T-Cell Receptor Repertoire Analysis with Computational Tools—An Immunologist’s Perspective

Over the last few years, there has been a rapid expansion in the application of information technology to biological data. Particularly the field of immunology has seen great strides in recent years. The development of next-generation sequencing (NGS) and single-cell technologies also brought forth a revolution in the characterization of immune repertoires. T-cell receptor (TCR) repertoires carry comprehensive information on the history of an individual’s antigen exposure. They serve as correlates of host protection and tolerance, as well as biomarkers of immunological perturbation by natural infections, vaccines or immunotherapies. Their interrogation yields large amounts of data. This requires a suite of highly sophisticated bioinformatics tools to leverage the meaning and complexity of the large datasets. Many different tools and methods, specifically designed for various aspects of immunological research, have recently emerged. Thus, researchers are now confronted with the issue of having to choose the right kind of approach to analyze, visualize and ultimately solve their task at hand. In order to help immunologists to choose from the vastness of available tools for their data analysis, this review addresses and compares commonly used bioinformatics tools for TCR repertoire analysis and illustrates the advantages and limitations of these tools from an immunologist’s perspective.

CAR-NK Cells: From Natural Basis to Design for Kill

Chimeric antigen receptors (CARs) are fusion proteins with an extracellular antigen recognition domain and numerous intracellular signaling domains that have been genetically modified. CAR-engineered T lymphocyte-based therapies have shown great success against blood cancers; however, potential fatal toxicity, such as in cytokine release syndrome, and high costs are some shortcomings that limit the clinical application of CAR-engineered T lymphocytes and remain to overcome. Natural killer (NK) cells are the focal point of current immunological research owing to their receptors that prove to be promising immunotherapeutic candidates for treating cancer. However, to date, manipulation of NK cells to treat malignancies has been moderately successful. Recent progress in the biology of NK cell receptors has greatly transformed our understanding of how NK cells recognize and kill tumor and infected cells. CAR-NK cells may serve as an alternative candidate for retargeting cancer because of their unique recognition mechanisms, powerful cytotoxic effects especially on cancer cells in both CAR-dependent and CAR-independent manners and clinical safety. Moreover, NK cells can serve as an ‘off-the-shelf product’ because NK cells from allogeneic sources can also be used in immunotherapies owing to their reduced risk of alloreactivity. Although ongoing fundamental research is in the beginning stages, this review provides an overview of recent developments implemented to design CAR constructs to stimulate NK activation and manipulate NK receptors for improving the efficiency of immunotherapy against cancer, summarizes the preclinical and clinical advances of CAR-NK cells against both hematological malignancies and solid tumors and confronts current challenges and obstacles of their applications. In addition, this review provides insights into prospective novel approaches that further enhance the efficiency of CAR-NK therapies and highlights potential questions that require to be addressed in the future.

Nature of Acquired Immune Responses, Epitope Specificity and Resultant Protection from SARS-CoV-2

The primary global response to the SARS-CoV-2 pandemic has been to bring to the clinic as rapidly as possible a number of vaccines that are predicted to enhance immunity to this viral infection. While the rapidity with which these vaccines have been developed and tested (at least for short-term efficacy and safety) is commendable, it should be acknowledged that this has occurred despite the lack of research into, and understanding of, the immune elements important for natural host protection against the virus, making this endeavor a somewhat unique one in medical history. In contrast, as pointed out in the review below, there were already important past observations that suggested that respiratory infections at mucosal surfaces were susceptible to immune clearance by mechanisms not typical of infections caused by systemic (blood-borne) pathogens. Accordingly, it was likely to be important to understand the role for both innate and acquired immunity in response to viral infection, as well as the optimum acquired immune resistance mechanisms for viral clearance (B cell or antibody-mediated, versus T cell mediated). This information was needed both to guide vaccine development and to monitor its success. We have known that many pathogens enter into a quasi-symbiotic relationship with the host, with each undergoing sequential change in response to alterations the other makes to its presence. The subsequent evolution of viral variants which has caused such widespread concern over the last 3–6 months as host immunity develops was an entirely predictable response. What is still not known is whether there will be other unexpected side-effects of the deployment of novel vaccines in humans which have yet to be characterized, and, if so, how and if these can be avoided. We conclude by remarking that to ignore a substantial body of well-attested immunological research in favour of expediency is a poor way to proceed.

