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The ability to identify and track T-cell receptor (TCR) sequences from patient samples is becoming central to the field of cancer research and immunotherapy. Tracking genetically engineered T cells expressing TCRs that target specific tumor antigens is important to determine the persistence of these cells and quantify tumor responses. The available high-throughput method to profile TCR repertoires is generally referred to as TCR sequencing (TCR-Seq). However, the available TCR-Seq data are limited compared with RNA sequencing (RNA-Seq). In this paper, we have benchmarked the ability of RNA-Seq-based methods to profile TCR repertoires by examining 19 bulk RNA-Seq samples across 4 cancer cohorts including both T-cell-rich and T-cell-poor tissue types. We have performed a comprehensive evaluation of the existing RNA-Seq-based repertoire profiling methods using targeted TCR-Seq as the gold standard. We also highlighted scenarios under which the RNA-Seq approach is suitable and can provide comparable accuracy to the TCR-Seq approach. Our results show that RNA-Seq-based methods are able to effectively capture the clonotypes and estimate the diversity of TCR repertoires, as well as provide relative frequencies of clonotypes in T-cell-rich tissues and low-diversity repertoires. However, RNA-Seq-based TCR profiling methods have limited power in T-cell-poor tissues, especially in highly diverse repertoires of T-cell-poor tissues. The results of our benchmarking provide an additional appealing argument to incorporate RNA-Seq into the immune repertoire screening of cancer patients as it offers broader knowledge into the transcriptomic changes that exceed the limited information provided by TCR-Seq. [ABSTRACT FROM AUTHOR]

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding motifs. Based on the discovery, we make the preprocessing and coding closer to the natural biological process. Besides, due to the input being based on multiple types of features and the attention module focused on the BiGRU hidden layer, TripHLApan has learned more sequence level binding information. The application of transfer learning strategies ensures the accuracy of prediction results under special lengths (peptides in length 8) and model scalability with the data explosion. Compared with the current optimal models, TripHLApan exhibits strong predictive performance in various prediction environments with different positive and negative sample ratios. In addition, we validate the superiority and scalability of TripHLApan's predictive performance using additional latest data sets, ablation experiments and binding reconstitution ability in the samples of a melanoma patient. The results show that TripHLApan is a powerful tool for predicting the binding of HLA-I and HLA-II molecular peptides for the synthesis of tumor vaccines. TripHLApan is publicly available at https://github.com/CSUBioGroup/TripHLApan.git. [ABSTRACT FROM AUTHOR]

People living with HIV on antiretroviral therapy often have undetectable virus levels by standard assays, but "latent" HIV still persists in viral reservoirs. Eliminating these reservoirs is the goal of HIV cure research. The quantitative viral outgrowth assay (QVOA) is commonly used to estimate the reservoir size, that is, the infectious units per million (IUPM) of HIV-persistent resting CD4+ T cells. A new variation of the QVOA, the ultra deep sequencing assay of the outgrowth virus (UDSA), was recently developed that further quantifies the number of viral lineages within a subset of infected wells. Performing the UDSA on a subset of wells provides additional information that can improve IUPM estimation. This paper considers statistical inference about the IUPM from combined dilution assay (QVOA) and deep viral sequencing (UDSA) data, even when some deep sequencing data are missing. Methods are proposed to accommodate assays with wells sequenced at multiple dilution levels and with imperfect sensitivity and specificity, and a novel bias-corrected estimator is included for small samples. The proposed methods are evaluated in a simulation study, applied to data from the University of North Carolina HIV Cure Center, and implemented in the open-source R package SLDeepAssay. [ABSTRACT FROM AUTHOR]

Motivation It has been proven that only a small fraction of the neoantigens presented by major histocompatibility complex (MHC) class I molecules on the cell surface can elicit T cells. This restriction can be attributed to the binding specificity of T cell receptor (TCR) and peptide-MHC complex (pMHC). Computational prediction of T cells binding to neoantigens is a challenging and unresolved task. Results In this paper, we proposed an attention-aware contrastive learning model, ATMTCR, to infer the TCR–pMHC binding specificity. For each TCR sequence, we used a transformer encoder to transform it to latent representation, and then masked a percentage of amino acids guided by attention weights to generate its contrastive view. Compared to fully-supervised baseline model, we verified that contrastive learning-based pretraining on large-scale TCR sequences significantly improved the prediction performance of downstream tasks. Interestingly, masking a percentage of amino acids with low attention weights yielded best performance compared to other masking strategies. Comparison experiments on two independent datasets demonstrated our method achieved better performance than other existing algorithms. Moreover, we identified important amino acids and their positional preference through attention weights, which indicated the potential interpretability of our proposed model. [ABSTRACT FROM AUTHOR]

Summary: The immune system plays a critical role in protecting the host against infection but is subject to numerous levels of control that are necessary to prevent pathological, tissue-damaging responses. Inappropriate inflammatory immune responses to self-antigens, innocuous commensal microorganisms, or environmental antigens can lead to chronic, debilitating, and degenerative diseases. Regulatory T cells have an essential, non-redundant, and dominant function in preventing pathological immune responses, as shown by the development of systemic fatal autoimmunity in humans and animals with a genetic deficiency in regulatory T cells. In addition to controlling immune responses, there is a growing understanding that regulatory T cells also contribute directly to tissue homeostasis by promoting tissue regeneration and repair. For these reasons, the prospect of enhancing regulatory T-cell numbers and/or function in patients represents an appealing therapeutic opportunity with potential applications in many diseases, including some where the pathological role of the immune system has only recently been recognized. Approaches to enhance regulatory T cells are now starting to be explored in clinical studies in humans. This review series brings together papers highlighting the Treg-enhancing approaches that are most advanced clinically and examples of therapeutic opportunities based on our growing understanding of regulatory T-cell functions. [ABSTRACT FROM AUTHOR]

Understanding the T-cell response to SARS-CoV-2 is key in patients who lack antibody production. We demonstrate the applicability of a functional assay to measure the T-cell response in a cohort of patients with immunodeficiency. T-cell responses to COVID are now linked to improved outcomes. This paper demonstrates a method to robustly test responses for routine diagnostic use in healthy controls and those unable to make a detectable antibody response due to underlying immune deficiency (primary or acquired). [ABSTRACT FROM AUTHOR]

The spleen is a complex secondary lymphoid organ that plays a crucial role in controlling blood‐stage infection with Plasmodium parasites. It is tasked with sensing and removing parasitized RBCs, erythropoiesis, the activation and differentiation of adaptive immune cells, and the development of protective immunity, all in the face of an intense inflammatory environment. This paper describes how these processes are regulated following infection and recognizes the gaps in our current knowledge, highlighting recent insights from human infections and mouse models. [ABSTRACT FROM AUTHOR]

Motivation Identifying rare subpopulations of cells is a critical step in order to extract knowledge from single-cell expression data, especially when the available data is limited and rare subpopulations only contain a few cells. In this paper, we present a data mining method to identify small subpopulations of cells that present highly specific expression profiles. This objective is formalized as a constrained optimization problem that jointly identifies a small group of cells and a corresponding subset of specific genes. The proposed method extends the max-sum submatrix problem to yield genes that are, for instance, highly expressed inside a small number of cells, but have a low expression in the remaining ones. Results We show through controlled experiments on scRNA-seq data that the MicroCellClust method achieves a high F 1 score to identify rare subpopulations of artificially planted human T cells. The effectiveness of MicroCellClust is confirmed as it reveals a subpopulation of CD4 T cells with a specific phenotype from breast cancer samples, and a subpopulation linked to a specific stage in the cell cycle from breast cancer samples as well. Finally, three rare subpopulations in mouse embryonic stem cells are also identified with MicroCellClust. These results illustrate the proposed method outperforms typical alternatives at identifying small subsets of cells with highly specific expression profiles. Availabilityand implementation The R and Scala implementation of MicroCellClust is freely available on GitHub, at https://github.com/agerniers/MicroCellClust/ The data underlying this article are available on Zenodo, at https://dx.doi.org/10.5281/zenodo.4580332. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

