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Systemic lupus erythematosus (SLE) is an autoimmune disease associated with hyperactive innate and adaptive immune systems that cause dermatological, cardiovascular, renal, and neuropsychiatric problems in patients. SLE's multifactorial nature and complex pathogenesis present significant challenges in its clinical classification. In addition, unpredictable treatment responses in patients emphasize the need for highly specific and sensitive SLE biomarkers that can assist in understanding the exact pathogenesis and, thereby, lead to the identification of novel therapeutic targets. Recent studies on microRNA (miRNA), a non-coding region involved in the regulation of gene expression, indicate its importance in the development of the immune system and thus in the pathogenesis of various autoimmune disorders such as SLE. miRNAs are fascinating biomarker prospects for SLE categorization and disease monitoring owing to their small size and high stability. In this paper, we have discussed the involvement of a wide range of miRNAs in the regulation of SLE inflammation and how their modulation can be a potential therapeutic approach. [ABSTRACT FROM AUTHOR]

Anomaly detection is an important issue, which has been deeply studied in different research domains and application fields. The dendritic cell algorithm (DCA) is one of the most popular artificial immune system inspired approaches to handle anomaly detection problems. The performance of DCA depends significantly on the parameters used to compute the relationship between input instance and detectors. However, we find that while the DCA's performance is good in practical applications, it is difficult to analyze due to the empirical based parameters and lacks adaptability. This paper studies how to effectively learn appropriate parameters for deterministic DCA (dDCA) for anomaly detection tasks. In particular, we propose a novel immune optimization based dDCA (IO-dDCA) for anomaly detection. It consists of dDCA classification, T cell (TC) classification, gradient descent optimization and immune nonlinear dynamic optimization. First, the dDCA is regarded as a binary classifier, and the data instances which are labeled as normal will be classified by a T cell inspired classification method, so as to improve the classification performance of dDCA. Then, to improve dDCA's adaptability, gradient descent is adopted for dDCA parameters' optimization. Finally, the immune nonlinear model is introduced to adjust learning rate in gradient descent to find the optimal parameters. The theoretical and experimental performance analysis of IO-dDCA show effectiveness of the novel approach through simulations, and the experimental results show that the proposed IO-dDCA has good classification accuracy. [ABSTRACT FROM AUTHOR]

Type I CRISPR-Cas systems employ multi-subunit effector Cascade and helicase-nuclease Cas3 to target and degrade foreign nucleic acids, representing the most abundant RNA-guided adaptive immune systems in prokaryotes. Their ability to cause long fragment deletions have led to increasing interests in eukaryotic genome editing. While the Cascade structures of all other six type I systems have been determined, the structure of the most evolutionarily conserved type I-B Cascade is still missing. Here, we present two cryo-EM structures of the Synechocystis sp. PCC 6714 (Syn) type I-B Cascade, revealing the molecular mechanisms that underlie RNA-directed Cascade assembly, target DNA recognition, and local conformational changes of the effector complex upon R-loop formation. Remarkably, a loop of Cas5 directly intercalated into the major groove of the PAM and facilitated PAM recognition. We further characterized the genome editing profiles of this I-B Cascade-Cas3 in human CD3+ T cells using mRNA-mediated delivery, which led to unidirectional 4.5 kb deletion in TRAC locus and achieved an editing efficiency up to 41.2%. Our study provides the structural basis for understanding target DNA recognition by type I-B Cascade and lays foundation for harnessing this system for long range genome editing in human T cells. Here the authors present two cryo-EM structures of the Synechocystis sp. PCC 6714 (Syn) type I-B Cascade, revealing the molecular mechanisms that underlie RNA-directed Cascade assembly, target DNA recognition and local conformational changes of the effector complex upon R-loop formation. [ABSTRACT FROM AUTHOR]

Systemic Lupus Erythematosus (SLE) is a progressive disease leading to immune-mediated tissue damage, associated with an alteration of lymphoid organs. Therapeutic strategies involving regulatory T (Treg) lymphocytes, which physiologically quench autoimmunity and support long-term immune tolerance, are considered, as conventional treatment often fails. We describe here a therapeutic strategy based on Tregs overexpressing FoxP3 and harboring anti-CD19 CAR (Fox19CAR-Tregs). Fox19CAR-Tregs efficiently suppress proliferation and activity of B cells in vitro, which are relevant for SLE pathogenesis. In an humanized mouse model of SLE, a single infusion of Fox19CAR-Tregs restricts autoantibody generation, delay lymphopenia (a key feature of SLE) and restore the human immune system composition in lymphoid organs, without detectable toxicity. Although a short survival, SLE target organs appear to be protected. In summary, Fox19CAR-Tregs can break the vicious cycle leading to autoimmunity and persistent tissue damage, representing an efficacious and safe strategy allowing restoration of homeostasis in SLE. Systemic Lupus Erythematosus (SLE) is a chronic and progressive autoimmune disease characterized by abnormally activated B cells causing organ damage. Here authors introduce an adoptive cell therapy involving regulatory T cells overexpressing FoxP3 and harboring an anti-CD19 CAR to inhibit pathological B cells and thus tissue-harming autoimmunity in a humanized mouse model. [ABSTRACT FROM AUTHOR]

