Abstract 2172: Proteogenomics of laser microdissected difficult-to-treat breast cancers identifies Basal and Her2 patients associated with outcome differences

• Published in: Cancer research (Chicago, Ill.) Ill.), 2021-07, Vol.81 (13_Supplement), p.2172-2172
• Main Authors: Raj-Kumar, Praveen-Kumar, Liu, Tao, Sturtz, Lori A., Kovatich, Albert J., Gritsenko, Marina A., Petyuk, Vladislav A., Deyarmin, Brenda, Liu, Jianfang, Praveen-Kumar, Anupama, McDermott, Jason E., Shukla, Anil K., Moore, Ronald J., Monroe, Matthew E., Webb-Robertson, Bobbie-Jo M., Hooke, Jeffrey A., Fantacone-Campbell, Leigh, Kvecher, Leonid, Kane, Jennifer, Melley, Jennifer, Somiari, Stella, Benz, Stephen C., Golovato, Justin, Rabizadeh, Shahrooz, Soon-Shiong, Patrick, Smith, Richard D., Mural, Richard J., Rodland, Karin D., Shriver, Craig D., Li, Zhaoyu, Hu, Hai
• Format: Article
• Language: English
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM2021-2172

Introduction: Breast cancer (BC) is the second most common cause of cancer death among women in the USA. Recent proteogenomic studies of human BC have identified many potential therapeutic biomarkers for the most common types of BC. Here, we strive to comprehensively understand the proteogenomic landscape of difficult-to-treat breast cancer (DTBC) tumors. Methods: 118 primary breast tumors, with a focus on DTBC patients, were selected from the IRB-approved protocol. The study cohort included 30 triple negative, 16 HER2+, 16 Luminal A, 39 Luminal B1, and 17 Luminal B2 selected by immunohistochemistry. Breast tumors were embedded in OCT (Optimum Cutting Temperature) and processed by laser microdissection (LMD) to remove non-tumorous tissue. DNA, RNA, and protein were simultaneously extracted from each tumor using the illustra triplePrep kit. Paired-end RNA sequencing and whole genome sequencing (WGS) were performed for 118 and 100 tumors, respectively, using the Illumina HiSeq platform. Quantitative global proteomics and phosphoproteomic analyses were performed on 113 and 50 tumors, respectively, using isobaric TMT 6-plex labeling with the “universal reference” strategy. Results: Unlike other BC cohorts, our WGS cohort had an almost equal number of Estrogen(ER)+ (55.6%) and ER- (44.4%) cases, which gave us a nominally higher percentage TP53 (57%) and lower PIK3CA (32%) non-silent somatic mutation. Similar to previous reports, GATA3 was mutated in 13% of only ER+ cases. Unlike a recent report on proteomics clustering of bulk-processed tumors, our data show that a stromal-enriched cluster was not mixed with all subtypes but a majority of Luminal A (LumA) subtype, probably because LMD excluded stromal components in other tumor subtypes. Consensus clustering of proteomics data separated intrinsic Her2 patients with outcome differences. Her2 patients associated with the Basal-enriched proteome cluster had better survival than those associated with the LumA-enriched proteome cluster. Previously reported marker PGK1, a predictor for poor survival in BC, was upregulated in Her2 tumors associated with the LumA-enriched proteome cluster. The clustering of phosphoproteomics data separated intrinsic Basal patients into groups with and without relapse. We identified 3 and 18 genes with upregulated kinase activities in the relapse-free and relapsed Basal patients, respectively. In conclusion, this study provides a high-quality proteogenomic resource for DTBC investigation