Fig 1.
Proteomics strategy leading to the discovery of the 5-protein signature predictive to lumretuzumab activity.
Cell- or patient-derived xenografts responsive (TGI>80) or resistant to lumretuzumab activity were lysed and mixed 1:1 (w/w) with super-SILAC-labelled cell extracts [17] prior to SDS-PAGE fractionation, tryptic digestion, and LC-MS/MS analysis. Protein identification and quantification relative to the super-SILAC standards was performed as previously described [17]. The lineage and the number of different cell- and patient-derived xenograft models included in the discovery step are indicated, as is the number of replicates per xenograft samples.
Table 1.
Assay development and qualification plan for the 5-protein signature in FFPE breast cancer tissue.
Table 2.
SRM reporting peptides assessed in the 5-protein signature in cell lines and in breast and lung tissue.
Fig 2.
Box plot representations and performance of the 5- and 3-protein signatures predictive for lumretuzumab activity in responder and non-responder FFPE xenograft models.
The box plots data distribution includes minimum, first quartile, median, third quartile, and maximum.
Fig 3.
(A) HER2 IRS scores measured by IHC and HER2 protein concentration measured by SRM (B) HER3 IRS scores measured by IHC and HER3 protein concentration measured by SRM (C) EGFR and HER3 versus HER2 protein concentration measured by SRM. The shaded area represents the 10% confidence interval of the linear fit.
Fig 4.
Box plot representations and correlation of the 5- and 3-protein signatures with patient response.
(A, C): Box plot representations of the 5-protein (A) and the 3-protein (C) signature separated by patient response; the box plots data distribution includes minimum, first quartile, median, third quartile, and maximum. (B, D): Correlation of the 5-protein (B) and the 3-protein (D) signature to the individual patient response assessed by RECIST; the signatures’ combined measure is obtained by summing the concentration of the proteins CLIC3+GM2A+OAT+PADI3-DPYSL2 (5-protein signature) or GM2A+OAT-DPYSL2 (3-proteins signature). PD: progressive disease; SD: stable disease; PR: partial response; CR: complete response.