Engineering chimeric autoantibody receptor T cells for targeted B cell depletion in multiple sclerosis model: An in-vitro study

The Evolution of Anti-CD20 Treatment for Multiple Sclerosis: Optimization of Antibody Characteristics and Function

B-cell depletion with CD20-targeted agents is commonly used for treatment of multiple sclerosis (MS), other autoimmune diseases, and certain hematologic malignancies. Initial apparent success with rituximab in MS and neuromyelitis optica spurred development of the anti-CD20 monoclonal antibody (mAb) therapies ocrelizumab, ofatumumab, and ublituximab as well as the anti-CD19 mAb inebilizumab. While each are effective at targeting and depleting B cells, structural differences translate into different mechanisms of action affecting maintenance of B-cell depletion and safety and tolerability. Although the anti-CD20 mAbs differ in degree of human versus mouse sequences as well as target CD20 epitope, these properties do not appear to substantially affect activity or tolerability. In contrast, an antibody-dependent cell-mediated cytotoxicity (ADCC) versus a complement-dependent cytotoxicity mechanism of action as well as subcutaneous versus intravenous administration may provide improved tolerability. Glycoengineering of the mAbs ublituximab and inebilizumab enhances ADCC and can overcome the reduced responses to mAb-mediated B-cell depletion associated with certain genetic polymorphisms. Other strategies for therapeutic targeting of CD20, including brain shuttle antibodies (e.g., RO7121932), bispecific antibodies, chimeric antigen receptor T-cell therapies, and antibody-drug conjugates, are in active clinical development and may be future treatment approaches in MS and other B-cell-mediated autoimmune diseases.

Chimeric Autoantibody Receptor- and/or Peptide-MHC-Based CAR Therapies for Targeted Elimination of Antigen-Specific B or T Cells in Hypersensitivity Disorders Such as Allergies and Autoimmune Diseases

Hypersensitivity reactions are dysregulated and potentially devastating immune responses, characterized by a tendency to become chronic. They target either self-proteins or harmless foreign proteins and are driven by both T and B cells. Although numerous symptomatic treatment options for hypersensitivity reactions have been established over recent decades, only a few antigen-specific, causal approaches capable of specifically targeting the pathogenic autoreactive T and/or B cells have been developed. Among these are cell-based treatment modalities involving chimeric antigen receptor (CAR)- or chimeric autoantibody-receptor (CAAR)-expressing cells. These therapies utilize B- or T-cell antigens, presented as B-cell epitopes or peptide-major histocompatibility complexes (pMHCs) to serve as bait. The latter are coupled to potent activation domains derived from the TCR/CD3 complex itself, such as the zeta or CD3 chains, as well as domains from bona fide co-stimulatory molecules (e.g., CD28, 4-1BB). Recent in vitro and in vivo studies have demonstrated the therapeutic potential of these ATMP-based strategies in eliminating autoreactive lymphocytes and alleviating hypersensitivity reactions. This systematic review provides a comprehensive overview of the current status of antigen-specific CAR and CAAR T-cell therapies, highlighting novel directions as well as the ongoing challenges within this promising research field.

New thoughts on the intestinal microbiome-B cell-IgA axis and therapies in IgA nephropathy

IgA nephropathy (IgAN), as the most common chronic glomerulonephritis worldwide, is often triggered by mucosal infections and follows a chronic progression, with the majority of patients ultimately progressing to end-stage renal disease (ESRD) during their lifetimes. Since the mystery of its complete pathogenesis has not been fully solved, the resulting lack of effective early diagnosis and treatment greatly affects the prognosis of patients. Given the well-defined pathological feature of IgA deposition in the mesangial region, the source and role of pathogenic IgA has been focused on. Starting from the microbiology and immunity of the gut, we systematically review both the physiological and the pathological process of microbiome-B cell-IgA axis, from microbial-induced IgA production to the role of IgA in the intestinal immune milieu, and ultimately end up with the various aspects of microbiome-B cell-IgA axis in the pathogenesis of IgAN as well as the corresponding therapeutic initiatives available. Our retrospective review helps researchers to systematically understand the complex role between intestinal flora dysbiosis and pathogenic IgA in IgAN. This understanding provides a foundation for in-depth explorations to uncover more detailed pathogenic mechanisms and to develop more precise and effective diagnostic and therapeutic approaches.

