背景:乳腺癌(BC)是最常见的癌症,也是全球女性癌症死亡的主要原因。尽管取得了进展,非腔A肿瘤患者的临床结局存在相当大的差异,分类为难以治疗的乳腺癌(DTBC)。这项研究旨在描绘DTBC肿瘤与腔A(LumA)肿瘤相比的蛋白质基因组景观。
方法:我们回顾性地收集了117个未经治疗的原发性乳腺肿瘤标本,重点关注DTBC亚型。通过激光显微切割(LMD)处理乳腺肿瘤以富集肿瘤细胞。DNA,RNA,同时从每种肿瘤制剂中提取蛋白质,然后是全基因组测序,配对末端RNA测序,全球蛋白质组学和磷酸蛋白质组学。差异特征分析,我们进行了通路分析和生存分析,以更好地了解DTBC和研究生物标志物.
结果:我们观察到基因突变的明显变异,结构变化,DTBC和LumA乳腺肿瘤之间的染色体改变。DTBC肿瘤主要在TP53、PLXNB3、锌指基因、SDC2,CDH1,PIK3CA中的突变较少,SVIL,和PTEN。值得注意的是,细胞带1q21,其中包含许多细胞增殖相关基因,在DTBC肿瘤中显著扩增。LMD成功地最小化基质成分和增加的RNA-蛋白质一致性,基质评分比较和蛋白质组学分析证明了这一点。通过蛋白质组学和磷酸蛋白质组学聚类分析观察到不同的DTBC和LumA富集簇,一些生存差异。磷酸化蛋白质组学确定了高复发风险和低复发风险基底样肿瘤的两种不同的磷酸化蛋白质组学图谱。涉及一些已知与乳腺癌的发生和进展有关的基因,包括KIAA1522,DCK,FOXO3,MYO9B,ARID1A,EPRS,ZC3HAV1和RBM14。最后,一项针对多组学数据的综合通路分析,突出了DTBC肿瘤中增殖通路的丰富.
结论:这项研究提供了DTBC与LumA的整合蛋白质基因组特征,并通过激光显微切割富集了肿瘤细胞。我们确定了DTBC肿瘤和磷酸肽的许多共同特征,这些特征可以作为高/低复发风险基底样BC的潜在生物标志物,并可能指导治疗选择。
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 survival 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 proteomic 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, and RBM14. Lastly, an integrated pathway analysis of multi-omics data highlighted a robust enrichment of proliferation pathways in DTBC tumors.
CONCLUSIONS: This study provides an integrated proteogenomic characterization of DTBC vs LumA with tumor cells enriched through laser microdissection. We identified many common features of DTBC tumors and the phosphopeptides that could serve as potential biomarkers for high/low relapse-risk basal-like BC and possibly guide treatment selections.