Antimicrobial Peptides Therapy: An Emerging Alternative for Treating Drug-Resistant Bacteria.

Microbial resistance to antibiotics is an ancient and dynamic issue that has brought a situation reminiscent of the pre-antibiotic era to the limelight. Currently, antibiotic resistance and the associated infections are widespread and pose significant global health and economic burden. Thus, the misuse of antibiotics, which has increased resistance, has necessitated the search for alternative therapeutic agents for combating resistant pathogens. Antimicrobial peptides (AMPs) hold promise as a viable therapeutic approach against drug-resistant pathogens. AMPs are oligopeptides with low molecular weight. They have broad-spectrum antimicrobial activities against pathogenic microorganisms. AMPs are nonspecific and target components of microbes that facilitate immune response by acting as the first-line defense mechanisms against invading pathogenic microbes. The diversity and potency of AMPs make them good candidates for alternative use. They could be used alone or in combination with several other biomaterials for improved therapeutic activity. They can also be employed in vaccine production targeting drug-resistant pathogens. This review covers the opportunities and advances in AMP discovery and development targeting antimicrobial resistance (AMR) bacteria. Briefly, it presents an overview of the global burden of the antimicrobial resistance crisis, portraying the global magnitude, challenges, and consequences. After that, it critically and comprehensively evaluates the potential roles of AMPs in addressing the AMR crisis, highlighting the major potentials and prospects.

Assessment of innate immune response modulating impurities in glucagon for injection.

Glucagon for Injection is a polypeptide hormone medication used to treat patients with severe hypoglycemia or low blood sugar. Only recently, was a generic version of glucagon for injection approved by the FDA. While the generic version was deemed equivalent to its brand-name counterpart, the two glucagon products were produced using different manufacturing processes. The brand-name glucagon is produced via recombinant DNA while the generic glucagon is produced by peptide synthesis. Different manufacturing processes can result in different levels of innate immune response modulating impurities (IIRMIs). This study utilized a cell-based assay method, which allows for detection of a broad spectrum of impurities, to investigate the IIRMI risks of the generic glucagon to make sure it has similar or less immunogenicity risks than the brand-name glucagon product. Three commercial cell lines (RAW-Blue™, HEK-Blue™-hNOD1 and HEK-Blue™-hNOD2) carrying a secreted embryonic alkaline phosphatase reporter construct were used to quantify the level of innate immune responses after being treated with the glucagon drugs. The study results showed that despite differences in manufacturing process, the innate immunogenicity risk in the synthetic (generic) glucagon was at negligible level and comparable to the recombinant (brand-name) glucagon product.

Assessment of Choroidal Vasculature and Innate Immune Cells in the Eyes of Albino and Pigmented Mice.

The visualization of choroidal vasculature and innate immune cells in the eyes of pigmented mice has been challenging due to the presence of a retinal pigment epithelium (RPE) layer separating the choroid and retina. Here, we established methods for visualizing the choroidal macrophages, mast cells, and vasculature in eyes of albino and pigmented mice using cell type-specific staining. We were able to visualize the choroidal arterial and venous systems. An arterial circle around the optic nerve was found in mice similar to the Zinn-Haller arterial circle that exists in humans and primates. Three different structural patterns of choriocapillaris were observed throughout the whole choroid: honeycomb-like, maze-like, and finger-like patterns. Choroidal mast cells were relatively few but dense around the optic nerve. Mast cell distribution in the middle and periphery was different among strains. Macrophages were found in all layers of the choroid. Thus, utilizing the simple and reliable methods described herein will allow the evaluation of transgenic and preclinical mouse models of ocular diseases that affect the choroid, including age-related macular degeneration (AMD), diabetic choroidopathy, and retinopathy of prematurity. These studies will advance our understanding of the pathophysiology, and molecular and cellular mechanisms that can be targeted therapeutically, in these diseases.

Understanding Host-Virus Interactions: Assessment of Innate Immune Responses in Mastomys natalensis Cells after Arenavirus Infection.

