Weighted gene coexpression network analysis and machine learning reveal oncogenome associated microbiome plays an important role in tumor immunity and prognosis in pan-cancer

BACKGROUND

For many years, the role of the microbiome in tumor progression, particularly the tumor microbiome, was largely overlooked. The connection between the tumor microbiome and the tumor genome still requires further investigation.

METHODS

The TCGA microbiome and genome data were obtained from Haziza et al.'s article and UCSC Xena database, respectively. Separate WGCNA networks were constructed for the tumor microbiome and genomic data after filtering the datasets. Correlation analysis between the microbial and mRNA modules was conducted to identify oncogenome associated microbiome module (OAM) modules, with three microbial modules selected for each tumor type. Reactome analysis was used to enrich biological processes. Machine learning techniques were implemented to explore the tumor type-specific enrichment and prognostic value of OAM, as well as the ability of the tumor microbiome to differentiate TP53 mutations.

RESULTS

We constructed a total of 182 tumor microbiome and 570 mRNA WGCNA modules. Our results show that there is a correlation between tumor microbiome and tumor genome. Gene enrichment analysis results suggest that the genes in the mRNA module with the highest correlation with the tumor microbiome group are mainly enriched in infection, transcriptional regulation by TP53 and antigen presentation. The correlation analysis of OAM with CD8+ T cells or TAM1 cells suggests the existence of many microbiota that may be involved in tumor immune suppression or promotion, such as Williamsia in breast cancer, Biostraticola in stomach cancer, Megasphaera in cervical cancer and Lottiidibacillus in ovarian cancer. In addition, the results show that the microbiome-genome prognostic model has good predictive value for short-term prognosis. The analysis of tumor TP53 mutations shows that tumor microbiota has a certain ability to distinguish TP53 mutations, with an AUROC value of 0.755. The tumor microbiota with high importance scores are Corallococcus, Bacillus and Saezia. Finally, we identified a potential anti-cancer microbiota, Tissierella, which has been shown to be associated with improved prognosis in tumors including breast cancer, lung adenocarcinoma and gastric cancer.

CONCLUSION

There is an association between the tumor microbiome and the tumor genome, and the existence of this association is not accidental and could change the landscape of tumor research.

Immuno-oncology-microbiome axis of gastrointestinal malignancy

Research on the relationship between the microbiome and cancer has been controversial for centuries. Recent works have discovered that the intratumor microbiome is an important component of the tumor microenvironment (TME). Intratumor bacteria, the most studied intratumor microbiome, are mainly localized in tumor cells and immune cells. As the largest bacterial reservoir in human body, the gut microbiome may be one of the sources of the intratumor microbiome in gastrointestinal malignancies. An increasing number of studies have shown that the gut and intratumor microbiome play an important role in regulating the immune tone of tumors. Moreover, it has been recently proposed that the gut and intratumor microbiome can influence tumor progression by modulating host metabolism and the immune and immune tone of the TME, which is defined as the immuno-oncology-microbiome (IOM) axis. The proposal of the IOM axis provides a new target for the tumor microbiome and tumor immunity. This review aims to reveal the mechanism and progress of the gut and intratumor microbiome in gastrointestinal malignancies such as esophageal cancer, gastric cancer, liver cancer, colorectal cancer and pancreatic cancer by exploring the IOM axis. Providing new insights into the research related to gastrointestinal malignancies.

Intratumour microbiome of pancreatic cancer

Pancreatic cancer is a high mortality malignancy with almost equal mortality and morbidity rates. Both normal and tumour tissues of the pancreas were previously considered sterile. In recent years, with the development of technologies for high-throughput sequencing, a variety of studies have revealed that pancreatic cancer tissues contain small amounts of bacteria and fungi. The intratumour microbiome is being revealed as an influential contributor to carcinogenesis. The intratumour microbiome has been identified as a crucial factor for pancreatic cancer progression, diagnosis, and treatment, chemotherapy resistance, and immune response. A better understanding of the biology of the intratumour microbiome of pancreatic cancer contributes to the establishment of better early cancer screening and treatment strategies. This review focuses on the possible origins of the intratumour microbiome in pancreatic cancer, the intratumour localization, the interaction with the tumour microenvironment, and strategies for improving the outcome of pancreatic cancer treatment. Thus, this review offers new perspectives for improving the prognosis of pancreatic cancer.

[Comparison between transoral radiofrequency coblation surgery and open partial laryngectomy for the treatment of supraglottic laryngeal carcinoma]

Objective: To explore the feasibility and efficacy of radiofrequency coblation assisted transoral surgery for the treatment of supraglottic laryngeal carcinoma by comparing with concurrent patients treated with conventional transcervical approach. To clarify the advantages of different surgical methods and to summarize the experience of supraglottic carcinoma radiofrequency ablation. Methods: Forty-six patients with supraglottic laryngeal carcinoma treated in department of otorhinolaryngology head and neck surgery, Peking University First Hospital from March 2014 to January 2021 were analyzed retrospectively. Among them(43 males, 3 females, aged from 45 to 79 years old), 23 patients were treated with radiofrequency coblation and 23 patients with partial laryngectomy with conventional transcervical approach. The operation time, intra-operative blood loss volume, recovery time, inpatient total medical cost and follow-up information of the two groups were analyzed. SPSS 26.0 software was used for statistical analysis. Results: There were no significant differences in age, gender, TNM staging,tumor staging and postoperative radiotherapy between the two groups (all P>0.05).The operation time, intra-operative blood loss volume, recovery time, inpatient total medical cost of the RFC-TOS group were110.0(60.0,150.0)min,5.0(5.0,30.0)ml,3.0(2.0,5.0)days,6.0(4.0,14.0)days and 26 100.7(16 145.5,47 044.4)yuan. The data of conventional transcervical approach group were 205.0(156.5,272.3)min, 150.0(50,200) ml, 18.0(16.3,22.8)days and 56520.1(440 992.5,67 109.9)yuan, (Z=-4.03, -4.94, -4.97, -4.98 and -4.13;all P<0.001).The 5-year local control rate, disease-specific survival rate and overall survival rate of the two groups were 86.96%,95.65%,91.30% and 86.96%,91.30%,73.90% renspectively, which had no significant difference between the two groups(all P>0.05). Conclusions: Compared with conventional transcervical surgeries, RFC-TOS could be a reliable new surgical option for organ-function preservation strategy in the treatment of supraglottic laryngeal carcinoma.The RFC is a suitable new technique and deserving more multi-center clinical trials for its clinical promotion.