Transcriptional landscape associated with TNBC resistance to neoadjuvant chemotherapy revealed by single-cell RNA-seq

• Published in: Molecular therapy. Oncolytics Vol. 23; pp. 151 - 162
• Main Authors: Vishnubalaji, Radhakrishnan, Alajez, Nehad M.
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 17.12.2021; American Society of Gene & Cell Therapy; Elsevier
• Subjects: gene signature; NAC; neoadjuvant chemotherapy; Original; resistance; single cell; TNBC; triple-negative breast cancer; neoadjuvant chemotherapy; NAC; triple-negative breast cancer; single cell; gene signature; TNBC; resistance
• ISSN: 2372-7705; 2372-7705
• DOI: 10.1016/j.omto.2021.09.002

Triple-negative breast cancer (TNBC) resistance to neoadjuvant chemotherapy (NAC) represents a major clinical challenge; therefore, delineating tumor heterogeneity can provide novel insight into resistance mechanisms and potential therapeutic targets. Herein, we identified the transcriptional landscape associated with TNBC resistance to NAC at the single-cell level by analyzing publicly available transcriptome data from more than 5,000 single cells derived from four extinction (responders) and four persistence (non-responders) patients, revealing remarkable tumor heterogeneity. Employing iterative clustering and guide-gene selection (ICGS) and uniform manifold approximation and projection (UMAP), we classified TNBC single cells into several clusters based on their distinct gene signatures. The presence of clusters indicative of immune cell activation was a hallmark of the extinction group pre-NAC, while post NAC, the extinction tissue consisted mostly of breast, omental fat, and fibroblasts. The persistent gene signatures of pre-NAC resembled the gene signature of lung epithelial, mammary, and salivary glands and acute myeloid leukemia blast cells, which were associated with enhanced cellular movement and activation of FOXM1, NOTCH1, and MYC and suppression of tumor necrosis factor (TNF) and IFNG mechanistic networks. Multivariate survival analysis identified persistence-derived three-gene signature (KIF5BhighHLA-ClowIGHG2low) predictive of relapse-free survival (hazard ratio [HR]: 2.2 [1.6–3.2, p < 0.0001]) in a second cohort of 360 TNBC patients. Mechanistically, loss of function of several upregulated genes in the persistent group (BYSL, FDPS, ENO1, MED20, MRPL9, MRPL37, NDUFB11, PMVK, MYC, and GSTP1) inhibited MDA-MB-231 and BT-549 TNBC models’ colony-forming unit (CFU) potential and enhanced their sensitivity to paclitaxel. Our data unraveled the transcriptional portrait associated with NAC resistance, identified several key genes, and suggested their potential utilization as prognostic markers and therapeutic targets in TNBC. [Display omitted] TNBC patients exhibit variable responses to neoadjuvant chemotherapy (NAC), suggesting an underlying clonal heterogeneity. Employing single-cell transcriptome analysis of TNBC responders and non-responders to NAC, we identified gene signature(s) associated with NAC resistance and survival and highlighted the presence of immune infiltration as the hallmark of NAC responsiveness.