The adaptive immune system is a natural diagnostic and therapeutic. It recognizes threats earlier than clinical symptoms manifest and neutralizes antigen with exquisite specificity. Recognition specificity and broad reactivity is enabled via adaptive B-and T-cell receptors: the immune receptor repertoire. The human immune system, however, is not omnipotent. Our natural defense system sometimes loses the battle to parasites and microbes and even turns against us in the case of cancer and (autoimmune) inflammatory disease. A long-standing dream of immunoengineers has been, therefore, to mechanistically understand how the immune system "sees", "reacts" and "remembers" (auto)antigens. Only very recently, experimental and computational methods have achieved sufficient quantitative resolution to start querying and engineering adaptive immunity with great precision. In specific, these innovations have been applied with the greatest fervency and success in immunotherapy, autoimmunity and vaccine design. The work here highlights advances, challenges and future directions of quantitative approaches which seek to advance the fundamental understanding of immunological phenomena, and reverse engineer the immune system to produce auspicious biopharmaceutical drugs and immunodiagnostics. Our review indicates that the merger of fundamental immunology, computational immunology and (digital) biotechnology minimizes black box engineering, thereby advancing both immunological knowledge and as well immunoengineering methodologies. Introduction 3Advancing immunology through engineering innovations 3Adaptive immune receptors are natural diagnostics and therapeutics 3Engineering the vast immune receptor sequence space requires quantitative approaches 4Current approaches for immune repertoire analysis and immunoengineering 4Computational immunology and immunoinformatics of adaptive immunity 4 B-and T-cell pattern mining using machine and deep learning 6Mathematical modeling of immune receptor recognition 8Computational modeling of immune receptor 3D structure 9Computational modeling of antibody-epitope interaction 10Genomic sequencing of immune repertoires 12Identifying candidate TCRs or antibodies via high-throughput library screens 13Proteomic sequencing and serological profiling of antibody repertoires 14 Future directions for quantitative immunoengineering and immune receptor analysis 15Setting targets on public and private immune receptors 15Efficient modification of immune receptor activity in vitro and in vivo 16De novo design of immune receptor sequences 18Closing the data gap between immune receptor sequence and cognate epitope for immune receptor and epitope engineering 21Challenges in machine learning analysis on immune receptor repertoires 21Relating immune receptor antigen specificity to cellular transcriptomic profile 24 Conclusion 25 Conflicts of Interest 25 Focus Boxes 26Focus Box 1: Brief summary of deep learning and its architectures. 26Focus Box 2: Recognition holes in the immune repertoire 26 Notes and references 30mo...

The ability to use mesenchymal stromal cells (MSC) directly out of cryostorage would significantly reduce the logistics of MSC therapy by allowing on-site cryostorage of therapeutic doses of MSC at hospitals and clinics. Such a paradigm would be especially advantageous for the treatment of acute conditions such as stroke and myocardial infarction, which are likely to require treatment within hours after ischemic onset. Recently, several reports have emerged that suggest MSC viability and potency are damaged by cryopreservation. Herein we examine the effect of cryopreservation on human MSC viability, immunomodulatory potency, growth factor secretion, and performance in an ischemia/ reperfusion injury model. Using modifications of established cryopreservation methods we developed MSC that retain >95% viability upon thawing, remain responsive to inflammatory signals, and are able to suppress activated human peripheral blood mononuclear cells. Most importantly, when injected into the eyes of mice 3 hours after the onset of ischemia and 2 hours after the onset of reperfusion, cryopreserved performed as well as fresh MSC to rescue retinal ganglion cells. Thus, our data suggests when viability is maintained throughout the cryopreservation process, MSC retain their therapeutic potency in both in vitro potency assays and an in vivo ischemia/reperfusion model.Mesenchymal stromal/stem cells (MSC) have been explored in hundreds of clinical trials for the treatment of dozens of conditions 1,2 . While MSC can be harvested from nearly any tissue 3 , they are a rare cell type 4 and thus typically require significant ex vivo expansion to generate therapeutic doses of cells. Allogeneic MSC are used in most clinical trials as MSC are immune evasive, allowing them to avoid immediate immune detection and clearance 2 . Allogeneic MSC are typically expanded in culture, cryopreserved, and banked for future use, creating the opportunity for an 'off-the-shelf ' therapy.Many proposed applications of MSC therapy would require on demand access to therapeutic doses of MSC and therefore necessitate access to cryopreserved MSC stocks. Acute conditions including acute graft versus host disease (GvHD), acute kidney injury, acute lung injury, and sudden onset ischemic events such as myocardial infarction, acute limb ischemia, retinal and optic neuropathies, and stroke would all benefit from rapid MSC administration within hours after the onset of symptoms. The mechanism of action of MSC in these conditions is thought to be mediated through both modulation of inflammatory reactions as well as secretion of protective growth factors 5 . Even if a disease indication could accommodate a post-thaw recovery period ranging from hours to days, logistically, use of MSC immediately post-thaw would still be preferable, since post-thaw recovery needs to be carried out by experienced technicians in dedicated facilities. This not only leads to quality control issues but also adds significant infrastructure requirements that will prevent the use of MSC therapies...

The use of mesenchymal stromal cell (MSC) therapy for the treatment of type 2 diabetes (T2D) and T2D complications is promising; however, the investigation of MSC function in the setting of T2D has not been thoroughly explored. In our current study, we investigated the phenotype and function of MSCs in a simulated in vitro T2D environment. We show that palmitate, but not glucose, exposure impairs MSC metabolic activity with moderate increases in apoptosis, while drastically affecting proliferation and morphology. In co-culture with peripheral blood mononuclear cells (PBMCs), we found that MSCs not only lose their normal suppressive ability in high levels of palmitate, but actively support and enhance inflammation, resulting in elevated PBMC proliferation and pro-inflammatory cytokine release. The pro-inflammatory effect of MSCs in palmitate was partially reversed via palmitate removal and fully reversed through pre-licensing MSCs with interferon-gamma and tumor necrosis factor alpha. Thus, palmitate, a specific metabolic factor enriched within the T2D environment, is a potent modulator of MSC immunosuppressive function, which may in part explain the depressed potency observed in MSCs isolated from T2D patients. Importantly, we have also identified a robust and durable pre-licensing regimen that protects MSC immunosuppressive function in the setting of T2D.