Variable Region Fragments Research Articles

Targeted degradation of oncogenic BCR-ABL by silencing the gene of NEDD8 E3 ligase RAPSYN

Tyrosine kinase inhibitors have been the standard treatment for patients with Philadelphia chromosome-positive (Ph+) leukemia. However, a series of issues, including drug resistance, relapse and intolerance, are still an unmet medical need. Here, we report the targeted siRNA-based lipid nanoparticles in Ph+ leukemic cell lines for gene therapy of Ph+ leukemia, which specifically targets a recently identified NEDD8 E3 ligase RAPSYN in Ph+ leukemic cells to disrupt the neddylation of oncogenic BCR-ABL. To achieve the specificity for Ph+ leukemia therapy, a single-chain fragment variable region (scFv) of anti-CD79B monoclonal antibody was covalently conjugated on the surface of OA2-siRAPSYN lipid nanoparticles to generate the targeted lipid nanoparticles (scFv-OA2-siRAPSYN). Through effectively silencing RAPSYN gene in leukemic cell lines by the nanoparticles, BCR-ABL was remarkably degraded accompanied by the inhibition of proliferation and the promotion of apoptosis. The specific targeting, therapeutic effects and systemic safety were further evaluated and demonstrated in cell line-derived mouse models. The present study has not only addressed the clinical need of Ph+ leukemia, but also enabled gene therapy against a less druggable target.Graphical

Aqueous humour protein dysregulation in Asian eyes with primary open angle glaucoma

The pathophysiology of Primary Open Angle Glaucoma (POAG) remains poorly understood. Through proteomic analysis of aqueous humour (AH) from POAG patients, we aim to identify changes in protein composition of these samples compared to control samples.High resolution mass spectrometry-based TMT6plex quantitative proteomics analysis is performed on AH samples collected from POAG patients, and compared against a control group of patients with cataracts. Data are available via ProteomeXchange with identifier PXD033153.1589 proteins were quantified from the aqueous samples using Proteome Discoverer version 2.2 software. Among these proteins, 210 were identified as unique master proteins. The proteins which were up or down-regulated by ±3 fold-change were considered significant. Human neuroblastoma full-length cDNA clone CS0DD006YL02 was significantly upregulated in patients with severe POAG on >2 medications, while actin, cytoplasmic 1, V2-7 protein (fragment), immunoglobulin-like polypeptide 1 and phosphatidylethanolamine-binding protein 4 were only present in these patients with severe POAG on >2 medications.Beta-crystallin B1 and B2, Gamma-crystallin C, D and S were significantly downregulated in the severe POAG ≤2 glaucoma medications group.Beta-crystallin B2, Gamma-crystallin D and GCT-A9 light chain variable region (fragment) were significantly downregulated in the non-severe POAG group.Actin, cytoplasmic 1 was significantly upregulated in subjects with severe POAG who required more than 2 glaucoma medications. Crystallins (Beta-crystallin B1 and B2, Gamma-crystallin C, D and S) were significantly downregulated in subjects with severe POAG who required less than 2 glaucoma medications.

Abstract 1860: The smallest antibody class: Cow ultralong CDR3 knobs as a new class of biomolecule for therapeutics and diagnostics

Abstract Engineered antibodies, including bispecifics and ADCs, are now a major drug class for oncology and other therapeutic areas. There are two fundamental antibody fragments: the Fv (heavy and light chain variable region fragments, derived from most species), and VHH (heavy chain ‘only’ V regions, derived from camelids and sharks). Cows produce antibodies with an unusually long VH CDR3 region, which can be up to seventy amino acids in length and is comprised of a β-ribbon “stalk” and disulfide-bonded “knob” minidomain which sits atop the stalk. The knob region is highly diverse and can bind cryptic epitopes with high affinity. We recently developed the technology to produce knob domains independently of the antibody, and at ~5 kDa are the smallest functional antibody fragment (https://doi.org/10.1073/pnas.2303455120). The high stability and small size could enable improved tissue penetration and development of novel therapeutics, including knob-drug conjugates or extremely small bispecific molecules. Citation Format: Vaughn Smider. The smallest antibody class: Cow ultralong CDR3 knobs as a new class of biomolecule for therapeutics and diagnostics [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 1860.

