Periodic Reporting for period 4 - vAMRes (Vaccines as a remedy for antimicrobial resistant bacterial infections)
Reporting period: 2023-05-01 to 2023-10-31
In the context of the ERC Advanced Grant vAMRes project we aimed to discover human monoclonal antibodies (mAbs) to address two main challenges for global health, antimicrobial resistance (AMR) and pandemic viral pathogens.
AMR represents one of the most challenging public health issues of our times and the World Health Organization (WHO) estimates more than 10 million deaths linked to AMR by 2050. Here, we tackled pan-resistant Neisseria gonorrhoeae (Gonococcus), a bacterium listed as high priority by the WHO, by identifying 17 mAbs able to kill this pathogen. The most potent mAb (01K12) was also tested in vivo showing protection from infection and highlighting its potential as countermeasure to gonococcus. In addition, these mAbs were used as tools to identify protective antigens that could be used to develop effective vaccines against this bacterium. The approach developed during the five years of the vAMRes project will be instrumental to develop new medical interventions against gonococcus and pave the way for new countermeasures to tackle AMR.
The coronavirus disease 2019 (COVID-19) pandemic was responsible for more than 7 million reported deaths worldwide, although its toll is estimated to be at least three times higher. Despite the WHO declared the end to COVID-19 emergency, the virus keeps evolving and to evade natural and vaccine induced immunity constituting a major global health problem. To put an end to this emergency, in the last three years we enrolled convalescent and vaccinated individuals, or people with hybrid immunity to isolate extremely potent neutralizing antibodies and study the evolution of the B cell response to SARS-CoV-2. Throughout the vAMRes project, we single cell sorted more than 14,000 Spike (S) protein-specific memory B cells (MBCs) and isolated over 700 neutralizing mAbs (nAbs). Among all nAbs, one antibody named MAD0004J08 was selected for clinical development and tested in phase II-III clinical trial for the treatment of COVID-19. This was the most potent nAb developed and manufactured within the European Union as countermeasure to COVID-19.
AMR represents one of the most challenging public health issues of our times and the World Health Organization (WHO) estimates more than 10 million deaths linked to AMR by 2050. Here, we tackled pan-resistant Neisseria gonorrhoeae (Gonococcus), a bacterium listed as high priority by the WHO, by identifying 17 mAbs able to kill this pathogen. The most potent mAb (01K12) was also tested in vivo showing protection from infection and highlighting its potential as countermeasure to gonococcus. In addition, these mAbs were used as tools to identify protective antigens that could be used to develop effective vaccines against this bacterium. The approach developed during the five years of the vAMRes project will be instrumental to develop new medical interventions against gonococcus and pave the way for new countermeasures to tackle AMR.
The coronavirus disease 2019 (COVID-19) pandemic was responsible for more than 7 million reported deaths worldwide, although its toll is estimated to be at least three times higher. Despite the WHO declared the end to COVID-19 emergency, the virus keeps evolving and to evade natural and vaccine induced immunity constituting a major global health problem. To put an end to this emergency, in the last three years we enrolled convalescent and vaccinated individuals, or people with hybrid immunity to isolate extremely potent neutralizing antibodies and study the evolution of the B cell response to SARS-CoV-2. Throughout the vAMRes project, we single cell sorted more than 14,000 Spike (S) protein-specific memory B cells (MBCs) and isolated over 700 neutralizing mAbs (nAbs). Among all nAbs, one antibody named MAD0004J08 was selected for clinical development and tested in phase II-III clinical trial for the treatment of COVID-19. This was the most potent nAb developed and manufactured within the European Union as countermeasure to COVID-19.
Neisseria gonorrhoeae: Gonococcus, a bacterium resistant to most antibiotics causing more than 80 million cases of gonorrhea annually, is a WHO high priority pathogen. Recently, vaccine development prospects were boosted by reports that licensed meningococcus serogroup B (MenB) vaccines provided partial protection against gonococcus infection. Thanks to a collaboration with the University Hospital in Siena (Italy), we enrolled donors immunized with the MenB vaccine 4CMenB (Bexsero) to collect their blood and isolate human peripheral blood mononuclear cells (PBMCs). From these samples over 3,000 MenB outer membrane vesicles (OMVs)-specific MBCs were single cell sorted and almost 400 antibodies showed to cross-bind MenB and gonococcus. To identify mAbs able to kill gonococcus and MenB strains, all cross-binding antibodies were tested through a bactericidal assay. From this screening we identified a panel of 17 gonococcus bactericidal mAbs (b-mAbs). In addition to the bactericidal screening, b-mAbs were also tested through innovative assays based on the high-content confocal microscopy platform Opera Phenix to evaluate their opsonophagocytic activity. All but one b-mAb were able to promote Opsonophagocytosis in vitro. Next, we aimed to identify the antigen targeted by identified b-mAbs. Our data revealed that the majority of b-mAbs targeted the PorB (n=9) antigen followed by antibodies directed against the LOS (n=4). The antigen recognized by the remaining 4 b-mAbs remained unknown. The most potent and broadly reactive b-mAb, named 01K12, was tested in vivo and demonstrated protection against gonococcus infection when administered prophylactically.
Thanks to our study we identified PorB and LOS as key antigens of gonococcal and meningococcal immunity providing a mechanistic explanation of the cross-protection observed in the clinic. In addition, we showed that isolating human monoclonal antibodies from vaccinees can be instrumental for rapid bacterial antigen discovery which can be used to address the challenge posed by AMR.
