TY - JOUR
T1 - Defining candidate mRNA and protein EV biomarkers to discriminate ccRCC and pRCC from non-malignant renal cells in vitro
AU - Zieren, Richard C.
AU - Dong, Liang
AU - Clark, David J.
AU - Kuczler, Morgan D.
AU - Horie, Kengo
AU - Moreno, Leandro Ferreira
AU - Lih, Tung-Shing M.
AU - Schnaubelt, Michael
AU - Vermeulen, Louis
AU - Zhang, Hui
AU - de Reijke, Theo M.
AU - Pienta, Kenneth J.
AU - Amend, Sarah R.
N1 - Funding Information: The authors thank Barbara Smith, microscopy specialist of the Microscope Facility at Johns Hopkins University School of Medicine, for acquiring TEM images. We thank all members of the Pienta, Amend, Zhang, and Vermeulen laboratories for their feedback. This work was supported by the Stichting Cure for Cancer foundation, Amsterdam, the Netherlands to RCZ; Japan Society for the Promotion of Science (KAKENHI: 19K18555) to KH; the New York Stem Cell Foundation as a Robertson Investigator to LV; the National Institutes of Health, National Cancer Institute, the Early Detection Research Network (EDRN, U01CA152813), the Clinical Proteomic Tumor Analysis Consortium (CPTAC, U24CA210985) to HZ; KJP was supported by the National Institutes of Health, NCI grants U54CA143803, CA163124, CA093900, and CA143055, the Prostate Cancer Foundation, and the William and Carolyn Stutt Research Fund, Ronald Rose, MC Dean, Inc., William and Marjorie Springer, Mary and Dave Stevens, Louis Dorfman, and the Jones Family Foundation to KJP; and the Patrick C. Walsh Prostate Cancer Research Fund, the Prostate Cancer Foundation, and CDMRP/PCRP grant W81XWH-20-10353 to SRA. Funding Information: The authors thank Barbara Smith, microscopy specialist of the Microscope Facility at Johns Hopkins University School of Medicine, for acquiring TEM images. We thank all members of the Pienta, Amend, Zhang, and Vermeulen laboratories for their feedback. This work was supported by the Stichting Cure for Cancer foundation, Amsterdam, the Netherlands to RCZ; Japan Society for the Promotion of Science (KAKENHI: 19K18555) to KH; the New York Stem Cell Foundation as a Robertson Investigator to LV; the National Institutes of Health, National Cancer Institute, the Early Detection Research Network (EDRN, U01CA152813), the Clinical Proteomic Tumor Analysis Consortium (CPTAC, U24CA210985) to HZ; KJP was supported by the National Institutes of Health, NCI grants U54CA143803, CA163124, CA093900, and CA143055, the Prostate Cancer Foundation, and the William and Carolyn Stutt Research Fund, Ronald Rose, MC Dean, Inc., William and Marjorie Springer, Mary and Dave Stevens, Louis Dorfman, and the Jones Family Foundation to KJP; and the Patrick C. Walsh Prostate Cancer Research Fund, the Prostate Cancer Foundation, and CDMRP/PCRP grant W81XWH-20-10353 to SRA. Publisher Copyright: © 2021, The Author(s).
PY - 2021/9/1
Y1 - 2021/9/1
N2 - Renal cell carcinoma (RCC) accounts for over 400,000 new cases and 175,000 deaths annually. Diagnostic RCC biomarkers may prevent overtreatment in patients with early disease. Extracellular vesicles (EVs) are a promising source of RCC biomarkers because EVs carry proteins and messenger RNA (mRNA) among other biomolecules. We aimed to identify biomarkers and assess biological functions of EV cargo from clear cell RCC (ccRCC), papillary RCC (pRCC), and benign kidney cell lines. EVs were enriched from conditioned cell media by size exclusion chromatography. The EV proteome was assessed using Tandem Mass Tag mass spectrometry (TMT-MS) and NanoString nCounter technology was used to profile 770 cancer-related mRNA present in EVs. The heterogeneity of protein and mRNA abundance and identification highlighted the heterogeneity of EV cargo, even between cell lines of a similar pathological group (e.g., ccRCC or pRCC). Overall, 1726 proteins were quantified across all EV samples, including 181 proteins that were detected in all samples. In the targeted profiling of mRNA by NanoString, 461 mRNAs were detected in EVs from at least one cell line, including 159 that were present in EVs from all cell lines. In addition to a shared EV cargo signature, pRCC, ccRCC, and/or benign renal cell lines also showed unique signatures. Using this multi-omics approach, we identified 34 protein candidate pRCC EV biomarkers and 20 protein and 8 mRNA candidate ccRCC EV biomarkers for clinical validation.
AB - Renal cell carcinoma (RCC) accounts for over 400,000 new cases and 175,000 deaths annually. Diagnostic RCC biomarkers may prevent overtreatment in patients with early disease. Extracellular vesicles (EVs) are a promising source of RCC biomarkers because EVs carry proteins and messenger RNA (mRNA) among other biomolecules. We aimed to identify biomarkers and assess biological functions of EV cargo from clear cell RCC (ccRCC), papillary RCC (pRCC), and benign kidney cell lines. EVs were enriched from conditioned cell media by size exclusion chromatography. The EV proteome was assessed using Tandem Mass Tag mass spectrometry (TMT-MS) and NanoString nCounter technology was used to profile 770 cancer-related mRNA present in EVs. The heterogeneity of protein and mRNA abundance and identification highlighted the heterogeneity of EV cargo, even between cell lines of a similar pathological group (e.g., ccRCC or pRCC). Overall, 1726 proteins were quantified across all EV samples, including 181 proteins that were detected in all samples. In the targeted profiling of mRNA by NanoString, 461 mRNAs were detected in EVs from at least one cell line, including 159 that were present in EVs from all cell lines. In addition to a shared EV cargo signature, pRCC, ccRCC, and/or benign renal cell lines also showed unique signatures. Using this multi-omics approach, we identified 34 protein candidate pRCC EV biomarkers and 20 protein and 8 mRNA candidate ccRCC EV biomarkers for clinical validation.
KW - Biomarkers
KW - EV cargo
KW - Extracellular vesicles
KW - Kidney cancer
KW - Multi-omics
UR - http://www.scopus.com/inward/record.url?scp=85111562000&partnerID=8YFLogxK
U2 - https://doi.org/10.1007/s12032-021-01554-2
DO - https://doi.org/10.1007/s12032-021-01554-2
M3 - Article
C2 - 34331598
SN - 1357-0560
VL - 38
JO - Medical oncology (Northwood, London, England)
JF - Medical oncology (Northwood, London, England)
IS - 9
M1 - 105
ER -