EXTH-01. STEM CELL THERAPY FOR LEPTOMENINGEAL DISEASE

Abstract Leptomeningeal disease (LMD), known as carcinomatous meningitis, occurs in approximately 5% of all cancer patients. LMD presents an extremely poor prognosis, with an average life expectancy of 4-6 weeks. Although, whole brain/spinal cord irradiation and intrathecal injection of anticancer drugs are sometimes performed, the effects are limited, so new therapeutic strategies for LMD are urgently needed. We have reported that treatment using engineered stem cells (SCs) may be effective treatment option against LMD of breast cancer, lung cancer, and malignant melanoma, which are types of cancer that tends to metastasize to the central nervous system. Specifically, we reported that engineered allogeneic SCs simultaneously targeting epidermal growth factor receptor (EGFR) and death receptor (DR) has efficacy for LMD of triple negative breast cancer. Also, we reported that twin SCs releasing oncolytic herpes virus, granulocyte-macrophage colony-stimulating factor (GM-CSF), and single-chain variable region fragments (scFv) against PD-1 has efficacy in LMD of malignant melanoma. The greatest advantage of SC based therapeutic strategy for LMD is summarized by these facts: (1) LMD is a condition in which cancer cells spread within a single closed space through cerebrospinal fluid, and the SCs characteristic of homing to tumor cells has an advantage; (2) Repetitive intrathecal injection of drugs for patients is an invasive procedure, but SCs can continuously secrete/release therapeutic agents into the spinal cavity after a single injection. We believe that stem cell therapy has the potential to become a new therapeutic option for LMD in the future.

Secretion of 4-1BB Ligand Crosslinked to PD-1 Checkpoint Inhibitor Potentiates Chimeric Antigen Receptor T Cell Solid Tumor Efficacy.

Chimeric antigen receptor (CAR) T cell therapy has transformed the treatment of hematological malignancies but has yet to achieve similar success in solid tumors due to a lack of persistence and function in the tumor microenvironment. We previously reported the augmentation of CAR T cell therapy in an engineered solid tumor model through the secretion of anti-PD-1 single-chain fragment variable region (scFv), as shown by enhanced CAR T cell antitumor efficacy, expansion, and vitality. We have since improved the platform to create a superior cellular product-CAR T cells secreting single-chain trimeric 4-1BB ligand fused to anti-PD-1 scFv (αPD1-41BBL). 4-1BB signaling promotes cytotoxic T lymphocyte proliferation and survival but targeting 4-1BB with agonist antibodies in the clinic has been hindered by low antitumor activity and high toxicity. CAR T cells using 4-1BB endodomain for costimulatory signals have demonstrated milder antitumor response and longer persistence compared to CAR T cells costimulated by CD28 endodomain. We have, for the first time, engineered CD28-costimulated CAR T cells to secrete a fusion protein containing the soluble trimeric 4-1BB ligand. In vitro and in vivo, CAR19.αPD1-41BBL T cells exhibited reduced inhibitory receptor upregulation, enhanced persistence and proliferation, and a less differentiated memory status compared to CAR T cells without additional 4-1BB:4-1BBL costimulation. Accordingly, CAR19.αPD1-41BBL T cell-treated mice displayed significantly improved tumor growth control and overall survival. Spurred on by our preclinical success targeting CD19 as a model antigen, we produced mesothelin-targeting CAR T cells and confirmed the enhanced solid tumor efficacy of αPD1-41BBL-secreting CAR T cells.

Yeast biopanning against site-specific phosphorylations in tau.

The detection of site-specific phosphorylation in the microtubule-associated protein tau is emerging as a means to diagnose and monitor the progression of Alzheimer's Disease and other neurodegenerative diseases. However, there is a lack of phospho-specific monoclonal antibodies and limited validation of their binding specificity. Here, we report a novel approach using yeast biopanning against synthetic peptides containing site-specific phosphorylations. Using yeast cells displaying a previously validated phospho-tau (p-tau) single-chain variable region fragment (scFv), we show selective yeast cell binding based on single amino acid phosphorylation on the antigen. We identify conditions that allow phospho-specific biopanning using scFvs with a wide range of affinities (KD = 0.2 to 60 nM). Finally, we demonstrate the capability of screening large libraries by performing biopanning in 6-well plates. These results show that biopanning can effectively select yeast cells based on phospho-site specific antibody binding, opening doors for the facile identification of high-quality monoclonal antibodies.