Optimized immunoglobulin knock-ins using Cas9 reveal peritoneal B cell lineage relationships in vivo

Immunoglobulin (Ig) knock-in mice are valuable tools in basic and translational immunological research. Here we present Speed-Ig, a rapid Cas9-based method for generating Ig knock-in mouse lines with high on-target integration rates at both heavy and light chain alleles. With standardized target sites and promoter regions, Speed-Ig mice can be used for comparative studies of B cell biology and vaccine optimization in vivo. We used Speed-Ig to create panels of mice with Ig pairs derived from B-1a, B-1b, and B-2 cells. Surprisingly, B-1b and B-2 Ig pairs drove both B-1b and B-2 phenotypes, suggesting a previously unknown lineage relationship between these subsets. We then confirmed the B-1:B-2 relationship with transcription factor reporter lines and through adoptive cell transfer experiments. In summary, our Ig knock-in approach facilitated the discovery of previously unappreciated aspect of innate-like B cell biology.

Clinical and immunological studies of humoral factors of inflammation and regeneration in patients with injuries of the frontal and basal area

The authors conducted clinical and immunological research on the identification of сytokine factors of inflammation and regeneration in patients with frontal bone trauma (29) and practically healthy donors (11). Factors of inflammation (interleukin-1β, γ-interferon), anti-inflammation and regeneration (interleukin-34 and transforming growth factor – TGF-1β) were determined in the blood serum by ELISA. It was found that the content of the factor of regeneration decreases and the levels of anti-inflammatory cytokines increase in the blood serum of the patients with frontal traumas with frontal sinus damage.

The Invasive Bank Vole (Myodes glareolus): A Model System for Studying Parasites and Ecoimmunology during a Biological Invasion

The primary driver of the observed increase in emerging infectious diseases (EIDs) has been identified as human interaction with wildlife and this increase has emphasized knowledge gaps in wildlife pathogens dynamics. Wild rodent models have proven excellent for studying changes in parasite communities and have been a particular focus of eco-immunological research. Helminth species have been shown to be one of the factors regulating rodent abundance and indirectly affect disease burden through trade-offs between immune pathways. The Myodes glareolus invasion in Ireland is a unique model system to explore the invasion dynamics of helminth species. Studies of the invasive population of M. glareolus in Ireland have revealed a verifiable introduction point and its steady spread. Helminths studies of this invasion have identified enemy release, spillover, spillback and dilution taking place. Longitudinal studies have the potential to demonstrate the interplay between helminth parasite dynamics and both immune adaptation and coinfecting microparasites as M. glareolus become established across Ireland. Using the M. glareolus invasion as a model system and other similar wildlife systems, we can begin to fill the large gap in our knowledge surrounding the area of wildlife pathogen dynamics.

Immunological research about ultra-high dilution and Homeopathy: From 1994 to 2014

Background: This review is part of a special issue of journal “Homeopathy” (ELSEVIER) scheduled for publication in 2015, about the follow-up of researches published in the book titled “Ultra-High Dilution, Physiology and Physics”, written and edited by PC Endler and J Schulte in 1994. In this book, Prof. Madeleine Bastide described experimental models in immunology that were used during the 1980s to investigate high dilution effects on several biological systems. Bastide categorized available papers in four categories: high dilutions of antigens; high dilutions of thymus, bursa and other hormones; high dilutions of cytokines and immunopharmacological activity of silica. The studies about high dilutions of antigens were interrupted from this time onwards. Only the in vitro models developed on antigens and histamine dilutions lasted up to 2009. During this process, a huge multi-centre study was performed, with high reproducibility, and involving different independent laboratories. The studies about highly diluted cytokines, thymulin and other hormones brought some regulatory properties of endogenous substances prepared homeopathically, with special focus on epigenetic mechanisms of highly diluted cytokines. The frequently studied substance was Thymulin 5cH, which improved the activity of phagocytes in viral, bacterial and parasitic infections. Studies about the immunopharmacological activity of silica have assumed a new focus: the putative role of silica as active contaminant present in high dilutions, that is still under discussion.

