See how researchers are using the PercayAI product suite to augment discovery.
For information on how to cite the platform in your research, learn more here.
'Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humans'
June 23, 2021
Authors investigated the linkage between consuming various specifically designed fibre snacks that target the features of the gut microbiota of adult humans with obesity by transplanting to gnotobiotic mice.
"This [CompBio] tool utilizes natural language processing and a biological language ‘dictionary’ that is not restricted to fixed pathway and ontology knowledge bases, and employs conditional probability analysis to calculate statistical enrichment of ‘biological concepts’ (biological processes/pathways) over those which occur by random sampling. The output of the engine enables rapid interpretation of cellular and molecular processes that change as a result of pea fiber supplementation."
'Human neutralizing antibodies against SARS-CoV-2 require intact Fc effector functions for optimal therapeutic protection'
February 12, 2021
Through the use of the PercayAI platform, the authors identified the associated cellular changes that are improved through monoclonal antibody treatment: diminished innate immune response and preserved tissue repair.
"When given after infection, intact mAbs [monoclonal antibodies] reduce SARS-CoV-2 burden and lung disease in mice and hamsters better than loss-of-function Fc variant mAbs. Fc engagement of neutralizing antibodies mitigates inflammation and improves respiratory mechanics, and transcriptional profiling suggests these phenotypes are associated with diminished innate immune signaling and preserved tissue repair. Immune cell depletions establish that neutralizing mAbs require monocytes and CD8+ T cells for optimal clinical and virological benefit. Thus, potently neutralizing mAbs utilize Fc effector functions during therapy to mitigate lung infection and disease."
'Proteomic Signatures of Heart Failure in Relation to Left Ventricular Ejection Fraction'
Journal of the American College of Cardiology
October 27, 2020
This study aims to develop a new proteomics-based method to more accurately characterize clinical phenotypes of patients with heart failure.
The PercayAI platform was used to perform network analysis to "evaluate circulating proteins that were differentially expressed in HFrEF, HFmrEF, and HFpEF patients." The themes list provided by the PercayAI platform analysis was then used to create " a pseudo heat map of the most salient biological themes that were differently expressed among the HFrEF, HFmrEF, and HFpEF cohorts."
'Ablation of Fat Cells in Adult Mice Induces Massive Bone Gain'
October 6, 2020
While other pathway and process analysis tools were unable to find a mechanism for the increased bone mass after the ablation of fat cells, PercayAI's platform presented a clear direction for the researchers.
"Through the use of CompBio, a computational biologist was able to rapidly form a testable hypothesis that the effect was likely to due to the repression of expression of multiple BMP inhibitory molecules," said Richard Head, Professor of Genetics and Pathology & Immunology, Washington University School of Medicine in St. Louis.
'Sox9 deletion causes severe intervertebral disc degeneration characterized by apoptosis, matrix remodeling, and compartment-specific transcriptomic changes'
October 4, 2020
This study identified a new therapeutic target that may mitigate disc degeneration. It used platform features such as concept filters to copare the nucleus pulposus and annulus fibrosus at the concept level to understand common underlying biology.
Authors used the PercayAI Software Platform to analyze"significantly differentially up- and down-regulated genes from the NP [nucleus pulposus] and AF [annulus fibrosus] compartments..."
Preprint: 'Activity dependent translation in astrocytes'
April 9, 2020
This study aims to find the activity-dependent translation response from astrocytes. Additionally, they addressed whether the astrocyte response depended on neuronal activity. Here, they were able to uncover the translational targets that were promoted in response to activity as well as find that neuronal activity was necessary for this response.
Both CompBio and GO analysis found pathways related to cytoskeleton, ribosomes and mitochondria. The authors note that these pathways suggest the astrocytes are poised by the neuronal activity to have increased perisynaptic process motility. CompBio identified genes associated with autism and neurodegenerative disorders in a non-obvious manner not identified by previous tools.
