Abstract 3753: Co-expression proteomic analysis of antibody drug conjugate receptor and payload biomarkers in breast cancer
Authors: Negin Ghafourian, Sheeno P. Thyparambil, Richard Mortensen, James Chou, Robert Heaton, Xuefeng B. Ling
Journal: Cancer Research (2024)

Abstract The use of antibody drug conjugates (ADC) targeting HER2, and Trop 2 has made a great difference in the treatment of breast cancer. Such agents consist of an antibody targeting the receptor which is conjugated to a payload chemotherapy agent. Chemotherapy involves the use of anti-tubulin agents (e.g. docetaxel), topoisomerase inhibitors etc. We examined 507 breast cancer samples using targeted proteomics to quantitate biomarkers for ADC targets such as HER2, HER3, EGFR and Trop2 in our clinical proteomics (CLIA) laboratory. We also measured biomarkers that are associated with response and biomarkers that are associated with resistance to chemotherapeutic agents. Resistance markers include TUBB3 (taxanes), and response markers include TOPO1 (irinotecan, topotecan). Methods: Formalin fixed, paraffin embedded (FFPE) tissues blocks of breast cancer were sectioned, marked for tumor, laser capture microdissected, digested and analyzed by LC-selected reaction monitoring mass spectrometry. Seventy-two proteins were quantitated. Discussion:In our previous work, we have determined that &amp;gt;740 amol/µg HER2 corresponds to IHC 3+/2+ and FISH +. Based on the HER2 quantitation for each sample, the samples were segregated into three groups. Negative (Group A, &amp;lt;150 amol/µg), High expressors (Group C, &amp;gt;740 amol/µg), and Detected (Group B, 151-739 amol/µg). Groups A, B, and C were 39%, 46%, and 43% of the cases respectively. In Group A (HER2 negative), HER3 was detected in 14% of cases with a 3x range (181-602 amol/µg), EGFR was detected in 53% of samples with 139x range (108-14986 amol/µg), Trop2 was detected in 59% of cases ranging from 256 to 11900 amol/µg, Topo1 was detected in 86% of cases with a 12x range (402-4870 amol/µg) and TUBB3 was detected in 63% of cases at levels ranging from 755 to 11750 amol/µg. In Group B (HER2 detected), HER3 was detected in 38% with a 3x range (178-565 amol/µg), EGFR was detected in 34% at levels ranging from 104-7040 amol/µg, Trop2 was detected in 63% ranging from 157 to 12808 amol/µg, Topo1 was detected in 94% with a 12x range (413-5100 amol/µg), and TUBB3 was detected in 51% of cases at levels ranging from 757 to 9311 amol/µg.In Group 3 (HER2 highly expressed), HER3 was detected in 43% with a 5x range (189- 890 amol/µg), EGFR was detected in 30% at levels ranging from 101 to 565 amol/µg, Trop2 was detected in 68% ranging from 310 to14650 amol/µg, Topo1 was detected in 95% with a 6x range (487- 2885 amol/µg), and TUBB3 was detected in 64% of samples at levels ranging from 829 to 2300 amol/µg. Conclusion:The capacity to multiplex 72 protein biomarkers from 2-3 FFPE sections will help in design of ADCs bispecific antibodies and/or bispecific ADCs. Citation Format: Negin Ghafourian, Sheeno P. Thyparambil, Richard Mortensen, James Chou, Robert Heaton, Xuefeng B. Ling. Co-expression proteomic analysis of antibody drug conjugate receptor and payload biomarkers in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3753.