PMN‐MDSC are pathologically activated neutrophils that acquire T cell (and NK cell) suppressive activity and thus function as negative regulators of effector lymphocytes in many disease conditions.[1] For many years, these PMN‐MDSC have mainly been seen as contributors to disease progression and severity, best exemplified in the context of cancer. However, more recently, PMN‐MDSC have also been described in newborn mice and humans.[2] This finding raised the question on the potential functional roles of these regulatory myeloid cells in neonate immunobiology. During the first days (mice) or weeks (human) of life, an initial seeding of microbiota in the gut takes place. The appearance of these microbiota triggers immune responses that could potentially lead to harmful inflammation and immunopathology. In this early phase of life, PMN‐MDSC could be beneficial by limiting overshooting immune responses. Indeed, a recent paper by He et al.[3] describes the transient presence of PMN‐MDSC during the first month of life. Such PMN‐MDSC have been shown to suppress T cells in a contact‐depended manner, but the mechanism behind the transitory nature of this phenomenon has not yet been elucidated. In this issue of the Journal of Leukocyte Biology Perego et al. describe molecular mechanisms that regulate this transient increase and subsequent decrease of PMN‐MDSC in newborn mice.[4] [ABSTRACT FROM AUTHOR]

Background Acute kidney injury (AKI) occurs in 30% of patients infused with chimeric antigen receptor (CAR) T-cells. The purpose of this study was to identify risk factors and long-term outcomes after AKI in patients who received CAR T-cell therapy. Methods Medical records of 115 adult patients with R/R hematological malignancies treated with CD19-targeted CAR T-cells at Vall d'Hebron University Hospital between July 2018 and May 2021. Baseline demographic data including age, gender, ethnicity, body mass index (BMI), and co-morbidities, as well as the type of hematological neoplasia and prior lines of therapy were collected. Laboratory parameters including serum creatinine and whole blood hemoglobin were retrospectively reviewed and values were gathered for days +1, +7, +14, +21, and +28 post-infusion. Results A total of 24/115 (21%) patients developed AKI related to CAR T-cell therapy; 6/24 with AKI over chronic kidney disease (CKD). Two patients had AKI in the context of lymphodepleting (LD) chemotherapy and the other 22 after CAR T-cell infusion, starting at day+1 in 3 patients, day+7 in 13 patients, day +14 in 1 patient, day+21 in 2 patients, and day+28 in 3 patients. Renal function was recovered in 19/24 (79%) patients within the first month after infusion. Male gender, CKD, cytokine release syndrome (CRS), and immune effector cell-associated neurotoxicity syndrome (ICANS) were associated with AKI. Male gender, CKD, ICANS grade ≥3 and CRS grade ≥2 were identified as independent risk factors for AKI on multivariable analysis. In terms of the most frequent CAR T-cell related complications, CRS was observed in 95 (82%) patients and ICANS in 33 (29%) patients. Steroids were required in 34 (30%) patients and tocilizumab in 37 (32%) patients. Six (5%) patients were admitted to the intensive care unit (1 for septic shock, 4 for CRS grade ≥2 associated to ICANS grade ≥2, and 1 for CRS grade ≥3). A total of 5 (4.4%) patients died in the first 30 days after CAR T-cell infusion for reasons other than disease progression, including 4 cases of infectious complications and 1 of heart failure. Conclusion Our results suggest that AKI is a frequent but mild adverse event, with fast recovery in most patients. [ABSTRACT FROM AUTHOR]

Summary Knowledge of immunoglobulin and T cell receptor encoding genes is derived from high-quality genomic sequencing. High-throughput sequencing is delivering large volumes of data, and precise, high-throughput approaches to annotation are needed. Digger is an automated tool that identifies coding and regulatory regions of these genes, with results comparable to those obtained by current expert curational methods. Availability and implementation Digger is published under open source license at https://github.com/williamdlees/Digger and is available as a Python package and a Docker container. [ABSTRACT FROM AUTHOR]

Objective: Chimeric antigen receptor (CAR) T-cell therapy is a promising treatment for relapsed/refractory acute lymphoblastic leukemia (ALL) in pediatric oncology. However, little is known about the cognitive functioning of these patients. This study examines the neuropsychological functioning of pediatric patients referred for CAR T-cell therapy. Method: Data was obtained from a longitudinal observational study of CAR T-cell therapy patients (ages 1–30 years) at the Children's Hospital of Philadelphia. Neuropsychological data and neurotoxicity ratings were collected before and after CAR T-cell infusion, with brief cognitive testing at 28 days and 180 days post-infusion to assess acute changes. Cognitive testing included pencil-and-paper measures of intellectual functioning, attention, processing speed, and psychological functioning, as well as NIH Toolbox subtests. Results: Of 13 patients completing pre-infusion cognitive testing, 44% of patients scored below average (1 SD below the mean) on a timed visual-motor processing speed test. 20–25% of the sample scored below average on measures of executive functioning, attention/working memory, and expre0111111ssive vocabulary, exceeding what would be expected in a normal distribution. Fewer patients completed post-infusion assessments (n = 8, 28 days; n = 5, 6 months; n = 3, 1 year), with up to 50% scoring below average on the timed visual-motor processing speed test and 33% scoring below average on a measure of inhibitory control and selective attention after 1 year. Conclusions: Pediatric CAR T-cell therapy patients have high rates of cognitive dysfunction prior to receiving infusions, with evidence for increasing problems with timed visual-motor and executive functioning. Findings highlight the need to monitor pediatric CAR T-cell therapy patients throughout treatment. [ABSTRACT FROM AUTHOR]

Neuroimmune connections have been revealed to play a central role in neurodegenerative diseases (NDs). However, the mechanisms that link the central nervous system (CNS) and peripheral immune cells are still mostly unknown. We recently found that specific ablation of the Arf1 gene in hindbrain and spinal cord neurons promoted NDs through activating the NLRP3 inflammasome in microglia via peroxided lipids and adenosine triphosphate (ATP) releasing. Here, we demonstrate that IL-1β with elevated chemokines in the neuronal Arf1-ablated mouse hindbrain and spinal cord recruited and activated γδ T cells in meninges. The activated γδ T cells then secreted IFN-γ that entered into parenchyma to activate the microglia-A1 astrocyte-C3-neuronal C3aR neurotoxic pathway. Remarkably, the neurodegenerative phenotypes of the neuronal Arf1 -ablated mice were strongly ameliorated by IFN- γ or C3 knockout. Finally, we show that the Arf1-reduction-induced neuroimmune- IFN- γ-gliosis pathway exists in human NDs, particularly in amyotrophic lateral sclerosis and multiple sclerosis. Together, our results uncover a previously unknown mechanism that links the CNS and peripheral immune cells to promote neurodegeneration. [ABSTRACT FROM AUTHOR]

Motivation T cells play an essential role in adaptive immune system to fight pathogens and cancer but may also give rise to autoimmune diseases. The recognition of a peptide–MHC (pMHC) complex by a T cell receptor (TCR) is required to elicit an immune response. Many machine learning models have been developed to predict the binding, but generalizing predictions to pMHCs outside the training data remains challenging. Results We have developed a new machine learning model that utilizes information about the TCR from both α and β chains, epitope sequence, and MHC. Our method uses ProtBERT embeddings for the amino acid sequences of both chains and the epitope, as well as convolution and multi-head attention architectures. We show the importance of each input feature as well as the benefit of including epitopes with only a few TCRs to the training data. We evaluate our model on existing databases and show that it compares favorably against other state-of-the-art models. Availability and implementation https://github.com/DaniTheOrange/EPIC-TRACE. [ABSTRACT FROM AUTHOR]

Motivation Molecular quantitative trait locus (QTL) mapping has proven to be a powerful approach for prioritizing genetic regulatory variants and causal genes identified by genome-wide association studies. Recently, this success has been extended to circular RNA (circRNA), a potential group of RNAs that can serve as markers for the diagnosis, prognosis, or therapeutic targets of various human diseases. However, a well-developed computational pipeline for circRNA QTL (circQTL) discovery is still lacking. Results We introduce an integrative method for circQTL mapping and implement it as an automated pipeline based on Nextflow, named cscQTL. The proposed method has two main advantages. Firstly, cscQTL improves the specificity by systematically combining outputs of multiple circRNA calling algorithms to obtain highly confident circRNA annotations. Secondly, cscQTL improves the sensitivity by accurately quantifying circRNA expression with the help of pseudo references. Compared to the single method approach, cscQTL effectively identifies circQTLs with an increase of 20%–100% circQTLs detected and recovered all circQTLs that are highly supported by the single method approach. We apply cscQTL to a dataset of human T cells and discover genetic variants that control the expression of 55 circRNAs. By colocalization tests, we further identify circBACH2 and circYY1AP1 as potential candidates for immune disease regulation. Availability and implementation cscQTL is freely available at: https://github.com/datngu/cscQTL and https://doi.org/10.5281/zenodo.7851982. [ABSTRACT FROM AUTHOR]

