Loss of long-range co-expression is a common trait in cancer

Abstract

Cancer cells display common traits and enabling-characteristics previously described as the Hallmarks of Cancer. These occur alongside alterations in the regulatory mechanisms controlling gene transcription. Gene co-expression networks (GCNs) identify correlated sets of genes that might share these mechanisms. We have previously reported loss of long-range co-expression for breast, lung, and kidney cancer GCNs. Here, we extend the study to fifteen tissues. Unlike in healthy phenotypes, the highest cancer gene-pair interactions are intra-chromosomal and their strength decays with base-pair distance. Communities in tumor GCNs are strongly associated with cancer related processes along with a wide presence of adaptive immune response. Riboproteins are highly co-expressed in cancer and normal GCNs, suggesting their relevance for cell viability. The loss of long-range co-expression is not observed in other chronic diseases such as Type-2 Diabetes or Alzheimer’s disease. These results suggest that the loss of long-range co-expression is a common trait in cancer.