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This document is a correction notice for a paper on the potential bioactive compound bromelain. The authors have identified errors in one section of the paper and provide revised references. The corrected table includes therapeutic studies of bromelain based on experimental studies. The document also includes a compilation of various scientific studies and articles related to the use of bromelain for various medical purposes. The studies explore the potential benefits of bromelain in treating conditions such as cancer, inflammation, thrombosis, and pain. The document provides a comprehensive overview of the scientific research on bromelain and its potential applications in medicine. [Extracted from the article]

Rheumatoid arthritis (RA) is a chronic autoimmune condition frequently found in rheumatological patients that sometimes raises diagnosis and management problems. The pathogenesis of the disease is complex and involves the activation of many cells and intracellular signaling pathways, ultimately leading to the activation of the innate and acquired immune system and producing extensive tissue damage. Along with joint involvement, RA can have numerous extra-articular manifestations (EAMs), among which lung damage, especially interstitial lung disease (ILD), negatively influences the evolution and survival of these patients. Although there are more and more RA-ILD cases, the pathogenesis is incompletely understood. In terms of genetic predisposition, external environmental factors act and subsequently determine the activation of immune system cells such as macrophages, neutrophils, B and T lymphocytes, fibroblasts, and dendritic cells. These, in turn, show the ability to secrete molecules with a proinflammatory role (cytokines, chemokines, growth factors) that will produce important visceral injuries, including pulmonary changes. Currently, there is new evidence that supports the initiation of the systemic immune response at the level of pulmonary mucosa where the citrullination process occurs, whereby the autoantibodies subsequently migrate from the lung to the synovial membrane. The aim of this paper is to provide current data regarding the pathogenesis of RA-associated ILD, starting from environmental triggers and reaching the cellular, humoral, and molecular changes involved in the onset of the disease. [ABSTRACT FROM AUTHOR]

Background: The tonsils operate as a protection ring of mucosa at the gates of the upper aero-digestive tract. They show similarities with lymph nodes and participate as inductive organs of systemic and mucosal immunity. Based on the reduction of their size since puberty, they are thought to experience involution in adulthood. In this context, we have used tonsillar mononuclear cells (TMC) isolated from patients at different stages of life, to study the effect of ageing and the concomitant persistent inflammation on these immune cells. Results: We found an age-dependent reduction in the proportion of germinal center B cell population (BGC) and its T cell counterpart (T follicular helper germinal center cells, TfhGC). Also, we demonstrated an increment in the percentage of local memory B cells and mantle zone T follicular helper cells (mTfh). Furthermore, younger tonsils rendered higher proportion of proliferative immune cells within the freshly isolated TMC fraction than those from older ones. We demonstrated the accumulation of a B cell subset (CD20+CD39highCD73+ cells) metabolically adapted to catabolize adenosine triphosphate (ATP) as patients get older. To finish, tonsillar B cells from patients at different ages did not show differences in their proliferative response to stimulation ex vivo, in bulk TMC cultures. Conclusions: This paper sheds light on the changing aspects of the immune cellular landscape, over the course of time and constant exposure, at the entrance of the respiratory and digestive systems. Our findings support the notion that there is a re-modelling of the immune functionality of the excised tonsils over time. They are indicative of a transition from an effector type of immune response, typically oriented to reduce pathogen burden early in life, to the development of an immunosuppressive microenvironment at later stages, when tissue damage control gets critical provided the time passed under immune attack. Noteworthy, when isolated from such histologic microenvironment, older tonsillar B cells seem to level their proliferation capacity with the younger ones. Understanding these features will not only contribute to comprehend the differences in susceptibility to pathogens among children and adults but would also impact on vaccine developments intended to target these relevant mucosal sites. [ABSTRACT FROM AUTHOR]

