Identifying and hurdling obstacles to translational research

Advancing mouse models for transplantation research

Mouse models have been instrumental in understanding mechanisms of transplant rejection and tolerance, but cross-study reproducibility and translation of experimental findings into effective clinical therapies are issues of concern. The Mouse Models in Transplantation symposium gathered scientists and physician-scientists involved in basic and clinical research in transplantation to discuss the strengths and limitations of mouse transplant models and strategies to enhance their utility. Participants recognized that increased procedure standardization, including the use of prespecified, defined endpoints, and statistical power analyses, would benefit the field. They also discussed the generation of new models that incorporate environmental and genetic variables affecting clinical outcomes as potentially important. If implemented, these strategies are expected to improve the reproducibility of mouse studies and increase their translation to clinical trials and, ideally, new Food and Drug Administration-approved drugs.

Innovative three-dimensional models for understanding mechanisms underlying lung diseases: powerful tools for translational research

Chronic lung diseases result from alteration and/or destruction of lung tissue, inevitably causing decreased breathing capacity and quality of life for patients. While animal models have paved the way for our understanding of pathobiology and the development of therapeutic strategies for disease management, their translational capacity is limited. There is, therefore, a well-recognised need for innovative in vitro models to reflect chronic lung diseases, which will facilitate mechanism investigation and the advancement of new treatment strategies. In the last decades, lungs have been modelled in healthy and diseased conditions using precision-cut lung slices, organoids, extracellular matrix-derived hydrogels and lung-on-chip systems. These three-dimensional models together provide a wide spectrum of applicability and mimicry of the lung microenvironment. While each system has its own limitations, their advantages over traditional two-dimensional culture systems, or even over animal models, increases the value of in vitro models. Generating new and advanced models with increased translational capacity will not only benefit our understanding of the pathobiology of lung diseases but should also shorten the timelines required for discovery and generation of new therapeutics. This article summarises and provides an outline of the European Respiratory Society research seminar "Innovative 3D models for understanding mechanisms underlying lung diseases: powerful tools for translational research", held in Lisbon, Portugal, in April 2022. Current in vitro models developed for recapitulating healthy and diseased lungs are outlined and discussed with respect to the challenges associated with them, efforts to develop best practices for model generation, characterisation and utilisation of models and state-of-the-art translational potential.

Vaccine-associated enhanced disease in humans and animal models: Lessons and challenges for vaccine development

The fight against infectious diseases calls for the development of safe and effective vaccines that generate long-lasting protective immunity. In a few situations, vaccine-mediated immune responses may have led to exacerbated pathology upon subsequent infection with the pathogen targeted by the vaccine. Such vaccine-associated enhanced disease (VAED) has been reported, or at least suspected, in animal models, and in a few instances in humans, for vaccine candidates against the respiratory syncytial virus (RSV), measles virus (MV), dengue virus (DENV), HIV-1, simian immunodeficiency virus (SIV), feline immunodeficiency virus (FIV), severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), and the Middle East respiratory syndrome coronavirus (MERS-CoV). Although alleviated by clinical and epidemiological evidence, a number of concerns were also initially raised concerning the short- and long-term safety of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is causing the ongoing COVID-19 pandemic. Although the mechanisms leading to this phenomenon are not yet completely understood, the individual and/or collective role of antibody-dependent enhancement (ADE), complement-dependent enhancement, and cell-dependent enhancement have been highlighted. Here, we review mechanisms that may be associated with the risk of VAED, which are important to take into consideration, both in the assessment of vaccine safety and in finding ways to define models and immunization strategies that can alleviate such concerns.

