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.

Tailoring MSCs to fit the disease. Fresh, cryopreserved and, prelicensed cryopreserved MSC are all being explored to treat numerous diseases, but all are not suitable to treat all conditions. injury. “*” denotes preferred therapeutic strategy when both fresh MSC and cryo‐MSC have shown utility in treating the disease but one is more efficacious or logistically suitable. Abbreviations: CLI, critical limb ischemia; GvHD. graft versus host disease; I/R, ischemia reperfusion (I/R); OI, osteogenesis imperfecta.

The purpose of this study was to determine mesenchymal stem cell (MSC) therapy efficacy on rescuing the visual system in the experimental autoimmune encephalomyelitis (EAE) model of multiple sclerosis (MS) and to provide new mechanistic insights. Methods: EAE was induced in female C57BL6 mice by immunization with myelin oligodendrocyte glycoprotein (MOG) 35-55 , complete Freund's adjuvant, and pertussis toxin. The findings were compared to sham-immunized mice. Half of the EAE mice received intraperitoneally delivered stem cells (EAE + MSC). Clinical progression was monitored according to a five-point EAE scoring scheme. Pattern electroretinogram (PERG) and retinal nerve fiber layer (RNFL) thickness were measured 32 days after induction. Retinas were harvested to determine retinal ganglion cell (RGC) density and prepared for RNAsequencing. Results: EAE animals that received MSC treatment seven days after EAE induction showed significantly lower motor-sensory impairment, improvement in the PERG amplitude, and preserved RNFL. Analysis of RNA-sequencing data demonstrated statistically significant differences in gene expression in the retina of MSC-treated EAE mice. Differentially expressed genes were enriched for pathways involved in endoplasmic reticulum stress, endothelial cell differentiation, HIF-1 signaling, and cholesterol transport in the MSC-treated EAE group. Conclusions: Systemic MSC treatment positively affects RGC function and survival in EAE mice. Better cholesterol handling by increased expression of Abca1, the cholesterol efflux regulatory protein, paired with the resolution of HIF-1 signaling activation might explain the improvements seen in PERG of EAE animals after MSC treatment. Translational Relevance: Using MSC therapy in a mouse model of MS, we discovered previously unappreciated biochemical pathways associated with RGC neuroprotection, which have the potential to be pharmacologically targeted as a new treatment regimen.

Melanoma represents the most serious type of skin cancer. Although recent years have seen advances using targeted and immunotherapies, most patients remain at high risk for tumor recurrence. Here we show that IRAK-M, a negative regulator of MyD88 signaling, is deficient or low in melanoma and expression levels correlate with patient survival. Inducing IRAK-M expression using genetic approaches or epigenetic modifiers initiates apoptosis by prompting its interaction with TRAF6 via IRAK-M's C-terminal domain. This complex recruits and degrades calpastatin which stimulates calpain activity and triggers caspase-3-dependent but caspase-8,−9-independent apoptosis. Using a drug screen, we identified compounds that induced IRAK-M expression. Administration of IRAK-M-inducing drugs reduced tumor growth in mice but was ineffective against IRAK-M knock-down tumors. These results uncover a previously uncharacterized apoptosis pathway, emphasize IRAK-M as a potential therapeutic target and suggest that the anticancer activity of certain drugs could do so through their ability to induce IRAK-M expression.

This protocol has been optimized for recombinant expression of molony virus based reverse transcriptases (RT). The plasmid used contains a reverse transcriptase gene which is derived from Moloney Murine Leukemia Virus. The enzyme when expressed recombinantly can synthesizes a complementary DNA strand from single-stranded RNA, DNA, or an RNA:DNA hybrid. Enzyme Engi ne e ri ng: Enzyme Engi ne e ri ng: The enzyme contains point mutations to generate a highly processive, thermostable, and improved fidelity mutant reverse transcriptase. Details, incluiding the sequence of this enzyme are published and can be found in the references below and addgene link. The e nzyme conta i ns a n a cti ve RNAse H doma i n a nd i s hi ghl y e nzyme conta i ns a n a cti ve RNAse H doma i n a nd i s hi ghl y the rmosta bl e the rmosta bl e. This MMLV construct contains the following mutations: D200N, L603W, T330P, L139P, E607K,D524G, E562Q, D583N and D653N. These appear to be the same set of mutations present in the T he rmo T he rmo Fi she r Ma xi ma H-RT Fi she r Ma xi ma H-RT , which is one of the best preforming RTs you can buy. The enzyme in our hands is extremely active. Moreover, while the MMLV RT is thermostable and will work up to 65°C it runs optimally at 42°C. The point muitations utilized here are currently filed under a provisional patent with Thermo Fisher Scientific. Commcercial use of this enzyme must go though Thermo Fisher Scientific.

Objective: Fat content of adipocytes derived from infant umbilical cord mesenchymal stem cells (MSCs) predicts adiposity in children through 4 to 6 years of age. This study tested the hypothesis that MSCs from infants born to mothers with obesity (Ob-MSCs) exhibit adipocyte hypertrophy and perturbations in genes regulating adipogenesis compared with MSCs from infants of mothers with normal weight (NW-MSCs).Methods: Adipogenesis was induced in MSCs embedded in three-dimensional hydrogel structures, and cell size and number were measured by three-dimensional imaging. Proliferation and protein markers of proliferation and adipogenesis in undifferentiated and adipocyte differentiating cells were measured. RNA sequencing was performed to determine pathways linked to adipogenesis phenotype.Results: In undifferentiated MSCs, greater zinc finger protein (Zfp)423 protein content was observed in Ob-versus NW-MSCs. Adipocytes from Ob-MSCs were larger but fewer than adipocytes from NW-MSCs. RNA sequencing analysis showed that Zfp423 protein correlated with mRNA expression of genes enriched for cell cycle, MSC lineage specification, inflammation, and metabolism pathways. MSC proliferation was not different before differentiation but declined faster in Ob-MSCs upon adipogenic induction.