2024 in review: Six impactful research studies using PEPperPRINT’s peptide microarray technology

In 2024, several impactful academic publications have highlighted the diverse applications of PEPperPRINT’s peptide microarray in a variety of research fields. From combating devastating diseases like African Swine Fever and schistosomiasis to uncovering novel diagnostic markers for Brugada syndrome, our technology is being leveraged to tackle some of the most pressing health challenges today.

This article highlights six key studies that demonstrate how our microarray platform is enabling researchers to make significant strides in areas ranging from vaccine development to cancer treatment, offering hope for more effective therapies and diagnostics that could benefit millions globally.

1. Mapping key targets to fight African Swine Fever

Overview: This study addresses the urgent challenge of African Swine Fever (ASF), a devastating pig disease with no effective vaccine. Using high-density peptide microarrays, researchers mapped ASF virus (ASFV) epitopes, identifying immune targets on key viral proteins like p54 and D117L. These insights aim to guide vaccine development and improve diagnostics, laying the groundwork for better ASF control strategies.

Why this matters: ASF poses a significant threat to global pig farming, with substantial economic and societal impacts. The identification of specific immune targets in ASFV proteins enhances our understanding of ASF immunity and provides a foundation for next-generation vaccines. Moreover, the findings suggest applications in serological diagnostics, particularly in challenging samples such as meat exudates.

How PEPperPRINT’s peptide microarray was used: Our microarray was pivotal in analyzing over 5,000 peptide sequences from ASFV proteins. This technology enabled the detection of antibody interactions with high resolution, highlighting critical immune epitopes like those in the p54 transmembrane domain and the p17 stabilizing protein. Combining epitope analysis with protein structure prediction modeling, this technology efficiently identified promising targets for vaccine development and diagnostic innovation.

Reference: Desmet, Cloé, et al. "ASFV epitope mapping by high density peptides microarrays." Virus Research 339 (2024): 199287. https://doi.org/10.1016/j.virusres.2023.199287. 

2. Insights into citrullination and autoimmune disease targets

Overview: This study generates a comprehensive, quantitative atlas of protein citrullination, focusing on over 14,000 citrullination sites identified in leukemia-derived HL60 cells differentiated into neutrophil-like cells. It highlights the PADI4 enzyme as a critical player in regulating histone modifications and immune function. These findings have implications for understanding autoimmune diseases and provide potential targets for therapeutic intervention.

Why this matters: Citrullination is a pivotal post-translational modification linked to diseases such as rheumatoid arthritis, neurodegeneration, and cancer. This research utilized advanced proteomics and mass spectrometry to map citrullination sites with high precision, revealing the extensive role of PADI4 in regulating both histones and non-histone proteins. This work opens new avenues for therapeutic strategies targeting PADI4 in autoimmune diseases.

How PEPperPRINT’s peptide microarray was used: PEPperPRINT microarrays played a crucial role in validating antibody reactivity against citrullinated peptides. These microarrays were used to study synovial fluid from individuals with rheumatoid arthritis, distinguishing between different antibody profiles. This, in conjunction with mass spectrometry, helped to connect biochemical modifications with clinical relevance, enhancing the translational impact of the research.

Reference: Rebak, Alexandra S., et al. "A quantitative and site-specific atlas of the citrullinome reveals widespread existence of citrullination and insights into PADI4 substrates." Nature Structural & Molecular Biology (2024): 1-19. https://doi.org/10.1038/s41594-024-01214-9 

3. Exploring heterologous DNA vaccines for broader protection against SARS-CoV-2 variants

Overview: SARS-CoV-2 research is crucial for developing vaccines that can protect against current and future variants of the virus. This study looked at how different types of DNA vaccines influence the immune response in mice by analyzing which parts of the SARS-CoV-2 virus the antibodies target. It compared homologous vaccines (from the same virus strain) with heterologous vaccines (a combination of strains) to determine which approach induces a stronger, broader immune response.