CAR T cells in autoimmunity: game changer or stepping stone?

ABSTRACT

The advent of chimeric antigen receptor (CAR) T cells has revolutionized the treatment landscape for hematologic malignancies, and emerging evidence suggests their potential in autoimmune diseases (AIDs). This article evaluates the early successes and future implications of B-cell-targeting CAR T-cell therapy in AIDs. Initial applications, particularly in refractory systemic lupus erythematosus, have demonstrated significant and durable clinical remissions, with accompanying evaluation of the immune system suggesting a so-called "reset" of innate inflammation and adaptive autoimmunity. This has generated widespread interest in expanding this therapeutic approach. CAR T cells offer unique advantages over other treatment modalities, including very deep B-cell depletion and unique therapeutic activity within inflamed tissues and associated lymphoid structures. However, the field must address key concerns, including long-term toxicity, particularly the risk of secondary malignancies, and future accessibility given the higher prevalence of AIDs compared with malignancies. Technological advances in cell therapy, such as next-generation CAR T cells, allogeneic off-the-shelf products, and alternative cell types, such as regulatory CAR T cells, are being explored in AIDs to improve efficacy and safety. In addition, bispecific antibodies are emerging as potential alternatives or complements to CAR T cells, potentially offering comparable efficacy without the need for complex logistics, lymphodepletion, and the risk of insertional mutagenesis. As the field evolves, cellular therapists will play a critical role in the multidisciplinary teams managing these complex cases. The transformative potential of CAR T cells in AIDs is undeniable, but careful consideration of safety, efficacy, and implementation is essential as this novel therapeutic approach moves forward.

A new therapeutic pathway in autoimmune diseases: chimeric antigen receptor T cells (CAR-T) targeting specific cell subtypes or antigen-specific B lymphocytes—a brief review

In hematological malignancies, autologous immunotherapy with T lymphocytes expressing a chimeric antigen receptor (CAR-T) has been successfully applied. CAR enhances the immuno-cellular effector system directly against cells expressing target antigens. The objective here was to discuss the prospects of applying CAR-T and its variants in autoimmune diseases (AIDs) to deplete pathogenic autoantibodies by eliminating B lymphocytes and plasma cells. B cells play a crucial role in the pathogenesis of AID through the production of autoantibodies, cytokine dysregulation, antigen presentation, and regulatory dysfunction. In AID with numerous autoreactive clones against various autoantigens, such as systemic lupus erythematosus, rheumatoid arthritis, vasculitis, myositis, and systemic sclerosis, CAR-T targeting CD19/CD20 and B-cell maturation antigen (BCMA) have shown success in preclinical and clinical studies, representing an innovative option for refractory patients when standard treatments fail. The suppression of B lymphocytes reactive against specific antigens using cytolytic T cells carrying a chimeric autoantibody receptor (CAAR-T) offers a promising approach for managing various AIDs, especially those with characterized pathogenic autoantibodies, such as pemphigus vulgaris, myasthenia gravis, and anti-NMDAR autoimmune encephalitis. CAAR-T allows the elimination of autoreactive B lymphocytes without compromising the general functionality of the immune system, minimizing common side effects in general immunosuppressive therapies, including immunobiologicals and CAR-T. In vitro, preclinical, and clinical (phase 1) studies have demonstrated the efficacy and specificity of CAR-T and CAAR-T in several AIDs; however, extensive clinical trials (phase 3) are required to assess their safety and clinical applicability. These advances promise to enhance precision medicine in the management of AIDs, offering personalized treatments for individual patients.

