Systems biology applied to vaccine and immunotherapy development

Tracking the pipeline: immunoinformatics and the COVID-19 vaccine design

With the onset of the COVID-19 pandemic, the amount of data on genomic and proteomic sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) stored in various databases has exponentially grown. A large volume of these data has led to the production of equally immense sets of immunological data, which require rigorous computational approaches to sort through and make sense of. Immunoinformatics has emerged in the recent decades as a field capable of offering this approach by bridging experimental and theoretical immunology with state-of-the-art computational tools. Here, we discuss how immunoinformatics can assist in the development of high-performance vaccines and drug discovery needed to curb the spread of SARS-CoV-2. Immunoinformatics can provide a set of computational tools to extract meaningful connections from the large sets of COVID-19 patient data, which can be implemented in the design of effective vaccines. With this in mind, we represent a pipeline to identify the role of immunoinformatics in COVID-19 treatment and vaccine development. In this process, a number of free databases of protein sequences, structures and mutations are introduced, along with docking web servers for assessing the interaction between antibodies and the SARS-CoV-2 spike protein segments as most commonly considered antigens in vaccine design.

The combination of artificial intelligence and systems biology for intelligent vaccine design

INTRODUCTION

A new body of evidence depicts the applications of artificial intelligence and systems biology in vaccine design and development. The combination of both approaches shall revolutionize healthcare, accelerating clinical trial processes and reducing the costs and time involved in drug research and development.

AREAS COVERED

This review explores the basics of artificial intelligence and systems biology approaches in the vaccine development pipeline. The topics include a detailed description of epitope prediction tools for designing epitope-based vaccines and agent-based models for immune system response prediction, along with a focus on their potentiality to facilitate clinical trial phases.

EXPERT OPINION

Artificial intelligence and systems biology offer the opportunity to avoid the inefficiencies and failures that arise in the classical vaccine development pipeline. One promising solution is the combination of both methodologies in a multiscale perspective through an accurate pipeline. We are entering an 'in silico era' in which scientific partnerships, including a more and more increasing creation of an 'ecosystem' of collaboration and multidisciplinary approach, are relevant for addressing the long and risky road of vaccine discovery and development. In this context, regulatory guidance should be developed to qualify the in silico trials as evidence for intelligent vaccine development.

Perspectives on Systems Modeling of Human Peripheral Blood Mononuclear Cells

Human peripheral blood mononuclear cells (PBMCs) are the key drivers of the immune responses. These cells undergo activation, proliferation and differentiation into various subsets. During these processes they initiate metabolic reprogramming, which is coordinated by specific gene and protein activities. PBMCs as a model system have been widely used to study metabolic and autoimmune diseases. Herein we review various omics and systems-based approaches such as transcriptomics, epigenomics, proteomics, and metabolomics as applied to PBMCs, particularly T helper subsets, that unveiled disease markers and the underlying mechanisms. We also discuss and emphasize several aspects of T cell metabolic modeling in healthy and disease states using genome-scale metabolic models.

Vaccination with human amniotic epithelial cells confer effective protection in a murine model of Colon adenocarcinoma

As a prophylactic cancer vaccine, human amniotic membrane epithelial cells (hAECs) conferred effective protection in a murine model of colon cancer. The immunized mice mounted strong cross-protective CTL and antibody responses. Tumor burden was significantly reduced in tumor-bearing mice after immunization with hAECs. Placental cancer immunotherapy could be a promising approach for primary prevention of cancer. In spite of being the star of therapeutic strategies for cancer treatment, the results of immunotherapeutic approaches are still far from expectations. In this regard, primary prevention of cancer using prophylactic cancer vaccines has gained considerable attention. The immunologic similarities between cancer development and placentation have helped researchers to unravel molecular mechanisms responsible for carcinogenesis and to take advantage of stem cells from reproductive organs to elicit robust anti-cancer immune responses. Here, we showed that vaccination of mice with human amniotic membrane epithelial cells (hAECs) conferred effective protection against colon cancer and led to expansion of systemic and splenic cytotoxic T cell population and induction of cross-protective cytotoxic responses against tumor cells. Vaccinated mice mounted tumor-specific Th1 responses and produced cross-reactive antibodies against cell surface markers of cancer cells. Tumor burden was also significantly reduced in tumor-bearing mice immunized with hAECs. Our findings pave the way for potential future application of hAECs as an effective prophylactic cancer vaccine.