"Ultra-high Dilution" 1994 revisited 2014: Follow up of experiments and theories

Background: “Research in ultra-high dilutions, and the interaction of ultra-high dilutions and living systems, has reached a level of quality and popularity that it is about to be taken seriously by current … sciences …” the editors wrote in their introduction to “Ultra High Dilution. Physiology and Physics”, published by Kluwer (now Springer) in 19941. Back then, this anthology assembled contributions of leading scientists in fundamental and clinical research on homeopathy. Over the following two decades, it became widely quoted within the homeopathic community and also known in other research communities. Aim: To re-visit and review the 1994 studies in biology, physics, biophysics and clinics from the perspective of 2014. Methods: As a rule, the original authors from 1994 or closed laboratory colleagues were asked to contribute papers covering their research efforts and learnings in the period from1994 up to 2014. These contributions were a) edited and cross-referenced and b) peer reviewed via the Elsevier Electronic System in preparation of a special issue of the journal “Homeopathy”, London, to appear in October 2015. Results: Part 1 (Biology) includes chapters • on dose-dependent hormesis effects in low and very low doses by Menachem Oberbaum, who was also the author on this topic in 1994; • on further results on the “classical” model with wheat and an ultra high dilution (UHD) of a silver salt by Waltraud Scherer-Pongratz, also author in 1994, et al.; on the model with highland amphibians and an UHD of the hormone thyroxine by Christian Endler, also author in 1994, et al.; and on a new model derived from the latter two, combining wheat and a plant hormone by Scherer-Pongratz and Endler; • on a botanical and a zoological survey on high dilution research by the new contributors Tim Jäger, Stephan Baumgartner et al. and Leoni Bonamin et al., as well as a survey on immunological research by Bernard Poitevin, also author in 1994. • on UHD research from the laboratory of Madeleine Bastide, decedée, now pursued by Bonamin, and from the laboratory of Jacques Benveniste, decedé, now pursued by Yoléne Thomas; Part 2 (Biophysics) includes chapters • on effects of homeopathic medicines in closed vials by Roeland van Wijk, also author in 1994, et al.; • on electromagnetic and magentic vector potential bio-information and water by Cyril Smith, also author in 1994; Part 3 (Physics) includes chapters • on investigation topics, models and theories presented by various authors in 1994, followed up by Jurgen Schulte; • on experimental methods by Schulte, also author in 1994; • on the recent discussion on the theory of entanglement by Schulte Part 4 (Clinics) includes chapters • on provings of UHDs on healthy volunteers by Harald Walach, also author in 1994; • on a review by Robert Mathie of clinical research on homeopathy, as a follow-up to Max Haidvogl’s contribution (Haidvogl being happily retired) referring to Klaus Linde in 1994. Furthermore, • a contribution on quality and standards of reporting in homeopathy research was added by Beate Stock-Schroer, • a bibliographic survey on repetitions of experiments on UHDs by Endler et al. was included, • the outlook on “preliminary elements of a theory on UHDs” from 1994 was updated by the editors; • and Marco Righetti, as well as Peter Fisher, also contributors in 1994, wrote prefaces. Conclusion: “Ultra High Dilution revisited”, the special issue of “Homeopathy”, October 2015, may be seen as a “buena vista social club” of homeopathy researchers 1994 (luckily supported by younger colleagues), as a disclosure of new results on the old models (what happened between 1994 and 2014?), as well as a general survey on the state of UHD research.

Multi-Omics Approaches in Immunological Research

The immune system plays a vital role in health and disease, and is regulated through a complex interactive network of many different immune cells and mediators. To understand the complexity of the immune system, we propose to apply a multi-omics approach in immunological research. This review provides a complete overview of available methodological approaches for the different omics data layers relevant for immunological research, including genetics, epigenetics, transcriptomics, proteomics, metabolomics, and cellomics. Thereafter, we describe the various methods for data analysis as well as how to integrate different layers of omics data. Finally, we discuss the possible applications of multi-omics studies and opportunities they provide for understanding the complex regulatory networks as well as immune variation in various immune-related diseases.