Abstract 2451: Physical, genomic, and proteomic characterization of a cancer cell line panel in an integrated dataset

Introduction: Recent work has linked cancer phenotype (e.g., metastatic ability) to physical properties (e.g., nuclear deformability), as well as genetic alterations (e.g., mutations in lamin genes affecting nuclear stiffness). However, while the genomics of immortalized human cell lines - important models for studying cancer disease pathogenesis and progression - have been relatively well studied, an integrative analysis of physical cell phenotypes with genomic, transcriptomic, and proteomics assays, spanning tissues of origins and culture environments (CE), has been lacking. The Physical Sciences in Oncology Network (PS-ON), a trans-disciplinary project established by the NCI, has generated a curated open dataset that is accessible to researchers via various database interfaces to address this need.

Methods: A panel of 39 cancerous and non-malignant cell lines frequently used in cancer research were selected to cover a set of nine tissues: breast, lung, pancreas, brain, prostate, colon, ovary, blood, and skin. Thirty of these cell lines (from all tissues except blood) were assayed by traction and atomic force microscopy and imaging to measure their cell morphology, proliferation, motility, and nuclear volume. Measurements were performed in seven CE of varying physical properties (e.g., stiffness) to recapitulate a range of realistic tissue conditions and frequently used reagents. All 39 cell lines were assayed via whole exome sequencing, mRNA-seq, and miRNA-seq (in a single CE), while nine cell lines were subjected to proteomic analysis (across seven CEs).

Results: All raw measurements and summary metrics from the study were incorporated into a data model compatible with established data stores (e.g., GDC, miRBase) and integrated in an open-access relational database (RDB). We performed several integrative analyses using the RDB. A broad set of interactions emerged between cell line CE characteristics (e.g., integrin ligands), the phenotypes of cells (e.g., motility) and gene expression, with effect-size varying by cell-line tissue of origin and cancer diagnosis. For instance, motility was significantly (FDR < 5%) correlated with expression of a small set of genes across tissues (e.g., BNP1 and PFKP in both skin and prostate cancers).

Conclusion: This PS-ON cell line characterization allows correlative analyses across CE, cells’ morphological and proliferation properties, and omics data. The integrated RDB facilitates these analyses via a unified interface and data model for the large collection of files comprising the resource. We demonstrated the utility of the RDB by using it to infer the relationship between differential gene expression, CE and resulting phenotypes, with potentially important downstream effects on hallmarks of cancer malignancy.

Citation Format: Milen Nikolov, Brian White, Adrian Pegoraro, Debra Hope, Mariam Eljanne, James Eddy, Paul Janmey, Parag Mallick, Kristen Dang. Physical, genomic, and proteomic characterization of a cancer cell line panel in an integrated dataset [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2451.

Drying kinetics of deformable and cracking nano-porous gels

The desiccation of porous materials encompasses a wide range of technological and industrial processes and is acutely sensitive to the hierarchical structure of the porous materials resulting in complex dynamics which are challenging to unravel. Macroscopic observations of the surface and geometry of model colloidal gels during desiccation under controlled air flow highlight the role of crack formation in drying. The density of cracks and their rate of appearance depend on the initial solid fraction of the gels and their adherence to the substrate. While under certain conditions cracking leads to an increase of the drying rate, in other cases cracking allows for its conservation over an extended period of the drying process. Nevertheless, as long as the sample is saturated with water, each piece within the sample shrinks isotropically as if it were an independent drying system. By simulating the airflow around the sample and inside the crack cavities, we show the existence of a perturbation in the air velocity in the vicinity of the crack cavity whose scale depends on the aspect ratio (depth/width) of the latter. On this basis, we propose a simple model which predicts the observed drying rate variations encountered while the sample cracks; and further enables to simulate the desiccation for a designated crack density.

Simplified screening for microalbuminuria

BACKGROUND

Screening for microalbuminuria is increasingly advocated as a way to diagnose early renal involvement in diabetes and other diseases. It usually entails the use of a radioimmunoassay that is expensive and not always readily available.

OBJECTIVE

To assess the efficacy of three simple and inexpensive tests for ruling out microalbuminuria.

DESIGN

Cross-sectional study.

SETTING

Outpatient clinics.

PATIENTS

221 patients from primary care clinics and a diabetes clinic.

MEASUREMENTS

Random urine specimens were tested for albumin by using Micral-Test immunoassay strips (Boehringer Mannheim, Mannheim, Germany) and for protein by using sulfosalicylic acid testing and impregnated dipsticks (Chemstrips, Boehringer Mannheim). Radioimmunoassay for albumin was used for all specimens as standard for comparison.

RESULTS

When less than 20 mg/L was considered the upper limit of normal for albumin concentration, Micral-Test, sulfosalicylic acid testing, and Chemstrips had negative predictive values of 99%, 95%, and 96%, respectively. Seventy-four specimens tested negative on both sulfosalicylic acid and Chemstrips; the negative predictive value of these two tests combined was 99%.

CONCLUSIONS

The combination of sulfosalicylic acid testing and Chemistrips was as good as and less expensive than Micral-Test in ruling out microalbuminuria.

An application of EDXRF on the study of barley seedlings growth on sewage sludge

An energy dispersive X-ray fluorescence method for trace element analysis in plants (leaves and roots) is presented. The method is characterized by the use of a secondary target excitation, thin specimen, and microwave acid digestion. The accuracy is about 10% and the sensitivity is in the range 10-50 ng/cm2. The analysis time (from dry sample to concentration data) is about 4 x 10(3) s. The effects of Cr in sewage sludge on barley seedling growth is presented.