Retrovirus-Based Virus-Like Particle Immunogenicity and Its Modulation by Toll-Like Receptor Activation

Retrovirus-derived virus-like particles (VLPs) are particularly interesting vaccine platforms, as they trigger efficient humoral and cellular immune responses and can be used to display heterologous antigens. In this study, we characterized the intrinsic immunogenicity of VLPs and investigated their possible adjuvantization by incorporation of Toll-like receptor (TLR) ligands. We designed a noncoding single-stranded RNA (ncRNA) that could be encapsidated by VLPs and induce TLR7/8 signaling. We found that VLPs efficiently induce in vitro dendritic cell activation, which can be improved by ncRNA encapsidation (_ncRNAVLPs). Transcriptome studies of dendritic cells harvested from the spleens of immunized mice identified antigen presentation and immune activation as the main gene expression signatures induced by VLPs, while TLR signaling and Th1 signatures characterize _ncRNAVLPs. In vivo and compared with standard VLPs, _ncRNAVLPs promoted Th1 responses and improved CD8⁺ T cell proliferation in a MyD88-dependent manner. In an HIV vaccine mouse model, HIV-pseudotyped _ncRNAVLPs elicited stronger antigen-specific cellular and humoral responses than VLPs. Altogether, our findings provide molecular evidence for a strong vaccine potential of retrovirus-derived VLPs that can be further improved by harnessing TLR-mediated immune activation.IMPORTANCE We previously reported that DNA vaccines encoding antigens displayed in/on retroviral VLPs are more efficient than standard DNA vaccines at inducing cellular and humoral immune responses. We aimed to decipher the mechanisms and investigated the VLPs' immunogenicity independently of DNA vaccination. We show that VLPs have the ability to activate antigen-presenting cells directly, thus confirming their intrinsic immunostimulatory properties and their potential to be used as an antigenic platform. Notably, this immunogenicity can be further improved and/or oriented by the incorporation into VLPs of ncRNA, which provides further TLR-mediated activation and Th1-type CD4⁺ and CD8⁺ T cell response orientation. Our results highlight the versatility of retrovirus-derived VLP design and the value of using ncRNA as an intrinsic vaccine adjuvant.

Early Transcriptome Signatures from Immunized Mouse Dendritic Cells Predict Late Vaccine-Induced T-Cell Responses

Systems biology offers promising approaches for identifying response-specific signatures to vaccination and assessing their predictive value. Here, we designed a modelling strategy aiming to predict the quality of late T-cell responses after vaccination from early transcriptome analysis of dendritic cells. Using standardized staining with tetramer, we first quantified antigen-specific T-cell expansion 5 to 10 days after vaccination with one of a set of 41 different vaccine vectors all expressing the same antigen. Hierarchical clustering of the responses defined sets of high and low T cell response inducers. We then compared these responses with the transcriptome of splenic dendritic cells obtained 6 hours after vaccination with the same vectors and produced a random forest model capable of predicting the quality of the later antigen-specific T-cell expansion. The model also successfully predicted vector classification as low or strong T-cell response inducers of a novel set of vaccine vectors, based on the early transcriptome results obtained from spleen dendritic cells, whole spleen and even peripheral blood mononuclear cells. Finally, our model developed with mouse datasets also accurately predicted vaccine efficacy from literature-mined human datasets.

Vaccines are designed to elicit effective immune responses against antigens. The various vector platforms used in vaccine development are diverse and complex, rendering the selection of promising vaccines vector challenging. We have designed a modeling strategy that predicts the propensity of vaccine vectors to elicit strong late T-cell responses using transcriptome material obtained 6 hours after vaccination. Our model, designed with mouse datasets, also predicted vector efficacy from mined human data. Thus, molecular signatures obtained 6 hours after vaccination can predict vaccine efficacy at 2 weeks post vaccination, which should help in vaccine development.