'Effects of Microbiota-Directed Foods in Gnotobiotic Animals and Undernourished Children'
July 12, 2019
Authors used metabolomics and metagenomic analyses of fecal and plasma samples to characterize Bangladeshi children as they progressed from severe to moderate accute malnutrition. After identifying underrepresented bacterial taxa in the malnourised children, authors used mouse and pig models to develop microbiota-directed complementary food (MDCF) prototypes, which were then tested in a randomized, double-blind controlled feeding study. A lead MDCF was identified to improve important markers of healthy development in children. CompBio identified the bone signature that related to the stunted growth found in patients.
'Mechanisms by Which Sialylated Milk Oligosaccharides Impact Bone Biology in a Gnotobiotic Mouse Model of Infant Undernutrition'
Proceedings of the National Academy of Sciences (PNAS)
June 20, 2019
Authors studied stunted grown in undernourished children by colonizing the gut of germ-free mice with the microbiome of a representative Severe Accute Malnourished child. These mice displayed reduced eosinphil cells and poor response from tufts cells in the gut and increased osteoclast mediated bone reabsorption. The addition of sialylated milk oligosaccharides to the diet increased bone volume, reduced osteoclasts and their progenitors, and altered regulators of osteoclastogenesis and mediators of Th2 responses.
Authors were able to show through use of CompBio that this treatment improved the immune and tuft cell response within the gut compared to the colonized mice not given sialylated milk oligosaccharides.
'Transcriptomic Analysis of Enteropathy in Zambian Children With Severe Acute Malnutrition'
June 20, 2019
Authors performed transcriptomic characterization of intestinal biopsies from children with Severe Accute Malnutrition. Several novel elements of pathology were identified, including genes related to nutrient transport, intestinal absorption, and xenobiotic metabolism. CompBio identified altered expression in processes that enable proper permeability, muscosal health and immune response.
'Interaction Between Smoking and ATG16L1T300A Triggers Paneth Cell Defects in Crohn's Disease'
The Journal of Clinical Investigation
Nov. 1, 2018
Authors developed a mouse model of Crohn's Disease Paneth cell defects using a gene x environment approach. Mice harboring a prevalent Crohn's Disease mutation (ATG16L1T300A) were exposed to cigarette smoke, a major environmental risk factor for Crohn's Disease, and Paneth cell defects were observed. Transcriptomic analyses identified pro-apoptosis and downregulation of PPARgamma as major hallmarks of Paneth cell defects. Paneth cell defects were rescued using either an apoptosis inhibitor or a PAPRgamma activator, supporting the role of these processes in the developement of Paneth cell defects.
CompBio identified the molecular target signatures underlying the mouse model of paneth cell defects that was leading to the phenotypes observed in patients, specifically crypt cell apoptosis and defects in the Paneth cells. This analysis led to identifying the downregulation of PPAR-gamma and metabolic defects along with the cell death as targets. Then, the apoptosis inhibitor and PPAR-gamma agonist and diabetic drug, rosiglitazone, was used to prevent the crypt cell apoptosis and defects in the Paneth cells.
'Single-Cell RNA-Seq Uncovers a Robust Transcriptional Response to Morphine by Glia'
Sept. 25, 2018
This study's aim was to understand the molecular alterations and cell types that mediate drug addiction. Within the nucleus accumbens of morphine treated mice, oligodendrocytes were identified as having an abundance of morphine-regulated genes. Further, there was an enrichment in pathways that impact oligodendrocyte maturation and myleination. The biological pathways described were identified by CompBio before the tool could be cited.
'Abnormal Small Intestinal Epithelial Microvilli in Patients With Crohn's Disease'
May 18, 2018
The aim of the publication was to identify the alterations that occur in intestinal cells that contribute to progression of Crohn's Disease. Sections of patient's intestinal tissue from inflammed and non-diseased areas were used from transcriptomics analysis. CompBio clearly identified reduced microvilli genes as an associated factor and reduced microvilli length was confirmed through histology.