Biology subjects

Dunn, P.

Publications and source records attributed to Dunn, P..

10 recordsLinked to original sources

bioRxiv2026

A semi-automated tool for improving Assessments and Lab Tests data annotation in ImmPort

Public data sharing in immunological and clinical research is essential for transparency, reproducibility, and secondary analysis. However, many datasets in repositories such as ImmPort lack sufficient structured data to enable reuse. ImmPort's Assessments and Lab Tests templates -- which capture critical clinical information -- are often incomplete or omitted due to their complexity and the manual effort required. To address this challenge, an application with a graphical user interface requiring no programming was developed to facilitate population of these templates. The tool streamlines the submission process by reducing time and complexity for data contributors while ensuring template formatting. It integrates ImmPort files, study-specific data files, and a curated data dictionary to automate the mapping of study variables to the required fields within each template. The tool was evaluated on seven ImmPort studies with diverse designs. It successfully generated submission-ready templates that passed ImmPort's internal validation and will be incorporated into the repository. By improving the feasibility and completeness of templates, this approach enhances the quality, findability, and reusability of data within ImmPort.

immunology↗

bioRxiv2025

Glucocorticoids unleash immune-dependent melanoma control through inhibition of the GARP/TGF-β axis

Half of advanced melanoma patients fail to benefit from immune checkpoint blockade and novel treatments are urgently required. Testing topical medications used in other skin diseases for anti-cancer activity in an immunotherapy-resistant murine melanoma model, we counterintuitively found that glucocorticoids elicit rapid cytotoxic T lymphocyte (CTL)-dependent tumor control. Genetic ablation of the glucocorticoid receptor in different cellular compartments revealed glucocorticoids acted not on immune cells but directly on tumor cells to downregulate expression of GARP (glycoprotein A repetitions predominant). This inhibited TGF-{beta} signaling and unleashed CTL killing. In agreement, glucocorticoids stimulated tumor control in multiple cancer models, but only if the tumors also responded to pharmacological inhibition of TGF-{beta} signaling. Furthermore, melanoma patients with high glucocorticoid receptor expression or signaling showed improved prognosis and lower TGF-{beta} signaling in tumor-infiltrating CTLs. Additionally, elevated GARP expression correlated with reduced survival, including in immunotherapy-treated patients. Thus, the GARP/TGF-{beta} axis emerges as a glucocorticoid-sensitive cancer cell-intrinsic immune evasive mechanism. SignificanceScreening widely used topical treatments in a melanoma model, this study uncovers a surprising role for glucocorticoids in triggering CD8+ T cell-dependent tumor control through downregulation of GARP and thus TGF-{beta} signaling. Melanoma patient sample analysis supported these findings suggesting GARP/TGF-{beta} activity functions as a tumor cell-intrinsic immune evasive mechanism, and GARP expression may serve as both a biomarker of poor antitumor immunity and a therapeutic target to improve the response to immunotherapy.

cancer biology↗

bioRxiv2025

Zinc Finger Repressors mediate widespread PRNP lowering in the nonhuman primate brain and profoundly extend survival in prion disease mice

Prion disease is a rapidly progressing and invariably fatal neurodegenerative disorder with no approved treatment. The disease is caused by the self-templated misfolding of the prion protein (PrP) into toxic species, ultimately leading to neurodegeneration and death. We evaluated a novel epigenetic regulation approach using Zinc Finger Repressors (ZFRs) to ablate PrP expression at the transcriptional level. When delivered using adeno-associated virus (AAV), ZFRs potently and specifically reduced prion mRNA expression by >95% in vitro and to near undetectable levels within single neurons in vivo. In wildtype mice, ZFRs stably lowered neuronal PrP expression throughout the central nervous system for at least 17 months. In mice inoculated with misfolded PrP, AAV-ZFRs given at either early or late disease stages profoundly extended lifespan, significantly reduced PrP in the brain, and improved an array of molecular, histological, biomarker, and behavioral readouts. Finally, we delivered a ZFR targeting the human prion gene (PRNP) to cynomolgus monkeys using a novel blood-brain-barrier penetrant AAV capsid. Extensive bulk and single-cell assessments revealed widespread ZFR expression and PRNP repression in all 35 brain regions assessed, providing the first demonstration of epigenetic regulation across the nonhuman primate neuraxis following a single intravenous (IV) dose. These results highlight the potential of a one-time IV administered ZFR treatment for prion disease and other neurological disorders.

neuroscience↗

bioRxiv2024

Potent and selective repression of SCN9A by engineered zinc finger repressors for the treatment of neuropathic pain

