Development of antibodies against the notch ligand Delta-Like-1 by phage display with activity against breast cancer cells

Notch signalling is a well-established oncogenic pathway, and its ligand Delta-like 1 (DLL1) is overexpressed in estrogen receptor-positive (ER⁺) breast cancers and associated with poor patient prognosis. Hence, DLL1 has become an interesting therapeutic target for breast cancer. Here, the development of specific functional blocking anti-DLL1 antibodies with potential activity against ER⁺ breast cancer cells is reported. Human DLL1 proteins, containing the essential regions for binding to the Notch receptor and Notch signalling activation, were produced and used to select specific scFv antibody fragments by phage display. Fifteen unique scFvs were identified and reformatted into full IgGs. Characterization of these antibodies by ELISA, surface plasmon resonance and flow cytometry enabled selection of three specific anti-DLL1 IgGs, sharing identical VH regions, with nM affinities. Cellular assays on ER⁺ breast cancer MCF-7 cells showed that one of the IgGs (IgG-69) was able to partially impair DLL1-mediated activation of the Notch pathway, as determined by Notch reporter and RT-qPCR assays, and to attenuate cell growth. Treatment of MCF-7 cells with IgG-69 reduced mammosphere formation, suggesting that it decreases the breast cancer stem cell subpopulation. These results support the use of this strategy to develop and identify potential anti-DLL1 antibodies candidates against breast cancer.

Production of high-quality SARS-CoV-2 antigens: Impact of bioprocess and storage on glycosylation, biophysical attributes, and ELISA serologic tests performance

Serological assays are valuable tools to study SARS-CoV-2 spread and, importantly, to identify individuals that were already infected and would be potentially immune to a virus reinfection. SARS-CoV-2 Spike protein and its receptor binding domain (RBD) are the antigens with higher potential to develop SARS-CoV-2 serological assays. Moreover, structural studies of these antigens are key to understand the molecular basis for Spike interaction with angiotensin converting enzyme 2 receptor, hopefully enabling the development of COVID-19 therapeutics. Thus, it is urgent that significant amounts of this protein became available at the highest quality. In this study, we produced Spike and RBD in two human derived cell hosts: HEK293-E6 and Expi293F™. We evaluated the impact of different and scalable bioprocessing approaches on Spike and RBD production yields and, more importantly, on these antigens' quality attributes. Using negative and positive sera collected from human donors, we show an excellent performance of the produced antigens, assessed in serologic enzyme-linked immunosorbent assay (ELISA) tests, as denoted by the high specificity and sensitivity of the test. We show robust Spike productions with final yields of approx. 2 mg/L of culture that were maintained independently of the production scale or cell culture strategy. To the best of our knowledge, the final yield of 90 mg/L of culture obtained for RBD production, was the highest reported to date. An in-depth characterization of SARS-CoV-2 Spike and RBD proteins was performed, namely the antigen's oligomeric state, glycosylation profiles, and thermal stability during storage. The correlation of these quality attributes with ELISA performance show equivalent reactivity to SARS-CoV-2 positive serum, for all Spike and RBD produced, and for all storage conditions tested. Overall, we provide straightforward protocols to produce high-quality SARS-CoV-2 Spike and RBD antigens, that can be easily adapted to both academic and industrial settings; and integrate, for the first time, studies on the impact of bioprocess with an in-depth characterization of these proteins, correlating antigen's glycosylation and biophysical attributes to performance of COVID-19 serologic tests.

Repair of Iron Centers RIC protein contributes to the virulence of Staphylococcus aureus

RICs are a family of bacterial proteins involved in the repair of iron centers containing proteins damaged by the antimicrobial reactive species liberated by the innate immune system of infected hosts. Staphylococcus aureus is a human pathogen with increasing antibiotic resistance that also contains a RIC-like protein. In this work, we show that the survival of S. aureus within macrophages decreases upon inactivation of ric, and that the viability was restored to levels similar to the wild-type strain by reintroduction of ric via in trans complementation. Importantly, in macrophages that do not produce reactive oxygen species, the lower survival of the ric mutant was no longer observed. In lung epithelial cells, the intracellular viability of the S. aureus ric mutant was also shown to be lower than that of the wild-type. The wax moth larvae Galleria mellonella infected with S. aureus ric mutant presented an approximately 2.5-times higher survival when compared to the wild-type strain. Moreover, significantly lower bacterial loads were determined in the larvae hemolymph infected with strains not expressing ric, and complementation assays confirmed that this behavior was related to RIC. Furthermore, expression of the S. aureus ric gene within the larvae increased along the course of infection with a ~20-fold increase after 8 h of infection. Altogether, the data show that RIC is important for the virulence of S. aureus.