All World Health Organization (WHO) pre-qualified rabies vaccines for humans are inactivated tissue culture rabies virus formulations produced for intramuscular (IM) administration. Due to costs and vaccine shortage, dose-saving intradermal (ID) administration of rabies post-exposure prophylaxis (PEP) is encouraged by WHO. This study compared the immunogenicity of the ID 2-site, 3-visit Institut Pasteur Cambodge (IPC) PEP regimen to the IM 1-site, 4-visit 4-dose Essen regimen using Verorab vaccine (Sanofi). The development of neutralizing antibodies (nAbs) and T cell response was assessed in 210 patients with a category II or III animal exposure in a rabies-endemic country. At day 28, all participants developed nAbs (≥0.5 IU/mL), irrespective of PEP scheme, age, or administration of rabies immunoglobulin. T cell response and nAb titers were similar for both PEP schemes. This study demonstrated that the 1-week ID IPC regimen is as effective as the 2-week IM 4-dose Essen regimen in inducing an anti-rabies immune response under real-life PEP. [ABSTRACT FROM AUTHOR]

Acute T-cell-mediated rejection (aTCMR) still remains a clinical problem after kidney transplantation despite significant improvements in immunosuppressive regimens. Polyfunctional T cells, i.e. T cells producing multiple pro-inflammatory cytokines, are believed to be the most relevant T cells in an immune response. The aim of this study was to determine whether polyfunctional donor-reactive T cells are associated with aTCMR. In a case–control study, 49 kidney transplant recipients with a biopsy-proven aTCMR in the first year after transplantation were included, as well as 51 controls without aTCMR. Circulating donor-reactive T cells were identified by the expression of CD137 after short-term co-culture with donor antigen-presenting cells. Polyfunctional donor-reactive T cells were further characterized by dissection into different T-cell subsets encompassing the spectrum of naïve to terminally differentiated effector T cells. Prior to kidney transplantation, proportions of donor-reactive CD4+ (0.03% versus 0.02%; P < 0.01) and CD8+ (0.18% versus 0.10%; P < 0.01) CD137++ T cells were significantly higher in recipients with a biopsy-proven aTCMR versus non-rejectors. Polyfunctionality was higher (P = 0.03) in this subset of CD137-expressing T cells. These cells were predominantly of the EM/EMRA-phenotype, with polyfunctional donor-reactive CD137++CD4+ T cells predominantly co-expressing CD28 whereas approximately half of the polyfunctional CD137++CD8+ T cells co-expressed CD28. In addition, at the time of aTCMR, polyfunctional donor-reactive CD137++ CD4+, but not CD8+, T cells, were specifically decreased by 75% compared to before transplantation in recipients with as well as those without an aTCMR. Prior to transplantation, the proportion of polyfunctional donor-reactive CD137++ T cells is associated with the occurrence of a biopsy-proven aTCMR within the first year after transplantation. Acute TCMR remains a clinical problem after kidney transplantation despite significant improvements in immunosuppressive regimens. Poly-functional (producing ≥2 cytokines) T cells are believed to be the most relevant T cells in an immune response. Prior to kidney transplantation proportions of poly-functional CD137 high expressing donor-reactive CD4+ and CD8+ T cells are higher in recipients experiencing an acute TCMR within the first year after transplantation compared to those who remained free of rejection. [ABSTRACT FROM AUTHOR]

Inflammation plays a significant role in lung infection including that caused by Mycobacterium tuberculosis , in which both adaptive and innate lymphocytes can affect infection control. How inflammation affects infection is understood in a broad sense, including inflammaging (chronic inflammation) seen in the elderly, but the explicit role that inflammation can play in regulation of lymphocyte function is not known. To fill this knowledge gap, we used an acute lipopolysaccharide (LPS) treatment in young mice and studied lymphocyte responses, focusing on CD8 T cell subsets. LPS treatment decreased the total numbers of T cells in the lungs of LPS mice while also increasing the number of activated T cells. We demonstrate that lung CD8 T cells from LPS mice became capable of an antigen independent innate-like IFN-γ secretion, dependent on IL-12p70 stimulation, paralleling innate-like IFN-γ secretion of lung CD8 T cells from old mice. Overall, this study provides information on how acute inflammation can affect lymphocytes, particularly CD8 T cells, which could potentially affect immune control of various disease states. [ABSTRACT FROM AUTHOR]

Some research has shown that PM2.5 causes Th1/Th2 immune imbalance and aggravates asthma. However, the exact mechanism of PM2.5 causing aggravation of asthma remains unclear. The purpose of this study was to investigate whether exposure to PM2.5 exacerbates Th1/Th2 immune imbalance through the Notch signaling pathway. Eight-week-old SPF female BALF/c mice were sensitized by ovalbumin to establish an asthma mouse model. PM2.5 exposure was carried out by aerosol inhalation of PM2.5 (510 μg/m3) after each provocation. The lung function of mice was measured and Splenic T lymphocyte subsets were detected. Notch signaling pathway was tested. The levels of interferon (IFN)-γ and interleukin (IL)-4 in serum and bronchoalveolar lavage fluid were determined. The results showed that the expression of the mRNA and protein of Notch1 and Hes1 in the asthma group were significantly higher than those in healthy controls. The levels of IL-4 were also remarkably high; while the levels of IFN-γ were remarkably low in serum and BALF, the Th1% and Th1/Th2 ratios were significantly lower, and Th2% was significantly higher in the asthma group than in the healthy controls. PM2.5 promoted further activation of the Notch signaling pathway and aggravated Th1/Th2 immune imbalance in asthmatic mice. γ-secretase inhibitor can partially inhibit the activation of the Notch signaling pathway and alleviate aggravation of immune imbalance. In conclusion, the asthmatic mice had a Th1/Th2 immune imbalance and an overactivated Notch signaling pathway. PM2.5 further aggravated Th1/Th2 immune imbalance by activating the Notch signaling pathway. [ABSTRACT FROM AUTHOR]

Psoriasis is a common chronic disease, and existing treatment regimens often exhibit certain toxicities and side effects. Zerumbone (Zer) may possess therapeutic effect, and the objective of this study is to investigate the effect of Zer on psoriasis. A mouse model of psoriasis was established using imiquimod cream, and the role of Zer on the pathological alterations in psoriatic mouse skin was evaluated by psoriasis area and severity index (PASI) score; the effect of Zer on keratinocyte proliferation was evaluated via hematoxylin and eosin staining, Zen image analysis, and immunofluorescence; Immunohistochemistry and enzyme-linked immunoassay were used to evaluate the effect of Zer on tissue inflammatory responses, while malondialdehyde (MDA) and glutathione (GSH) levels were measured to elucidate the role of Zer in modulating oxidative stress; the signaling pathway regulated by Zer was evaluated by western blotting. The results demonstrated that Zer could alleviate the pathological manifestations of psoriasis, reduce PASI score, reduce skin pathological damage and epidermal hyperplasia, diminish the number of CD8+ T cells and cytokine expression levels, decrease the level of MDA and GSH and increase the expression of Nrf and HO-1. Zer was found to regulate the NLRP3/nuclear factor-kappa B (NF-κB) signaling pathway. In conclusion, Zer ameliorated the symptoms of psoriasis in mice, suppressed the keratinocyte hyperproliferation, and mitigates inflammation and oxidative stress in psoriatic skin tissue by regulating the NLRP3/NF-κB pathway. [ABSTRACT FROM AUTHOR]

