Abstract
BackgroundTranscription Factors (TFs), essential for many cellular processes, generally work coordinately to induce transcriptional change in response to internal and external signals. Disrupted cooperation between TFs, leading to dysregulation of target genes, contributes to the pathogenesis of many diseases, including cancer. Although the aberrant activation of individual TFs and the functional effects have been widely studied, the perturbation of TF cooperativity in cancer has rarely been explored.ResultsWe used TF co-expression as proxy as cooperativity and performed a large-scale study on disrupted TF cooperation across seven cancer types. While the connectivity of downstream effectors, like metabolic genes and TF targets, were more or similarly disrupted than/with non-TFs, the cooperativity of TFs (upstream regulators) were consistently less disturbed in all studied cancer types. Highly coordinated TFs in normal, however, generally lost that cooperation in cancer. Although different types of cancer shared very few TF pairs with highly disrupted cooperation, the cooperativity of interferon regulatory factors (IRF) was highly disrupted in six cancer types. Specifically, the cooperativity of IRF8 was highly perturbed in lung cancer, which was further validated by two independent lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD) datasets. More interestingly, the cooperativity of IRF8 was markedly associated with tumor progression and even contributed to the patient survival independent of tumor stage.ConclusionsOur findings underscore the far more important role of TF cooperativity in tumorigenesis than previously appreciated. Disrupted cooperation of TFs provides potential clinical utility as prognostic markers for predicting the patient survival.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2842-8) contains supplementary material, which is available to authorized users.
Highlights
Transcription Factors (TFs), essential for many cellular processes, generally work coordinately to induce transcriptional change in response to internal and external signals
TF cooperativity is less disturbed than non-TF in cancer We obtained 1991 human TFs in total by combining three databases, AnimalTFDB [22], TRANSFAC [23], and TFCat [24] (Methods)
We studied seven cancer types and each cancer type had mRNA expression profiles measured for both tumor and matched normal samples (Table 1)
Summary
Transcription Factors (TFs), essential for many cellular processes, generally work coordinately to induce transcriptional change in response to internal and external signals. Disrupted cooperation between TFs, leading to dysregulation of target genes, contributes to the pathogenesis of many diseases, including cancer. The aberrant activation of individual TFs and the functional effects have been widely studied, the perturbation of TF cooperativity in cancer has rarely been explored. Transcription factors (TFs) are proteins that bind to either promoter or enhancer regions of a gene, thereby regulating the transcription activity of the gene [1, 2]. About 10 % of genes in the human genome encode TFs and they are essential for many cellular processes [3]. Like aberrant activation of individual TFs, disruption of TF cooperativity alters the expression of downstream genes and contributes to disease pathogenesis.
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