title: Influence of biospecimen variables on proteomic biomarkers in breast cancer.
abstract: 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 who did 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.
authors.affiliation: Authors' Affiliations: Departments of Investigational Cancer Therapeutics, Surgical Oncology, fmeric@mdanderson.org.
authors.forename: Funda
authors.initials: F
authors.lastname: Meric-Bernstam
authors.affiliation: Authors' Affiliations: Departments of Investigational Cancer Therapeutics.
authors.forename: Argun
authors.initials: A
authors.lastname: Akcakanat
authors.affiliation: Biostatistics.
authors.forename: Huiqin
authors.initials: H
authors.lastname: Chen
authors.affiliation: Pathology.
authors.forename: Aysegul
authors.initials: A
authors.lastname: Sahin
authors.affiliation: Authors' Affiliations: Departments of Investigational Cancer Therapeutics.
authors.forename: Emily
authors.initials: E
authors.lastname: Tarco
authors.affiliation: Radiology, Current Institution Department of Radiology, Ohio State University, Columbus, Ohio.
authors.forename: Selin
authors.initials: S
authors.lastname: Carkaci
authors.affiliation: Radiology.
authors.forename: Beatriz E
authors.initials: BE
authors.lastname: Adrada
authors.affiliation: Authors' Affiliations: Departments of Investigational Cancer Therapeutics.
authors.forename: Gopal
authors.initials: G
authors.lastname: Singh
authors.affiliation: Biostatistics.
authors.forename: Kim-Anh
authors.initials: KA
authors.lastname: Do
authors.affiliation: Authors' Affiliations: Departments of Investigational Cancer Therapeutics.
authors.forename: Zerzhinski M
authors.initials: ZM
authors.lastname: Garces
authors.affiliation: Surgical Oncology.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Mittendorf
authors.affiliation: Surgical Oncology.
authors.forename: Gildy
authors.initials: G
authors.lastname: Babiera
authors.affiliation: Surgical Oncology.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Bedrosian
authors.affiliation: Surgical Oncology.
authors.forename: Rosa
authors.initials: R
authors.lastname: Hwang
authors.affiliation: Pathology.
authors.forename: Savitri
authors.initials: S
authors.lastname: Krishnamurthy
authors.affiliation: Pathology.
authors.forename: William F
authors.initials: WF
authors.lastname: Symmans
authors.affiliation: Breast Medical Oncology, Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas; and.
authors.forename: Ana Maria
authors.initials: AM
authors.lastname: Gonzalez-Angulo
authors.affiliation: Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas; and.
authors.forename: Gordon B
authors.initials: GB
authors.lastname: Mills
mesh_terms: D014408:Biomarkers, Tumor / Q000378:metabolism*; D001943:Breast Neoplasms / Q000378:metabolism* / Q000473:pathology; D005260:Female; D006801:Humans; D019869:Phosphatidylinositol 3-Kinases / Q000378:metabolism; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction; D047368:Tumor Burden
chemical_list: D014408:Biomarkers, Tumor; D020543:Proteome; D019869:Phosphatidylinositol 3-Kinases