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Discover how PEPperPRINT Peptide Microarray products have been used in different fields of research.

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Characterization of antibodies against the replication protein (Rep) encoded by bovine meat and milk factors (BMMFs)

Frehtman, Veronika; Shukla, Gunjan; Gentz, Michael; Müller, Marcus; Duduyemi, Oladimeji Paul; Grewe, Imke; Ernst, Claudia; Tessmer, Claudia; Didier, Andrea; Hofmann, Ilse; Bund, Timo; Leuchs, Barbara
Appl Microbiol Biotechnol.
Apr 2026
10.1007/s00253-026-13809-x
Abstract Bovine Meat and Milk Factors (BMMFs) are DNA elements with similarity to bacterial plasmids, are frequently identified in bovine meat and milk and were proposed to contribute to cancer development. All known BMMFs encode a conserved replication protein (Rep), allowing for histologic BMMF detection in clinical specimens based on Rep-directed mouse monoclonal antibodies (mAbs), which, however, have only been partially characterized so far. Here, 20 anti-BMMF Rep antibodies were assessed for biophysical properties, reactivity, specificity and binding sensitivity to five distinct BMMF Reps and other prokaryotic/eukaryotic target antigens using an enzyme-linked immunosorbent assay (ELISA)-based anti-BMMF Rep antibody binding assay. We demonstrated sensitive and specific antibody reaction with their respective Rep targets, according to the antibody immunization. Consensus antibodies raised against defined peptides of conserved Rep amino acid stretches interacted with most of the Rep antigens. Antibodies produced based on immunization with the Rep encoded on the BMMF isolate H1MSB.1, including rabbit and human chimeric variants, reacted only with the cognate H1MSB.1 Rep, with only two outliers targeting additional Reps. Completely new antibodies raised against the Rep of another isolate (C1HB.4) specifically detected the cognate C1HB.4 Rep antigen – not interacting with other Reps. New antibodies generated by triple Rep immunization (H1MSB.2/C1MI.3M.1/C1MI.9M.1 Rep) reacted to either all three or two immunization antigens without interacting with any other Reps. None of the antibodies cross-reacted against Reps of bacteria occurring during milk production or lysates of mammalian hosts. Competitive inhibition confirmed antigen-specificity across the antibody panel, which additionally did not show aberrancies concerning purity or antibody size for the majority of the tested Abs. These findings authenticate a highly specific panel of anti-BMMF Rep antibodies, which can serve as tools for BMMF detection in cancer and chronic diseases.**Key Points** • Anti-BMMF Rep antibodies are important to judge BMMFs’ role as cancer risk factors. • Selective binding of anti-BMMF Rep antibodies to BMMF Rep antigens. • No cross-reactivity of anti-BMMF Rep antibodies with bacterial and mammalian outgroup specimens.

Integrated reiterative pipeline for rapid epitope-based pan-alphavirus vaccines

Versiani, Alice F.; McCaffrey, Peter; Ribeiro-Filho, Helder V.; Silva, Natalia I. O.; Lopes-de-Oliveira, Paulo S.; Carrera, Jean-Paul; Nogueira, Mauricio L.; Marques, Rafael E.; Rossi, Shannan L.; Vasilakis, Nikos
Sci Adv.
Mar 2026
10.1126/sciadv.aeb2066
The vast diversity of the virosphere underscores the need for rapid, adaptable vaccine development infrastructures. Arthropod-borne zoonotic alphaviruses, in particular, continue to pose substantial threats to human and animal health. We present a fast, multitarget vaccine design pipeline integrating machine learning-based epitope prediction, protein modeling, and docking to prioritize viral peptides by immunogenicity, allele coverage, solubility, and stability. T cell epitopes were validated using peptide microarrays and molecular dynamics simulations, confirming receptor binding accuracy. Flow cytometry of murine and human peripheral blood mononuclear cells demonstrated robust T cell activation and cytokine secretion (IFN-γ, TNF-α, or IL-2), dependent on species and HLA allele. Final candidates were selected by composite immunogenicity scores. While this study primarily validates the T cell-specific arm of our predictive pipeline, complementary B cell epitope analyses are ongoing. Our findings support the development of broadly protective pan-alphaviral vaccines and the establishment of efficient, tunable processes for global vaccine development.

