open access

Vol 25, No 5 (2020)
Original research articles
Published online: 2020-09-01
Submitted: 2018-11-12
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Label-free quantitative mass spectrometry from formalin-fixed paraffin-embedded samples of nasopharyngeal carcinoma: Preliminary results from a non-endemic European cohort of patients

Eduardo Netto, Hugo Santos, Luís Carvalho, José Luis Capelo-Martínez, Miguel Rito, José Cabeçadas, Margarida Roldão
DOI: 10.1016/j.rpor.2020.05.007
·
Rep Pract Oncol Radiother 2020;25(5):746-753.

open access

Vol 25, No 5 (2020)
Original research articles
Published online: 2020-09-01
Submitted: 2018-11-12

Abstract

Aim

Report our results of biomarker discovery in formalin-fixed paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) via proteomic analysis.

Background

Nasopharyngeal carcinoma (NPC) is a rare cancer in Western countries. Proteomic analysis have already been reported as a useful tool to provide biomarkers. Formalin-fixed paraffin-embedded (FFPE) samples, despite largely underused, can provide invaluable information for biomarker research via proteomic analysis.

Methods

FFPE samples of NPC were submitted to protein extraction followed by FASP-digestion and label-free quantitative mass spectrometry (MS). Patients’ received concurrent chemoradiation with or without adjuvant chemotherapy as per Intergroup 0099 trial. IMRT was delivered following the RTOG0615 specifications. Toxicity was scored using the CTCAE 4.03 tables. Survival was estimated using Kaplan–Meier curves. Log-rank was used to detect differences. KEGG ontology graphics were generated.

Results

28 FFPE samples from NPC patients were used. Patients were: 79% male, 97% Caucasians, 86% WHO type 3, 40% T1, 10% T2, 25% T3, and 25% T4. With a median follow up of 37 months, local control was 83 (T1, 100% T2, T3 and T4), overall survival was 84%, and six patients developed distant metastases. All five patients that died were due to metastatic disease. Tumor samples contained a median of 75% of tumor material. We found Epstein–Barr (EBV) and Herpes simplex (HSV) viruses’ related proteins significantly present in early-stage primary NPC (T1 and T2, p<0.01). A pool of 10 proteins was statistically up-regulated in the metastatic group of patients (p<0.01). Median survival from this M1 group was <1 year (p<0.001).

Conclusions

FFPE samples yielded adequate material for MS analysis. We found EBV and HSV related proteins on early-stage NPC, and proteomic profiling associated with distant metastases, potential candidates of disease biomarkers. Validation is needed.

Abstract

Aim

Report our results of biomarker discovery in formalin-fixed paraffin-embedded (FFPE) nasopharyngeal carcinoma (NPC) via proteomic analysis.

Background

Nasopharyngeal carcinoma (NPC) is a rare cancer in Western countries. Proteomic analysis have already been reported as a useful tool to provide biomarkers. Formalin-fixed paraffin-embedded (FFPE) samples, despite largely underused, can provide invaluable information for biomarker research via proteomic analysis.

Methods

FFPE samples of NPC were submitted to protein extraction followed by FASP-digestion and label-free quantitative mass spectrometry (MS). Patients’ received concurrent chemoradiation with or without adjuvant chemotherapy as per Intergroup 0099 trial. IMRT was delivered following the RTOG0615 specifications. Toxicity was scored using the CTCAE 4.03 tables. Survival was estimated using Kaplan–Meier curves. Log-rank was used to detect differences. KEGG ontology graphics were generated.

Results

28 FFPE samples from NPC patients were used. Patients were: 79% male, 97% Caucasians, 86% WHO type 3, 40% T1, 10% T2, 25% T3, and 25% T4. With a median follow up of 37 months, local control was 83 (T1, 100% T2, T3 and T4), overall survival was 84%, and six patients developed distant metastases. All five patients that died were due to metastatic disease. Tumor samples contained a median of 75% of tumor material. We found Epstein–Barr (EBV) and Herpes simplex (HSV) viruses’ related proteins significantly present in early-stage primary NPC (T1 and T2, p<0.01). A pool of 10 proteins was statistically up-regulated in the metastatic group of patients (p<0.01). Median survival from this M1 group was <1 year (p<0.001).

Conclusions

FFPE samples yielded adequate material for MS analysis. We found EBV and HSV related proteins on early-stage NPC, and proteomic profiling associated with distant metastases, potential candidates of disease biomarkers. Validation is needed.

Get Citation

Keywords

Nasopharyngeal carcinoma; Biomarkers; Proteomic analysis; Metastases prediction

About this article
Title

Label-free quantitative mass spectrometry from formalin-fixed paraffin-embedded samples of nasopharyngeal carcinoma: Preliminary results from a non-endemic European cohort of patients

Journal

Reports of Practical Oncology and Radiotherapy

Issue

Vol 25, No 5 (2020)

Pages

746-753

Published online

2020-09-01

DOI

10.1016/j.rpor.2020.05.007

Bibliographic record

Rep Pract Oncol Radiother 2020;25(5):746-753.

Keywords

Nasopharyngeal carcinoma
Biomarkers
Proteomic analysis
Metastases prediction

Authors

Eduardo Netto
Hugo Santos
Luís Carvalho
José Luis Capelo-Martínez
Miguel Rito
José Cabeçadas
Margarida Roldão

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