Examining the antimicrobial activity and toxicity to animal cells of different types of CO-releasing molecules

Transition metal carbonyl complexes used as CO-releasing molecules (CORMs) for biological and therapeutic applications may exhibit interesting antimicrobial activity. However, understanding the chemical traits and mechanisms of action that rule this activity is required to establish a rationale for the development of CORMs into useful antibiotics. In this work the bactericidal activity, the toxicity to eukaryotic cells, and the ability of CORMs to deliver CO to bacterial and eukaryotic cells were analysed for a set of seven CORMs that differ in the transition metal, ancillary ligands and the CO release profile. Most of these CORMs exhibited bactericidal properties that decrease in the following order: CORM-2 > CORM-3 > ALF062 > ALF850 > ALF186 > ALF153 > [Fe(SBPy3)(CO)](BF4)2. A similar yet not entirely coincident decreasing order was found for their induction of intracellular reactive oxygen species (ROS) in E. coli. In contrast, studies in model animal cells showed that for any given CORM, the level of intracellular ROS generated was negligible when compared with that measured inside bacteria. Importantly, these CORMs were in general not toxic to eukaryotic cells, namely murine macrophages, kidney LLC-PK1 epithelial cells, and liver cell line HepG2. CORM-2 and CORM-3 delivered CO to the intracellular space of both E. coli and the two types of tested eukaryotic cells, yet toxicity was only elicited in the case of E. coli. CO delivered by ALF186 into the intercellular space did not enter E. coli cells and the compound was not toxic to either bacteria or to eukaryotic cells. The Fe(ii) carbonyl complex [Fe(SBPy3)(CO)](2+) had the reverse, undesirable toxicity profile, being unexpectedly toxic to eukaryotic cells and non-toxic to E. coli. ALF153, the most stable complex in the whole set, was essentially devoid of toxicity or ROS induction ability in all cells. These results suggest that CORMs have a relevant therapeutic potential as antimicrobial drugs since (i) they can show opposite toxicity profiles towards bacteria and eukaryotic cells; (ii) their activity can be modulated through manipulation of the ancillary ligands, as shown with the three {Ru(CO)3}(2+) and two zerovalent Mo based CORMs; and (iii) their toxicity to eukaryotic cells can be made acceptably low. With this new approach, this work contributes to the understanding of the roots of the bactericidal action of CORMs and helps in establishing strategies for their development into a new class of antibiotics.

Trichomonas vaginalis Repair of Iron Centres Proteins: The Different Role of Two Paralogs

Trichomonas vaginalis, the causative parasite of one of the most prevalent sexually transmitted diseases is, so far, the only protozoan encoding two putative Repair of Iron Centres (RIC) proteins. Homologs of these proteins have been shown to protect bacteria from the chemical stress imposed by mammalian immunity. In this work, the biochemical and functional characterisation of the T. vaginalis RICs revealed that the two proteins have different properties. Expression of ric1 is induced by nitrosative stress but not by hydrogen peroxide, while ric2 transcription remained unaltered under similar conditions. T. vaginalis RIC1 contains a di-iron centre, but RIC2 apparently does not. Only RIC1 resembles bacterial RICs on spectroscopic profiling and repairing ability of oxidatively-damaged iron-sulfur clusters. Unexpectedly, RIC2 was found to bind DNA plasmid and T. vaginalis genomic DNA, a function proposed to be related with its leucine zipper domain. The two proteins also differ in their cellular localization: RIC1 is expressed in the cytoplasm only, and RIC2 occurs both in the nucleus and cytoplasm. Therefore, we concluded that the two RIC paralogs have different roles in T. vaginalis, with RIC2 showing an unprecedented DNA binding ability when compared with all other until now studied RICs.