The Role of Gastrin and CCK Receptors in Pancreatic Cancer and other Malignancies

The gastrointestinal (GI) peptide gastrin is an important regulator of the release of gastric acid from the stomach parietal cells and it also plays an important role in growth of the gastrointestinal tract. It has become apparent that gastrin and its related peptide cholecystokinin (CCK) are also significantly involved with growth of GI cancers as well as other malignancies through activation of the cholecystokinin-B (CCK-B) receptor. Of interest, gastrin is expressed in the embryologic pancreas but not in the adult pancreas; however, gastrin becomes re-expressed in pancreatic cancer where it stimulates growth of this malignancy by an autocrine mechanism. Strategies to down-regulate gastrin or interfere with its interface with the CCK receptor with selective antibodies or receptor antagonists hold promise for the treatment of pancreatic cancer and other gastrin--responsive tumors.

Live attenuated and inactivated viral vaccine formulation and nasal delivery: potential and challenges

Vaccines are cost-effective for the prevention of infectious diseases and have significantly reduced mortality and morbidity. Novel approaches are needed to develop safe and effective vaccines against disease. Major challenges in vaccine development include stability in a suitable dosage form and effective modes of delivery. Many live attenuated vaccines are capable of eliciting both humoral and cell mediated immune responses if physicochemically stable in an appropriate delivery vehicle. Knowing primary stresses that impart instability provides a general rationale for formulation development and mode of delivery. Since most pathogens enter the body through the mucosal route, live-attenuated vaccines have the advantage of mimicking natural immunization via non-invasive delivery. This presentation will examine aspects of formulation design, types of robust dosage forms to consider, effective routes of delivery (invasive and noninvasive), and distinctions between live attenuated or inactivated vaccines.

High-throughput data analysis and data integration for vaccine trials

Rational vaccine development can benefit from biomarker studies, which help to predict, optimize and evaluate the immunogenicity of vaccines and ultimately provide surrogate endpoints for vaccine trials. Systems biology approaches facilitate acquisition of both simple biomarkers and complex biosignatures. Yet, evaluation of high-throughput (HT) data requires a plethora of tools for data integration and analysis. In this review, we present an overview of methods for evaluation and integration of large amounts of data collected in vaccine trials from similar and divergent molecular HT techniques, such as transcriptomic, proteomic and metabolic profiling. We will describe a selection of relevant statistical and bioinformatic approaches that are frequently associated with systems biology. We will present data dimension reduction techniques, functional analysis approaches and methods of integrating heterogeneous HT data. Finally, we will provide a few examples of applications of these techniques in vaccine research and development.

Genomics and infectious disease: a call to identify the ethical, legal and social implications for public health and clinical practice

Advances in genomics are contributing to the development of more effective, personalized approaches to the prevention and treatment of infectious diseases. Genetic sequencing technologies are furthering our understanding of how human and pathogen genomic factors - and their interactions - contribute to individual differences in immunologic responses to vaccines, infections and drug therapies. Such understanding will influence future policies and procedures for infectious disease management. With the potential for tailored interventions for particular individuals, populations or subpopulations, ethical, legal and social implications (ELSIs) may arise for public health and clinical practice. Potential considerations include balancing health-related benefits and harms between individuals and the larger community, minimizing threats to individual privacy and autonomy, and ensuring just distribution of scarce resources. In this Opinion, we consider the potential application of pathogen and host genomic information to particular viral infections that have large-scale public health consequences but differ in ELSI-relevant characteristics such as ease of transmission, chronicity, severity, preventability and treatability. We argue for the importance of anticipating these ELSI issues in advance of new scientific discoveries, and call for the development of strategies for identifying and exploring ethical questions that should be considered as clinical, public health and policy decisions are made.