Peripheral neuropathies are estimated to affect several million patients in the US with no long-lasting therapy currently available. In humans, the Nav1.7 sodium channel, encoded by the SCN9A gene, is involved in a spectrum of inherited neuropathies, and has emerged as a promising target for analgesic drug development. The development of a selective Nav1.7 inhibitor has been challenging, in part due to structural similarities among other Nav channels. Here we present preclinical studies for the first genomic medicine approach using engineered zinc finger repressors (ZFRs) specifically targeting human/nonhuman primate (NHP) SCN9A. AAV-mediated delivery of ZFRs in human iPSC-derived neurons resulted in 90% reduction of SCN9A with no detectable off-target activity. To establish proof-of-concept, a ZFR targeting the mouse Scn9a was assessed in the SNI neuropathic pain mouse model, which resulted in up to 70% repression of Scn9a in mouse DRGs and was associated with reduction in pain hypersensitivity as measured by increased mechanical- and cold-induced pain thresholds. AAV-mediated intrathecal delivery of ZFR in NHPs demonstrated up to 60% repression of SCN9A in bulk DRG tissue and on single-cell levels in the nociceptors. The treatment was well tolerated in NHPs, and no dose-limiting findings were observed four weeks after a single intrathecal injection. Taken together, our results demonstrate that AAV-delivered ZFR targeting the SCN9A gene is promising and supports further development as a potential therapy for peripheral neuropathies.

neuroscience↗

bioRxiv2023

Evidence for a role of 5-HT-glutamate co-releasing neurons in acute stress mechanisms

The majority of midbrain 5-hydroxytryptamine (5-HT) neurons express the vesicular glutamate transporter 3 (VGLUT3) and co-release 5-HT and glutamate, but the function of this co-release is unclear. Given the strong links between 5-HT and uncontrollable stress, we used a combination of c-Fos immunocytochemistry and conditional gene knock out in mice to test the hypothesis that glutamate co-releasing 5-HT neurons would be activated by stress and involved in stress coping. Acute, uncontrollable swim stress increased c-Fos immunoreactivity in neurons co-expressing VGLUT3 and the 5-HT marker tryptophan hydroxylase 2 (TPH2) in the dorsal raphe nucleus (DRN). This effect was localised in the ventral DRN subregion and prevented by the antidepressant fluoxetine. In contrast, a more controllable stressor, acute social defeat, had no effect on c-Fos immunoreactivity in VGLUT3-TPH2 co-expressing neurons in the DRN. To test whether activation of glutamate co-releasing 5-HT neurons was causally linked to stress coping, mice with a specific deletion of VGLUT3 in 5-HT neurons were exposed to acute swim stress. Compared to wildtype controls, the mutant mice showed increased climbing behaviour, a measure of active coping. Wildtype mice also showed increased climbing when administered fluoxetine, revealing an interesting parallel between the behavioural effects of genetic loss of VGLUT3 in 5-HT neurons and 5-HT reuptake inhibition. We conclude that 5-HT-glutamate co-releasing neurons are recruited by exposure to uncontrollable stress. Furthermore, natural variation in the balance of 5-HT and glutamate released at the 5-HT synapse may impact on stress susceptibility.

neuroscience↗

bioRxiv2022

Transcriptional atlas of the human immune response to 13 vaccines reveals a common predictor of vaccine-induced antibody responses

Systems biology approaches have been used to define molecular signatures and mechanisms of immunity to vaccination. However, most such studies have been done with single vaccines, and comparative analysis of the response to different vaccines is lacking. We integrated temporal transcriptional data of over 3,000 samples, obtained from 820 healthy adults across 28 studies of 13 different vaccines and analyzed vaccination-induced signatures associated with the antibody response. Most vaccines induced similar kinetics of shared transcriptional signatures, including signatures of innate immunity occurring 1-3 days post-vaccination, as well as the canonical plasmablast and cell cycle signatures appearing 7 days post-vaccination. However, the yellow fever vaccine YF-17D uniquely induced an early transient signature of T and B cell activation at Day 1, followed by delayed antiviral/interferon and plasmablast signatures that peaked at Days 7 and 14-21, respectively. Thus, despite the shared transcriptional response to most vaccines, at any given time point there was no evidence for a "universal signature" that could be used to predict the antibody response to all vaccines. However, accounting for the asynchronous nature of responses led to the identification of a time-adjusted signature that improved prediction antibody of responses across vaccines. These results provide a transcriptional atlas of the human immune response to vaccination and define a common, time-adjusted signature of antibody responses to vaccination.

immunology↗

bioRxiv2021

The Immune Signatures Data Resource: A compendium of systems vaccinology datasets

Vaccines are among the most cost-effective public health interventions for preventing infection-induced morbidity and mortality, yet much remains to be learned regarding the mechanisms by which vaccines protect. Systems immunology combines traditional immunology with modern omic profiling techniques and computational modeling to promote rapid and transformative advances in vaccinology and vaccine discovery. The NIH/NIAID Human Immunology Project Consortium (HIPC) has leveraged systems immunology approaches to identify molecular signatures associated with the immunogenicity of many vaccines, including those targeting seasonal influenza, yellow fever, and hepatitis B. These data are made available to the broader scientific community through the ImmuneSpace data portal and analysis engine leveraging the NIH/NIAID ImmPort repository1,2. However, a barrier to progress in this area is that comparative analyses have been limited by the distributed nature of some data, potential batch effects across studies, and the absence of multiple relevant studies from non-HIPC groups in ImmPort. To support comparative analyses across different vaccines, we have created the Immune Signatures Data Resource, a compendium of standardized systems vaccinology datasets. This data resource is available through ImmuneSpace, along with code to reproduce the processing and batch normalization starting from the underlying study data in ImmPort and the Gene Expression Omnibus (GEO). The current release comprises 1405 participants from 53 cohorts profiling the response to 24 different vaccines and includes transcriptional profiles and antibody response measurements. This novel systems vaccinology data release represents a valuable resource for comparative and meta-analyses that will accelerate our understanding of mechanisms underlying vaccine responses. [Table 1]

systems biology↗

bioRxiv2021

An innate immune activation state prior to vaccination predicts responsiveness to multiple vaccines