The identification of the mechanisms by which T-cell receptors (TCRs) interact with human antigens provides a crucial opportunity to develop new vaccines, diagnostics and immunotherapies. However, the accurate prediction and recognition of TCR–antigen pairing represents a substantial computational challenge in immunology. Existing tools only learn the binding patterns of antigens from many known TCR binding repertoires and fail to recognize antigens that have never been presented to the immune system or for which only a few TCR binding repertoires are known. However, the binding specificity for neoantigens or exogenous peptides is crucial for immune studies and immunotherapy. Therefore, we developed Pan-Peptide Meta Learning (PanPep), a general and robust framework to recognize TCR–antigen binding, by combining the concepts of meta-learning and the neural Turing machine. The neural Turing machine adds external memory to avoid forgetting previously learned tasks, which is used here to accurately predict TCR binding specificity with any peptide, particularly unseen ones. We applied PanPep to various challenging clinical tasks, including (1) qualitatively measuring the clonal expansion of T cells; (2) efficiently sorting responsive T cells in tumour neoantigen therapy; and (3) accurately identifying immune-responsive TCRs in a large cohort from a COVID-19 study. Our comprehensive tests show that PanPep outperforms existing tools. PanPep also offers interpretability, revealing the nature of peptide and TCR interactions in 3D crystal structures. We believe PanPep can be a useful tool to decipher TCR–antigen interactions and that it has broad clinical applications. Machine learning methods can predict and recognize binding patterns between T-cell receptors and human antigens, but they struggle with antigens for which no or little data exist regarding interactions with the immune system. A new method called PanPep based on meta-learning can learn quickly on new binding prediction tasks and accurately predicts pairing between T-cell receptors and new antigens. [ABSTRACT FROM AUTHOR]

Pemphigus vulgaris is a potential life-threatening autoimmune bullous disorder. The significant role of autoreactive B cells in the pathogenesis of PV has been explained extensively by producing autoantibodies. Recently, attention has been directed toward the role of T cells in the pathogenesis of PV; in other words, the underlying etiology of PV depends on the interaction between T cells and B cells resulting in antibody secretion. Herein, we systematically review the current literature on the emerging role of T cells in PV. To perform this systematic review, an extensive search through EMBASE, PubMed, Scopus, and ISI databases was performed from 1976 through 2021. Articles investigating the function of T cell subgroups in the pathogenesis or treatment of pemphigus vulgaris were included and reviewed. It is evidenced that T cells play a pivotal role in PV pathogenesis. Th1 and Th2 dichotomy including Th1 suppression and Th2 elevation may induce antibody production against desmoglein in keratinocytes. Furthermore, increased level of Th17 and decreased level of regulatory T cells have been detected in PV patients. However, further studies on the exact role of γδ-T cells in PV are required in order to clarify the pathogenesis of PV. T cells and their subtypes can be involved in the pathogenesis of PV. Thus, they can be considered as tentative targets of novel therapies for PV. [ABSTRACT FROM AUTHOR]

Studying the interplay between genetic variation, epigenetic changes, and regulation of gene expression is crucial to understand the modification of cellular states in various conditions, including immune diseases. In this study, we characterize the cell-specificity in three key cells of the human immune system by building cis maps of regulatory regions with coordinated activity (CRDs) from ChIP-seq peaks and methylation data. We find that only 33% of CRD-gene associations are shared between cell types, revealing how similarly located regulatory regions provide cell-specific modulation of gene activity. We emphasize important biological mechanisms, as most of our associations are enriched in cell-specific transcription factor binding sites, blood-traits, and immune disease-associated loci. Notably, we show that CRD-QTLs aid in interpreting GWAS findings and help prioritize variants for testing functional hypotheses within human complex diseases. Additionally, we map trans CRD regulatory associations, and among 207 trans-eQTLs discovered, 46 overlap with the QTLGen Consortium meta-analysis in whole blood, showing that mapping functional regulatory units using population genomics allows discovering important mechanisms in the regulation of gene expression in immune cells. Finally, we constitute a comprehensive resource describing multi-omics changes to gain a greater understanding of cell-type specific regulatory mechanisms of immunity. An analysis of cis-regulatory domains (CRDs) among monocytes, neutrophils, and T cells derived from ChIP-seq peaks and methylation data suggests cell-type specific regulatory mechanisms of immunity. [ABSTRACT FROM AUTHOR]

