Biology subjects

Newhouse, D.

Publications and source records attributed to Newhouse, D..

7 recordsLinked to original sources

bioRxiv2023

Spatial transcriptomics reveals molecular dysfunction associated with Lewy pathology

Lewy pathology composed of -synuclein is the key pathological hallmark of Parkinsons disease (PD), found both in dopaminergic neurons that control motor function, and throughout cortical regions that control cognitive function. Recent work has investigated which dopaminergic neurons are most susceptible to death, but little is known about which neurons are vulnerable to developing Lewy pathology and what molecular changes an aggregate induces. In the current study, we use spatial transcriptomics to selectively capture whole transcriptome signatures from cortical neurons with Lewy pathology compared to those without pathology in the same brains. We find, both in PD and in a mouse model of PD, that there are specific classes of excitatory neurons that are vulnerable to developing Lewy pathology in the cortex. Further, we identify conserved gene expression changes in aggregate-bearing neurons that we designate the Lewy-associated molecular dysfunction from aggregates (LAMDA) signature. This gene signature indicates that neurons with aggregates downregulate synaptic, mitochondrial, ubiquitin-proteasome, endo-lysosomal, and cytoskeletal genes and upregulate DNA repair and complement/cytokine genes. However, beyond DNA repair gene upregulation, we find that neurons also activate apoptotic pathways, suggesting that if DNA repair fails, neurons undergo programmed cell death. Our results identify neurons vulnerable to Lewy pathology in the PD cortex and identify a conserved signature of molecular dysfunction in both mice and humans.

neuroscience↗

bioRxiv2023

Agreement between the ventilated capsule and the KuduSmart(R) device for measuring sweating responses to passive heat stress and exercise

The present study assessed agreement between the KuduSmart(R) device and the ventilated capsule (VC) technique for measuring: i) minute-averaged local sweat rate (LSR); ii) sweating onset; iii) thermosensitivity; and iv) steady-state LSR, during passive heat stress and exercise. On two separate occasions for each heat stress intervention, participants were either passively heated by recirculating hot water (49{degrees}C) through a tube-lined garment until rectal temperature increased 1{degrees}C over baseline (n=8), or walked on a treadmill for 60 minutes at a fixed rate of heat production (n=9). LSR of the forearm was concurrently measured with a VC and the KuduSmart(R) device secured within [~]2 cm. Mean body temperature was calculated as the weighted average between rectal (80%) and mean skin (20%) temperature. Using a ratio scale Bland-Altman analysis with the VC as the reference, the KuduSmart(R) device demonstrated systematic bias for minute-averaged LSR (1.19 [1.09, 1.28]) and steady-state LSR (1.16 [1.09,1.23]), however no bias for thermosensitivity (1.08 [1.00, 1.16]) or sweating onset (1.00 [1.00, 1.00]). Although poor agreement was observed for minute-averaged LSR (CV = 43.3%), more than 73% of all observations with the KuduSmart(R) device (n=2795) were within an absolute error of < 0.2 mg/cm2/min to the VC. The KuduSmart(R) device demonstrated acceptable agreement for steady-state LSR (CV = 19.5%) and thermosensitivity (CV = 21.7%), and almost perfect agreement for sweating onset (CV = 0.14%). Collectively, the KuduSmart(R) device may be a satisfactory in-field solution for assessing the sweating response to heat stress.

physiology↗

bioRxiv2023

GSK-3 inhibitor elraglusib enhances tumor-infiltrating immune cell activation in tumor biopsies and synergizes with anti-PD-L1 in a murine model of colorectal cancer