In this brief opinion piece, we highlight our studies characterizing adaptive SARS-CoV-2 immune responses in infection and vaccination, and the ability of SARS-CoV-2-specific T cells to recognize emerging variants of concern, and the role of pre-existing cross-reactive T cells. In the context of the debate on correlates of protection, the pandemic's progression in the past 3 years underlined the need to consider how different adaptive immune responses might differentially contribute to protection from SARS-CoV-2 infection versus COVID-19 disease. Lastly, we discuss how cross-reactive T cell responses may be useful in generating a broad adaptive immunity, recognizing different variants and viral families. Considering vaccines with broadly conserved antigens could improve preparedness for future infectious disease outbreaks. [ABSTRACT FROM AUTHOR]

Summary: Regulatory T cells (Tregs) are a subtype of CD4+ T cells that can mediate immune tolerance by a multitude of immunomodulatory mechanisms. Treg-based adoptive immunotherapy is currently being tested in multiple phases I and II clinical trials in transplantation and autoimmune diseases. We have learned from the work done on conventional T cells that distinct mechanistic states can define their dysfunctions, such as exhaustion, senescence, and anergy. All three can negatively impact the therapeutic effectiveness of T-cell-based therapies. However, whether Tregs are susceptible to such dysfunctional states is not well studied, and results are sometimes found to be controversial. In addition, Treg instability and loss of FOXP3 expression is another Treg-specific dysfunction that can decreasein their suppressive potential. A better understanding of Treg biology and pathological states will be needed to compare and interpret the results of the different clinical and preclinical trials. We will review herein Tregs' mechanisms of action, describe different T-cell dysfunction subtypes and how and if they apply to Tregs (exhaustion, senescence, anergy, and instability), and finally how this knowledge should be taken into consideration when designing and interpreting Treg adoptive immunotherapy trials. Recent advances in Treg-based immunotherapy, as an immune tolerance approach for transplantation and autoimmune diseases, exhibited the need for a better understanding of Treg biology. Classical mechanisms of dysfunction in T cells such as exhaustion, senescence, and anergy are poorly understood in Tregs. Previous works in auto- and alloimmune diseases, as well as in cell-engineering, have shown susceptibility of Tregs to such complications, furthering the importance of this knowledge for future design and interpretation of Treg adoptive immunotherapy trials. [ABSTRACT FROM AUTHOR]

Summary: Innate lymphoid cells (ILCs) are tissue resident cells that are triggered through a relatively broad spectrum of alarmins, inflammatory cues, neuropeptides, and hormones. Functionally, ILCs are akin to subsets of helper T cells and are characterized by a similar effector cytokine profile. They also share a dependency on many of the same essential transcription factors identified for the maintenance and survival of T cells. The key distinguishing factor between the ILC family and T cells is the lack of antigen-specific T cell receptor (TCR) on ILCs and, thus, they can be considered the "ultimate invariant T cells". ILCs, like T cells, orchestrate downstream effector inflammatory responses by adjusting the cytokine microenvironment in a fashion that promotes protection, health, and homeostasis at mucosal barrier sites. But also, like T cells, ILCs have recently been implicated in several pathological inflammatory disease states. This review focuses on the selective role of ILCs in the development of allergic airway inflammation (AAI) and fibrosis in the gut where a complex ILC interplay has been shown to either attenuate or worsen disease. Finally, we discuss new data on TCR gene rearrangements in subsets of ILCs that challenge the current dogma linking their origin to committed bone marrow progenitors and instead propose a thymic origin for at least some ILCs. In addition, we highlight how naturally occurring TCR rearrangements and the expression of major histocompatibility (MHC) molecules in ILCs provide a useful natural barcode for these cells and may prove instrumental in studying their origins and plasticity. In the lungs, in response to local insult ILC2s initiate a cascade of events that culminate in the expansion and polarization of CD4+ T cells to Th2 cells creating a type 2 immune environment leading to allergic airway inflammation. In the gut, RORα-deficient mice are protected from salmonella-induced intestinal fibrosis due to the failure of RORα-deficient ILC3 to produce functional IL-17. Finally, a new ILC development dogma is proposed where some ILCs undergo non-productive TCR generearrangements in the thymus prior to moving into the periphery and other tissues. [ABSTRACT FROM AUTHOR]

Summary: The immune system is composed of a variety of different T-cell lineages distributed through both secondary lymphoid tissue and non-lymphoid tissue. The intestinal epithelium is a critical barrier surface that contains numerous intraepithelial lymphocytes that aid in maintaining homeostasis at that barrier. This review focuses on T-cell receptor αβ (TCRαβ) CD8αα intraepithelial lymphocytes, and how recent advances in the field clarify how this unique T-cell subset is selected, matures, and functions in the intestines. We consider how the available evidence reveals a story of ontogeny starting from agonist selection of T cells in the thymus and finishing through the specific signaling environment of the intestinal epithelium. We conclude with how this story raises further key questions about the development of different ontogenic waves of TCRαβ CD8αα IEL and their importance for intestinal epithelial homeostasis. The intestine is home to a variety of T-cell subsets. One particular T-cell subset, TCRαβ CD8αα intraepithelial lymphocytes (IELs), is selected in the thymus. This review discusses the factors and events that regulate the selection of TCRαβ CD8αα IELs. [ABSTRACT FROM AUTHOR]

Summary: The Forkhead Box P3 (FOXP3) protein is an essential transcription factor for the development and function of regulatory T cells (Tregs), involved in the maintenance of immunological tolerance. Although extensive research over the last decade has investigated the critical role of FOXP3+ cells in preserving immune homeostasis, our understanding of their specific functions remains limited. Therefore, unveiling the molecular mechanisms underpinning the up- and downstream transcriptional regulation of and by FOXP3 is crucial for developing Treg-targeted therapeutics. Dysfunctions in FOXP3+ Tregs have also been found to be inherent drivers of autoimmune disorders and have been shown to exhibit multifaceted functions in the context of cancer. Recent research suggests that these cells may also be involved in tissue-specific repair and regeneration. Herein, we summarize current understanding of the thymic-transcriptional regulatory landscape of FOXP3+ Tregs, their epigenetic modulators, and associated signaling pathways. Finally, we highlight the contributions of FOXP3 on the functional development of Tregs and reflect on the clinical implications in the context of pathological and physiological immune responses. A subset of CD4+ T cells, recognized as FOXP3+ regulatory T (Treg) cells, are involved in preserving immune tolerance. Defects in these cells drive the pathogenesis of autoimmune diseases. In this review, we discuss the functions and dysfunctions in the developmental pathways of FOXP3+ Tregs, their emerging roles, and explore potential therapeutic targets. [ABSTRACT FROM AUTHOR]

Summary: Most CD4 and CD8 T cells are restricted by conventional major histocompatibility complex (MHC) molecules and mount TCR-dependent adaptive immune responses. In contrast, MAIT, iNKT, and certain γδ TCR bearing cells are characterized by their abilities to recognize antigens presented by unconventional antigen-presenting molecules and to mount cytokine-mediated TCR-independent responses in an "innate-like" manner. In addition, several more diverse T-cell subsets have been described that in a similar manner are restricted by unconventional antigen-presenting molecules but mainly depend on their TCRs for activation. Vice versa, innate-like behaviour was reported in defined subpopulations of conventional T cells, particularly in barrier sites, showing that these two features are not necessarily linked. The abilities to recognize antigens presented by unconventional antigen-presenting molecules or to mount TCR-independent responses creates unique niches for these T cells and is linked to wide range of functional capabilities. This is especially exemplified by unconventional and innate-like T cells present at barrier sites where they are involved in pathogen defense, tissue homeostasis as well as in pathologic processes. T cells can recognize conventional (peptide-major histocompatibility complex) or unconventional ligands. In many cases, "unconventional" T cells such as MAIT cells also show innate-like features and can respond independently of their TCR. Recent data have indicated innate-like features in conventional T cells, such as the recently described TMICpopulation in gut. [ABSTRACT FROM AUTHOR]