Why this matters: The study used peptide microarray technology to map B-cell epitopes recognized by antibodies in three groups of mice. Each group received a different vaccination regimen: one group received a DNA vaccine encoding the spike protein of the SARS-CoV-2 Index strain, another received the Beta variant spike protein, and the third group received a combination (heterologous prime-boost) of both vaccines. The findings showed that the heterologous regimen triggered a broader antibody response, increasing the potential for cross-neutralization against multiple SARS-CoV-2 variants. This approach could lead to more versatile vaccines that offer better protection against emerging strains.

How PEPperPRINT’s peptide microarray was used: Our peptide microarray was used to map the B-cell epitopes targeted by antibodies in the pooled sera from each group of vaccinated mice. The array featured cyclic overlapping peptides — short sequences of amino acids arranged in a closed loop structure that overlap with each other — covering the full spike protein of the SARS-CoV-2 Index strain and including key mutations. This setup helped identify the specific virus regions recognized by antibodies, enabling researchers to map out immune responses and identify potential areas crucial for designing vaccines effective against multiple variants.

Reference: Frische, Anders, et al. "Antigen-Heterologous Vaccination Regimen Triggers Alternate Antibody Targeting in SARS-CoV-2-DNA-Vaccinated Mice." Vaccines 12.3 (2024): 218. https://doi.org/10.3390/vaccines12030218 

4. Uncovering autoantibodies as a key diagnostic factor in Brugada syndrome

Overview: The study examined plasma from 50 Brugada syndrome (BrS) patients and 50 control subjects to identify anti-NaV1.5 autoantibodies using advanced assays. It found that 90% of BrS patients had detectable autoantibodies, compared to only 6% in controls. The specificity of these autoantibodies was confirmed by their absence in a cohort of patients with other cardiac diseases such as long QT syndrome, heart failure, and structural cardiomyopathies. The autoantibodies were shown to reduce sodium current density in cells by approximately 40%, suggesting a direct pathogenic impact on heart function, and the findings were confirmed through in vivo mouse models exhibiting Brugada-like electrocardiographic (ECG) patterns.

Why this matters: BrS is a life-threatening arrhythmia disorder that remains challenging to diagnose, with the hallmark ECG pattern often being difficult to detect. Only 25% of patients show detectable SCN5A gene mutations, complicating the diagnosis further. This discovery reveals a significant diagnostic potential, with high sensitivity and specificity for identifying BrS in patients, potentially revolutionizing how the syndrome is detected and managed.

How PEPperPRINT’s peptide microarray was used: Our peptide microarray was used to identify the specific regions on the NaV1.5 protein where the anti-NaV1.5 autoantibodies bind. These regions are part of the extracellular loops of the NaV1.5 sodium channel, which are the parts of the protein that are exposed on the outside of the cell. By combining this method with other techniques like western blotting and immunofluorescence, the study not only confirmed the specificity of the autoantibodies but also provided deeper insights into how these antibodies may interfere with NaV1.5 channel function, contributing to the pathology of BrS.

Reference: Tarantino, Adriana, et al. "NaV1. 5 autoantibodies in Brugada syndrome: pathogenetic implications." European heart journal 45.40 (2024): 4336-4348. https://doi.org/10.1093/eurheartj/ehae480

5. Discovering a novel PSCA antibody and its application as an antibody-drug conjugate in prostate cancer

Overview: This study introduces F12, a novel, highly specific, fully human antibody fragment targeting Prostate Stem Cell Antigen (PSCA) and its application as an antibody-drug conjugate (ADC) for prostate cancer treatment. The antibody, identified through phage display and affinity maturation, was shown to bind PSCA with high specificity, without interacting with 6,000 other human membrane proteins tested in a membrane proteome array assay. When conjugated with the cytotoxic agent monomethyl auristatin E (MMAE), the F12-MMAE ADC demonstrated dose-dependent efficacy in prostate cancer xenograft models. This approach offers a promising new therapeutic strategy, particularly for advanced prostate cancer, including hormone-independent forms and metastases.

