TY - JOUR
T1 - Absolute quantitative proteomics using the total protein approach to identify novel clinical immunohistochemical markers in renal neoplasms
AU - Jorge, Susana
AU - Capelo, José L.
AU - LaFramboise, William
AU - Satturwar, Swati
AU - Korentzelos, Dimitrios
AU - Bastacky, Sheldon
AU - Quiroga-Garza, Gabriela
AU - Dhir, Rajiv
AU - Wiśniewski, Jacek R.
AU - Lodeiro, Carlos
AU - Santos, Hugo M.
N1 - info:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDB%2F50006%2F2020/PT#
info:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UIDP%2F50006%2F2020/PT#
info:eu-repo/grantAgreement/FCT/Investigador FCT/IF%2F00007%2F2015%2FCP1293%2FCT0001/PT#
info:eu-repo/grantAgreement/FCT/OE/SFRH%2FBD%2F120537%2F2016/PT#
Funding Information:
PROTEOMASS Scientific Society is acknowledged by the funding provided to the Laboratory for Biological Mass Spectrometry Isabel Moura (#PM001/2019 and #PM003/2016).) .. This project utilized the University of Pittsburgh Hillman Cancer Center shared resource facilities (Cancer Genomics Facility and The Health Science Tissue Bank) supported in part by award P30CA047904 (Dr. W. LaFramboise and R. Dhir).
PY - 2021/12
Y1 - 2021/12
N2 - Background: Renal neoplasms encompass a variety of malignant and benign tumors, including many with shared characteristics. The diagnosis of these renal neoplasms remains challenging with currently available tools. In this work, we demonstrate the total protein approach (TPA) based on high-resolution mass spectrometry (MS) as a tool to improve the accuracy of renal neoplasm diagnosis. Methods: Frozen tissue biopsies of human renal tissues [clear cell renal cell carcinoma (n = 7), papillary renal cell carcinoma (n = 5), chromophobe renal cell carcinoma (n = 5), and renal oncocytoma (n = 5)] were collected for proteome analysis. Normal adjacent renal tissue (NAT, n = 5) was used as a control. Proteins were extracted and digested using trypsin, and the digested proteomes were analyzed by label-free high-resolution MS (nanoLC-ESI-HR-MS/MS). Quantitative analysis was performed by comparison between protein abundances of tumors and NAT specimens, and the label-free and standard-free TPA was used to obtain absolute protein concentrations. Results: A total of 205 differentially expressed proteins with the potential to distinguish the renal neoplasms were found. Of these proteins, a TPA-based panel of 24, including known and new biomarkers, was selected as the best candidates to differentiate the neoplasms. As proof of concept, the diagnostic potential of PLIN2, TUBB3, LAMP1, and HK1 was validated using semi-quantitative immunohistochemistry with a total of 128 samples assessed on tissue micro-arrays. Conclusions: We demonstrate the utility of combining high-resolution MS and the TPA as potential new diagnostic tool in the pathology of renal neoplasms. A similar TPA approach may be implemented in any cancer study with solid biopsies.
AB - Background: Renal neoplasms encompass a variety of malignant and benign tumors, including many with shared characteristics. The diagnosis of these renal neoplasms remains challenging with currently available tools. In this work, we demonstrate the total protein approach (TPA) based on high-resolution mass spectrometry (MS) as a tool to improve the accuracy of renal neoplasm diagnosis. Methods: Frozen tissue biopsies of human renal tissues [clear cell renal cell carcinoma (n = 7), papillary renal cell carcinoma (n = 5), chromophobe renal cell carcinoma (n = 5), and renal oncocytoma (n = 5)] were collected for proteome analysis. Normal adjacent renal tissue (NAT, n = 5) was used as a control. Proteins were extracted and digested using trypsin, and the digested proteomes were analyzed by label-free high-resolution MS (nanoLC-ESI-HR-MS/MS). Quantitative analysis was performed by comparison between protein abundances of tumors and NAT specimens, and the label-free and standard-free TPA was used to obtain absolute protein concentrations. Results: A total of 205 differentially expressed proteins with the potential to distinguish the renal neoplasms were found. Of these proteins, a TPA-based panel of 24, including known and new biomarkers, was selected as the best candidates to differentiate the neoplasms. As proof of concept, the diagnostic potential of PLIN2, TUBB3, LAMP1, and HK1 was validated using semi-quantitative immunohistochemistry with a total of 128 samples assessed on tissue micro-arrays. Conclusions: We demonstrate the utility of combining high-resolution MS and the TPA as potential new diagnostic tool in the pathology of renal neoplasms. A similar TPA approach may be implemented in any cancer study with solid biopsies.
KW - Mass spectrometry-based proteomics
KW - Renal neoplasms, Immunohistochemistry
KW - Tissue micro-array (TMA)
KW - Total protein approach (TPA)
UR - http://www.scopus.com/inward/record.url?scp=85114375618&partnerID=8YFLogxK
U2 - 10.1186/s12916-021-02071-9
DO - 10.1186/s12916-021-02071-9
M3 - Article
C2 - 34482820
AN - SCOPUS:85114375618
VL - 19
JO - BMC Medicine
JF - BMC Medicine
IS - 1
M1 - 196
ER -