Mastomys natalensis is the natural host of various arenaviruses, including the human-pathogenic Lassa virus. Homologous arenaviruses, defined here as those having M. natalensis as a natural host, can establish long-lasting infection in M. natalensis, while these animals rapidly clear arenaviruses having another rodent species as a natural host (heterologous viruses). Little is known about the mechanisms behind the underlying arenavirus-host barriers. The innate immune system, particularly the type I interferon (IFN) response, might play a role. In this study, we developed and validated RT-PCR assays to analyse the expression of M. natalensis interferon-stimulated genes (ISGs). We then used these assays to study if homologous and heterologous viruses induce different IFN responses in M. natalensis cells. Infection experiments were performed with the homologous Lassa and Morogoro viruses and the related but heterologous Mobala virus. Compared to the direct induction with IFN or Poly(I:C), arenaviruses generally induced a weak IFN response. However, the ISG-expression profiles of homologous and heterologous viruses were similar. Our data indicate that, at least in M. natalensis cells, the IFN system is not a major factor in the virus-host barrier for arenaviruses. Our system provides a valuable tool for future in vivo investigation of arenavirus host restrictions at the level of the innate immune response.

Immunogenicity Risk Assessment of Spontaneously Occurring Therapeutic Monoclonal Antibody Aggregates.

Aggregates of therapeutic proteins have been associated with increased immunogenicity in pre-clinical models as well as in human patients. Recent studies to understand aggregates and their immunogenicity risks use artificial stress methods to induce high levels of aggregation. These methods may be less biologically relevant in terms of their quantity than those that occur spontaneously during processing and storage. Here we describe the immunogenicity risk due to spontaneously occurring therapeutic antibody aggregates using peripheral blood mononuclear cells (PBMC) and a cell line with a reporter gene for immune activation: THP-1 BLUE NFκB. The spontaneously occurring therapeutic protein aggregates were obtained from process intermediates and final formulated drug substance from stability retains. Spontaneously occurring aggregates elicited innate immune responses for several donors in a PBMC assay with cytokine and chemokine production as a readout for immune activation. Meanwhile, no significant adaptive phase responses to spontaneously occurring aggregate samples were detected. While the THP-1 BLUE NFκB cell line and PBMC assays both responded to high stress induced aggregates, only the PBMC from a limited subset of donors responded to processing-induced aggregates. In this case study, levels of antibody aggregation occurring at process relevant levels are lower than those induced by stirring and may pose lower risk in vivo. Our methodologies can further inform additional immunogenicity risk assessments using a pre-clinical in vitro risk assessment approach utilizing human derived immune cells.

Innate immune detection of lipid oxidation as a threat assessment strategy.

Oxidized phospholipids that result from tissue injury operate as immunomodulatory signals that, depending on the context, lead to proinflammatory or anti-inflammatory responses. In this Perspective, we posit that cells of the innate immune system use the presence of oxidized lipids as a generic indicator of threat to the host. Similarly to how pathogen-associated molecular patterns represent general indicators of microbial encounters, oxidized lipids may be the most common molecular feature of an injured tissue. Therefore, microbial detection in the absence of oxidized lipids may indicate encounters with avirulent microorganisms. By contrast, microbial detection and detection of oxidized lipids would indicate encounters with replicating microorganisms, thereby inducing a heightened inflammatory and defensive response. Here we review recent studies supporting this idea. We focus on the biology of oxidized phosphocholines, which have emerged as context-dependent regulators of immunity. We highlight emerging functions of oxidized phosphocholines in dendritic cells and macrophages that drive unique inflammasome and migratory activities and hypermetabolic states. We describe how these lipids hyperactivate dendritic cells to stimulate antitumour CD8+ T cell immunity and discuss the potential implications of the newly described activities of oxidized phosphocholines in host defence.

CXCL10 levels at hospital admission predict COVID-19 outcome: hierarchical assessment of 53 putative inflammatory biomarkers in an observational study.

BACKGROUND: Host inflammation contributes to determine whether SARS-CoV-2 infection causes mild or life-threatening disease. Tools are needed for early risk assessment. METHODS: We studied in 111 COVID-19 patients prospectively followed at a single reference Hospital fifty-three potential biomarkers including alarmins, cytokines, adipocytokines and growth factors, humoral innate immune and neuroendocrine molecules and regulators of iron metabolism. Biomarkers at hospital admission together with age, degree of hypoxia, neutrophil to lymphocyte ratio (NLR), lactate dehydrogenase (LDH), C-reactive protein (CRP) and creatinine were analysed within a data-driven approach to classify patients with respect to survival and ICU outcomes. Classification and regression tree (CART) models were used to identify prognostic biomarkers. RESULTS: Among the fifty-three potential biomarkers, the classification tree analysis selected CXCL10 at hospital admission, in combination with NLR and time from onset, as the best predictor of ICU transfer (AUC [95% CI] = 0.8374 [0.6233-0.8435]), while it was selected alone to predict death (AUC [95% CI] = 0.7334 [0.7547-0.9201]). CXCL10 concentration abated in COVID-19 survivors after healing and discharge from the hospital. CONCLUSIONS: CXCL10 results from a data-driven analysis, that accounts for presence of confounding factors, as the most robust predictive biomarker of patient outcome in COVID-19.

