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458 Loss of COP9 Signalosome Gene-Containing 2q Region Is Associated with Lenalidomide and Pomalidomide Resistance in Myeloma Patients

Program: Oral and Poster Abstracts
Type: Oral
Session: 652. Multiple Myeloma and Plasma cell Dyscrasias: Clinical and Epidemiological: Multiple Myeloma and Waldenstrom Macroglobulinemia: Exploring Biomarkers in the Era of Personalized Medicine
Hematology Disease Topics & Pathways:
Genomics, Translational Research, Non-Biological, Clinically Relevant, Therapies, Biological Processes
Sunday, December 12, 2021: 12:15 PM

Sarah Gooding, MD PhD1,2,3,4*, Naser Ansari-Pour, BSc, PhD3,4*, Mohammad H Kazeroun3,4*, Kubra Karagoz, PhD5*, Mirian Angulo Salazar3,4*, Evelyn Fitzsimons, BSc6*, Maria Ortiz Estevez, PhD7*, Fadi Towfic, PhD8*, Erin Flynt5*, William E. Pierceall, PhD5, Kwee Yong, MD, PhD6,9*, Paresh Vyas, DPhil, FRCP, FRCPath, MRCP, MRCPath2,4,10 and Anjan Thakurta, PhD3,5*

1Oxford Centre for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
2Department of Clinical Haematology, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
3Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
4MRC Molecular Haematology Unit and Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
5Translational Development and Diagnostics, Bristol Myers Squibb, Summit, NJ
6Cancer Institute, Department of Haematology, University College London, London, United Kingdom
7Research Analytics, Celgene Institute for Translational Research Europe (CITRE), Seville, Spain
8Bristol Myers Squibb, San Diego, CA
9Department of Haematology, University College London Hospitals, London, United Kingdom
10Weatherall Institute of Molecular Medicine, Weatherall Inst. of Molecular Medicine, Oxford, United Kingdom

Introduction

Identification of the causes of, and biomarkers for, drug resistance in myeloma is important for understanding treatment failures, and for future instigation of targeted therapeutics for myeloma. Using the largest set of whole genome sequencing (WGS) of advanced and drug resistant multiple myelomas to date, we reported that even heterozygous loss of the 3p region, which harbours immunomodulatory drug (IMiD) and CRBN E3 ligase modulator drug (CELMoD)-binding protein Cereblon (CRBN), undergoes strong therapeutic selection on lenalidomide (LEN) and/or pomalidomide (POM) treatment (Gooding et al 2021, PMC7893409). We hypothesized that copy loss of other genes required for IMiD activity may also have clinical relevance. Several groups have reported pharmacogenetic screens identifying genes essential for IMiD sensitivity in vitro, particularly genes required for the maintenance of the CUL4-DDB1-CRBN E3 Ubiquitin Ligase, such as members of the COP9 signalosome complex, function of which prevents CRBN protein degradation. However, loss of these genes has hitherto not been reported in myeloma.

Methods and results

We identified candidate genes whose loss may favor IMiD drug resistance from published pharmacogenetic screens (n=5), and shortlisted genes consistently identified as essential for LEN or POM function in ≥2 screens (n=23). In our WGS dataset of 455 patients (cohorts: newly diagnosed (ND) n = 198, LEN-refractory n = 203; and LEN-then-POM-refractory n = 54), the incidence of mutation of shortlisted LEN/POM-essential genes in drug-refractory cohorts was rare (<5% combined), as found with CRBN. We next identified all those with overall incidence of >10% copy loss at the LEN-then-POM-refractory state, plus incidence of copy loss that increased from ND to LEN-then-POM-refractory states by ≥1.5-fold. This delivered 3 copy loss regions for further investigation: a) 3p, which we had already reported; b) 17p, loss of which is known to be strongly selected in myeloma as the site of TP53; and c) 2q, previously unidentified as relevant in myeloma, but whose minimal common region contained two members of the COP9 signalosome (COPS7B, COPS8). Proportion of loss of this region increased between ND (5.5%), LEN-refractory (9.8%) and LEN-then-POM-refractory states (16.6%), p=0.009. Those patients who had lost a copy of these genes also demonstrated a significant reduction in COPS7B/COPS8 gene expression (p<0.01 both genes).

In a separate cohort of myeloma patients (n=24) with sequential sample WGS analysis before and after LEN and/or POM resistance acquisition, we traced acquisition of CNA-defined subclones. 5/24 (21%) patients had acquired either clonal or subclonal loss of the 2q region containing COPS7B and COPS8 at IMID resistance, which had been either absent or below limit of detection pre-IMiD exposure. No other CNA newly-emerged in such a high proportion during IMiD treatment. Relative decrease in even one COP9 signalosome gene has been shown to cause CRBN protein level to fall, and reduce LEN efficacy (Sievers et al 2018, PMC6148446). We are now analysing CRBN protein levels in sequential biopsies from these cases.

Conclusion

Copy number aberrations have not previously been shown to drive a therapy-specific clonal advantage in myeloma in the clinic. We have now identified a second novel CNA, 2q loss, which increases in incidence through LEN- and POM-refractory states to emerge as a marker of dominant clones in advanced, IMiD-resistant disease. Whether these CNAs will mark resistance to novel CELMoDs remains to be seen. The CRBN protein is key to the function of these drugs, and many novel proteolysis targeting chimeras (PROTACs) in development, but whether the kinetics of their CRBN binding are as sensitive to relative CRBN protein loss remains a key question. CNAs may be easily and cost-effectively detected in the clinic by targeted sequencing approaches, and may prove valuable in future therapeutic decision making.

Disclosures: Gooding: Bristol Myers Squibb: Research Funding. Ansari-Pour: Bristol Myers Squibb: Consultancy. Karagoz: h.: Research Funding. Ortiz Estevez: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Towfic: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Flynt: BMS: Current Employment, Current equity holder in publicly-traded company. Pierceall: BMS: Current Employment, Current equity holder in publicly-traded company. Yong: Sanofi: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Takeda: Honoraria; GSK: Honoraria; Amgen: Honoraria; BMS: Research Funding; Autolus: Research Funding. Vyas: Astellas: Consultancy, Honoraria; Takeda: Honoraria; Janssen: Honoraria; Novartis: Honoraria; Pfizer: Honoraria; Daiichi Sankyo: Honoraria; Bristol Myers Squibb: Consultancy, Honoraria, Research Funding; Gilead: Honoraria; Jazz: Honoraria; AbbVie: Consultancy, Honoraria. Thakurta: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company, Patents & Royalties.

*signifies non-member of ASH