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Microorganisms are shown to actively partition their intracellular resources, such as proteins, for growth optimization. Recent experiments have begun to reveal molecular components unpinning the partition; however, quantitatively, it remains unclear how individual parts orchestrate to yield precise resource allocation that is both robust and dynamic. Here, we developed a coarse-grained mathematical framework that centers on guanosine pentaphosphate (ppGpp)-mediated regulation and used it to systematically uncover the design principles of proteome allocation in Escherichia coli . Our results showed that the cellular ability of resource partition lies in an ultrasensitive, negative feedback-controlling topology with the ultrasensitivity arising from zero-order amino acid kinetics and the negative feedback from ppGpp-controlled ribosome synthesis. In addition, together with the time-scale separation between slow ribosome kinetics and fast turnovers of ppGpp and amino acids, the network topology confers the organism an optimization mechanism that mimics sliding mode control, a nonlinear optimization strategy that is widely used in man-made systems. We further showed that such a controlling mechanism is robust against parameter variations and molecular fluctuations and is also efficient for biomass production over time. This work elucidates the fundamental controlling mechanism of E. coli proteome allocation, thereby providing insights into quantitative microbial physiology as well as the design of synthetic gene networks.

Radioresistance is still an emerging problem for radiotherapy of oral cancer. Aberrant epigenetic alterations play an important role in cancer development, yet the role of such alterations in radioresistance of oral cancer is not fully explored. Using a methylation microarray, we identified promoter hypermethylation of FHIT (fragile histidine triad) in radioresistant OML1-R cells, established from hypo-fractionated irradiation of parental OML1 radiosensitive oral cancer cells. Further analysis confirmed that transcriptional repression of FHIT was due to promoter hypermethylation, H3K27me3 and overexpression of methyltransferase EZH2 in OML1-R cells. Epigenetic interventions or depletion of EZH2 restored FHIT expression. Ectopic expression of FHIT inhibited tumor growth in both in vitro and in vivo models, while also resensitizing radioresistant cancer cells to irradiation, by restoring Chk2 phosphorylation and G2/M arrest. Clinically, promoter hypermethylation of FHIT inversely correlated with its expression and independently predicted both locoregional control and overall survival in 40 match-paired oral cancer patient samples. Further in vivo therapeutic experiments confirmed that inhibition of DNA methylation significantly resensitized radioresistant oral cancer cell xenograft tumors. These results show that epigenetic silencing of FHIT contributes partially to radioresistance and predicts clinical outcomes in irradiated oral cancer. The radiosensitizing effect of epigenetic interventions warrants further clinical investigation.

Gene therapy mediated by murine leukemia virus (MLV)-based replicating retrovirus vector (RRV) was previously proven to be highly effective in tumor cell killing, resulting in significant suppression of tumor growth in vivo. Recently, we developed a different form of RRV which is derived from another retrovirus, gibbon ape leukemia virus (GALV), as a cancer therapeutic agent. We compared the gene delivery efficiency and antitumor effects in the two types of RRV in experimental hepatocellular carcinoma (HCC). Our results show that both RRVs can efficiently spread throughout entire HCC cell populations in vitro and achieve high transduction efficiency in HCC xenografts in vivo, while GALV RRV, in general, exhibited more rapid replication kinetics in the tumors. In vitro, substantial HCC cell killing was achieved even when initially only 1% of the HCC cells were producing RRVs that express the yeast cytosine deaminase suicide gene, indicating that the high efficiency of gene transfer by replicative spread of RRVs greatly increased suicide gene toxicity. In vivo, GALV RRV-mediated suicide gene therapy efficiently suppressed HCC tumor growth and no detectable RRV signals were observed in extratumoral tissues, showing promise in using GALV RRV as a cancer therapeutic agent.