Current advancements in cellular immunotherapy for autoimmune disease

The management of autoimmune diseases is currently limited by therapies that largely suppress the immune system, often resulting in partial and temporary remissions. Cellular immunotherapies offer a targeted approach by redirecting immune cells to correct the underlying autoimmunity. This review explores the latest advances in cellular immunotherapies for autoimmune diseases, focusing on various strategies, such as the use of chimeric antigen receptor (CAR) T cells, chimeric auto-antibody receptor (CAAR) T cells, regulatory T cells (Tregs), and tolerogenic dendritic cells (TolDCs). We review recent preclinical studies and results from clinical trials that demonstrate the potential for these therapies to either deplete autoreactive cells or promote immune tolerance through broad or selective targeting of immune cell populations. Key challenges such as ensuring specificity, preventing off-target effects, and improving the longevity of therapeutic effects are discussed. The evolving landscape of cellular immunotherapies holds promise for more durable treatment responses and increased specificity for autoimmune disease treatment.

Cars pick up another passenger: Organ transplantation

With over 30,000 patients having received CAR T cells as a treatment for malignancy, our experience in oncology has facilitated numerous efforts to adapt the CAR therapeutic platform for diseases and conditions beyond cancer. Recognition of their efficacy, where traditional small molecule or biologic therapies fail, has spurred multiple efforts leveraging CAR T cells for immune modulation in the setting of organ/tissue transplantation. In the present review, we discuss CAR T cell approaches that are currently under development, to target both humoral and cellular alloimmunity. These include CAR T platforms repurposed from oncology and autoimmune diseases, as well as ones designed specifically to target alloimmunity in transplant. We also present important challenges and application considerations that will need to be addressed before we can expect successful clinical translation. Finally, we highlight a few of the exciting advances currently in development that are likely to pave a smoother path to translating CAR T cell therapies into transplant patients.

Chimeric HLA antibody receptor T cell therapy for humoral transplant rejection

Antibody-mediated rejection (ABMR) is a significant obstacle to achieving optimal long-term outcomes after solid organ transplantation. The presence of donor-specific antibodies (DSAs), particularly against human leucocyte antigen (HLA), increases the risk of allograft rejection and subsequent graft loss. No effective treatment for ABMR currently exists, warranting novel approaches to target the HLA-specific humoral alloimmune response. Cellular therapies may hold promise to this end. According to publicly available sources as of now, three independent laboratories have genetically engineered a chimeric HLA antibody receptor (CHAR) and transduced it into human T cells, based on the demonstrated efficacy of chimeric antigen receptor T cell therapies in malignancies. These CHAR-T cells are designed to exclusively eliminate B cells that produce donor-specific HLA antibodies, which form the cornerstone of ABMR. CHAR technology generates potent and functional human cytotoxic T cells to target alloreactive HLA-specific B cells, sparing B cells with other specificities. Thus CHAR technology may be used as a selective desensitization protocol and to treat ABMR after solid organ transplantation.

CAR T-cell therapy for systemic lupus erythematosus: current status and future perspectives

Systemic lupus erythematosus (SLE) and lupus nephritis (LN) are debilitating autoimmune disorders characterized by pathological autoantibodies production and immune dysfunction, causing chronic inflammation and multi-organ damage. Despite current treatments with antimalarial drugs, glucocorticoids, immunosuppressants, and monoclonal antibodies, a definitive cure remains elusive, highlighting an urgent need for novel therapeutic strategies. Recent studies indicate that chimeric antigen receptor T-cell (CAR-T) therapy has shown promising results in treating B-cell malignancies and may offer a significant breakthrough for non-malignant conditions like SLE. In this paper, we aim to provide an in-depth analysis of the advancements in CAR-T therapy for SLE, focusing on its potential to revolutionize treatment for this complex disease. We explore the fundamental mechanisms of CAR-T cell action, the rationale for its application in SLE, and the immunological underpinnings of the disease. We also summarize clinical data on the safety and efficacy of anti-CD19 and anti-B cell maturation antigen (BCMA) CAR-T cells in targeting B-cells in SLE. We discuss the clinical implications of these findings and the potential for CAR-T therapy to improve outcomes in severe or refractory SLE cases. The integration of CAR-T therapy into the SLE treatment paradigm presents a new horizon in autoimmunity research and clinical practice. This review underscores the need for continued exploration and optimization of CAR-T strategies to address the unmet needs of SLE patients.