Inhibition of GSK-3 using small-molecule elraglusib has shown promising preclinical antitumor activity. Using in vitro systems, we found that elraglusib promotes immune cell-mediated tumor cell killing, enhances tumor cell pyroptosis, decreases tumor cell NF-{kappa}B-regulated survival protein expression, and increases immune cell effector molecule secretion. Using in vivo systems, we observed synergy between elraglusib and anti-PD-L1 in an immunocompetent murine model of colorectal cancer. Murine responders had more tumor-infiltrating T-cells, fewer tumor-infiltrating Tregs, lower tumorigenic circulating cytokine concentrations, and higher immunostimulatory circulating cytokine concentrations. To determine the clinical significance, we utilized human plasma samples from patients treated with elraglusib and correlated cytokine profiles with survival. Using paired tumor biopsies, we found that CD45+ tumor-infiltrating immune cells had lower expression of inhibitory immune checkpoints and higher expression of T-cell activation markers in post-elraglusib patient biopsies. These results introduce several immunomodulatory mechanisms of GSK-3 inhibition using elraglusib, providing a rationale for the clinical evaluation of elraglusib in combination with immunotherapy. Statement of significancePharmacologic inhibition of GSK-3 using elraglusib sensitizes tumor cells, activates immune cells for increased anti-tumor immunity, and synergizes with anti-PD-L1 immune checkpoint blockade. These results introduce novel biomarkers for correlations with response to therapy which could provide significant clinical utility and suggest that elraglusib, and other GSK-3 inhibitors, should be evaluated in combination with immune checkpoint blockade.

cancer biology↗

bioRxiv2022

Ultra High-Plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles

A deeper understanding of complex biological processes, including tumor development and immune response, requires ultra high-plex, spatial interrogation of multiple "omes". Here we present the development and implementation of a novel spatial proteogenomic (SPG) assay on the GeoMx(R) Digital Spatial Profiler platform with NGS readout that enables ultra high-plex digital quantitation of proteins (> 100-plex) and RNA (whole transcriptome, > 18,000-plex) from a single FFPE sample. This study highlighted the high concordance, R > 0.85, and <11% change in sensitivity between SPG assay and the single analyte -assays on various cell lines and tissues from human and mouse. Furthermore, we demonstrate that the SPG assay was reproducible across multiple users. When used in conjunction with advanced cellular neighborhood segmentation, distinct immune or tumor RNA and protein targets were spatially resolved within individual cell subpopulations in human colorectal cancer and non-small cell lung cancer. We used the SPG assay to interrogate 23 different glioblastoma multiforme samples across 4 pathologies. The study revealed distinct clustering of both RNA and protein based on pathology and anatomic location. The in-depth investigation of giant cell glioblastoma multiforme revealed distinct protein and RNA expression profiles compared to that of the more common glioblastoma multiforme. More importantly, the use of spatial proteogenomics allowed simultaneous interrogation of critical protein post-translational modifications alongside whole transcriptomic profiles within the same distinct cellular neighborhoods.

