Peptide Arrays Research Articles

Positive charges promote the recognition of proteins by the chaperone SlyD from Escherichia coli.

SlyD is a widely-occurring prokaryotic FKBP-family prolyl isomerase with an additional chaperone domain. Often, such as in Escherichia coli, a third domain is found at its C-terminus that binds nickel and provides it for nickel-enzyme biogenesis. SlyD has been found to bind signal peptides of proteins that are translocated by the Tat pathway, a system for the transport of folded proteins across membranes. Using peptide arrays to analyze these signal peptide interactions, we found that SlyD interacted only with positively charged peptides, with a preference for arginines over lysines, and large hydrophobic residues enhanced binding. Especially a twin-arginine motif was recognized, a pair of highly conserved arginines adjacent to a stretch of hydrophobic residues. Using isothermal titration calorimetry (ITC) with purified SlyD and a signal peptide-containing model Tat substrate, we could show that the wild type twin-arginine signal peptide was bound with higher affinity than an RR>KK mutated variant, confirming that positive charges are recognized by SlyD, with a preference of arginines over lysines. The specific role of negative charges of the chaperone domain surface and of hydrophobic residues in the chaperone active site was further analyzed by ITC of mutated SlyD variants. Our data show that the supposed key hydrophobic residues of the active site are indeed crucial for binding, and that binding is influenced by negative charges on the chaperone domain. Recognition of positive charges is likely achieved by a large negatively charged surface region of the chaperone domain, which is highly conserved although individual positions are variable.

Expansion and differentiation of human neural stem cells on synthesized integrin binding peptide surfaces

The extracellular matrix plays a crucial role in the growth of human neural stem cells (hNSCs) by forming a stem cell niche, both in vitro and in vivo. The demand for defined synthetic substrates has been increasing recently in stem cell research, reflecting the requirements for precise functions and safety concerns in potential clinical approaches. In this study, we tested the adhesion and expansion of one of the most representative hNSC lines, the ReNcell VM Human Neural Progenitor Cell Line, in a pure-synthesized short peptide-based in vitro niche using a previously established integrin-binding peptide array. Spontaneous cell differentiation was then induced using two different in vitro approaches to further confirm the multipotent features of cells treated with the peptides. Twelve different integrin-binding peptides were capable of supporting hNSC adhesion and expansion at varied proliferation rates. In the ReNcell medium-based differentiation approach, cells detached in almost all peptide-based groups, except integrin α5β1 binding peptide. In an altered differentiation process induced by retinoic acid containing neural differentiation medium, cell adhesion was retained in all 12 peptide groups. These peptides also appeared to have varied effects on the differentiation potential of hNSCs towards neurons and astrocytes. Our findings provide abundant options for the development of in vitro neural stem cell niches and will help develop promising tools for disease modeling and future stem cell therapies for neurological diseases.

PdPANA: phagemid display as peptide array for neutralizing antibodies, an engineered in silico vaccine candidate against COVID-19

The COVID-19 pandemic has tested the technical, scientific, and industrial resources of all countries worldwide. Faced with the absence of pharmacological strategies against the disease, an effective plan for vaccinating against SARS-CoV-2 has been essential. Due to the lack of production means and necessary infrastructure, only a few nations could adequately confront this pathogen with a production, storage, and distribution scheme in place. This disease has become endemic in many countries, especially in those that are developing, thus necessitating solutions tailored to their reality. In this paper, we propose an in silico method to guide the design towards a thermally stable, universal, efficient, and safe COVID-19 vaccine candidate against SARS-CoV-2 using bioinformatics, immunoinformatics, and molecular modeling approaches for the selection of antigens with higher immunogenic potential, incorporating them into the surface of the M13 phage. Our work focused on using phagemid display as peptide array for neutralizing antibodies (PdPANA). This alternative approach might be useful during the vaccine development process, since it could bring improvements in terms of cost-effectiveness in production, durability, and ease of distribution of the vaccine under less stringent thermal conditions compared to existing methods. Our results suggest that in the heavily glycosylated region of SARS-CoV-2 Spike protein (aa 344–583), from its inter-glycosylated regions, useful antigenic peptides can be obtained to be used in M13 phagemid display system. PdPANA, our proposed method might be useful to overcome the classic shortcoming posed by the phage-display technique (i.e., the time-consuming task of in vitro screening through great sized libraries with non-useful recombinant proteins) and obtain the most ideal recombinant proteins for vaccine design purposes.

