NGS of Nanobodies against endogenous Plasmodium falciparum Pfs230
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB85614 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The bacterial pathogen, Acinetobacter baumannii, is a leading cause of drug-resistant infections. Here, we investigated the potential of developing nanobodies that specifically recognize A. baumannii over other Gram-negative bacteria. Through generation and panning of a synthetic nanobody library, we identified several potential lead candidates. We demonstrate how incorporation of next generation sequencing analysis can aid in selection of lead candidates for further characterization. Using monoclonal phage display, we validated the binding of several lead nanobodies to A. baumannii. Subsequent purification and biochemical characterization revealed one particularly robust nanobody that broadly and specifically bound A. baumannii compared to other common drug resistant pathogens. These findings support the potentially for nanobodies to selectively target A. baumannii and the identification of lead candidates for possible future diagnostic and therapeutic development.
2023-06-21 | GSE202972 | GEO
Project description:Selection of Novel Nanobodies Targeting EGFR Using Phage Display Library
| PRJEB35883 | ENA
Project description:NGS of phage antibody outputs from whole-cell panning
| PRJNA923794 | ENA
Project description:Nanobodies are emerging as ideal instruments for drug design and several have recently been created to block SARS-Cov-2 entry in the host cell by targeting surface-exposed Spike protein. However, due to the high frequency of mutations that affect Spike, these nanobodies may not efficiently target Spike during viral entry. Here we have established a pipeline that instead targets highly conserved viral proteins that are made only after viral entry into the host cell when the SARS-Cov-2 RNA-based genome is translated. As proof of principle, we designed nanobodies against the SARS-CoV-2 non-structural protein Nsp9, required for replication of the viral genome. To find out if this strategy efficiently blocked viral replication, one of these anti-Nsp9 nanobodies, 2NSP23, previously characterized using immunoassays and NMR spectroscopy for epitope mapping, was encapsulated into lipid nanoparticles (LNP) as mRNA. We show that this nanobody, hereby referred to as LNP-mRNA-2NSP23, is internalized and translated in HEK293 cells. We next infected HEK293-ACE2 cells subjected to LNP-mRNA-2NSP23 with multiple SARS-CoV-2 variants. Analysis of total RNA isolated form infected cells treated or untreated with LNP-mRNA-2NSP23 using qPCR and RNA deep sequencing shows that the LNP-mRNA-2NSP23 nanobody protects HEK293-ACE2 cells and suppresses replication of several SARS-CoV-2 variants. These observations indicate that following translation, the nanobody 2NSP23 inhibits viral replication by targeting Nsp9 in living cells. We propose that LNP-mRNA-2NSP23 may be translated into an innovative technology to generate novel antiviral drugs highly efficient across coronaviruses.
2023-10-10 | GSE244714 | GEO
Project description:Plasmodium falciparum Pfs230 and Pfs48/45 are the leading candidates for malaria transmission-blocking vaccines. However, it remains unknown how the two interact and if additional domains in Pfs230 are potential vaccine candidates. Here we report a 3.36 Å resolution cryo-electron microscopy structure of the endogenous Pfs230-Pfs48/45 complex. We show that Pfs48/45 interacts with Pfs230 domains 13 and 14, which are distinct from domains included in current Pfs230 vaccine immunogens. Using a transgenic line with a domain 13 to 14 deletion, we show that these domains are essential for Pfs230 localization on the gamete surface. Nanobodies against these domains inhibit Pfs230-Pfs48/45 complex formation, reduce transmission and structural analyses reveal their binding epitopes. Pfs230 domains 13 and 14 are targets of naturally acquired immunity and when delivered as mRNA-LNP vaccines induced potent immune responses. Our comprehensive structural insights on a core P. falciparum fertilization complex guide the design of novel transmission-blocking vaccine candidates against malaria.