Antibody-based Radiopharmaceuticals as Theranostic Agents: An Overview.

Since the inception of antibodies as magic bullets for targeting antigens with high specificity for various in vitro and in-vivo detection and therapy applications, the field has evolved, and remarkable success has been achieved not only in the methods of development of these targeting agents but also in their applications. The utilization of these moieties for the development of antibody-based radiopharmaceuticals for diagnostic and therapy (theranostic) purposes has resulted in the availability of various cancer-targeting agents suitable for clinical applications. The high affinity and specificity of antibodies towards the target antigens overexpressed on tumors render them an excellent carrier molecules for radionuclide delivery. Although intact antibodies have high potential as imaging and therapeutic agents, a major drawback of intact antibody-based radionuclide targeting is their slow pharmacokinetics and poor penetration into solid tumors. In contrast to large intact antibodies, engineered antibody fragments, such as minibodies, diabodies, single-chain variable region fragments (scFvs), nanobodies, and non-antibody protein scaffolds-based moieties, retain the specificities and affinities of intact antibodies in addition to improved pharmacokinetics for imaging and therapy of solid tumors. These engineered carrier molecules are not only amenable for simple and robust radiolabeling procedures but also provide high contrast images with minimal radiotoxicity to vital organs. However, in various instances, rapid clearance with sub-optimal tumor accumulation, limiting renal dose, and cross-reactivity of these radiolabeled engineered smaller molecules have also been observed. Herein, we review current knowledge of the recent methods for the development of antibody-based targeting moieties, the suitability of various engineered formats for targeting tumors, and radiolabeling strategies for the development of radioformulations. We discuss promising antibody-based and non-antibody- based affibody radiopharmaceuticals reported for clinical applications. Finally, we highlight how emerging technologies in antibody engineering and drug development can be amalgamated for designing novel strategies for cancer imaging and therapy.

Gold nanoparticles-decorated M13 phage SPR probe for dual detection of antigen biomarkers in serum

Label-free SPR is rarely used for biomarker detection in real samples due to its low sensitivity. Herein, we report a phage-based SPR (P-SPR) strategy for the detection of carcinoembryonic antigen (CEA) in undiluted serums. M13 phage is genetically engineered to display an anti-CEA single-chain variable region fragment on pIII protein for antigen targeting and to display the gold binding peptide (GBP) at the pVIII protein for gold nanoparticles (GNPs) binding to form the GNPs decorated M13 phage probe that can amplify the plasmon resonance signal. The proposed P-SPR method demonstrated ultrasensitive detection of CEA within 10 min. Under ideal conditions, P-SPR showed exceptional sensitivity with a limit of detection (LOD) of 0.83 fM, which is approximately 2000 times that of the conventional SPR and four orders of magnitude more sensitive than enzyme-linked immunosorbent assay. In particular, the proposed strategy can cross-validate the SPR results through naked-eye counting of the plaques generated by the P-SPR probes, enabling a reliable dual detection system. In addition, P-SPR scheme has excellent sensing performance for the detection of real samples at concentrations lower than LOD of ELISA. Therefore, the proposed P-SPR strategy holds potential for early detection of tumour biomarkers in liquid biopsy.

Modified Therapeutic Antibodies: Improving Efficacy

Abstract The prosperity of the biotherapeutics market reflects the feasibility and effectiveness of therapeutic antibodies for the treatment of cancers, inflammatory disorders, and refractory infections. As drawbacks emerge in clinical trials and practice, such as impeded binding, reduced effector functions, and frequent adverse reactions, modifications of therapeutic antibodies are unprecedently burgeoning in research and development (RD ② fragment of crystallizable domain (Fc) amino acid alterations; ③ cross-isotype or cross-subclass exchanges; ④ antibody–drug conjugates (ADCs); ⑤ single chain of variable region fragment (scFv) for chimeric antigen receptor T (CAR-T) cells; and ⑥ bispecific antibodies (bsAbs) in order to promote binding affinity, half-life in circulation, effectiveness toward target cells and, ultimately, to achieve overall improved efficacy. While many achievements have been made around the world in the past decades, China has been playing an active role in this realm, with its great demand for biotherapeutics with R&D potential. This review recapitulates the international progress that has been achieved with modified therapeutic antibodies, and then focuses on that of China in an independent section.