Exploring Syndecan-4 and MLP and Their Interaction in Primary Cardiomyocytes and H9c2 Cells.

The transmembrane proteoglycan syndecan-4 is known to be involved in the hypertrophic response to pressure overload. Although multiple downstream signaling pathways have been found to be involved in this response in a syndecan-4-dependent manner, there are likely more signaling components involved. As part of a larger syndecan-4 interactome screening, we have previously identified MLP as a binding partner to the cytoplasmic tail of syndecan-4. Interestingly, many human MLP mutations have been found in patients with hypertrophic (HCM) and dilated cardiomyopathy (DCM). To gain deeper insight into the role of the syndecan-4-MLP interaction and its potential involvement in MLP-associated cardiomyopathy, we have here investigated the syndecan-4-MLP interaction in primary adult rat cardiomyocytes and the H9c2 cell line. The binding of syndecan-4 and MLP was analyzed in total lysates and subcellular fractions of primary adult rat cardiomyocytes, and baseline and differentiated H9c2 cells by immunoprecipitation. MLP and syndecan-4 localization were determined by confocal microscopy, and MLP oligomerization was determined by immunoblotting under native conditions. Syndecan-4-MLP binding, as well as MLP self-association, were also analyzed by ELISA and peptide arrays. Our results showed that MLP-WT and syndecan-4 co-localized in many subcellular compartments; however, their binding was only detected in nuclear-enriched fractions of isolated adult cardiomyocytes. In vitro, syndecan-4 bound to MLP at three sites, and this binding was reduced in some HCM-associated MLP mutations. While MLP and syndecan-4 also co-localized in many subcellular fractions of H9c2 cells, these proteins did not bind at baseline or after differentiation into cardiomyocyte-resembling cells. Independently of syndecan-4, mutated MLP proteins had an altered subcellular localization in H9c2 cells, compared to MLP-WT. The DCM- and HCM-associated MLP mutations, W4R, L44P, C58G, R64C, Y66C, K69R, G72R, and Q91L, affected the oligomerization of MLP with an increase in monomeric at the expense of trimeric and tetrameric recombinant MLP protein. Lastly, two crucial sites for MLP self-association were identified, which were reduced in most MLP mutations. Our data indicate that the syndecan-4-MLP interaction was present in nuclear-enriched fractions of isolated adult cardiomyocytes and that this interaction was disrupted by some HCM-associated MLP mutations. MLP mutations were also linked to changes in MLP oligomerization and self-association, which may be essential for its interaction with syndecan-4 and a critical molecular mechanism of MLP-associated cardiomyopathy.

Increase of Cardiac Autoantibodies Against Beta-2-adrenergic Receptor During Acute Cellular Heart Transplant Rejection.

Acute cellular rejection (ACR) in heart transplant (HTx) recipients may be accompanied by cardiac cell damage with subsequent exposure to cardiac autoantigens and the production of cardiac autoantibodies (aABs). This study aimed to evaluate a peptide array screening approach for cardiac aABs in HTx recipients during ACR (ACR-HTx). In this retrospective single-center observational study, sera from 37 HTx recipients, as well as age and sex-matched healthy subjects were screened for a total of 130 cardiac aABs of partially overlapping peptide sequences directed against structural proteins using a peptide array approach. In ACR-HTx, troponin I (TnI) serum levels were found to be elevated. Here, we could identify aABs against beta-2-adrenergic receptor (β-2AR: EAINCYANETCCDFFTNQAY) to be upregulated in ACR-HTx (intensities: 0.80 versus 1.31, P = 0.0413). Likewise, patients positive for β-2AR aABs showed higher TnI serum levels during ACR compared with aAB negative patients (10.0 versus 30.0 ng/L, P = 0.0375). Surprisingly, aABs against a sequence of troponin I (TnI: QKIFDLRGKFKRPTLRRV) were found to be downregulated in ACR-HTx (intensities: 3.49 versus 1.13, P = 0.0025). A comparison in healthy subjects showed the same TnI sequence to be upregulated in non-ACR-HTx (intensities: 2.19 versus 3.49, P = 0.0205), whereas the majority of aABs were suppressed in non-ACR-HTx. Our study served as a feasibility analysis for a peptide array screening approach in HTx recipients during ACR and identified 2 different regulated aABs in ACR-HTx. Hence, further multicenter studies are needed to evaluate the prognostic implications of aAB testing and diagnostic or therapeutic consequences.

