Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer

Zhao, Xiaozheng; Huffman, Kenneth E.; Fujimoto, Junya; Canales, Jamie Rodriguez; Girard, Luc; Nie, Guangjun; Heymach, John V.; Wistuba, Igacio I.; Minna, John D.; Yu, Yonghao

doi:10.1007/S13361-017-1706-Z

Title: Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer

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Abstract

With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT. Here we present a simple workflow for whole proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple trichloroacetic acid precipitation step. Comparisons of protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200 proteins identified. Using an isobaric labeling strategy, we quantified more than 5400 proteins in tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as squamous cell carcinoma (SqCC) marker proteins were overexpressed in the tumor, consistent with the patient’s pathology based diagnosis of “poorly differentiated SqCC”. Among the most downregulated proteins in the tumor sample, we noted a number of proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed proteins using amore »« less

Authors:

Zhao, Xiaozheng ^[1]; Huffman, Kenneth E. ^[2]; Fujimoto, Junya; Canales, Jamie Rodriguez ^[3]; Girard, Luc ^[2]; Nie, Guangjun ^[1]; Heymach, John V. ^[4]; Wistuba, Igacio I. ^[3]; Minna, John D. ^[2]; Yu, Yonghao ^[5]

National Center for Nanoscience and Technology, CAS Center for Excellence in Nanoscience (China)
University of Texas Southwestern Medical Center, Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Pharmacology and Internal Medicine (United States)
University of Texas MD Anderson Cancer Center, Department of Translational Molecular Pathology (United States)
University of Texas MD Anderson Cancer Center, Department of Head and Neck and Thoracic Oncology (United States)
University of Texas Southwestern Medical Center, Department of Biochemistry (United States)

Publication Date:: Sun Oct 15 00:00:00 EDT 2017

OSTI Identifier:: 22776853

Resource Type:: Journal Article

Journal Name:: Journal of the American Society for Mass Spectrometry

Additional Journal Information:: Journal Volume: 28; Journal Issue: 10; Other Information: Copyright (c) 2017 American Society for Mass Spectrometry; http://www.springer-ny.com; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 1044-0305

Country of Publication:: United States

Language:: English

Subject:: 62 RADIOLOGY AND NUCLEAR MEDICINE; ANIMAL TISSUES; BIOLOGICAL MARKERS; BIOPSY; CARCINOMAS; COMPARATIVE EVALUATIONS; DIAGNOSIS; DNA DAMAGES; DNA REPLICATION; LUNGS; MASS SPECTROSCOPY; PATHOLOGY; PROTEINS; TEMPERATURE MEASUREMENT

Citation Formats


                    Zhao, Xiaozheng, Huffman, Kenneth E., Fujimoto, Junya, Canales, Jamie Rodriguez, Girard, Luc, Nie, Guangjun, Heymach, John V., Wistuba, Igacio I., Minna, John D., and Yu, Yonghao. Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer.  United States: N. p., 2017. 
        Web.  doi:10.1007/S13361-017-1706-Z.

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                    Zhao, Xiaozheng, Huffman, Kenneth E., Fujimoto, Junya, Canales, Jamie Rodriguez, Girard, Luc, Nie, Guangjun, Heymach, John V., Wistuba, Igacio I., Minna, John D., & Yu, Yonghao. Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer.  United States.  https://doi.org/10.1007/S13361-017-1706-Z

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                    Zhao, Xiaozheng, Huffman, Kenneth E., Fujimoto, Junya, Canales, Jamie Rodriguez, Girard, Luc, Nie, Guangjun, Heymach, John V., Wistuba, Igacio I., Minna, John D., and Yu, Yonghao. 2017.  
        "Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer".  United States.  https://doi.org/10.1007/S13361-017-1706-Z.

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@article{osti_22776853,

  title        = {Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer},

  author       = {Zhao, Xiaozheng and Huffman, Kenneth E. and Fujimoto, Junya and Canales, Jamie Rodriguez and Girard, Luc and Nie, Guangjun and Heymach, John V. and Wistuba, Igacio I. and Minna, John D. and Yu, Yonghao},

  abstractNote = {With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT. Here we present a simple workflow for whole proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple trichloroacetic acid precipitation step. Comparisons of protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200 proteins identified. Using an isobaric labeling strategy, we quantified more than 5400 proteins in tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as squamous cell carcinoma (SqCC) marker proteins were overexpressed in the tumor, consistent with the patient’s pathology based diagnosis of “poorly differentiated SqCC”. Among the most downregulated proteins in the tumor sample, we noted a number of proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed proteins using a candidate approach and cross-referencing with publicly available databases led to the identification of potential druggable targets in DNA replication and DNA damage repair pathways. We conclude that our approach allows LC-MS/MS proteomic analyses on OCT-embedded lung cancer specimens, opening the way to bring powerful proteomics into the clinic. .},

  doi          = {10.1007/S13361-017-1706-Z},

  url          = {https://www.osti.gov/biblio/22776853},
  journal      = {Journal of the American Society for Mass Spectrometry},

  issn         = {1044-0305},

  number       = 10,

  volume       = 28,

  place        = {United States},

  year         = {Sun Oct 15 00:00:00 EDT 2017},

  month        = {Sun Oct 15 00:00:00 EDT 2017}

}

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