Cell-free DNA for the detection of emerging treatment failure in relapsed/ refractory multiple myeloma

Johannes M Waldschmidt, Andrew J Yee, Tushara Vijaykumar, Ricardo A Pinto, Julia Frede, Praveen Anand, Giada Bianchi, Guangwu Guo, Sayalee Potdar, Charles Seifer, Monica S Nair, Antonis Kokkalis, Jake A Kloeber, Samantha Shapiro, Lillian Budano, Mason Mann, Robb Friedman, Brea Lipe, Erica Campagnaro, Elizabeth K O'Donnell, Cheng-Zhong Zhang, Jacob P Laubach, Nikhil C Munshi, Paul G Richardson, Kenneth C Anderson, Noopur S Raje, Birgit Knoechel, Jens G Lohr, Johannes M Waldschmidt, Andrew J Yee, Tushara Vijaykumar, Ricardo A Pinto, Julia Frede, Praveen Anand, Giada Bianchi, Guangwu Guo, Sayalee Potdar, Charles Seifer, Monica S Nair, Antonis Kokkalis, Jake A Kloeber, Samantha Shapiro, Lillian Budano, Mason Mann, Robb Friedman, Brea Lipe, Erica Campagnaro, Elizabeth K O'Donnell, Cheng-Zhong Zhang, Jacob P Laubach, Nikhil C Munshi, Paul G Richardson, Kenneth C Anderson, Noopur S Raje, Birgit Knoechel, Jens G Lohr

Abstract

Interrogation of cell-free DNA (cfDNA) represents an emerging approach to non-invasively estimate disease burden in multiple myeloma (MM). Here, we examined low-pass whole genome sequencing (LPWGS) of cfDNA for its predictive value in relapsed/ refractory MM (RRMM). We observed that cfDNA positivity, defined as ≥10% tumor fraction by LPWGS, was associated with significantly shorter progression-free survival (PFS) in an exploratory test cohort of 16 patients who were actively treated on diverse regimens. We prospectively determined the predictive value of cfDNA in 86 samples from 45 RRMM patients treated with elotuzumab, pomalidomide, bortezomib, and dexamethasone in a phase II clinical trial (NCT02718833). PFS in patients with tumor-positive and -negative cfDNA after two cycles of treatment was 1.6 and 17.6 months, respectively (HR 7.6, P < 0.0001). Multivariate hazard modelling confirmed cfDNA as independent risk factor (HR 96.6, P = 6.92e-05). While correlating with serum-free light chains and bone marrow, cfDNA additionally discriminated patients with poor PFS among those with the same response by IMWG criteria. In summary, detectability of MM-derived cfDNA, as a measure of substantial tumor burden with therapy, independently predicts poor PFS and may provide refinement for standard-of-care response parameters to identify patients with poor response to treatment earlier than is currently feasible.

Conflict of interest statement

Competing interest statement:

J.M.W.: Advisory boards of Janssen and Sanofi. B.L.: Research funding from Amgen and Cellectar. Advisory boards of Bristol-Myers Squibb, Janssen and GlaxoSmithKline. C.-Z.Z.: Co-founder, advisor, and equity holder of Pillar BioSciences. P.G.R.: Research grants from Bristol-Myers Squibb, Oncopeptides, Celgene, Takeda, and Karyopharm. Advisory boards of Oncopeptides, Janssen, Sanofi, and Secura Bio. K.C.A.: Consultant to Bristol-Myers Squibb, Millennium, Janssen, Sanofi, Amgen, Gilead, Precision Biosciences. Scientific founder of Oncopep and C4 Therapeutics. N.S.R.: Consultant to Amgen, Bristol-Myers Squibb, Janssen, Sanofi, Takeda, AstraZeneca and C4 Therapeutics. Advisory boards of Caribou and Immuneel. Research funding from BluebirdBio. J.G.L.: Consultant for T2 Biosystems. Research funding from Bristol-Myers Squibb, Celgene. All other authors declare no conflicts of interest.

No disclosures related to this publication.

