Cargando…

Optimization of a high-throughput whole blood expression profiling methodology and its application to assess the pharmacodynamics of interferon (IFN) beta-1a or polyethylene glycol-conjugated IFN beta-1a in healthy clinical trial subjects

BACKGROUND: Clinical trials offer a unique opportunity to study human disease and response to therapy in a highly controlled setting. The application of high-throughput expression profiling to peripheral blood from clinical trial subjects could facilitate the identification of transcripts that funct...

Descripción completa

Detalles Bibliográficos
Autores principales: Allaire, Normand E, Bushnell, Steven E, Bienkowska, Jadwiga, Brock, Graham, Carulli, John
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3560109/
https://www.ncbi.nlm.nih.gov/pubmed/23289891
http://dx.doi.org/10.1186/1756-0500-6-8
_version_ 1782257733802655744
author Allaire, Normand E
Bushnell, Steven E
Bienkowska, Jadwiga
Brock, Graham
Carulli, John
author_facet Allaire, Normand E
Bushnell, Steven E
Bienkowska, Jadwiga
Brock, Graham
Carulli, John
author_sort Allaire, Normand E
collection PubMed
description BACKGROUND: Clinical trials offer a unique opportunity to study human disease and response to therapy in a highly controlled setting. The application of high-throughput expression profiling to peripheral blood from clinical trial subjects could facilitate the identification of transcripts that function as prognostic or diagnostic markers of disease or treatment. The paramount issue for these methods is the ability to produce robust, reproducible, and timely mRNA expression profiles from peripheral blood. Single-stranded complementary DNA (sscDNA) targets derived from whole blood exhibit improved detection of transcripts and reduced variance as compared to their complementary RNA counterparts and therefore provide a better option for interrogation of peripheral blood on oligonucleotide arrays. High-throughput microarray technologies such as the high-throughput plate array platform offer several advantages compared with slide- or cartridge-based arrays; however, manufacturer’s protocols do not support the use of sscDNA targets. RESULTS: We have developed a highly reproducible, high-through put, whole blood expression profiling methodology based on sscDNA and used it to analyze human brain reference RNA and universal human reference RNA samples to identify experimental conditions that most highly correlated with a gold standard quantitative polymerase chain reaction reference dataset. We then utilized the optimized method to analyze whole blood samples from healthy clinical trial subjects treated with different versions of interferon (IFN) beta-1a. Analysis of whole blood samples before and after treatment with intramuscular [IM] IFN beta-1a or polyethylene glycol-conjugated IFN (PEG-IFN) beta-1a under optimized experimental conditions demonstrated that PEG-IFN beta-1a induced a more sustained and prolonged pharmacodynamic response than unmodified IM IFN beta-1a. These results provide validation of the utility of this new methodology and suggest the potential therapeutic benefit of a sustained pharmacodynamic response to PEG-IFN beta-1a. CONCLUSIONS: This novel microarray methodology is ideally suited for utilization in large clinical studies to identify expressed transcripts for the elucidation of disease mechanisms of action and as prognostic, diagnostic, or toxicity markers.
format Online
Article
Text
id pubmed-3560109
institution National Center for Biotechnology Information
language English
publishDate 2013
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-35601092013-02-04 Optimization of a high-throughput whole blood expression profiling methodology and its application to assess the pharmacodynamics of interferon (IFN) beta-1a or polyethylene glycol-conjugated IFN beta-1a in healthy clinical trial subjects Allaire, Normand E Bushnell, Steven E Bienkowska, Jadwiga Brock, Graham Carulli, John BMC Res Notes Research Article BACKGROUND: Clinical trials offer a unique opportunity to study human disease and response to therapy in a highly controlled setting. The application of high-throughput expression profiling to peripheral blood from clinical trial subjects could facilitate the identification of transcripts that function as prognostic or diagnostic markers of disease or treatment. The paramount issue for these methods is the ability to produce robust, reproducible, and timely mRNA expression profiles from peripheral blood. Single-stranded complementary DNA (sscDNA) targets derived from whole blood exhibit improved detection of transcripts and reduced variance as compared to their complementary RNA counterparts and therefore provide a better option for interrogation of peripheral blood on oligonucleotide