Single-cell long noncoding RNA (lncRNA) transcriptome implicates MALAT1 in triple-negative breast cancer (TNBC) resistance to neoadjuvant chemotherapy

Hibah Shaath,Shahryar Khattak,Radhakrishnan Vishnubalaji,Nehad M Alajez,Ramesh Elango

doi:10.1038/s41420-020-00383-y

Hibah Shaath, Shahryar Khattak + Show 3 more

Open Access

https://doi.org/10.1038/s41420-020-00383-y

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Abstract

Cumulative evidence suggests added benefit for neoadjuvant chemotherapy (NAC) in a subset of triple-negative breast cancer (TNBC) patients. Herein we identified the long noncoding RNA (lncRNA) transcriptional landscape associated with TNBC resistance to NAC, employing 1758 single cells from three extinction and three persistence TNBC patients. Using Iterative Clustering and Guide-gene Selection (ICGS) and uniform manifold approximation and projection (UMAP) dimensionality reduction analysis, we observed single cells derived from each patient to largely cluster together. Comparing the lncRNA transcriptome from single cells through the course of NAC treatment revealed minimal overlap based on lncRNA transcriptome, suggesting substantial effects of NAC on lncRNA transcription. The differential analysis revealed upregulation of 202 and downregulation of 19 lncRNAs in the persistence group, including upregulation of five different transcripts encoding for the MALAT1 lncRNA. CRISPR/Cas9-mediated MALAT1 promoter deletion in BT-549 TNBC model enhanced sensitivity to paclitaxel and doxorubicin, suggesting a role for MALAT1 in conferring resistance. Mechanistically, whole transcriptome analysis of MALAT1-KO cells revealed multiple affected mechanistic networks as well as oxidative phosphorylation canonical and angiogenesis functional category. Interestingly, lncRNA profiling of MALAT1-depleted TNBC also revealed a number of altered lncRNAs in response to MALAT1 deletion, suggesting a reciprocal relationship between MALAT1 and a number of lncRNAs, including NEAT1, USP3-AS1, and LINC-PINT, in TNBC. Elevated expression of MALAT1, USP3-AS1, and LINC-PINT correlated with worse clinical outcomes in BC patients. Our data revealed the lncRNA transactional portrait and highlighted a complex regulatory network orchestrated by MALAT1 in the context of TNBC resistance to NAC therapy.

Highlights

Breast cancer (BC) is the most prevalent type of cancer and the most common cause of cancer-related deaths among women worldwide[1]
In order to identify potential long noncoding RNA (lncRNA)-based signatures predictive of response to Neoadjuvant chemotherapy (NAC) treatment, sequencing data derived from 872 single cells from three extinction and three persistent Triple-negative breast cancer (TNBC) patients prior to neoadjuvant therapy were subjected to hierarchical clustering
Clustering patterns displayed that single cells derived from the extinction and the persistence group clustered into eight different subgroups (x-axis), which clustered into three different clusters (y-axis) based on their lncRNA profile

Summary

Introduction

Breast cancer (BC) is the most prevalent type of cancer and the most common cause of cancer-related deaths among women worldwide[1]. Despite many successes in the field of BC therapy, treatment regimen and the response rate among various molecular subtypes varies. Triple-negative breast cancer (TNBC) is characterized by the absence of receptors commonly used for classification and as targets. These include the estrogen receptor (ER), human epidermal growth factor receptor-2 (HER2), and progesterone receptor (PR). Neoadjuvant chemotherapy (NAC) remains the gold standard form of therapy for TNBC patients, with limited effectiveness, narrower durations of response, and considerably toxic profiles[2]. As a highly heterogeneous BC subtype, there are very few options for treating TNBC patients that confer resistance to conventional chemotherapy[3].

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