Changing face of vaccination in immunocompromised hosts

Infection prevention is a key component of care and an important determinant of clinical outcomes in a diverse population of immunocompromised hosts. Vaccination remains a fundamental preventative strategy, and clear guidelines exist for the vaccination of immunocompromised individuals and close contacts. Unfortunately, adherence to such guidelines is frequently suboptimal, with consequent missed opportunities to prevent infection. Additionally, vaccination of immunocompromised individuals is known to produce responses inferior to those observed in immunocompetent hosts. Multiple factors contribute to this finding, and developing improved vaccination strategies for those at high risk of infectious complications remains a priority of care providers. Herein, we review potential factors contributing to vaccine outcomes, focusing on host immune responses, and propose a means for applying modern, innovative systems biology technology to model critical determinants of vaccination success. With influenza vaccine in solid organ transplants used as a case in point, novel means for stratifying individuals using a host "immunophenotype" are explored, and strategies for individualizing vaccine approaches tailored to safely optimize vaccine responses in those most at risk are discussed.

Systems vaccinology for cancer vaccine development

Results of therapeutic vaccines for established chronic infections or cancers are still unsatisfactory. The only therapeutic cancer vaccine approved for clinical use is the sipuleucel-T, for the treatment of metastatic prostate cancer, which induces a limited 4-month improvement in the overall survival of vaccinated patients compared to controls. This represents a remarkable advancement in the cancer immunotherapy field, although the clinical outcome of cancer vaccines needs to be substantially improved. To this aim, a multipronged strategy is required, including the evaluation of mechanisms underlying the effective elicitation of immune responses by cancer vaccines. The recent development of new technologies and computational tools allows the comprehensive and quantitative analysis of the interactions between all of the components of innate and adaptive immunity over time. Here we review the potentiality of systems biology in providing novel insights in the mechanisms of action of vaccines to improve their design and effectiveness.

Protein turnover forms one of the highest maintenance costs in Lactococcus lactis

Protein turnover plays an important role in cell metabolism by regulating metabolic fluxes. Furthermore, the energy costs for protein turnover have been estimated to account for up to a third of the total energy production during cell replication and hence may represent a major limiting factor in achieving either higher biomass or production yields. This work aimed to measure the specific growth rate (μ)-dependent abundance and turnover rate of individual proteins, estimate the ATP cost for protein production and turnover, and compare this with the total energy balance and other maintenance costs. The lactic acid bacteria model organism Lactococcus lactis was used to measure protein turnover rates at μ = 0.1 and 0.5 h(-1) in chemostat experiments. Individual turnover rates were measured for ~75% of the total proteome. On average, protein turnover increased by sevenfold with a fivefold increase in growth rate, whilst biomass yield increased by 35%. The median turnover rates found were higher than the specific growth rate of the bacterium, which suggests relatively high energy consumption for protein turnover. We found that protein turnover costs alone account for 38 and 47% of the total energy produced at μ = 0.1 and 0.5 h(-1), respectively, and gene ontology groups Energy metabolism and Translation dominated synthesis costs at both growth rates studied. These results reflect the complexity of metabolic changes that occur in response to changes in environmental conditions, and signify the trade-off between biomass yield and the need to produce ATP for maintenance processes.

Prediction of individual immune responsiveness to a candidate vaccine by a systems vaccinology approach

Background

We have previously shown that a candidate idiotype vaccine, based on the IGKV3-20 light chain protein, is able to induce activation of circulating antigen presenting cells (APCs) in both HCV-positive and HCV-negative subjects, with production of Th2-type cytokines. In addition, such a candidate idiotype vaccine induces an early gene expression pattern, characterized by the strong induction of an innate immune response, and a late pattern, characterized by a prevalent B cell response. Nonetheless, some HCV-positive individuals showed a complete lack of maturation of circulating APCs with low levels of cytokine production, strongly suggesting the possible identification of selective impairments in immune response in individual subjects.

Method

Peripheral blood mononuclear cells (PBMCs) were stimulated ex vivo with IGKV3-20 for 24 h and 6 days. Analysis of the global gene expression profile as well as the cytokine pattern was performed for individual subjects.

