Cellular mechanisms associated with sub-optimal immune responses to SARS-CoV-2 bivalent booster vaccination in patients with Multiple Myeloma

Abstract

Background: The real-world impact of bivalent vaccines for wild type (WA.1) and Omicron variant (BA.5) is largely unknown in immunocompromised patients with Multiple Myeloma (MM). We characterize the humoral and cellular immune responses in patients with MM before and after receiving the bivalent booster, including neutralizing assays to identify patterns associated with continuing vulnerability to current variants (XBB1.16, EG5) in the current post-pandemic era.

Methods: We studied the humoral and cellular immune responses before and after bivalent booster immunization in 48 MM patients. Spike binding IgG antibody levels were measured by SARS-CoV-2 spike binding ELISA and neutralization capacity was assessed by a SARS-CoV-2 multi-cycle microneutralization assays to assess inhibition of live virus. We measured spike specific T-cell function using the QuantiFERON SARS-CoV-2 (Qiagen) assay as well as flow-cytometry based T-cell. In a subset of 38 patients, high-dimensional flow cytometry was performed to identify immune cell subsets associated with lack of humoral antibodies.

Findings: We find that bivalent vaccination provides significant boost in protection to the omicron variant in our MM patients, in a treatment specific manner. MM patients remain vulnerable to newer variants with mutations in the spike portion. Anti-CD38 and anti-BCMA therapies affect the immune machinery needed to produce antibodies.

Interpretation: Our study highlights varying immune responses observed in MM patients after receiving bivalent COVID-19 vaccination. Specifically, a subgroup of MM patients undergoing anti-CD38 and anti-BCMA therapy experience impairment in immune cells such DCs, B cells, NK cells and TFH cells, leading to an inability to generate adequate humoral and cellular responses to vaccination.

Funding: National Cancer Institute (National Institutes of Health), National Institute of Allergy and Infectious Diseases (National Institutes of Health), NCI Serological Sciences Network for COVID-19 (SeroNet) and The Icahn School of Medicine at Mount Sinai.

Keywords: Bivalent vaccine; COVID-19; Hematological malignancy; Multiple Myeloma; Omicron; SARS-CoV-2.

Fig. 1

Humoral responses to Bivalent Vaccination in patients with Multiple Myeloma. (A) Left panel: anti-SARS-CoV-2 spike IgG antibody levels before and after SARS-CoV-2 bivalent vaccination in MM patients. Right panel: anti-SARS-CoV-2 spike IgG antibody levels before and after SARS-CoV-2 bivalent vaccination by major treatment groups. Antibody concentrations measured in artificial units per mL (AU/mL) and are depicted on a log-10 scale. The gray horizontal dotted line indicates the lower limit of detection (5 AU/mL). (B) Neutralizing antibody ID50 to WA.1 wild-type SARS-CoV-2 strain for MM subject groups split according to major treatment groups. Neutralizing antibody ID50 to Omicron SARS-CoV-2 strain for MM subject groups split according to major treatment groups. The gray horizontal dotted line indicates the lower limit of detection. Dots are colored to indicate treatment regimen at the time of vaccination. p-values represent comparison using the paired Wilcoxon signed-rank test. (C) Percent of MM patients that are unable to neutralize ancestral strain (WA.1) and variants of interest BA.5, XBB1.16, EG.1 and XBB1.5.1 pre and post bivalent vaccination. Threshold for neutralization was at least 30% inhibition of variant. Gray denotes patients able to neutralize while red denotes those not able to neutralize.

Fig. 2

T Cell responses to Bivalent Vaccination in patients with Multiple Myeloma. (A) SARS-CoV-2 specific CD4+ T cell responses in MM patients measured by Qiagen QuantiFERON assay. Results show IFN gamma in IU/mL produced by AG1 peptide pool stimulation containing CD4+ epitopes from the S1 subunit of the ancestral Spike protein minus the IFN gamma produced from negative control condition. Dots are colored to indicate treatment regimen at the time of vaccination. p-values represent comparison using the paired Wilcoxon signed-rank test. (B and C) Representative FACS dot plots of IFN gamma expressing CD4+ T cells in a MM patient, pre and post bivalent vaccination, after 6 h stimulation with (B) ancestral SARS-CoV-2 CD4 peptide pools and (C) Omicron BA.5 SARS-CoV-2 CD4 peptide pools. Cytokine expressing CD4+ T cells were identified within activation gates defined by expression of CD4+ T cell activation markers CD154 and CD69. (D) Spearman’s rank correlation between SARS-CoV-2 specific T cell response from Qiagen QuantiFERON kit and IFN gamma producing CD4+ T cells stimulated with ancestral peptide strains. Shaded gray indicates the 95% confidence bands for the regression line and values in parenthesis indicate 95% confidence intervals for correlation coefficient. IFN gamma-expressing CD4+ T cells were calculated by subtracting water control frequencies from the CD4+ T cell response for each subject. (E) Spearman’s rank correlation between SARS-CoV-2 specific T cell response from Qiagen QuantiFERON kit and IFN gamma producing CD4+ T cells stimulated with Omicron BA.5 peptide strains. Shaded gray indicates the 95% confidence bands for the regression line and values in parenthesis indicate 95% confidence intervals for correlation coefficient. IFN gamma-expressing CD4+ T cells were calculated by subtracting water control frequencies from the CD4+ T cell response for each subject. Colors of dots indicate treatment regimen at the time of vaccination.

Fig. 3

CD38 and BCMA expression in MM patient Samples. (A) Median CD38 expression in immune cell types in 5 MM patients receiving anti-CD38 targeting therapy and 5 MM patients receiving other treatment regimens not including an anti-CD38 targeting therapy in peripheral blood patients. (B–E) Representative histogram of CD38 expression by flow cytometry in the peripheral blood of patients receiving anti-CD38 therapy compared to patients not undergoing any active therapy. (B) CD38 expression on B cells (C) CD38 expression on NK Cells (D) CD38 expression on Dendritic Cells (DCs) (E) CD38 expression on CD4+ T cells. (F) Histogram of BCMA expression in the plasma cell B cell subset in the bone marrow sample of an MM patient. (G–I) Representative TSNE illustrating the composition of the immune cell milieu in (G) Reference patient currently not on any active treatment (H) patients receiving anti-BCMA bispecific therapy and (I) patients on anti-CD38 therapy.

Fig. 4

Phenotypic differences between responding and sub-optimal Multiple Myeloma patients during bivalent vaccination. Suboptimal MM patients are denoted as the lowest quartile of anti-SARS-CoV-2 spike IgG antibody levels antibody production compared to responding MM patients. (A) Frequencies of CD1c+ dendritic cells in peripheral blood mononuclear cells pre and post bivalent vaccination. (B) Absolute NK Cell counts in peripheral blood pre and post bivalent vaccination in MM patients. (C) Absolute B Cell counts in peripheral blood pre and post bivalent vaccination in MM patients. (D) Frequency of CXCR5+ CD4+ (TFH cells) expressing a Th2 phenotype (CXCR3-CCR6-CCR4+) in peripheral blood peripheral blood pre and post bivalent vaccination in MM patients. Dots are colored to indicate treatment regimen at the time of vaccination. p-values represent comparison using Mann–Whitney U test.