Bringing systems biology to cancer,immunology and infectious disease

A report on the seventh annual ‘International Conference on Systems Biology of Human Disease’ held in Boston, Massachusetts, USA, 17–19 June, 2014.     

Transaldolase: From biochemistry to human disease

The role of the enzyme transaldolase (TAL) in central metabolism, its biochemical properties, structure, and role in human disease is reviewed. The nearly ubiquitous enzyme transaldolase is a part of the pentose phosphate pathway and transfers a dihydroxyacetone group from donor compounds (fructose 6-phosphate or sedoheptulose 7-phosphate) to aldehyde acceptor compounds. The phylogeny of transaldolases shows that five subfamilies can be distinguished, three of them with proven TAL enzyme activity, one with unclear function, and the fifth subfamily comprises transaldolase-related enzymes, the recently discovered fructose 6-phosphate aldolases. The three-dimensional structure of a bacterial (Escherichia coli TAL B) and the human enzyme (TALDO1) has been solved. Based on the 3D-structure and mutagenesis studies, the reaction mechanism was deduced. The cofactor-less enzyme proceeds with a Schiff base intermediate (bound dihydroxyacetone). While a transaldolase deficiency is well tolerated in many microorganisms, it leads to severe symptoms in homozygous TAL-deficient human patients. The involvement of TAL in oxidative stress and apoptosis, in multiple sclerosis, and in cancer is discussed.     

Understanding the contribution of synonymous mutations to human disease

Synonymous mutations - sometimes called 'silent' mutations - are now widely acknowledged to be able to cause changes in protein expression, conformation and function. The recent increase in knowledge about the association of genetic variants with disease, particularly through genome-wide association studies, has revealed a substantial contribution of synonymous SNPs to human disease risk and other complex traits. Here we review current understanding of the extent to which synonymous mutations influence disease, the various molecular mechanisms that underlie these effects and the implications for future research and biomedical applications.     

Modelling infectious disease to support human health

During the current COVID-19 pandemic, there has been renewed scientific and public focus on understanding the pathogenesis of infectious diseases and investigating vaccines and therapies to combat them. In addition to the tragic toll of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we also recognize increased threats from antibiotic-resistant bacterial strains, the effects of climate change on the prevalence and spread of human pathogens, and the recalcitrance of other infectious diseases – including tuberculosis, malaria, human immunodeficiency virus (HIV) and fungal infections – that continue to cause millions of deaths annually. Large amounts of funding have rightly been redirected toward vaccine development and clinical trials for COVID-19, but we must continue to pursue fundamental and translational research on other pathogens and host immunity. Now more than ever, we need to support the next generation of researchers to develop and utilize models of infectious disease that serve as engines of discovery, innovation and therapy.

Summary: This Editorial considers how knowledge from animal and other models of infectious disease can impact our understanding of human biology and potential therapies, focusing largely on zebrafish. It also highlights ways in which DMM is supporting these areas.