Signaling Pathways Involved in Myocardial Ischemia-Reperfusion Injury and Cardioprotection: A Systematic Review of Transcriptomic Studies in Sus scrofa

Myocardial damage in acute myocardial infarctions (AMI) is primarily the result of ischemia−reperfusion injury (IRI). Recognizing the timing of transcriptional events and their modulation by cardioprotective strategies is critical to address the pathophysiology of myocardial IRI. Despite the relevance of pigs for translational studies of AMI, only a few have identified how transcriptomic changes shape cellular signaling pathways in response to injury. We systematically reviewed transcriptomic studies of myocardial IRI and cardioprotection in Sus scrofa. Gene expression datasets were analyzed for significantly enriched terms using the Enrichr analysis tool, and statistically significant results (adjusted p-values of <0.05) for Signaling Pathways, Transcription Factors, Molecular Functions, and Biological Processes were compared between eligible studies to describe how these dynamic changes transform the myocardium from an injured and inflamed tissue into a scar. Then, we address how cardioprotective interventions distinctly modulate the myocardial transcriptome and discuss the implications of uncovering gene regulatory networks for cardiovascular pathologies and translational applications.

Artificial Intelligence Pipeline to Bridge the Gap between Bench Researchers and Clinical Researchers in Precision Medicine

Precision medicine informatics is a field of research that incorporates learning systems that generate new knowledge to improve individualized treatments using integrated data sets and models. Given the ever-increasing volumes of data that are relevant to patient care, artificial intelligence (AI) pipelines need to be a central component of such research to speed discovery. Applying AI methodology to complex multidisciplinary information retrieval can support efforts to discover bridging concepts within collaborating communities. This dovetails with precision medicine research, given the information rich multi-omic data that are used in precision medicine analysis pipelines. In this perspective article we define a prototype AI pipeline to facilitate discovering research connections between bioinformatics and clinical researchers. We propose building knowledge representations that are iteratively improved through AI and human-informed learning feedback loops supported through crowdsourcing. To illustrate this, we will explore the specific use case of nonalcoholic fatty liver disease, a growing health care problem. We will examine AI pipeline construction and utilization in relation to bench-to-bedside bridging concepts with interconnecting knowledge representations applicable to bioinformatics researchers and clinicians.

Humanized Mouse Models of Rheumatoid Arthritis for Studies on Immunopathogenesis and Preclinical Testing of Cell-Based Therapies

Rodent models of rheumatoid arthritis (RA) have been used over decades to study the immunopathogenesis of the disease and to explore intervention strategies. Nevertheless, mouse models of RA reach their limit when it comes to testing of new therapeutic approaches such as cell-based therapies. Differences between the human and the murine immune system make it difficult to draw reliable conclusions about the success of immunotherapies. To overcome this issue, humanized mouse models have been established that mimic components of the human immune system in mice. Two main strategies have been pursued for humanization: the introduction of human transgenes such as human leukocyte antigen molecules or specific T cell receptors, and the generation of mouse/human chimera by transferring human cells or tissues into immunodeficient mice. Recently, both approaches have been combined to achieve more sophisticated humanized models of autoimmune diseases. This review discusses limitations of conventional mouse models of RA-like disease and provides a closer look into studies in humanized mice exploring their usefulness and necessity as preclinical models for testing of cell-based therapies in autoimmune diseases such as RA.

Influence of Genetic Background on Hematologic and Histopathologic Alterations during Acute Granulocytic Anaplasmosis in 129/SvEv and C57BL/6J Mice Lacking Type I and Type II Interferon Signaling

The role of host type I IFN signaling and its interaction with other immune pathways during bacterial infections is incompletely understood. Type II IFN signaling plays a key role during numerous bacterial infections including granulocytic anaplasmosis (GA) caused by Anaplasma phagocytophilum infection. The function of combined type I and type II IFN signaling and their potential synergism during GA and similar tick-borne diseases is a topic of current research investigation. The goal of this study was to evaluate 2 mouse models of absent type I/type II IFN signaling in experimental A. phagocytophilum infection to determine the effects of background strain. Mice lacking both type I and type II IFN receptor signaling (IFNAR-/-/IFNGR-/-) on either the 129/SvEv or C57BL/6J genetic background were evaluated at days 0, 6, 8, and 12 of infection. Pathogen burden in multiple organs was largely similar between strains of infected mice, with few significant differences. Background strain influenced the immune response to infection. Mice of the 129/SvEv strain developed more severe hematologic abnormalities, particularly more severe leukocytosis with marked neutrophilia and lymphocytosis, throughout acute infection. Histopathologic changes occurred in infected mice of both strains and varied in severity by organ. 129/SvEv mice developed more severe pathologic changes in spleen and bone marrow, whereas C57BL/6J mice developed more severe renal pathology. This work highlights the importance of mouse background strain in dictating pathophysiologic response to infection and informs future work regarding the loss of type I and type II IFN signaling on the immune response during GA.