Assessment of TLR3 and MDA5-Mediated Immune Responses Using Knockout Quail Fibroblast Cells.

Toll-like receptor 3 (TLR3) and melanoma differentiation-associated gene 5 (MDA5) are double-stranded RNA (dsRNA)-recognizing receptors that mediate innate immune responses to virus infection. However, the roles played by these receptors in the pathogenesis of avian viruses are poorly understood. In this study, we generated TLR3 and MDA5 single knockout (SKO) and TLR3-MDA5 double knockout (DKO) quail fibroblast cells and examined dsRNA receptor-mediated innate immune responses in vitro. The knockout cells were then stimulated with a synthetic dsRNA ligand polyinosinic:polycytidylic acid [poly(I:C)] or influenza A virus. Endosomal stimulation of TLR3 by adding poly(I:C) in cell culture media or cytoplasmic stimulation of MDA5 by transfecting poly(I:C) resulted in significant increases of TLR3, MDA5, interferon (IFN) ß, and interleukin 8 gene expression levels in wild type (WT) cells. Endosomal poly(I:C) treatment induced a higher level expression of most of the genes tested in MDA5 SKO cells compared with WT cells, but not in TLR3 SKO and DKO cells. Cytoplasmic transfection of poly(I:C) led to significant upregulation of all four genes in WT, TLR3 SKO, and MDA5 SKO cells at 8 hr posttransfection and negligible gene expression changes in TLR3-MDA5 DKO cells. Upon infection with a strain of influenza virus with compromised IFN antagonistic capability, WT cells produced the highest amount of biologically active type I IFN followed by TLR3 SKO and MDA5 SKO cells. DKO cells did not produce detectable amounts of type I IFN. However, the IFN did not induce an antiviral state fast enough to block virus replication, even in WT cells under the experimental conditions employed. In summary, our data demonstrate that TLR3 and MDA5 are the key functional dsRNA receptors in quail and imply their coordinated roles in the induction of innate immune responses upon virus infection.

Evaluación de las respuestas inmunitarias mediadas por TLR3 y MDA5 utilizando células de fibroblastos de codorniz con genes eliminados. El receptor tipo Toll 3 (TLR3) y el gene 5 asociado a la diferenciación de melanoma (MDA5) son receptores de reconocimiento de ARN de doble cadena (dsRNA) que median las respuestas inmunitarias innatas a la infección por virus. Sin embargo, no se conocen bien las funciones que desempeñan estos receptores en la patogenia de los virus aviares. En este estudio, se generaron células de fibroblastos de codorniz con eliminación simple de los genes TLR3 y MDA5 (SKO) y eliminación doble de los genes TLR3-MDA5 (DKO) y se examinaron las respuestas inmunitarias innatas mediadas por el receptor de dsRNA in vitro. Posteriormente, las células con genes eliminados se estimularon con un ligando sintético de ARN de doble cadena poliinosínico: ácido policitidílico [poli (I: C)] o con el virus de la influenza A. La estimulación endosómica de TLR3 mediante la adición de poli(I: C) en medios de cultivo celular, o la estimulación citoplásmica de MDA5 mediante la transfección de poli(I: C), dieron como resultado aumentos significativos de los niveles de expresión de los genes para TLR3, MDA5, interferón (IFN) ß e interleucina 8 en células de tipo silvestre (WT). El tratamiento con poli(I: C) endosómico indujo un nivel de expresión más alto de la mayoría de los genes analizados en las células con eliminación simple del gene MDA5 en comparación con las células silvestres, pero no en las células con eliminación simple del gene TLR3 y con eliminación doble de genes. La transfección citoplásmica de poli(I: C) condujo a una regulación positiva significativa de los cuatro genes en las células silvestres, en las células con eliminación simple del gene TLR3 y en las células con eliminación simple del gene MDA5 a las ocho horas posteriores a la transfección y cambios insignificantes en la expresión de genes en las células con eliminación doble de los genes TLR3 y MDA5. Durante la infección con una cepa del virus de la influenza con una capacidad antagonista para IFN comprometida, las células silvestres produjeron la mayor cantidad de IFN de tipo I biológicamente activo, seguidas de las células con eliminación simple del gene TLR3 y de las células con eliminación simple del gene MDA5. Las células con eliminación doble de genes no produjeron cantidades detectables de IFN de tipo I. Sin embargo, el IFN no indujo un estado antiviral lo suficientemente rápido como para bloquear la replicación del virus, incluso en células silvestres bajo las condiciones experimentales empleadas. En resumen, los datos de este estudio demuestran que TLR3 y MDA5 son los receptores de ARN de doble cadena funcionales clave en la codorniz e implican sus funciones coordinadas en la inducción de respuestas inmunitarias innatas durante la infección por virus.