Remitting seronegative symmetrical synovitis with pitting oedema (RS3PE) syndrome was first described by McCarty in 1985 and is characterized by pitting oedema and an acute symmetrical synovitis of small joints. Self-directed inflammation in autoimmune disorders is caused by an abnormal activation of the adaptive immune system, while in autoinflammatory disorders, it is due to aberrant activation of the innate immune system without autoantibodies or autoreactive T cells. The role of autoimmunity in the pathogenesis of RS3PE syndrome is suggested by possible associations with some autoimmune diseases and human leukocyte antigen (HLA) haplotypes. However, several other features point to a possible role of autoinflammation in RS3PE syndrome. In this review, the relative contributions of both innate and adaptive immune systems to the pathogenesis of RS3PE syndrome are discussed. [ABSTRACT FROM AUTHOR]

Accurately predicting the antigen-binding specificity of adaptive immune receptors (AIRs), such as T-cell receptors (TCRs) and B-cell receptors (BCRs), is essential for discovering new immune therapies. However, the diversity of AIR chain sequences limits the accuracy of current prediction methods. This study introduces SC-AIR-BERT, a pre-trained model that learns comprehensive sequence representations of paired AIR chains to improve binding specificity prediction. SC-AIR-BERT first learns the 'language' of AIR sequences through self-supervised pre-training on a large cohort of paired AIR chains from multiple single-cell resources. The model is then fine-tuned with a multilayer perceptron head for binding specificity prediction, employing the K-mer strategy to enhance sequence representation learning. Extensive experiments demonstrate the superior AUC performance of SC-AIR-BERT compared with current methods for TCR- and BCR-binding specificity prediction. [ABSTRACT FROM AUTHOR]

CD8+ T cells can recognize peptides presented by class I human leukocyte antigen (HLA-I) of nucleated cells. Exploring this immune mechanism is essential for identifying T-cell vaccine targets in cancer immunotherapy. Over the past decade, the wealth of data generated by experiments has spawned many computational approaches for predicting HLA-I binding, antigen presentation and T-cell immune responses. Nevertheless, existing HLA-I binding and antigen presentation prediction approaches suffer from low precision due to the absence of T-cell receptor (TCR) recognition. Direct modeling of T-cell immune responses is less effective as TCR recognition's mechanism still remains underexplored. Therefore, directly applying these existing methods to screen cancer neoantigens is still challenging. Here, we propose a novel immune epitope prediction method termed IEPAPI by effectively incorporating antigen presentation and immunogenicity. First, IEPAPI employs a transformer-based feature extraction block to acquire representations of peptides and HLA-I proteins. Second, IEPAPI integrates the prediction of antigen presentation prediction into the input of immunogenicity prediction branch to simulate the connection between the biological processes in the T-cell immune response. Quantitative comparison results on an independent antigen presentation test dataset exhibit that IEPAPI outperformed the current state-of-the-art approaches NetMHCpan4.1 and mhcflurry2.0 on 100 (25/25) and 76% (19/25) of the HLA subtypes, respectively. Furthermore, IEPAPI demonstrates the best precision on two independent neoantigen datasets when compared with existing approaches, suggesting that IEPAPI provides a vital tool for T-cell vaccine design. [ABSTRACT FROM AUTHOR]

Motivation T-cell receptor beta chain (TCRB) repertoires are crucial for understanding immune responses. However, their high diversity and complexity present significant challenges in representation and analysis. The main motivation of this study is to develop a unified and compact representation of a TCRB repertoire that can efficiently capture its inherent complexity and diversity and allow for direct inference. Results We introduce a novel approach to TCRB repertoire encoding and analysis, leveraging the Lempel-Ziv 76 algorithm. This approach allows us to create a graph-like model, identify-specific sequence features, and produce a new encoding approach for an individual's repertoire. The proposed representation enables various applications, including generation probability inference, informative feature vector derivation, sequence generation, a new measure for diversity estimation, and a new sequence centrality measure. The approach was applied to four large-scale public TCRB sequencing datasets, demonstrating its potential for a wide range of applications in big biological sequencing data. Availability and implementation Python package for implementation is available https://github.com/MuteJester/LZGraphs. [ABSTRACT FROM AUTHOR]

Background: Resveratrol has been reported to reverse the imbalance of T helper 17/regulatory T (Th17/Treg) by inhibiting the aryl hydrocarbon receptor pathway to treat immune thrombocytopenia. However, the regulation mechanism of the Notch signaling pathway by resveratrol has not been reported in purpura. This study is aimed to explore the mechanism of resveratrol ultrafine nanoemulsion (Res-mNE) in immune thrombocytopenia. Methods: The immune thrombocytopenia mouse model was constructed to explore the effect of RES-mNE on immune thrombocytopenia. Cluster of differentiation 4 (CD4+) T cells were isolated and treated with different medications. CD4+ T cells were induced to differentiate into Th17 cells and Treg cells. Flow cytometry was used to detect the proportion of Th17 cells and Treg cells. The secretion was measured by the enzyme-linked immunosorbent assay (ELISA). Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) and western blot were used to detect the mRNA and protein levels. Results: Th17 cells, IL-17A and IL-22 increased in the immune thrombocytopenia mouse model, and the Treg cells and IL-10 decreased. Res-mNE promoted Treg cell differentiation and IL-10 secretion in CD4+ T cells while inhibiting Th17 cell differentiation and IL-17A and IL-22 levels. The AhR activator 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) reversed the effect of Res-mNE. Notch inhibitors reduced the ratio of Th17/Treg differentiation. Res-mNE activated the expression of Foxp3 by mediating AhR/Notch signaling to reverse the imbalance of Th17/Treg differentiation in immune thrombocytopenia. Conclusion: Taken together, our findings demonstrated that RES-mNE inhibited the AhR/Notch axis and reversed Th17/Treg imbalance by activating Foxp3. [ABSTRACT FROM AUTHOR]

T cells play key protective but also pathogenic roles in COVID-19. We studied the expression of long non-coding RNAs (lncRNAs) in COVID-19 T-cell transcriptomes by integrating previously published single-cell RNA sequencing datasets. The long intergenic non-coding RNA MALAT1 was the most highly transcribed lncRNA in T cells, with Th1 cells demonstrating the lowest and CD8+ resident memory cells the highest MALAT1 expression, amongst CD4+ and CD8+ T-cells populations, respectively. We then identified gene signatures that covaried with MALAT1 in single T cells. A significantly higher number of transcripts correlated negatively with MALAT1 than those that correlated. Enriched functional annotations of the MALAT1- anti-correlating gene signature included processes associated with T-cell activation such as cell division, oxidative phosphorylation, and response to cytokine. The MALAT1 anti-correlating gene signature shared by both CD4+ and CD8+ T-cells marked dividing T cells in both the lung and blood of COVID-19 patients. Focussing on the tissue, we used an independent patient cohort of post-mortem COVID-19 lung samples and demonstrated that MALAT1 suppression was indeed a marker of MKI67+ proliferating CD8+ T cells. Our results reveal MALAT1 suppression and its associated gene signature are a hallmark of human proliferating T cells. T cells play important roles in the body's response to COVID-19. We found gene signatures anti-correlating to MALAT1 expression as a marker of proliferating CD4+ Th1 and CD8+ exhausted sub-populations. [ABSTRACT FROM AUTHOR]

Background The impact of different therapeutic classes of drugs in antiretroviral therapy (ART) regimens on the CD4/CD8 ratio is not well documented in people treated for HIV. The objective of this study was to analyze the long-term effect of exposure to integrase strand transfer inhibitor (INSTI) on CD4/CD8 ratio compared with nonnucleoside reverse transcriptase inhibitor (NNRTI) or protease inhibitor (PI) among ART-treated persons with HIV (PWH). Methods Data from the Quebec HIV Cohort collected from 31 August 2017 were used. Our analysis included all patients in the cohort who received a first or subsequent ART regimen composed of 2 nucleoside reverse transcriptase inhibitors (NRTIs) and a third active drug of a different class (NNRTI, PI, or INSTI) for at least 16 weeks. Marginal structural Cox models were constructed to estimate the effect of different therapeutic classes on the CD4/CD8 ratio outcome. Results Among the 3907 eligible patients, 972 (24.9%), 1996 (51.1%), and 939 (24.0%) were exposed to an ART regimen whose third active agent was an NNRTI, PI, or INSTI, respectively. The total follow-up time was 13 640.24 person-years. The weighted hazard ratio for the association between the third active class and CD4/CD8 ratio ≥1 was.56 (95% confidence interval [CI]:.48–.65) for patients exposed to NNRTI + 2 NRTIs and.41 (95% CI:.35–.47) for those exposed to PI + 2 NRTIs, compared with those exposed INSTI + 2 NRTIs. Conclusions For people treated for HIV, INSTI-based ART appears to be associated with a higher CD4/CD8 ratio than NNRTI and PI-based ART. [ABSTRACT FROM AUTHOR]