Objectives: The aim of this data paper is to describe a collection of 33 genomic, transcriptomic and epigenomic sequencing datasets of the B-cell acute lymphoblastic leukemia (ALL) cell line REH. REH is one of the most frequently used cell lines for functional studies of pediatric ALL, and these data provide a multi-faceted characterization of its molecular features. The datasets described herein, generated with short- and long-read sequencing technologies, can both provide insights into the complex aberrant karyotype of REH, and be used as reference datasets for sequencing data quality assessment or for methods development. Data description: This paper describes 33 datasets corresponding to 867 gigabases of raw sequencing data generated from the REH cell line. These datasets include five different approaches for whole genome sequencing (WGS) on four sequencing platforms, two RNA sequencing (RNA-seq) techniques on two different sequencing platforms, DNA methylation sequencing, and single-cell ATAC-sequencing. [ABSTRACT FROM AUTHOR]

Head and neck squamous cell carcinoma (HNSCC) is a common malignant tumour. Despite advancements in surgery, radiotherapy and chemotherapy, which have improved the prognosis of most patients, a subset of patients with poor prognoses still exist due to loss of surgical opportunities, postoperative recurrence, and metastasis, among other reasons. The tumour microenvironment (TME) is a complex organization composed of tumour, stromal, and endothelial cells. Communication and interaction between tumours and immune cells within the TME are increasingly being recognized as pivotal in inhibiting or promoting tumour development. Previous studies on T cells in the TME of HNSCC have yielded novel therapeutic possibilities. However, the function of B cells, another adaptive immune cell type, in the TME of HNSCC patients has yet to be determined. Recent studies have revealed various distinct subtypes of B cells and tertiary lymphoid structures (TLSs) in the TME of HNSCC patients, which are believed to impact the efficacy of immune checkpoint inhibitors (ICIs). Therefore, this paper focuses on B cells in the TME to explore potential directions for future immunotherapy for HNSCC. [ABSTRACT FROM AUTHOR]

Helminths are multicellular parasites that are a substantial problem for both human and veterinary medicine. According to estimates, 1.5 billion people suffer from their infection, resulting in decreased life quality and burdens for healthcare systems. On the other hand, these infections may alleviate autoimmune diseases and allergy symptoms. The immune system is programmed to combat infections; nevertheless, its effector mechanisms may result in immunopathologies and exacerbate clinical symptoms. This review summarizes the role of the immune response against worms, with an emphasis on the Th2 response, which is a hallmark of helminth infections. We characterize non-immune cells (enteric tuft cells—ETCs) responsible for detecting parasites, as well as the role of hematopoietic-derived cells (macrophages, basophils, eosinophils, neutrophils, innate lymphoid cells group 2—ILC2s, mast cells, T cells, and B cells) in initiating and sustaining the immune response, as well as the functions they play in granulomas. The aim of this paper is to review the existing knowledge regarding the immune response against helminths, to attempt to decipher the interactions between cells engaged in the response, and to indicate the gaps in the current knowledge. [ABSTRACT FROM AUTHOR]

This paper formulates and analyzes two mathematical models that describe the within-host dynamics of human immunodeficiency virus type 1 (HIV-1) with impairment of both cytotoxic T lymphocytes (CTLs) and B cells. Both viral transmission (VT) and cellular infection (CT) mechanisms are considered. The second model is a generalization of the first model that includes distributed time delays. For the two models, we establish the non-negativity and boundedness of the solutions, find the basic reproductive numbers, determine all possible steady states and establish the global asymptotic stability properties of all steady states by means of the Lyapunov method. We confirm the theoretical results by conducting numerical simulations. We conduct a sensitivity analysis to show the effect of the values of the parameters on the basic reproductive number. We discuss the results, showing that impaired B cells and CTLs, time delay and latent CT have significant effects on the HIV-1 dynamics. [ABSTRACT FROM AUTHOR]