Identification of a conformational epitope on the E antigen implicated in anti-E alloimmunization

Matsuura, Hideaki; Yamada, Ayuna; Doi, Hiroki; Fujii, Sumie; Miura, Yasuo
Blood Adv.
Mar 2026
10.1182/bloodadvances.2025018046

Selective Targeting of Tip Endothelial Cells as a Therapeutic Strategy for Tumor Angiogenesis

Kim, Byoungmo; Lee, Ha Kyeong; Azam, Zulfikar; Choi, Jeong Uk; Wahab, Riajul; Lee, Na Kyeong; Ko, Yoon Gun; Choi, So‐Young; Lee, Se‐Ra; Shim, Wan Seob; Kim, Taeeung; Kim, In‐San; Alam, Farzana; Kim, Sang Yoon; Kim, Seong Who; Byun, Youngro; Al‐Hilal, Taslim A
Advanced Science.
Mar 2026
10.1002/advs.202512975
ABSTRACT Tip endothelial cells (TipEC), the leading edge of angiogenic sprouts, are essential for pathological neo‐vascularization but remain difficult to target due to the lack of specific druggable markers. Here, we identify Doppel as a selective and druggable regulator of endothelial tip cell function. Doppel expression enhances TipEC selection, directional migration, and regulates tip‐stalk cell dynamics by spatially controlling VEGFR2/Dll4/Src pathway. Genetic ablation of PRND (Doppel) reduces tip cell formation without affecting the stalk cells (StalkECs) number in tumors, indicating its selective role in TipECs. Importantly, depletion of TipECs using the first‐in‐class monoclonal antibodies against a highly conserved WQF‐motif of Doppel robustly decreased the growth of tumors by selectively downregulating VEGFR2+ TipECs but not StalkECs. These findings position Doppel as a tumor TipEC‐specific, druggable target that may offer a new avenue to enhance and refine anti‐angiogenic therapies in cancer treatment.

Clinical outcomes-dependent IgG epitope profiling in HTLV-1 reveals differential recognition of pathogen-derived antigens

Cilento, Natali Espasiani; Borges, João Vitor Da Silva; Machado, Nicolle Rakanidis; Do Nascimento, Lais Alves; Moreira, Anna Luisa Baratelli; Passos, Lhays Ozório; Santamarina, Aline Boveto; Casseb, Jorge; Sanabani, Sabri Saeed; Victor, Jefferson Russo
Front. Immunol..
Feb 2026
10.3389/fimmu.2026.1755133
Human T-lymphotropic virus type 1 (HTLV-1) infection presents a wide clinical spectrum ranging from lifelong asymptomatic carriage to severe inflammatory neurodegeneration (HAM/TSP) or adult T-cell leukemia/lymphoma (ATLL). Although IgG responses contribute to viral control and immunopathology, the extent to which HTLV-1 clinical outcomes shape pathogen-derived IgG repertoires remains unclear. In this study, we applied a high-density infectious-disease epitope microarray containing 4,345 linear epitopes from viral, bacterial, parasitic, and fungal pathogens to profile IgG responses in healthy controls (HCs), asymptomatic carriers (ACs), HAM/TSP patients, and ATLL patients. Signal intensities were quantified in arbitrary units, and recognized epitopes were evaluated using similarity clustering (80% identity threshold) to assess repertoire structure. HTLV-1–infected individuals exhibited extensive remodeling of humoral immunity, with marked differences in the breadth and intensity of IgG recognition across clinical groups. HAM/TSP patients displayed broad and high-magnitude responses consistent with chronic inflammation and heightened Th1 activation, whereas ATLL patients recognized the largest number of epitopes but with distinct patterns indicative of altered B-cell regulation. Enhanced IgG responses to Mycobacterium tuberculosis, Strongyloides stercoralis, Toxoplasma gondii, and Plasmodium species were consistent with known co-infection susceptibilities in HTLV-1. Epitope similarity analysis revealed hundreds of low-redundancy clusters across all groups, arguing against simple linear cross-reactivity and suggesting phenotype-specific reshaping of B-cell selection and idiotypic networks. These findings demonstrate that HTLV-1 infection produces distinct, clinically dependent IgG epitope signatures across multiple pathogen classes, with potential relevance for understanding HTLV-1 pathogenesis and informing future studies integrating epitope mapping with B-cell repertoire analysis.

