Influence of biospecimen variables on proteomic biomarkers in breast cancer

Funda Meric-Bernstam, Argun Akcakanat, Huiqin Chen, Aysegul Sahin, Emily Tarco, Selin Carkaci, Beatriz E. Adrada, Gopal Singh, Kim Anh Do, Zerzhinski M. Garces, Elizabeth Mittendorf, Gildy Babiera, Isabelle Bedrosian, Rosa Hwang, Savitri Krishnamurthy, William F. Symmans, Ana Maria Gonzalez-Angulo, Gordon B. Mills

Research output: Contribution to journalArticlepeer-review

40 Scopus citations


Background: PI3K/Akt/mTOR signaling is being actively pursued as a therapeutic target for breast cancer. We sought to determine if tumor heterogeneity and biospecimen variables affect the evaluation of PI3K/Akt/mTOR pathway markers. Methods: Intraoperative image-guided core-needle biopsies (CNB), and central and peripheral surgical tumor specimens were prospectively collected in 53 patients with invasive breast cancer. Specimens were assessed with reverse-phase protein arrays (RPPA) and immunohistochemistry (IHC). Results: There was a moderate or strong correlation between the expression of 149 (97%) of the 154 different RPPA markers in the center and periphery. Correlation was higher for smaller tumors, in patients whodid not undergo neoadjuvant therapy, and with shorter cold ischemia time. Of 154 markers, 132 (86%) were not statistically different between the center and periphery, and 97 (63%) were not different between the CNB and the surgical specimen (average of the central and peripheral specimen). pAkt S473 and PTEN had a significant correlation between central and peripheral specimens, and between CNB and surgical specimen. However, pAkt S473, pS6 S235/236, and pS6 240/244 levels were significantly higher in CNB than the central specimens both by RPPA and by IHC. Conclusions: Most individual proteomic biomarkers studied do not have significant intratumoral heterogeneity. However, protein and phosphoprotein levels are affected by biospecimen type and other preanalytic variables. PI3K pathway activation is greater in CNB compared with postexcision surgical samples suggesting a potential loss of phosphorylation during surgical manipulation, or with cold ischemia of surgical specimens.

Original languageEnglish (US)
Pages (from-to)3870-3883
Number of pages14
JournalClinical Cancer Research
Issue number14
StatePublished - Jul 15 2014
Externally publishedYes

ASJC Scopus subject areas

  • Oncology
  • Cancer Research


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