Simple Summary: This article addresses the topic of primary immunodeficiencies, with particular emphasis on antibody deficiencies with near-normal immunoglobulin levels or hyperimmunoglobulinemia. This paper goes beyond genetics and emphasizes the importance of the immune system and particularly immune checkpoints and Epstein–Barr virus (EBV) reactivation in the context of these disorders. The article delves into the immune dysregulations occurring in the course of this type of disease and the potential role of EBV reactivation, which affects the clinical picture of patients and, in the future, may contribute to the development of cancer, especially those related to hematological malignancies. Disturbances observed in the immunopathogenesis of the presented diseases go beyond the accepted scheme, with the development of PID largely associated only with genetic disorders, and the article emphasizes that the regulation of immunity and virus reactivation also contributes to the progression of PID. This study delves into the intricate landscape of primary immunodeficiencies, with a particular focus on antibody deficiencies characterized by near-normal immunoglobulin levels or hyperimmunoglobulinemia. Contrary to the conventional focus on genetic dysregulation, these studies investigate the key roles of immune checkpoints, such as PD-1/PD-L1, CTLA-4/CD86, and CD200R/CD200, on selected subpopulations of T and B lymphocytes and their serum concentrations of soluble forms in patients recruited for the studies in healthy volunteers. In addition, the studies also show the role of Epstein–Barr virus (EBV) reactivation and interactions with tested pathways of immune checkpoints involved in the immunopathogenesis of this disease. By examining the context of antibody deficiencies, this study sheds light on the nuanced interplay of factors beyond genetics, particularly the immune dysregulations that occur in the course of this type of disease and the potential role of EBV reactivation, which affects the clinical presentation of patients and may contribute to the development of cancer in the future, especially related to hematological malignancies. [ABSTRACT FROM AUTHOR]

Linear-B cell epitopes (LBCE) play a vital role in vaccine design; thus, efficiently detecting them from protein sequences is of primary importance. These epitopes consist of amino acids arranged in continuous or discontinuous patterns. Vaccines employ attenuated viruses and purified antigens. LBCE stimulate humoral immunity in the body, where B and T cells target circulating infections. To predict LBCE, the underlying protein sequences undergo a process of feature extraction, feature selection, and classification. Various system models have been proposed for this purpose, but their classification accuracy is only moderate. In order to enhance the accuracy of LBCE classification, this paper presents a novel 2-step metaheuristic variant-feature selection method that combines a linear support vector classifier (LSVC) with a Modified Genetic Algorithm (MGA). The feature selection model employs mono-peptide, dipeptide, and tripeptide features, focusing on the most diverse ones. These selected features are fed into a machine learning (ML)-based parallel ensemble classifier. The ensemble classifier combines correctly classified instances from various classifiers, including k-Nearest Neighbor (kNN), random forest (RF), logistic regression (LR), and support vector machine (SVM). The ensemble classifier came up with an impressively high accuracy of 99.3% as a result of its work. This accuracy is superior to the most recent models that are considered to be state-of-the-art for linear B-cell classification. As a direct consequence of this, the entire system model can now be utilised effectively in real-time clinical settings. [ABSTRACT FROM AUTHOR]

Since the pioneering works of Berg and Purcell, discriminating between diffusion followed by binding has played a central role in understanding cell signaling. B cell receptors (BCR) and antibodies (Ab) challenge that simplified view as binding to the antigen follows after a chain of diffusion and rotations, including whole molecule rotation and independent tilts and twists of their Fab arms due to their Yshaped structure and flexibility. In this paper, we combine analytical calculations with Brownian simulations to derive the first-passage times due to these three rotations positioning the Fab paratopes at a proper distance and orientation required for antigen binding. Our results indicate that when measuring Ab--Ag effective kinetic binding rates, using experimental methods in which the analyte is in solution only gives values proportional to the intrinsic binding rates, k+, and k-, for values of k+ up to 109 s-1. Beyond that, a plateau of the effective 3D on rate between 108 M-1s-1 and 109 M-1s-1 is attained. Additionally, for BCR--Ag interactions, the effective 2D on and off binding rates can only be inferred from the corresponding effective 3D on and off rates for values of effective 3D on rates lower than 106 M-1s-1. This is highly relevant when trying to relate BCR--antigen-binding strength and B cell response, especially during germinal center reactions. Therefore, there is a pressing need to reexamine our current understanding of the BCR--antigen kinetic rates in germinal centers using the latest experimental assays for BCR--Ag interactions. [ABSTRACT FROM AUTHOR]