Why this matters: The study of PSCA as a therapeutic target is crucial due to its consistent overexpression in various stages of prostate cancer, including metastatic and hormone-resistant cases. PSCA also serves as a potential marker for other solid tumors, such as pancreatic and renal cancers. Traditional therapies for advanced prostate cancer have limited efficacy, particularly when the disease becomes resistant to hormone therapy. This new research addresses the need for more effective treatments by developing a high-affinity, fully human PSCA-targeting antibody. By improving the specificity and potency of PSCA-targeting therapies, this approach could help overcome common barriers in prostate cancer treatment, such as antigen heterogeneity and the immunosuppressive tumor microenvironment.

How PEPperPRINT’s peptide microarray was used: The peptide microarray technology played a crucial role in mapping the precise epitope targeted by the F12 antibody. This microarray approach, using a library of cyclic peptides, allowed researchers to pinpoint the exact sequence of PSCA amino acids (63–69) that F12 binds to, ensuring the antibody's specificity. This precise targeting is vital, as it minimizes the risk of off-target effects and increases the therapeutic potential of the antibody. Additionally, the microarray analysis was combined with other technologies like membrane proteome arrays to confirm that F12 did not bind to any other human proteins, supporting its high specificity. These methods are integral in optimizing antibody development, ensuring that candidates like F12 are both effective and safe for therapeutic use.

Reference: Chu, Xiaojie, et al. "Discovery of a novel highly specific, fully human PSCA antibody and its application as an antibody-drug conjugate in prostate cancer." mAbs. Vol. 16. No. 1. Taylor & Francis, 2024. https://doi.org/10.1080/19420862.2024.2387240 

6. Using AI to identify key peptides for schistosomiasis, a neglected parasitic disease

Overview: In the fight against schistosomiasis, a neglected tropical disease, this study uses the power of AI and AlphaFold technology to identify promising linear B-cell epitopes for diagnosing Schistosoma haematobium and Schistosoma mansoni infections. The study integrates in-silico immunoinformatic tools with peptide microarray validation to identify peptides that can serve as reliable diagnostic markers. Peptide AAB81008-19-30, in particular, demonstrated excellent diagnostic potential in distinguishing infected individuals from healthy controls, while nine other peptides showed acceptable diagnostic performance.

Why this matters: Schistosomiasis remains one of the most pressing neglected tropical diseases, with millions affected, particularly in regions like sub-Saharan Africa. Traditional diagnostic methods such as microscopy, have limitations, especially in detecting low-intensity infections. As control programs reduce disease prevalence, there is an increasing need for more sensitive and specific diagnostic tools. Current serological tests suffer from low specificity, often cross-reacting with other infections. The identification of species-specific peptides, like those discovered in this study, offers a pathway to more reliable, cost-effective diagnostics that can be used in remote, resource-poor settings, providing better surveillance and control.

How PEPperPRINT’s peptide microarray was used: The study used our peptide microarray technology to validate the identified B-cell epitopes. The arrays featured 122 peptides from S. haematobium and S. mansoni, selected through in-silico prediction using AI tools like AlphaFold. Serum samples from infected individuals were tested against the peptides to assess their diagnostic performance. The microarray platform enabled high-throughput screening, revealing which peptides effectively distinguished infected individuals from healthy controls. This approach, combining AI-based predictions and peptide microarrays, ensured high specificity and minimized cross-reactivity, offering a more reliable method for diagnosing schistosomiasis, especially in low-endemic regions.

Reference: Vengesai, Arthur, et al. "Identification of Schistosoma haematobium and Schistosoma mansoni linear B-cell epitopes with diagnostic potential using in silico immunoinformatic tools and peptide microarray technology." PLOS Neglected Tropical Diseases 18.8 (2024): e0011887. https://doi.org/10.1371/journal.pntd.0011887 

How PEPperPRINT can support your research

In conclusion, the studies highlighted in this article demonstrate the broad potential of PEPperPRINT’s peptide microarray technology to drive forward impactful research across a wide range of fields, from infectious diseases to cancer therapy. These breakthroughs not only showcase the versatility and precision of our platform but also highlight the real-world applications that can improve diagnostics and treatments globally. 

If you’re looking to explore how peptide microarrays can advance your own research or would like to learn more about our technology, we invite you to get in touch with PEPperPRINT. Together, we can make a meaningful impact on global health and scientific progress.