As an Editor at Disease Models & Mechanisms (DMM) and an academic researcher using zebrafish as a model to study tuberculosis, it is especially exciting to read and publish research in zebrafish to obtain, in a whole, live vertebrate, insights into infectious diseases and therapies (Box 1). Indeed, zebrafish provide a remarkable vertebrate model for many questions related to infectious disease. Embryos and larvae are optically transparent, enabling microscopy of both pathogen and host that would be more challenging or cumbersome in other systems (Fig. 1). Knock-in of fluorescent tags at endogenous loci allows direct and detailed in vivo visualization of the host immune response (Cronan et al., 2018). Both forward and reverse genetic approaches for understanding infection are straightforward and are buttressed by the high-throughput capabilities of this model, in which a single tank of adult zebrafish can produce hundreds of embryos per week. Furthermore, chemical biology screens and interventions using intact, living animals are uniquely accessible to researchers, as zebrafish larvae and embryos are permeable to diverse small molecules and fit within a single well of 96-well and 384-well plates (Patton et al., 2021). Open in a separate windowFig. 1.Zebrafish larva infected with fluorescent Mycobacterium abscessus expressing TdTomato, shown in red. Image courtesy of Matt Johansen (Johansen et al., 2021).Box 1. DMM highlights zebrafish advancing knowledge in infectious diseaseRecent publications in DMM show the potential of the zebrafish model system to provide new or fuller insights into infectious diseases and therapies. One question being addressed is how basic cell-autonomous immune processes function in the context of a full organism. Various Reviews have highlighted what we have learned about the role of pyroptosis in host defence against bacterial infections (Brokatzky and Mostowy, 2022), as well as advances in understanding the diverse roles that macrophages and neutrophils play during the initial response to a variety of infectious and inflammatory stimuli (Rosowski, 2020). Zebrafish can also provide models for parasitic diseases that are relatively neglected, and we were pleased to publish a zebrafish model that provides insight into Toxoplasma pathogenesis, particularly the in vivo interactions of Toxoplasma with macrophages (Yoshida et al., 2020). Research dissecting the role of host immune cells in pathogen responses can be further potentiated by new tools, such as those developed by the Lieschke laboratory using macrophage and neutrophil-specific Cas9 driver lines to allow cell-specific genetic perturbation (Isiaku et al., 2021).Non-tuberculous mycobacteria causing pulmonary disease are a growing threat worldwide, with an antibiotic resistance profile that makes them very difficult to treat (Stout et al., 2016; Vinnard et al., 2016). An exploration of phage therapy for non-tuberculous mycobacteria in the zebrafish provides new insights into exciting clinical work that bookends this publication (Johansen et al., 2021). Engineered bacteriophages targeting specific strains of Mycobacterium abscessus have now been used clinically in cases of advanced lung disease (Dedrick et al., 2019; Nick et al., 2022). In other work, Habjan et al. employed the zebrafish mycobacterial infection model as an early screening step for anti-tuberculosis hits from in vitro screens that might have the best chance for in vivo translation. Following up on a screen for novel in vitro activity against Mycobacterium tuberculosis that identified ∼240 compounds, they identified 14 compounds with good in vivo activity. Impressively, they went on to identify the target of the strongest in vivo hit as being a mycobacterial aspartyl-tRNA synthase through screening for resistant mutants in both Mycobacterium marinum and Mycobacterium tuberculosis (Habjan et al., 2021).Drug screens, like those discussed above, are possible due to the permeability of the zebrafish to small molecules, which also allows creative ways to control the induction of host cytokines. DMM published an approach that enables drug-inducible, tissue-specific, titratable expression of different cytokines (Ibrahim et al., 2020). Harnessing this permeability in zebrafish can also enable detailed exploration of the effects of drugs, such as broadly used glucocorticoids, on specific innate immune cell types (Xie et al., 2019).The zebrafish has also been used as a model to understand infectious disease therapies targeting the pathogen directly. A recent paper describes the in vivo efficacy of nanoparticle-based delivery of lipophilic antibiotics, as well as use of the zebrafish to screen different formulations (Knudsen Dal et al., 2022). Finally, in the adult zebrafish sphere, a recent Review focused on how zebrafish can inform vaccine development strategies (Saralahti et al., 2020).These recent publications highlight some of the strengths of the zebrafish model for infectious disease research. DMM aims to be at the forefront in encouraging scientists and clinicians to leverage these insights for future therapies.Although efforts in zebrafish are often recognized and valued within the model organism community and beyond, it can sometimes be hard to break through to the world of clinical research. I vividly remember the excitement of being invited to present my work as a starting assistant professor at an early-career researcher lunch with a prominent visiting scientist, only to have my research and plans dismissed with some variation of “Well, why don''t you try to figure out what''s actually going on in people?”.Indeed, this is what many zebrafish researchers are ultimately trying to do by a different route. The goal of harnessing the knowledge we generate in models to impact human biology and therapies is an important part of the scientific enterprise. Many of us want and expect our findings to be relevant beyond the context of a model system. In my field, it has been exciting to see work in the zebrafish emerge that has led to the discovery of fundamentally conserved features of tuberculosis and host immunity – from zebrafish to humans – and has since translated to ongoing clinical trials.However, although we might hope that our work will be inherently understood and utilized in the clinical context, maximizing the potential of this research requires community advocates and communicators to help place the work in context. This can be achieved through ongoing dialogue among researchers, clinicians and patients to understand medical needs and perspectives. For example, DMM and The Company of Biologists have been long-time supporters of societies, such as the Zebrafish Disease Models Society, which focuses on the translational potential of zebrafish for understanding human disease and for developing new therapies, including some being investigated in clinical trials.Thus, it is useful to consider the following three broad themes when using model organisms in infectious disease research:

