Plasma acylcarnitines and amino acids in dyslipidemia: An integrated metabolomics and machine learning approach.

Purpose: The Discovery of underlying intermediates associated with the development of dyslipidemia results in a better understanding of pathophysiology of dyslipidemia and their modification will be a promising preventive and therapeutic strategy for the management of dyslipidemia. Methods: The entire dataset was selected from the Surveillance of Risk Factors of Noncommunicable Diseases (NCDs) in 30 provinces of Iran (STEPs 2016 Country report in Iran) that included 1200 subjects and was stratified into four binary classes with normal and abnormal cases based on their levels of triglyceride (TG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), and non-HDL-C.Plasma concentrations of 20 amino acids and 30 acylcarnitines in each class of dyslipidemia were evaluated using Tandem mass spectrometry. Then, these attributes, along with baseline characteristics data, were used to check whether machine learning (ML) algorithms could classify cases and controls. Results: Our ML framework accurately predicts TG binary classes. Among the models tested, the SVM model stood out, performing slightly better with an AUC of 0.81 and a standard deviation of test accuracy at 0.04. Consequently, it was chosen as the optimal model for TG classification. Moreover, the findings showed that alanine, phenylalanine, methionine, C3, C14:2, and C16 had great power in differentiating patients with high TG from normal TG controls. Conclusions: The comprehensive output of this work, along with sex-specific attributes, will improve our understanding of the underlying intermediates involved in dyslipidemia. Supplementary Information: The online version contains supplementary material available at 10.1007/s40200-024-01384-9.

An Anti-TAZ Monoclonal Antibody Recognizing Cell Surface Expressed TAZ Protein in Human Tumor Cells.

Background: WWTR1 or TAZ is a transcriptional co-activator protein expressed in cytoplasm which functions as the main downstream effector of the Hippo signaling pathway. This pathway is an evolutionally conserved signal cascade, which plays a pivotal role in organ size control and tumorigenesis. Ectopic expression of TAZ has already been observed in many malignancies, while the ectopic localization of TAZ is reported for the first time. The aim of this study was to produce a specific monoclonal antibody (mAb) against a synthetic peptide derived from WWTR1 protein to be used as a research tool in human carcinomas. Methods: A 21-mer synthetic peptide (derived from human TAZ protein) was used for immunization of BALB/c mice after conjugation with Keyhole Limpet Haemocyanin (KLH) using hybridoma technology. The generated mAb reacted with the immunizing peptide employing ELISA assay. The reactivity of the antibody with native TAZ protein was assessed through Western blot, immunocytochemistry, and flow cytometry using different cancer cell lines. Results: The produced mAb could recognize the immunizing peptide in ELISA and Kaff was 0.6×10-9 M. The produced anti-TAZ mAb unlike available commercial anti-TAZ antibody, was capable of specifically recognizing cell surface TAZ in human carcinoma cell lines including MCF-7, Raji, and A431 in Western blot, immunocytochemistry, and flow cytometry assays. As expected, no reactivity was observed using normal Peripheral Blood Mononuclear Cell (PBMC) from healthy donors. Conclusion: Based on the results, TAZ is ectopically expressed on the surface of tumor cell lines which is not the case in normal cells. The generated mAb has a potential to be used as a research tool in studying the expression of TAZ in human carcinomas in different applications.

Design of a dual-function agent by fusing a designed anti-VEGF-A binder and CPG-2 enzyme.

Anti-VEGF therapies are common for the treatment of cancer. Carboxypeptidase G (CPG-2) enzyme is a zinc-dependent metalloenzyme that metabolizes non-toxic synthetic 'benzoic mustard prodrugs' to cytotoxic moieties in tumor cells. In this study, we designed a dual-activity agent by combining a designed anti-VEGF- and CPG-2 enzyme to convert methotrexate (MTX). VEGF-A was docked against a set of scaffolds, and suitable inverse rotamers were made. Rosetta design was used for the interface design. The top 1200 binders were chosen by flow cytometry and displayed in yeast. The activity of CPG-2 enzyme was analyzed at different temperature conditions and in the presence of the substrate, MTX. Optimal binders were selected and protein was eluted using immobilized metal affinity chromatography and size-exclusion chromatography. Both, native PAGE and on-yeast flow cytometry confirmed the binding of the binder to VEGF-A. The activity of truncated enzymes was slightly lower than that of full-length enzymes linked to VEGF-A. The method should be generally useful as a dual-activity agent for targeting VEGF-A and combination therapy with the enzyme CPG-2 for metabolizing non-toxic prodrugs to cytotoxic moieties.Communicated by Ramaswamy H. Sarma.

A novel ADC targeting cell surface fibromodulin in a mouse model of triple-negative breast cancer.