Detection of a single circulating tumor cell using a genetically engineered antibody-like phage nanofiber probe

Detection of circulating tumor cells (CTCs), at the single-cell level, can be of great value for subsequent treatment of tumors but remains a significant challenge. Herein, we report a phage-based detection strategy for the identification of single CTC. The key assay component is the flexible recombinant M13@anti-CEA-scFv probe (M13, CEA, and scFv stand for M13 phage, carcinoembryonic antigen, and single-chain variable region fragment, respectively), which has a high, monoclonal antibody-like binding affinity for tumor cell-expressed CEA antigen, as confirmed by enzyme-linked immunosorbent assay (ELISA). Cell immunofluorescence experiments by confocal microscopy also demonstrate that the M13@anti-CEA-scFv could specifically bind to CEA-positive colon cancer cells such as Caco-2 and HT29, instead of CEA-negative HEK293T cells even when in great excess. Quantitative polymerase chain reaction (qPCR) further proves the ability to pin down single Caco-2 cell in 1 mL of spiked samples by 1,000 copies of M13@anti-CEA-scFv probe, after merely 15 min incubation. Another probe, the rigid magnetic microparticle (MMP), loaded with anti-CEA antibody, is used for the initial screening of the single CTC, which is mixed with numerous lymphocytes. The CEA on the resultant MMPs/CTC complex is subsequently recognized by numerous copies of M13@anti-CEA-scFv to form an MMP/CTC/M13@anti-CEA-scFv sandwich complex. Probing the phage DNA in this complex by qPCR leads to the unambiguous identification of the single Caco-2 cell in 1 mL of spiked blood samples. The phage-based detection strategy holds promise for the single-cell detection of any CTCs since the scFv displayed at the end of phage can be customized to the unique antigen of a specific CTC.

Construction of a full-length antibody phage display vector

Antibody phage display technology plays an important role in the development of monoclonal antibodies, humanization, and affinity evolution of antibodies. Thus far, antibody phage display mainly focuses on the display of antibody variable region or antigen-binding fragments. In this study, we constructed a new phage display system that can display full-length IgG antibodies on M13 phage. The phage display vector contains open reading frames (ORFs) encoding full-length the heavy and light chains of the antibody. NcoI/XhoI restriction enzyme sites were used to clone the variable region of the heavy chain into the heavy chain ORF, and SalI/NotI sites were used to clone the light chain variable region. SnaBI and SbfI restriction enzyme sites were designed between the cloning sites of heavy and light chains, respectively, to increase the cloning efficiency. The full-length antibodies of nivolumab against programmed death factor 1, trastuzumab against human epidermal growth factor 2, diL2K against the cluster of differentiation 3 epsilon, and adalimumab against tumor necrosis factor- alpha were displayed on phage with the vector. Phage-displayed antibodies showed their original antigen-binding activity. An amber codon shifted the vector to express IgG in non-suppressed Escherichia coli. The heavy and light chains of the E. coli-expressed antibodies could be detected through western blotting, and the antigen-binding activity was confirmed using an enzyme-linked immunosorbent assay. Biopanning was carried out with a model phage display antibody library, and the results showed that the novel phage system could be used for antibody library construction and highly efficient antibody screening. The reported system is the first full-length antibody phage display system.

Development of diagnostic antibodies against immunoglobulin heavy chain variable region for heavy chain amyloidosis (AH amyloidosis).