Energy expenditure across immune challenge severities in a lizard: consequences for innate immunity, locomotor performance and oxidative status.

Reptiles, like other vertebrates, rely on immunity to defend themselves from infection. The energetic cost of an immune response is liable to scale with infection severity, prompting constraints on other self-maintenance traits if immune prioritization exceeds energy budget. In this study, adult male side-blotched lizards (Uta stansburiana) were injected with saline (control) or high (20 µg g-1 body mass) or low (10 µg g-1 body mass) concentrations of lipopolysaccharide (LPS) to simulate bacterial infections of discrete severities. The costs and consequences of the immune response were assessed through comparisons of change in resting metabolic rate (RMR), energy metabolites (glucose, glycerol, triglycerides), innate immunity (bactericidal ability), sprint speed and oxidative status (antioxidant capacity, reactive oxygen metabolites). High-LPS lizards had the lowest glucose levels and greatest sprint reductions, while their RMR and bactericidal ability were similar to those of control lizards. Low-LPS lizards had elevated RMR and bactericidal ability, but glucose levels and sprint speed changes between those of high-LPS and control lizards. Levels of glycerol, triglycerides, reactive oxygen metabolites and antioxidant capacity did not differ by treatment. Taken together, energy expenditure for the immune response varies in a non-linear fashion with challenge severity, posing consequences for performance and self-maintenance processes in a reptile.

A unifying model to estimate the effect of heat stress in the human innate immunity during physical activities.

Public health is threatened by climate change and extreme temperature events worldwide. Differences in health predispositions, access to cooling infrastructure and occupation raises an issue of heat-related health inequality in those vulnerable and disadvantaged demographic groups. To address these issues, a comprehensive understanding of the effect of elevated body temperatures on human biological systems and overall health is urgently needed. In this paper we look at the inner workings of the human innate immunity under exposure to heat stress induced through exposure to environment and physical exertion. We couple two experimentally validated computational models: the innate immune system and thermal regulation of the human body. We first study the dynamics of critical indicators of innate immunity as a function of human core temperature. Next, we identify environmental and physical activity regimes that lead to core temperature levels that can potentially compromise the performance of the human innate immunity. Finally, to take into account the response of innate immunity to various intensities of physical activities, we utilise the dynamic core temperatures generated by a thermal regulation model. We compare the dynamics of all key players of the innate immunity for a variety of stresses like running a marathon, doing construction work, and leisure walking at speed of 4 km/h, all in the setting of a hot and humid tropical climate such as present in Singapore. We find that exposure to moderate heat stress leading to core temperatures within the mild febrile range (37, 38][Formula: see text], nudges the innate immune system into activation and improves the efficiency of its response. Overheating corresponding to core temperatures beyond 38[Formula: see text], however, has detrimental effects on the performance of the innate immune system, as it further induces inflammation, which causes a series of reactions that may lead to the non-resolution of the ongoing inflammation. Among the three physical activities considered in our simulated scenarios (marathon, construction work, and walking), marathon induces the highest level of inflammation that challenges the innate immune response with its resolution. Our study advances the current state of research towards understanding the implications of heat exposure for such an essential physiological system as the innate immunity. Although we find that among considered physical activities, a marathon of 2 h and 46 min induces the highest level of inflammation, it must be noted that construction work done on a daily basis under the hot and humid tropical climate, can produce a continuous level of inflammation triggering moieties stretched at a longer timeline beating the negative effects of running a marathon. Our study demonstrates that the performance of the innate immune system can be severely compromised by the exposure to heat stress and physical exertion. This poses significant risks to health especially to those with limited access to cooling infrastructures. This is due in part to having low income, or having to work on outdoor settings, which is the case for construction workers. These risks to public health should be addressed through individual and population-level measures via behavioural adaptation and provision of the cooling infrastructure in outdoor environments.