Merging Flow Synthesis and Enzymatic Maturation to Expand the Chemical Space of Lasso Peptides.

Many peptidic natural products, such as lasso peptides, cyclic peptides, and cyclotides, are conformationally constrained and show biological stability, making them attractive scaffolds for drug development. Although many peptides can be synthesized and modified through chemical methods, knot-like lasso peptides such as microcin J25 (MccJ25) and their analogues remain elusive. As the chemical space of MccJ25 analogues accessible through purely biological methods is also limited, we proposed a hybrid approach: flow-based chemical synthesis of non-natural precursor peptides, followed by in vitro transformation with recombinant maturation enzymes, to yield a more diverse array of lasso peptides. Herein, we established the rapid, flow-based synthesis of chemically modified MccJ25 precursor peptides (57 amino acids). Heterologous expression of enzymes McjB and McjC was extensively optimized to improve yields and facilitate the synthesis of multiple analogues of MccJ25, including the incorporation of non-canonical tyrosine and histidine derivatives into the lasso scaffold. Finally, using our chemoenzymatic strategy, we produced a biologically active analogue containing three d-amino acids in the loop region and incorporated backbone N-methylations. Our method provides rapid access to chemically modified lasso peptides that could be used to investigate structure-activity relationships, epitope grafting, and the improvement of therapeutic properties.

Human antibody signatures towards the Chlamydia trachomatis major outer membrane protein after natural infection and vaccination

Chlamydia trachomatis (CT) Major Outer Membrane Protein (MOMP) holds a neutralising epitope in the Variable Domain 4 (VD4), and this region's immune dominance during infection is well known. This study aimed to assess the antibody response induced after infection and compare it for specificity and functionality to the response following vaccination with the vaccine CTH522, which contains VD4's from serovars D, E, F, and G. We assessed the antibody epitopes in MOMP by a high density peptide array. Furthermore, the role of the VD4 epitope in neutralisation was explored by competitive inhibition experiments with a fusion protein holding the neutralising VD4 linear epitope. This was done in two independent groups: 1) MOMP seropositive individuals infected with CT (n=10, from case-control study) and 2) CTH522/CAF®01-vaccinated females (n=14) from the CHLM-01 clinical trial. We identified the major antigenic regions in MOMP as VD4 and the conserved region just before VD3 in individuals infected with CT. The same regions, with the addition of VD1, were identified in vaccine recipients. Overall, the VD4 peptide responses were uniform in vaccinated individuals and led to inhibition of infection invitro in all tested samples, whereas the VD4 responses were more heterogenous in individuals infected with CT, and only 2 out of 10 samples had VD4-mediated neutralising antibody responses. These data provide insights into the role of antibodies against MOMP VD4 induced after infection and vaccination, and show that their functionality differs. The induction of functional VD4-specific antibodies in vaccine recipients mimics previous results from animal models. This work was supported by the European Commission through contract FP7-HEALTH-2011.1.4-4-280873 (ADITEC) and Fonden til Lægevidenskabens Fremme.

The intrinsic substrate specificity of the human tyrosine kinome

Phosphorylation of proteins on tyrosine (Tyr) residues evolved in metazoan organisms as a mechanism of coordinating tissue growth1. Multicellular eukaryotes typically have more than 50 distinct protein Tyr kinases that catalyse the phosphorylation of thousands of Tyr residues throughout the proteome1–3. How a given Tyr kinase can phosphorylate a specific subset of proteins at unique Tyr sites is only partially understood4–7. Here we used combinatorial peptide arrays to profile the substrate sequence specificity of all human Tyr kinases. Globally, the Tyr kinases demonstrate considerable diversity in optimal patterns of residues surrounding the site of phosphorylation, revealing the functional organization of the human Tyr kinome by substrate motif preference. Using this information, Tyr kinases that are most compatible with phosphorylating any Tyr site can be identified. Analysis of mass spectrometry phosphoproteomic datasets using this compendium of kinase specificities accurately identifies specific Tyr kinases that are dysregulated in cells after stimulation with growth factors, treatment with anti-cancer drugs or expression of oncogenic variants. Furthermore, the topology of known Tyr signalling networks naturally emerged from a comparison of the sequence specificities of the Tyr kinases and the SH2 phosphotyrosine (pTyr)-binding domains. Finally we show that the intrinsic substrate specificity of Tyr kinases has remained fundamentally unchanged from worms to humans, suggesting that the fidelity between Tyr kinases and their protein substrate sequences has been maintained across hundreds of millions of years of evolution.

