Sickle cell disease (SCD) afflicts millions of people worldwide and is associated with considerable morbidity and mortality. Chronic and acute vaso-occlusion are the clinical hallmarks of SCD and can result in pain crisis, widespread organ damage, and early movtality. Even though the molecular underpinnings of SCD were identified more than 60 years ago, there are no molecular or biophysical markers of disease severity that are feasibly measured in the clinic. Abnormal cellular adhesion to vascular endothelium is at the root of vaso-occlusion. However, cellular adhesion is not currently evaluated clinically. Here, we present a clinically applicable microfluidic device (SCD biochip) that allows serial quantitative evaluation of red blood cell (RBC) adhesion to endothelium-associated protein-immobilized microchannels, in a closed and preprocessing-free system. With the SCD biochip, we have analyzed blood samples from more than 100 subjects and have shown associations between the measured RBC adhesion to endothelium-associated proteins (fibronectin and laminin) and individual RBC characteristics, including hemoglobin content, fetal hemoglobin concentration, plasma lactate dehydrogenase level, and reticulocyte count. The SCD biochip is a functional adhesion assay, reflecting quantitative evaluation of RBC adhesion, which could be used at baseline, during crises, relative to various long-term complications, and before and after therapeutic interventions.

Over the last 7 years, we have focused our experimental and computational research efforts on improving our understanding of the biochemical, molecular, and cellular processing of iododeoxyuridine (IUdR) and ionizing radiation (IR) induced DNA base damage by DNA mismatch repair (MMR). These coordinated research efforts, sponsored by the National Cancer Institute Integrative Cancer Biology Program (ICBP), brought together system scientists with expertise in engineering, mathematics, and complex systems theory and translational cancer researchers with expertise in radiation biology. Our overall goal was to begin to develop computational models of IUdR- and/or IR-induced base damage processing by MMR that may provide new clinical strategies to optimize IUdR-mediated radiosensitization in MMR deficient (MMR−) “damage tolerant” human cancers. Using multiple scales of experimental testing, ranging from purified protein systems to in vitro (cellular) and to in vivo (human tumor xenografts in athymic mice) models, we have begun to integrate and interpolate these experimental data with hybrid stochastic biochemical models of MMR damage processing and probabilistic cell cycle regulation models through a systems biology approach. In this article, we highlight the results and current status of our integration of radiation biology approaches and computational modeling to enhance IUdR-mediated radiosensitization in MMR− damage tolerant cancers.

Base Excision Repair (BER) is a major DNA repair pathway involved in the processing of exogenous nonbulky base damages from certain classes of cancer chemotherapy drugs as well as ionizing radiation. Methoxyamine (MX) is a small molecule chemical inhibitor of BER that is shown to enhance chemotherapy and/or ionizing radiation cytotoxicity in human cancers. In this paper, we have analysed the inhibitory effect of MX on the base excision repair pathway kinetics using a computational model of the repair pathway. The inhibitory effect of MX depends on the base excision repair efficiency. We have generated variable efficiency groups using different sets of protein concentrations generated by Latin hypercube sampling, and we have clustered simulation results into high, medium and low efficiency repair groups. From analysis of the inhibitory effect of MX on each of the three groups, it is found that the inhibition is most effective for high efficiency base excision repair, and least effective for low efficiency repair.

In this study, we develop asynchronous probabilistic cell cycle models to quantitatively assess the effect of ionizing radiation on a human colon cancer cell line. We use both synchronous and asynchronous cell populations and follow treated cells for up to 2 cell cycle times. The model outputs quantify the changes in cell cycle dynamics following ionizing radiation treatment, principally in the duration of both G1 and G2/M phases.

The purpose of this study is to develop a comprehensive mathematical model of DNA double-strand break (DSB) repair in a cell cycle-dependent manner to analyze the improved radiosensitivity of prostate cancer (PCa) cells to ionizing radiation (IR) when radiation treatment is combined with androgen deprivation therapy (ADT). The effectiveness of the combination treatment, which is currently a standard treatment for PCa, depend on DSB repair capacity of the cells as these are the main lesions following IR. It is reported in the literature that the major DSB repair pathways, non-homologous end joining (NHEJ) and homologous recombination (HR), are both impaired after ADT, which then resulted in increased radiosensitivity and better IR treatment outcomes in PCa. In our previous work, we have developed quantitative models for NHEJ and HR individually to analyze the mechanism of the effect of ADT on IR treatment outcomes through impaired repair dynamics. The present work combines these two models in a cell cycle-dependent manner in order to develop a comprehensive model to analyze the repair dynamics after IR only and IR+ADT treatments. NHEJ is the major pathway, whereas HR is restricted to S- or G2-phases of the cell cycle after DNA replication has been completed and we have incorporated the cell cycle dependent contributions of the NHEJ and HR models in our comprehensive model. The literature data used in the development of these previous models were from both in vitro experiments as well as clinical data from PCa patients. In our comprehensive model, we have used the data from the literature to determine the distribution of the initial DSBs for cells in different cell cycle phases as the damage depends on the cell cycle phase at the time of radiation. We have incorporated the data on the percent contributions of NHEJ and HR repair in different cell cycle phases into the model and calculated the repair outcomes from NHEJ and HR models according to these ratios. Cell cycle arrest is implemented in relation to the amount of remaining DSBs in each cell cycle phase after repair. Using the number of unrepaired DSBs, we have calculated the proportion of cells that would progress to the next cell cycle phase as well as the proportion for which the cell death mechanism is triggered. The simulation results showed that ADT combined with IR has enhanced the treatment outcome. The cell survival rate was lower for the combination treatment case (55.7% compared to 62.1 % of IR only case). The cell proliferation was also significantly slower (85-95h doubling time compared to 35-45h of IR only case). The results agreed well with the experimental data that showed 30h and 95.5 h of doubling times for IR only and IR+ADT treatment respectively. The comprehensive model outcomes show that impaired NHEJ and HR dynamics as a result of ADT have the potential to enhance the IR treatment outcomes for PCa patients. Citation Format: Mengdi Qian, Alexandru Almasan, Evren Gurkan-Cavusoglu. Cell cycle-dependent, comprehensive mathematical modeling of the role of DNA repair in response to radiotherapy for prostate cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5499.