Immunological Aspects of Isolation and Confinement.

Beyond all doubts, the exploration of outer space is a strategically important and priority sector of the national economy, scientific and technological development of every and particular country, and of all human civilization in general. A number of stress factors, including a prolonged confinement in a limited hermetically sealed space, influence the human body in space on board the spaceship and during the orbital flight. All these factors predominantly negatively affect various functional systems of the organism, in particular, the astronaut's immunity. These ground-based experiments allow to elucidate the effect of confinement in a limited space on both the activation of the immunity and the changes of the immune status in dynamics. Also, due to simulation of one or another emergency situation, such an approach allows the estimation of the influence of an additional psychological stress on the immunity, particularly, in the context of the reserve capacity of the immune system. A sealed chamber seems a convenient site for working out the additional techniques for crew members selection, as well as the countermeasures for negative changes in the astronauts' immune status. In this review we attempted to collect information describing changes in human immunity during isolation experiments with different conditions including short- and long-term experiments in hermetically closed chambers with artificial environment and during Antarctic winter-over.

Activity of the Toll-like receptor ligands in children with high and low socioeconomic backgrounds.

BACKGROUND: Adjuvants are essential in the induction of immunity by vaccines and interact with receptors, including the Toll-like receptors (TLRs). Responsiveness of these receptors differs between and within populations, which impacts vaccine effectiveness. OBJECTIVE: Here we examine how the innate cytokine response towards TLR ligands differs between high and low socioeconomic status (SES) school-aged children from Makassar, Indonesia. METHODS: We stimulated whole blood from children, of which 27 attended a high SES school and 27 children a low SES school, with ligands for TLR-2/1, -2/6, -3, -4, -5, -7, -9 and measured pro- (TNF) and anti-inflammatory (IL-10) cytokines released. RESULTS: In the low SES there is an increased pro-inflammatory response after 24 h stimulation with TLR-2/1 ligand Pam3 and TLR-4 ligand LPS compared to the high SES. Comparison of the response to LPS after 24 h versus 72 h stimulation revealed that the pro-inflammatory response in the low SES after 24 h shifts to an anti-inflammatory response, whereas in the high SES the initial anti-inflammatory response shifts to a strong pro-inflammatory response after 72 h stimulation. CONCLUSION: We observed differences in the TLR-mediated innate immune response between children attending low and high SES schools, which can have important implications for vaccine development.

Assessment of severity and mortality of COVID-19 with anti-A1 and anti-B IgM isohaemagglutinins, a reflection of the innate immune status.

AIMS: The relationship between the innate immune system that creates the polysaccharide antibody response and COVID-19 is not fully understood. In this study, it was aimed to determine the predictive values of isohaemagglutinins in COVID-19 severity/mortality. METHODS: Approximately 15 440 patients diagnosed with COVID-19 were examined, and a total of 286 patients with anti-B and anti-A1 IgM isohaemagglutinins test results were randomly enrolled in the study. These patients were stratified into two groups according to anti-A1 (n: 138 blood type B or O) and anti-B (n: 148 blood type A) IgM isohaemagglutinins. Anti-A1 or/and anti-B IgM, biochemical parameters, symptoms, chronic diseases, hospitalisation status, intubation status, admission to intensive care unit (ICU) and exitus status were recorded and evaluated for all patients. RESULTS: Anti-A1 IgM and anti-B IgM were significantly lower in ICU patients (7.5 ± 9.9 vs 18.0 ± 20.4 and 5.5 ± 6.3 vs 19.3 ± 33.6 titres, respectively; P < .01) and in exitus patients (3.8 ± 3.6 vs 16.7 ± 18.7 and 3.5 ± 4.7 vs 16.9 ± 29.6 titres respectively; P < .01). In the ROC analysis performed to differentiate between exitus and discharge within groups, the sensitivity of anti-B IgM and anti-A1 IgM at cut-off ≤4 was 88.9% and 79.6%, specificity 66.0% and 73.4%, and AUC 0.831 and 0.861, respectively (P < .01). Anti-A1 IgM decreased the mortality risk 0.811 times per unit while anti-B IgM decreased 0.717 times (P < .01). CONCLUSION: Anti-B and anti-A1 isohaemagglutinins, which are an expression of the innate immune system, can be used to predict the severity and mortality of COVID-19 disease.

