瘤和免疫细胞中的外源序列 (外来):用于估计瘤RNA-seq数据中的微生物丰度的工具
Rebecca Hoyd1, Caroline E Wheeler1, YunZhou Liu1
1Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio.
Cancer research communications
|October 18, 2023
概括
我们开发了一种工具,使用RNA测序数据识别瘤中的微生物. 这项研究揭示了瘤微生物组与临床结果之间的新联系,为新型癌症诊断和治疗铺平了道路.
科学领域:
- 在瘤学瘤学.
- 微生物学 微生物学
- 生物信息学是一种生物信息学.
背景情况:
- 瘤微生物组影响癌症的发展和治疗反应.
- 有证据表明,微生物存在于瘤中,但它们对癌症生物学和结果的影响需要进一步调查.
- 对瘤微生物组数据的全面分析对于确定可靠的相关性至关重要.
研究的目的:
- 开发和验证一种计算工具, {exotic} (瘤和免疫细胞中的外源序列),用于从RNA测序 (RNA-seq) 数据中识别瘤微生物群.
- 通过将微生物丰度与临床和瘤特征相关联,评估瘤微生物组的临床相关性.
- 探索微生物与瘤相互作用的潜在机制.
主要方法:
- 创建了 {exotic} 工具,用于检测RNA-seq数据集中的微生物序列.
- 应用 {exotic} 来分析来自瘤研究信息交换网络 (ORIEN) 和癌症基因组图谱 (TCGA) 的样本.
- 与临床变量 (例如年龄,瘤缺氧) 和免疫细胞组成相关联的确定的微生物丰度,重点关注跨数据集的一致关联.
主要成果:
- 该工具有效地去除污染物和批量效应,产生与其他测序方法一致的微生物丰度.
- 确定了微生物丰度和临床变量 (包括生存率) 之间的癌症特异性关联.
- 通过网络分析观察到与免疫组成的有限相关性,但突出显示Alistipes作为与代谢和炎症基因相关的关键微生物.
结论:
- 该工具可以在现有的RNA-seq数据集中稳定地发现与瘤相关的微生物.
- 建立了瘤微生物组和临床癌症特征之间的新联系,支持潜在的生物标志物应用.
- 这些发现需要进一步研究瘤微生物组对癌症进展和治疗结果的影响的机制.
相关概念视频
03:21RNA-seq
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
02:24Ribosome Profiling
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...