It is difficult to diagnose immunoglobulin heavy chain amyloidosis (AH amyloidosis) without proteomic analysis due to no useful diagnostic antibodies. The aim of this study was to develop diagnostic antibodies available to immunohistochemistry and immunoblotting. Two rabbit anti-heavy chain variable region antibodies were generated and evaluated in immunohistochemical studies performed on 11 AH amyloidosis patients and 64 patients with other systemic amyloidoses. Additionally, immunoblotting was performed using extracted amyloid protein from one patient and serum samples from two patients with AH amyloidosis. Immunohistochemical analysis generated a positive outcome in 10 of 11 AH amyloidosis patients (sensitivity 90.9%). While positive staining was also observed in 9 of 64 non-AH amyloidosis patients (specificity 85.9%), substitution of the blocking agent reversed the positive reactivity in 5 of 9 patients. Amyloid protein band was clearly detected via immunoblotting analysis, and protein bands with similar molecular weights of amyloid protein were observed in serum samples from patients with AH amyloidosis. The two antibodies may represent a powerful diagnostic tool for AH amyloidosis. In addition, our data revealed the existence of amyloidogenic variable region fragments in the serum of patients, suggesting their potential as diagnostic markers for AH amyloidosis.

An immunotoxin targeting Ebola virus glycoprotein inhibits Ebola virus production from infected cells.

Ebola virus (EBOV), a member of the mononegaviral family Filoviridae, causes severe disease associated with high lethality in humans. Despite enormous progress in development of EBOV medical countermeasures, no anti-EBOV treatment has been approved. We designed an immunotoxin in which a single-chain variable region fragment of the EBOV glycoprotein-specific monoclonal antibody 6D8 was fused to the effector domains of Pseudomonas aeruginosa exotoxin A (PE38). This immunotoxin, 6D8-PE38, bound specifically to cells expressing EBOV glycoproteins. Importantly, 6D8-PE38 targeted EBOV-infected cells, as evidenced by inhibition of infectious EBOV production from infected cells, including primary human macrophages. The data presented here provide a proof of concept for immunotoxin-based targeted killing of infected cells as a potential antiviral intervention for Ebola virus disease.

An Open Sandwich Immunochromatography for Non-competitive Detection of Small Antigens.

Immunochromatography assay is an easy and rapid on-site detection method. However, conventional sandwich immunochromatographies using two antibodies can only detect target molecules above a threshold size. Small molecules below 1000 in molecular weight are usually detected using competitive immunoassay. However, competitive immunoassay is not suitable for visual detection of low concentration samples. Based on the principles of open sandwich immunoassay, which detects small molecules via interchain interaction of separated variable region fragments (VH and VL) from a single antibody, we developed non-competitive open sandwich immunochromatography. Bone Gla protein (BGP)-C7, a peptide containing the seven C-terminal amino acids of human osteocalcin, was selected as the target. By using VL fragments fixed on a nitrocellulose membrane, and colored cellulose bead-labeled VH fragments, we specifically detected 10 ng/mL of BGP-C7. This is the first report of open sandwich immunochromatography, which is an easy and rapid method for on-site, signal-on detection of small molecules.

Identification of an anti–SARS–CoV-2 receptor-binding domain–directed human monoclonal antibody from a naïve semisynthetic library

There is a desperate need for safe and effective vaccines, therapies, and diagnostics for SARS– coronavirus 2 (CoV-2), the development of which will be aided by the discovery of potent and selective antibodies against relevant viral epitopes. Human phage display technology has revolutionized the process of identifying and optimizing antibodies, providing facile entry points for further applications. Herein, we use this technology to search for antibodies targeting the receptor-binding domain (RBD) of CoV-2. Specifically, we screened a naïve human semisynthetic phage library against RBD, leading to the identification of a high-affinity single-chain fragment variable region (scFv). The scFv was further engineered into two other antibody formats (scFv-Fc and IgG1). All three antibody formats showed high binding specificity to CoV-2 RBD and the spike antigens in different assay systems. Flow cytometry analysis demonstrated specific binding of the IgG1 format to cells expressing membrane-bound CoV-2 spike protein. Docking studies revealed that the scFv recognizes an epitope that partially overlaps with angiotensin-converting enzyme 2 (ACE2)–interacting sites on the CoV-2 RBD. Given its high specificity and affinity, we anticipate that these anti-CoV-2 antibodies will be useful as valuable reagents for accessing the antigenicity of vaccine candidates, as well as developing antibody-based therapeutics and diagnostics for CoV-2.

