Performance in omics analyses of blood samples in long-term storage

Opportunities for the exploitation of existing biobanks in environmental health research

Dennie G A J Hebels, Panagiotis Georgiadis, Hector C. Keun, Toby J. Athersuch, Paolo Vineis, Roel Vermeulen, Ützen Portengen, Ingvar A. Bergdahl, Göran Hallmans, Domenico Palli, Benedetta Bendinelli, Vittorio Krogh, Rosario Tumino, Carlotta Sacerdote, Salvatore Panico, Jos C S Kleinjans, Theo M C M de Kok, Martyn T. Smith, Soterios A. Kyrtopoulos

Research output: Contribution to journalArticle

84 Citations (Scopus)

Abstract

Background: The suitability for omic analysis of biosamples collected in previous decades and currently stored in biobanks is unknown. Objectives: We evaluated the influence of handling and storage conditions of blood-derived biosamples on transcriptomic, epigenomic (CpG methylation), plasma metabolomic [UPLC-ToFMS (ultra performance liquid chromatography-time-of-flight mass spectrometry)], and wide-target proteomic profiles. Methods: We collected fresh blood samples without RNA preservative in heparin, EDTA, or citrate and held them at room temperature for ≤ 24 hr before fractionating them into buffy coat, erythrocytes, and plasma and freezing the fractions at-80°C or in liquid nitrogen. We developed methodology for isolating RNA from the buffy coats and conducted omic analyses. Finally, we analyzed analogous samples from the EPIC-Italy and Northern Sweden Health and Disease Study biobanks. Results: Microarray-quality RNA could be isolated from buffy coats (including most biobank samples) that had been frozen within 8 hr of blood collection by thawing the samples in RNA preservative. Different anticoagulants influenced the metabolomic, proteomic, and to a lesser extent transcriptomic profiles. Transcriptomic profiles were most affected by the delay (as little as 2 hr) before blood fractionation, whereas storage temperature had minimal impact. Effects on metabolomic and proteomic profiles were noted in samples processed ≥ 8 hr after collection, but no effects were due to storage temperature. None of the variables examined significantly influenced the epigenomic profiles. No systematic influence of tim-in-storage was observed in samples stored over a period of 13-17 years. Conclusions: Most samples currently stored in biobanks are amenable to meaningful omics analysis, provided that they satisfy collection and storage criteria defined in this study.

Original languageEnglish
Pages (from-to)480-487
Number of pages8
JournalEnvironmental Health Perspectives
Volume121
Issue number4
DOIs
Publication statusPublished - Apr 2013

Fingerprint

Environmental Health
Metabolomics
RNA
Proteomics
Research
Epigenomics
Temperature
Sweden
Edetic Acid
Citric Acid
Liquid Chromatography
Anticoagulants
Methylation
Italy
Freezing
Heparin
Mass Spectrometry
Nitrogen
Erythrocytes
Health

Keywords

  • Biomarkers
  • Epigenomics
  • Metabolomics
  • Metabonomics
  • Molecular epidemiology
  • Proteomics
  • Transcriptomics

ASJC Scopus subject areas

  • Health, Toxicology and Mutagenesis
  • Public Health, Environmental and Occupational Health

Cite this

Performance in omics analyses of blood samples in long-term storage : Opportunities for the exploitation of existing biobanks in environmental health research. / Hebels, Dennie G A J; Georgiadis, Panagiotis; Keun, Hector C.; Athersuch, Toby J.; Vineis, Paolo; Vermeulen, Roel; Portengen, Ützen; Bergdahl, Ingvar A.; Hallmans, Göran; Palli, Domenico; Bendinelli, Benedetta; Krogh, Vittorio; Tumino, Rosario; Sacerdote, Carlotta; Panico, Salvatore; Kleinjans, Jos C S; de Kok, Theo M C M; Smith, Martyn T.; Kyrtopoulos, Soterios A.

