstract
- Head and Neck Squamous Cell Carcinoma (HNSCC) comprises a diverse group of tumors with variable treatment response and prognosis. The tumor microenvironment (TME), which includes microbiome and immune cells, can impact outcomes. Here, we sought to relate the presence of specific microbes, gene expression, and tumor immune infiltration using tumor transcriptomics from The Cancer Genome Atlas (TCGA) and associate these with overall survival (OS). RNA sequencing (RNAseq) from HNSCC tumors in TCGA was processed through the exogenous sequences in tumors and immune cells (exotic) pipeline to identify and quantify low-abundance microbes. The detection of the Papillomaviridae family of viruses assessed HPV status. All statistical analyses were performed using R. A total of 499 RNAseq samples from TCGA were analyzed. HPV was detected in 111 samples (22%), most commonly Alphapapillomavirus 9 (90.1%). The presence of Alphapapillomavirus 9 was associated with improved OS [HR = 0.60 (95%CI: 0.40-0.89, p = .01)]. Among other microbes, Yersinia pseudotuberculosis was associated with the worst survival (HR = 3.88; p = .008), while Pseudomonas viridiflava had the best survival (HR = 0.05; p = .036). Microbial species found more abundant in HPV- tumors included several gram-negative anaerobes. HPV- tumors had a significantly higher abundance of M0 ( p < .001) and M2 macrophages ( p = .035), while HPV+ tumors had more T regulatory cells ( p < .001) and CD8+ T-cells ( p < .001). We identified microbes in HNSCC tumor samples significantly associated with survival. A greater abundance of certain anaerobic microbes was seen in HPV tumors and pro-tumorigenic macrophages. These findings suggest that TME can be used to predict patient outcomes and may help identify mechanisms of resistance to systemic therapies.
- Subjects :
- Humans
Female
Male
Prognosis
Middle Aged
Papillomaviridae genetics
Aged
Head and Neck Neoplasms virology
Head and Neck Neoplasms mortality
Head and Neck Neoplasms immunology
Head and Neck Neoplasms microbiology
Head and Neck Neoplasms pathology
Head and Neck Neoplasms genetics
Papillomavirus Infections virology
Papillomavirus Infections immunology
Papillomavirus Infections complications
Microbiota genetics
Tumor Microenvironment immunology
Squamous Cell Carcinoma of Head and Neck virology
Squamous Cell Carcinoma of Head and Neck microbiology
Squamous Cell Carcinoma of Head and Neck immunology
Squamous Cell Carcinoma of Head and Neck mortality
Subjects
Details
- Language :
- English
- ISSN :
- 1555-8576
- Volume :
- 25
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Cancer biology & therapy
- Publication Type :
- Academic Journal
- Accession number :
- 38722731
- Full Text :
- https://doi.org/10.1080/15384047.2024.2350249