Objectives: This study evaluated the characteristics of serosal involvement in adult-onset Still’s disease (AOSD). Methods: Patients meeting the Yamaguchi classification criteria were classified into AOSD with and without serosal involvement according to their manifestations and sonography/radiography. Clinical data was retrospectively reviewed from 102 patients with AOSD in two centres. Results: Forty-two patients (41.2%) had serosal involvement. The frequencies of pulmonary infiltrate and impaired liver function were significantly higher in patients with serosal involvement (푝 = .002 and 푝 = .007, respectively), who also had a higher modified systemic score (푝 = .009). In addition, the percentages of CD3+ T cells (푝 < .001) and, especially, the CD8+ T cells (푝 = .004) were significantly increased in the peripheral blood of AOSD patients with serosal involvement. Notably, patients with serosal involvement were more likely to develop macrophage activation syndrome (푝 = .047) and a chronic pattern (푝 = .016) during the follow-up. Conclusions: Patients with serosal involvement demonstrated the more severe disease activity and different immune phenotypes; these patients were more likely to develop macrophage activation syndrome, and they may require more aggressive treatment at an early time to control their systemic inflammation. [ABSTRACT FROM AUTHOR]

Major histocompatibility complex (MHC) class II molecules play a pivotal role in antigen presentation and CD4+ T cell response. Accurate prediction of the immunogenicity of MHC class II-associated antigens is critical for vaccine design and cancer immunotherapies. However, current computational methods are limited by insufficient training data and algorithmic constraints, and the rules that govern which peptides are truly recognized by existing T cell receptors remain poorly understood. Here, we build a transfer learning-based, long short-term memory model named 'TLimmuno2' to predict whether epitope-MHC class II complex can elicit T cell response. Through leveraging binding affinity data, TLimmuno2 shows superior performance compared with existing models on independent validation datasets. TLimmuno2 can find real immunogenic neoantigen in real-world cancer immunotherapy data. The identification of significant MHC class II neoantigen-mediated immunoediting signal in the cancer genome atlas pan-cancer dataset further suggests the robustness of TLimmuno2 in identifying really immunogenic neoantigens that are undergoing negative selection during cancer evolution. Overall, TLimmuno2 is a powerful tool for the immunogenicity prediction of MHC class II presented epitopes and could promote the development of personalized immunotherapies. [ABSTRACT FROM AUTHOR]

Dysregulation of leukocyte trafficking, lipid metabolism, and other metabolic processes are the hallmarks that underpin and drive pathology in obesity. Current clinical management targets alternations in lifestyle choices (e.g. exercise, weight loss) to limit the impact of the disease. Crucially, re-gaining control over the pathogenic cellular and molecular processes may offer an alternative, complementary strategy for obese patients. Here we investigate the impact of the immunopeptide, PEPITEM, on pancreas homeostasis and leukocyte trafficking in mice on high-fed obesogenic diet (HFD). Both prophylactic and therapeutic treatment with PEPITEM alleviated the effects of HFD on the pancreas, reducing pancreatic beta cell size. Moreover, PEPITEM treatment also limited T-cell trafficking (CD4+ T-cells and KLRG1+ CD3+ T-cells) to obese visceral, but not subcutaneous, adipose tissue. Similarly, PEPITEM treatment reduced macrophage numbers within the peritoneal cavity of mice on HFD diet at both 6 and 12 weeks. By contrast, PEPITEM therapy elevated numbers of T and B cells were observed in the secondary lymphoid tissues (e.g. spleen and inguinal lymph node) when compared to the untreated HFD controls. Collectively our data highlights the potential for PEPITEM as a novel therapy to combat the systemic low-grade inflammation experienced in obesity and minimize the impact of obesity on pancreatic homeostasis. Thus, offering an alternative strategy to reduce the risk of developing obesity-related co-morbidities, such as type 2 diabetes mellitus, in individuals at high risk and struggling to control their weight through lifestyle modifications. In this manuscript, we demonstrate for the first time that therapeutic administration of the immunopeptide, PEPITEM, limits the pathological impact of obesity on the pancreas and systemic leukocyte trafficking, dampening the effects of obesity-induced systemic low-grade inflammation. Further work is required to determine the utility of PEPITEM as an alternative strategy to reduce the risk of developing obesity-related co-morbidities, such as type-2 diabetes, in individuals at high risk and struggling to control their weight through lifestyle modifications. [ABSTRACT FROM AUTHOR]

The trafficking of autoreactive leukocytes across the blood-brain barrier (BBB) endothelium is a hallmark of multiple sclerosis (MS) pathogenesis. Although the BBB endothelium represents one of the main central nervous system (CNS) borders to interact with the infiltrating leukocytes, its exact contribution to neuroinflammation remains understudied. Here, we show that Mcam identifies inflammatory brain endothelial cells (ECs) with pro-migratory transcriptomic signature during experimental autoimmune encephalomyelitis (EAE). In addition, MCAM was preferentially upregulated on BBB ECs in MS lesions in situ and at EAE disease onset by molecular magnetic resonance imaging. In vitro and in vivo, we demonstrate that MCAM on BBB ECs contributes to EAE development by promoting the cellular trafficking of TH1 and TH17 lymphocytes across the BBB. Lastly, we showcase ST14 as an immune ligand to brain endothelial MCAM, enriched on CD4+ T lymphocytes that cross the BBB in vitro, in vivo and in MS lesions as detected by flow cytometry on rapid autopsy derived brain tissue from MS patients. Collectively, our findings reveal that MCAM is at the center of a pathological pathway used by brain ECs to recruit pathogenic CD4+ T lymphocyte from circulation early during neuroinflammation. The therapeutic targeting of this mechanism is a promising avenue to treat MS. [ABSTRACT FROM AUTHOR]

Mitochondria are the controllers of cell metabolism and are recognized as decision makers in cell death pathways, organizers of cytoplasmic signaling networks, managers of cellular stress responses, and regulators of nuclear gene expression. Cells of the immune system are particularly dependent on mitochondrial resources, as they must swiftly respond to danger signals with activation, trafficking, migration, and generation of daughter cells. Analogously, faulty immune responses that lead to autoimmunity and tissue inflammation rely on mitochondria to supply energy, cell building blocks and metabolic intermediates. Emerging data endorse the concept that mitochondrial fitness, and the lack of it, is of particular relevance in the autoimmune disease rheumatoid arthritis (RA) where deviations of bioenergetic and biosynthetic flux affect T cells during early and late stages of disease. During early stages of RA, mitochondrial deficiency allows naïve RA T cells to lose self-tolerance, biasing fundamental choices of the immune system toward immune-mediated tissue damage and away from host protection. During late stages of RA, mitochondrial abnormalities shape the response patterns of RA effector T cells engaged in the inflammatory lesions, enabling chronicity of tissue damage and tissue remodeling. In the inflamed joint, autoreactive T cells partner with metabolically reprogrammed tissue macrophages that specialize in antigen-presentation and survive by adapting to the glucose-deplete tissue microenvironment. Here, we summarize recent data on dysfunctional mitochondria and mitochondria-derived signals relevant in the RA disease process that offer novel opportunities to deter autoimmune tissue inflammation by metabolic interference. [ABSTRACT FROM AUTHOR]

T-cell receptors (TCRs) play an essential role in the adaptive immune system. Probabilistic models for TCR repertoires can help decipher the underlying complex sequence patterns and provide novel insights into understanding the adaptive immune system. In this work, we develop TCRpeg, a deep autoregressive generative model to unravel the sequence patterns of TCR repertoires. TCRpeg largely outperforms state-of-the-art methods in estimating the probability distribution of a TCR repertoire, boosting the average accuracy from 0.672 to 0.906 measured by the Pearson correlation coefficient. Furthermore, with promising performance in probability inference, TCRpeg improves on a range of TCR-related tasks: profiling TCR repertoire probabilistically, classifying antigen-specific TCRs, validating previously discovered TCR motifs, generating novel TCRs and augmenting TCR data. Our results and analysis highlight the flexibility and capacity of TCRpeg to extract TCR sequence information, providing a novel approach for deciphering complex immunogenomic repertoires. [ABSTRACT FROM AUTHOR]