© 2021. The Author(s), under exclusive licence to Springer Nature Limited.

Figures

Figure 1.. Tumor fraction in cfDNA as…
Figure 1.. Tumor fraction in cfDNA as proxy for tumor burden and as prognostic marker.
A. Primary analysis of cfDNA in a test cohort of MM patients (n=16) undergoing a variety of therapeutic regimens. Tumor fraction in cfDNA was measured after a minimum of two months on the current regimen using ichorCNA. In a second validation cohort, patients with RRMM (n=45) received uniform treatment with elotuzumab, pomalidomide, bortezomib and dexamethasone (elo-PVD, clinicaltrials.gov identifier: NCT02718833). Tumor fraction in cfDNA was measured at baseline (n=44 available), and at cycle 3 day 1 (C3D1, n=42 available) of treatment. B. Kaplan-Meier curve for PFS (months) in MM patients with tumor fraction positivity (≥10%) or negativity (<10%) in cfDNA. C,D. Serial copy number profile, cfDNA tumor fraction and iFLC obtained at multiple time points in two patients, Pt01T (C, PFS 2.8 months) and Pt02T (D, PFS, 2.4 months). Abbreviations: RRMM= relapsed/refractory multiple myeloma, LPWGS= low-pass whole genome sequencing, elo-PVD= elotuzumab-pomalidomide-bortezomib-dexamethasone, C3D1= cycle 3 day 1 of elo-PVD treatment, TF= tumor fraction, EoT= end of treatment.
Figure 2.. Tumor fraction in cfDNA is…
Figure 2.. Tumor fraction in cfDNA is predictive of progression-free survival.
Kaplan-Meier survival for PFS (months) in MM patients with tumor fraction positive or negative results at screening (A, n=44) and C3D1 (B, n=42). Abbreviations: TF= tumor fraction.
Figure 3.. Comparing MM-derived cfDNA with serological…
Figure 3.. Comparing MM-derived cfDNA with serological parameters and bone marrow infiltration.
Correlation of paired samples between cfDNA tumor fraction and iFLC (A, n=79) or bone marrow infiltration (B, n=56). C. Copy number profile and matched bone marrow result for Pt01V (PFS 3.8 months) and Pt02V (PFS 1.2 months). Abbreviations: iFLC= involved serum-free light chain, BM= bone marrow, PFS= progression-free survival, TF= tumor fraction.
Figure 4.. Refining IMWG response criteria with…
Figure 4.. Refining IMWG response criteria with cfDNA as an orthogonal marker of response.
A. Kaplan-Meier survival for PFS (months) in 33 MM pts with SD or PR according to IMWG criteria separated by tumor fraction positive or negative cfDNA testing at C3D1. B. Detailed median PFS and hazard ratio values for patients with SD or PR according to respective cfDNA status at C3D1. C,D. Copy number profile, cfDNA tumor fraction, iFLC and serum M-protein over time in two patients, Pt03V (C, PFS 3.3 months) and Pt04V (D, PFS 4.3 months). Abbreviations: IMWG= International Myeloma Working Group, C3D1= cycle 3 day 1 (of elo-PVD treatment), PFS= progression-free survival, PR= partial response, SD= stable disease, TF= tumor fraction.
Figure 5.. Cox proportional hazard model for…
Figure 5.. Cox proportional hazard model for PFS and cfDNA tumor fraction after two cycles of elo-PVD.
Forest plots of hazard ratios for PFS according to cfDNA positivity (P=6.92e-05) at cycle 3 day 1 (C3D1) compared to achievement of VGPR (P=0.646) and PR (P=0.315) at the same time point (n=42), as well as age, having received >1 treatment, ISS stage III and high-risk cytogenetics. Cytogenetic information was not available for n=4 patients (*). Abbreviations: C3D1= cycle 3 day 1 (of elo-PVD treatment), TF= tumor fraction, VGPR= very good partial response, PR= partial response, SD= stable disease, ISS= International Staging System, HR= high-risk (del17p, t(4;14), t(14;16), t(14;20)).

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