Biology subjects

Greene, J. M.

Publications and source records attributed to Greene, J. M..

5 recordsLinked to original sources

bioRxiv2025

Antigen presenting cells play a critical role in determining response to regulatory T cell therapy in type 1 diabetes

Type 1 diabetes (T1D) is an autoimmune disease in which the immune system attacks pancreatic beta cells, leading to high blood glucose levels and requiring lifelong insulin therapy. There is no cure, and individuals with T1D may face a reduced lifespan of up to 12 years. Defects in regulatory T cells (Tregs) are a key contributor to disease onset and are being explored as a therapeutic avenue. However, the effectiveness of Treg therapy remains uncertain. Research is further limited by the inability to directly observe pancreatic and lymph node activity during the long presymptomatic stage of T1D. In this study, we develop a mathematical model for beta and T cell dynamics. We find both Treg quality and quantity affect disease progression, and that antigen-presenting cell (APC) dynamics play a central role. Notably, Treg therapy combined with APC depletion improves outcomes, especially with strong peptide-induced APC activation.

immunology↗

bioRxiv2022

Reactive Oxygen Species Signaling Differentially Controls Wound Healing and Regeneration

Reactive oxygen species (ROS), such as hydrogen peroxide, are conserved and critical components of both wound healing and regeneration. Even though millions are affected each year by poor wound healing and an inability to restore functional tissue, how the same ROS-mediated signaling regulates these two different processes is not fully understood. Here, we investigate the role(s) of ROS during planarian wound healing and regeneration. We show ROS accumulate after injury and are required for wound closure (by promoting cytoskeletal movements) and regrowth (by promoting blastema formation). We found that different threshold levels of ROS regulate separate downstream targets to control wound healing (jun-1) versus regeneration (hsp70). By only manipulating ROS levels, we were able to control which injury-induced program was initiated: failure to close (chronic wound), healing only (no blastema), or full regeneration. Our results demonstrate that healing versus regenerative outcomes are based on differential ROS-mediated gene expression soon after injury. This study highlights ROS signaling as a potential therapeutic means to control wound repair mechanisms in multiple contexts. Therefore, investigating the mechanisms by which ROS control different tissue repair processes will be necessary not only for regenerative medicine but to improve clinical outcomes for chronic wounds and fibrosis.

developmental biology↗

bioRxiv2019

Validation of a Mathematical Model of Cancer Incorporating Spontaneous and Induced Evolution to Drug Resistance

This paper continues the study of a model which was introduced in earlier work by the authors to study spontaneous and induced evolution to drug resistance under chemotherapy. The model is fit to existing experimental data, and is then validated on additional data that had not been used when fitting. In addition, an optimal control problem is studied numerically.

cancer biology↗

bioRxiv2017

A mathematical approach to differentiate spontaneous and induced evolution to drug resistance during cancer treatment

Drug resistance is a major impediment to the success of cancer treatment. Resistance is typically thought to arise through random genetic mutations, after which mutated cells expand via Darwinian selection. However, recent experimental evidence suggests that the progression to drug resistance need not occur randomly, but instead may be induced by the treatment itself, through either genetic changes or epigenetic alterations. This relatively novel notion of resistance complicates the already challenging task of designing effective treatment protocols. To better understand resistance, we have developed a mathematical modeling framework that incorporates both spontaneous and drug-induced resistance. Our model demonstrates that the ability of a drug to induce resistance can result in qualitatively different responses to the same drug dose and delivery schedule. We have also proven that the induction parameter in our model is theoretically identifiable, and proposed an in vitro protocol which could be used to determine a treatments propensity to induce resistance.

cancer biology↗

bioRxiv2017

Translation Inhibition And Resource Balance In The Cell-Free Gene Expression System

Quantifying the effect of vital resources on transcription and translation helps to understand the degree to which the concentration of each resource must be regulated for achieving homeostasis. Utilizing the synthetic transcription-translation (TX-TL) system, we study the impact of nucleotide triphosphates (NTPs) and magnesium (Mg2+), on gene expression. Recent observations of the counterintuitive phenomenon of suppression of gene expression at high NTP concentrations have led to the speculation that such suppression is due to the consumption of resources by transcription, hence leaving fewer resources for translation. In this work, we investigate an alternative hypothesis: direct suppression of the translation rate via stoichiometric mismatch in necessary reagents. We observe NTP-dependent suppression even in the early phase of gene expression, contradicting the resource limitation argument. To further decouple the contributions of transcription and translation, we performed gene expression experiments with purified mRNA. Simultaneously monitoring mRNA and protein abundances allowed us to extract a time-dependent translation rate. Measuring translation rates for different Mg2+ and NTP concentrations, we observe a complex resource dependence. We demonstrate that translation is the rate-limiting process that is directly inhibited by high NTP concentrations. Additional Mg2+ can partially reverse this inhibition. In several experiments, we observe two maxima of the translation rate viewed as a function of both Mg2+ and NTP concentration, which can be explained in terms of an NTP-independent effect on the ribosome complex and an NTP-Mg2+ titration effect. The non-trivial compensatory effects of abundance of different vital resources signals the presence of complex regulatory mechanisms to achieve optimal gene expression.

synthetic biology↗