Summary: The actions of the immune system are finely tuned, involving complex communication and coordination between diverse immune and non-immune cells across the tissues of the body. A healthy immune system requires a precise balance between immunity and tolerance. Regulatory T cells (Tregs) have long been appreciated as one of the master regulators of this balance; their importance is underscored by the autoimmunity that develops in mice and humans when Tregs are missing or dysfunctional. In addition to the immunoregulatory roles of Tregs in suppressing autoimmunity and inflammation via control of adaptive and innate immune responses, several non-immune modulatory functions of Tregs have been identified in recent years. In this review, we have highlighted the growing literature on the action of Tregs in metabolism, stem cell maintenance, tissue repair, and angiogenesis. Alongside Tregs' immune suppressive role, these non-suppressive activities comprise a key function of Tregs in regulating health and disease. As Tregs receive increasing attention as therapeutic targets, understanding their non-canonical functions may become an important feature of Treg-directed interventions. Diverse functions of Tregs beyond immune suppression. As detailed in the canonical suppression box, Tregs use several mechanisms to dampen proliferation and function of effector T cells and other immune cells. Tregs also have myriad effects on tissue repair, angiogenesis, basal metabolism, and maintenance of the stem cell niche. [ABSTRACT FROM AUTHOR]

Summary: Immune homeostasis is heavily dependent on the action of regulatory T cells (Tregs) which act to suppress the activation of many immune cell types including autoreactive conventional T cells. A body of evidence has shown that Tregs are intrinsically defective in many common autoimmune diseases, and gene polymorphisms which increase the susceptibility of autoimmune disease development have implicated the interleukin-2 (IL-2) signaling pathway as a key dysregulated mechanism. IL-2 is essential for Treg function and survival, and Tregs are highly sensitive to low levels of this cytokine in their environment. This review will revisit the rationale behind using low-dose IL-2 as a therapy to treat autoimmune diseases and evaluate the outcomes of trials to date. Furthermore, novel engineered IL-2 therapies with increased Treg specificity have shown promise in pre-clinical studies and human clinical trials for some agents have begun. Future studies will determine whether low-dose IL-2 or engineered IL-2 therapies can change the course of autoimmune and inflammatory diseases in patients. [ABSTRACT FROM AUTHOR]

Objectives To analyse humoral and cellular immune response to mRNA COVID-19 vaccines in patients with GCA. Methods Consecutive patients with a diagnosis of GCA receiving two doses of BNT162b2 vaccine were assessed at baseline and 3 weeks from the second vaccine dose. Healthy subjects (n  = 51) were included as controls (HC). Humoral response was assessed with Spike-specific IgG antibody response (S-IgG) and neutralizing antibodies (NtAb). Specific T cell response was assessed by enzyme linked immunosorbent spot (ELISpot). Results Of 56 included patients with GCA, 44 were eligible after exclusion of previous evidence of COVID-19 and incomplete follow-up. A significant proportion of patients with GCA (91%) demonstrated antibody (S-IgG) response, but this was significantly lower than HCs (100%); P  < 0.0001. Neutralizing activity was not detected in 16% of patients with GCA. Antibody titres (S-IgG and NtAb) were significantly lower compared with HCs. Humoral response (S-IgG and NtAb) was significantly hampered by treatment with MTX. Cellular response was lacking in 30% of patients with GCA (vs 0% in HCs; P  < 0.0001). Cellular response was significantly influenced by the levels of baseline peripheral T-lymphocytes and by glucocorticoid treatment. Treatment with tocilizumab did not affect any level of the immune response elicited by vaccination. Conclusions Although patients with GCA apparently achieve a robust antibody seroconversion, there is a significant impairment of the neutralizing activity. MTX significantly reduced all levels of the humoral response. Up to one-third of patients do not develop a cellular immune protection in response to COVID-19 vaccination. [ABSTRACT FROM AUTHOR]

Computational prediction of T cell epitopes is a crucial component in the development of novel vaccines. T cells in a healthy vertebrate host can recognize as non-self only those peptides that are present in the parasite's proteins but absent in the host's proteins. This principle enables us to determine the current and past host specificity of a parasite and to predict peptides capable of eliciting a T cell response. Building upon the detailed mapping of T cell clone specificity for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antigens, we employed Monte Carlo tests to determine that empirically confirmed T cell-stimulating peptides have a significantly increased proportion of pentapeptides, hexapeptides and heptapeptides not found in the human proteome (P  < 0.0001, Cohen's d  > 4.9). We observed a lower density of potential pentapeptide targets for T cell recognition in the spike protein from the human-adapted SARS-CoV-2 ancestor compared to 10 other SARS-CoV-2 proteins originating from the horseshoe bat-adapted ancestor. Our novel method for predicting T cell immunogenicity of SARS-CoV-2 peptides is four times more effective than previous approaches. We recommend utilizing our theory-based method where efficient empirically based algorithms are unavailable, such as in the development of certain veterinary vaccines, and combining it with empirical methods in other cases for optimal results. [ABSTRACT FROM AUTHOR]

Summary: Background: Primary cutaneous peripheral T‐cell lymphomas with a T‐follicular helper phenotype (pcTFH‐PTCL) are poorly characterized, and often compared to, but not corresponding with, mycosis fungoides (MF), Sézary syndrome, primary cutaneous CD4+ lymphoproliferative disorder, and skin manifestations of angioimmunoblastic T‐cell lymphomas (AITL). Objectives: We describe the clinicopathological features of pcTFH‐PTCL in this original series of 23 patients, and also characterize these cases molecularly. Methods: Clinical and histopathological data of the selected patients were reviewed. Patient biopsy samples were also analysed by targeted next‐generation sequencing. Results: All patients (15 men, eight women; median age 66 years) presented with skin lesions, without systemic disease. Most were stage T3b, with nodular (n = 16), papular (n = 6) or plaque (atypical for MF, n = 1) lesions. Three (13%) developed systemic disease and died of lymphoma. Nine (39%) patients received more than one line of chemotherapy. Histologically, the lymphomas were CD4+ T‐cell proliferations, usually dense and located in the deep dermis (n = 14, 61%), with the expression of at least two TFH markers (CD10, CXCL13, PD1, ICOS, BCL6), including three markers in 16 cases (70%). They were associated with a variable proportion of B cells. Eight patients were diagnosed with an associated B‐cell lymphoproliferative disorder (LPD) on biopsy, including Epstein–Barr virus (EBV)‐positive diffuse large B‐cell lymphoma (n = 3), EBV+ LPD (n = 1) and monotypic plasma cell LPD (n = 4). Targeted sequencing showed four patients to have a mutated TET2–RHOAG17V association (as frequently seen in AITL) and another a TET2/DNMT3A/PLCG1/SETD2 mutational profile. The latter patient, one with a TET2–RHOA association, and one with no detected mutations, developed systemic disease and died. Five other patients showed isolated mutations in TET2 (n = 1), PLCG1 (n = 2), SETD2 (n = 1) or STAT5B (n = 1). Conclusions: Patients with pcTFH‐PTCL have pathological and genetic features that overlap with those of systemic lymphoma of TFH derivation. Clinically, most remained confined to the skin, with only three patients showing systemic spread and death. Whether pcTFH‐PTCL should be integrated as a new subgroup of TFH lymphomas in future classifications is still a matter of debate. What is already known about this topic?There is a group of cutaneous lymphomas that express T‐follicular helper (TFH) markers that do not appear to correspond to existing World Health Organization diagnostic entities.These include mycosis fungoides, Sézary syndrome, or primary cutaneous CD4+ small/medium‐sized T‐cell lymphoproliferative disorder or cutaneous extensions of systemic peripheral T‐cell lymphomas (PTCL) with TFH phenotype. What does this study add?This is the first large original series of patients with a diagnosis of primary cutaneous PTCL with a TFH phenotype (pcTFH‐PTCL) to be molecularly characterized.pcTFH‐PTCL may be a standalone group of cutaneous lymphomas with clinicopathological and molecular characteristics that overlap with those of systemic TFH lymphomas, such as angioimmunoblastic T‐cell lymphoma, and does not belong to known diagnostic groups of cutaneous lymphoma.This has an impact on the treatment and follow‐up of patients; the clinical behaviour needs to be better clarified in further studies to tailor patient management. [ABSTRACT FROM AUTHOR]