Astragaloside IV (AS-IV) is one of the main active components extracted from the Chinese medicinal herb Astragali and serves as a marker for assessing the herb's quality. AS-IV is a tetracyclic triterpenoid saponin in the form of lanolin ester alcohol and exhibits various biological activities. This review article summarizes the chemical structure of AS-IV, its pharmacological effects, mechanism of action, applications, future prospects, potential weaknesses, and other unexplored biological activities, aiming at an overall analysis. Papers were retrieved from online electronic databases, such as PubMed, Web of Science, and CNKI, and data from studies conducted over the last 10 years on the pharmacological effects of AS—IV as well as its impact were collated. This review focuses on the pharmacological action of AS-IV, such as its anti-inflammatory effect, including suppressing inflammatory factors, increasing T and B lymphocyte proliferation, and inhibiting neutrophil adhesion-associated molecules; antioxidative stress, including scavenging reactive oxygen species, cellular scorching, and regulating mitochondrial gene mutations; neuroprotective effects, antifibrotic effects, and antitumor effects. [ABSTRACT FROM AUTHOR]

Prediction of conformational B-cell epitopes (CBCE) is an essential phase for vaccine design, drug invention, and accurate disease diagnosis. Many laboratorial and computational approaches have been developed to predict CBCE. However, laboratorial experiments are costly and time consuming, leading to the popularity of Machine Learning (ML)-based computational methods. Although ML methods have succeeded in many domains, achieving higher accuracy in CBCE prediction remains a challenge. To overcome this drawback and consider the limitations of ML methods, this paper proposes a novel DL-based framework for CBCE prediction, leveraging the capabilities of deep learning in the medical domain. The proposed model is named Deep Learning-based Temporal Convolutional Neural Network (DL-TCNN), which hybridizes empirical hyper-tuned 1D-CNN and TCN. TCN is an architecture that employs causal convolutions and dilations, adapting well to sequential input with extensive receptive fields. To train the proposed model, physicochemical features are firstly extracted from antigen sequences. Next, the Synthetic Minority Oversampling Technique (SMOTE) is applied to address the class imbalance problem. Finally, the proposed DL-TCNN is employed for the prediction of CBCE. The model's performance is evaluated and validated on a benchmark antigen–antibody dataset. The DL-TCNN achieves 94.44% accuracy, and 0.989 AUC score for the training dataset, 78.53% accuracy, and 0.661 AUC score for the validation dataset; and 85.10% accuracy, 0.855 AUC score for the testing dataset. The proposed model outperforms all the existing CBCE methods. [ABSTRACT FROM AUTHOR]

Epigallocatechin‐3‐gallate (EGCG) is a major bioactive compound in tea polyphenol extract. After ingestion, EGCG reaches the intestine and may commence anti‐inflammation in the intestinal organ. Thus, in this paper, the anti‐inflammatory effect of EGCG was studied using lipopolysaccharide (LPS)‐induced inflammation in RAW 264.7 cells. LPS induction instigated morphological deformation extensively which was normalized by EGCG. In LPS‐induced macrophage cells, EGCG was found to lower cellular nitric oxide (32% of LPS group) and intercellular ROS level (45.4% of LPS group). It also suppressed the expression of IL‐1β (LPS 132.6 ± 14.6, EGCG 10.67 ± 3.65), IL‐6 (LPS 2994.44 ± 178.5, EGCG 408.33 ± 52.34), TNF‐α (LPS 27.11 ± 2.84, EGCG 1.22 ± 0.03), and iNOS (LPS 40.45 ± 11.17, EGCG 10.24 ± 0.89). The GO function analysis identified that these differential genes involved 24 biological processes, 18 molecular functions, and 19 cellular component‐related processes. KEGG pathway enrichment analysis revealed that LPS significantly affects NF‐κB, TNF, and TLR signaling pathways. Western blotting revealed that EGCG diminished P‐IκB/IκB ratio by 75% and p‐p65/p65 by 50% compared to the LPS group. Finally, Arg‐1 and CD‐206 mRNA expression were determined by RT‐PCR, which was consistent with the RNA‐Seq result. These findings indicate that EGCG exerts an anti‐inflammatory effect by reducing NO and ROS production, suppressing TLR4 protein expression, and inhibiting IκB and p65 phosphorylation. [ABSTRACT FROM AUTHOR]