Antigen-specific immunotherapy for platelet alloimmune disorders

Fetal/Neonatal Alloimmune Thrombocytopenia (FNAIT) is a significant hematologic disorder arising from maternal immune responses to fetal platelet alloantigens, predominantly Human Platelet Antigen (HPA)-1a. This review first describes the pathogenesis of FNAIT, highlighting the roles of HPA-specific antibodies, particularly HPA-1a, in causing severe thrombocytopenia and intracranial hemorrhage in affected neonates. Current management strategies, including intravenous immunoglobulin and investigational therapies like Nipocalimab, are evaluated for their efficacy and limitations. The review also discusses promising antigen-specific therapies, such as effector-silent monoclonal antibodies and innovative approaches targeting alloantibody-producing B cells. Additionally, the potential of Chimeric Autoantibody Receptor (CAAR) T cell therapy for selective elimination of pathogenic B cells is examined. The necessity for a prophylactic strategy similar to RhD immunoprophylaxis in preventing FNAIT is emphasized, along with the importance of identifying at-risk pregnancies. The development of renewable monoclonal antibodies and suitable animal models are critical steps toward effective prevention and treatment of this disorder.

PeptiHub: a curated repository of precisely annotated cancer-related peptides with advanced utilities for peptide exploration and discovery

Peptihub (https://bioinformaticscollege.ir/peptihub/) is a meticulously curated repository of cancer-related peptides (CRPs) that have been documented in scientific literature. A diverse collection of CRPs is included in the PeptiHub, showcasing a spectrum of effects and activities. While some peptides demonstrated significant anticancer efficacy, others exhibited no discernible impact, and some even possessed alternative non-drug functionalities, including drug carrier or carcinogenic attributes. Presently, Peptihub houses 874 CRPs, subjected to evaluation across 10 distinct organism categories, 26 organs, and 438 cell lines. Each entry in the database is accompanied by easily accessible 3D conformations, obtained either experimentally or through predictive methodology. Users are provided with three search frameworks offering basic, advanced, and BLAST sequence search options. Furthermore, precise annotations of peptides enable users to explore CRPs based on their specific activities (anticancer, no effect, insignificant effect, carcinogen, and others) and their effectiveness (rate and IC50) under cancer conditions, specifically within individual organs. This unique property facilitates the construction of robust training and testing datasets. Additionally, PeptiHub offers 1141 features with the convenience of selecting the most pertinent features to address their specific research questions. Features include aaindex1 (in six main subcategories: alpha propensities, beta propensity, composition indices, hydrophobicity, physicochemical properties, and other properties), amino acid composition (Amino acid Composition and Dipeptide Composition), and Grouped Amino Acid Composition (Grouped amino acid composition, Grouped dipeptide composition, and Conjoint triad) categories. These utilities not only speed up machine learning-based peptide design but also facilitate peptide classification. Database URL: https://bioinformaticscollege.ir/peptihub/.

Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases

Accurate knowledge of the genome, virus and bacteria that have invaded our bodies is crucial for diagnosing many human diseases. The field of bioinformatics encompasses the complex computational methods required for this purpose. Metagenomics employs next-generation sequencing (NGS) technology to study and identify microbial communities in environmental samples. This technique allows for the measurement of the relative abundance of different microbes. Various tools are available for detecting bacterial species in sequenced metagenomic samples. In this study, we focus on well-known taxonomic classification tools such as MetaPhlAn4, Centrifuge, Kraken2, and Bracken, and evaluate their performance at the species level using synthetic and real datasets. The results indicate that MetaPhlAn4 exhibited high precision in identifying species in the simulated dataset, while Kraken2 had the best area under the precision-recall curve (AUPR) performance. Centrifuge, Kraken2, and Bracken showed accurate estimation of species abundances, unlike MetaPhlAn4, which had a higher L2 distance. In the real dataset analysis with samples from an inflammatory bowel disease (IBD) research, MetaPhlAn4, and Kraken2 had faster execution times, with differences in performance at family and species levels among the tools. Enterobacteriaceae and Pasteurellaceae were highlighted as the most abundant families by Centrifuge, Kraken2, and MetaPhlAn4, with variations in abundance among ulcerative colitis (UC), Crohn's disease (CD), and control non-IBD (CN) groups. Escherichia coli (E. coli) has the highest abundance among Enterobacteriaceae species in the CD and UC groups in comparison with the CN group. Bracken overestimated E. coli abundance, emphasizing result interpretation caution. The findings of this research can assist in selecting the appropriate short-read classifier, thereby aiding in the diagnosis of target diseases.

