Development of a Robust Ultrasonic-Based Sample Treatment to Unravel the Proteome of OCT-Embedded Solid Tumor Biopsies

Susana Jorge, José L. Capelo, William Laframboise, Rajiv Dhir, Carlos Lodeiro, Hugo M. Santos

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

An effective three-step proteomics workflow is proposed to overcome the pitfalls caused by polymers present in optimum cutting temperature (OCT)-embedded tissue during its preparation for mass spectrometry analysis. First, the OCT-embedded tissue biopsies are cleaned using ethanol and water in a sequential series of ultrasonic washes in an ultrasound bath (35 kHz ultrasonic frequency, 100% ultrasonic amplitude, 2 min of ultrasonic duty time). Second, a fast ultrasonic-assisted extraction of proteins is done using an ultrasonic probe (30 kHz ultrasonic frequency, 50% ultrasonic amplitude, 2 min of ultrasonic duty time, 1 mm diameter tip). Third, a rapid ultrasonic digestion of complex proteomes is performed using a microplate horn assembly device (20 kHz ultrasonic frequency, 25% ultrasonic amplitude, 4 min of ultrasonic duty time). As a proof of concept, the new workflow was applied to human normal and tumor kidney biopsies including chromophobe renal cell carcinomas (chRCCs) and renal oncocytomas (ROs). A successful cluster of proteomics profiles was obtained comprising 511 and 172 unique proteins found in chRCC and RO samples, respectively. The new method provides high sample throughput and comprehensive protein recovery from OCT samples.

Original languageEnglish
Pages (from-to)2979-2986
JournalJournal Of Proteome Research
Volume18
Issue number7
DOIs
Publication statusPublished - 1 Jan 2019

Keywords

  • chromophobe renal cell carcinoma
  • label-free quantification
  • mass spectrometry
  • OCT-embedded tissues
  • renal oncocytoma
  • ultrasound energy

Fingerprint Dive into the research topics of 'Development of a Robust Ultrasonic-Based Sample Treatment to Unravel the Proteome of OCT-Embedded Solid Tumor Biopsies'. Together they form a unique fingerprint.

  • Cite this