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Ye X. Quantitative Membrane Proteomics for Discovery of Actionable Drug Targets at the Surface of RAS-Driven Human Cancer Cells. Methods Mol Biol 2024; 2823:27-46. [PMID: 39052212 DOI: 10.1007/978-1-0716-3922-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
With the advent of promising lung cancer immunotherapies targeting proteins at the cell surface of RAS-driven human cancers, the mass spectrometry (MS)-based surfaceomics remains a feasible strategy for therapeutic target discovery. This chapter describes a protocol for discovery of druggable protein targets at the surface of RAS-driven human cancer cells. This method relies on bottom-up MS-based quantitative surfaceomics that employs in parallel, targeted hydrazide-based cell-surface glycoproteomics and global shotgun membrane proteomics to enable unbiased quantitative profiling of thousands of cell surface membrane proteins. A large-scale molecular map of the KRASG12V surface was attained, resulting in confident detection and quantitation of more than 500 cell surface membrane proteins that were found to be unique or upregulated at the surface of cells harboring the KRASG12V mutant. A multistep bioinformatic progression revealed a subset of unique and/or significantly upregulated proteins as priority drug targets selected for orthogonal cross-validation using immunofluorescence, structured illumination microscopy, and western blotting. Among cross-validated targets, CUB domain containing protein 1 (CDCP1) and basigin (BSG-CD147) were selected as leading targets due to their involvement in cell adhesion and migration, consistent with the KRASG12V malignant phenotype as revealed by scanning electron microscopy and phenotypic cancer cell assays. Follow-up studies confirmed CDCP1 as an actionable therapeutic target, resulting in development of recombinant antibodies capable of killing KRAS-transformed cancer cells in preclinical setting. The present MS-based surfaceomics workflow represents a powerful drug target discovery platform that enables development of innovative immunotherapeutics (e.g., antibody drug conjugate against CDCP1) for attacking oncogenic RAS-driven cancers at the cell surface.
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Affiliation(s)
- Xiaoying Ye
- Analytical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA.
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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Kaczmarczyk JA, Roberts RR, Luke BT, Chan KC, Van Wagoner CM, Felder RA, Saul RG, Simona C, Blonder J. Comparative microsomal proteomics of a model lung cancer cell line NCI-H23 reveals distinct differences between molecular profiles of 3D and 2D cultured cells. Oncotarget 2021; 12:2022-2038. [PMID: 34611477 PMCID: PMC8487723 DOI: 10.18632/oncotarget.28072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022] Open
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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Affiliation(s)
- Jan A. Kaczmarczyk
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Rhonda R. Roberts
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Brian T. Luke
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - King C. Chan
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Current address: The Center for Cell Clearance, University of Virginia, Charlottesville, VA 22908, USA
| | - Carly M. Van Wagoner
- Protein Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Current address: The Center for Cell Clearance, University of Virginia, Charlottesville, VA 22908, USA
| | - Robin A. Felder
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Richard G. Saul
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Colantonio Simona
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Josip Blonder
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
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Huang P, Kong Q, Gao W, Chu B, Li H, Mao Y, Cai Z, Xu R, Tian R. Spatial proteome profiling by immunohistochemistry-based laser capture microdissection and data-independent acquisition proteomics. Anal Chim Acta 2020; 1127:140-148. [PMID: 32800117 DOI: 10.1016/j.aca.2020.06.049] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 12/11/2022]
Abstract
Understanding the tumor heterogeneity through spatially resolved proteome profiling is important for biomedical research and clinical application. Laser capture microdissection (LCM) is a powerful technology for exploring local cell populations without losing spatial information. Conventionally, tissue sections are stained with hematoxylin and eosin (H&E) for cell-type identification before LCM. However, it generally requires experienced pathologists to distinguish different cell types, which limits the application of LCM to broad cancer research field. Here, we designed an immunohistochemistry (IHC)-based workflow for cell type-resolved proteome analysis of tissue samples. Firstly, targeted cell type was marked by IHC using antibody targeting cell-type specific marker to improve accuracy and efficiency of LCM. Secondly, to increase protein recovery from chemically crosslinked IHC tissues, we optimized a decrosslinking procedure to seamlessly combine with the integrated spintip-based sample preparation technology SISPROT. This newly developed approach, termed IHC-SISPROT, has comparable performance as H&E staining-based proteomic analysis. High sensitivity and reproducibility of IHC-SISPROT were achieved by combining with data independent acquisition proteomics. More than 3500 proteins were identified from only 0.2 mm2 and 12 μm thickness of hepatocellular carcinoma (HCC) tissue section. Furthermore, using 5 mm2 and 12 μm thickness of HCC tissue section, 6660 and 6052 protein groups were quantified from cancer cells and cancer-associated fibroblasts (CAFs) by the IHC-SISPROT workflow. Bioinformatic analysis revealed the enrichment of cell type-specific ligands and receptors and potentially new communications between cancer cells and CAFs by these signaling proteins. Therefore, IHC-SISPROT is a sensitive and accurate proteomic approach for spatial profiling of cell type-specific proteome from tissues.
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Affiliation(s)
- Peiwu Huang
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China; State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Qian Kong
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China; State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Weina Gao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Bizhu Chu
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Hua Li
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China; SUSTech Core Research Facilities, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yiheng Mao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR, China
| | - Ruilian Xu
- Shenzhen People's Hospital, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, 518020, China
| | - Ruijun Tian
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Shenzhen, 518055, China.