Syndecan-1-targeted therapeutic antibody impairs macropinocytosis and elicits antitumor immunity in pancreatic cancer

Yang, Zecheng; Theardy, Madelaine S.; Chen, Shuaitong; Wei, Yongkun; Takeda, Mitsunobu; Zeng, Yue; Wang, Xiaofei; Yao, Jun; Li, Jennifer; Thirasastr, Prapassorn; Park, Jangho; Zheng, Yangxi; Vien, Long T.; Wani, Khalida M.; Wang, Huamin; Gao, Sisi; Heffernan, Tim; Kwong, Lawrence; Wistuba, Ignacio I.; Bover, Laura; Draetta, Giulio F.; Ying, Haoqiang; Yao, Wantong
Cell Reports Medicine.
Feb 2026
10.1016/j.xcrm.2026.102613
Pancreatic ductal adenocarcinoma (PDAC) remains one of the deadliest malignancies, with a 5-year survival rate of just 13%. While the development and early clinical use of small molecules targeting oncogenic KRAS mutations, key drivers of PDAC, have shown promise, resistance to these targeted therapies remains a significant challenge. We recently identified Syndecan-1 (SDC1), a highly expressed heparan sulfate proteoglycan, as a critical KRAS effector protein that promotes nutrient salvage and tumor growth. Here, we report the development of a human-specific monoclonal antibody (anti-SDC1 mAb) that inhibits PDAC cell proliferation in vitro and suppresses PDAC tumor growth in vivo. Mechanistically, the anti-SDC1 mAb blocks macropinocytosis and induces antibody-dependent cellular cytotoxicity (ADCC). In vivo, anti-SDC1 mAb synergizes with standard chemotherapy, KRAS∗ inhibitors, and immunotherapies, resulting in tumor regression and near-complete response. These findings highlight the anti-SDC1 mAb as a promising therapeutic strategy for PDAC and potentially other KRAS∗ and SDC1-driven tumors.

Non-Neutralizing Antibody Functions Predict Susceptibility to SARS-CoV-2 Infection after mRNA Booster Vaccination

Levy, Shlomia; Trifkovic, Sanja; Mielke, Dieter; Oppenheimer, Hannah; Goodman, Derrick; Ostrovsky, Daniel; Sanfield-Oakley, Sherry A.; Brackett, Caroline; Friedman, Lilach M; Kerkau, Melissa; Webby, Richard; Tomaras, Georgia; Guido, Ferrari; Nesher, Lior; Hertz, Tomer
Jan 2026
10.2139/ssrn.6019238
Previous studies have shown that neutralizing and binding antibody titers are correlates of protection for symptomatic SARS-CoV-2 infection. We previously reported that individuals with low IgG and IgA baseline immune history (BIH) to SARS-CoV-2 variants were at increased risk of symptomatic infection in study of healthcare workers that received 3 or 4 doses of the Pfizer BNT-1262b2 vaccine. We also found that 1-month post-vaccination with the 4th booster dose, individuals with low-BIH mounted significant rises in binding and neutralizing antibody titers, to levels comparable to those of individuals with high-BIH, demonstrating that their increased risk was not due to inability to respond to vaccination. To further study the underlying factors that are associated with increased risk, we conducted a systems serology study of 40 low-BIH and 40 high-BIH individuals across 7 months of follow-up. We found that individuals with low BIH exhibited a significantly higher risk of symptomatic infection (HR=2.691, p=0.0065) and mounted weaker IgA and antibody-dependent cellular cytotoxicity (ADCC) responses compared to high-BIH individuals, particularly against Omicron and Delta variants. Baseline levels of the chemokine CXCL-11 were elevated in the low-BIH group. We then showed that baseline immune profiles can be used to train a prediction model of infection risk across 7 months of follow-up with 76% accuracy. IgA, ADCC and ADCP baseline features were dominant predictors of susceptibility. Our findings suggest that non-neutralizing antibody functions, especially IgA and ADCC, contribute to protection against symptomatic SARS-CoV-2 infection and that serology-guided stratification can enhance discovery of immune correlates of risk informing future vaccine design and deployment strategies.

