Biology subjects

Pullen, K. M.

Publications and source records attributed to Pullen, K. M..

5 recordsLinked to original sources

bioRxiv2024

Cross species modeling reveals a role for the unfolded protein response in shaping the transcriptional reaction to Mycobacterium tuberculosis infection

Numerous blood mRNA signatures have been developed to diagnose tuberculosis (TB) disease. The utility of these signatures in diverse populations depends on the inclusion of ubiquitously expressed features, such as type 1 interferon (IFN) production and innate immune cell activities. As a result, these signatures are generally insensitive to heterogeneous responses between individuals. Designing more effective therapies will require understanding the diverse mechanisms underlying pathogenesis by associating them with appropriate preclinical animal models. To address this critical animal-to-human gap, we applied a modeling framework, Translatable Components Regression, which is designed to account for biological heterogeneity by identifying multiple orthogonal axes of variation that are common to humans and animal models. Our framework was capable of distinguishing human active TB from latent TB infection using a model derived from murine data. This discrimination was based on differential expression of numerous biological pathways in addition to the common IFN and neutrophil signatures. Prominent among these predictive pathways was protein translation, which we show is a feature of the Mtb infection-induced Unfolded Protein Response (UPR) in macrophages. We show that this cellular stress pathway controls a variety of immune-related functions in Mtb-infected mouse macrophages, suggesting a possible causative role during the development of TB disease. Significance StatementDespite tuberculosis being one of the top causes of global mortality, the mechanisms that control the progression of disease are still not fully understand. Here we leverage a systems-level modeling approach that incorporates transcriptomics data across thousands of genes from both a traditional tuberculosis mouse model and human clinical samples to implicate a previously unappreciated mechanism in pathogenesis, the unfolded protein response. We validate these findings in a mouse macrophage model and pinpoint which branch of the unfolded protein response might be activated during tuberculosis infection. These insights, originally derived from our cross-species model, may allow us to better understand human tuberculosis pathogenesis and potentially identify therapeutic targets to prevent active tuberculosis.

systems biology↗

bioRxiv2023

Autoencoder Model for Translating Omics Signatures

The development of effective therapeutics and vaccines for human diseases requires a systematic understanding of human biology. While animal and in vitro culture models have successfully elucidated the molecular mechanisms of diseases in many studies, they yet fail to adequately recapitulate human biology as evidenced by the predominant likelihood of failure in clinical trials. To address this broadly important problem, we developed AutoTransOP, a neural network autoencoder framework to map omics profiles from designated species or cellular contexts into a global latent space, from which germane information can be mapped between different contexts. This approach performs as well or better than extant machine learning methods and can identify animal/culture-specific molecular features predictive of other contexts, without requiring homology matching. For an especially challenging test case, we successfully apply our framework to a set of inter-species vaccine serology studies, where no 1-1 mapping between human and non-human primate features exists.

bioinformatics↗

bioRxiv2022

3D RNA-scaffolded wireframe origami

Hybrid RNA:DNA origami, in which a long RNA scaffold strand is folded into a target nanostructure via thermal annealing with complementary DNA oligos, has only been explored to a limited extent despite its unique potential for biomedical delivery of mRNA, tertiary structure characterization of long RNAs, and fabrication of artificial ribozymes. Here, we investigate design principles of wireframe RNA-scaffolded origami in three dimensions rendered as polyhedra composed of dual-duplex edges. We computationally designed, fabricated, and characterized tetrahedra folded from an EGFP-encoding messenger RNA and de Bruijn sequences, an octahedron folded with M13 transcript RNA, and an octahedron and pentagonal bipyramids folded with 23S ribosomal RNA, demonstrating the ability to make diverse polyhedral shapes with distinct structural and functional RNA scaffolds. We characterized secondary and tertiary structures using dimethyl sulfate mutational profiling and cryo-electron microscopy, revealing for the first time insight into both global and local, base-level structures of origami. Our top-down sequence design strategy enables the use of long RNAs as functional scaffolds for complex wireframe origami.

bioengineering↗

bioRxiv2021

Sexually dimorphic placental responses to maternal SARS-CoV-2 infection

There is a persistent male bias in the prevalence and severity of COVID-19 disease. Underlying mechanisms accounting for this sex difference remain incompletely understood. Interferon responses have been implicated as a modulator of disease in adults, and play a key role in the placental anti-viral response. Moreover, the interferon response has been shown to alter Fc-receptor expression, and therefore may impact placental antibody transfer. Here we examined the intersection of viral-induced placental interferon responses, maternal-fetal antibody transfer, and fetal sex. Placental interferon stimulated genes (ISGs), Fc-receptor expression, and SARS-CoV-2 antibody transfer were interrogated in 68 pregnancies. Sexually dimorphic placental expression of ISGs, interleukin-10, and Fc receptors was observed following maternal SARS-CoV-2 infection, with upregulation in males. Reduced maternal SARS-CoV-2-specific antibody titers and impaired placental antibody transfer were noted in pregnancies with a male fetus. These results demonstrate fetal sex-specific maternal and placental adaptive and innate immune responses to SARS-CoV-2.

immunology↗

bioRxiv2020

Morphological profiling of tubercule bacilli identifies drug pathways of action

Morphological profiling is a method to classify target pathways of antibacterials based on how bacteria respond to treatment through changes to cellular shape and spatial organization. Here, we utilized the cell-to-cell variation in morphological features of Mycobacterium tuberculosis bacilli to develop a rapid profiling platform called Morphological Evaluation and Understanding of Stress (MorphEUS). MorphEUS classified 94% of tested drugs correctly into broad categories according to modes of action previously identified in the literature. In the other 6%, MorphEUS pointed to key off-target or secondary bactericidal activities. We observed cell-wall damaging activity induced by bedaquiline and moxifloxacin through secondary effects downstream from their main target pathways. We implemented MorphEUS to correctly classify three compounds in a blinded study and identified an off-target effect for one compound that was not readily apparent in previous studies. We anticipate that the ability of MorphEUS to rapidly identify pathways of drug action and the proximal cause of bactericidal activity in tubercule bacilli will make it applicable to other pathogens and cell types where morphological responses are subtle and heterogeneous. Significance StatementTuberculosis is a leading cause of death in the world and requires treatment with an arduous multidrug regimen. Many new tuberculosis drugs are in development, and the drug development pipeline would benefit from more rapid methods to learn drug mechanism of action and off-target effects. Here, we describe a high throughput imaging method for rapidly classifying drugs into categories based on the primary and secondary cellular damage called Morphological Evaluation and Understanding of drug-Stress (MorphEUS). We anticipate that MorphEUS will assist in rapidly pinpointing causes of cellular death in response to drug treatment in tuberculosis and other bacterial pathogens.

microbiology↗