Reportable EGFR levels were found in only 5 of the 17 investigated samples (EGFR amounts below LLOQ were detected in two additional samples), in good agreement with the low signal for this protein measured by IHC. of the 5-proteins signature in responder and non-responder FFPE xenografts. (XLSX) pone.0213892.s008.xlsx (87K) GUID:?58725F11-1BF3-4575-A407-DDA3C10BF0D0 S6 Table: Measurement of the 5-protein response signature in lung and breast cancer FFPE tissue and in two selected xenografts. (XLSX) pone.0213892.s009.xlsx (49K) GUID:?40161929-88D2-47FD-845E-FE6A2E4171A2 S7 Table: Summary of patient clinical data enrolled in trial BP27582. (XLSX) pone.0213892.s010.xlsx (10K) GUID:?C1BB5EE6-F557-4662-8103-C7EC9481B2EF S8 Table: Measurement of the 5-protein signature in FFPE tissue samples from patients enrolled in the trial BP27582. (XLSX) pone.0213892.s011.xlsx (36K) GUID:?BEF4D388-AA43-48CF-BD2A-C8927679C960 Data Availability StatementRaw data files supporting the data presented in S1A Fig can be found at the PeptideAtlas data repository under accession http://www.peptideatlas.org/PASS/PASS01330. Raw data files supporting the data presented in Fig 2 and S5 Table can be found at the PeptideAtlas data repository under accession http://www.peptideatlas.org/PASS/PASS01332. Raw data files supporting the data presented in Fig 3, S3 Fig, S6 Table and S8 Table can be found at the PeptideAtlas data repository under accession accession http://www.peptideatlas.org/PASS/PASS01332. Abstract Human protein biomarker discovery relies heavily on pre-clinical models, in particular established cell lines and patient-derived xenografts, but confirmation studies in primary tissue are essential to demonstrate clinical relevance. We describe in this study the process that was followed to clinically translate a 5-protein response signature predictive for the activity of an anti-HER3 monoclonal antibody (lumretuzumab) originally measured in fresh frozen xenograft tissue. We detail the development, qualification, and validation of the multiplexed targeted mass spectrometry assay used to assess the signature performance in formalin-fixed, paraffin-embedded human clinical samples collected in a phase Ib trial designed to evaluate lumretuzumab in patients with metastatic breast cancer. We believe that the strategy delineated here provides a path forward to avoid the time- and cost-consuming step of having to develop L 006235 immunological reagents against unproven targets. We expect that mass spectrometry-based platforms may become part of a rational process to rapidly test and qualify large number of candidate biomarkers to identify the few that stand a chance for further development and validation. Introduction In the last few years, pre-clinical research has gradually shifted from studying cell lines to patient-derived xenografts (PDX) as source of biomarkers, in particular in the oncology arena [1C3]. In breast cancer, for instance, a consortium of academic laboratories from Europe, Australia, and L 006235 North America has recently described and released data on over 500 stably transplantable PDX models representing all three clinical subtypes of breast cancer (reviewed in detail in [2]) with most of these models characterized with respect to their genetics, transcriptomics and proteomics features. Remarkably, PDX models have been shown to retain a significant degree of biological and histological fidelity with their tumors of origin. Thus, a recent study including 22 patient-derived breast cancer xenografts demonstrated that PDX tumors recapitulated the proteomic diversity of human breast cancers [4], and, more specifically, that the proteogenomic signatures of PDXs resembled most findings from breast cancer patients. An attractive aspect of PDX models is that they may show comparable responses to the originating tumor, which make them suitable for screening against specific therapeutics [2] and for discovering biomarkers for drug sensitivity and response. Lumretuzumab (RG7116) is a humanized, glycoengineered immunoglobulin-G1 antibody that binds with high sensitivity and specificity to the extracellular domain of the human epidermal growth factor receptor 3 (HER3) [5], one of the members of HER family receptors playing a critical role L 006235 in tumor growth, proliferation, and progression of numerous epithelial malignancies (reviewed in [6,7]). In particular, HER3 up-regulation has been correlated with resistance to HER2-targeting inhibitors in breast cancer due to the unique ability of the HER2:HER3 heterodimer to activate the PI3K/AKT-mTOR signaling pathway (reviewed in [8C10]). Lumretuzumab hinders the binding of heregulin (a native HER3 ligand) to HER3, resulting in almost total Rabbit Polyclonal to TOP2A inhibition of HER3 heterodimerization and subsequent phosphorylation, and causing tumor arrest of cell lineCbased xenografts in mouse models up to total remission compared to controls. A first in-human, dose escalation phase I study to characterize security, effectiveness, and pharmacokinetic and pharmacodynamic properties of lumretuzumab L 006235 recently reported L 006235 the molecule was well tolerated and showed evidence of medical activity [11]. However, the functions of HER3 or heregulin as prognostic markers for HER3-targeted treatment response have remained controversial and no marker have been identified so far for breast malignancy. High heregulin manifestation.