Dissecting the Origin of Breast Cancer Subtype Stem Cell and the Potential Mechanism of Malignant Transformation

<div><p>Background</p><p>Breast cancer is the most common incident form of cancer in women including different subtypes. Cancer stem cells (CSCs) have been confirmed to exist in breast cancer. But the research on the origin of breast cancer subtype stem cells (BCSSCs) is still inadequate.</p><p>Methods</p><p>We identified the putative origin cells of BCSSCs through comparing gene signatures between BCSSCs and normal mammary cells from multiple perspectives: common signature, expression consistency, functional similarity and shortest path length. First, the potential origin cells were ranked according to these measures separately. Then Q statistic was employed to combine all rank lists into a unique list for each subtype, to prioritize the origin cells for each BCSSC. Next, we identified origin-related gene modules through integrating functional interaction network with differentially expressed genes. Finally, transcription factors of significant gene modules were predicted by Match^TM.</p><p>Results</p><p>The results showed that Luminal A CSC was most relevant to luminal progenitor cell or mature luminal cell; luminal B and HER2 CSC were most relevant to bipotent-enriched progenitor cell; basal-like CSC was most relevant to bipotent-enriched progenitor cell or mature luminal cell. Network modules analysis revealed genes related to mitochondrial respiratory chain (MRC) were significantly dysregulated during the origin of luminal B CSC. In addition, SOX10 emerged as a key regulator of MRC.</p><p>Conclusions</p><p>Our study supports substantive evidence for the possible origin of four kinds of BCSSCs. Dysfunction of MRC may contribute to the origin of luminal B CSC. These findings may have important implications to treat and prevent breast cancer.</p></div

The work flow of our approach.

<p>Firstly, we downloaded gene expression profiles of normal mammary cells and BCSSCs data from GEO. We indentified signature genes for each type of normal mammary cells and BCSSCs. Secondly, we compared the gene signatures including enrichment analysis of signature gene sets, BCSSC GSS, GO-term’s SSS and the shortest path in HPRD network for up-regulated/over-expressed and down-regulated/under-expressed genes. We obtained eight rank lists of potential origin cells of BCSSCs for each expression profile. In order to prioritize the origin cells for each BCSSC, <i>Q</i> statistic was employed to combine all rank lists into a unique list. We discovered that luminal B subtype was most associated with bipotent-enriched progenitor cell. Next, we analyzed expression data of luminal B CSC and bipotent-enriched progenitor cell through a network module-based method in protein FI network. The result showed that genes related to the function of MRC were significantly dysregulated between normal and cancer condition. Bi, lp, ml and mb are abbreviation for bipotent-enriched progenitor cell, luminal progenitor cell, mature luminal and mature basal cell respectively. A, B, basal and HER are abbreviation for luminal A, luminal B, basal-like and HER2 subtypes, respectively.</p

Differentially expressed genes between luminal B CSC and bipotent-enriched progenitor cell.

<p><b>A</b>, heat map of differentially expressed genes between luminal B CSC and bipotent-enriched progenitor cell. Each row represents a gene; each column, a sample. Colored bar indicates the expression level. <b>B</b>, the result of functional enrichment analysis of differentially expressed genes based on GO. The terms in red are related to mitochondrion. The disconnected bar represents <i>p</i>-value of the term is zero.</p

The rank lists for four subtypes of breast cancer.

<p>The rank lists were integrated by <i>Q</i> statistic. Rank 1 and rank 2 were the integrated rank list for GSE7513 and GSE7515, separately. Overall rank was the average of rank 1 and rank 2. U, up-regulated/over-expressed genes; d, down-regulated/under-expressed genes. Colored bar indicates the ranking of each pair of relationship. The lighter presents the higher ranking; the darker presents the lower ranking.</p

Identification of origin-specific gene modules.

<p><b>A</b>, module 1 from luminal B CSC (left) and module 3 from bipotent-enriched progenitor cell (right). <b>B</b>, the result of functional enrichment analysis of module 1. The terms in red are related to mitochondrion. <b>C</b>, heat map of genes in module 1. Each row represents a gene; each column, a sample. Colored bar indicates the expression level. <b>D</b>, the result of prediction of transcription factor for module 1 by Match^TM. Each row represents a transcript. The number indicates the upstream distance from transcription start site.</p

Number of normal cells signature genes.

<p>Number of normal cells signature genes.</p

Bar plot of the length distribution of the cascades.

<p>Bar plot of the length distribution of the cascades.</p

Bar plot of the number of cascades in the clusters.

<p>Bar plot of the number of cascades in the clusters.</p