Gene regulation strategies underlying skeletal muscle atrophy in cancer cachexia

Cancer cachexia is a syndrome characterized by the severe skeletal muscle wasting tissue; that affects more than 50% of all cancer patients and results in lower quality of life due to compromised fatigue, weakness, decreased immune function, insulin resistance and poor tolerance and response to radio and chemotherapy. Remarkably, approximately 20% of cancer-related deaths are estimated to be directly caused by cachexia. There is currently no effective targeted therapy and the main limitation lays on the traditional approaches that not deal with the inherent complexity, characterized by non-linear interactions, of gene regulatory networks (GRN). Thus, a clear identification of the components of gene regulation, and a quantitative understanding of their temporal integration to control cellular responses is fundamental for capture essential mechanistic details that will ultimately enable the development of direct therapeutic strategies for the treatment of cancer cachexia. Here, we examine genome-wide gene expression of muscle wasting under two different frameworks, using static and dynamic gene expression data. We structure this approach as follow: Chapter 1 presents a quantitative characterization of the signaling pathways and a GRN reconstruction of muscle wasting in Lewis Lung Carcinoma (LLC) tumor-bearing mice by integrating static mRNAs and microRNAs expression profiles. The results show that LLC mice reduced body weight in 20% and presented muscle and fat tissue wasting after 23 days of tumor induction. In addition, we found 1008 differential expressed mRNAs (487 up-regulated and 521 down-regulated) and eighteen deregulated miRNAs (13 up-regulated and 5 down-regulated). Our data suggest activation of the transcriptional factor NF-κB and Stat3, which have been described in the activation of atrophic gene programs. Moreover, we ident potential posttranscriptional regulation by miRNAs of three important biological process: extracellular matrix organization, cell migration and transcription factor binding. Overall our results identify a set of signaling pathways that may contribute to muscle wasting in cancer cachexia, between them extracellular matrix genes with potential regulatory mechanism mediated by miRNAs. Chapter 2 provides further dissection of the NF-κB signaling pathway in atrophying muscle cells. Here, we examine quantitatively the genome-wide dynamic gene expression effects of the activation of NF-κB by the exposure of tumor necrosis factor – alpha (TNF-α) on skeletal muscle cells (C2C12). We characterize the regulatory strategies of gene induction and repression by measuring both mRNA transcription and degradation rates and connecting these processes via mathematical modeling. Our data points to a dominant role of transcription dynamics in the regulation of both gene induction and repression programs in response to TNF; and unveils a decrease in mRNA degradation rate as strategy for genes of late response to increase their intracellular concentrations. Furthermore, our analysis shows constitutive degradation as an intrinsic characteristic of genes that determines most of temporal ranks of gene expression profiles. Using a non-degradable form of inhibitor kappa B alpha and RelA knockout C2C12 cells we found that NF-κB is responsible for both gene induction and gene repression during muscle cell atrophy induced by TNF-α. Our fine-grained data highlights the importance of signaling dynamics in mediating the TNF-α effects on skeletal muscle cells and reveals a critical interplay between synthesis and degradation control in that regulates dynamic gene expression programs. (AU)