Ontological representation, integration, and analysis of LINCS cell line cells and their cellular responses

Abstract Background Aiming to understand cellular responses to different perturbations, the NIH Common Fund Library of Integrated Network-based Cellular Signatures (LINCS) program involves many institutes and laboratories working on over a thousand cell lines. The community-based Cell Line Ontology (CLO) is selected as the default ontology for LINCS cell line representation and integration. Results CLO has consistently represented all 1097 LINCS cell lines and included information extracted from the LINCS Data Portal and ChEMBL. Using MCF 10A cell line cells as an example, we demonstrated how to ontologically model LINCS cellular signatures such as their non-tumorigenic epithelial cell type, three-dimensional growth, latrunculin-A-induced actin depolymerization and apoptosis, and cell line transfection. A CLO subset view of LINCS cell lines, named LINCS-CLOview, was generated to support systematic LINCS cell line analysis and queries. In summary, LINCS cell lines are currently associated with 43 cell types, 131 tissues and organs, and 121 cancer types. The LINCS-CLO view information can be queried using SPARQL scripts. Conclusions CLO was used to support ontological representation, integration, and analysis of over a thousand LINCS cell line cells and their cellular responses.https://deepblue.lib.umich.edu/bitstream/2027.42/140390/1/12859_2017_Article_1981.pd

Mass spectrometry database of lacrimal gland adenoid cystic carcinoma and normal lacrimal gland tissue identifies extracellular matrix remodeling in these tumors

Adenoid cystic carcinoma of the lacrimal gland (LGACC) is a slow-growing but aggressive orbital malignancy. Due to the rarity of LGACC, it is poorly understood, which makes diagnosing, treating, and monitoring disease progression difficult. The aim is to understand the molecular drivers of LGACC further to identify potential targets for treating this cancer. Mass spectrometry was performed on LGACC and normal lacrimal gland samples to examine the differentially expressed proteins to understand this cancer's proteomic characteristics. Downstream gene ontology and pathway analysis revealed the extracellular matrix is the most upregulated process in LGACC. This data serves as a resource for further understanding LGACC and identifying potential treatment targets. This dataset is publicly available

Identifying Glioblastoma Gene Networks Based on Hypergeometric Test Analysis

Patient specific therapy is emerging as an important possibility for many cancer patients. However, to identify such therapies it is essential to determine the genomic and transcriptional alterations present in one tumor relative to control samples. This presents a challenge since use of a single sample precludes many standard statistical analysis techniques. We reasoned that one means of addressing this issue is by comparing transcriptional changes in one tumor with those observed in a large cohort of patients analyzed by The Cancer Genome Atlas (TCGA). To test this directly, we devised a bioinformatics pipeline to identify differentially expressed genes in tumors resected from patients suffering from the most common malignant adult brain tumor, glioblastoma (GBM). We performed RNA sequencing on tumors from individual GBM patients and filtered the results through the TCGA database in order to identify possible gene networks that are overrepresented in GBM samples relative to controls. Importantly, we demonstrate that hypergeometric-based analysis of gene pairs identifies gene networks that validate experimentally. These studies identify a putative workflow for uncovering differentially expressed patient specific genes and gene networks for GBM and other cancers

Gene Networks created by Pairs with high PCC (greater than 0.7) and high hypergeometric p-value yield less experimentally verified interactions.

<p>The number of connections identified was calculated for gene pairs with high PCC and high hypergeometric p-values. These connections were then compared to those identified in the literature. Note that few connections were found to be experimentally validated.</p

Pipeline for identifying patient-specific gene association in GBM.

<p>Our first step in our pipeline is to identify Differentially Expressed (DE) genes that are represented in 3 out of 4 algorithms. Next, we filter this DE gene list for those genes that overlapped with DE genes in the TCGA GBM Database. We then calculate the Correlation Coefficient and a hypergeometric p-value for every gene pair. Finally, by selecting the gene pairs with the highest correlation values we create a patient specific gene correlation network, which can be experimentally verified. As a starting point for our experiments, we can use the sub-networks in which, already verified connections exist in the literature.</p

Correlation networks created by using the top gene pairs for each patient.

<p>The number of connections we identified were compared to those previously described in the literature (red). Yellow indicates connections, which were identified in protein-protein interaction databases.</p

Novel Curcumin Inspired Bis-Chalcone Promotes Endoplasmic Reticulum Stress and Glioblastoma Neurosphere Cell Death

Glioblastoma (GBM) has a dismal prognosis and successful elimination of GBM stem cells (GSCs) is a high-priority as these cells are responsible for tumor regrowth following therapy and ultimately patient relapse. Natural products and their derivatives continue to be a source for the development of effective anticancer drugs and have been shown to effectively target pathways necessary for cancer stem cell self-renewal and proliferation. We generated a series of curcumin inspired bis-chalcones and examined their effect in multiple patient-derived GSC lines. Of the 19 compounds synthesized, four analogs robustly induced GSC death in six separate GSC lines, with a half maximal inhibitory concentration (IC50) ranging from 2.7&ndash;5.8 &mu;M and significantly reduced GSC neurosphere formation at sub-cytotoxic levels. Structural analysis indicated that the presence of a methoxy group at position 3 of the lateral phenylic appendages was important for activity. Pathway and drug connectivity analysis of gene expression changes in response to treatment with the most active bis-chalcone 4j (the 3,4,5 trimethoxy substituted analog) suggested that the mechanism of action was the induction of endoplasmic reticulum (ER) stress and unfolded protein response (UPR) mediated cell death. This was confirmed by Western blot analysis in which 4j induced robust increases in CHOP, p-jun and caspase 12. The UPR is believed to play a significant role in GBM pathogenesis and resistance to therapy and as such represents a promising therapeutic target