Oncotarget

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Comparative microsomal proteomics of a model lung cancer cell line NCI-H23 reveals distinct differences between molecular profiles of 3D and 2D cultured cells

Jan A. Kaczmarczyk, Rhonda R. Roberts, Brian T. Luke, King C. Chan, Carly M. Van Wagoner, Robin A. Felder, Richard G. Saul, Colantonio Simona and Josip Blonder _

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Oncotarget. 2021; 12:2022-2038. https://doi.org/10.18632/oncotarget.28072

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Abstract

Jan A. Kaczmarczyk1, Rhonda R. Roberts1, Brian T. Luke2, King C. Chan3,5, Carly M. Van Wagoner3,5, Robin A. Felder4, Richard G. Saul1, Colantonio Simona1 and Josip Blonder1

1 Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA

2 Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA

3 Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA

4 Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA

5 Current address: The Center for Cell Clearance, University of Virginia, Charlottesville, VA 22908, USA

Correspondence to:

Josip Blonder, email: [email protected]

Keywords: lung cancer; proteomics; 2D vs. 3D cultured cells; preclinical testing model; drug target discovery

Received: June 15, 2021     Accepted: August 31, 2021     Published: September 28, 2021

Copyright: © 2021 Kaczmarczyk et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

ABSTRACT

Lung cancer is the leading cause of cancer-related deaths in the USA and worldwide. Yet, about 95% of new drug candidates validated in preclinical phase eventually fail in clinical trials. Such a high attrition rate is attributed mostly to the inability of conventional two-dimensionally (2D) cultured cancer cells to mimic native three-dimensional (3D) growth of malignant cells in human tumors.

To ascertain phenotypical differences between these two distinct culture conditions, we carried out a comparative proteomic analysis of a membrane fraction obtained from 3D- and 2D-cultured NSCLC model cell line NCI-H23. This analysis revealed a map of 1,166 (24%) protein species regulated in culture dependent manner, including differential regulation of a subset of cell surface-based CD molecules. We confirmed exclusive expression of CD99, CD146 and CD239 in 3D culture. Furthermore, label-free quantitation, targeting KRas proteoform-specific peptides, revealed upregulation of both wild type and monoallelic KRas4BG12C mutant at the surface of 3D cultured cells.

In order to reduce the high attrition rate of new drug candidates, the results of this study strongly suggests exploiting base-line molecular profiling of a large number of patient-derived NSCLC cell lines grown in 2D and 3D culture, prior to actual drug candidate testing.


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