The Pre-Existing T Cell Landscape Is Associated with Response to High Dose Melphalan and Autologous Stem Cell Transplant in Multiple Myeloma

Introduction: High dose melphalan and autologous stem cell transplant (ASCT) remain a cornerstone of therapy for transplant-eligible newly diagnosed multiple myeloma (MM) patients. The bone marrow microenvironment may affect the response of MM cells to high dose melphalan and ASCT. The changes in the immune landscape and associations with response to ASCT remain largely unknown. Here we investigate the role of the microenvironment in response to high dose melphalan using scRNA and TCR sequencing in paired pre- and post-ASCT bone marrow samples from the Indiana Myeloma Registry.

Methods: Paired bone marrow (BM) aspirates were collected from MM patients (n=40) after induction therapy but before ASCT and again after ASCT but prior to maintenance therapy (range 58-142 days post-ASCT). All patients had measurable disease after induction therapy. After ASCT, patients were evaluated based on their response to ASCT and divided into those who achieved a stringent complete response (n=17) and were negative for measurable residual disease (MRD) at 10^-6 by flow cytometry (responders), or those who achieved a partial response or less (n=23) (non-responders).

BM mononuclear cells were isolated by Ficoll and CD138 magnetic bead selection into CD138+ve and CD138-ve subsets. Paired pre- and post-ASCT CD138-ve samples underwent scRNA and TCR sequencing (10X Genomics), resulting in 488,479 high quality cells. Samples were independently normalized, cells integrated, and clusters annotated for cell type. Significant gene expression differences between clusters were calculated.

Results: Significant differences in the proportions of different immune cells in pre- vs. post-ASCT samples were identified with increases in B cells (2.6% vs 19.6%; P<.001) and B-cell progenitors (1.5% vs 8.9%; P<0.001) and decreases in CD4 T cells (24.8% vs 10.2%; P<0.001) and monocytes/myeloid cells (27.8% vs 21.0%; P=0.005) in post-ASCT samples. The overall proportions of CD8 T cells remained stable (27.1% vs 25.1%; P=0.2), but there were significant differences in the proportion of cells within the CD8 T cell clusters, including an increase in effector CD8 T cells (8.6% vs 10.7%; P=0.01) that expressed IFNG, KLRG1, TBX21, and PRF1 as well as a decrease in second cluster of CD8 T cells (2.3% vs 0.6%; P<0.01) expressing IL7R and TCF7. When comparing responder and non-responder pre-ASCT samples, we found a higher percentage of a CD4 T cell subset (10.0% vs 7.6%; P=0.04) in responders, which expressed SELL, CCR7, and ICOS indicating they are likely non-effector memory cells or naïve cells. There was also a higher proportion of myeloid dendritic cells (1.47% vs 1.08%; P=0.05) and granulocyte progenitors (0.98% vs 0.62%; P=0.04) in responders in post-ASCT samples. TCR sequencing revealed expanded CD8 T cells but not CD4 T cells, suggesting the CD4 T cell subset of interest may have a modulating effect of MM cells response to high dose melphalan rather than a specific anti-myeloma immune response.

Conclusions: We comprehensively describe the immune microenvironment in the BM of MM patients around ASCT and identify a pre-existing CD4 T cell subset that is associated with depth of response to ASCT. Further studies are required to better define the role of this population in modulating the response to melphalan. Prospective follow up of patients is ongoing to assess which clusters are associated with progression-free and overall survival.

Abu Zaid:Pharmacyclics: Research Funding; BMS: Research Funding; Janssen: Research Funding; Cormedix: Current equity holder in publicly-traded company; Ossium Health: Consultancy; Pieris: Current equity holder in publicly-traded company; Genentech: Research Funding. Johnson:Genentech: Research Funding. Chopra:Genentech/Roche: Current Employment, Current equity holder in publicly-traded company. Dos Santos:Genentech: Current Employment, Current equity holder in publicly-traded company. Nixon:Roche / Genentech: Current Employment, Current equity holder in publicly-traded company, Current holder of stock options in a privately-held company. Suvannasankha:Regeneron: Research Funding; Janssen Oncology: Consultancy, Honoraria, Research Funding; BMS/Celgene: Consultancy, Honoraria, Research Funding; Sutro Biopharma: Research Funding; GSK: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding. Abonour:Janssen: Honoraria, Research Funding, Speakers Bureau; Takeda: Honoraria, Research Funding; Amgen: Honoraria; Bristol Myers Squibb: Honoraria, Research Funding; GSK: Honoraria, Research Funding; Prothena: Honoraria. Walker:Bristol Myers Squibb: Research Funding; Genentech: Research Funding.