A decision tree model for neuroimmune guidance of allergic immunity.

The immune system defends the body from infectious and non-infectious threats. Distinct recognition strategies have evolved to generate antigen-specific immunity against pathogens or toxins versus antigen-independent tissue repair. Structural recognition, or the sensing of conserved motifs, guides the immune response to viruses, bacteria, fungi, and unicellular parasites. Functional recognition, which is sensing that is based on the activities of an input, guides antigen-independent tissue healing and antigen-specific Type 2 immunity to toxins, allergens, and helminth parasites. Damage-associated molecular patterns (DAMPs), released from damaged and dying cells, permit functional recognition by immune cells. However, the DAMP paradigm alone does not explain how functional recognition can lead to such disparate immune responses, namely wound healing and Type 2 immunity. Recent work established that sensory neurons release neuropeptides in response to a variety of toxins and allergens. These neuropeptides act on local innate immune cells, stimulating or inhibiting their activities. By integrating our knowledge on DAMP function with new information on the role of neuropeptides in innate immune activation in Type 2 immunity, we describe a decision tree model of functional recognition. In this model, neuropeptides complement or antagonize DAMPs to guide the development of antigen-specific Type 2 immunity through the activation of innate immune cells. We discuss why this decision tree system evolved and its implications to allergic diseases.

Molecular characterization for food safety assessment of a genetically modified late blight resistant potato: an unusual case.

Standard food safety assessments of genetically modified crops require a thorough molecular characterization of the novel DNA as inserted into the plant that is intended for commercialization, as well as a comparison of agronomic and nutritional characteristics of the genetically modified to the non-modified counterpart. These characterization data are used to identify any unintended changes in the inserted DNA or in the modified plant that would require assessment for safety in addition to the assessment of the intended modification. An unusual case of an unintended effect discovered from the molecular characterization of a genetically modified late blight resistant potato developed for growing in Bangladesh and Indonesia is presented here. Not only was a significant portion of the plasmid vector backbone DNA inserted into the plant along with the intended insertion of an R-gene for late blight resistance, but the inserted DNA was split into two separate fragments and inserted into two separate chromosomes. One fragment carries the R-gene and the other fragment carries the NPTII selectable marker gene and the plasmid backbone DNA. The implications of this for the food safety assessment of this late blight resistant potato are considered.

Assessment of the pulmonary adaptive immune response to Cladosporium cladosporioides infection using an experimental mouse model.

Cladosporium cladosporioides causes asthma and superficial and deep infections, mostly in immunodeficient individuals and animals. This study aimed to investigate whether C. cladosporioides spores can enter the lungs through pulmonary circulation and influence pulmonary immune response. We intravenously injected mice with C. cladosporioides spore suspension and conducted several assays on the lungs. Pulmonary hemorrhage symptoms and congestion were most severe on days 1, 2, and 3 post-inoculation (PI). Extensive inflammatory cell infiltration occurred throughout the period of infection. More spores and hyphae colonizing the lungs were detected on days 1, 2, and 3 PI, and fewer spores and hyphae were observed within 21 d of infection. Numerous macrophages, dendritic cells, and neutrophils were observed on day 5 PI, along with upregulation of CD54, an intercellular adhesion molecule. Th1 and Th2 cells increased after infection; specifically, Th2 cells increased considerably on day 5 PI. These results suggest that days 2 and 5 PI represent the inflammatory peak in the lungs and that the Th2 and Th1 signaling pathways are potentially involved in pulmonary immune responses. In conclusion, the further adaptive immune responses played important roles in establishing effective pulmonary immunity against C. cladosporioides systemic infections based on innate immune responses.

TIAMMAt: Leveraging Biodiversity to Revise Protein Domain Models, Evidence from Innate Immunity.

