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Proteogenomics of laser microdissected difficult-to-treat breast cancers identifies Basal and Her2 patients associated with outcome differences Praveen-Kumar Raj-Kumar1, Tao Liu2, Lori A. Sturtz1, Albert J. Kovatich3,4, Marina A. Gritsenko2, Vladislav A. Petyuk2, Tyler J Sagendorf2, Brenda Deyarmin1, Jianfang Liu1, Anupama Praveen-Kumar1, Guisong Wang3,4, Viswanadham Sridhara1, James Craig1, Jason E. McDermott2, Anil K. Shukla2, Ronald J. Moore2, Matthew E. Monroe2, Bobbie-Jo M.Webb-Robertson2, Jeffrey A. Hooke3,4, Leigh Fantacone-Campbell3,4, Leonid Kvecher1, Jennifer Kane1, JenniferMelley1, Stella Somiari1, Stephen C Benz5, Justin Golovato6, Shahrooz Rabizadeh6, Patrick Soon-Shiong6, Richard D. Smith2, Richard J. Mural1, Karin D. Rodland2,#, Craig D. Shriver7,#, Xiaoying Lin1, Hai Hu1,# 1Chan Soon-Shiong Institute of Molecular Medicine at Windber, Windber, PA. 2Pacific Northwest National Laboratory, Richland, WA. 3Clinical Breast Care Project, Murtha Cancer Center Research Program, Uniformed Services University /Walter Reed National Military Medical Center, Bethesda, MD. 4Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD. 5NantOmics, Culver City, CA. 6NantWorks, Culver City, CA. 7Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University of the Health Sciences, Bethesda, MD. #Co-corresponding authors BACKGROUND CONCLUSION RESULTS Breast cancer has high molecular heterogeneity, organ-of-origin specific treatments are not adequate. There are four well-defined subtypes based on transcripts (PAM50): Basal-like, Her2 enriched, Luminal A, and Luminal B. Clinical subtyping are based on IHC markers (ER, PR, HER2, and Ki67): Triple-negative (TN), HER2+, Luminal A (LA), Luminal B1 (LB1) and Luminal B2 (LB2) Subtypes like TN, luminal B (LB1 and LB2) and HER2+ are identified as Difficult-to-Treat BC (DTBC) because of its aggressiveness and proliferative property. Previous proteogenomic work (TCGA, CPTAC et, RITM0027712, ?Breast cancer has high molecular heterogeneity, organ-of-origin specific treatments are not adequate. ?There are four well-defined subtypes based on transcripts (PAM50): Basal-like, Her2 enriched, Luminal A, and Luminal B. ?Clinical subtyping are based on IHC markers (ER, PR, HER2, and Ki67): Triple-negative (TN), HER2+, Luminal A (LA), Luminal B1 (LB1) and Luminal B2 (LB2) ?Subtypes like TN, luminal B (LB1 and LB2) and HER2+ are identified as Difficult-to-Treat BC (DTBC) because of its aggressiveness and proliferative property. ?Previous proteogenomicwork (TCGA, CPTAC etc.) analyzed BCs from the general population with bulk tissue processing. ?Herein, we focus on DTBC tumors (~87%) from patients with long follow-up using Laser Microdissection (LMD) processing.