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Technology Insight: application of molecular techniques to formalin-fixed paraffin-embedded tissues from breast cancer

Nature Clinical Practice Oncology volume 2, pages 246–254 (2005)Cite this article

Abstract

Breast cancer is a heterogenous disease in terms of both clinical behavior and molecular characteristics. To develop prognostic and predictive markers for breast cancer, it would be useful to be able to analyze formalin-fixed paraffin-embedded tissue (FPET) collected and banked from completed clinical trials. RNAs extracted from FPETs are chemically modified and fragmented, and are therefore not ideal substrates for gene-expression profiling assays. However, methods are being developed to optimize the use of such RNAs for high-throughput gene expression profiling assays. For microarray analysis, existing methods may be adequate for fresh FPET, but they do not work well with older FPET. For older samples, real-time reverse transcription-polymerase chain reaction is the method of choice for gene-expression profiling.

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Figure 1: Ideal management of breast cancer patients.
Figure 2: General steps involved in gene expression profiling of formalin-fixed paraffin-embedded tissue.
Figure 3: Size distribution of fixed, paraffin-embedded tissue RNA from 12 tumor specimens.
Figure 4: TaqMan® real-time reverse-transcription polymerase chain reaction assay.
Figure 5: Mean cycling threshold values for 92 genes in 62 patient samples as a function of paraffin-block archive-storage time.
Figure 6: Strategy used in development of Oncotype DX™ multi-gene prognostic assay for estrogen-receptor-positive node-negative tamoxifen-treated patients with breast cancer.
Figure 7: The cDNA-mediated annealing, selection, extension and ligation (DASL™) assay monitors gene expression by targeting sequences in cDNAs with sets of query oligonucleotides, which are composed of multiple parts.
Figure 8: Result of unsupervised clustering of 987 node-positive breast cancer samples according to amplification status of 10 different genes.

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Acknowledgements

The studies mentioned in this article were in part funded by the following grants: NCI grant U10CA12027 awarded to NSABP Foundation Inc (Pittsburgh, PA), Common Wealth Universal Research Enhancement Program from PA State Department of Health fiscal year 2003 awarded to Soonmyung Paik

Author information

Authors and Affiliations

  1. Director of the Division of Pathology at the National Surgical Adjuvant Breast and Bowel Project (NSABP), Pittsburgh, USA

    Soonmyung Paik

  2. Director of Division of Pathology, Molecular Pathology Laboratory, NSABP, Pittsburgh, USA

    Chung-yeul Kim

  3. Postdoctoral Fellow of Center for Cancer Research at the National Cancer Institute, Bethesda, Maryland, USA

    Yong-kuk Song

  4. Assistant Professor of the Department of Pathology at the KonKuk University Hospital, Seoul, Korea

    Wan-seop Kim

Authors
  1. Soonmyung Paik
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  2. Chung-yeul Kim
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  3. Yong-kuk Song
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  4. Wan-seop Kim
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Corresponding author

Correspondence to Soonmyung Paik.

Ethics declarations

Competing interests

S Paik has received honorarium less than $10,000 in total amount during the past two years from Genomic Health, Inc for invited lectures arranged by the company. Genomic Health Inc developed and markets Oncotype DX™ assay as a commercial reference laboratory. Dr Paik is listed as one of the co-inventors in patent filings for Oncotype DX™ assay with all rights released to NSABP Foundation Inc. He does not hold any position or own stocks of the Genomic Health Inc. He does not have any loyalty payment arrangement for his involvement in developing the Oncotype DX™ test.

Glossary

MKI67

Gene that enclodes an antigen identified by monoclonal antibody Ki-67

AURKA

Aurora kinase A, also known as STK15

BIRC5

Baculoviral IAP repeat-containing 5 (Survivin)

CCNB1

Cyclin B1

MYBL2

Gene for v-myb myeloblastosis viral oncogene homolog (avian)-like 2

GRB7

Growth factor receptor-bound protein 7

ERBB2

v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, a neuro/glioblastoma-derived oncogene homolog. It codes for a transmembrane glycoprotein (HER2) that possesses tyrosine kinase activity.

BCL2

B-cell chronic lymphocytic leukemia/lymphoma 2

SCUBE2

Signal peptide, CUB domain, EGF-like 2

MMP11

Matrix metalloproteinase 11 (stromelysin 3)

CTSL2

Cathepsin L2

GSTM1

Glutathione S-transferase M1

BAG1

BCL2-associated athanogene

NATIONAL SURGICAL ADJUVANT BREAST AND BOWEL PROJECT (NSABP)

A clinical trials cooperative group supported by the National Cancer Institute (NCI)

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Paik, S., Kim, Cy., Song, Yk. et al. Technology Insight: application of molecular techniques to formalin-fixed paraffin-embedded tissues from breast cancer. Nat Rev Clin Oncol 2, 246–254 (2005). https://doi.org/10.1038/ncponc0171

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