癌症中細菌轉錄圖譜之資料庫

Abstract

微生物族群大量存在於人體內，而微生物失衡被報導與許多疾病相關，包括各種癌症。大多數研究都聚焦在腸道微生物菌相上，而參與腫瘤微環境中之細菌仍舊不太清楚。先前的研究已經從癌症基因組圖譜 (TCGA) 之核糖核酸定序、全基因組定序和全外顯子定序中獲得了細菌表達之資訊。卻很少使用微小核糖核酸定序之資料。我們的先導研究發現，使用 TCGA 微小核糖核酸定序資料發現大腸直腸癌 (CRC) 微生物與 16S 核糖體去氧核醣核酸定序技術中發現之微生物組相似。在本研究中，我們使用 TCGA 微小核糖核酸定序資料評估了 32 種癌症中之細菌相對表現量。為了發現與癌症關聯之細菌，我們使用了一種分析方法將未對應上人類之定序片段與細菌參考進行比對，並建立了 BIC 資料庫網站—癌症中細菌轉錄圖譜之資料庫。 BIC 提供與癌症相關之細菌資訊，包含細菌相對表現量、細菌多樣性、與臨床指標關聯性、細菌間、細菌和人類基因間之共表現網絡及其相關之生物功能性。這些結果可以互補先前已發表之資料庫。使用者可以輕鬆下載輸出結果之圖、表，或下載細菌相對表現量之矩陣做更進一步之分析。總而言之， BIC 可以提供腫瘤微環境中細菌相關之資訊。 BIC 可在下方網址中獲得：http://bic.jhlab.tw/。

Microbial communities are massively resident in the human body, yet dysbiosis has been reported to correlate with many diseases, including various cancers. Most studies focus on the gut microbiome, while the bacteria that participate in tumor microenvironments on site remain unclear. Previous studies have acquired the bacteria expression profiles from RNA-Seq, whole genome sequencing, and whole exon sequencing in The Cancer Genome Atlas (TCGA). However, small-RNA sequencing data were rarely used. Our pilot study found that the colorectal cancer (CRC) microbiome discovered with TCGA micro-RNA sequencing data is similar to those found in the 16S-rDNA sequencing technique. Using TCGA miRNA-Seq, we evaluated bacterial abundance in 32 types of cancer in this study. To uncover the bacteria involved in cancer, we applied an analytical process to align unmapped human reads to bacterial references and developed the bacteria in cancer (BIC) database for the transcriptional landscape of bacteria in cancer. BIC provides cancer-associated bacterial information, including the relative abundance of bacteria, bacterial diversity, associations with clinical relevance, the co-expression network of bacteria and human genes, and their associated biological functions. These results can complement previously published databases. Users can easily download the result plots and tables, or download the bacterial abundance matrix for further analyses. In summary, BIC can provide information on cancer microenvironments related to microbial communities. BIC is available at: http://bic.jhlab.tw/.