Results

The gene expression profile showed a strong agreement with the cytokine pattern. Indeed, the expression pattern of immune-related genes is highly predictive of the individual immunological phenotype.

Conclusion

The overall results represent a proof of concept, indicating the efficacy of such an ex vivo screening platform for predicting individual’s responsiveness to an antigen as well as guiding optimization of vaccine design. Larger cohort study will be needed to validate results observed in the study.

Food, nutrigenomics, and neurodegeneration--neuroprotection by what you eat!

Diet in human health is no longer simple nutrition, but in light of recent research, especially nutrigenomics, it is linked via evolution and genetics to cell health status capable of modulating apoptosis, detoxification, and appropriate gene response. Nutritional deficiency and disease especially lack of vitamins and minerals is well known, but more recently, epidemiological studies suggest a role of fruits and vegetables, as well as essential fatty acids and even red wine (French paradox), in protection against disease. In the early 1990s, various research groups started considering the use of antioxidants (e.g., melatonin, resveratrol, green tea, lipoic acid) and metabolic compounds (e.g., nicotinamide, acetyl-L-carnitine, creatine, coenzyme Q10) as possible candidates in neuroprotection. They were of course considered on par with snake oil salesman (women) at the time. The positive actions of nutritional supplements, minerals, and plant extracts in disease prevention are now mainstream and commercial health claims being made are subject to regulation in most countries. Apart from efficacy and finding, the right dosages, the safety, and especially the level of purification and lack of contamination are all issues that are important as their use becomes widespread. From the mechanistic point of view, most of the time these substances replenish the body's deficiency and restore normal function. However, they also exert actions that are not sensu stricto nutritive and could be considered pharmacological especially that, at times, higher intake than recommended (RDA) is needed to see these effects. Free radicals and neuroinflammation processes underlie many neurodegenerative conditions, even Parkinson's disease and Alzheimer's disease. Curcumin, carotenoids, acetyl-L-carnitine, coenzyme Q10, vitamin D, and polyphenols and other nutraceuticals have the potential to target multiple pathways in these conditions. In summary, augmenting neuroprotective pathways using diet and finding new natural substances that can be more efficacious, i.e., induction of health-promoting genes and reduction of the expression of disease-promoting genes, could be incorporated into neuroprotective strategies of the future.

Applications of selected reaction monitoring (SRM)-mass spectrometry (MS) for quantitative measurement of signaling pathways

Quantitative measurement of the major regulatory proteins in signaling networks poses several technical challenges, including low abundance, the presence of post-translational modifications (PTMs), and the lack of suitable affinity detection reagents. Using the innate immune response (IIR) as a model signaling pathway, we illustrate the approach of stable isotope dilution (SID)-selected reaction monitoring (SRM)-mass spectrometry (MS) assays for quantification of low abundance signaling proteins. A work flow for SID-SRM-MS assay development is established for proteins with experimentally observed MS spectra and for those without. Using the interferon response factor (IRF)-3 transcription factor as an example, we illustrate the steps in high responding signature peptide identification, SID-SRM-MS assay optimization, and evaluation. SRM assays for normalization of IIR abundance to invariant housekeeping proteins are presented. We provide an example of SID-SRM assay development for post-translational modification (PTM) detection using an activating phospho-Ser modified NF-κB/RelA transcription factor, and describe challenges inherent in PTM-SID-SRM-MS assay development. Application of highly qualified quantitative, SID-SRM-MS assays will enable a systems-level approach to understanding the dynamics and kinetics of signaling in host cells, such as the IIR.

Human embryonic stem cells--a potential vaccine for ovarian cancer

OBJECTIVE

To investigate the therapeutic potential of human embryonic stem cells (hESCs) as a vaccine to induce an immune response and provide antitumor protection in a rat model.

