Omics
Graph Algorithms for Condensing and Consolidating Gene Set Analysis ResultsWeighted set cover and affinity propagation algorithms are used to combine results from multiple enrichment analyses. Weighted set cover first condenses enriched gene sets to use the fewest number of gene sets that cover all relevant genes. Affinity propagation then clusters the enriched pathways and selects the most representative set. Together they facilitate interpretation of multiple enrichment analysis results. A demonstration of its utility highlights both general and unique pathways associated with cancer survival across seven cancer types.
Correlation Analysis of Histopathology and Proteogenomics Data for Breast CancerHistopathology images are important for cancer diagnosis and prognosis. We extracted quantitative morphological features from breast cancers images and systematically analyzed their relationships with proteins and mRNAs. We observed concordant correlation patterns between image-protein and image-RNA and identified four cancer-related biological processes associated with morphological features related to different tumor components. Further, we observed that proteomic data reveal unique protein-related biological processes associated with morphology. Finally, prognostic morphological features were identified, and their roles are consistent with the underlying biological processes.
Hdac4 Interactions in Huntington's Disease Viewed Through the Prism of MultiomicsThe histone deacetylase Hdac4 is known to contribute to the progression of Huntington's Disease (HD), but the underlying mechanisms remain unknown. Here, we defined the endogenous interactome of Hdac4 in the brain of HD mouse models, characterizing their polyQ- and age-dependence in affected tissues. Further integration with proteome and transcriptome data sets reveals the disease-induced enhancement of Hdac4 interactions with vesicular sorting proteins, including the WASH complex. This may contribute to the known decreased synaptic functions in Huntington's Disease.
Simultaneous Improvement in the Precision, Accuracy, and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation ChainsHigh-quality label-free proteome quantification (LFQ) is valuable for clinical and pharmaceutical studies yet remains extremely challenging despite technical advances. Particularly, fluctuating precision, limited robustness, and compromised accuracy are known issues. Here, we described and validated a new strategy enabling the discovery of the LFQs of simultaneously enhanced precision, robustness, and accuracy from thousands of LFQ manipulation chains. In the proof-of-concept study, this strategy showed superior ability in identifying well-performing LFQs. An online tool incorporating this novel strategy was also developed.
High-throughput Exploration of the Network Dependent on AKT1 in Mouse Ovarian Granulosa CellsThe PI3K/AKT signaling pathway is known to regulate a broad range of cellular processes, and it is often altered in cancer. We have performed high-throughput analyses of the proteins and transcripts deregulated after Akt1 depletion in primary murine granulosa cells, which are the supporting cells of the oocyte. We found known and novel cellular processes perturbed by AKT1 knock-down. Our results confirm and extend the role of this kinase in critical cellular processes, such as directional migration, and provide a series of new substrate candidates that deserve further investigation.
Loss of BAP1 Results in Growth Inhibition and Enhances Mesenchymal–Epithelial Transition in Kidney Tumor CellsLower expression of WT BAP1 was correlated with longer overall survival in ccRCC patients. Quantitative proteomic analysis revealed that BAP1 was largely involved in cytoskeletal remodeling and cell proliferation. Functional assays determined that loss of BAP1 decreased cell motility and inhibited cell proliferation in ccRCC cell lines. BAP1 knockout rendered accumulation of H2AK119ub on the Snail gene region and inhibited Snail transcription, and thus led to mesenchymal-epithelial transition in ccRCC tumor cells.
Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent AcquisitionData-independent acquisition proteomics was used to study proteome changes of naive human neutrophils in rare monogenic diseases affecting their functions. Neutrophils of patients with mutations in the neutrophil elastase gene ELANE demonstrated global proteome dysregulation, whereas chronic granulomatous disease and leukocyte adhesion deficiency had modest effects on the respective neutrophil proteomes. Proteomics then guided targeted genetic assays to resolve two clinical cases with undetermined genetic causes, highlighting the usefulness of mass spectrometry-based clinical diagnostics.
Proteins, Transcripts, and Genetic Architecture of Seminal Fluid and Sperm in the Mosquito Aedes aegyptiAn expanded understanding of mosquito reproductive biology may assist efforts to control wild mosquito populations by manipulating reproduction. Given that molecular mechanisms of seminal fluid and sperm function are poorly understood, we have catalogued proteins that compose the ejaculate in Aedes aegypti,—the vector of dengue, Zika, and other viruses. The sperm and seminal fluid proteomes characterized herein represent a valuable tool for investigations of mosquito biology and the development of molecular targets by which mosquito populations may be suppressed.