Chronic rhinosinusitis with nasal polyps (CRSwNP) has long been considered a benign, chronic inflammatory, and hyperplastic disease. Recent studies have shown that autoimmune-related mechanisms are involved in the pathology of nasal polyps. Activated plasma cells, eosinophils, basophils, innate type 2 lymphocytes, mast cells, and proinflammatory cytokine in polyp tissue indicate the mobilization of innate and adaptive immune pathways during polyp formation. The discovery of a series of autoantibodies further supports the autoimmune nature of nasal polyps. Local homeostasis dysregulation, infection, and chronic inflammation may trigger autoimmunity through several mechanisms, including autoantigens overproduction, microbial translocation, molecular mimicry, superantigens, activation or inhibition of receptors, bystander activation, dysregulation of Toll-Like Receptors (TLRs), epitope spreading, autoantigens complementarity. In this paper, we elaborated on the microbiome-mediated mechanism, abnormal host immunity, and genetic changes to update the role of autoimmunity in the pathogenesis of chronic rhinosinusitis with nasal polyps. [ABSTRACT FROM AUTHOR]

The purpose of this paper was to assess the value of ultrasonography in the prognosis of diffuse large b-cell lymphoma (DLBCL) by developing a new prognostic model. One hundred and eleven DLBCL patients with complete clinical information and ultrasound findings were enrolled in our study. Univariate and multivariate regression analyses were used to identify independent risk factors for progression-free survival (PFS) and overall survival (OS). Receiver operator characteristic (ROC) curves were plotted and the corresponding area under the curve (AUC) was calculated to assess the accuracy of the international prognostic index (IPI) and new model in DLBCL risk stratification. The results suggested that hilum loss and ineffective treatment were independent risk variables for both PFS and OS in DLBCL patients. Additionally, the new model that added hilum loss and ineffective treatment to IPI had a better AUC for PFS and OS than IPI alone (AUC: 0.90, 0.88, and 0.82 vs. 0.71, 0.74, and 0.68 for 1-, 3-, and 5-year PFS, respectively; AUC: 0.92, 0.85 and 0.86 vs. 0.71, 0.75 and 0.76, for 1-, 3-, and 5-year OS, respectively). The model based on ultrasound images could better suggest PFS and OS of DLBCL, allowing for better risk stratification. [ABSTRACT FROM AUTHOR]

