Molecular Biomarker Core, Case Western Reserve University, Cleveland, OH, USA; School of Nursing, Case Western Reserve University, Cleveland, OH, USA.
Molecular Biomarker Core, Case Western Reserve University, Cleveland, OH, USA; School of Nursing, Case Western Reserve University, Cleveland, OH, USA.
Genomics. 2023 Nov;115(6):110708. doi: 10.1016/j.ygeno.2023.110708. Epub 2023 Sep 18.
It has become widely accepted that sample cellular composition is a significant determinant of the gene expression patterns observed in any transcriptomic experiment performed with bulk tissue. Despite this, many investigations currently performed with whole blood do not experimentally account for possible inter-specimen differences in cellularity, and often assume that any observed gene expression differences are a result of true differences in nuclear transcription. In order to determine how confounding of an assumption this may be, in this study, we recruited a large cohort of human donors (n = 138) and used a combination of next generation sequencing and flow cytometry to quantify and compare the underlying contributions of variance in leukocyte counts versus variance in other biological factors to overall variance in whole blood transcript levels. Our results suggest that the combination of donor neutrophil and lymphocyte counts alone are the primary determinants of whole blood transcript levels for up to 75% of the protein-coding genes expressed in peripheral circulation, whereas the other factors such as age, sex, race, ethnicity, and common disease states have comparatively minimal influence. Broadly, this infers that a majority of gene expression differences observed in experiments performed with whole blood are driven by latent differences in leukocyte counts, and that cell count heterogeneity must be accounted for to meaningfully biologically interpret the results.
人们普遍认为，样本细胞组成是任何使用组织进行的转录组实验中观察到的基因表达模式的重要决定因素。尽管如此，目前许多使用全血进行的研究并没有在实验上考虑细胞成分在个体间可能存在的差异，并且通常假设任何观察到的基因表达差异都是核转录真实差异的结果。为了确定这种假设可能存在多大的混淆，在这项研究中，我们招募了一大群人类供体（n=138），并结合下一代测序和流式细胞术来量化和比较白细胞计数的差异与其他生物学因素的差异对全血转录水平总变异的潜在贡献。我们的研究结果表明，供体中性粒细胞和淋巴细胞计数的组合是外周循环中多达 75%表达的蛋白编码基因的全血转录水平的主要决定因素，而其他因素，如年龄、性别、种族、民族和常见疾病状态的影响相对较小。总体而言，这意味着在使用全血进行的实验中观察到的大多数基因表达差异是由白细胞计数的潜在差异驱动的，并且必须考虑细胞计数异质性才能对结果进行有意义的生物学解释。
