Biology subjects

Sperling, A.

Publications and source records attributed to Sperling, A..

4 recordsLinked to original sources

bioRxiv2026

A Lenalidomide-Inducible Suicide Switch for Gene- and Cell-Based Therapy

Genetically modified immune effector cells, including chimeric antigen receptor (CAR) T cells, have emerged as transformative anti-cancer agents. However, these autonomous, living therapies are limited by difficult-to-control hyperactivation toxicities. To achieve their full potential as therapies for a broader range of diseases, CAR T cells must target novel antigens and integrate further potency enhancements that raise the possibility of novel and intensified toxicities. High performance safety systems are needed to restrain these highly active next-generation gene- and cell-based therapies. Cell therapy suicide switches remain infrequently used, and are currently limited by inaccessible controller drugs, incomplete cell depletion, fitness cost, and immunogenicity. To address these issues, we engineered a fully human sequence-based cell therapy suicide switch based on the overexpression of Caspase-Activated DNase (CAD) and its stoichiometric chaperone/inhibitor ICAD fused to a lenalidomide-inducible degron. Acute destabilization of ICAD with the broadly available, off-patent molecular glue degrader drug lenalidomide uncaged CAD to induce DNA damage and cell death. By this degradable cage mechanism, the ICAD-CAD suicide switch achieved long-term expression in primary human T cells without detectable leakiness, and deep drug-induced cell depletion. The ICAD-CAD switch was generalizable to alternative acute destabilization systems. Genome-wide CRISPR screening established the necessity of CAD and the lenalidomide-interacting E3 ubiquitin ligase substrate adaptor CRBN for switch function. When co-delivered with a CAR, ICAD-CAD CAR T cells retained effector functions and could be rapidly depleted with lenalidomide.

synthetic biology↗

bioRxiv2026

Computational Analysis of Fibroblast Subpopulation Dynamics as a Driver of Fibrotic Foci Formation

Fibroblasts maintain the extracellular matrix (ECM) to support tissue homeostasis and wound healing. In fibrotic diseases, fibroblasts are a primary driver of disease progression through excess collagen secretion and enhanced contractility. Replacing native tissue with a collagen rich fibrotic scar leads to a decline in tissue function. Recent research into idiopathic pulmonary fibrosis (IPF) has identified fibroblast subpopulations that may be primed for the hyper-activation that leads to increased progression of fibrotic disease. Understanding the contribution of these subpopulations to disease progression requires integrating experimental and computational techniques to understand their dynamic contributions to tissue phenotype. Herein, we introduce a framework for modeling subpopulations using a multiscale mechanistic computational model to understand differences within subpopulations, at the intracellular level and how these differences contribute to cell-and tissue-level pathology. We build and validate this framework using two well-defined subpopulations of fibroblasts in IPF. The subpopulations are defined by the presence or absence of Thy-1, a cell-surface protein that regulates fibroblast mechanosensing. We first developed a logic-based network model of a fibroblast. We then applied this model to identify sub-networks that regulate myofibroblast marker expression in the two subpopulations. Coupling this with an agent-based model (ABM) of the lung microenvironment, we observed how different rules regulating cell fate decisions in each subpopulation affected collagen content. Computational image outputs were analyzed with the open-source biological image analysis software QuPath to quantify how changes in subpopulation dynamics change model-predicted foci characteristics such as size and collagen density. We find that the ability for Thy-1+ fibroblasts to transition to Thy-1- fibroblasts significantly increases total collagen content, as well as influences fibrotic foci characteristics. Overall, we present a combined experimental and computational framework for studying how dynamic changes in fibroblast subpopulations lead to tissue-level disease phenotypes. Author SummaryIn wound healing fibroblasts are responsible for rebuilding the scaffolding, called the extracellular matrix (ECM), of the damaged tissue to aid in regeneration. In fibrosis, the normal wound healing processes are hijacked leading to overproduction of ECM proteins, such as collagen, by fibroblasts leading to fibrosis. In fibrotic diseases with no known cause, such as idiopathic pulmonary fibrosis (IPF), subpopulations of fibroblasts have been identified as possible drivers of disease. Herein, we use a multiscale computational model that represents intracellular, cellular, and tissue level signaling to study how the presence or absence of a single protein on a fibroblasts surface, Thy-1, affects the formation of fibrotic scar in IPF. Thy-1 regulates how a fibroblast senses the stiffness of the microenvironment. The absence of Thy-1 impacted intracellular signaling and when combined across many cells led to fibrosis at the tissue level. Additionally, if normal Thy-1+ fibroblasts could dynamically lose Thy-1 expression the amount of collagen they produced correlated with that in end stage IPF lungs. This model presents a framework for studying different fibroblast subpopulations using multiscale computational modeling to understand how changes in a single protein in one cell can, over an entire population, affect the dynamics of disease progression.

bioengineering↗

bioRxiv2024

The origin, deployment, and evolution of a plant-parasitic nematode effectorome

Plant-parasitic nematodes constrain global food security. During parasitism, they secrete effectors into the host plant from two types of pharyngeal gland cells. These effectors elicit profound changes in host biology to suppress immunity and establish a unique feeding organ from which the nematode draws nutrition. Despite the importance of effectors in nematode parasitism, there has been no comprehensive identification and characterisation of the effector repertoire of any plant-parasitic nematode. To address this, we advance techniques for gland cell isolation and transcriptional analysis to define a stringent annotation of putative effectors for the cyst nematode Heterodera schachtii at three key life-stages. We define 659 effector gene loci: 293 "known" high-confidence homologs of plant-parasitic nematode effectors, and 366 "novel" effectors with high gland cell expression. In doing so we define a comprehensive "effectorome" of a plant-parasitic nematode. Using this effector definition, we provide the first systems-level understanding of the origin, deployment and evolution of a plant-parasitic nematode effectorome. The robust identification of the comprehensive effector repertoire of a plant-parasitic nematode will underpin our understanding of nematode pathology, and hence, inform strategies for crop protection.

plant biology↗

bioRxiv2021

SARS-CoV-2 infection reduces Krüppel-Like Factor 2 in human lung autopsy

Acute respiratory distress syndrome (ARDS) occurred in ~12% of hospitalized COVID-19 patients in a recent New York City cohort. Pulmonary endothelial dysfunction, characterized by increased expression of inflammatory genes and increased monolayer permeability, is a major component of ARDS. Vascular leak results in parenchymal accumulation of leukocytes, protein, and extravascular water, leading to pulmonary edema, ischemia, and activation of coagulation associated with COVID-19. Endothelial inflammation further contributes to uncontrolled cytokine storm in ARDS. We have recently demonstrated that Kruppel-like factor 2 (KLF2), a transcription factor which promotes endothelial quiescence and monolayer integrity, is significantly reduced in experimental models of ARDS. Lung inflammation and high-tidal volume ventilation result in reduced KLF2, leading to pulmonary endothelial dysfunction and acute lung injury. Mechanistically, we found that KLF2 is a potent transcriptional activator of Rap guanine nucleotide exchange factor 3 (RAPGEF3) which orchestrates and maintains vascular integrity. Moreover, KLF2 regulates multiple genome-wide association study (GWAS)-implicated ARDS genes. Whether lung KLF2 is regulated by SARS-CoV-2 infection is unknown. Here we report that endothelial KLF2 is significantly reduced in human lung autopsies from COVID-19 patients, which supports that ARDS due to SARS-CoV-2 is a vascular phenotype possibly attributed to KLF2 down-regulation. We provide additional data demonstrating that KLF2 is down-regulated in SARS-CoV infection in mice.

pathology↗