Malik Sarah A, Zhu Chencan, Li Jinyu, LaComb Joseph F, Denoya Paula I, Kravets Igor, Miller Joshua D, Yang Jie, Kramer Melissa, McCombie W Richard, Robertson Charles E, Frank Daniel N, Li Ellen
Department of Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, United States.
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794, United States.
World J Gastroenterol. 2021 Apr 14;27(14):1465-1482. doi: 10.3748/wjg.v27.i14.1465.
Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human diseases. Short-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer (CRC) resections. We hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk factors.
To assess the impact of preoperative antibiotics and other variables on integrated microbiome and human transcriptomic data generated from archived CRC resection samples.
Genomic DNA (gDNA) and RNA were extracted from prospectively collected 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center from 2010-2020. The 16S rRNA gene sequencing (V3V4 region, paired end, 300 bp) and confirmatory quantitative polymerase chain reaction (qPCR) assays were conducted on gDNA. RNA sequencing (IPE, 125 bp) was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers scores ≥ 6.
PERMANOVA detected significant effects of tumor nontumor histology ( = 0.002) and antibiotics ( = 0.001) on microbial β-diversity, but CRC tumor location (left right), diabetes mellitus not diabetic and Black/African Ancestry (AA) not Black/AA, did not reach significance. Linear mixed models detected significant tumor nontumor histology*antibiotics interaction terms for 14 genus level taxa. QPCR confirmed increased abundance in tumor nontumor groups, and detected significantly reduced bacterial load in the (+)antibiotics group. Principal coordinate analysis of the transcriptomic data showed a clear separation between tumor and nontumor samples. Differentially expressed genes obtained from separate analyses of tumor and nontumor samples, are presented for the antibiotics, CRC location, diabetes and Black/AA race groups.
Recent adoption of additional preoperative antibiotics as standard of care, has a measurable impact on -omics analysis of resected specimens. This study still confirmed increased in tumor.
整合多组学方法已越来越多地应用于复杂人类疾病的发现和功能研究。短期术前抗生素已被用于降低结直肠癌（CRC）切除术中的手术部位感染。我们假设抗生素会影响从切除样本中生成的多组学数据集的分析，以研究结直肠癌的生物学危险因素。
评估术前抗生素和其他变量对存档的结直肠癌切除样本所产生的整合微生物组和人类转录组数据的影响。
从2010年至2020年在单个医疗中心存档的50例CRC患者中前瞻性收集51对冷冻的散发性CRC肿瘤及相邻非肿瘤黏膜样本，提取基因组DNA（gDNA）和RNA。对gDNA进行16S rRNA基因测序（V3V4区域，双端，300 bp）和验证性定量聚合酶链反应（qPCR）检测。对RNA完整性数值评分≥6的平行肿瘤和非肿瘤RNA样本进行RNA测序（IPE，125 bp）。
PERMANOVA检测到肿瘤与非肿瘤组织学（P = 0.002）和抗生素（P = 0.001）对微生物β多样性有显著影响，但结直肠癌肿瘤位置（左与右）、糖尿病与非糖尿病以及黑人/非洲裔（AA）与非黑人/AA未达到显著水平。线性混合模型检测到14个属水平分类群存在显著的肿瘤与非肿瘤组织学*抗生素交互作用项。qPCR证实肿瘤与非肿瘤组中[具体名称]丰度增加，并检测到（+）抗生素组细菌载量显著降低。转录组数据的主坐标分析显示肿瘤和非肿瘤样本之间有明显分离。分别对肿瘤和非肿瘤样本进行分析得到的差异表达基因，针对抗生素、结直肠癌位置、糖尿病和黑人/AA种族组进行了展示。
近期将额外的术前抗生素作为标准治疗方法的应用，对切除标本的组学分析有可测量的影响。本研究仍证实肿瘤中[具体名称]增加。