cancer biology↗

bioRxiv2021

Sustained IL-15 response signature predicts RhCMV/SIV vaccine efficacy

Simian immunodeficiency virus (SIV) challenge of rhesus macaques (RMs) vaccinated with Rhesus Cytomegalovirus (RhCMV) vectors expressing SIV proteins (RhCMV/SIV) results in a binary outcome: stringent control and subsequent clearance of highly pathogenic SIV in ~55% of vaccinated RMs with no protection in the remaining 45%. Although previous work suggests that unconventionally restricted, SIV-specific, effector-memory (EM)-biased CD8+ T cell responses are necessary for efficacy, the magnitude of these responses does not predict efficacy, and the basis of protection vs. non-protection in RhCMV/SIV vector-vaccinated RMs has not been elucidated. Here, we report that RhCMV/SIV vector administration strikingly alters the whole blood transcriptome of vaccinated RMs, with the sustained induction of specific immune-related pathways, including non-canonical T cell receptor (TCR), toll-lie receptor (TLR), inflammasome/cell death, and interleukin-15 (IL-15) signaling, significantly predicting protection. The IL-15 gene expression signature was further evaluated in an independent RM IL-15 treatment cohort, revealing that in whole blood the response to IL-15 is inclusive of innate and adaptive immune gene expression networks that link with RhCMV/SIV vaccine efficacy. We also show that this IL-15 response signature similarly tracks with vaccine protection in an independent RhCMV/SIV vaccination/SIV challenge RM validation cohort. Thus, the RhCMV/SIV vaccine imparts a coordinated and persistent induction of innate and adaptive immune pathways featuring IL-15, a known regulator of CD8+ T cell function, that enable vaccine-elicited CD8+ T cells to mediate protection against highly pathogenic SIV challenge. Author SummarySIV insert-expressing vaccine vectors based on strain 68-1 RhCMV elicit robust, highly effector-memory-biased T cell responses that are associated with an unprecedented level of SIV control after challenge (replication arrest leading to clearance) in slightly over half of vaccinated monkeys. Since efficacy is not predicted by standard measures of immunogenicity, we used functional genomics analysis of RhCMV/SIV vaccinated monkeys with known challenge outcomes to identify immune correlates of protection. We found that arrest of viral replication after challenge significantly correlates with a vaccine-induced response to IL-15 that includes modulation of T cell, inflammation, TLR signaling, and cell death programming. These data suggest that RhCMV/SIV efficacy is not based on chance, but rather, results from a coordinated and sustained vaccine-mediated induction of innate and adaptive immune pathways featuring IL-15, a known regulator of CD8+ effector-memory T cell function, that enable vaccine-elicited CD8+ T cells to mediate efficacy.

genomics↗

bioRxiv2018

Parent and offspring genotypes influence gene expression in early life

Parents can have profound effects on offspring fitness. Little, however, is known about the mechanisms through which parental care variation influences offspring physiology in natural systems. White-throated sparrows Zonotrichia albicollis (WTSPs) exist in two genetic morphs, tan and white, controlled by a large polymorphic supergene. Morphs mate disassortatively, resulting in two pair types: tan male x white female (TxW) pairs, which provide biparental care and white male x tan female (WxT) pairs, which provide female-biased care. To investigate the effects of parental care variation, we performed RNA-seq on WTSP nestlings sampled from nests of both pair types. Pair type had the largest effect on nestling gene expression, with 881 genes differentially expressed (DE) and seven correlated gene co-expression modules. The DE genes and modules up-regulated in nests with female-biased parental care primarily function in metabolism and stress-related pathways resulting from the overrepresentation of stress response and proteolysis genes. These results show that parental genotypes, a proxy for parental care in this system, alter nestling physiology and highlight avenues of further research investigating the ultimate implications of alternative parental care strategies. Nestlings also exhibited morph-specific gene expression, driven by innate immunity genes and co-expression of genes located in the supergene. Remarkably, we identified the same regulatory hub genes in these blood-derived expression networks as were previously identified in WTSP brains (EPM2A, BPNT1, TAF5L). These hub genes were located within the supergene, highlighting the importance of this gene complex in structuring regulatory networks across diverse tissues.

genomics↗

bioRxiv2017

Transcriptional response to West Nile virus infection in the zebra finch (Taeniopygia guttata), a songbird model for immune function

West Nile Virus (WNV) is the one of most widespread arboviruses worldwide. WNV exists in a bird-mosquito transmission cycle where passerine birds act as the primary reservoir host. As a public health concern, the mammalian immune response to WNV has been studied in detail. Little, however, is known about the avian immune response to WNV. Avian taxa show variable susceptibility to WNV and what drives this variation is unknown. Thus, to study the immune response to WNV in birds, we experimentally infected captive zebra finches (Taeniopygia guttata). Zebra finches provide a useful model, as like many natural avian hosts they are moderately susceptible to WNV and thus provide sufficient viremia to infect mosquitoes. We performed splenic RNAseq during peak viremia to provide an overview of the transcriptional response. In general, we find strong parallels with the mammalian immune response to WNV, including up-regulation of five genes in the Rig-I-like receptor signaling pathway, and offer insights into avian specific responses. Together with complementary immunological assays, we provide a model of the avian immune response to WNV and set the stage for future comparative studies among variably susceptible populations and species.

genomics↗