Escherichia coli RIC is able to donate iron to iron-sulfur clusters

Escherichia coli RIC (Repair of Iron Centers) is a diiron protein previously reported to be involved in the repair of iron-sulfur proteins damaged by oxidative or nitrosative stresses, and proposed to act as an iron donor. This possible role of RIC was now examined specifically by evaluating its ability to donate iron ions to apo-iron-sulfur proteins, determining the iron binding constants and assessing the lability of its iron ions. We show, by UV-visible, EPR and resonance Raman spectroscopies that RIC may participate in the synthesis of an iron-sulfur cluster in the apo-forms of the spinach ferredoxin and IscU when in the presence of the sulfide donating system IscS and L-cysteine. Iron binding assays allowed determining the as-isolated and fully reduced RIC dissociation constants for the ferric and ferrous iron of 10-27 M and 10-13 M, respectively. Mössbauer studies revealed that the RIC iron ions are labile, namely when the center is in the mixed-valence redox form as compared with the (μ-oxo) diferric one. Altogether, these results suggest that RIC is capable of delivering iron for the formation of iron-sulfur clusters.

Effect of combined oxidative and nitrosative stresses on Staphylococcus aureus transcriptome

Staphylococcus aureus is a pathogen responsible for severe community- and nosocomially acquired infections. To fight pathogen intrusion, the innate immune system uses a plethora of weapons, with the generation of oxidative and nitrosative stresses among the most efficient. In this work, the S. aureus genome-wide transcriptional responses to oxidative stress generated by hydrogen peroxide, to nitrosative stress imposed by S-nitrosoglutathione (GSNO), and to the combination of the two were investigated using microarray analysis. The results showed that these stresses have a significant impact on the transcriptome of S. aureus. Hydrogen peroxide modified mainly the mRNA abundance of genes involved in oxidative detoxification and DNA metabolism, which together represent 14 % of the total number of upregulated genes. GSNO caused significant alteration of the expression of gene products with regulatory function. However, the simultaneous addition of GSNO and hydrogen peroxide was found to cause the more significant transcriptomic alteration, affecting ∼10 % of the total transcriptome. In particular, exposure of S. aureus to GSNO plus hydrogen peroxide modified the transcription of genes associated with cell envelope and iron metabolism, including induction of ftnA and dps genes that encode iron-storage and oxidative-protecting proteins. Further studies revealed that when exposed to combined GSNO-hydrogen peroxide stresses, S. aureus has decreased viability, which is enhanced in the presence of iron, and low siderophore activity. Altogether, this study revealed, for the first time, how the combined oxidative and nitrosative stresses inflicted during phagocytosis interfere at the transcriptional level with the S. aureus cellular metabolism.

A role for reactive oxygen species in the antibacterial properties of carbon monoxide-releasing molecules

Carbon monoxide-releasing molecules (CO-RMs) are, in general, transition metal carbonyl complexes that liberate controlled amounts of CO. In animal models, CO-RMs have been shown to reduce myocardial ischaemia, inflammation and vascular dysfunction, and to provide a protective effect in organ transplantation. Moreover, CO-RMs are bactericides that kill both Gram-positive and Gram-negative bacteria such as Staphylococcus aureus and Pseudomonas aeruginosa. Herein are reviewed the microbial genetic and biochemical responses associated with CO-RM-mediated cell death. Particular emphasis is given to the data revealing that CO-RMs induce the generation of reactive oxygen species (ROS), which contribute to the antibacterial activity of these compounds.

Bacterioferritin protects the anaerobe Desulfovibrio vulgaris Hildenborough against oxygen

Intracellular free iron, is under aerobic conditions and via the Fenton reaction a catalyst for the formation of harmful reactive oxygen species. In this article, we analyzed the relation between intracellular iron storage and oxidative stress response in the sulfate reducing bacterium Desulfovibrio vulgaris Hildenborough, an anaerobe that is often found in oxygenated niches. To this end, we investigated the role of the iron storage protein bacterioferritin using transcriptomic and physiological approaches. We observed that transcription of bacterioferritin is strongly induced upon exposure of cells to an oxygenated atmosphere. When grown in the presence of high concentrations of oxygen the D. vulgaris bacterioferritin mutant exhibited, in comparison with the wild type strain, lower viability and a higher content of intracellular reactive oxygen species. Furthermore, the bacterioferritin gene is under the control of the oxidative stress response regulator D. vulgaris PerR. Altogether the data revealed a previously unrecognized ability for the iron storage bacterioferritin to contribute to the oxygen tolerance exhibited by D. vulgaris.