Induced Polyspecificity of Human Secretory Immunoglobulin A Antibodies: Is It Possible to Improve Their Ability to Bind Pathogens?

Gorshkova, Ekaterina N.; Pashova, Shina; Vasilenko, Ekaterina A.; Tchurina, Tatiana S.; Razzorenova, Elizaveta A.; Starkina, Olga V.; Dimitrova, Petya; Pashov, Anastas; Vassilev, Tchavdar Lubenov
Pharmacology.
Dec 2021
10.1159/000520343
Introduction: As has been shown previously, various protein-modifying agents can change the antigen-binding properties of immunoglobulins. However, induced polyspecificity of human secretory immunoglobulin A (sIgA) has not been previously characterized in detail. Methods: In the present study, human secretory immunoglobulin A (IgA) was exposed to buffers with acidic pH, to free heme, or to pro-oxidative ferrous ions, and the antigen-binding behavior of the native and modified IgA to viral and bacterial antigens was compared using Western blotting and enzyme-linked immunosorbent assay. The ability of these agents to modulate the antigen-binding properties of human sIgA toward a wide range of pathogen peptides was investigated using an epitope microarray. Results: We have shown that acidic pH, heme, and pro-oxidative ferrous ions influenced the binding of secretory IgA in opposite directions (either increasing or decreasing); however, the strongest effect was observed when using buffers with low pH. This fraction had the highest number of affected reactivities; most of them were increased and most of the new ones were toward common pathogens. Conclusions: Thus, it was shown that all investigated treatments can alter to some degree the antigen-binding of secretory IgA, but acidic pH has the most potentially beneficial effect by increasing binding to a largest number of common pathogens’ antigens.

Influenza‐associated thrombotic thrombocytopenic purpura: A report of two cases and a brief review of the literature

Onkarappa Mangala, Yashvin; Sweeney, Joseph D.
Vox Sanguinis.
Nov 2021
10.1111/vox.13227
Background and Objectives Thrombotic thrombocytopenic purpura (TTP) is often preceded by a recent history of an acute infection and influenza is the most implicated virus. Materials and Methods We identified two cases of TTP, which were preceded by influenza between 2010 and 2021. In one patient, we epitope mapped the binding specificity of antibodies using an overlapping peptide approach of the stalk protein of Influenza B and the cysteine-rich spacer domain (CRSD) of ADAMTS13. A literature search was performed for reports of influenza-associated TTP over the period 1980–2021. Results Two patients were identified in which TTP was preceded by influenza, one Influenza A and the other Influenza B. Epitope mapping of the latter’s plasma identified target epitopes in both the stalk protein of Influenza B and CRSD of ADAMTS13. The literature review revealed only seven case reports, all but one from Europe or Asia and associated with Influenza A. Severe ADAMTS13 deficiency was demonstrated in only four cases. Conclusion We report the first small case series of influenza-associated TTP. Moreover, it is the first case implicating Influenza B and a mechanism favouring polyclonal B-cell proliferation rather than molecular mimicry as the stimulus to form anti-ADAMTS13 auto-antibodies is suggested.

The Potential Role of Human NME1 in Neuronal Differentiation of Porcine Mesenchymal Stem Cells: Application of NB-hNME1 as a Human NME1 Suppressor