1. Conserved host–pathogen interactions in model systems. Although we all recognize, even at a strictly visual level, the many differences between the biology of a model organism and human biology, there is fundamentally conserved biology to be explored. Immune signalling pathways and underlying principles, as well as molecular and cellular details, first discovered and dissected in worms, flies, fish, mice and other model organisms, have translated remarkably well to human biology in many cases.
2. Model diversity. Divergent biology – in addition to being fascinating and important for the sake of knowledge itself – also leads to vital new insights and therapeutic approaches. As just one example, bacteriophages were instrumental in the discovery of fundamental aspects of gene regulation, have been used to facilitate genetic manipulation of seemingly genetically intractable pathogens, and are now being engineered and deployed therapeutically. And the study of bacterial–bacteriophage interactions of course led to all the advances made possible by CRISPR. These and many other examples from models that diverge from humans all support open-mindedness in science and emphasize the strength of laboratories taking diverse approaches and using diverse models. Pressing questions and opportunities in this realm are many, including investigation of how some non-human immune systems – those of bats, as just one example – permit asymptomatic tolerance of viruses that may be pathogenic in humans (Hayman, 2019). Which animal species restrict human pathogens via immune mechanisms that might eventually be harnessed therapeutically? Some of these topics will be prominent in a 2023 meeting organized by DMM entitled ‘Infectious Diseases Through an Evolutionary Lens’, which will take place in London at the British Medical Association House (Fig. 2).Open in a separate windowFig. 2.DMM''s 2023 meeting is entitled ‘Infectious Diseases Through an Evolutionary Lens’ and will take place in London at the British Medical Association House. Register your interest here: https://www.biologists.com/infectious-diseases-through-an-evolutionary-lens-contact-form/.
3. Engineering preclinical and predictive models of infectious disease. With advances in gene editing and the ability to make specific base edits, it is possible to precisely model human variants in an in vivo context during infection. Organisms like the zebrafish can provide useful models to delve into the specific consequences of these variants. Orthogonal approaches include mammalian animal models and advanced human cell models (Leist et al., 2020; van der Vaart et al., 2021). Discussion between scientists doing this preclinical work and clinical collaborators will be needed to determine to what degree the model recapitulates human disease and how these models can be used to advance new therapies. Recently, we have seen some of the landscape for clinical trials change, and in public health emergencies, collaborations would ideally accelerate the time from discovery to clinic. Again, this will require dialogue with and buy-in from clinical researchers to put together rigorous clinical trials.

DMM seeks to create and contribute to the ongoing conversations among and between basic scientists, clinical researchers and clinicians, with insights and criticisms from each of these domains. By highlighting rigorous, high-quality science in these areas, we hope to contribute to improved understanding of infectious diseases and new approaches to treatment.     

117例医院真菌感染分析及预防

目的 了解佛山市南海人民医院真菌感染的分布,探讨有效预防和控制真菌感染的措施。方法 对该院117例真菌感染病例作回顾性分析。结果 3583例送检标本中真菌检出率为3．27％（117／3583）,医院内真菌感染率为2．95％（106／3583）。分离出真菌以白色念珠菌为主（70／117．59．8％）、热带念珠菌次之（17／117,14．5％）、霉菌居第3位（9／117．7．69％）。药敏显示：5-氟胞嘧啶、两性霉素B和制霉素敏感率较高,分别为92．4％、93．3％和92．5％,咪康唑、酮康唑和益康唑敏感率较低．为52．0％、49．0％和36．0％。结论 医院内真菌感染占真菌感染绝大部分,感染真菌以白色念珠菌为主。感染部位以呼吸道为主;临床规范、合理使用广谱抗生素,加强消毒护理工作。是预防控制真菌感染发生的最有效措施。     

The clinical immunology of human Chagas disease

Human infection with the protozoan parasite Trypanosoma cruzi leads to Chagas disease, which affects approximately 17 million people in Latin America. A significant percentage of the infected population will develop clinical symptoms or present changes in laboratory and/or image evaluation. The existence of a large spectrum of clinical manifestations--with patients ranging from asymptomatic to severe cardiac involvement--emphasizes the need to use standardized and well-defined clinical criteria among different research groups. In this article, we carry out a systematic review of the immunology in human Chagas disease, discussing recent findings in the context of a clinical perspective.     