SARS-CoV-2: The coronavirus disease 2019 (COVID-19) pandemic has had a devastating economic and health impact on our society. Over 7 million deaths worldwide have been attributed to SARS-CoV-2, the causative agent of COVID-19. Since the beginning of 2020, we started isolating MBCs from the blood of COVID-19 survivors to discover extremely potent nAbs and develop new medical countermeasures. We isolated over 4,000 S protein-specific MBCs by single cell sorting from 14 donors and identified 453 nAbs. Only 1.4% of them neutralized the authentic virus in vitro with a potency of 1-10 ng/mL. The lead candidate, named J08 (or MAD0004J08), showed to neutralize SARS-CoV-2 and the initial variants (Alpha, Beta, Gamma and Delta) with a 100% inhibitory concentration (IC100) below 10 ng/ml and to protect and treat SARS-CoV-2 infection in vivo at a concentration as low as 0.25 mg/Kg. MAD0004J08 was developed, manufactured and tested in a Phase II/III clinical trial. Unfortunately, after treating around hundreds of individuals, the phase II/III trial was suspended as MAD0004J08 showed a reduced neutralization activity against the newly emerged and globally spread omicron variant.
From 2021 until the end of the vAMRes project we enrolled donors that received two (seronegative 2 doses; SN2) and three vaccine doses (seronegative 3 doses; SN3), and individuals with hybrid immunity, i.e. infection followed by 2 mRNA vaccine doses. From these cohorts, we isolated over 10,000 S protein-specific MBCs, identifying over 700 nAbs against the live SARS-CoV-2 virus. All antibodies were tested in neutralization against emerging SARS-CoV-2 variants to identify the most potent and broadly reactive nAbs. All nAbs were also characterized to understand their epitope region, evaluate their Fc functions and identify their germlines. Thanks to the work performed through the vAMRes project we were able to identify potent and variant resistant nAbs, define protective epitope regions and shed light on the evolution of the B cell and antibody response during infection and after vaccination. This information will be instrumental to design the next generation of therapeutics and vaccines against COVID-19 and human coronavirus related threats.
From the above projects, seventeen manuscripts were published in top tier journals including PNAS, Cell, Nature, Nature Medicine, Nature communications and Journal of Experimental Medicine.
Thanks to our study we identified PorB and LOS as key antigens of gonococcal and meningococcal immunity providing a mechanistic explanation of the cross-protection observed in the clinic. In addition, we showed that isolating human monoclonal antibodies from vaccinees can be instrumental for rapid bacterial antigen discovery which can be used to address the challenge posed by AMR.
SARS-CoV-2: The coronavirus disease 2019 (COVID-19) pandemic has had a devastating economic and health impact on our society. Over 7 million deaths worldwide have been attributed to SARS-CoV-2, the causative agent of COVID-19. Since the beginning of 2020, we started isolating MBCs from the blood of COVID-19 survivors to discover extremely potent nAbs and develop new medical countermeasures. We isolated over 4,000 S protein-specific MBCs by single cell sorting from 14 donors and identified 453 nAbs. Only 1.4% of them neutralized the authentic virus in vitro with a potency of 1-10 ng/mL. The lead candidate, named J08 (or MAD0004J08), showed to neutralize SARS-CoV-2 and the initial variants (Alpha, Beta, Gamma and Delta) with a 100% inhibitory concentration (IC100) below 10 ng/ml and to protect and treat SARS-CoV-2 infection in vivo at a concentration as low as 0.25 mg/Kg. MAD0004J08 was developed, manufactured and tested in a Phase II/III clinical trial. Unfortunately, after treating around hundreds of individuals, the phase II/III trial was suspended as MAD0004J08 showed a reduced neutralization activity against the newly emerged and globally spread omicron variant.
From 2021 until the end of the vAMRes project we enrolled donors that received two (seronegative 2 doses; SN2) and three vaccine doses (seronegative 3 doses; SN3), and individuals with hybrid immunity, i.e. infection followed by 2 mRNA vaccine doses. From these cohorts, we isolated over 10,000 S protein-specific MBCs, identifying over 700 nAbs against the live SARS-CoV-2 virus. All antibodies were tested in neutralization against emerging SARS-CoV-2 variants to identify the most potent and broadly reactive nAbs. All nAbs were also characterized to understand their epitope region, evaluate their Fc functions and identify their germlines. Thanks to the work performed through the vAMRes project we were able to identify potent and variant resistant nAbs, define protective epitope regions and shed light on the evolution of the B cell and antibody response during infection and after vaccination. This information will be instrumental to design the next generation of therapeutics and vaccines against COVID-19 and human coronavirus related threats.
From the above projects, seventeen manuscripts were published in top tier journals including PNAS, Cell, Nature, Nature Medicine, Nature communications and Journal of Experimental Medicine.
Thanks to the antibody discovery platform developed during the ERC Advanced Grant vAMRes we were able to address two main challenges for global health: AMR and pandemic viral pathogens. The tools and assays developed in our projects will bring the field of microbiology into the 21st century, opening avenues for new studies addressing AMR. In addition, our ability to isolate extremely potent and broadly protective nAbs has allowed us to develop new countermeasures against COVID-19 bringing one antibody (MAD0004J08) to phase II/III clinical trial. Finally, our single cell level characterization of the B cell and antibody responses has shed light on key features of the immune response that could support the design of the next generation of therapeutics and vaccines to tackle human coronaviruses.