Periodic Reporting for period 4 - B-DOMINANCE (B Cell Immunodominance in Antiviral Immunity)
Berichtszeitraum: 2024-06-01 bis 2025-05-31
B-DOMINANCE addressed several fundamental gaps of knowledge in B cell biology, using immunity to influenza virus as a research tool. Influenza virus infection causes significant morbidity and mortality, and vaccines are partially effective and need yearly reformulation due to ongoing antigenic drift. This situation is becoming evident to society with the COVID19 pandemic, where SARS-CoV2 is presenting similar challenges.
B-DOMINANCE posited that, by having a better understanding of immunodominance in B cell responses we would be able to improve current influenza vaccines. Indeed, most of the important discoveries made in B cell biology utilized as tools simple, artificial antigens which have only one or two epitope targets.
In details, B-DOMINANCE has three main objectives:
The first objective is to understand how and if B cells, specific for different epitopes on influenza virus, are different and how can this impact their response.
For the second objective, we want to investigate the memory B cell response and how those are influenced by pre-existing immunity. In humans, we all get infected with influenza by the age of three, so by the time that we get re-infected we already have existing antibodies or memory B cells. As mentioned above, the virus mutates, so these antibodies are not fully effective in protecting from infection. Here we want to investigate how different component of the immune system (B cells or antibodies), which have specificity for certain epitopes of influenza, can get reactivated after infection or vaccination with a drifted virus. This information is essential to design effective novel vaccines that can help focusing the immune responses on the right targets.
The third objective was amended after the outbreak of the COVID19 pandemic. Here the goal is to study how pre-existing immunity can influence the B cell responses to COVID vaccines and subsequent break-through infection.
By the end of the action (May 2025) three major conclusions have emerged.
First, memory B cells that ultimately protect the lungs do not arise in situ: they are generated in conventional lymphoid organs during persistent germinal centers and only later migrate to the lung parenchyma, where they adopt a distinct tissue-resident transcriptional programme.
Second, bona-fide germinal centres—the structures in which B-cell affinity maturation takes place—also form in the nasal mucosa of both mice and humans.
Third, pre-existing antibodies influence subsequent responses only under specific structural conditions: they modulate recall immunity when the incoming antigen is multivalent and when antibody and memory-B-cell binding sites are co-located in space, but they are largely ineffective when antigen is monovalent or differently arrayed.
Together these findings offer tangible directions for next-generation intranasal vaccines and for antigen-display platforms that can be tuned to recruit the most protective B-cell clones.
B-DOMINANCE posited that, by having a better understanding of immunodominance in B cell responses we would be able to improve current influenza vaccines. Indeed, most of the important discoveries made in B cell biology utilized as tools simple, artificial antigens which have only one or two epitope targets.
In details, B-DOMINANCE has three main objectives:
The first objective is to understand how and if B cells, specific for different epitopes on influenza virus, are different and how can this impact their response.
For the second objective, we want to investigate the memory B cell response and how those are influenced by pre-existing immunity. In humans, we all get infected with influenza by the age of three, so by the time that we get re-infected we already have existing antibodies or memory B cells. As mentioned above, the virus mutates, so these antibodies are not fully effective in protecting from infection. Here we want to investigate how different component of the immune system (B cells or antibodies), which have specificity for certain epitopes of influenza, can get reactivated after infection or vaccination with a drifted virus. This information is essential to design effective novel vaccines that can help focusing the immune responses on the right targets.
The third objective was amended after the outbreak of the COVID19 pandemic. Here the goal is to study how pre-existing immunity can influence the B cell responses to COVID vaccines and subsequent break-through infection.
By the end of the action (May 2025) three major conclusions have emerged.
First, memory B cells that ultimately protect the lungs do not arise in situ: they are generated in conventional lymphoid organs during persistent germinal centers and only later migrate to the lung parenchyma, where they adopt a distinct tissue-resident transcriptional programme.
Second, bona-fide germinal centres—the structures in which B-cell affinity maturation takes place—also form in the nasal mucosa of both mice and humans.
Third, pre-existing antibodies influence subsequent responses only under specific structural conditions: they modulate recall immunity when the incoming antigen is multivalent and when antibody and memory-B-cell binding sites are co-located in space, but they are largely ineffective when antigen is monovalent or differently arrayed.
Together these findings offer tangible directions for next-generation intranasal vaccines and for antigen-display platforms that can be tuned to recruit the most protective B-cell clones.
A cornerstone of the project was the construction of an integrated experimental-computational pipeline capable of reading, for each individual B cell, its full transcriptome together with the paired immunoglobulin heavy- and light-chain sequences. The pipeline has been released under an open-source license. All raw and processed datasets have been deposited in ArrayExpress, and their reuse by external groups has already generated more than thirty data-driven publications, attesting to the resource’s broad utility.
Using this platform, we first characterized the fate of B cells specific for wild-type influenza hemagglutinin (HA) across spleen, lymph nodes and lungs. We revealed that memory cells destined for the lung are generated in lymphoid organs and later acquire a tissue-resident phenotype upon arrival in the lung. This work provided the first high-resolution map of lung-resident B-cell memory and has become a frequently cited reference in the field. The discovery prompted two follow-up investigations. In the first we found that Streptococcus pneumoniae, after influenza, disrupted the recruitment signal, thereby preventing memory B cells from establishing residency and compromising protection against a subsequent influenza challenge. In the second we demonstrated the presence of active germinal centers in the nasal mucosa of mice and humans and documented their clonal relationship to systemic responses.
