Durable T cell immunity to COVID-19 vaccines in MS patients on B cell depletion therapy

Abstract

Immune-mediated protection generated to COVID-19 mRNA vaccines is associated with anti-Spike (S) protein neutralizing antibodies. However, humoral immunity is compromised in B cell depleting (BCD) therapies, used to treat autoimmune diseases such as Multiple Sclerosis (MS). To study the effect of BCD on the durability and protective efficacy of vaccine-induced immunity, we evaluated S-reactive antibodies and T cell responses 1-70 weeks post-vaccination in MS cohorts treated with BCD compared to non-BCD therapies from four centers. BCD-treated participants had significantly reduced antibody levels and enhanced frequencies of S-reactive CD4⁺ and CD8⁺ memory T cells to COVID-19 vaccination compared to the non-BCD group, with some variations among different BCD formulations. T cell memory responses persisted up to 14 months post-vaccination in both BCD and non-BCD cohorts, who experienced similar clinical protection from COVID-19. Together, our results establish a critical role for T cell-mediated immunity in anti-viral protection independent of humoral immunity.

Fig. 1. Long-term reduction of humoral responses to COVID-19 vaccines in participants with MS on BCD therapies.

a Schematic of sample collection for participants with MS on non-BCD therapies (black) and BCD therapies (red) after initial two dose vaccine series. Samples were collected 4–483 days following completion of the vaccine series. b CD19⁺B cells in non-BCD (black) and BCD (red) participants shown in representative flow cytometry plots (left) and graphs of compiled data (right). c Area under the curve (AUC) of IgG specific for S (left) and RBD (right) in non-BCD (black) and BCD (red) participants. d Same as (c) for BCD participants taking various B cell depleting therapies. e Relationship of AUC of IgG specific for SARS-CoV-2 S (left) and RBD (right) with time post-vaccination in days for non-BCD (black) and BCD (red) participants. Inset graphs show results for only BCD participants. Statistics: (b–d) Bar plots represent data as mean ± standard deviation. b A t-test was used to compare the frequency of B cells in non-BCD and BCD participants. c, d A one-way analysis of covariance (ANCOVA) was used to evaluate the difference in antibody titers between cohorts after controlling for age, sex, vaccine type, and time-post vaccination. e Both Pearson’s correlation and a linear model was used to investigate the relationship between antibody titers and time-post vaccination controlling for age, sex, and vaccine type. ****p < 0.0001, *p < 0.05 Abbreviations: BCD (B cell depleting/depleted), non-BCD (non-B cell depleting/depleted), S (Spike protein), RBD (receptor binding domain).

Fig. 2. Enhancement of the T cell response to COVID-19 vaccines in BCD participants with MS.

S-reactive T cells were identified following stimulation with S peptide pools using the activation-induced marker (AIM) assay (see methods). Representative flow cytometry plots of CD4⁺ (a) and CD8⁺ (b) T cells (see gating strategy Supplementary Fig. 1a) expressing activation markers after control DMSO stimulation (top) or S peptide stimulation (bottom) in non-BCD (left) or BCD (right) participants. S-reactive CD4⁺ (c) and CD8⁺ (d) T cells in non-BCD (black) vs BCD (red) participants (left) and BCD participants taking OCR (dark red), RTX (red), and OFA (pink) (right) shown as a percentage of non-naïve T cells in each site. e S-reactive CD4⁺T cells over time post-vaccination for non-BCD (black, left) and BCD (red, right) participants. f Same as (e) for CD8⁺T cells. Statistics: (c–d) Bar plots represent data as mean ± standard deviation and a one-way analysis of covariance (ANCOVA) was used to evaluate the difference in quantities of S-reactive T cells between cohorts after controlling for age, sex, vaccine type, and time-post vaccination. e–f A linear model was used to investigate the relationship between S-reactive T cell frequency and time post-vaccination controlling for age, sex, and vaccine-type. **p < 0.01, *p < 0.05, ns p ≥ 0.05 Abbreviations: BCD (B cell depleting/depleted), non-BCD (non B cell depleting/depleted), OCR (Ocrelizumab), RTX (Rituximab), OFA (Ofatumumab), S (Spike protein).

Fig. 3. Variations in S-reactive T cell phenotypes in BCD participants with MS.

a T cell subset phenotypes of S-reactive CD4⁺T cells shown in representative flow cytometry plots of total CD4⁺T cells (black contour) and S-reactive T cells (red dots) from non-BCD (left) or BCD (right) participants (b) or stacked bar plots of averaged data across all non-BCD (black) and BCD (red) participants. c–d Same as (A-B) for CD8⁺T cells. e Representative flow cytometry plots of total CD4⁺T cells (black contour) and S-reactive CD4⁺T cells (red dots) expressing T_FH markers PD-1 and CXCR5 in non-BCD (left) and BCD (right) participants (right) and compiled expression of S-specific T_FH shown as percentage of PD-1 and CXCR5 expressing S-reactive CD4⁺T cells. Bar plots represent data as mean ± standard deviation. f Relationship of quantity of S-reactive T_FH with time post-vaccination in days for non-BCD (black, left) and BCD (red, right) participants. Statistics: (b,d,e) A one-way analysis of covariance (ANCOVA) was used to evaluate the difference in proportions of S-reactive T cell phenotypes between cohorts after controlling for age, sex, vaccine type, and time-post vaccination. f A linear model was used to investigate the relationship between S-reactive T_FH and time post-vaccination controlling for age, sex, and vaccine type. *p < 0.05, ns p ≥ 0.05 Abbreviations: S (Spike protein), BCD (B cell depleting/depleted), non-BCD (non B cell depleting/depleted), T_CM (central memory T cells), T_EMRA (terminally differentiated effector memory T cells), T_EM (effector memory T cells), T_FH (T follicular helper cells).

Fig. 4. Role of dose and specific BCD drug in participants with MS from four academic centers.

Quantification of the humoral and cellular response following two or three doses of COVID-19 vaccines in participants with MS compiled from four academic centers (see methods). a–b Quantity of anti-Spike and anti-RBD antibodies were normalized as a percent of the maximum of anti-Spike or anti-RBD antibody titer within each test method (see “methods”). a Normalized anti-Spike value is shown for non-BCD (black) and BCD (red) participants who have received two (closed circle) or three (open circle) doses of a COVID-19 vaccine (left) or BCD participants taking OCR, RTX, or OFA after two doses of the COVID-19 vaccine (right). b Same as (a) for anti-RBD antibodies. c Fraction of S-specific CD4⁺T cells shown for non-BCD (black) and BCD (red) participants who have received two (closed circle) or three (open circle) doses of a COVID-19 vaccine (left) or BCD participants taking OCR, RTX, or OFA after two doses of the COVID-19 vaccine (right). d Same as (c) for CD8⁺ T cells. Statistics: (a–d) Bar plots represent data as mean ± standard deviation and a one-way analysis of covariance (ANCOVA) was used to evaluate the difference in quantities of vaccine-induced immunity between cohorts after controlling for age, sex, vaccine type, and time-post vaccination. ****p < 0.0001, *** p < 0.001, ** p < 0.01, *p < 0.05 Abbreviations: BCD (B cell depleting/depleted), non-BCD (non B cell depleting/depleted), OCR (Ocrelizumab), RTX (Rituximab), OFA (Ofatumumab), S (Spike protein).