Rethinking biobanking and translational medicine in the Netherlands: how the research process stands to matter for patient care

Biobanking has been identified as one of the key components of translational medicine, and while current models for translation tend to focus their attention on how the products of research projects are fed back into health-care practices, we suggest that in addition to that the research process itself can have beneficial effects on the delivery of high-quality health care by streamlining diagnostic and follow-up protocols, reduced patient waiting times, and facilitating data comparison across patients. This Viewpoint is based on experiences with, and observations of, the neurodegenerative component of a clinical biobanking initiative in the Netherlands called the Parelsnoer Institute (PSI), which links all eight of the University Medical Centers for harmonized and standardized collection and storage processes for multiple disease conditions.

Large-scale polymorphism discovery in macaque G-protein coupled receptors

BACKGROUND

G-protein coupled receptors (GPCRs) play an inordinately large role in human health. Variation in the genes that encode these receptors is associated with numerous disorders across the entire spectrum of disease. GPCRs also represent the single largest class of drug targets and associated pharmacogenetic effects are modulated, in part, by polymorphisms. Recently, non-human primate models have been developed focusing on naturally-occurring, functionally-parallel polymorphisms in candidate genes. This work aims to extend those studies broadly across the roughly 377 non-olfactory GPCRs. Initial efforts include resequencing 44 Indian-origin rhesus macaques (Macaca mulatta), 20 Chinese-origin rhesus macaques, and 32 cynomolgus macaques (M. fascicularis).

RESULTS

Using the Agilent target enrichment system, capture baits were designed for GPCRs off the human and rhesus exonic sequence. Using next generation sequencing technologies, nearly 25,000 SNPs were identified in coding sequences including over 14,000 non-synonymous and more than 9,500 synonymous protein-coding SNPs. As expected, regions showing the least evolutionary constraint show greater rates of polymorphism and greater numbers of higher frequency polymorphisms. While the vast majority of these SNPs are singletons, roughly 1,750 non-synonymous and 2,900 synonymous SNPs were found in multiple individuals.

CONCLUSIONS

In all three populations, polymorphism and divergence is highly concentrated in N-terminal and C-terminal domains and the third intracellular loop region of GPCRs, regions critical to ligand-binding and signaling. SNP frequencies in macaques follow a similar pattern of divergence from humans and new polymorphisms in primates have been identified that may parallel those seen in humans, helping to establish better non-human primate models of disease.

Development of a new humanized mouse model to study acute inflammatory arthritis

BACKGROUND

Substantial advances have been generated in understanding the pathogenesis of rheumatoid arthritis (RA). Current murine models of RA-like disease have provided great insights into the molecular mechanism of inflammatory arthritis due to the use of genetically deficient or transgenic mice. However, these studies are limited by differences that exist between human and murine immune systems. Thus, the development of an animal model that utilizes human immune cells, will afford the opportunity to study their function in the initiation and propagation of inflammatory arthritis.

METHODS

One to two-day old irradiated NOD-scid IL2rγ(null) (NSG) mice were reconstituted with human CD34+ cord blood stem cells. Leukocytes were analyzed by flow cytometry and circulating antibodies were determined by ELISA. Arthritis was induced by injecting complete Freund's adjuvant into knee or ankle joints. Mice were also treated with the TNF inhibitor, Etanercept, or PBS and joints were analyzed histologically.

