The aim of this work was to design and test a vaccine regimen focusing the immune response on targets associated with infection prevention. We demonstrated that priming with a DNA vaccine expressing only the HIV Env V1V2 region induces Ab responses targeting the critical region in V2 associated with protection. This work shows that V1V2 scaffold DNA priming immunization provides a method to focus immune responses to the desired target region, in the absence of immune interference by other epitopes. This induced immune responses with improved recognition of epitopes important for protective immunity, namely, V2-specific humoral immune responses inversely correlating with HIV risk of infection in the RV144 trial.
Abstract Background We evaluated a novel DNA vaccine delivery by LION™ nanoparticles for its ability to induce innate and adaptive immune responses in Rhesus macaques. Methods CoV-2 Spike or HIV Env DNA were formulated with a cationic nanocarrier (Lipid InOrganic Nanoparticle; LION™) administered via the IM route. Chemokine/cytokine and vaccine-specific responses were monitored in blood and lymph nodes (LN) by proteomics, flow, antibody assays. Results DNA/LION™ induced strong cellular and higher humoral responses than DNA/Electroporation and induced rapid (4-24hr) transient innate responses. Flow analysis showed activation of T, B, myeloid incl. dendritic cells in blood and their trafficking to LN with a strong increase of Tfh, Germinal Center Tfh CD4 and CD8 cells. Cell subsets were activated by cytokine networks incl. CXCL11, IL-7 and IL-15. GC-B cell activation directly correlated with increase of FLT3L and CXCL12 and importantly with antibody levels. Conclusion DNA/LION™ led to robust induction of cellular and humoral responses against different immunogens, serving as promising platform of effective nucleic acid vaccine delivery. Transient cytokine responses, incl. IL-15, resulted in strong activation of draining lymph nodes, and contributed to shaping adaptive (cellular and humoral) immunity. Our data showed rapid and coordinated cytokine responses to the vaccine and highlight the important role of innate responses to vaccination in modulating adaptive immunity.
The speed of development, versatility and efficacy of mRNA-based vaccines have been amply demonstrated in the case of SARS-CoV-2. DNA vaccines represent an important alternative since they induce both humoral and cellular immune responses in animal models and in human trials. We tested the immunogenicity and protective efficacy of DNA-based vaccine regimens expressing different prefusion-stabilized Wuhan-Hu-1 SARS-CoV-2 Spike antigens upon intramuscular injection followed by electroporation in rhesus macaques. Different Spike DNA vaccine regimens induced antibodies that potently neutralized SARS-CoV-2 in vitro and elicited robust T cell responses. The antibodies recognized and potently neutralized a panel of different Spike variants including Alpha, Delta, Epsilon, Eta and A.23.1, but to a lesser extent Beta and Gamma. The DNA-only vaccine regimens were compared to a regimen that included co-immunization of Spike DNA and protein in the same anatomical site, the latter of which showed significant higher antibody responses. All vaccine regimens led to control of SARS-CoV-2 intranasal/intratracheal challenge and absence of virus dissemination to the lower respiratory tract. Vaccine-induced binding and neutralizing antibody titers and antibody-dependent cellular phagocytosis inversely correlated with transient virus levels in the nasal mucosa. Importantly, the Spike DNA+Protein co-immunization regimen induced the highest binding and neutralizing antibodies and showed the strongest control against SARS-CoV-2 challenge in rhesus macaques.
Immunocompromised individuals including patients with hematological malignancies constitute a population at high risk of developing severe disease upon SARS-CoV-2 infection. Protection afforded by vaccination is frequently low and the biology leading to altered vaccine efficacy is not fully understood. A patient cohort who had received bone marrow transplantation or CAR-T cells was studied following a 2-dose BNT162b2 mRNA vaccination and compared to healthy vaccine recipients. Anti-Spike antibody and systemic innate responses were compared in the two vaccine cohorts. The patients had significantly lower SARS-CoV-2 Spike antibodies to the Wuhan strain, with proportional lower cross-recognition of Beta, Delta, and Omicron Spike-RBD proteins. Both cohorts neutralized the wildtype WA1 and Delta but not Omicron. Vaccination elicited an innate cytokine signature featuring IFN-γ, IL-15 and IP-10/CXCL10, but most patients showed a diminished systemic cytokine response. In patients who failed to develop antibodies, the innate systemic response was dominated by IL-8 and MIP-1α with significant attenuation in the IFN-γ, IL-15 and IP-10/CXCL10 signature response. Changes in IFN-γ and IP-10/CXCL10 at priming vaccination and IFN-γ, IL-15, IL-7 and IL-10 upon booster vaccination correlated with the Spike antibody magnitude and were predictive of successful antibody development. Overall, the patients showed heterogeneous adaptive and innate responses with lower humoral and reduced innate cytokine responses to vaccination compared to naïve vaccine recipients. The pattern of responses described offer novel prognostic approaches for potentiating the effectiveness of COVID-19 vaccination in transplant patients with hematological malignancies.
