DNA microarray profiling of genes differentially regulated by the histone deacetylase inhibitors vorinostat and LBH589 in colon cancer cell lines

<p>Abstract</p> <p>Background</p> <p>Despite the significant progress made in colon cancer chemotherapy, advanced disease remains largely incurable and novel efficacious chemotherapies are urgently needed. Histone deacetylase inhibitors (HDACi) represent a novel class of agents which have demonstrated promising preclinical activity and are undergoing clinical evaluation in colon cancer. The goal of this study was to identify genes in colon cancer cells that are differentially regulated by two clinically advanced hydroxamic acid HDACi, vorinostat and LBH589 to provide rationale for novel drug combination partners and identify a core set of HDACi-regulated genes.</p> <p>Methods</p> <p>HCT116 and HT29 colon cancer cells were treated with LBH589 or vorinostat and growth inhibition, acetylation status and apoptosis were analyzed in response to treatment using MTS, Western blotting and flow cytometric analyses. In addition, gene expression was analyzed using the Illumina Human-6 V2 BeadChip array and Ingenuity^®Pathway Analysis.</p> <p>Results</p> <p>Treatment with either vorinostat or LBH589 rapidly induced histone acetylation, cell cycle arrest and inhibited the growth of both HCT116 and HT29 cells. Bioinformatic analysis of the microarray profiling revealed significant similarity in the genes altered in expression following treatment with the two HDACi tested within each cell line. However, analysis of genes that were altered in expression in the HCT116 and HT29 cells revealed cell-line-specific responses to HDACi treatment. In addition a core cassette of 11 genes modulated by both vorinostat and LBH589 were identified in both colon cancer cell lines analyzed.</p> <p>Conclusion</p> <p>This study identified HDACi-induced alterations in critical genes involved in nucleotide metabolism, angiogenesis, mitosis and cell survival which may represent potential intervention points for novel therapeutic combinations in colon cancer. This information will assist in the identification of novel pathways and targets that are modulated by HDACi, providing much-needed information on HDACi mechanism of action and providing rationale for novel drug combination partners. We identified a core signature of 11 genes which were modulated by both vorinostat and LBH589 in a similar manner in both cell lines. These core genes will assist in the development and validation of a common gene set which may represent a molecular signature of HDAC inhibition in colon cancer.</p

Rollback-Recovery for Middleboxes

Network middleboxes must offer high availability, with automatic failover when a device fails. Achieving high availability is challenging because failover must correctly restore lost state (e.g., activity logs, port mappings) but must do so quickly (e.g., in less than typical transport timeout values to minimize disruption to applications) and with little overhead to failure-free operation (e.g., additional per-packet latencies of 10-100s of µs). No existing middlebox design provides failover that is correct, fast to recover, and imposes little increased latency on failure-free operations. We present a new design for fault-tolerance in middleboxes that achieves these three goals. Our system, FTMB (for Fault-Tolerant MiddleBox), adopts the classical approach of “rollback recovery” in which a system uses information logged during normal operation to correctly reconstruct state after a failure. However, traditional rollback recovery cannot maintain high throughput given the frequent output rate of middleboxes. Hence, we design a novel solution to record middlebox state which relies on two mechanisms: (1) ‘ordered logging’, which provides lightweight logging of the information needed after recovery, and (2) a ‘parallel release’ algorithm which, when coupled with ordered logging, ensures that recovery is always correct. We implement ordered logging and parallel release in Click and show that for our test applications our design adds only 30µs of latency to median per packet latencies. Our system introduces moderate throughput overheads (5-30%) and can reconstruct lost state in 40-275ms for practical systems