Many factors determine whether an individual responding to vaccination will generate an immune response that can lead to protection. Several studies have shown that the pre-vaccination immune state is associated with the antibody response to vaccines. However, the generalizability and mechanisms that underlie this association remain poorly defined. Here, we sought to identify a common pre-vaccination signature and mechanisms that could predict the immune response across a wide variety of vaccines. We leveraged the "Immune Signatures Data Resource" created by the NIH Human Immunology Project Consortium (HIPC) to integrate data from 28 studies involving 13 different vaccines and associate the blood transcriptional status of 820 healthy young adults with their responses. An unsupervised analysis of blood transcriptional profiles across studies revealed three distinct pre-vaccination states, characterized by the differential expression of genes associated with a pro-inflammatory response, cell proliferation, and metabolism alterations downstream of NF{kappa}B and IRF7. Innate and adaptive immune cell subset-specific genes were also associated with the three pre-vaccination states. Importantly, individuals whose pre-vaccination state was enriched in pro-inflammatory response genes known to be downstream of NF{kappa}B tended to have higher serum antibody responses one month after vaccination. A supervised analysis of the same data resulted in a single classifier, also enriched for NF{kappa}B regulated genes, that predicted the antibody response across most of the vaccines. Projection into single-cell RNA-sequencing data suggested that this pre-vaccination state was attributable to the signature of activation of non-classical monocytes and myeloid dendritic cells. Transcriptional signatures of acute responses to bacterial and not viral infections were enriched in the high pro-inflammatory pre-vaccination state and also included NF{kappa}B regulated genes. The pro-inflammatory pre-vaccination state was highly reminiscent of the innate activation state triggered by TLR ligands or adjuvants. These results demonstrate that wide variations in the transcriptional state of the immune system in humans can be a key determinant of responsiveness to vaccination. They also define a transcriptional signature NF{kappa}B activation at baseline, that is associated with a greater magnitude of antibody response to multiple vaccines, and suggest that modulation of the innate immune system by next-generation adjuvants targeting NF{kappa}B before vaccine administration may improve vaccine responsiveness.

systems biology↗

bioRxiv2017

The 10,000 Immunomes Project: A resource for human immunology

New immunological assays now enable rich measurements of human immune function, but difficulty attaining enough measurements across sufficiently large and diverse cohorts has hindered describing normal human immune physiology on a large scale. Here we present the 10,000 Immunomes Project (10KIP), a diverse human immunology reference derived from over 44,000 individuals across 242 studies from ImmPort, a publicly available resource of raw immunology study data and protocols. We carefully curated datasets, aggregating subjects from healthy/control arms and harmonizing data across studies. We demonstrate 10KIPs utility by describing variations in serum cytokines and leukocytes by age, race, and sex; defining a baseline cell-cytokine network; and using 10KIP as a common control to describe immunologic changes in pregnancy. Subject-level data is available for interactive visualization and download at http://10kImmunomes.org/. We believe 10KIP can serve as a common control cohort and will accelerate hypothesis generation by clinical and basic immunologists across diverse populations.\n\nOne Sentence SummaryAn open online resource of human immunology data from more than 10,000 normal subjects including interactive data visualization and download enables a new look at immune system differences across age and sex, rapid hypothesis generation, and creation of custom control cohorts.

immunology↗

bioRxiv2017

Meta-analysis of Cytometry Data Reveals Racial Differences in Immune Cells

While meta-analysis has demonstrated increased statistical power and more robust estimations in studies, the application of this commonly accepted methodology to cytometry data has been challenging. Different cytometry studies often involve diverse sets of markers. Moreover, the detected values of the same marker are inconsistent between studies due to different experimental designs and cytometer configurations. As a result, the cell subsets identified by existing auto-gating methods cannot be directly compared across studies. We developed MetaCyto for automated meta-analysis of both flow and mass cytometry (CyTOF) data. By combining clustering methods with a silhouette scanning method, MetaCyto is able to identify commonly labeled cell subsets across studies, thus enabling meta-analysis. Applying MetaCyto across a set of 10 heterogeneous cytometry studies totaling 2926 samples enabled us to identify multiple cell populations exhibiting differences in abundance between White and Asian adults. Software is released to the public through GitHub (github.com/hzc363/MetaCyto).

bioinformatics↗