Abstract The speed of development, versatility and efficacy of mRNA-based vaccines have been amply demonstrated in the case of SARS-CoV-2. DNA vaccines represent an important alternative since they induce both humoral and cellular immune responses in animal models and in human trials. We tested the immunogenicity and protective efficacy of DNA-based vaccine regimens expressing different prefusion-stabilized SARS-CoV-2 Spike antigens upon intramuscular injection followed by electroporation in rhesus macaques. Different Spike DNA vaccine regimens induced antibodies that potently neutralized SARS-CoV-2 in vitro and elicited robust T cell responses. The DNA-only vaccine regimens were compared to a regimen that included co- immunization of Spike DNA and protein in the same anatomical site, the latter of which showed significant higher antibody responses. All vaccine regimens led to control of SARS-CoV-2 intranasal/intratracheal challenge and absence of virus dissemination to the lower respiratory tract. Vaccine-induced binding and neutralizing antibody titers and antibody-dependent cellular phagocytosis inversely correlated with transient virus levels in the nasal mucosa. Importantly, the Spike DNA+Protein co-immunization regimen induced the highest binding and neutralizing antibodies and showed the strongest control against SARS-CoV-2 challenge in rhesus macaques. Author summary Anti-Spike neutralizing antibodies provide strong protection against SARS-CoV-2 infection in animal models, and correlate with protection in humans, supporting the notion that induction of strong humoral immunity is key to protection. We show induction of robust antibody and T cell responses by different Spike DNA-based vaccine regimens able to effectively mediate protection and to control SARS-CoV-2 infection in the rhesus macaque model. This study provides the opportunity to compare vaccines able to induce different humoral and cellular immune responses in an effort to develop durable immunity against the SARS-CoV-2. A vaccine regimen comprising simultaneous co-immunization of DNA and Protein at the same anatomical site showed best neutralizing abilities and was more effective than DNA alone in inducing protective immune responses and controlling SARS-CoV-2 infection. Thus, an expansion of the DNA vaccine regimen to include co-immunization with Spike protein may be of advantage also for SARS-CoV-2.
The COVID-19 virus has evolved significantly from the ancestral WA1/2020 strain over the past 3 years with new sublineages, subvariants, and recombinant strains emerging and causing new waves of infections.1 During 2022, the Omicron B.1.1.529 sublineages have been spreading world-wide and a recent emerging rapidly spreading XBB.1.5 variant has been reported (www.gisaid.org). This prompted the analysis of vaccine induced neutralizing antibody (NAb) to evaluate protective efficacy to the newly circulating variants. Our results show lower but detectable neutralizing activity to the newer circulating variants including XBB.1.5, suggesting a continuing benefit of the current bivalent (WA1/BA.5) vaccine. Because anti-Spike immunity is known to decline overtime, bivalent booster vaccinations in previously boosted individuals or after BA.5 breakthrough infection are justified because they increase immunity and enhance the probability to neutralize further evolving variants. Due to continuing erosion of immunity by the newly emerging variants, the timely updating of future booster vaccines remains one of the most important issues in the fight against COVID. Although different COVID-19 proteins contribute to SARS-CoV-2 pathogenesis, the different evolving Spike variants are of particular interest because they facilitate cell entry via the ACE2 receptor protein, an interaction that directly affects virus transmissibility and impacts on the vaccine efficacy. The first generation of COVID-19 vaccines used the WA1/2020 Spike protein. We and others reported that the vaccine-induced immunity provided reduced neutralization of the Omicron BA.1.529.1 subvariants BA.4 and BA.5, which share identical Spike proteins (Supplemental Methods). The BA.4/5 Spike differs from the ancestral WA1 Spike at 18 amino acids (AA) located within Receptor Binding Domain (RBD) including the mutations L452R, F486V, R493Q (Figure 1A). The second generation COVID-19 vaccine comprising a bivalent mRNA vaccine including both the ancestral WA1 and Omicron BA.5 Spike proteins, improved neutralization of BA.4/5. However, the recent emergence of additional Omicron sublineages raised concerns about the breadth and strength of the bivalent vaccine-induced NAb. Of concern are the multiple changes in RBD located in key interaction sites with the ACE2 receptor. The RBD of the BQ.1 sublineage has additional mutations at positions R346T, K444T, and N460K. The RBDs of XBB and XBB1.5 share additional mutations at L368I, V445P, N460K, and F490S and differ by an