METHODS

Cross-reactivity of antigens between hESCs and tumour cells was screened by immunohistochemistry. Fischer 344 rats were divided into 7 groups, with 6 rats in each, immunized with: Group 1, hESC; Group 2, pre-inactivated mitotic NuTu-19; Group 3 PBS; Group 4, hESC; Group 5, pre-inactivated mitotic NuTu-19; Group 6, PBS; Group 7, hESC only. At 1 (Groups 1-3) or 4 weeks (Groups 4-6) after the last vaccination, each rat was challenged intraperitoneally with NuTu-19. Tumor growth and animal survival were closely monitored. Rats immunized with H9 and NuTu- 19 were tested by Western blot analysis of rat orbital venous blood for cytokines produced by Th1 and Th2 cells.

RESULTS

hESCs presented tumour antigens, markers, and genes related to tumour growth, metastasis, and signal pathway interactions. The vaccine administered to rats in Group 1 led to significant antitumor responses and enhanced tumor rejection in rats with intraperitoneal inoculation of NuTu-19 cells compared to control groups. In contrast, rats in Group 4 did not display any elevation of antitumour responses. Western blot analysis found cross-reactivity among antibodies generated between H9 and NuTu-19. However, the cytokines did not show significant differences, and no side effects were detected.

CONCLUSION

hESC-based vaccination is a promising modality for immunotherapy of ovarian cancer.

Quantitation of the dynamic profiles of the innate immune response using multiplex selected reaction monitoring-mass spectrometry

The innate immune response (IIR) is a coordinated intracellular signaling network activated by the presence of pathogen-associated molecular patterns that limits pathogen spread and induces adaptive immunity. Although the precise temporal activation of the various arms of the IIR is a critical factor in the outcome of a disease, currently there are no quantitative multiplex methods for its measurement. In this study, we investigate the temporal activation pattern of the IIR in response to intracellular double-stranded RNA stimulation using a quantitative 10-plex stable isotope dilution-selected reaction monitoring-MS assay. We were able to observe rapid activation of both NF-κB and IRF3 signaling arms, with IRF3 demonstrating a transient response, whereas NF-κB underwent a delayed secondary amplification phase. Our measurements of the NF-κB-IκBα negative feedback loop indicate that about 20% of IκBα in the unstimulated cell is located within the nucleus and represents a population that is rapidly degraded in response to double-stranded RNA. Later in the time course of stimulation, the nuclear IκBα pool is repopulated first prior to its cytoplasmic accumulation. Examination of the IRF3 pathway components shows that double-stranded RNA induces initial consumption of the RIG-I PRR and the IRF3 kinase (TBK1). Stable isotope dilution-selected reaction monitoring-MS measurements after siRNA-mediated IRF3 or RelA knockdown suggests that a low nuclear threshold of NF-κB is required for inducing target gene expression, and that there is cross-inhibition of the NF-κB and IRF3 signaling arms. Finally, we were able to measure delayed noncanonical NF-κB activation by quantifying the abundance of the processed (52 kDa) NF-κB2 subunit in the nucleus. We conclude that quantitative proteomics measurement of the individual signaling arms of the IIR in response to system perturbations is significantly enabled by stable isotope dilution-selected reaction monitoring-MS-based quantification, and that this technique will reveal novel insights into the dynamics and connectivity of the IIR.

Immunogenomics approaches for vaccine evaluation

Vaccines represent a potent tool to prevent or contain diseases with high morbidity or mortality. However, despite their widespread use, there is still a limited understanding of the mechanisms underlying the effective elicitation of protective immune responses by vaccines. The integrated co-operation between cells and molecules of innate and adaptive immune systems is under intense study by several groups and constantly updated. The recent development of new technologies and computational tools permits the comprehensive and quantitative analysis of the interactions between all of the components of immunity over time. This study reviews recent progress in exploiting an immunogenomics approach, within the systems biology strategy, to study and evaluate vaccine strategies for infectious and neoplastic diseases. The final goal of this approach is 2-fold, looking for novel and unpredictable mechanisms as well as identifying common immune signatures, relevant for predicting immune responsiveness to improve the design of vaccine strategies. Such approach, indeed, would enable the switch from 'empirical' to 'knowledge-based' vaccinology, leading to a patient-tailored treatment.