PM Q-probe: A fluorescent binding protein that converts many antibodies to a fluorescent biosensor

Quenchbody (Q-body) is a fluorescent biosensor in which a fluorescent dye is tagged near the antigen binding site of an antibody. The fluorescence of the dye is quenched by the tryptophan residues present in the variable region of the antibody, and is recovered when the antigen binds. Q-bodies have been prepared using recombinant DNA technology by introducing one or more tag sequence(s) at either the N-terminal of the Fab or the single chain variable region fragment of the antibody, and labeling the tag with a fluorescent dye. However, preparation of recombinant antibody fragments is time-consuming and the performance of the Q-body is unpredictable. Here we report an antibody-binding quenching probe made from protein M from Mycoplasma genitalium that can transform the IgG antibody into an immunosensor. By using bacterially expressed and purified protein M and labeling the C-terminal cysteine-containing tag, we prepared a TAMRA-labeled PM Q-probe. When the Q-probe was incubated with Fab or IgG recognizing the bone Gla protein, the fluorescence of the probe was quenched and subsequently recovered by the adding of antigens in a dose-dependent manner. We also succeeded in detecting several small biomarkers with nanomolar sensitivity, including thyroxine extracted from human serum. The clone found to be suitable for the detection of cortisol was confirmed to work as a recombinant Q-body as well, which also worked in 50% human serum. The results suggest that the Q-probe can quickly convert an IgG to a biosensor, which will be useful in rapid diagnosis of small biomarkers.

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Administration of recombinant single chain fragment of variable region (hScFv) of IgG suppresses development of murine vasculitis induced with Candida albicans water-soluble fraction: An animal model of Kawasaki disease.

Administration of recombinant single chain fragment of variable region (hScFv) of IgG suppresses development of murine vasculitis induced with Candida albicans water-soluble fraction: An animal model of Kawasaki disease.

Intrabody-based FRET probe to visualize endogenous histone acetylation

Post-translational histone modifications are major regulators of gene expression. However, conventional immunoassays do not provide sufficient information regarding their spatial and temporal dynamic changes. Fluorescence/Förster resonance energy transfer (FRET)-based probes are capable of monitoring the dynamic changes associated with histone modifications in real-time by measuring the balance between histone-modifying enzyme activities. Recently, a genetically encoded histone-modification fluorescent probe using a single-chain variable region (scFv) fragment of a specific antibody was developed. The probe, modification-specific intracellular antibody, is capable of monitoring histone-acetylation levels in both cultured cells and living organisms based on the ratio of fluorescence intensities between the cell nucleus and cytoplasm. In this study, we constructed a FRET probe composed of yellow fluorescent protein attached at the N-terminus of an acetyl H3K9-specific scFv, tethered to a cyan fluorescent protein. When the FRET probe was expressed in human cells, both FRET efficiency and fluorescence intensity in the nucleus increased following histone-deacetylase inhibitor treatment. Using these two parameters, endogenous histone-acetylation levels were quantified over a high dynamic range. This probe provides a simple approach to quantify spatial and temporal dynamic changes in histone acetylation.

Cancer cell killing by target antigen engagement with engineered complementary intracellular antibody single domains fused to pro-caspase3

Many tumour causing proteins, such as those expressed after chromosomal translocations or from point mutations, are intracellular and are not enzymes per se amenable to conventional drug targeting. We previously demonstrated an approach (Antibody-antigen Interaction Dependent Apoptosis (AIDA)) whereby a single anti-β-galactosidase intracellular single chain Fv antibody fragment, fused to inactive procaspase-3, induced auto-activation of caspase-3 after binding to the tetrameric β-galactosidase protein. We now demonstrate that co-expressing an anti-RAS heavy chain single VH domain, that binds to mutant RAS several thousand times more strongly than to wild type RAS, with a complementary light chain VL domain, caused programmed cell death (PCD) in mutant RAS expressing cells when each variable region is fused to procaspase-3. The effect requires binding of both anti-RAS variable region fragments and is RAS-specific, producing a tri-molecular complex that auto-activates the caspase pathway leading to cell death. AIDA can be generally applicable for any target protein inside cells by involving appropriate pairs of antigen-specific intracellular antibodies.