In vitro and ex vivo gene expression profiling reveals differential kinetic response of HSPs and UPR genes is associated with PI resistance in multiple myeloma

Amit Kumar Mitra,Brian G Van Ness,Vijay Ramakrishnan,Harish Kumar,Linda Baughn,Shaji Kumar,S Vincent Rajkumar,Li Chen

doi:10.1038/s41408-020-00344-9

Abstract

Extensive inter-individual variation in response to chemotherapy (sensitive vs resistant tumors) is a serious cause of concern in the treatment of multiple myeloma (MM). In this study, we used human myeloma cell lines (HMCLs), and patient-derived CD138+ cells to compare kinetic changes in gene expression patterns between innate proteasome inhibitor (PI)-sensitive and PI-resistant HMCLs following test dosing with the second-generation PI Ixazomib. We found 1553 genes that changed significantly post treatment in PI-sensitive HMCLs compared with only seven in PI-resistant HMCLs (p < 0.05). Genes that were uniquely regulated in PI-resistant lines were RICTOR (activated), HNF4A, miR-16-5p (activated), MYCN (inhibited), and MYC (inhibited). Ingenuity pathway analysis (IPA) using top kinetic response genes identified the proteasome ubiquitination pathway (PUP), and nuclear factor erythroid 2-related factor 2 (NRF2)-mediated oxidative stress response as top canonical pathways in Ix-sensitive cell lines and patient-derived cells, whereas EIF2 signaling and mTOR signaling pathways were unique to PI resistance. Further, 10 genes were common between our in vitro and ex vivo post-treatment kinetic PI response profiles and Shaughnessy’s GEP80-postBz gene expression signature, including the high-risk PUP gene PSMD4. Notably, we found that heat shock proteins and PUP pathway genes showed significant higher upregulation in Ix-sensitive lines compared with the fold-change in Ix-resistant myelomas.

Highlights

Multiple myeloma (MM) remains an incurable disease with 5-year survival rate of 48.5% (NCI-SEER Cancer statistics)[1]
Extensive inter-individual variation in response to chemotherapy is a serious cause of concern in the treatment of myeloma[2,3]
Response to Ix in human myeloma cell lines (HMCLs) and patient-derived human myeloma cells are provided in Fig. 1a, b

Summary

Introduction

Multiple myeloma (MM) remains an incurable disease with 5-year survival rate of 48.5% (NCI-SEER Cancer statistics)[1]. Not all patients respond well to treatment and those who do often develop resistance over the course of treatment. Drug resistance may be categorized into: (1) innate resistance already present in drug-naive patients who never respond to treatment, or (2) emerging/acquired resistance where a patient’s tumor undergoes relapse or “acquires” the ability to resist therapy in course of treatment despite good response to initial treatment[3,4]. Proteasome inhibitors (PIs) are standard-of-care chemotherapeutic agents for myeloma that impede tumor metastasis and angiogenesis by accelerating unfolded protein response (UPR) and by interfering with the nuclear factor-κB-enabled regulation of cell adhesion-mediated drug resistance[3,5,6]. Alterations in gene expression levels have been shown to be associated with response to cancer drugs, including PIs in myeloma[7,8].

Methods

Results

Conclusion