Microarray gene expression analysis of fixed archival tissue permits molecular classification and identification of potential therapeutic targets in diffuse large B-cell lymphoma

Kim Linton, Christopher Howarth, Mark Wappett, Gillian Newton, Cynthia Lachel, Javeed Iqbal, Stuart Pepper, Richard Byers, Wing Chan, John Radford

Research output: Contribution to journalArticle

19 Citations (Scopus)

Abstract

Refractory/relapsed diffuse large B-cell lymphoma (DLBCL) has a poor prognosis. Novel drugs targeting the constitutively activated NF-κB pathway characteristic of ABC-DLBCL are promising, but evaluation depends on accurate activated B cell-like (ABC)/germinal center B cell-like (GCB) molecular classification. This is traditionally performed on gene microarray expression profiles of fresh biopsies, which are not routinely collected, or by immunohistochemistry on formalin-fixed, paraffin-embedded (FFPE) tissue, which lacks reproducibility and classification accuracy. We explored the possibility of using routine archival FFPE tissue for gene microarray applications. We examined Affymetrix HG U133 Plus 2.0 gene expression profiles from paired archival FFPE and fresh-frozen tissues of 40 ABC/GCB-classified DLBCL cases to compare classification accuracy and test the potential for this approach to aid the discovery of therapeutic targets and disease classifiers in DLBCL. Unsupervised hierarchical clustering of unselected present probe sets distinguished ABC/GCB in FFPE with remarkable accuracy, and a Bayesian classifier correctly assigned 32 of 36 cases with >90% probability. Enrichment for NF-κB genes was appropriately seen in ABC-DLBCL FFPE tissues. The top discriminatory genes expressed in FFPE separated cases with high statistical significance and contained novel biology with potential therapeutic insights, warranting further investigation. These results support a growing understanding that archival FFPE tissues can be used in microarray experiments aimed at molecular classification, prognostic biomarker discovery, and molecular exploration of rare diseases.

Original languageEnglish (US)
Pages (from-to)223-232
Number of pages10
JournalJournal of Molecular Diagnostics
Volume14
Issue number3
DOIs
StatePublished - May 1 2012

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Lymphoma, Large B-Cell, Diffuse
Paraffin
Formaldehyde
B-Lymphocytes
Gene Expression
Transcriptome
Therapeutics
Genes
Germinal Center
Drug Delivery Systems
Rare Diseases
Cluster Analysis
Biomarkers
Immunohistochemistry
Biopsy

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine

Cite this

Microarray gene expression analysis of fixed archival tissue permits molecular classification and identification of potential therapeutic targets in diffuse large B-cell lymphoma. / Linton, Kim; Howarth, Christopher; Wappett, Mark; Newton, Gillian; Lachel, Cynthia; Iqbal, Javeed; Pepper, Stuart; Byers, Richard; Chan, Wing; Radford, John.

In: Journal of Molecular Diagnostics, Vol. 14, No. 3, 01.05.2012, p. 223-232.

Research output: Contribution to journalArticle

Linton, Kim ; Howarth, Christopher ; Wappett, Mark ; Newton, Gillian ; Lachel, Cynthia ; Iqbal, Javeed ; Pepper, Stuart ; Byers, Richard ; Chan, Wing ; Radford, John. / Microarray gene expression analysis of fixed archival tissue permits molecular classification and identification of potential therapeutic targets in diffuse large B-cell lymphoma. In: Journal of Molecular Diagnostics. 2012 ; Vol. 14, No. 3. pp. 223-232.
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