RESULTS

Humanized mice were established with high reconstitution rates and were able to spontaneously produce human immunoglobulins as well as specific IgG in response to immunization. Intraperitoneal injection of thioglycolate or injection of complete Freund's adjuvant into joints resulted in migration of human immune cells to the injected sites. Arthritic humanized mice treated with Etanercept had markedly less inflammation, which was associated with decreased total numbers of human CD45+ cells, including human lymphocytes and neutrophils.

CONCLUSIONS

The humanized mouse model is a new model to study inflammatory arthritis disease using human leukocytes without rejection of engrafted tissue. Future studies may adapt this system to incorporate RA patient cord blood and develop a chimeric animal model of inflammatory arthritis using genetically predisposed immune cells.

The airway epithelium as regulator of inflammation patterns in asthma

INTRODUCTION

Asthma is a complex, heterogeneous and mutifactorial disease and represents a major health problem in Westernized countries. The airway epithelium, with its direct physical contact with luminal triggers, has a major role in determining the nature of inflammation that develops in asthmatic airways.

OBJECTIVE

The present review aims to provide a brief overview of the numerous ways the airway epithelium can affect and influence the histopathological picture in asthma.

RESULTS AND CONCLUSION

The ways the epithelium aggravates inflammation range from acute responses to luminal triggers such as allergens and infections to the multipathogenic events occurring as a consequence of repeated epithelial damage-repair responses. The airway epithelium also facilitates the selective migration of leukocytes into the airway lumen, a process that is important in regulating inflammatory cell homeostasis. The fact that only some of the important leukocyte subtypes participate in this process cause translational problems and difficulties in the interpretation of luminal samples. To further reveal the nature of the multifaceted involvement of the airway epithelium in inflamed asthmatic airways emerges as a promising goal for identifying new therapeutic strategies.

The diverse ethics of translational research

Commentators on the ethics of translational research find it morally problematic. Types of translational research are said to involve questionable benefits, special risks, additional barriers to informed consent, and severe conflicts of interest. Translational research conducted on the global poor is thought to exploit them and increase international disparities. Some commentators support especially stringent ethical review. However, such concerns are grounded only in pre-approval translational research (now called T1). Whether or not T1 has these features, translational research beyond approval (T2: phase IV, health services, and implementation research) is unlikely to and, when conducted on the global poor, may support development. Therefore, insofar as T1 is morally problematic, and no independent objections to T2 exist, the ethics of translational research is diverse: while some translational research is problematic, some is not. Funding and oversight should reflect this diversity, and T2 should be encouraged, particularly when conducted among the global poor.

Life-science research within US academic medical centers

CONTEXT

Besides the generic "basic" vs "applied" labels, little information is known about the types of life-science research conducted within academic medical centers (AMCs).

OBJECTIVE

To determine the relative proportion, characteristics, funding, and productivity of AMC faculty by the type of research they conduct.

DESIGN

Mailed survey conducted in 2007 of 3080 life-science faculty at the 50 universities with medical schools that received the most funding from the National Institutes of Health in 2004. Response rate was 74%.

SETTING AND PARTICIPANTS

Research faculty affiliated with a medical school or teaching hospital, representing 77% of respondents (n = 1663).

MAIN OUTCOME MEASURES

Type of research (basic, translational, clinical trials, health services research/clinical epidemiology, multimode, other), total funding, industry funding, publications, professional activities, patenting behavior, and industry relationships.

RESULTS

Among AMC research faculty, 33.6% exclusively conducted basic science research as principal investigators compared with translational researchers (9.1%), clinical trial investigators (7.1%), and health services researchers/clinical epidemiologists (9.0%). While principal investigators garnered a mean of $410,755 in total annual research funding, 22.1% of all AMC research faculty were unsponsored, a proportion that ranged from 11.5% for basic science researchers to 46.8% for health services researchers (P < .001). The average AMC faculty member received $33,417 in industry-sponsored funding, with most of this money concentrated among clinical trial ($110,869) and multimode ($59,916) principal investigators. Translational (61.3%), clinical trial (67.3%), and multimode (70.9%) researchers were significantly more likely than basic science researchers (41.9%) to report a relationship with industry and that these relationships contributed to their most important scientific work (P < .05 for all comparisons).