Sequence annotation is fundamental for studying the evolution of protein families, particularly when working with nonmodel species. Given the rapid, ever-increasing number of species receiving high-quality genome sequencing, accurate domain modeling that is representative of species diversity is crucial for understanding protein family sequence evolution and their inferred function(s). Here, we describe a bioinformatic tool called Taxon-Informed Adjustment of Markov Model Attributes (TIAMMAt) which revises domain profile hidden Markov models (HMMs) by incorporating homologous domain sequences from underrepresented and nonmodel species. Using innate immunity pathways as a case study, we show that revising profile HMM parameters to directly account for variation in homologs among underrepresented species provides valuable insight into the evolution of protein families. Following adjustment by TIAMMAt, domain profile HMMs exhibit changes in their per-site amino acid state emission probabilities and insertion/deletion probabilities while maintaining the overall structure of the consensus sequence. Our results show that domain revision can heavily impact evolutionary interpretations for some families (i.e., NLR's NACHT domain), whereas impact on other domains (e.g., rel homology domain and interferon regulatory factor domains) is minimal due to high levels of sequence conservation across the sampled phylogenetic depth (i.e., Metazoa). Importantly, TIAMMAt revises target domain models to reflect homologous sequence variation using the taxonomic distribution under consideration by the user. TIAMMAt's flexibility to revise any subset of the Pfam database using a user-defined taxonomic pool will make it a valuable tool for future protein evolution studies, particularly when incorporating (or focusing) on nonmodel species.

Host permissiveness to baculovirus influences time-dependent immune responses and fitness costs.

Insects possess specific immune responses to protect themselves from different types of pathogens. Activation of immune cascades can inflict significant developmental costs on the surviving host. To characterize infection kinetics in a surviving host that experiences baculovirus inoculation, it is crucial to determine the timing of immune responses. Here, we investigated time-dependent immune responses and developmental costs elicited by inoculations from each of two wild-type baculoviruses, Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and Helicoverpa zea single nucleopolyhedrovirus (HzSNPV), in their common host H. zea. As H. zea is a semi-permissive host of AcMNPV and fully permissive to HzSNPV, we hypothesized there are differential immune responses and fitness costs associated with resisting infection by each virus species. Newly molted 4th-instar larvae that were inoculated with a low dose (LD15 ) of either virus showed significantly higher hemolymph FAD-glucose dehydrogenase (GLD) activities compared to the corresponding control larvae. Hemolymph phenoloxidase (PO) activity, protein concentration and total hemocyte numbers were not increased, but instead were lower than in control larvae at some time points post-inoculation. Larvae that survived either virus inoculation exhibited reduced pupal weight; survivors inoculated with AcMNPV grew slower than the control larvae, while survivors of HzSNPV pupated earlier than control larvae. Our results highlight the complexity of immune responses and fitness costs associated with combating different baculoviruses.

Innate responses to gut microbiota; critical assessment of the necessary experimental controls.

The intestinal microbiota is comprises a diverse community of micro-organisms that interact with many host processes. Innate immune responses to the gut microbiota are of particular importance as they influence many other downstream responses. This fascinating host-microbe crosstalk is a rapidly expanding field of study; thus, it is critical to ensure reproducibility between studies and applicability to human clinical trials through standardization of experiments. We discuss here recent advances in the field including the spectrum of colonization statuses available, the critical importance of colonization timing, the dynamics of the microbial community, and the required housing of animals, as they pertain to appropriate experimental control and design.

Chimeric antigen receptor (CAR) natural killer (NK)-cell therapy: leveraging the power of innate immunity.

Chimeric antigen receptor (CAR) T cells are a rapidly emerging form of cancer treatment, and have resulted in remarkable responses in refractory lymphoid malignancies. However, their widespread clinical use is limited by toxicity related to cytokine release syndrome and neurotoxicity, the logistic complexity of their manufacturing, cost and time-to-treatment for autologous CAR-T cells, and the risk of graft-versus-host disease (GvHD) associated with allogeneic CAR-T cells. Natural killer (NK) cells have emerged as a promising source of cells for CAR-based therapies due to their ready availability and safety profile. NK cells are part of the innate immune system, providing the first line of defence against pathogens and cancer cells. They produce cytokines and mediate cytotoxicity without the need for prior sensitisation and have the ability to interact with, and activate other immune cells. NK cells for immunotherapy can be generated from multiple sources, such as expanded autologous or allogeneic peripheral blood, umbilical cord blood, haematopoietic stem cells, induced pluripotent stem cells, as well as cell lines. Genetic engineering of NK cells to express a CAR has shown impressive preclinical results and is currently being explored in multiple clinical trials. In the present review, we discuss both the preclinical and clinical trial progress made in the field of CAR NK-cell therapy, and the strategies to overcome the challenges encountered.