Abstract PO5-05-09: Testing AI-Predicted Protein Motifs that Direct Constitutive Genomic AR Activity in Endocrine Resistant Breast Cancer

Abstract Testing AI-Predicted Protein Motifs that Direct Constitutive Genomic AR Activity in Endocrine-Resistant Breast Cancer Ashfia F. Khan 1,2, Anthony S. Peidl 1,2, Shaymaa Bahnassy 3, Henry Vo2, Micah B. Castillo 2, Sarah K Herzog4,5, Suzanne AW Fuqua4,6, Preethi Gunaratne 2, Xiaolian Gao 2, Subash C. Pakhrin7, Tasneem Bawa-Khalfe1,2 1 Center for Nuclear Receptors & Cell Signaling, University of Houston, Houston, TX 2 Department of Biology & Biochemistry, University of Houston, Houston, TX 3 Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 4 Lester & Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 5 Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX 6 Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 7 Department of Computer Science & Engineering Technology, University of Houston-Downtown, Houston, TX Background: Endocrine therapy (ET) remains the first-line treatment for hormone-receptor positive (HR+) breast cancer (BCa). Approximately 15–20% of HR+ BCa are intrinsically resistant to ET, and 30–40% of patients acquire resistance. Resistance to ET (ET-R) supports cancer progression with reduced disease-free survival and greater incidence of metastatic disease. Hence, therapeutic strategies for ET-R HR+ BCa remain an overarching challenge. The androgen receptor (AR) is emerging as an attractive alternative target for BCa subtypes, and elevated AR levels drive HR+ BCa progression. Targeting AR in HR+ BCa is proving difficult with preclinical studies showing conflicting results for AR antagonists. Yet clinical trials with several AR-targeting drugs are ongoing. Our recent report highlights a unique constitutively active modified AR population that drives HR+ BCa metastatic properties and is insensitive to AR inhibitors. Our current objectives are to 1) use a novel machine-learning model to predict AR modifications and 2) establish a strategy to identify patients with high modified AR levels. Methods: An advanced artificial intelligence (AI) tool and mid-throughput microfluidic peptide array technology were used to map modification domains on AR. SUMO post-translational modification of AR (SUMO-AR) was eliminated in HR+ BCa using CRISPR-Cas9 technology. RNA-seq was employed to identify a unique gene signature for SUMO-AR, and comparative bioinformatic analysis stratified patients with high versus low SUMO-AR. Results: A novel deep-learning AI platform SumoPred-PLM is trained to identify consensus, non-consensus, and SUMO2/3-specific motifs on AR. We verified SUMO2/3-specific sites on AR with a mid-throughput microfluidic peptide array. The identified SUMO2/3-acceptor site of AR is important for HR+ BCa cell pathophysiology; loss of this SUMO2/3-acceptor site impacts endogenous AR SUMOylation, cell morphology, and proliferation/apoptosis. Using both high and low SUMO-AR BCa lines, a unique SUMO-AR gene profile was established. Our SUMO-AR gene signature identifies HR+ BCa patients with greater susceptibility to metastatic progression. Conclusion: Our studies present a unique pipeline that incorporates deep-learning AI technology to identify vulnerable motifs in AR for future drug discovery. Drug screens are currently ongoing. In addition, we establish a SUMO-AR gene signature that stratifies HR+ BCa patients with high/low SUMO-AR and predicts disease progression. We expect the results could be utilized to identify responders to AR inhibitors in ongoing clinical trials. Citation Format: Ashfia Khan, Anthony Peidl, Shaymaa Bahnassy, Henry Vo, Micah Castillo, Sarah Herzog, Suzanne Fuqua, Preethi Gunaratne, Xiaolian Gao, Subash Pakhrin, Tasneem Bawa-Khalfe. Testing AI-Predicted Protein Motifs that Direct Constitutive Genomic AR Activity in Endocrine Resistant Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-05-09.