additional mutation F486S (XBB) and F486P (XBB.1.5), a rarely seen AA change emerged late in 2022.2, 3 The rapidly spreading XBB.1.5 alerted the medical community about possible impact on the protective efficacy of the NAb induced by the current bivalent COVID-19 vaccine. In this part of the NCT04743388 study, we evaluated the NAb magnitude and breadth targeting ancestral WA1, different Omicron sublineages, including the recently emerging XBB.1.5, in different SARS CoV-2 vaccinated (monovalent or bivalent) cohorts and a COVID-19 breakthrough cohort in Greece. Major inclusion criteria included: (i) age above 18 years; (II) ability to sign the informed consent form and (iii) eligibility for vaccination, according to the national program for COVID-19 vaccination. Major exclusion criteria included the presence of: (i) autoimmune disorder under immunosuppressive therapy; (ii) active malignant disease and (iii) end-stage renal disease, as previously described.4 The BA.1/BA.2 sublineages circulating during spring 2022 in Greece were largely replaced by BA.5 in the summer5 (Figure 1B). The more recent circulating variants include BQ.1.1 and the newly introduced XBB and XBB.1.5.5 The median age of the participants (n = 79) was 56.5 years (range 22–100), whereas 28 (35.4%) were males and the median body mass index was 25.6 kg/m2 (range 17.6–35.9). Ten (12.6%) individuals had hypercholesterolemia and 21 (26.5%) had hypertension. The participants share a history of COVID-19 WA1 monovalent vaccination and differ by the bivalent booster vaccination or lack thereof (Figure 1C). The bivalent booster cohort (n = 21) had received prior three doses of the monovalent BNT162b2 mRNA (Pfizer/BioNTech) vaccine (Table S1). Fourteen individuals were also infected by COVID-19 (likely BA.1/BA.2, the circulating strains in spring 2022; www.gisaid.org) and they received the bivalent booster vaccine in October 2022 at 3–7 months post-infection. The monovalent vaccinated cohort (n = 37) had received three doses of BNT162b2 mRNA (Pfizer/BioNTech) (Figure 1C). The COVID-19 breakthrough cohort had received monovalent WA1 vaccinations from different manufacturers (n = 21) but did not receive the bivalent booster vaccination (Table S2). The COVID-19 infection in this cohort occurred during July and August 2022, when BA.5 was the dominant circulating SARS-CoV-2 sublineage in Greece (Figure 1B). The cohorts were analyzed for the presence of cross-neutralizing NAb 1 month after the last vaccination or at 3–5 months post-COVID (BA.5) infection. Sera were tested for their ability to neutralize pseudotyped viruses carrying one of a panel of different Spike proteins including WA1, BA.5, the sublineages BQ.1.1 and XBB, as well as the recent XBB.1.5 (Supplemental Information). The WA1 Spike used in this assay has the D614G mutation, which is shared with all the other Spike proteins (Figure 1A). All cohorts showed robust neutralization of WA1. Both the bivalent booster cohort and the breakthrough cohort had ~3-5-fold higher titers against WA1 than BA.5 (Figure 1D, E). In contrast, the monovalent vaccine cohort (Figure 1F) showed significantly (>10-fold) lower levels of NAb to BA.5, as we described previously for patients with multiple myeloma or Waldenstrom's Macroglobulinemia.6 In agreement with others, these data show that the bivalent booster vaccine greatly augmented the level of the strain-specific NAb and showed the limited breadth of the WA1-induced NAb against BA.5. To address cross-neutralization to recently spreading variants, the neutralization capability of BA.5 was compared against BQ.1.1, a sublineage of BA.5, the more divergent XBB, a BA.2 recombinant, and the rapidly spreading more infectious XBB.1.5. The bivalent boosted cohort and the breakthrough infection cohort showed similar readouts being marked by significant reductions of NAb titers to BQ.1.1 (~5-fold) and XBB and XBB.1.5 (~10-fold), demonstrating significant escape from the host immune responses. No difference in the relative decreases were found when comparing the two cohorts. Importantly, of great concern is the finding that 20–30% of individuals have very low or no NAb, with titers below the threshold of the assay (Figure 1D, E). Prior history of bivalent booster vaccination or breakthrough infection did not change the outcome. This analysis suggested the need for future additional booster vaccination because there is no demonstrated superiority in breadth after BA.4/5 breakthrough infection. NAb titers are known to wane over time both after vaccination and/or infection. We further compared the NAb titers of BQ.1.1 to the other new variants, namely XBB and XBB.1.5. There was a significant decrease in NAb titers found in both cohorts against the XBB variants. Interestingly, no difference between XBB and XBB.1.5 was found, indicating that the F480S to P mutation had no further effect on antigenic escape. Thus, despite the rapid emergence of