Reactive oxygen species mediate bactericidal killing elicited by carbon monoxide-releasing molecules

CO-releasing molecules (CO-RMs) were previously shown by us to be more potent bactericides than CO gas. This suggests a mechanism of action for CO-RM, which either potentiates the activity of CO or uses another CO-RM-specific effect. We have also reported that CORM-2 induces the expression of genes related to oxidative stress. In the present study we intend to establish whether the generation of reactive oxygen species by CO-RMs may indeed result in the inhibition of bacterial cellular function. We now report that two CO-RMs (CORM-2 and ALF062) stimulate the production of ROS in Escherichia coli, an effect that is abolished by addition of antioxidants. Furthermore, deletion of genes encoding E. coli systems involved in reactive oxygen species scavenging, namely catalases and superoxide dismutases, potentiates the lethality of CORM-2 due to an increase of intracellular ROS content. CORM-2 also induces the expression of the E. coli DNA repair/SOS system recA, and its inactivation enhances toxicity of CORM-2. Moreover, fluorescence microscopy images reveal that CORM-2 causes DNA lesions to bacterial cells. We also demonstrate that cells treated with CORM-2 contain higher levels of free iron arising from destruction of iron-sulfur proteins. Importantly, we show that CO-RMs generate hydroxyl radicals in a cell-free solution, a process that is abolished by scavenging CO. Altogether, we provide a novel insight into the molecular basis of CO-RMs action by showing that their bactericidal properties are linked to cell damage inflicted by the oxidative stress that they are able to generate.

Exploring the antimicrobial action of a carbon monoxide-releasing compound through whole-genome transcription profiling of Escherichia coli

We recently reported that carbon monoxide (CO) has bactericidal activity. To understand its mode of action we analysed the gene expression changes occurring when Escherichia coli, grown aerobically and anaerobically, is treated with the CO-releasing molecule CORM-2 (tricarbonyldichlororuthenium(II) dimer). Microarray analysis shows that the E. coli CORM-2 response is multifaceted, with a high number of differentially regulated genes spread through several functional categories, namely genes involved in inorganic ion transport and metabolism, regulators, and genes implicated in post-translational modification, such as chaperones. CORM-2 has a higher impact in E. coli cells grown anaerobically, as judged by the repression of genes belonging to eight functional classes which are not seen in the response of aerobically CORM-2-treated cells. The biological relevance of the variations caused by CORM-2 was substantiated by studying the CORM-2 sensitivity of selected E. coli mutants. The results show that the deletion of redox-sensing regulators SoxS and OxyR increased the sensitivity to CORM-2 and suggest that while SoxS plays an important role in protection against CORM-2 under both growth conditions, OxyR seems to participate only in the aerobic CORM-2 response. Under anaerobic conditions, we found that the heat-shock proteins IbpA and IbpB contribute to CORM-2 defence since the deletion of these genes increases the sensitivity of the strain. The induction of several met genes and the hypersensitivity to CORM-2 of the ΔmetR, ΔmetI and ΔmetN mutant strains suggest that CO has effects on the methionine metabolism of E. coli. CORM-2 also affects the transcription of several E. coli biofilm-related genes and increases biofilm formation in E. coli. In particular, the absence of tqsA or bhsA increases the resistance of E. coli to CORM-2, and deletion of tsqA leads to a strain that has lost its capacity to form biofilm upon treatment with CORM-2. In spite of the relatively stable nature of the CO molecule, our results show that CO is able to trigger a significant alteration in the transcriptome of E. coli which necessarily has effects in several key metabolic pathways.

Flavohemoglobin requires microaerophilic conditions for nitrosative protection ofStaphylococcus aureus

Flavohemoglobins and flavodiiron proteins are two families of enzymes involved in nitrosative detoxification. However, the physiological oxygen-related conditions under which they work and their relative role are still a matter of debate. To address this question we analyzed the function of the putative flavohemoprotein of Staphylococcus aureus, an organism that lacks a flavodiiron-like gene. In this report we show that the recombinant protein contains all features typical of canonical flavohemoglobins and that the transcription of flavohemoglobin gene was upregulated by nitrosative stress in an oxygen-dependent manner. However, and in contrast to other bacterial flavohemoglobins, the S. aureus protein has no apparent role in aerobic nitrosative protection, being only beneficial when cells of S. aureus are submitted to nitrosative stress in a microaerophilic environment. The in vivo data corroborates the proposal that Hmp acts physiologically as a denitrosylase.