Abstract 3081: Competitive Inhibition Of Tlt-1/fibrinogen Molecular Interaction Disrupts Platelet Function In Ex Vivo Platelet Assays

Background: Platelets facilitate thrombosis, hemostasis, and immunity through their interaction with fibrinogen. Fibrinogen is the ligand for the platelet receptors αIIbβ3 and T REM- L ike T ranscript-1 (TLT-1), TLT-1 is an Ig-domain containing receptor released from platelet α-granules upon platelet activation. Unlike αIIbβ3, little is known about the TLT-1/fibrinogen interaction. Aims: Delineate the TLT-1/fibrinogen molecular interaction and determine if, peptides representing this interaction can regulate platelet function and inflammatory hemostasis. Methods: Octet Qke Bio-layer Interferometry and atomic force microscopy (AFM) were used to evaluate soluble TLT-1 binding to fibrinogen. Immunoprecipitation and a peptide array were used to determine which fibrinogen peptides bound TLT-1. Flow cytometry using FITC-labelled fibrinogen binding to activated human platelets and human platelet aggregometry in the presence of these peptides were used in competitive inhibition assays. Additionally, competitive ELISAs using peptides representing regions the TLT-1 extracellular domain incubated with soluble TLT-1 in a fibrinogen coated wells were used to identify the region(s) on TLT-1 interaction with fibrinogen. Results: We obtained an equilibrium dissociation constant (KD) of 3.02 ± 0.20 nM for the TLT-1/Fibrinogen interaction. AFM suggests that sTLT-1 mediates fibrinogen polymerization. Competitive inhibition assays suggest complementary determining loop-1 and LP-17 (a 17 amino acid region of TLT-1) mediate TLT-1’s interaction to fibrinogen. The 3D modeling of our identified peptides show that they form a binding complex on the B module of the D-domain rather than a single binding site. These peptides competitively reduce platelet aggregation in aggregation assays and decrease fibrinogen binding to platelets in flow cytometry assays compared to controls. Cell binding and clotting assays are underway and the current status of projected will be reported here. Conclusions: TLT-1 uses LP17 and CDR-1 to interact with the newly identified TLT-1 binding complex on fibrinogen. This TLT-1 binding surface may represent a targetable intervention to regulate thrombosis and inflammation.

A Review of Bioactive Compound Effects from Primary Legume Protein Sources in Human and Animal Health.

The global demand for sustainable and nutritious food sources has catalyzed interest in legumes, known for their rich repertoire of health-promoting compounds. This review delves into the diverse array of bioactive peptides, protein subunits, isoflavones, antinutritional factors, and saponins found in the primary legume protein sources-soybeans, peas, chickpeas, and mung beans. The current state of research on these compounds is critically evaluated, with an emphasis on the potential health benefits, ranging from antioxidant and anticancer properties to the management of chronic diseases such as diabetes and hypertension. The extensively studied soybean is highlighted and the relatively unexplored potential of other legumes is also included, pointing to a significant, underutilized resource for developing health-enhancing foods. The review advocates for future interdisciplinary research to further unravel the mechanisms of action of these bioactive compounds and to explore their synergistic effects. The ultimate goal is to leverage the full spectrum of benefits offered by legumes, not only to advance human health but also to contribute to the sustainability of food systems. By providing a comprehensive overview of the nutraceutical potential of legumes, this manuscript sets a foundation for future investigations aimed at optimizing the use of legumes in the global pursuit of health and nutritional security.

Interaction of SMAC with a survivin-derived peptide alters essential cancer hallmarks: Tumor growth, inflammation, and immunosuppression

