Molecular Portrait of Hypoxia in Breast Cancer: A Prognostic Signature and Novel HIF-Regulated Genes

Abstract

: Intratumoral hypoxia has been associated with invasion, metastasis, and treatment failure, prompting the need for a global characterization of the response to hypoxic conditions. The current study presents the results of a large-scale RNA sequencing (RNA-seq) effort, analyzing 31 breast cancer cell lines representative of breast cancer subtypes or normal mammary epithelial (NME) cells exposed to control tissue culture conditions (20% O) or hypoxic conditions (1% O). The results demonstrate that NME have a stronger response to hypoxia both in terms of number of genes induced by hypoxia as well as level of expression. A conserved 42-gene hypoxia signature shared across PAM50 subtypes and genes that are exclusively upregulated in Luminal A, Luminal B, and normal-like mammary epithelial cells is identified. The 42-gene expression signature is enriched in a subset of basal-like cell lines and tumors and differentiates survival among patients with basal-like tumors. Mechanistically, the hypoxia-inducible factors (HIF-1 and/or HIF-2) mediate the conserved hypoxic response. Also, four novel hypoxia-regulated and HIF-1-responsive genes were identified as part of the conserved signature. This dataset provides a novel resource to query transcriptional changes that occur in response to hypoxia and serves as a starting point for a clinical assay to aid in stratifying patients that would benefit from hypoxia-targeted therapies, some of which are currently in clinical trials. IMPLICATIONS: RNA-seq of 31 breast cancer cells exposed to control or hypoxic conditions reveals a conserved genomic signature that contains novel HIF-regulated genes and is prognostic for the survival of patients with triple-negative breast cancer.

Calpain-2 regulates hypoxia/HIF-induced amoeboid reprogramming and metastasis

“…22 After HIF-stabilization, invasive tumor cells retain sustained hypoxia-related transcriptional programs and metastatic ability. [22][23][24][25][26] In response to hypoxic challenge, adaptive switching between migration modes may equip moving cancer cells with a repertoire of escape strategies, yet the molecular mechanisms mediating amoeboid conversion and their relevance for hypoxia-induced metastasis remain unclear.…”

“…22 After HIF-stabilization, invasive tumor cells retain sustained hypoxia-related transcriptional programs and metastatic ability. [22][23][24][25][26] In response to hypoxic challenge, adaptive switching between migration modes may equip moving cancer cells with a repertoire of escape strategies, yet the molecular mechanisms mediating amoeboid conversion and their relevance for hypoxia-induced metastasis remain unclear.We used invasive and metastatic epithelial breast cancer and head and neck squamous carcinoma cells (HN-SCC), which invade collectively into 3D fibrillar collagen in tumoroid culture upon normoxia and undergo rapid amoeboid conversion in response to hypoxia or pharmacological stabilization of HIF-1.We then mapped the induced amoeboid variants, pathways of migration mode switching, and their implications for metastatic organ colonization. Hypoxia/HIF stabilization induces conversion to blebbing-amoeboid movement by upregulating activity of the cysteine protease calpain-2, which cleaves the focal adhesion adapter talin-1, limits β1 integrin activity, and strongly enhances metastasis.…”

RhoB is regulated by hypoxia and modulates metastasis in breast cancer

“…We recently performed an RNA sequencing analysis of 31 cell lines exposed to 20% or 1% O 2 conditions . The RhoB transcript was reliably detected in 9 out of 31 cell lines analyzed by RNA sequencing.…”

Deregulation of miR‐27a may contribute to canine fibroblast activation after coculture with a mast cell tumour cell line

“…Three additional upregulated genes in our coculture system further indicated a possible cellular response of PF to an enhanced metabolic status. Canine PF expressed increased mRNA levels of FGF11 and EGLN1 after 96 h. Both genes have been associated with adaptations to metabolic changes that improve cancer cell survival [61]. In contrast to other FGF family members, FGF11 is an intracellular nonsecreted growth factor and shows promitogenic and procell survival activities [62] and is therefore likely to be involved in the fibroblast activation itself.…”