From fundamental immunology to development of vaccinology

In the last ten years research in vaccinology has been developed in the world to conceive new vaccine approaches against infections like HIV/AIDS. Jean-Gérard Guillet is a pioneer in the development of new vaccine strategies. From the first results he obtained in the late 80's on the presentation of antigenic peptides to T cells, he axed his work on the study of induction mechanisms of T cell mediated immune responses. The selection of antigenic peptides and the search to enhance antigen immunogenicity led him to elaborate lipopeptides as new vaccine formulae. The efficacy of these preparations was tested in animal models (mouse, macaque) and, thereafter, in humans with clinical trials promoted by the French National Agency for AIDS and viral hepatitis (ANRS). The study of T-cell induced responses in vaccinated volunteers was implemented following the creation of two facilities, an immuno-monitoring platform and the Clinical Investigation Centre Cochin-Pasteur, a structure specialized in vaccinology.     

Implementation of hypocalcaemia prevention programmes in commercial dairy herds: From theory to practice

Hypocalcaemia prevention programmes have been widely studied in experimental settings, but their feasibility has not been assessed under field conditions. The main objective of this study was to evaluate, in the context of small dairy farms in western France, whether and how dairy farmers implement prevention programmes and manage the feeding of dry cows to prevent hypocalcaemia. Seventy-nine commercial Holstein dairy farms in Brittany (France) were enrolled in a qualitative study in 2019. We conducted in-person interviews with the farmers to 1) understand the rationale behind the type and seasonality of prevention programmes they implemented and 2) assess how closely they followed common recommendations when implementing them. Most farmers (80 %) used at least one prevention programme, especially supplying a mineral mix formulated to meet the needs of dry cows in late gestation (53 %), acidifying the diet in late gestation (37 %), and supplying calcium at calving (oral or injectable form, 37 %). The use of programmes depended on whether the diet composition varied throughout the year. Among farmers who provided an acidified diet, 25 % did not supply a specific mineral mix to dry cows to ensure an adequate amount of P, Ca, and Mg, which could decrease the effectiveness of the acidification programme. A lack of reliability in feeding practices, such as not weighing feed or not delivering feed frequently enough, was identified for 61 % of contributing farms. Management practices could result in supplying an unsuitable amount of P, Ca, or Mg immediately before calving; for example, inappropriate batching practices around calving were identified for 22 % (cows) to 32 % (heifers) of farms. In addition, nearly all contributing farmers had no processes in place to monitor the effectiveness of the programmes implemented. Reasons for this overall lack of compliance should be explored.     

The contribution of dormant origins to genome stability: From cell biology to human genetics

The ability of a eukaryotic cell to precisely and accurately replicate its DNA is crucial to maintain genome stability. Here we describe our current understanding of the process by which origins are licensed for DNA replication and review recent work suggesting that fork stalling has exerted a strong selective pressure on the positioning of licensed origins. In light of this, we discuss the complex and disparate phenotypes observed in mouse models and humans patients that arise due to defects in replication licensing proteins.     

Golgi inCOGnito: From vesicle tethering to human disease

The Conserved Oligomeric Golgi (COG) complex, a multi-subunit vesicle tethering complex of the CATCHR (Complexes Associated with Tethering Containing Helical Rods) family, controls several aspects of cellular homeostasis by orchestrating retrograde vesicle traffic within the Golgi. The COG complex interacts with all key players regulating intra-Golgi trafficking, namely SNAREs, SNARE-interacting proteins, Rabs, coiled-coil tethers, and vesicular coats. In cells, COG deficiencies result in the accumulation of non-tethered COG-complex dependent (CCD) vesicles, dramatic morphological and functional abnormalities of the Golgi and endosomes, severe defects in N- and O- glycosylation, Golgi retrograde trafficking, sorting and protein secretion. In humans, COG mutations lead to severe multi-systemic diseases known as COG-Congenital Disorders of Glycosylation (COG-CDG). In this report, we review the current knowledge of the COG complex and analyze COG-related trafficking and glycosylation defects in COG-CDG patients.     

The contribution of immunology to the rational design of novel antibacterial vaccines

In most cases, a successful vaccine must induce an immune response that is better than the response invoked by natural infection. Vaccines are still unavailable for several bacterial infections and vaccines to prevent such infections will be best developed on the basis of our increasing insights into the immune response. Knowledge of the signals that determine the best possible acquired immune response against a given pathogen - comprising a profound T- and B-cell memory response as well as long-lived plasma cells - will provide the scientific framework for the rational design of novel antibacterial vaccines.