Frontiers in CAR-T cell therapy for autoimmune diseases

Chimeric antigen receptor (CAR)-engineered T (CAR-T) cell therapy has demonstrated significant success in treating cancers. The potential of CAR-T cells is now being explored in the context of autoimmune diseases. Recent clinical trials have shown sustained and profound elimination of autoreactive B cells by CAR-T cells, leading to promising autoimmune disease control with minimal safety concerns. These encouraging results have inspired further investigation into CAR-T cell applications for a broader range of autoimmune diseases and the development of advanced cell products with improved efficacy and safety. In this review, we discuss the mechanisms by which CAR-T cells target autoimmune conditions, summarize current preclinical models, and highlight ongoing clinical trials, including CAR-T therapy design, clinical outcomes, and challenges. Additionally, we discuss the limitations and future directions of CAR-T therapy in the treatment of autoimmune diseases.

Adoptive Cell Therapy in Mice Sensitized to a Grass Pollen Allergen

The proportion of patients with type I allergy in the world population has been increasing and with it the number of people suffering from allergic symptoms. Recently we showed that prophylactic cell therapy employing allergen-expressing bone marrow (BM) cells or splenic B cells induced allergen-specific tolerance in naïve mice. Here we investigated if cell therapy can modulate an established secondary allergen-specific immune response in pre-immunized mice. We sensitized mice against the grass pollen allergen Phl p 5 and an unrelated control allergen, Bet v 1, from birch pollen before the transfer of Phl p 5-expressing BM cells. Mice were conditioned with several combinations of low-dose irradiation, costimulation blockade, rapamycin and T cell-depleting anti-thymocyte globulin (ATG). Levels of allergen-specific IgE and IgG1 in serum after cell transfer were measured via ELISA and alterations in cellular responses were measured via an in vitro proliferation assay and transplantation of Phl p 5+ skin grafts. None of the tested treatment protocols impacted Phl p 5-specific antibody levels. Transient low-level chimerism of Phl p 5+ leukocytes as well as a markedly prolonged skin graft survival were observed in mice conditioned with high numbers of Phl p 5+ BMC or no sensitization events between the day of cell therapy and skin grafting. The data presented herein demonstrate that a pre-existing secondary allergen-specific immune response poses a substantial hurdle opposing tolerization through cell therapy and underscore the importance of prophylactic approaches for the prevention of IgE-mediated allergy.

Precise Targeting of Autoantigen-Specific B Cells in Lupus Nephritis with Chimeric Autoantibody Receptor T Cells

Despite conventional therapy, lupus nephritis (LN) remains a significant contributor to short- and long-term morbidity and mortality. B cell abnormalities and the production of autoantibodies against nuclear complexes like anti-dsDNA are recognised as key players in the pathogenesis of LN. To address the challenges of chronic immunosuppression associated with current therapies, we have engineered T cells to express chimeric autoantibody receptors (DNA-CAART) for the precise targeting of B cells expressing anti-dsDNA autoantibodies. T cells from LN patients were transduced using six different CAAR vectors based on their antigen specificity, including alpha-actinin, histone-1, heparan sulphate, or C1q. The cytotoxicity, cytokine production, and cell-cell contact of DNA-CAART were thoroughly investigated in co-culture experiments with B cells isolated from patients, both with and without anti-dsDNA positivity. The therapeutic effects were further evaluated using an in vitro immune kidney LN organoid. Among the six proposed DNA-CAART, DNA4 and DNA6 demonstrated superior selectively cytotoxic activity against anti-dsDNA+ B cells. Notably, DNA4-CAART exhibited improvements in organoid morphology, apoptosis, and the inflammatory process in the presence of IFNα-stimulated anti-dsDNA+ B cells. Based on these findings, DNA4-CAART emerge as promising candidates for modulating autoimmunity and represent a novel approach for the treatment of LN.

