Biology subjects

Sample, P. J.

Publications and source records attributed to Sample, P. J..

3 recordsLinked to original sources

bioRxiv2026

A Dynamically Regulated Designed IL-2 for Tumor-localized Signaling

Cytokines mediate cell-cell communication to coordinate immune responses and hold clinical promise as immunotherapies. While natural cytokines are exquisitely regulated by immune cells, engineered cytokines have not yet matched this sophisticated regulation, limiting clinical efficacy and safety. IL-2 is an important cytokine involved in antitumor response, but its production is disrupted in the immune-suppressive tumor microenvironment. Here we designed a regulated IL-2 module, OUTSMART designed IL-2 (dIL-2), that functions robustly in solid tumors and reduces systemic activity that could trigger toxicity: we computationally redesigned IL-2 to have a novel topology that increases stability, preserves native IL-2R{beta}{gamma} interfaces, ablates IL-2R binding, and delivers IL-2 signaling to CD8+ immune-effector cells. This designed cytokine is genetically regulated by a T cell activation-responsive promoter, allowing dynamic production from chimeric antigen receptor (CAR) T cells. Like wild type IL-2, OUTSMART dIL-2 drives T cell proliferation and enhances effector function. Unlike wild type IL-2, it preferentially stimulates CD8+ T cells and Natural Killer (NK) cells, avoids T regulatory cells, and stimulates CAR-T proliferation while preserving stemness, achieving durable tumor elimination in two solid tumor animal models. These design principles can be applied to create other dynamically-regulated cytokine systems that address mechanisms of complex disease.

synthetic biology↗

bioRxiv2026

A Rationally Designed Transgene Drives CAR T Functional Persistence and Durable Regression of Solid Tumors

The eradication of solid tumors by chimeric antigen receptor (CAR) T cells requires dynamic therapies capable of outlasting an immune suppressive tumor microenvironment (TME). However, biological barriers--including rapid exhaustion, poor expansion, and loss of stem-like memory--quickly neutralize these therapies. Because single-technology interventions often introduce unacceptable tradeoffs between efficacy and safety, durable remission demands a paradigm where multiple engineered solutions work in concert. To holistically address these mechanisms, we rationally designed a single-vector transgene that intrinsically drives CAR T functional persistence. The platform integrates four synergistic technologies: a high-avidity mesothelin (MSLN)-targeting CAR optimized to resist shed decoy antigens, a T-cell activation-responsive promoter (OUTLAST OP1) resisting exhaustion, a CD8-targeted designed IL-2 cytokine (OUTSMART dIL-2) driving intratumoral CAR-T expansion, and an EGFRopt safety switch. In lung and ovarian cancer models, this rational integration was required to drive antigen-dependent T cell expansion and eradicate established tumors at extremely low CAR T doses. Furthermore, engineered cells established a self-renewing pool of stem-like memory T cells capable of rejecting tumor rechallenge months later. Ultimately, this work demonstrates that intrinsic T cell dysfunction and extrinsic tumor-derived barriers can be simultaneously overcome by integrating synergistic technologies.

synthetic biology↗

bioRxiv2018

Human 5′ UTR design and variant effect prediction from a massively parallel translation assay

Predicting the impact of cis-regulatory sequence on gene expression is a foundational challenge for biology. We combine polysome profiling of hundreds of thousands of randomized 5' UTRs with deep learning to build a predictive model that relates human 5' UTR sequence to translation. Together with a genetic algorithm, we use the model to engineer new 5' UTRs that accurately target specified levels of ribosome loading, providing the ability to tune sequences for optimal protein expression. We show that the same approach can be extended to chemically modified RNA, an important feature for applications in mRNA therapeutics and synthetic biology. We test 35,000 truncated human 5' UTRs and 3,577 naturally-occurring variants and show that the model accurately predicts ribosome loading of these sequences. Finally, we provide evidence of 47 SNVs associated with human diseases that cause a significant change in ribosome loading and thus a plausible molecular basis for disease.

synthetic biology↗