Parallel experiments addressed the role of T-cell help and of pre-existing humoral immunity. We showed that CD4 T cells present before infection accelerate extrafollicular plasmablast production without increasing germinal-centre entry . A more ambitious series of reinfection, monoclonal-antibody transfer and mixed-cell-transfer models clarified how antibody valency and topology dictate whether memory clones re-enter germinal centres or whether naïve B cells dominate secondary responses. We found that antibody feedback does not hamper vaccine responses.
The COVID-19 amendment yielded two complementary outputs. Longitudinal sampling of hospitalised patients, combined with the single-cell pipeline from aim 1, uncovered B-cell clones that originated from seasonal coronavirus memory, rapidly differentiated into plasmablasts and gradually broadened their neutralisation breadth. Furthermore, we also identified a transcriptomic “affinity signature” that identifies high-affinity SARS-CoV-2-specific B cells for therapeutic antibody isolation.
Overall, the unifying model posit that viral infections elicit persistent germinal centers in lymphoid organs that, in turn, fuel the generation of variable memory that takes residency in lungs and upper respiratory tract and it is equipped to defend us against new emerging viral variants.
Over the funding period we produced twelve peer-reviewed articles, two invited reviews and three preprints; delivered approximately fifteen invited lectures at invited seminars or major conferences (Keystone, EMBO, WIRM, SSI, among others); and made all code, data and protocols freely accessible. Early-career researchers received training and moved on to new positions.
Using this platform, we first characterized the fate of B cells specific for wild-type influenza hemagglutinin (HA) across spleen, lymph nodes and lungs. We revealed that memory cells destined for the lung are generated in lymphoid organs and later acquire a tissue-resident phenotype upon arrival in the lung. This work provided the first high-resolution map of lung-resident B-cell memory and has become a frequently cited reference in the field. The discovery prompted two follow-up investigations. In the first we found that Streptococcus pneumoniae, after influenza, disrupted the recruitment signal, thereby preventing memory B cells from establishing residency and compromising protection against a subsequent influenza challenge. In the second we demonstrated the presence of active germinal centers in the nasal mucosa of mice and humans and documented their clonal relationship to systemic responses.
Parallel experiments addressed the role of T-cell help and of pre-existing humoral immunity. We showed that CD4 T cells present before infection accelerate extrafollicular plasmablast production without increasing germinal-centre entry . A more ambitious series of reinfection, monoclonal-antibody transfer and mixed-cell-transfer models clarified how antibody valency and topology dictate whether memory clones re-enter germinal centres or whether naïve B cells dominate secondary responses. We found that antibody feedback does not hamper vaccine responses.
The COVID-19 amendment yielded two complementary outputs. Longitudinal sampling of hospitalised patients, combined with the single-cell pipeline from aim 1, uncovered B-cell clones that originated from seasonal coronavirus memory, rapidly differentiated into plasmablasts and gradually broadened their neutralisation breadth. Furthermore, we also identified a transcriptomic “affinity signature” that identifies high-affinity SARS-CoV-2-specific B cells for therapeutic antibody isolation.
Overall, the unifying model posit that viral infections elicit persistent germinal centers in lymphoid organs that, in turn, fuel the generation of variable memory that takes residency in lungs and upper respiratory tract and it is equipped to defend us against new emerging viral variants.
Over the funding period we produced twelve peer-reviewed articles, two invited reviews and three preprints; delivered approximately fifteen invited lectures at invited seminars or major conferences (Keystone, EMBO, WIRM, SSI, among others); and made all code, data and protocols freely accessible. Early-career researchers received training and moved on to new positions.
At the outset of the project no public resource combined single-cell transcriptomics with paired B-cell-receptor sequencing for antigen-defined cells. The pipeline and datasets generated here therefore set a new methodological benchmark, lowering the entry barrier for laboratories worldwide to perform similar integrative analyses. Furthermore, the discovery of nasal germinal centers fundamentally adds to immunology textbooks and supplies a mechanistic rationale for intranasal vaccine formulations aimed at inducing local affinity maturation where pathogens first land. Overall our results significantly add to the current knowledge and offer mechanistic insights into B cell differentiation, migration and reactivation after respiratory viral infections
Although the funded action concludes in 2025, the project’s tangible outputs: research results, open software, curated databases, affinity-based cell-sorting signatures and validated nanobodies will remain available to academic and industrial stakeholders.
In sum, the project has advanced immunological knowledge from descriptive snapshots to a dynamic, tissue-resolved understanding of B-cell memory, and it has translated those insights into publicly shared tools and actionable vaccine strategies with lasting societal benefit.
Although the funded action concludes in 2025, the project’s tangible outputs: research results, open software, curated databases, affinity-based cell-sorting signatures and validated nanobodies will remain available to academic and industrial stakeholders.
In sum, the project has advanced immunological knowledge from descriptive snapshots to a dynamic, tissue-resolved understanding of B-cell memory, and it has translated those insights into publicly shared tools and actionable vaccine strategies with lasting societal benefit.