SMAC/Diablo is known as a pro-apoptotic mitochondrial protein released into the cytosol in response to apoptotic signals. We recently reported SMAC overexpression in cancers as essential for cell proliferation and tumor growth due to non-apoptotic functions including phospholipid synthesis regulation. These functions may be associated with its interactions with partner proteins. Using a peptide array with 768 peptides derived from 11 selected SMAC-interacting proteins, we identified SMAC-interacting sequences. These SMAC-binding sequences were produced as cell penetrating peptides targeted to the cytosol, mitochondria, or nucleus, inhibiting cell proliferation and inducing apoptosis in several cell lines. For in-vivo study, a survivin/BIRC5-derived peptide was selected due to its overexpression in many cancers, and involvement in mitosis, apoptosis, autophagy, cell proliferation, inflammation, and immune responses, as a target for cancer therapy. Specifically, a SMAC-targeting survivin/BIRC5-derived peptide, given intratumorally or intravenously, strongly inhibited lung tumor growth, cell proliferation, angiogenesis, and inflammation, induced apoptosis, and remodeled the tumor microenvironment. The peptide promoted tumor infiltration of CD8+ cells and increased cell-intrinsic PD-1/PD-L1 expression, resulting in cancer cell self-destruction and increased tumor cell death, preserving immune cells. Thus, targeting the interaction between the multifunctional proteins SMAC and survivin represents a innovative therapeutic cancer paradigm.

Epistasis Between HLA-DRB1*16:02:01 and SLC16A11 T-C-G-T-T Reduces Odds for Type 2 Diabetes in Southwest American Indians.

We sought to identify genetic/immunologic contributors of type 2 diabetes in an indigenous American community by genotyping all study participants for both high resolution HLA-DRB1 alleles and SLC16A11 to test their risk and/or protection for T2D. These genes were selected based on independent reports that HLA-DRB1*16:02:01 is protective for T2D and that SLC16A11 associates with T2D in individuals with BMI<35kg/m2, and here test the interaction of the two loci with a more complete dataset and perform a BMI sensitivity test. We define the risk-protection haplotype of SLC16A11, T-C-G-T-T, as allele "2" of a di-allelic genetic model with three genotypes, SLC16A11*11, *12, and *22, where allele "1" is the wildtype. Both earlier findings were confirmed. Together in the same logistic model with BMI≥35, DRB1*16:02:01 remains protective, 0.73, while SLC16A11 switches from risk to protection OR = 0.57 (*22) and 0.78 (*12), respectively; an added interaction term was statistically significant (OR = 0.49 with *12). Bootstrapped (b=10,000) statistical power of interaction, 0.4801, yielded mean OR = 0.43. Sensitivity analysis demonstrated the interaction significant in BMI range 30-41. To investigate the epistasis we used the primary function of the HLA-DRB1 molecule, peptide binding and presentation, to search the entire array of 15mer peptides for both the wildtype and ancient human SLC16A11 molecules for a pattern of strong binding that was associated with risk and protection for T2D. Applying computer binding algorithms suggests the core peptide at SLC16A11 D127G, FSAFASGLL, might be key for moderating risk for T2D with potential implications for T1D.

Abstract 4370: Functional characterisation of a novel mutation in PRKCA, a major driver of chordoid gliomas

Abstract Chordoid gliomas (ChG) are a rare low-grade brain tumor, believed to be derived from tanycytes. An analysis by the team identified a novel mutation present in all ChGs: PRKCA p.D463H. This mutation involves a D463H substitution at the kinase domain of the Protein kinase C alpha (PKCα), it is not found in any other cancer, and represents the hallmark of ChG. The aim of the project is to identify novel and biologically relevant PKCαD463H signaling pathways, which will demonstrate the involvement and the role of this mutated kinase in cellular functions implicated in the development of ChGs. The D463H mutation affects a critical residue of the kinase domain of PKCα, suggesting that such a change modifies substrate affinity. Following the purification of PKCαD463H, we have shown its inactivation via in vitro kinase assays and peptide array. In cellulo fret-based activity reporter assays have shown that PKCαD463H has a dominant negative effect over PKCαWT. Through co-immunoprecipitation we have shown that the mutant protein can bind the WT form and also colocalizes in the cell. Our results also show that the mutation affects the tertiary structure of the protein, resulting in a more open, unstable protein compared to the WT. Phosphoproteomic analysis of HEK cells overexpressing PKC⍺D463H show a decrease of phosphorylation specifically on proteins involved with cell-cell adhesion, including functionally relevant phosphosites. This is in line with our Co-IP mass spectrometry data which shows a decrease in interaction of PKC⍺D463H with proteins involved in cell junctions. The cell of origin, tanycytes, are highly specialized cells that contain important cell-cell junctions and therefore their perturbation could be a potential route of tumorigenesis. By understanding these changes integrated with our snRNAseq and bulk RNAseq of ChGs, and exploration in cellular models, we hope to elucidate the mechanism by which the mutation leads to the development of Chordoid Glioma. Citation Format: Charlotte Bellamy, Hannah Tovell, Florent Dingli, Damarys Loew, Stephane Liva, Selina Schwaighofer, Eduard Stefan, Alexandra Newton, Marc Sanson, Franck Bielle. Functional characterisation of a novel mutation in PRKCA, a major driver of chordoid gliomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4370.

