Easy NanoString nCounter data analysis with the NanoTube

Class, Caleb A.; Lukan, Caiden J; Bristow, Christopher A.; Do, Kim‐Anh

doi:10.1093/bioinformatics/btac762

Cited by 10 publications

(10 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…After normalization, expression values were compiled into a single matrix for differential expression (DE) analysis. DE genes were estimated using R packages Limma ( 36 ) & NanoTube ( 37 ), with chip-to-chip variation modeled into the analysis. DE genes meeting a p-value>0.01 were used to identify enriched Gene Ontologies for biological processes using the R package ClusterProfiler v4.0 ( 38 ).…”

Section: Methodsmentioning

confidence: 99%

Early host immune responses in a human organoid-derived gallbladder monolayer to Salmonella Typhi strains from patients with acute and chronic infections: a comparative analysis

Salerno-Goncalves,

Chen,

Bafford

et al. 2024

Front. Immunol.

View full text Add to dashboard Cite

Salmonella enterica serovar Typhi (S. Typhi), a human-restricted pathogen, invades the host through the gut to cause typhoid fever. Recent calculations of the typhoid fever burden estimated that more than 10 million new typhoid fever cases occur in low and middle-income countries, resulting in 65,400-187,700 deaths yearly. Interestingly, if not antibiotic-treated, upon the resolution of acute disease, 1%-5% of patients become asymptomatic chronic carriers. Chronically infected hosts are not only critical reservoirs of infection that transmit the disease to naive individuals but are also predisposed to developing gallbladder carcinoma. Nevertheless, the molecular mechanisms involved in the early interactions between gallbladder epithelial cells and S. Typhi remain largely unknown. Based on our previous studies showing that closely related S. Typhi strains elicit distinct innate immune responses, we hypothesized that host molecular pathways activated by S. Typhi strains derived from acutely and chronically infected patients would differ. To test this hypothesis, we used a novel human organoid-derived polarized gallbladder monolayer model, and S. Typhi strains derived from acutely and chronically infected patients. We found that S. Typhi strains derived from acutely and chronically infected patients differentially regulate host mitogen-activated protein kinase (MAPK) and S6 transcription factors. These variations might be attributed to differential cytokine signaling, predominantly via TNF-α and IL-6 production and appear to be influenced by the duration the isolate was subjected to selective pressures in the gallbladder. These findings represent a significant leap in understanding the complexities behind chronic S. Typhi infections in the gallbladder and may uncover potential intervention targets.

show abstract

Section: Methodsmentioning

confidence: 99%

Early host immune responses in a human organoid-derived gallbladder monolayer to Salmonella Typhi strains from patients with acute and chronic infections: a comparative analysis

Salerno-Goncalves,

Chen,

Bafford

et al. 2024

Front. Immunol.

View full text Add to dashboard Cite

show abstract

“…Quality control and normalization were done on raw data with the NanoTube 113 R package. Differential expression (DGE) was performed with the same package, referring to the Limma DGE method, integrated in the package and accounting for known cofounders, according to the following design: ∼ diagnosis + batch + age + sex .…”

Section: Methodsmentioning

confidence: 99%

Altered astrocytic and microglial homeostasis characterizes a decreased proinflammatory state in bipolar disorder

Amossé,

Tournier,

Badina

et al. 2023

Preprint

View full text Add to dashboard Cite

Multiple lines of evidence point to peripheral immune alterations in bipolar disorder (BD) although the activity of brain immune mechanisms remain largely unexplored. To identify the cell type-specific immune alterations in the BD brain, we performed a proteomic and single nuclear transcriptomic analysis ofpostmortemcingulate cortex samples from BD and control subjects. Our results showed that genes associated to the genetic risk for BD are enriched in microglia and astrocytes. Transcriptomic alterations in microglia point to a reduced proinflammatory phenotype, associated to reduced resistance to oxidative stress and apoptosis, which was confirmed with immunohistochemical quantification of IBA1 density. Astrocytes show transcriptomic evidence of an imbalance of multiple metabolic pathways, extracellular matrix composition and downregulated immune signalling. These alterations are associated toADCY2andNCAN,two GWAS genes upregulated in astrocytes. Finally, cell-cell communication analysis prioritized upregulated SPP1-CD44 signalling to astrocytes as a potential regulator of the transcriptomic alterations in BD. Our results indicate that microglia and astrocytes are characterized by downregulated immune responses associated to a dysfunction of core mechanisms via which these cells contribute to brain homeostasis.

show abstract

“…S1C), so this gene was removed. Data were then normalized using the NanoTube package 71 with the RUVg method from the RUVSeq package 72 , which uses only high-confidence housekeeper probes and removes unwanted technical variance while preserving biological variance. This strategy has been shown to outperform NanoString's commercial normalization strategy, which uses only centrality measures from the housekeeper probes included in the panel 73 .…”

Section: Nanostring Ncounter Gene Expression Analysismentioning

confidence: 99%

Section: Nanostring Ncounter Gene Expression Analysismentioning

confidence: 99%

Locus coeruleus injury modulates ventral midbrain neuroinflammation during DSS-induced colitis

Boles,

Holt,

Cole

et al. 2024

Preprint

View full text Add to dashboard Cite

Parkinson's disease (PD) is characterized by a decades-long prodrome, consisting of a collection of non-motor symptoms that emerges prior to the motor manifestation of the disease. Of these non-motor symptoms, gastrointestinal dysfunction and deficits attributed to central norepinephrine (NE) loss, including mood changes and sleep disturbances, are frequent in the PD population and emerge early in the disease. Evidence is mounting that injury and inflammation in the gut and locus coeruleus (LC), respectively, underlie these symptoms, and the injury of these systems is central to the progression of PD. In this study, we generate a novel two-hit mouse model that captures both features, using dextran sulfate sodium (DSS) to induce gut inflammation and N-(2-chloroethyl)-N-ethyl-2-bromobenzylamine (DSP-4) to lesion the LC. We first confirmed the specificity of DSP-4 for central NE using neurochemical methods and fluorescence light-sheet microscopy of cleared tissue, and established that DSS-induced outcomes in the periphery, including weight loss, gross indices of gut injury and systemic inflammation, the loss of tight junction proteins in the colonic epithelium, and markers of colonic inflammation, were unaffected with DSP-4 pre-administration. We then measured alterations in neuroimmune gene expression in the ventral midbrain in response to DSS treatment alone as well as the extent to which prior LC injury modified this response. In this two-hit model we observed that DSS-induced colitis activates the expression of key cytokines and chemokines in the ventral midbrain only in the presence of LC injury and the typical DSS-associated neuroimmune is blunted by pre-LC lesioning with DSP-4. In all, this study supports the growing appreciation for the LC as neuroprotective against inflammation-induced brain injury and draws attention to the potential for NEergic interventions to exert disease-modifying effects under conditions where peripheral inflammation may compromise ventral midbrain dopaminergic neurons and increase the risk for development of PD.

show abstract

Easy NanoString nCounter data analysis with the NanoTube

Cited by 10 publications

References 16 publications

Early host immune responses in a human organoid-derived gallbladder monolayer to Salmonella Typhi strains from patients with acute and chronic infections: a comparative analysis

Early host immune responses in a human organoid-derived gallbladder monolayer to Salmonella Typhi strains from patients with acute and chronic infections: a comparative analysis

Altered astrocytic and microglial homeostasis characterizes a decreased proinflammatory state in bipolar disorder

Locus coeruleus injury modulates ventral midbrain neuroinflammation during DSS-induced colitis

Contact Info

Product

Resources

About