CONCLUSION

The research function of AMCs is active and diverse, incorporating a substantial proportion of faculty who are conducting research and publishing without sponsorship.

Evaluation of animal models of neurobehavioral disorders

Animal models play a central role in all areas of biomedical research. The process of animal model building, development and evaluation has rarely been addressed systematically, despite the long history of using animal models in the investigation of neuropsychiatric disorders and behavioral dysfunctions. An iterative, multi-stage trajectory for developing animal models and assessing their quality is proposed. The process starts with defining the purpose(s) of the model, preferentially based on hypotheses about brain-behavior relationships. Then, the model is developed and tested. The evaluation of the model takes scientific and ethical criteria into consideration.Model development requires a multidisciplinary approach. Preclinical and clinical experts should establish a set of scientific criteria, which a model must meet. The scientific evaluation consists of assessing the replicability/reliability, predictive, construct and external validity/generalizability, and relevance of the model. We emphasize the role of (systematic and extended) replications in the course of the validation process. One may apply a multiple-tiered 'replication battery' to estimate the reliability/replicability, validity, and generalizability of result.Compromised welfare is inherent in many deficiency models in animals. Unfortunately, 'animal welfare' is a vaguely defined concept, making it difficult to establish exact evaluation criteria. Weighing the animal's welfare and considerations as to whether action is indicated to reduce the discomfort must accompany the scientific evaluation at any stage of the model building and evaluation process. Animal model building should be discontinued if the model does not meet the preset scientific criteria, or when animal welfare is severely compromised. The application of the evaluation procedure is exemplified using the rat with neonatal hippocampal lesion as a proposed model of schizophrenia.In a manner congruent to that for improving animal models, guided by the procedure expounded upon in this paper, the developmental and evaluation procedure itself may be improved by careful definition of the purpose(s) of a model and by defining better evaluation criteria, based on the proposed use of the model.

Translational integrity and continuity: personalized biomedical data integration

Translational research data are generated in multiple research domains from the bedside to experimental laboratories. These data are typically stored in heterogeneous databases, held by segregated research domains, and described with inconsistent terminologies. Such inconsistency and fragmentation of data significantly impedes the efficiency of tracking and analyzing human-centered records. To address this problem, we have developed a data repository and management system named TraM (http://tram.uchicago.edu), based on a domain ontology integrated entity relationship model. The TraM system has the flexibility to recruit dynamically evolving domain concepts and the ability to support data integration for a broad range of translational research. The web-based application interfaces of TraM allow curators to improve data quality and provide robust and user-friendly cross-domain query functions. In its current stage, TraM relies on a semi-automated mechanism to standardize and restructure source data for data integration and thus does not support real-time data application.

First-in-human trial participants: not a vulnerable population, but vulnerable nonetheless

The 21st-century translational science campaign could lead to an increase in first-in-human (FIH) trials. As tests of investigational interventions move from the laboratory to human research, scientists, officials, and review committees should address ongoing concerns about the ethics of FIH trials. In this article, I describe three ethical considerations relevant to all FIH trials: (1) the requirement for adequate preclinical research; (2) study design safeguards; and (3) choice of subject population. I also examine specific ethical considerations relevant to the three subject populations (healthy volunteers, seriously ill patients lacking standard treatment options, and stable patients) involved in FIH research. I recommend a variety of actions that could increase subject protection and the value of the information generated in FIH trials.