The neurodegenerative diseases Alzheimer's disease (AD) and Parkinson's disease (PD) both have a myriad of risk factors including genetics, environmental exposures, and lifestyle. However, aging is the strongest risk factor for both diseases. Aging also profoundly influences the immune system, with immunosenescence perhaps the most prominent outcome. Through genetics, mouse models, and pathology, there is a growing appreciation of the role the immune system plays in neurodegenerative diseases. In this review, we explore the intersection of aging and the immune system in AD and PD. [ABSTRACT FROM AUTHOR]

Immune checkpoint molecules play critical roles in regulating the anti-tumor immune response, and tumor cells often exploit these pathways to inhibit and evade the immune system. The B7-family immune checkpoint B7x is widely expressed in a broad variety of cancer types, and is generally associated with advanced disease progression and poorer clinical outcomes, but the underlying mechanisms are unclear. Here, we show that transduction and stable expression of B7x in multiple syngeneic tumor models leads to the expansion of immunosuppressive regulatory T cells (Tregs). Mechanistically, B7x does not cause increased proliferation of Tregs in tumors, but instead promotes the conversion of conventional CD4+ T cells into Tregs. Further, we find that B7x induces global transcriptomic changes in Tregs, driving these cells to adopt an activated and suppressive phenotype. B7x increases the expression of the Treg-specific transcription factor Foxp3 in CD4+ T cells by modulating the Akt/Foxo pathway. B7x-mediated regulation of Tregs reduces the efficacy of anti-CTLA-4 treatment, a therapeutic that partially relies on Treg-depletion. However, combination treatment of anti-B7x and anti-CTLA-4 leads to synergistic therapeutic efficacy and overcomes the B7x-mediated resistance to anti-CTLA-4. Altogether, B7x mediates an immunosuppressive Treg-promoting pathway within tumors and is a promising candidate for combination immunotherapy. B7x is a B7-family ligand with suppressive effects on effector T cells. Here the authors show that tumor-expressed B7x promotes the conversion of conventional CD4+ T cells into regulatory T cells within the tumor microenvironment to promote immune evasion and resistance to anti-CTLA-4 therapy. [ABSTRACT FROM AUTHOR]

Progressive multifocal leukoencephalopathy (PML) is an opportunistic viral disease of the brain—caused by human polyomavirus 2. It affects patients whose immune system is compromised by a corresponding underlying disease or by drugs. Patients with an underlying lymphoproliferative disease have the worst prognosis with a mortality rate of up to 90%. Several therapeutic strategies have been proposed but failed to show any benefit so far. Therefore, the primary therapeutic strategy aims to reconstitute the impaired immune system to generate an effective endogenous antiviral response. Recently, anti-PD-1 antibodies and application of allogeneic virus-specific T cells demonstrated promising effects on the outcome in individual PML patients. This article aims to provide a detailed overview of the literature with a focus on these two treatment approaches. [ABSTRACT FROM AUTHOR]

Dysregulated immune responses against the SARS-CoV-2 virus are instrumental in severe COVID-19. However, the immune signatures associated with immunopathology are poorly understood. Here we use multi-omics single-cell analysis to probe the dynamic immune responses in hospitalized patients with stable or progressive course of COVID-19, explore V(D)J repertoires, and assess the cellular effects of tocilizumab. Coordinated profiling of gene expression and cell lineage protein markers shows that S100Ahi/HLA-DRlo classical monocytes and activated LAG-3hi T cells are hallmarks of progressive disease and highlights the abnormal MHC-II/LAG-3 interaction on myeloid and T cells, respectively. We also find skewed T cell receptor repertories in expanded effector CD8+ clones, unmutated IGHG+ B cell clones, and mutated B cell clones with stable somatic hypermutation frequency over time. In conclusion, our in-depth immune profiling reveals dyssynchrony of the innate and adaptive immune interaction in progressive COVID-19. SARS-CoV-2 infection can lead to progressive pathology in patients with COVID-19, but information for this disease progression is sparse. Here the authors use multi-omics approach to profile the immune responses of patients, assessing immune repertoire and effects of tocilizumab treatments, to find a dyssynchrony between innate and adaptive immunity in progressive COVID-19. [ABSTRACT FROM AUTHOR]