Cho, Jin Hyoung; Ju, Won Seok; Seo, Sang Young; Kim, Bo Hyun; Kim, Ji-Su; Kim, Jong-Geol; Park, Soon Ju; Choo, Young-Kug
Int J Mol Sci.
Nov 2021
10.3390/ijms222212194
This study aimed to investigate the effects of the human macrophage (MP) secretome in cellular xenograft rejection. The role of human nucleoside diphosphate kinase A (hNME1), from the secretome of MPs involved in the neuronal differentiation of miniature pig adipose tissue-derived mesenchymal stem cells (mp AD-MSCs), was evaluated by proteomic analysis. Herein, we first demonstrate that hNME1 strongly binds to porcine ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1 (pST8SIA1), which is a ganglioside GD3 synthase. When hNME1 binds with pST8SIA1, it induces degradation of pST8SIA1 in mp AD-MSCs, thereby inhibiting the expression of ganglioside GD3 followed by decreased neuronal differentiation of mp AD-MSCs. Therefore, we produced nanobodies (NBs) named NB-hNME1 that bind to hNME1 specifically, and the inhibitory effect of NB-hNME1 was evaluated for blocking the binding between hNME1 and pST8SIA1. Consequently, NB-hNME1 effectively blocked the binding of hNME1 to pST8SIA1, thereby recovering the expression of ganglioside GD3 and neuronal differentiation of mp AD-MSCs. Our findings suggest that mp AD-MSCs could be a potential candidate for use as an additive, such as an immunosuppressant, in stem cell transplantation.

A high-throughput pipeline for design and selection of peptides targeting the SARS-Cov-2 Spike protein

Wolfe, Monica; Webb, Sean; Chushak, Yaroslav; Krabacher, Rachel; Liu, Yi; Swami, Nathan; Harbaugh, Svetlana; Chávez, Jorge
Sci Rep.
Nov 2021
10.1038/s41598-021-01225-2
Rapid design, screening, and characterization of biorecognition elements (BREs) is essential for the development of diagnostic tests and antiviral therapeutics needed to combat the spread of viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To address this need, we developed a high-throughput pipeline combining in silico design of a peptide library specific for SARS-CoV-2 spike (S) protein and microarray screening to identify binding sequences. Our optimized microarray platform allowed the simultaneous screening of ~ 2.5 k peptides and rapid identification of binding sequences resulting in selection of four peptides with nanomolar affinity to the SARS-CoV-2 S protein. Finally, we demonstrated the successful integration of one of the top peptides into an electrochemical sensor with a clinically relevant limit of detection for S protein in spiked saliva. Our results demonstrate the utility of this novel pipeline for the selection of peptide BREs in response to the SARS-CoV-2 pandemic, and the broader application of such a platform in response to future viral threats.

The cellular modifier MOAG-4/SERF drives amyloid formation through charge complementation

Pras, Anita; Houben, Bert; Aprile, Francesco A.; Seinstra, Renée; Gallardo, Rodrigo; Janssen, Leen; Hogewerf, Wytse; Gallrein, Christian; De Vleeschouwer, Matthias; Mata-Cabana, Alejandro; Koopman, Mandy; Stroo, Esther; de Vries, Minke; Louise Edwards, Samantha; Kirstein, Janine; Vendruscolo, Michele; Falsone, Salvatore Fabio; Rousseau, Frederic; Schymkowitz, Joost; Nollen, Ellen A. A.
EMBO J.
Nov 2021
10.15252/embj.2020107568
While aggregation-prone proteins are known to accelerate aging and cause age-related diseases, the cellular mechanisms that drive their cytotoxicity remain unresolved. The orthologous proteins MOAG-4, SERF1A, and SERF2 have recently been identified as cellular modifiers of such proteotoxicity. Using a peptide array screening approach on human amyloidogenic proteins, we found that SERF2 interacted with protein segments enriched in negatively charged and hydrophobic, aromatic amino acids. The absence of such segments, or the neutralization of the positive charge in SERF2, prevented these interactions and abolished the amyloid-promoting activity of SERF2. In protein aggregation models in the nematode worm Caenorhabditis elegans, protein aggregation and toxicity were suppressed by mutating the endogenous locus of MOAG-4 to neutralize charge. Our data indicate that MOAG-4 and SERF2 drive protein aggregation and toxicity by interactions with negatively charged segments in aggregation-prone proteins. Such charge interactions might accelerate primary nucleation of amyloid by initiating structural changes and by decreasing colloidal stability. Our study points at charge interactions between cellular modifiers and amyloidogenic proteins as potential targets for interventions to reduce age-related protein toxicity.

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