Novel in situ collection of tumor interstitial fluid from a head and neck squamous carcinoma reveals a unique proteome with diagnostic potential

Matthew D. Stone; Rick M. Odland; Thomas McGowan; Getiria Onsongo; Chaunning Tang; Nelson L. Rhodus; Pratik Jagtap; Sricharan Bandhakavi; Timothy J. Griffin

doi:10.1007/s12014-010-9050-3

Novel in situ collection of tumor interstitial fluid from a head and neck squamous carcinoma reveals a unique proteome with diagnostic potential

Matthew D. Stone, Rick M. Odland, Thomas McGowan, Getiria Onsongo, Chaunning Tang, Nelson L. Rhodus, Pratik Jagtap, Sricharan Bandhakavi, Timothy J. Griffin

Research output: Contribution to journal › Article › peer-review

21 Scopus citations

Abstract

Introduction: Tumors lack normal drainage of secreted fluids and consequently build up tumor interstitial fluid (TIF). Unlike other bodily fluids, TIF likely contains a high proportion of tumor-specific proteins with potential as biomarkers. Methods: Here, we evaluated a novel technique using a unique ultrafiltration catheter for in situ collection of TIF and used it to generate the first catalog of TIF proteins from a head and neck squamous cell carcinoma (HNSCC). To maximize proteomic coverage, TIF was immunodepleted for high abundance proteins and digested with trypsin, and peptides were fractionated in three dimensions prior to mass spectrometry. Results: We identified 525 proteins with high confidence. The HNSCC TIF proteome was distinct compared to proteomes of other bodily fluids. It contained a relatively high proportion of proteins annotated by Gene Ontology as " extracellular" compared to other secreted fluid and cellular proteomes, indicating minimal cell lysis from our in situ collection technique. Several proteins identified are putative biomarkers of HNSCC, supporting our catalog's value as a source of potential biomarkers. Conclusions: In all, we demonstrate a reliable new technique for in situ TIF collection and provide the first HNSCC TIF protein catalog with value as a guide for others seeking to develop tumor biomarkers.

Original language	English (US)
Pages (from-to)	75-82
Number of pages	8
Journal	Clinical Proteomics
Volume	6
Issue number	3
DOIs	https://doi.org/10.1007/s12014-010-9050-3
State	Published - Sep 2010

Bibliographical note

Funding Information:
Acknowledgments This research was funded in part by NIH grant 1R01DE017734. We are thankful to Mark Nelson and John Chilton at the University of Minnesota Supercomputing Institute for computational support for database searching. We are thankful to Todd Markowski of the University of Minnesota Proteomics Core Facility for SCX fractionation. We are also thankful to the members of the Griffin laboratory for helpful discussions and comments.

Keywords

Biomarker discovery
Head and neck squamous cell carcinoma
In situ collection
Tumor interstitial fluid

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This output contributes to the following UN Sustainable Development Goals (SDGs)

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title = "Novel in situ collection of tumor interstitial fluid from a head and neck squamous carcinoma reveals a unique proteome with diagnostic potential",

abstract = "Introduction: Tumors lack normal drainage of secreted fluids and consequently build up tumor interstitial fluid (TIF). Unlike other bodily fluids, TIF likely contains a high proportion of tumor-specific proteins with potential as biomarkers. Methods: Here, we evaluated a novel technique using a unique ultrafiltration catheter for in situ collection of TIF and used it to generate the first catalog of TIF proteins from a head and neck squamous cell carcinoma (HNSCC). To maximize proteomic coverage, TIF was immunodepleted for high abundance proteins and digested with trypsin, and peptides were fractionated in three dimensions prior to mass spectrometry. Results: We identified 525 proteins with high confidence. The HNSCC TIF proteome was distinct compared to proteomes of other bodily fluids. It contained a relatively high proportion of proteins annotated by Gene Ontology as {"} extracellular{"} compared to other secreted fluid and cellular proteomes, indicating minimal cell lysis from our in situ collection technique. Several proteins identified are putative biomarkers of HNSCC, supporting our catalog's value as a source of potential biomarkers. Conclusions: In all, we demonstrate a reliable new technique for in situ TIF collection and provide the first HNSCC TIF protein catalog with value as a guide for others seeking to develop tumor biomarkers.",

