Biology subjects

Aagaard, K. M.

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

5 recordsLinked to original sources

bioRxiv2026

Maternal Western-style Diet Promotes Immune Tolerance and Liver Sinusoidal Endothelial Cell Dysfunction in Nonhuman Primate Juvenile Offspring Liver

Maternal Western-style diet (mWSD) consumption during pregnancy and lactation is associated with developmental programming of metabolic dysfunction-associated steatotic liver disease (MASLD) in offspring. To understand the roles of immune and endothelial cells, we used single-cell RNA-sequencing of liver non-parenchymal cells from 3-year-old juvenile nonhuman primates exposed to mWSD during their gestation through weaning, followed by control diet consumption after weaning. We identified unique clusters of macrophages in mWSD-exposed juvenile livers with non-reparative, pro-fibrotic phenotypes characterized by predicted inactivation of NF-{kappa}B, decreased oxidative phosphorylation, and gene expression facilitating hepatic stellate cell-macrophage interactions. Kupffer cell and dendritic cell (DC) numbers were decreased by mWSD exposure, with inactivation of inflammatory and antigen presentation pathways in DCs, supporting DC immaturity. B cells increased in mWSD-exposed offspring, with RNA showing reduced inflammation and impaired differentiation, while T cells had RNA profiles consistent with apoptosis and reduced inflammatory function. mWSD exposure increased clusters of liver sinusoidal endothelial cells (LSECs), with activation of inflammation and proliferation pathways but decreased immune cell communication. Immunocytochemistry and RNAscope identified increased association of LSECs and immune cells in periportal regions. In summary, mWSD exposure during gestation and lactation selectively modulated LSEC-immune cell interactions consistent with immune tolerant B and T cells and fibrogenic pathways together with decreased pro-resolving macrophages in juvenile offspring. We conclude that mWSD exposure establishes an immune-tolerant environment in offspring liver, marked by a durable, pro-fibrotic microenvironment that resists postnatal dietary correction.

immunology↗

bioRxiv2024

Maternal Western-style diet programs skeletal muscle gene expression in lean adolescent Japanese macaque offspring

Early-life exposure to maternal obesity or a maternal calorically dense Western-style diet (WSD) is strongly associated with a greater risk of metabolic diseases in offspring, most notably insulin resistance and metabolic dysfunction-associated steatotic liver disease (MASLD). Prior studies in our well-characterized Japanese macaque model demonstrated that offspring of dams fed a WSD, even when weaned onto a control (CTR) diet, had reductions in skeletal muscle mitochondrial metabolism and increased skeletal muscle insulin resistance compared to offspring of dams on CTR diet. In the current study, we employed a nested design to test for differences in gene expression in skeletal muscle from lean 3-year-old adolescent offspring from dams fed a maternal WSD in both the presence and absence of maternal obesity or lean dams fed a CTR diet. We included offspring weaned to both a WSD or CTR diet to further account for differences in response to post-weaning diet and interaction effects between diets. Overall, we found that a maternal WSD fed to dams during pregnancy and lactation was the principal driver of differential gene expression (DEG) in offspring muscle at this time point. We identified key gene pathways important in insulin signaling including PI3K-Akt and MAP-kinase, regulation of muscle regeneration, and transcription-translation feedback loops, in both male and female offspring. Muscle DEG showed no measurable difference between offspring of obese dams on WSD compared to those of lean dams fed WSD. A post-weaning WSD effected offspring transcription only in individuals from the maternal CTR diet group but not in maternal WSD group. Collectively, we identify that maternal diet composition has a significant and lasting impact on offspring muscle transcriptome and influences later transcriptional response to WSD in muscle, which may underlie the increased metabolic disease risk in offspring.

physiology↗

bioRxiv2021

Squeegee: de-novo identification of reagent and laboratory induced microbial contaminants in low biomass microbiomes

Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low biomass environments. Our hypothesis is that contamination from DNA extraction kits or sampling lab environments will leave taxonomic "bread crumbs" across multiple distinct sample types, allowing for the detection of microbial contaminants when negative controls are unavailable. To test this hypothesis we implemented Squeegee, a de novo contamination detection tool. We tested Squeegee on simulated and real low biomass metagenomic datasets. On the low biomass samples, we compared Squeegee predictions to experimental negative control data and show that Squeegee accurately recovers known contaminants. We also analyzed 749 metagenomic datasets from the Human Microbiome Project and identified likely previously unreported kit contamination. Collectively, our results highlight that Squeegee can identify microbial contaminants with high precision. Squeegee is open-source and available at: https://gitlab.com/treangenlab/squeegee

bioinformatics↗

bioRxiv2020

Hidden genomic diversity of SARS-CoV-2: implications for qRT-PCR diagnostics and transmission

The COVID-19 pandemic has sparked an urgent need to uncover the underlying biology of this devastating disease. Though RNA viruses mutate more rapidly than DNA viruses, there are a relatively small number of single nucleotide polymorphisms (SNPs) that differentiate the main SARS-CoV-2 clades that have spread throughout the world. In this study, we investigated over 7,000 SARS-CoV-2 datasets to unveil both intrahost and interhost diversity. Our intrahost and interhost diversity analyses yielded three major observations. First, the mutational profile of SARS-CoV-2 highlights iSNV and SNP similarity, albeit with high variability in C>T changes. Second, iSNV and SNP patterns in SARS-CoV-2 are more similar to MERS-CoV than SARS-CoV-1. Third, a significant fraction of small indels fuel the genetic diversity of SARS-CoV-2. Altogether, our findings provide insight into SARS-CoV-2 genomic diversity, inform the design of detection tests, and highlight the potential of iSNVs for tracking the transmission of SARS-CoV-2.

genomics↗

bioRxiv2018

Experimental Zika Virus Infection in the Pregnant Common Marmoset Induces Spontaneous Fetal Loss and Neurodevelopmental Abnormalities

During its most recent outbreak across the Americas, Zika virus (ZIKV) was surprisingly shown to cause fetal loss and congenital malformations in acutely and chronically infected pregnant women. However, understanding the underlying pathogenesis of ZIKV congenital disease has been hampered by a lack of relevant in vivo experimental models. Here we present a candidate New World monkey model of ZIKV infection in pregnant marmosets that faithfully recapitulates human disease. ZIKV inoculation at the human-equivalent of early gestation caused an asymptomatic seroconversion, induction of type I/II interferon-associated genes and proinflammatory cytokines, and persistent viremia and viruria. Spontaneous pregnancy loss was observed 16-18 days post-infection, with extensive active placental viral replication and fetal neurocellular disorganization similar to that seen in humans. These findings underscore the key role of the placenta as a conduit for fetal infection, and demonstrate the utility of marmosets as a highly relevant model for studying congenital ZIKV disease and pregnancy loss.

microbiology↗