Manipulation of immunodominant dengue virus E protein epitopes reduces potential antibody-dependent enhancement

Background

Dengue viruses (DENV) are the most important arboviruses of humans and cause significant disease. Infection with DENV elicits antibody responses to the envelope glycoprotein, predominantly against immunodominant, cross-reactive, weakly-neutralizing epitopes. These weakly-neutralizing antibodies are implicated in enhancing infection via Fcγ receptor bearing cells and can lead to increased viral loads that are associated with severe disease. Here we describe results from the development and testing of cross-reactivity reduced DENV-2 DNA vaccine candidates that contain substitutions in immunodominant B cell epitopes of the fusion peptide and domain III of the envelope protein.

Results

Cross-reactivity reduced and wild-type vaccine candidates were similarly immunogenic in outbred mice and elicited high levels of neutralizing antibody, however mice immunized with cross-reactivity reduced vaccines produced significantly reduced levels of immunodominant cross-reactive antibodies. Sera from mice immunized with wild-type, fusion peptide-, or domain III- substitution containing vaccines enhanced heterologous DENV infection in vitro, unlike sera from mice immunized with a vaccine containing a combination of both fusion peptide and domain III substitutions. Passive transfer of immune sera from mice immunized with fusion peptide and domain III substitutions also reduced the development of severe DENV disease in AG129 mice when compared to mice receiving wild type immune sera.

Conclusions

Reducing cross-reactivity in the envelope glycoprotein of DENV may be an approach to improve the quality of the anti-DENV immune response.

Delivery success rate of engineered nanoparticles in the presence of the protein corona: a systems-level screening

Nanoparticles (NPs) for medical applications are often introduced into the body via intravenous injections, leading to the formation of a protein corona on their surface due to the interaction with blood plasma proteins. Depending on its composition and time evolution, the corona will modify the biological behavior of the particle. For successful delivery and targeting, it is therefore important to assess on a quantitative basis how and to what extent the presence of the corona perturbs the specific interaction of a designed NP with its cellular target. We present a theoretical systems-level analysis, in which peptides have been covalently coupled to the surface of nanoparticles, describing the delivery success rate in varying conditions, with regard to protein composition of the surrounding fluid. Dynamic modeling and parameter sensitivity analysis proved to be useful and computationally affordable tools to aid in the design of NPs with increased success rate probability in a biological context.

FROM THE CLINICAL EDITOR

The formation of a protein corona consisting of blood plasma proteins on the surface of intravenously delivered nanoparticles may modify the biological behavior of the particles. This team of investigators present a theoretical systems-level analysis of this important and often neglected phenomenon.

Overlap of genetic influences in phenotypes classically categorized as psychiatric vs medical disorders

Psychiatric disorders have traditionally been segregated from medical disorders in terms of drugs, treatment, insurance coverage and training of clinicians. This segregation is consistent with the long-standing observation that there are inherent differences between psychiatric disorders (diseases relating to thoughts, feelings and behavior) and medical disorders (diseases relating to physical processes). However, these differences are growing less distinct as we improve our understanding of the roles of epistasis and pleiotropy in medical genetics. Both psychiatric and medical disorders are predisposed in part by genetic variation, and psychiatric disorders tend to be comorbid with medical disorders. One hypothesis on this interaction posits that certain combinations of genetic variants (epistasis) influence psychiatric disorders due to their impact on the brain, but the associated genes are also expressed in other tissues so the same groups of variants influence medical disorders (pleiotropy). The observation that psychiatric and medical disorders may interact is not novel. Equally, both epistasis and pleiotropy are fundamental concepts in medical genetics. However, we are just beginning to understand how genetic variation can influence both psychiatric and medical disorders. In our recent work, we have discovered gene networks significantly associated with psychiatric and substance use disorders. Invariably, these networks are also significantly associated with medical disorders. Recognizing how genetic variation can influence both psychiatric and medical disorders will help us to understand the etiology of the individual and comorbid disease phenotypes, predict and minimize side effects in drug and other treatments, and help to reduce stigma associated with psychiatric disorders.