Gp120-derived amyloidogenic peptides form amyloid fibrils that increase HIV-1 infectivity.

Apart from mediating viral entry, the function of the free HIV-1 envelope protein (gp120) has yet to be elucidated. Our group previously showed that EP2 derived from one β-strand in gp120 can form amyloid fibrils that increase HIV-1 infectivity. Importantly, gp120 contains ~30 β-strands. We examined whether gp120 might serve as a precursor protein for the proteolytic release of amyloidogenic fragments that form amyloid fibrils, thereby promoting viral infection. Peptide array scanning, enzyme degradation assays, and viral infection experiments in vitro confirmed that many β-stranded peptides derived from gp120 can indeed form amyloid fibrils that increase HIV-1 infectivity. These gp120-derived amyloidogenic peptides, or GAPs, which were confirmed to form amyloid fibrils, were termed gp120-derived enhancers of viral infection (GEVIs). GEVIs specifically capture HIV-1 virions and promote their attachment to target cells, thereby increasing HIV-1 infectivity. Different GAPs can cross-interact to form heterogeneous fibrils that retain the ability to increase HIV-1 infectivity. GEVIs even suppressed the antiviral activity of a panel of antiretroviral agents. Notably, endogenous GAPs and GEVIs were found in the lymphatic fluid, lymph nodes, and cerebrospinal fluid (CSF) of AIDS patients in vivo. Overall, gp120-derived amyloid fibrils might play a crucial role in the process of HIV-1 infectivity and thus represent novel targets for anti-HIV therapeutics.

Role of the leucine-rich repeat protein kinase 2 C-terminal tail in domain cross-talk.

Leucine-rich repeat protein kinase 2 (LRRK2) is a multi-domain protein encompassing two of biology's most critical molecular switches, a kinase and a GTPase, and mutations in LRRK2 are key players in the pathogenesis of Parkinson's disease (PD). The availability of multiple structures (full-length and truncated) has opened doors to explore intra-domain cross-talk in LRRK2. A helix extending from the WD40 domain and stably docking onto the kinase domain is common in all available structures. This C-terminal (Ct) helix is a hub of phosphorylation and organelle-localization motifs and thus serves as a multi-functional protein : protein interaction module. To examine its intra-domain interactions, we have recombinantly expressed a stable Ct motif (residues 2480-2527) and used peptide arrays to identify specific binding sites. We have identified a potential interaction site between the Ct helix and a loop in the CORB domain (CORB loop) using a combination of Gaussian accelerated molecular dynamics simulations and peptide arrays. This Ct-Motif contains two auto-phosphorylation sites (T2483 and T2524), and T2524 is a 14-3-3 binding site. The Ct helix, CORB loop, and the CORB-kinase linker together form a part of a dynamic 'CAP' that regulates the N-lobe of the kinase domain. We hypothesize that in inactive, full-length LRRK2, the Ct-helix will also mediate interactions with the N-terminal armadillo, ankyrin, and LRR domains (NTDs) and that binding of Rab substrates, PD mutations, or kinase inhibitors will unleash the NTDs.

Interaction of T-cell-specific adapter protein with Src- and Tec-family kinases.

Adapter proteins are flexible and dynamic modulators of cellular signalling that are important for immune cell function. One of these, the T-cell-specific adapter protein (TSAd), interacts with the non-receptor tyrosine kinases Src and Lck of the Src family kinases (SFKs) and Itk of the Tec family kinases (TFKs). Three tyrosine residues in the TSAd C-terminus are phosphorylated by Lck and serve as docking sites for the Src homology 2 (SH2) domains of Src and Lck. The TSAd proline-rich region (PRR) binds to the Src homology 3 (SH3) domains found in Lck, Src and Itk. Despite known interactors, the role TSAd plays in cellular signalling remains largely unknown. TSAd's ability to bind both SFKs and TFKs may point to its function as a general scaffold for both kinase families. Using GST-pulldown as well as peptide array experiments, we found that both the SH2 and SH3 domains of the SFKs Fyn and Hck, as well as the TFKs Tec and Txk, interact with TSAd. This contrasts with Itk, which interacts with TSAd only through its SH3 domain. Although our analysis showed that TSAd is both co-expressed and may interact with Fyn, we were unable to co-precipitate Fyn with TSAd from Jurkat cells, as detected by Western blotting and affinity purification mass spectrometry. This may suggest that TSAd-Fyn interaction in intact cells may be limited by other factors, such as the subcellular localization of the two molecules or the co-expression of competing binding partners.