Simple Summary: B cells are increasingly appreciated as important contributors to the tumor microenvironment in a myriad of cancer histologies, including sarcoma. In sarcoma, recent investigations have revealed associations between B cell expression signatures, the presence of tertiary lymphoid structures, and responses to immunotherapy. In this paper, we aim to provide a comprehensive review of the multiple putative roles of B cells in sarcoma, including a historical overview, an assessment of B cells within the sarcoma microenvironment, the role of tertiary lymphoid structures, the relationship between immunotherapy efficacy and B cell signatures, sarcoma antigens and anti-tumor antibodies, pro-tumor B cell relationships, and future research directions. Despite being one of the first types of cancers studied that hinted at a major role of the immune system in pro- and anti-tumor biology, little is known about the immune microenvironment in sarcoma. Few types of sarcoma have shown major responses to immunotherapy, and its rarity and heterogeneity makes it challenging to study. With limited systemic treatment options, further understanding of the underlying mechanisms in sarcoma immunity may prove crucial in advancing sarcoma care. While great strides have been made in the field of immunotherapy over the last few decades, most of these efforts have focused on harnessing the T cell response, with little attention on the role B cells may play in the tumor microenvironment. A growing body of evidence suggests that B cells have both pro- and anti-tumoral effects in a large variety of cancers, and in the age of bioinformatics and multi-omic analysis, the complexity of the humoral response is just being appreciated. This review explores what is currently known about the role of B cells in sarcoma, including understanding the various B cell populations associated with sarcoma, the organization of intra-tumoral B cells in tertiary lymphoid structures, recent trials in immunotherapy in sarcoma, intra-tumoral immunoglobulin, the pro-tumor effects of B cells, and exciting future areas for research. [ABSTRACT FROM AUTHOR]

This paper studies a mechanical metamaterial with tetrachiral topology by mathematical modeling. Chirality is the property of an object that makes the object distinguishable from its mirror image; chirality can be left- or right-handed. The mechanical response of two metamaterial unit cells with different configurations (patterns A and B) is investigated. It is found that the cubic cell with a regular pattern A exhibits orthotropic mechanical behavior under loading along three coordinate axes. An irregular pattern B differs from pattern A in that the upper face of the unit cell has an opposite chirality. This architectural transformation is considered as a topological defect, which enhances the twisting effect in the loaded metamaterial. Analysis of displacements and stresses shows that the mechanical behavior of the pattern B cell is described by the model of a transversely isotropic material. The orthotropic and transversely isotropic behavior of the cells of given configurations is also confirmed by the values of the effective elastic constants. Microstructural geometry and mechanical deformation of metamaterials are shown to be closely related. It is shown that a topological defect in a unit cell of a tetrachiral metamaterial strongly determines its twisting behavior. [ABSTRACT FROM AUTHOR]

Simple Summary: Colic, a condition affecting the digestive tract of horses, manifests itself in severe pain and may be life-threatening. Recurrent colic is usually caused by ongoing, chronic inflammatory process (and may be defied as: ≥3 episodes of colic within a 6-month period, with at least 48 h between colic episodes), associated with a chronic process, often of an inflammatory nature. Multiple causes of recurrent colic may exist, including, for an improper diet, management changes, stress, or parasites infestation. During the diagnostic process, a noninvasive test in the form of taking a biopsy of the duodenal or rectal mucosa proves to be useful, but its usefulness is limited only to diffuse processes. The study presented here depicts a retrospective analysis of the histopathological findings of samples taken from 77 horses with recurrent colic, focusing on cellular infiltration, fibrosis, and erosions. All samples from the duodenum showed the presence of leukocytes infiltrates in the mucosal lamina propria, of which almost 70% were diffuse infiltrates. The most frequently observed cellular infiltration was a moderate infiltration consisting of lymphocytes and plasma cells. More than one-fourth of the horses were also found to have shortened intestinal villi. Similarly, in biopsies from the rectum, cellular infiltration was observed in all horses in this section, which consisted of a mixed population of plasma cells, lymphocytes, and eosinophilia. Analysis of the inflammatory lesions present may help in understanding the pathogenesis of chronic colic in horses. Colic, a condition affecting the gastrointestinal tract of horses, manifests as severe pain and may be a life-threatening condition. It is possible to distinguish between an acute, disposable process, as well as recurrent colic symptoms (abdominal pain) caused by an ongoing chronic inflammatory process. This paper presents a retrospective analysis of the histopathological findings of duodenal and rectal samples taken from horses with recurrent colic, with the aim to determine the frequency and extent of inflammation. The samples, i.e., duodenal biopsy (60 samples) and rectal biopsy (17 samples), were taken from 77 horses showing recurrent colic symptoms. Histopathological examination included staining with hematoxylin and eosin. The examination included evaluation of the superficial epithelium, mucosal lamina propria, and submucosa. All samples from the duodenum and rectum showed the presence of leukocyte infiltration in the mucosal lamina propria. The most frequently observed cellular infiltration was a moderate infiltration consisting of lymphocytes and plasma cells in duodenum and mixed populations of plasma cells, lymphocytes, and eosinophilia in the rectum. Mott cells were also noted among the inflammatory infiltrates. More than one-fourth of the horses were found to have shortened intestinal villi. The results presented here showed the involvement of inflammation in the course of recurrent colic, which can be both its cause (by impairing motility and absorption) and its effect (as a result of obstruction or ischemia). [ABSTRACT FROM AUTHOR]