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Leal-Egaña A, Balland M, Boccaccini AR. Re-engineering Artificial Neoplastic Milieus: Taking Lessons from Mechano- and Topobiology. Trends Biotechnol 2020; 38:142-153. [DOI: 10.1016/j.tibtech.2019.08.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 08/14/2019] [Accepted: 08/15/2019] [Indexed: 12/30/2022]
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Morley-Bunker A, Pearson J, Currie MJ, Morrin H, Whitehead MR, Eglinton T, Walker LC. Assessment of intra-tumoural colorectal cancer prognostic biomarkers using RNA in situ hybridisation. Oncotarget 2019; 10:1425-1439. [PMID: 30858927 PMCID: PMC6402718 DOI: 10.18632/oncotarget.26675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 02/01/2019] [Indexed: 01/01/2023] Open
Abstract
Genome-wide expression studies using microarrays and RNAseq have increased our understanding of colorectal cancer development. Translating potential gene biomarkers from these studies for clinical utility has typically relied on PCR-based technology and immunohistochemistry. Results from these techniques are limited by tumour sample heterogeneity and the lack of correlation between mRNA transcript abundance and corresponding protein levels. The aim of this research was to investigate the clinical utility of the RNA in situ hybridisation technique, RNAscope®, for measuring intra-tumoural gene expression of potential prognostic markers in a colorectal cancer cohort. Two candidate gene markers (GFI1 and TNFRSF11A) assessed in this study were identified from a previous study led by the The Cancer Genome Atlas (TCGA) Network, and analysis was performed on 112 consecutively collected, archival FFPE colorectal cancer tumour samples. Consistent with the TCGA Network study, we found reduced GFI1 expression was associated with high-grade and left-sided tumours, and reduced TNFRSF11A expression was associated with metastasis and high nodal involvement. RNAscope® combined with image analysis also enabled quantification of GFI1 and TNFRSF11A mRNA expression levels at the single cell level, allowing cell-type determination. These data showed that reduced mRNA transcript abundance measured in patients with poorer prognosis occurred in carcinoma cells, and not lymphocytes, stromal cells or normal epithelial cells. To our knowledge, this is the first study to assess the intra-tumoural expression patterns of GFI1 and TNFRSF11A and to validate their microarray expression profiles using RNAscope. We also demonstrate the utility of RNAscope® technology to show that expression differences are derived from carcinoma cells rather than from cells located in the tumour microenvironment.
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Affiliation(s)
- Arthur Morley-Bunker
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - John Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - Margaret J Currie
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Helen Morrin
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.,Cancer Society Tissue Bank, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Martin R Whitehead
- Canterbury Health Laboratories, Christchurch Hospital, Christchurch, New Zealand
| | - Tim Eglinton
- Department of Surgery, University of Otago, Christchurch, New Zealand
| | - Logan C Walker
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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Wang Y, Lu S, Xiong J, Singh K, Hui Y, Zhao C, Brodsky AS, Yang D, Jolly G, Ouseph M, Schorl C, DeLellis RA, Resnick MB. ColXα1 is a stromal component that colocalizes with elastin in the breast tumor extracellular matrix. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2018; 5:40-52. [PMID: 30207088 PMCID: PMC6317058 DOI: 10.1002/cjp2.115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 12/21/2022]
Abstract
The tumor microenvironment regulates tissue development and homeostasis, and its dysregulation contributes to neoplastic progression. Increased expression of type X collagen α‐1 (ColXα1) in tumor‐associated stroma correlates with poor pathologic response to neoadjuvant chemotherapy in estrogen receptor (ER) and human epidermal growth factor receptor 2 (HER2)‐positive breast cancers. Evaluation of ColXα1 expression patterns suggests a potential connection with elastin fibers. To investigate the possible interaction between ColXα1 and elastin, we evaluated the expression of ColXα1 in relation to elastin fibers in normal breast tissue, ductal carcinoma in situ, and invasive breast carcinomas at cellular and subcellular levels. Our findings demonstrate that ColXα1 colocalizes with elastin in invasive breast cancer‐associated stroma by immunohistochemistry, immunofluorescence, and electron microscopy. In 212 invasive breast carcinomas, this complex was aberrantly and selectively expressed in tumor extracellular matrix in 79% of ER+/HER2−, 80% of ER+/HER2+, 76% of ER−/HER2+, and 58% of triple negative breast cancers. In contrast, ColXα1 was generally absent, while elastin was present perivascularly in normal breast tissue. ColXα1 and elastin were coexpressed in 58% of ductal carcinoma in situ (DCIS) in periductal areas. In mass‐forming DCIS with desmoplastic stroma, the complex was intensely expressed in periductal areas as well as within the tumor‐associated stroma in all cases. Our data suggest that the breast carcinoma neoplastic process may involve aberrant expression of ColXα1 and elastin in the tumor microenvironment emerging early at the DCIS stage. Enrichment of these complexes in tumor‐associated stroma may represent a stromal signature indicative of intrinsic differences between breast cancers. These findings shed light on investigation into the role of aberrant collagen complex expression in tumorigenesis and tumor progression which may be leveraged in therapeutic and theranostic applications.
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Affiliation(s)
- Yihong Wang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Shaolei Lu
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Jinjun Xiong
- Department of Pathology, Women and Infants Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Kamaljeet Singh
- Department of Pathology, Women and Infants Hospital, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Yiang Hui
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Chaohui Zhao
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Alexander S Brodsky
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Dongfang Yang
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Grant Jolly
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Madhu Ouseph
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Christoph Schorl
- Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Ronald A DeLellis
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Murray B Resnick
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital and Lifespan Medical Center, Warren Alpert Medical School of Brown University, Providence, RI, USA
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