In: Environmental Health Perspectives, Vol. 121, No. 4, 04.2013, p. 480-487.

Research output: Contribution to journalArticle

Hebels, DGAJ, Georgiadis, P, Keun, HC, Athersuch, TJ, Vineis, P, Vermeulen, R, Portengen, Ü, Bergdahl, IA, Hallmans, G, Palli, D, Bendinelli, B, Krogh, V, Tumino, R, Sacerdote, C, Panico, S, Kleinjans, JCS, de Kok, TMCM, Smith, MT & Kyrtopoulos, SA 2013, 'Performance in omics analyses of blood samples in long-term storage: Opportunities for the exploitation of existing biobanks in environmental health research', Environmental Health Perspectives, vol. 121, no. 4, pp. 480-487. https://doi.org/10.1289/ehp.1205657
Hebels, Dennie G A J ; Georgiadis, Panagiotis ; Keun, Hector C. ; Athersuch, Toby J. ; Vineis, Paolo ; Vermeulen, Roel ; Portengen, Ützen ; Bergdahl, Ingvar A. ; Hallmans, Göran ; Palli, Domenico ; Bendinelli, Benedetta ; Krogh, Vittorio ; Tumino, Rosario ; Sacerdote, Carlotta ; Panico, Salvatore ; Kleinjans, Jos C S ; de Kok, Theo M C M ; Smith, Martyn T. ; Kyrtopoulos, Soterios A. / Performance in omics analyses of blood samples in long-term storage : Opportunities for the exploitation of existing biobanks in environmental health research. In: Environmental Health Perspectives. 2013 ; Vol. 121, No. 4. pp. 480-487.
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AU - Hebels, Dennie G A J

AU - Georgiadis, Panagiotis

AU - Keun, Hector C.

AU - Athersuch, Toby J.

AU - Vineis, Paolo

AU - Vermeulen, Roel

AU - Portengen, Ützen

AU - Bergdahl, Ingvar A.

AU - Hallmans, Göran

AU - Palli, Domenico

AU - Bendinelli, Benedetta

AU - Krogh, Vittorio

AU - Tumino, Rosario

AU - Sacerdote, Carlotta

AU - Panico, Salvatore

AU - Kleinjans, Jos C S

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AU - Kyrtopoulos, Soterios A.

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N2 - Background: The suitability for omic analysis of biosamples collected in previous decades and currently stored in biobanks is unknown. Objectives: We evaluated the influence of handling and storage conditions of blood-derived biosamples on transcriptomic, epigenomic (CpG methylation), plasma metabolomic [UPLC-ToFMS (ultra performance liquid chromatography-time-of-flight mass spectrometry)], and wide-target proteomic profiles. Methods: We collected fresh blood samples without RNA preservative in heparin, EDTA, or citrate and held them at room temperature for ≤ 24 hr before fractionating them into buffy coat, erythrocytes, and plasma and freezing the fractions at-80°C or in liquid nitrogen. We developed methodology for isolating RNA from the buffy coats and conducted omic analyses. Finally, we analyzed analogous samples from the EPIC-Italy and Northern Sweden Health and Disease Study biobanks. Results: Microarray-quality RNA could be isolated from buffy coats (including most biobank samples) that had been frozen within 8 hr of blood collection by thawing the samples in RNA preservative. Different anticoagulants influenced the metabolomic, proteomic, and to a lesser extent transcriptomic profiles. Transcriptomic profiles were most affected by the delay (as little as 2 hr) before blood fractionation, whereas storage temperature had minimal impact. Effects on metabolomic and proteomic profiles were noted in samples processed ≥ 8 hr after collection, but no effects were due to storage temperature. None of the variables examined significantly influenced the epigenomic profiles. No systematic influence of tim-in-storage was observed in samples stored over a period of 13-17 years. Conclusions: Most samples currently stored in biobanks are amenable to meaningful omics analysis, provided that they satisfy collection and storage criteria defined in this study.

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