B cells are classically considered solely as antibody-producing cells driving humoral immune responses to foreign antigens in infections and vaccinations as well as self-antigens in pathological settings such as autoimmunity. However, it has now become clear that B cells can also secrete a vast array of cytokines, which influence both pro- and anti-inflammatory immune responses. Indeed, similarly to T cells, there is significant heterogeneity in cytokine-driven responses by B cells, ranging from the production of pro-inflammatory effector cytokines such as IL-6, through to the release of immunosuppressive cytokines such as IL-10. In this review, focusing on human B cells, we summarize the key findings that have revealed that cytokine-producing B cell subsets have critical functions in healthy immune responses and contribute to the pathophysiology of autoimmune diseases. B cells are classically considered solely as antibody-producing cells driving humoral immune responses to foreign antigens in infections and vaccinations as well as self-antigens in pathological settings such as autoimmunity. However, it has now become clear that B cells can also secrete a vast array of cytokines, which influence both pro- and anti-inflammatory immune responses. In this review, focusing on human B cells, we summarise the key findings that have revealed that cytokine-producing B cell subsets have critical functions in healthy immune responses and contribute to the pathophysiology of autoimmune diseases. [ABSTRACT FROM AUTHOR]

Lung squamous cell carcinoma (LUSC) is a common subtype of lung cancer. Th1 cells contribute to antitumor immune responses. However, there are few studies on Th1 cells in LUSC. CD8+ T cells are the main driver of the antitumor immunity, targeting tumor cells killing. Th1 cells play an important auxiliary role in this process. Here, we used single‐cell RNA‐seq (scRNA‐seq) to analyze qualified CD4+ T cells and Th1 cells (defined CD4+ T cells with 1 or more of STAT1+, STAT4+, T‐bet+, and IFN‐γ+ as Th1 cells) from tissues of 8 LUSC patients. Then, we validated Th1 cells and CD8+ T cells of 32 LUSC patients by multiplex immunofluorescence staining and immunohistochemistry. Finally, we used flow cytometry to detect IFN‐γ of CD4+ T cells in human PBMCs coincubated with LUSC‐derived supernatant to simulate a tumor inhibitory microenvironment. ScRNA‐seq showed IFN‐γ+ Th1 cells account for 25.28% of all Th1 cells. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses of differentially expressed genes between IFN‐γ+ Th1 cells and IFN‐γ– Th1 cells confirmed the decreased IFN‐γ is associated with endoplasmic reticulum stress (ER stress). Multiplex immunofluorescence staining and immunohistochemistry proved there was a positive correlation between IFN‐γ+ STAT1+ T‐bet+ Th1 cells and CD8+ T cells. Flow cytometry showed IFN‐γ secreted by Th1 cells is decreased. These findings support the claim that Th1 cells' function is suppressed in LUSC. Through scRNA‐seq, we found that the decreased Th1 cells' function is associated with ER stress, which requires further study. Overall, these findings may produce a new method for the treatment of LUSC. [ABSTRACT FROM AUTHOR]

Recent studies have established that the innate immune system of reptiles is broad and robust, but the question remains: What role does the reptilian adaptive immune system play? Conventionally, adaptive immunity is described as involving T and B lymphocytes that display variable receptors, is highly specific, improves over the course of the response, and produces a memory response. While reptiles do have B and T lymphocytes that utilize variable receptors, their adaptive response is relatively non-specific, generates a prolonged antibody response, and does not produce a typical memory response. This alternative adaptive strategy may allow reptiles to produce a broad adaptive response that complements a strong innate system. Further studies into reptile adaptive immunity cannot only clarify outstanding questions on the reptilian immune system but can shed light on a number of important immunological concepts, including the evolution of the immune system and adaptive immune responses that take place outside of germinal centers. [ABSTRACT FROM AUTHOR]

The rheumatoid arthritis (RA) inflammatory process occurs in the joints where immune cells are attracted into the synovium to promote remodeling and tissue damage. GPR15 is a G protein‐coupled receptor (GPCR) located on chromosome 3 and has similarity in its sequence with chemokine receptors. Recent evidence indicates that GPR15 may be associated with modulation of the chronic inflammatory response. We evaluated the expression of GPR15 and GPR15L in blood and synovial tissue samples from RA patients, as well as to perform a functional migration assay in response to GPR15L. The expression of GPR15 and c10orf99/gpr15l mRNA was analyzed by RT‐qPCR. Samples of synovial fluid and peripheral blood were analyzed for CD45+CD3+CD4+GPR15+ and CD45+CD3+CD8+GPR15+ T cell frequency comparing RA patients versus control subjects by flow cytometry. Migration assays were performed using PBMCs isolated from these individuals in response to the synthetic GPR15 ligand. Statistical analysis included Kruskal–Wallis test, T‐test, or Mann–Whitney U test, according to data distribution. A higher expression in the mRNA for GPR15 was identified in early RA subjects. The frequencies of CD4+/CD8+ GPR15+ T lymphocytes are higher in RA patients comparing with healthy subjects. Also, the frequency CD4+/CD8+ GPR15+ T lymphocytes are higher in synovial fluid of established RA patients comparing with OA patients. GPR15 and GPR15L are present in the synovial tissue of RA patients and GPR15L promotes migration of PBMCs from RA patients and healthy subjects. Our results suggest that GPR15/GPR15L have a pathogenic role in RA and their antagonizing could be a therapeutic approach in RA. [ABSTRACT FROM AUTHOR]

Macrophages play a significant role in HIV infection and contribute to pathogenesis of comorbidities as well as establishment of the viral reservoir in people living with HIV. While CD4+ T cells are considered the main targets of HIV infection, infected macrophages resist the cytopathic effects of infection, contributing to the persistent HIV reservoir. Furthermore, activated macrophages drive inflammation and contribute to the development of comorbidities, including HIV‐associated CNS dysfunction. Better understanding the role of macrophages in HIV infection, persistence, and comorbidities can lead to development of innovative therapeutic strategies to address HIV‐related outcomes in people living with HIV. In October 2021, the National Institute of Mental Health and the Ragon Institute of MGH, MIT, and Harvard conducted a virtual meeting on role of macrophages in HIV infection, pathogenesis, and cure. This review article captures the key highlights from this meeting and provides an overview of interests and activities of various NIH institutes involved in supporting research on macrophages and HIV. [ABSTRACT FROM AUTHOR]

In addition to CD4+ T lymphocytes, cells of the myeloid lineage such as macrophages, dendritic cells (DCs), and osteoclasts (OCs) are emerging as important target cells for HIV‐1, as they likely participate in all steps of pathogenesis, including sexual transmission and early virus dissemination in both lymphoid and nonlymphoid tissues where they can constitute persistent virus reservoirs. At least in vitro, these myeloid cells are poorly infected by cell‐free viral particles. In contrast, intercellular virus transmission through direct cell‐to‐cell contacts may be a predominant mode of virus propagation in vivo leading to productive infection of these myeloid target cells. HIV‐1 cell‐to‐cell transfer between CD4+ T cells mainly through the formation of the virologic synapse, or from infected macrophages or dendritic cells to CD4+ T cell targets, have been extensively described in vitro. Recent reports demonstrate that myeloid cells can be also productively infected through virus homotypic or heterotypic cell‐to‐cell transfer between macrophages or from virus‐donor‐infected CD4+ T cells, respectively. These modes of infection of myeloid target cells lead to very efficient spreading in these poorly susceptible cell types. Thus, the goal of this review is to give an overview of the different mechanisms reported in the literature for cell‐to‐cell transfer and spreading of HIV‐1 in myeloid cells. [ABSTRACT FROM AUTHOR]