XBB.1.5, the majority of the individuals had detectable NAb against this variant, albeit at greatly reduced level. Of note, ~30% of the cohorts have levels below the threshold of detection. The real-life efficacy of these overall low NAb levels remains to be evaluated. In light of the previously observed waning of NAb upon WA1 vaccinations, which largely relate to SARS-CoV-2 evolutionary leaps, the current low levels of cross-neutralizing NAb found 1 month after the bivalent vaccination raises a concern and makes updating of future COVID-19 booster vaccines an important development and urgent matter. In contrast to the data on the booster cohort, the monovalent vaccination cohort showed a dramatically lower neutralization to the different sublineages of Spike proteins with lack of neutralization of BQ1.1 in ~50% and of XBB and XBB.1.5. in ~80% of vaccine recipients. Together, these data show the benefit of the bivalent vaccine over the WA-1 induced immunity and corroborate the importance of additional vaccinations to current spreading virus variants. As expansion of previous reports on the effectiveness of the mono- and bivalent vaccines addressing BQ.1 and XBB2, 3, 7-10 but not XBB.1.5, in this report, we provide new insights on neutralization breadth and strength showing that recently evolved Spike mutants, including XBB.1.5, have enhanced immune evasive properties compared to Spike from the ancestral WA1 and the BA.5 sublineages. The more rapid spread of XBB.1.5 is likely associated with increased transmissibility rather than increased immune evasion. Importantly, the overall low response rate to the BQ and XBB sublineages, including the rapidly spreading XBB.1.5, after bivalent vaccination is of great concern. The continuous and rapid evolution of COVID-19 variants diminishing neutralization magnitude and breadth, supports the development of additional vaccines using new Spike variants. Evangelos Terpos, Meletios-Athanasios Dimopoulos, George N. Pavlakis, Barbara K. Felber conceived and designed the study. Ioannis Ntanasis-Stathopoulos, Stamatia Skourti, Panagiotis Malandrakis, Ioannis P Trougakos, Evangelos Terpos, Meletios-Athanasios Dimopoulos provided resources, supervised, collected, and processed patient data and samples; Santhi Devasundaram, Margherita Rosati, Jenifer Bear, Robert Burns, Barbara K. Felber, George N. Pavlakis performed the experiments and data analysis; Barbara K. Felber, George N. Pavlakis, Evangelos Terpos drafted the manuscript. All authors reviewed and edited the manuscript and gave final approval for the submitted version. The authors thank members of the Felber and Terpos labs for discussions, and T. Jones for assistance. We also thank T. Bagratuni, A. Papadimou, and C-I. Liacos for technical assistance. This work was supported by funding from the Intramural Research Program, National Institutes of Health, National Cancer Institute, Center for Cancer Research to Barbara K. Felber. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organizations imply endorsement by the U.S. Government. This work was supported by funding from the Intramural Research Program, National Institutes of Health, National Cancer Institute, Center for Cancer Research to Barbara K. Felber. Evangelos Terpos has received honoraria from Astra/Zeneca and Pfizer. All other authors have declared no conflicts. The data that support the findings of this study are available from the corresponding authors upon reasonable request. Table S1. Bivalent booster cohort Table S2. Breakthrough infection cohort Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Patients with symptomatic monoclonal gammopathies have impaired humoral responses to COVID-19 vaccination. Their ability to recognize SARS-CoV-2 Omicron variants is of concern. We compared the response to BNT162b2 mRNA vaccinations of patients with multiple myeloma (MM, n = 60) or Waldenstrom’s macroglobulinemia (WM, n = 20) with healthy vaccine recipients (n = 37). Patient cohorts on active therapy affecting B cell development had impaired binding and neutralizing antibody (NAb) response rate and magnitude, including several patients lacking responses, even after a 3rd vaccine dose, whereas non-B cell depleting therapies had a lesser effect. In contrast, MM and WM cohorts off-therapy showed increased NAb with a broad response range. ELISA Spike-Receptor Binding Domain (RBD) Ab titers in healthy vaccine recipients and patient cohorts were good predictors of the ability to neutralize not only the original WA1 but also the most divergent Omicron variants BA.4/5. Compared to WA1, significantly lower NAb responses to BA.4/5 were found in all patient cohorts on-therapy. In contrast, the MM and WM cohorts off-therapy showed a higher probability to neutralize BA.4/5 after the 3rd vaccination. Overall, the boost in NAb after the 3rd dose suggests that repeat vaccination of MM and WM patients is beneficial even under active therapy.