BACKGROUND: Triple-negative breast cancers (TNBCs) are highly aggressive and metastatic. To date, finding efficacious targeted therapy molecules might be the only window of hope to cure cancer. Fibromodulin (FMOD), is ectopically highly expressed on the surface of Chronic Lymphocytic Leukemia (CLL) and bladder carcinoma cells; thus, it could be a promising molecule for targeted therapy of cancer. The objective of this study was to evaluate cell surface expression of FMOD in two TNBC cell lines and develop an antibody-drug conjugate (ADC) to target FMOD positive TNBC in vitro and in vivo. MATERIALS AND METHODS: Two TNBC-derived cell lines 4T1 and MDA-MB-231 were used in this study. The specific binding of anti-FMOD monoclonal antibody (mAb) was evaluated by flow cytometry and its internalization was verified using phAb amine reactive dye. A microtubulin inhibitor Mertansine (DM1) was used for conjugation to anti-FMOD mAb. The binding efficacy of FMOD-ADC was assessed by immunocytochemistry technique. The anti-FMOD mAb and FMOD-ADC apoptosis induction were measured using Annexin V-FITC and flow cytometry. Tumor growth inhibition of anti-FMOD mAb and FMOD-ADC was evaluated using BALB/c mice injected with 4T1 cells. RESULTS: Our results indicate that both anti-FMOD mAb and FMOD-ADC recognize cell surface FMOD molecules. FMOD-ADC could induce apoptosis in 4T1 and MDA-MB-231 cells in vitro. In vivo tumor growth inhibition was observed using FMOD-ADC in 4T1 inoculated BALB/c mice. CONCLUSION: Our results suggests high cell surface FMOD expression could be a novel bio-marker TNBCs. Furthermore, FMOD-ADC could be a promising candidate for targeting TNBCs.

Screening of candidate genes associated with high titer production of oncolytic measles virus based on systems biology approach.

The number of viral particles required for oncolytic activity of measles virus (MV) can be more than a million times greater than the reported amount for vaccination. The aim of the current study is to find potential genes and signaling pathways that may be involved in the high-titer production of MV. In this study, a systems biology approach was considered including collection of gene expression profiles from the Gene Expression Omnibus (GEO) database, obtaining differentially expressed genes (DEGs), performing gene ontology, functional enrichment analyses, and topological analyses on the protein-protein interaction (PPI) network. Then, to validate the in-silico data, total RNA was isolated from five cell lines, and full-length cDNA from template RNA was synthesized. Subsequently, quantitative reverse transcription-PCR (RT-qPCR) was employed. We identified five hub genes, including RAC1, HSP90AA1, DNM1, LTBP1, and FSTL1 associated with the enhancement in MV titer. Pathway analysis indicated enrichment in PI3K-Akt signaling pathway, axon guidance, proteoglycans in cancer, regulation of actin cytoskeleton, focal adhesion, and calcium signaling pathways. Upon verification by RT-qPCR, the relative expression of candidate genes was generally consistent with our bioinformatics analysis. Hub genes and signaling pathways may be involved in understanding the pathological mechanisms by which measles virus manipulates host factors in order to facilitate its replication. RAC1, HSP90AA1, DNM1, LTBP1, and FSTL1 genes, in combination with genetic engineering techniques, will allow the direct design of high-throughput cell lines to answer the required amounts for the oncolytic activity of MV.

Binder design for targeting SARS-CoV-2 spike protein: An in silico perspective.

INTRODUCTION: The COVID-19 pandemic is now affecting all people around the world and getting worse. New antiviral medications are desperately needed other than the few approved medications that have shown no promising efficacy so far. METHODS: Here we report three blocking binders for targeting SARS-CoV-2 spike protein to block the interaction between the spike protein on the SARS-CoV-2 and the angiotensin-converting enzyme 2 (ACE2) receptors, responsible for viral homing into the alveolar epithelium type II cells (AECII). RESULTS: The design process is based on the collected natural scaffolds and using Rosetta interface for designing the binders. CONCLUSION: Based on the structural analysis, three binders were selected, and the results showed that they might be promising as new therapeutic targets for blocking COVID-19.

Designed proteins assemble antibodies into modular nanocages.

Multivalent display of receptor-engaging antibodies or ligands can enhance their activity. Instead of achieving multivalency by attachment to preexisting scaffolds, here we unite form and function by the computational design of nanocages in which one structural component is an antibody or Fc-ligand fusion and the second is a designed antibody-binding homo-oligomer that drives nanocage assembly. Structures of eight nanocages determined by electron microscopy spanning dihedral, tetrahedral, octahedral, and icosahedral architectures with 2, 6, 12, and 30 antibodies per nanocage, respectively, closely match the corresponding computational models. Antibody nanocages targeting cell surface receptors enhance signaling compared with free antibodies or Fc-fusions in death receptor 5 (DR5)-mediated apoptosis, angiopoietin-1 receptor (Tie2)-mediated angiogenesis, CD40 activation, and T cell proliferation. Nanocage assembly also increases severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pseudovirus neutralization by α-SARS-CoV-2 monoclonal antibodies and Fc-angiotensin-converting enzyme 2 (ACE2) fusion proteins.

Designed proteins assemble antibodies into modular nanocages.

Antibodies are widely used in biology and medicine, and there has been considerable interest in multivalent antibody formats to increase binding avidity and enhance signaling pathway agonism. However, there are currently no general approaches for forming precisely oriented antibody assemblies with controlled valency. We describe the computational design of two-component nanocages that overcome this limitation by uniting form and function. One structural component is any antibody or Fc fusion and the second is a designed Fc-binding homo-oligomer that drives nanocage assembly. Structures of 8 antibody nanocages determined by electron microscopy spanning dihedral, tetrahedral, octahedral, and icosahedral architectures with 2, 6, 12, and 30 antibodies per nanocage match the corresponding computational models. Antibody nanocages targeting cell-surface receptors enhance signaling compared to free antibodies or Fc-fusions in DR5-mediated apoptosis, Tie2-mediated angiogenesis, CD40 activation, and T cell proliferation; nanocage assembly also increases SARS-CoV-2 pseudovirus neutralization by α-SARS-CoV-2 monoclonal antibodies and Fc-ACE2 fusion proteins. We anticipate that the ability to assemble arbitrary antibodies without need for covalent modification into highly ordered assemblies with different geometries and valencies will have broad impact in biology and medicine.