Proteogenomic characterization of difficult-to-treat breast cancer with tumor cells enriched through laser microdissection

Sep 22, 2026

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Breast cancer is the most commonly diagnosed cancer and a leading cause of death among women globally, yet non-luminal A tumors show substantial variability in clinical outcomes. This study delineates the proteogenomic landscape of difficult-to-treat breast cancer (DTBC) compared with luminal A (LumA) tumors. Using laser microdissection to enrich tumor cells from 117 untreated specimens, DNA, RNA, and proteins were extracted for whole-genome sequencing, paired-end RNA sequencing, and global proteomics/phosphoproteomics, followed by differential, pathway, and survival analyses.

LanguageEnglish

CategoryResearch & Report

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Pages24

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Abstract

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Raj‑Kumar et al. Breast Cancer Research (2024) 26:76 [https://doi.org/10.1](https://doi.org/10.1) 186/s13058‑024‑01835‑4 Breast Cancer Research RESEARCH Open Access Proteogenomic characterization of difficult‑to‑treat breast cancer with tumor cells enriched through laser microdissection Praveen‑Kumar Raj‑Kumar 1,2, Xiaoying Lin 1,2, Tao Liu3, Lori A. Sturtz 1,2, Marina A. Gritsenko3, Vladislav A. Petyuk3, Tyler J. Sagendorf3, Brenda Deyarmin1, Jianfang Liu1, Anupama Praveen‑Kumar1, Guisong Wang2,4, Jason E. McDermott3, Anil K. Shukla3, Ronald J. Moore3, Matthew E. Monroe3, Bobbie‑Jo M. Webb‑Robertson3, Jeffrey A. Hooke2,4, Leigh Fantacone‑Campbell2,4, Brad Mostoller 1, Leonid Kvecher 1,2, Jennifer Kane1, Jennifer Melley1, Stella Somiari1, Patrick Soon‑Shiong5, Richard D. Smith3, Richard J. Mural 1^, Karin D. Rodland3, Craig D. Shriver2,6*, Albert J. Kovatich2,4 and Hai Hu 1,2* Abstract Background Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of cancer death among women globally. Despite advances, there is considerable variation in clinical outcomes for patients with non‑ luminal A tumors, classified as difficult‑to‑treat breast cancers (DTBC) . This study aims to delineate the proteogenomic landscape of DTBC tumors compared to luminal A (LumA) tumors. Methods We retrospectively collected a total of 117 untreated primary breast tumor specimens, focusing on DTBC subtypes. Breast tumors were processed by laser microdissection (LMD) to enrich tumor cells. DNA, RNA, and protein were simultaneously extracted from each tumor preparation, followed by whole genome sequencing, paired‑end RNA sequencing, global proteomics and phosphoproteomics. Differential feature analysis, pathway analysis and sur‑ vival analysis were performed to better understand DTBC and investigate biomarkers. Results We observed distinct variations in gene mutations, structural variations, and chromosomal alterations between DTBC and LumA breast tumors. DTBC tumors predominantly had more mutations in TP53, PLXNB3, Zinc finger genes, and fewer mutations in SDC2, CDH1, PIK3CA, SVIL, and PTEN. Notably, Cytoband 1q21, which contains numerous cell proliferation‑related genes, was significantly amplified in the DTBC tumors. LMD successfully minimized stromal components and increased RNA–protein concordance, as evidenced by stromal score comparisons and pro‑ teomic analysis. Distinct DTBC and LumA‑enriched clusters were observed by proteomic and phosphoproteomic clustering analysis, some with survival differences. Phosphoproteomics identified two distinct phosphoproteomic profiles for high relapse‑risk and low relapse‑risk basal‑like tumors, involving several genes known to be associated with breast cancer oncogenesis and progression, including KIAA1522, DCK, FOXO3, MYO9B, ARID1A, EPRS, ZC3HAV1, ^Richard J. Mural: Deceased. *Correspondence: Craig D. Shriver [craig.shriver@usuhs.edu](craig.shriver@usuhs.edu)[ ](craig.shriver@usuhs.edu)Hai Hu[h.hu@wriwindber.org](h.hu@wriwindber.org) Full list of author information is available at the end of the article This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permit‑ ted use, you will need to obtain permission directly from

FAQs

What is the main purpose of this study?

To define the proteogenomic landscape of difficult-to-treat breast cancer (DTBC) tumors and compare it with luminal A (LumA) tumors.

How were tumor cells enriched for analysis?

Tumor samples were processed by laser microdissection (LMD) to enrich tumor cells, minimizing stromal components and improving RNA–protein concordance.

What kinds of differences were observed between DTBC and LumA tumors?

The study found distinct patterns in gene mutations, structural variations, and chromosomal alterations, including predominant TP53 and other gene mutation changes and significant amplification of cytoband 1q21 in DTBC.

Sep 22, 2026

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