Ultrasonic-assisted extraction and digestion of proteins from solid biopsies followed by peptide sequential extraction hyphenated to MALDI-based profiling holds the promise of distinguishing renal oncocytoma from chromophobe renal cell carcinoma

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Abstract

A novel analytical approach is proposed to discriminate between solid biopsies of chromophobe renal cell carcinoma (chRCC) and renal oncocytoma (RO). The method comprises the following steps: (i) ultrasonic extraction of proteins from solid biopsies, (ii) protein depletion with acetonitrile, (iii) ultrasonic assisted in-solution digestion using magnetic nanoparticle with immobilized trypsin, (iv) C18 tip-based preconcentration of peptides, (v) sequential extraction of the peptides with ACN, (vi) MALDI-snapshot of the extracts and (vii) investigation of the extract containing the most discriminating features using high resolution mass spectrometry. With this approach we have been able to differentially cluster renal oncocytoma and chromophobe renal cell carcinoma and identified 18 proteins specific to chromophobe and seven unique to renal oncocytoma. Chromophobes express proteins associated with ATP function (ATP5I & 5E; VATE1 & G2; ADT2), glycolysis (PGK1) and neuromedin whilst oncocytomas express ATP5H, ATPA, DEPD7 and TRIPB thyroid receptor interacting protein.

Original languageEnglish
Article number120180
JournalTalanta
Volume206
DOIs
Publication statusPublished - 1 Jan 2020

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Biopsy
Ultrasonics
Cells
Peptides
Proteins
Receptor-Interacting Protein Serine-Threonine Kinases
Trypsin
Mass spectrometry
Adenosine Triphosphate
Nanoparticles

Keywords

  • Chromophobe renal cell carcinoma
  • MALDI
  • Profiling ESI
  • Renal cancer
  • Renal oncocytoma
  • Sequential extraction

Cite this

@article{1095d29b1a4e4bffb167a21c7b2b4220,
title = "Ultrasonic-assisted extraction and digestion of proteins from solid biopsies followed by peptide sequential extraction hyphenated to MALDI-based profiling holds the promise of distinguishing renal oncocytoma from chromophobe renal cell carcinoma",
abstract = "A novel analytical approach is proposed to discriminate between solid biopsies of chromophobe renal cell carcinoma (chRCC) and renal oncocytoma (RO). The method comprises the following steps: (i) ultrasonic extraction of proteins from solid biopsies, (ii) protein depletion with acetonitrile, (iii) ultrasonic assisted in-solution digestion using magnetic nanoparticle with immobilized trypsin, (iv) C18 tip-based preconcentration of peptides, (v) sequential extraction of the peptides with ACN, (vi) MALDI-snapshot of the extracts and (vii) investigation of the extract containing the most discriminating features using high resolution mass spectrometry. With this approach we have been able to differentially cluster renal oncocytoma and chromophobe renal cell carcinoma and identified 18 proteins specific to chromophobe and seven unique to renal oncocytoma. Chromophobes express proteins associated with ATP function (ATP5I & 5E; VATE1 & G2; ADT2), glycolysis (PGK1) and neuromedin whilst oncocytomas express ATP5H, ATPA, DEPD7 and TRIPB thyroid receptor interacting protein.",
keywords = "Chromophobe renal cell carcinoma, MALDI, Profiling ESI, Renal cancer, Renal oncocytoma, Sequential extraction",
author = "Susana Jorge and Kevin Pereira and Hugo L{\'o}pez-Fern{\'a}ndez and William LaFramboise and Rajiv Dhir and Javier Fern{\'a}ndez-Lodeiro and Carlos Lodeiro and Santos, {Hugo M.} and Capelo-Mart{\'i}nez, {Jose L.}",
note = "PROTEOMASS Scientific Society is acknowledged by the funding provided to the Laboratory for Biological Mass Spectrometry Isabel Moura. Authors acknowledge the funding provided by the Associate Laboratory for Green Chemistry LAQV which is financed by national funds from FCT / MEC ( UID/QUI/50006/2019 ). H. M. S. is funded by the FCT 2015 Investigator Program ( IF/00007/2015 ). S. J. thanks FCT / MEC (Portugal) for her research contract as PhD student with the grant SFRH/BD/120537/2016 . J.F.L. Acknowledges FCT/MEC (Portugal) SFRH/BPD/93982/2013 and FCT-UNL for the DL57/2016 Assistant Researcher Contract. H. L{\'o}pez-Fern{\'a}ndez is supported by a post-doctoral fellowship from Xunta de Galicia ( ED481B 2016/068-0 ). This project utilized the University of Pittsburgh Hillman Cancer Center shared resource facility (Cancer Genomics Facility) supported in part by award P30CA047904 (Dr. LaFramboise).",
year = "2020",
month = "1",
day = "1",
doi = "10.1016/j.talanta.2019.120180",
language = "English",
volume = "206",
journal = "Talanta",
issn = "0039-9140",
publisher = "Elsevier",