Comprehensive Epitope Analysis of Monoclonal Antibodies Binding to Hen Egg Ovalbumin Using a Peptide Array

Food allergies are a significant health issue worldwide. In many countries, labeling of primary allergens in food products has been made mandatory to ensure consumer safety. In food manufacturing settings, the lateral flow immunoassay (LFI)—based on antigen–antibody reactions—is a rapid and accurate method for allergen testing and is widely used. Peptide arrays are tools that enable the synthesis of peptides of any sequence on a substrate and high-throughput analysis of their interactions with chemicals. This study aimed to investigate a new application of peptide arrays in the field of food technology, particularly in the development of antibodies for food allergen testing. First, monoclonal antibodies against hen egg ovalbumin, a major food allergen, were produced. Then, using a peptide array, the epitope and specificity of the antibodies were comprehensively and precisely analyzed. Finally, an LFI kit incorporating the antibodies demonstrated both high specificity and detection sensitivity for food allergen testing. These findings indicate that peptide arrays are valuable tools in the development of antibodies for food allergen testing, ensuring reliability and accuracy at the molecular level.

Highly heterogenous humoral immune response in Lyme disease patients revealed by broad machine learning-assisted antibody binding profiling with random peptide arrays.

Lyme disease (LD), a rapidly growing public health problem in the US, represents a formidable challenge due to the lack of detailed understanding about how the human immune system responds to its pathogen, the Borrelia burgdorferi bacterium. Despite significant advances in gaining deeper insight into mechanisms the pathogen uses to evade immune response, substantial gaps remain. As a result, molecular tools for the disease diagnosis are lacking with the currently available tests showing poor performance. High interpersonal variability in immune response combined with the ability of the pathogen to use a number of immune evasive tactics have been implicated as underlying factors for the limited test performance. This study was designed to perform a broad profiling of the entire repertoire of circulating antibodies in human sera at the single-individual level using planar arrays of short linear peptides with random sequences. The peptides sample sparsely, but uniformly the entire combinatorial sequence space of the same length peptides for profiling the humoral immune response to a B.burg. infection and compare them with other diseases with etiology similar to LD and healthy controls. The study revealed substantial variability in antibody binding profiles between individual LD patients even to the same antigen (VlsE protein) and strong similarity between individuals diagnosed with Lyme disease and healthy controls from the areas endemic to LD suggesting a high prevalence of seropositivity in endemic healthy control. This work demonstrates the utility of the approach as a valuable analytical tool for agnostic profiling of humoral immune response to a pathogen.

Human Hsp70 Substrate-Binding Domains Recognize Distinct Client Proteins.

The 13 Hsp70 proteins in humans act on unique sets of substrates with diversity often being attributed to J-domain-containing protein (Hsp40 or JDP) cofactors. We were therefore surprised to find drastically different binding affinities for Hsp70-peptide substrates, leading us to probe substrate specificity among the 8 canonical Hsp70s from humans. We used peptide arrays to characterize Hsp70 binding and then mined these data using machine learning to develop an algorithm for isoform-specific prediction of Hsp70 binding sequences. The results of this algorithm revealed recognition patterns not predicted based on local sequence alignments. We then showed that none of the human isoforms can complement heat-shocked DnaK knockout Escherichia coli cells. However, chimeric Hsp70s consisting of the human nucleotide-binding domain and the substrate-binding domain of DnaK complement during heat shock, providing further evidence in vivo of the divergent function of the Hsp70 substrate-binding domains. We also demonstrated that the differences in heat shock complementation among the chimeras are not due to loss of DnaJ binding. Although we do not exclude JDPs as additional specificity factors, our data demonstrate substrate specificity among the Hsp70s, which has important implications for inhibitor development in cancer and neurodegeneration.