Metabolite signature of human malignant thyroid tissue: A systematic review and meta-analysis

BACKGROUND

Thyroid cancer (TC) is the predominant malignancy within the endocrine system. However, the standard method for TC diagnosis lacks the capability to identify the pathological condition of all thyroid lesions. The metabolomics approach has the potential to manage this problem by identifying differential metabolites.

AIMS

This study conducted a systematic review and meta-analysis of the NMR-based metabolomics studies in order to identify significant altered metabolites associated with TC.

METHODS

A systematic search of published literature in any language in three databases including Embase, PubMed, and Scopus was conducted. Out of 353 primary articles, 12 studies met the criteria for inclusion in the systematic review. Among these, five reports belonging to three articles were eligible for meta-analysis. The correlation coefficient of the orthogonal partial least squares discriminant analysis, a popular model in the multivariate statistical analysis of metabolomic data, was chosen for meta-analysis. The altered metabolites were chosen based on the fact that they had been found in at least three studies.

RESULTS

In total, 49 compounds were identified, 40 of which were metabolites. The increased metabolites in thyroid lesions compared normal samples included lactate, taurine, alanine, glutamic acid, glutamine, leucine, lysine, phenylalanine, serine, tyrosine, valine, choline, glycine, and isoleucine. Lipids were the decreased compounds in thyroid lesions. Lactate and alanine were increased in malignant versus benign thyroid lesions, while, myo-inositol, scyllo-inositol, citrate, choline, and phosphocholine were found to be decreased. The meta-analysis yielded significant results for three metabolites of lactate, alanine, and citrate in malignant versus benign specimens.

DISCUSSION

In this study, we provided a concise summary of 12 included metabolomic studies, making it easier for future researchers to compare their results with the prior findings.

CONCLUSION

It appears that the field of TC metabolomics will experience notable advancement, leading to the discovery of trustworthy diagnostic and prognostic biomarkers.

Potential clinical implications of molecular mimicry-induced autoimmunity

BACKGROUND

Molecular mimicry is hypothesized to be a mechanism by which autoimmune diseases are triggered. It refers to sequence or structural homology between foreign antigens and self-antigens, which can activate cross-reactive lymphocytes that attack host tissues. Elucidating the role of molecular mimicry in human autoimmunity could have important clinical implications.

OBJECTIVE

To review evidence for the role of molecular mimicry in major autoimmune diseases and discuss potential clinical implications.

METHODS

Comprehensive literature review of clinical trials, observational studies, animal models, and immunology studies on molecular mimicry in multiple sclerosis, type 1 diabetes, rheumatoid arthritis, lupus, Guillain-Barre syndrome, autoimmune myocarditis, and primary biliary cirrhosis published from 2000-2023.

RESULTS

Substantial indirect evidence supports molecular mimicry as a contributor to loss of self-tolerance in several autoimmune conditions. Proposed microbial triggers include Epstein-Barr virus, coxsackievirus, Campylobacter jejuni, and bacterial commensals. Key mechanisms involve cross-reactive T cells and autoantibodies induced by epitope homology between microbial and self-antigens. Perpetuation of autoimmunity involves epitope spreading, inflammatory mediators, and genetic factors.

CONCLUSIONS

Molecular mimicry plausibly explains initial stages of autoimmune pathogenesis induced by infection or microbiota disturbances. Understanding mimicry antigens and pathways could enable improved prediction, monitoring, and antigen-specific immunotherapy for autoimmune disorders. However, definitive proof of causation in humans remains limited. Further research should focus on establishing clinical evidence and utility.