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author = "Stone, {Matthew D.} and Odland, {Rick M.} and Thomas McGowan and Getiria Onsongo and Chaunning Tang and Rhodus, {Nelson L.} and Pratik Jagtap and Sricharan Bandhakavi and Griffin, {Timothy J.}",

note = "Funding Information: Acknowledgments This research was funded in part by NIH grant 1R01DE017734. We are thankful to Mark Nelson and John Chilton at the University of Minnesota Supercomputing Institute for computational support for database searching. We are thankful to Todd Markowski of the University of Minnesota Proteomics Core Facility for SCX fractionation. We are also thankful to the members of the Griffin laboratory for helpful discussions and comments.",

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doi = "10.1007/s12014-010-9050-3",

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AU - Stone, Matthew D.

AU - Odland, Rick M.

AU - McGowan, Thomas

AU - Onsongo, Getiria

AU - Tang, Chaunning

AU - Rhodus, Nelson L.

AU - Jagtap, Pratik

AU - Bandhakavi, Sricharan

AU - Griffin, Timothy J.

N1 - Funding Information: Acknowledgments This research was funded in part by NIH grant 1R01DE017734. We are thankful to Mark Nelson and John Chilton at the University of Minnesota Supercomputing Institute for computational support for database searching. We are thankful to Todd Markowski of the University of Minnesota Proteomics Core Facility for SCX fractionation. We are also thankful to the members of the Griffin laboratory for helpful discussions and comments.

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N2 - Introduction: Tumors lack normal drainage of secreted fluids and consequently build up tumor interstitial fluid (TIF). Unlike other bodily fluids, TIF likely contains a high proportion of tumor-specific proteins with potential as biomarkers. Methods: Here, we evaluated a novel technique using a unique ultrafiltration catheter for in situ collection of TIF and used it to generate the first catalog of TIF proteins from a head and neck squamous cell carcinoma (HNSCC). To maximize proteomic coverage, TIF was immunodepleted for high abundance proteins and digested with trypsin, and peptides were fractionated in three dimensions prior to mass spectrometry. Results: We identified 525 proteins with high confidence. The HNSCC TIF proteome was distinct compared to proteomes of other bodily fluids. It contained a relatively high proportion of proteins annotated by Gene Ontology as " extracellular" compared to other secreted fluid and cellular proteomes, indicating minimal cell lysis from our in situ collection technique. Several proteins identified are putative biomarkers of HNSCC, supporting our catalog's value as a source of potential biomarkers. Conclusions: In all, we demonstrate a reliable new technique for in situ TIF collection and provide the first HNSCC TIF protein catalog with value as a guide for others seeking to develop tumor biomarkers.

AB - Introduction: Tumors lack normal drainage of secreted fluids and consequently build up tumor interstitial fluid (TIF). Unlike other bodily fluids, TIF likely contains a high proportion of tumor-specific proteins with potential as biomarkers. Methods: Here, we evaluated a novel technique using a unique ultrafiltration catheter for in situ collection of TIF and used it to generate the first catalog of TIF proteins from a head and neck squamous cell carcinoma (HNSCC). To maximize proteomic coverage, TIF was immunodepleted for high abundance proteins and digested with trypsin, and peptides were fractionated in three dimensions prior to mass spectrometry. Results: We identified 525 proteins with high confidence. The HNSCC TIF proteome was distinct compared to proteomes of other bodily fluids. It contained a relatively high proportion of proteins annotated by Gene Ontology as " extracellular" compared to other secreted fluid and cellular proteomes, indicating minimal cell lysis from our in situ collection technique. Several proteins identified are putative biomarkers of HNSCC, supporting our catalog's value as a source of potential biomarkers. Conclusions: In all, we demonstrate a reliable new technique for in situ TIF collection and provide the first HNSCC TIF protein catalog with value as a guide for others seeking to develop tumor biomarkers.

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Novel in situ collection of tumor interstitial fluid from a head and neck squamous carcinoma reveals a unique proteome with diagnostic potential

Abstract

Bibliographical note

Keywords

UN SDGs

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