Distinct Splice Variants and Pathway Enrichment in the Cell-Line Models of Aggressive Human Breast Cancer Subtypes

This
study was conducted as a part of the Chromosome-Centric Human
Proteome Project (C-HPP) of the Human Proteome Organization. The United
States team of C-HPP is focused on characterizing the protein-coding
genes in chromosome 17. Despite its small size, chromosome 17 is rich
in protein-coding genes; it contains many cancer-associated genes,
including BRCA1, ERBB2, (Her2/neu), and TP53. The goal of this study
was to examine the splice variants expressed in three ERBB2 expressed
breast cancer cell-line models of hormone-receptor-negative breast
cancers by integrating RNA-Seq and proteomic mass spectrometry data.
The cell lines represent distinct phenotypic variations subtype: SKBR3
(ERBB2+ (overexpression)/ER–/PR–; adenocarcinoma), SUM190
(ERBB2+ (overexpression)/ER–/PR–; inflammatory breast
cancer), and SUM149 (ERBB2 (low expression) ER–/PR–;
inflammatory breast cancer). We identified more than one splice variant
for 1167 genes expressed in at least one of the three cancer cell
lines. We found multiple variants of genes that are in the signaling
pathways downstream of ERBB2 along with variants specific to one cancer
cell line compared with the other two cancer cell lines and with normal
mammary cells. The overall transcript profiles based on read counts
indicated more similarities between SKBR3 and SUM190. The top-ranking
Gene Ontology and BioCarta pathways for the cell-line specific variants
pointed to distinct key mechanisms including: amino sugar metabolism,
caspase activity, and endocytosis in SKBR3; different aspects of metabolism,
especially of lipids in SUM190; cell-to-cell adhesion, integrin, and
ERK1/ERK2 signaling; and translational control in SUM149. The analyses
indicated an enrichment in the electron transport chain processes
in the ERBB2 overexpressed cell line models and an association of
nucleotide binding, RNA splicing, and translation processes with the
IBC models, SUM190 and SUM149. Detailed experimental studies on the
distinct variants identified from each of these three breast cancer
cell line models that may open opportunities for drug target discovery
and help unveil their specific roles in cancer progression and metastasis.

本研究作为人类蛋白质组组织（Human Proteome Organization）旗下以染色体为中心的人类蛋白质组计划（Chromosome-Centric Human Proteome Project, C-HPP）的一部分开展。C-HPP的美国团队聚焦于对17号染色体上的编码蛋白基因进行系统表征。尽管17号染色体体积较小，却富含编码蛋白基因，其中包含诸多癌症相关基因，例如BRCA1、ERBB2（Her2/neu）以及TP53。本研究的目标为，通过整合RNA测序（RNA-Seq）与蛋白质组质谱（proteomic mass spectrometry）数据，探究三种表达ERBB2的激素受体阴性乳腺癌细胞系模型中所表达的可变剪接变体。这三种细胞系分别对应不同的表型变异亚型：SKBR3（ERBB2+（过表达）/ER–/PR–；腺癌）、SUM190（ERBB2+（过表达）/ER–/PR–；炎性乳腺癌）以及SUM149（ERBB2（低表达）/ER–/PR–；炎性乳腺癌）。研究人员在这三种癌细胞系中至少一种的表达基因中，鉴定出1167个基因存在至少一种可变剪接变体。研究发现，ERBB2下游信号通路中的基因存在多种可变剪接变体，同时还发现相较于另外两种癌细胞系以及正常乳腺细胞，仅在某一种癌细胞系中特异性表达的变体。基于测序读段计数的整体转录本表达谱显示，SKBR3与SUM190的表达谱更为相似。针对细胞系特异性可变剪接变体，排名靠前的基因本体（Gene Ontology, GO）与BioCarta通路指向了不同的关键机制：SKBR3涉及氨基糖代谢、半胱天冬酶活性以及内吞作用；SUM190涉及代谢的多个方面，尤其是脂质代谢；SUM149则涉及细胞间黏附、整合素与ERK1/ERK2信号通路以及翻译调控。分析结果还显示，在ERBB2过表达的细胞系模型中，电子传递链相关过程存在富集；而在炎性乳腺癌模型SUM190与SUM149中，核苷酸结合、RNA剪接以及翻译过程存在显著关联。针对从这三种乳腺癌细胞系模型中鉴定出的特异性可变剪接变体开展详细实验研究，有望为药物靶点发现提供新机遇，并帮助阐明这些变体在癌症进展与转移中的特定作用。