Basic science of the innate immune system and the lung

Infections of the lung are prevented first by denial of access, mediated by humoral and cellular systems that obscure the pathogen's target, simultaneously acting to kill and clear the pathogen. Where pathogens penetrate these initial defence systems, rapid detection of their presence is achieved by their engagement with a large family of pattern recognition receptors, including Toll-like receptors, retinoic-acid-inducible gene-like helicases and Nod-like receptors. Activation of a coordinated inflammatory response is achieved by cooperative signalling between sentinel leucocytes such as alveolar macrophages and lung tissue, following which a profound pro-inflammatory response mobilizes phagocytes such as neutrophils and monocytes to the lung. Resolution of the innate immune response, largely dependent upon neutrophil apoptosis, results in restoration of normal tissue architecture. In chronic disease, dysregulated inflammation maintains these systems in a state of constant activation, potentially resulting in tissue damage and progressive disease.

People and organizational issues in research systems implementation

Knowledge about people and organizational issues pertinent to implementation and maintenance of clinical systems has grown steadily over the past fifteen years. Less is known about implementation of systems used for clinical and biomedical research. In conjunction with current National Institutes of Health Roadmap efforts that promote translational research, these issues should now be identified and addressed. During the 2007 American College of Medical Informatics Symposium, members discussed behavioral aspects of translational informatics. This article summarizes that discussion, which covered organizational issues, implications of how knowledge about clinical systems implementation can inform research systems implementation, and those issues unique to each kind of system.

The role of TLR activation in inflammation

The Toll-like receptor family was originally identified in Drosophila, where it provides important developmental and immunological signalling. In mammals, the developmental signal appears to have been lost, but the immunological defence role of these receptors has been expanded to provide broad recognition of bacterial, fungal, viral and parasitic pathogens. There is increasing evidence that these receptors go beyond the recognition of microbial molecules to sense host tissue damage. Recognition of host molecules and commensal microbes is also involved in the restoration of normal tissue architecture after injury and in maintenance of epithelial health. Recent developments in the TLR field highlight the importance of these molecules to human health and disease and demonstrate that their targeting, to boost immunity or inhibit inflammation, is both feasible and also potentially challenging.

Toll-like receptor (TLR)-based networks regulate neutrophilic inflammation in respiratory disease

The neutrophil is a crucial early defence against microbial infection, but neutrophilic inflammation can result in devastating acute and chronic inflammatory diseases. In the lungs, the neutrophil is a principal part of the pathology of the acute respiratory distress syndrome, and its activation may also be of substantial importance in chronic obstructive pulmonary disease and some forms of asthma. Induction of neutrophil recruitment in response to microbial attack requires activation of TLR (Toll-like receptor)-based signalling pathways and the concerted actions of multiple cell types, including sentinel cells such as monocytes and macrophages acting together with tissue cell types such as the epithelium or smooth-muscle cell. The present review describes some of these networks and the resulting potential for their targeting in respiratory disease.

miniTUBA: medical inference by network integration of temporal data using Bayesian analysis

MOTIVATION

Many biomedical and clinical research problems involve discovering causal relationships between observations gathered from temporal events. Dynamic Bayesian networks are a powerful modeling approach to describe causal or apparently causal relationships, and support complex medical inference, such as future response prediction, automated learning, and rational decision making. Although many engines exist for creating Bayesian networks, most require a local installation and significant data manipulation to be practical for a general biologist or clinician. No software pipeline currently exists for interpretation and inference of dynamic Bayesian networks learned from biomedical and clinical data.

RESULTS

miniTUBA is a web-based modeling system that allows clinical and biomedical researchers to perform complex medical/clinical inference and prediction using dynamic Bayesian network analysis with temporal datasets. The software allows users to choose different analysis parameters (e.g. Markov lags and prior topology), and continuously update their data and refine their results. miniTUBA can make temporal predictions to suggest interventions based on an automated learning process pipeline using all data provided. Preliminary tests using synthetic data and laboratory research data indicate that miniTUBA accurately identifies regulatory network structures from temporal data.

AVAILABILITY

miniTUBA is available at http://www.minituba.org.