Intratumoral heterogeneity of microRNA expression in breast cancer.
Author(s): Raychaudhuri M, Schuster T, Buchner T, Malinowsky K, Bronger H, Schwarz-Boeger U, Höfler H, Avril S
Publication: J Mol Diagn, 2012, Vol. 14, Page 376-84
PubMed ID: 22704963 PubMed Review Paper? No
Purpose of Paper
Conclusion of Paper
Studies
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Study Purpose
The purpose of this study was to determine the effects of tumor heterogeneity and section number and thickness on miRNA levels and the effects of tumor heterogeneity on ki-67 IHC in FFPE breast tumors and lymph node metastases. All primary breast tumors were >3 cm and contained >70% tumor. 2-3 samples, at least 5 mm apart from the periphery (within 5 mm of the edge), center (within 10 mm of center) and intermediate zones (between periphery and central), were taken, and RNA was extracted after proteinase K digestion using FFPE miRNeasy. When available (8 of 16 patients), RNA was also obtained from lymph node metastases.
Summary of Findings:
The number of sections, section thickness, and amount of extraction buffer used did not affect miRNA expression profiles. Further, a high degree of reproducibility in miRNA expression was found between repeat extractions from the same and replicate samples. The small nucleolar RNA U48 showed low intratumoral and intertumoral variation, but the small nucleolar RNA U44, and the miRNAs miR-16 and let-7a showed higher intratumoral heterogeneity (p=0.005). The intratumoral heterogeneity was 30% for miR-10b, 33% for miR-210, 44% for miR-335, and 51% for miR-31. Within zone heterogeneity and between zone heterogeneity led to similar variability in expression of all 4 miRNAs, but for miR-31, miR-10b, and miR-210, the intermediate zone showed less heterogeneity than the center and periphery. The authors report that tumor diameter, tumor cell content, or using primary tumor versus metastasis had no effects on the expression variability of miRNA levels, but miRNA expression differed greatly between the patients. Ki-67 immunostaining showed a coefficient of variance (CV) of 28% in primary tumors and 17% in lymph node metastases, and CVs of 5% in the intermediate zone, 22% in the center, and 23% in the periphery. Ki-67 expression was highly variable between patients (CV of 63-112%).
Biospecimens
Preservative Types
- Formalin
Diagnoses:
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform RNA Real-time qRT-PCR Protein Immunohistochemistry Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Aliquots and Components Biospecimen heterogeneity Biospecimen core
Biospecimen periphery
Between core and periphery
Biospecimen Aliquots and Components Aliquot size/volume 2 sections
4 sections
5 um section
10 um section
Biospecimen Acquisition Biospecimen location Breast
Lymph node metastasis
Real-time qRT-PCR Specific Targeted nucleic acid miR-10b
miR-210
miR-31
miR-335
let-7a
miR-16
RNU33
RNU48
Immunohistochemistry Specific Targeted peptide/protein Ki-67
Analyte Extraction and Purification Analyte isolation method 150 uL extraction buffer
240 uL extraction buffer