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TY - JOUR

T1 - Ultrasonic-assisted extraction and digestion of proteins from solid biopsies followed by peptide sequential extraction hyphenated to MALDI-based profiling holds the promise of distinguishing renal oncocytoma from chromophobe renal cell carcinoma

AU - Jorge, Susana

AU - Pereira, Kevin

AU - López-Fernández, Hugo

AU - LaFramboise, William

AU - Dhir, Rajiv

AU - Fernández-Lodeiro, Javier

AU - Lodeiro, Carlos

AU - Santos, Hugo M.

AU - Capelo-Martínez, Jose L.

N1 - PROTEOMASS Scientific Society is acknowledged by the funding provided to the Laboratory for Biological Mass Spectrometry Isabel Moura. Authors acknowledge the funding provided by the Associate Laboratory for Green Chemistry LAQV which is financed by national funds from FCT / MEC ( UID/QUI/50006/2019 ). H. M. S. is funded by the FCT 2015 Investigator Program ( IF/00007/2015 ). S. J. thanks FCT / MEC (Portugal) for her research contract as PhD student with the grant SFRH/BD/120537/2016 . J.F.L. Acknowledges FCT/MEC (Portugal) SFRH/BPD/93982/2013 and FCT-UNL for the DL57/2016 Assistant Researcher Contract. H. López-Fernández is supported by a post-doctoral fellowship from Xunta de Galicia ( ED481B 2016/068-0 ). This project utilized the University of Pittsburgh Hillman Cancer Center shared resource facility (Cancer Genomics Facility) supported in part by award P30CA047904 (Dr. LaFramboise).

PY - 2020/1/1

Y1 - 2020/1/1

N2 - A novel analytical approach is proposed to discriminate between solid biopsies of chromophobe renal cell carcinoma (chRCC) and renal oncocytoma (RO). The method comprises the following steps: (i) ultrasonic extraction of proteins from solid biopsies, (ii) protein depletion with acetonitrile, (iii) ultrasonic assisted in-solution digestion using magnetic nanoparticle with immobilized trypsin, (iv) C18 tip-based preconcentration of peptides, (v) sequential extraction of the peptides with ACN, (vi) MALDI-snapshot of the extracts and (vii) investigation of the extract containing the most discriminating features using high resolution mass spectrometry. With this approach we have been able to differentially cluster renal oncocytoma and chromophobe renal cell carcinoma and identified 18 proteins specific to chromophobe and seven unique to renal oncocytoma. Chromophobes express proteins associated with ATP function (ATP5I & 5E; VATE1 & G2; ADT2), glycolysis (PGK1) and neuromedin whilst oncocytomas express ATP5H, ATPA, DEPD7 and TRIPB thyroid receptor interacting protein.

AB - A novel analytical approach is proposed to discriminate between solid biopsies of chromophobe renal cell carcinoma (chRCC) and renal oncocytoma (RO). The method comprises the following steps: (i) ultrasonic extraction of proteins from solid biopsies, (ii) protein depletion with acetonitrile, (iii) ultrasonic assisted in-solution digestion using magnetic nanoparticle with immobilized trypsin, (iv) C18 tip-based preconcentration of peptides, (v) sequential extraction of the peptides with ACN, (vi) MALDI-snapshot of the extracts and (vii) investigation of the extract containing the most discriminating features using high resolution mass spectrometry. With this approach we have been able to differentially cluster renal oncocytoma and chromophobe renal cell carcinoma and identified 18 proteins specific to chromophobe and seven unique to renal oncocytoma. Chromophobes express proteins associated with ATP function (ATP5I & 5E; VATE1 & G2; ADT2), glycolysis (PGK1) and neuromedin whilst oncocytomas express ATP5H, ATPA, DEPD7 and TRIPB thyroid receptor interacting protein.

KW - Chromophobe renal cell carcinoma

KW - MALDI

KW - Profiling ESI

KW - Renal cancer

KW - Renal oncocytoma

KW - Sequential extraction

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DO - 10.1016/j.talanta.2019.120180

M3 - Article

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JO - Talanta

JF - Talanta

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