arrays. High-throughput microarray technologies such as the high-throughput plate array platform offer several advantages compared with slide- or cartridge-based arrays; however, manufacturer’s protocols do not support the use of sscDNA targets. RESULTS: We have developed a highly reproducible, high-through put, whole blood expression profiling methodology based on sscDNA and used it to analyze human brain reference RNA and universal human reference RNA samples to identify experimental conditions that most highly correlated with a gold standard quantitative polymerase chain reaction reference dataset. We then utilized the optimized method to analyze whole blood samples from healthy clinical trial subjects treated with different versions of interferon (IFN) beta-1a. Analysis of whole blood samples before and after treatment with intramuscular [IM] IFN beta-1a or polyethylene glycol-conjugated IFN (PEG-IFN) beta-1a under optimized experimental conditions demonstrated that PEG-IFN beta-1a induced a more sustained and prolonged pharmacodynamic response than unmodified IM IFN beta-1a. These results provide validation of the utility of this new methodology and suggest the potential therapeutic benefit of a sustained pharmacodynamic response to PEG-IFN beta-1a. CONCLUSIONS: This novel microarray methodology is ideally suited for utilization in large clinical studies to identify expressed transcripts for the elucidation of disease mechanisms of action and as prognostic, diagnostic, or toxicity markers. BioMed Central 2013-01-05 /pmc/articles/PMC3560109/ /pubmed/23289891 http://dx.doi.org/10.1186/1756-0500-6-8 Text en Copyright ©2013 Allaire et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Allaire, Normand E
Bushnell, Steven E
Bienkowska, Jadwiga
Brock, Graham
Carulli, John
Optimization of a high-throughput whole blood expression profiling methodology and its application to assess the pharmacodynamics of interferon (IFN) beta-1a or polyethylene glycol-conjugated IFN beta-1a in healthy clinical trial subjects
title Optimization of a high-throughput whole blood expression profiling methodology and its application to assess the pharmacodynamics of interferon (IFN) beta-1a or polyethylene glycol-conjugated IFN beta-1a in healthy clinical trial subjects
title_full Optimization of a high-throughput whole blood expression profiling methodology and its application to assess the pharmacodynamics of interferon (IFN) beta-1a or polyethylene glycol-conjugated IFN beta-1a in healthy clinical trial subjects
title_fullStr Optimization of a high-throughput whole blood expression profiling methodology and its application to assess the pharmacodynamics of interferon (IFN) beta-1a or polyethylene glycol-conjugated IFN beta-1a in healthy clinical trial subjects
title_full_unstemmed Optimization of a high-throughput whole blood expression profiling methodology and its application to assess the pharmacodynamics of interferon (IFN) beta-1a or polyethylene glycol-conjugated IFN beta-1a in healthy clinical trial subjects
title_short Optimization of a high-throughput whole blood expression profiling methodology and its application to assess the pharmacodynamics of interferon (IFN) beta-1a or polyethylene glycol-conjugated IFN beta-1a in healthy clinical trial subjects
title_sort optimization of a high-throughput whole blood expression profiling methodology and its application to assess the pharmacodynamics of interferon (ifn) beta-1a or polyethylene glycol-conjugated ifn beta-1a in healthy clinical trial subjects
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3560109/
https://www.ncbi.nlm.nih.gov/pubmed/23289891
http://dx.doi.org/10.1186/1756-0500-6-8
work_keys_str_mv AT allairenormande optimizationofahighthroughputwholebloodexpressionprofilingmethodologyanditsapplicationtoassessthepharmacodynamicsofinterferonifnbeta1aorpolyethyleneglycolconjugatedifnbeta1ainhealthyclinicaltrialsubjects
AT bushnellstevene optimizationofahighthroughputwholebloodexpressionprofilingmethodologyanditsapplicationtoassessthepharmacodynamicsofinterferonifnbeta1aorpolyethyleneglycolconjugatedifnbeta1ainhealthyclinicaltrialsubjects
AT bienkowskajadwiga optimizationofahighthroughputwholebloodexpressionprofilingmethodologyanditsapplicationtoassessthepharmacodynamicsofinterferonifnbeta1aorpolyethyleneglycolconjugatedifnbeta1ainhealthyclinicaltrialsubjects
AT brockgraham optimizationofahighthroughputwholebloodexpressionprofilingmethodologyanditsapplicationtoassessthepharmacodynamicsofinterferonifnbeta1aorpolyethyleneglycolconjugatedifnbeta1ainhealthyclinicaltrialsubjects
AT carullijohn optimizationofahighthroughputwholebloodexpressionprofilingmethodologyanditsapplicationtoassessthepharmacodynamicsofinterferonifnbeta1aorpolyethyleneglycolconjugatedifnbeta1ainhealthyclinicaltrialsubjects