Science - USA (2021-12-03)

Goelet al.,Science 374 , eabm0829 (2021) 3 December 2021 9 of 17

Gated on Non-Naive CD4+ T

A

Activation

Markers

24 hours

CD4+ T

CD8+ T

Quantify

Frequency/Phenotype

Stimulate with Spike

Peptide Megapools

CD40LCD107a

CD200IFN-

4-1BB

Flow Cytometry

A

B

0.058 0.059 0.039 0.66

0.039 0.032 0.015 0.20

Gated on Non-Naive CD8+ T

Pre-Immune Post-Vaccine

Pre-Immune Post-Vaccine

CD200

CD40L

IFN-

4-1BB

Unstimulated + Peptide Pool Unstimulated + Peptide Pool

Unstimulated + Peptide Pool Unstimulated + Peptide Pool

* **

CM

EM1

EM2

EM3

EMRA

3m6m

% of Peak Response

Total CD4 Durability

(% of Peak Magnitude)

= 0.5 ,p= 0.0062

0.0

0.3

0.6

0.9

0.00 0.25 0.50 0.75

% EM1 at 1 Month

6 Month Durability

AIM+ cTfh AIM+ Th1 AIM+ Th2 AIM+ Th17 AIM+ Th1/17

Naive

Recovered

(^0) 0.50.75 (^1360) 0.50.75 (^1360) 0.50.75 (^1360) 0.50.75 (^1360) 0.50.75 1 36
0.001
0.010
0.100
1.000
0.001
0.010
0.100
1.000
Months Post−Vaccine
% of nnCD4+
CD4+ Helper Subsets

**

****ns

**
0.053

• ns
  nsns
  AIM+ CM AIM+ EM1 AIM+ EM2 AIM+ EM3 AIM+ EMRA
  Naive
  Recovered
  (^0) 0.50.75 (^1360) 0.50.75 (^1360) 0.50.75 (^1360) 0.50.75 (^1360) 0.50.75 1 36
  0.001
  0.010
  0.100
  0.001
  0.010
  0.100
  Months Post−Vaccine
  % of nnCD4+
  CD4+ Memory Subsets


• 
  

  *ns
  ns
  nsns

  
  

  ---

  
  


• 
  

  ---

  
  

  ---

  
  

  ***ns
  Naive Recovered
  (^050100150200050100150200)
  0.001
  0.010
  0.100
  1.000
  Days Post−Vaccine
  % of nnCD4+
  AIM+ CD4 T (CD200+ CD40L+)
  0.01
  0.03
  0.10
  0.30
  0 2 4 6
  Months
  % of nnCD4+
  CD4+ AIM+
  Naive Recovered
  (^050100150200050100150200)
  0.001
  0.010
  0.100
  1.000
  Days Post−Vaccine
  % of nnCD8+
  AIM+ CD8 T (4 of 5 markers)
  0.001
  0.010
  0.100
  0 2 4 6
  Months
  % of nnCD8+
  CD8+ AIM+
  41/41 37/39 28/31
  36/41 27/39 13/31
  14/15 8/13 3/9
  10/15 3/13 2/9
  t1/2 = 47d t1/2 = 187d
  SARS-CoV-2 Naive
  N = 42
  SARS-CoV-2 Recovered
  N = 16

  
  

• mRNA
  Vaccine
  C
  D
  CXCR5
  SSC-A
  CXCR3
  CCR6
  CD4+ Helper Subsets
  cTfh
  Th17 Th1/17
  Th2 Th1
  IJ
  E
  FG
  H
  CCR7+: CM
  CCR7-: EM1
  CCR7+: EM2
  CCR7-: EM3CCR7-: EMRA
  Naive
  CD45RA
  CD27
  CD4+ Memory Subsets
  t1/2 = 27dt1/2 = NA
  p = 0.33
  Decay Rates = ns
  Decay Rates = ns
  p = 0.11
  AIM+ Cells
  Pfizer
  Moderna
  ns
  ns

  ---

  
  

  ---

  
  

  ns
  ns

  
  

  ---

  
  

  **

  
  

  ---

  
  

  ns
  ns
  ns
  nsns ns ns
  nsns

  
  

  ---

  
  

  ---

  
  

ns

• ns ns nsns
  ns
  
  ns


• ns

  ---

  
  

  ---

  
  

  * ns
  nsns
  ns
  ** nsns

  
  


• 
  


• 
  

  ---

  
  

  ns

  
  

  ---

  
  

  0.099 ns
  nsns

  
  


• 
  

  
  < 0.05
  < 0.01
  P value
  −1
  −0.5
  0
  0.5
  1
  Fig. 5. SARS-CoV-2 mRNA vaccines generate durable memory T cell
  responses.(AandB) Experimental design (A) and gating strategy (B) for
  quantifying the frequency of SARS-CoV-2–specific CD4+and CD8+T cells by
  AIM assay. For CD4+T cells, antigen specificity was defined on the basis of
  coexpression of CD40L and CD200. For CD8+T cells, antigen specificity was
  defined on the basis of expression of at least four of five activation markers,
  as indicated in (A). (CandD) Frequencies of AIM+CD4+T cells (C) and AIM+
  CD8+T cells (D) over time in PBMC samples from vaccinated individuals.
  Data were background subtracted using a paired unstimulated control for each
  time point and are represented as a percentage of non-naïve CD4+or CD8+
  T cells. Black triangles indicate time of vaccine doses, fractions above plots
  indicate the number of individuals above their individual baseline at memory time
  points, and summary plots show mean values with the 95% confidence interval.
  Decay rates were calculated using a piecewise linear mixed-effects model
  with censoring.DDecay Rates indicates whether decay rates were different
  in SARS-CoV-2–naïve and–recovered groups. (E) AIM+CD4+T cell memory
  subsets were identified on the basis of surface expression of CD45RA, CD27,
  and CCR7. (F) Frequencies of AIM+CD4+T cell memory subsets over time.
  (G) Correlation matrix of memory subset skewing at peak (1-month) response
  with total AIM+CD4+T cell durability at 3 and 6 months. Durability was measured
  as the percentage of peak response maintained at memory time points for
  each individual. (H) Correlation between percent of EM1 cells at peak response
  and 6-month durability. (I) AIM+CD4+T helper subsets were defined on the basis
  of chemokine receptor expression. (J) Frequencies of AIM+CD4+T helper
  subsets over time. For (F) and (J), lines connect mean values at different time
  points. Dotted lines indicate the limit of detection for the assay. Statistics
  were calculated using unpaired nonparametric Wilcoxon test with BH correction
  for multiple comparisons. Correlations were calculated using nonparametric
  Spearman rank correlation. *P< 0.05; *P< 0.01; P< 0.001; ****P< 0.0001;
  ns, not significant.
  RESEARCH | RESEARCH ARTICLE