2025-08-08 | PXD060667 | Pride
Project description:Since the start of the coronavirus disease-2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has caused more than 2 million deaths worldwide. Many vaccines have been deployed to date; however, the continual evolution of the viral receptor binding domain (RBD) has recently challenged their efficacy. In particular, SARS-CoV-2 variants originating in South Africa (B.1.351) and the U.K. (B.1.1.7) have reduced plasma neutralization activity and crippled antibody cocktails that received emergency use authorization1-3. Whereas vaccines can be updated periodically to account for emerging variants, complementary strategies are urgently needed to overcome viral escape. One potential alternative are camelid VHHs (also known as nanobodies), which can access conserved epitopes often hidden to conventional antibodies4-6. We here isolate anti-RBD nanobodies from llamas and mice engineered to produce VHHs from alpacas, dromedaries and camels. Through neutralization assays and cryo-electron microscopy we identify two “nanomouse” VHHs that circumvent RBD antigenic drift by recognizing a domain conserved in coronaviruses, away from the ACE2 binding motif. Conversely, llama nanobodies recognize the RBD-ACE2 interphase and as monomers they are ineffective against E484K or N501Y substitutions. Notably, as homotrimers those same VHHs neutralize RBD variants with ultrahigh (pM) affinity, rivaling the most potent antibodies produced to date against SARS-CoV-2. We conclude that multivalent nanobodies can avert SARS-CoV-2 escape mutants and thus they represent promising tools to prevent COVID-19 mortality when vaccines are compromised.
2021-05-18 | GSE167310 | GEO
Project description:Digoxin is a well-recognized cardiovascular medication; however, epidemiological investigations have associated its clinical application with an elevated risk of malignancy. To elucidate it, we discovered, for the first time, that therapeutic digoxin can facilitate tumor metastasis by acting as an inducer of immune checkpoints, including PD-1, PD-L1/2, CTLA-4, LAG-3, ICOS, TIM-3, and TIGIT, among others. The PD-1/PD-L1 axis plays a pivotal role. Digoxin upregulates PD-L1 production in cancer cells through multiple mechanisms, including digoxin-PKM2 interaction, liquid-liquid phase separation, and Na,K-ATPase degradation. Notably, endogenous digoxin (ED) was significantly upregulated in breast cancer, correlating with increased metastasis. When specific nanobodies (Nbs) were developed to functionally inhibit ED in vivo, pulmonary tumor metastasis was reduced. However, the efficacy of ED-targeting Nbs was limited by endogenous ouabain (EO), another hormone structurally similar to digoxin. To address this, Nbs co-targeting ED and EO demonstrated an increased anti-metastatic effect and a notable reduction in immune checkpoint expression. Furthermore, Nbs simultaneously targeting ED, EO, and PD-1 exhibited significant synergy in suppressing tumor progression with a favorable safety profile. In conclusion, therapeutic digoxin and ED are potent inducers of immune checkpoints. Engineered nanobodies co-targeting cardiotonic hormones (ED, EO) and immune checkpoints present a promising novel approach in the treatment of breast cancer metastasis.
2025-09-18 | GSE308027 | GEO
Project description:Digoxin is a well-recognized cardiovascular medication; however, epidemiological investigations have associated its clinical application with an elevated risk of malignancy. To elucidate it, we discovered, for the first time, that therapeutic digoxin can facilitate tumor metastasis by acting as an inducer of immune checkpoints, including PD-1, PD-L1/2, CTLA-4, LAG-3, ICOS, TIM-3, and TIGIT, among others. The PD-1/PD-L1 axis plays a pivotal role. Digoxin upregulates PD-L1 production in cancer cells through multiple mechanisms, including digoxin-PKM2 interaction, liquid-liquid phase separation, and Na,K-ATPase degradation. Notably, endogenous digoxin (ED) was significantly upregulated in breast cancer, correlating with increased metastasis. When specific nanobodies (Nbs) were developed to functionally inhibit ED in vivo, pulmonary tumor metastasis was reduced. However, the efficacy of ED-targeting Nbs was limited by endogenous ouabain (EO), another hormone structurally similar to digoxin. To address this, Nbs co-targeting ED and EO demonstrated an increased anti-metastatic effect and a notable reduction in immune checkpoint expression. Furthermore, Nbs simultaneously targeting ED, EO, and PD-1 exhibited significant synergy in suppressing tumor progression with a favorable safety profile. In conclusion, therapeutic digoxin and ED are potent inducers of immune checkpoints. Engineered nanobodies co-targeting cardiotonic hormones (ED, EO) and immune checkpoints present a promising novel approach in the treatment of breast cancer metastasis.
2025-09-20 | GSE308031 | GEO
Project description:Rapid detection and capture of clinical Escherichia coli strains mediated by OmpA-targeting nanobodies
| PRJEB78364 | ENA
Project description:Generation of synthetic Acinetobacter baumannii specific nanobodies
| PRJNA837907 | ENA