Next generation sequencing of B cell receptor (BCR) repertoires has become a ubiquitous tool for understanding the antibody-mediated immune response: it is now common to have large volumes of sequence data coding for both the heavy and light chain subunits of the BCR. However, until the recent development of high throughput methods of preserving heavy/light chain pairing information, these samples contained no explicit information on which heavy chain sequence pairs with which light chain sequence. One of the first steps in analyzing such BCR repertoire samples is grouping sequences into clonally related families, where each stems from a single rearrangement event. Many methods of accomplishing this have been developed, however, none so far has taken full advantage of the newly-available pairing information. This information can dramatically improve clustering performance, especially for the light chain. The light chain has traditionally been challenging for clonal family inference because of its low diversity and consequent abundance of non-clonal families with indistinguishable naive rearrangements. Here we present a method of incorporating this pairing information into the clustering process in order to arrive at a more accurate partition of the data into clonally related families. We also demonstrate two methods of fixing imperfect pairing information, which may allow for simplified sample preparation and increased sequencing depth. Finally, we describe several other improvements to the partis software package. Author summary: Antibodies form part of the adaptive immune response, and are critical to immunity acquired by both vaccination and infection. Next generation sequencing of the B cell receptor (BCR) repertoire provides a broad and highly informative view of the DNA sequences from which antibodies arise. Until recently, however, this sequencing data was not able to pair together the two domains (from separate chromosomes) that make up a functional antibody. In this paper we present several methods to improve analysis of the new paired data that does pair together sequence data for complete antibodies. We first show a method that better groups together sequences stemming from the same ancestral cell, solving a problem called "clonal family inference." We then show two methods that can correct for various imperfections in the data's identification of which sequences pair together to form complete antibodies, which together may allow for significantly simplified experimental methods. [ABSTRACT FROM AUTHOR]

Increasing interest is being addressed to the development of a reliable, reproducible and relevant in vitro model of intestinal barrier, mainly for engineered nanomaterials hazard and risk assessment, in order to meet regulatory and scientific demands. Starting from the consolidated Caco-2 cell model, widely used for determining translocation of drugs and chemicals, the establishment of an advanced intestinal barrier model with different level of complexity is important for overcoming Caco-2 monoculture limitations. For this purpose, a tri-culture model, consisting of two human intestinal epithelial cells (Caco-2 and HT29-MTX) and a human lymphocyte B cell (Raji B), was developed by several research groups to mimic the in vivo intestinal epithelium, furnishing appropriate tools for nanotoxicological studies. However, tri-culture model shows high levels of variability in ENM uptake/translocation studies. With the aim of implementing the standardization and optimization of this tri-culture for ENM translocation studies, the present paper intends to identify and discuss such relevant parameters involved in model establishment as: tri-culture condition set-up, barrier integrity evaluation, mucus characterization, M-cell induction. SiO2 fluorescent nanoparticles were used to compare the different models. Although a low level of SiO2 translocation is reported for all the different culture conditions. a relevant role of mucus and M-cells in NPs uptake/translocation has been highlighted. [ABSTRACT FROM AUTHOR]

The main target cells for Epstein-Barr virus (EBV) infection and persistence are B lymphocytes, although T and NK cells can also become infected. In this paper, we characterize the EBV present in 21 pediatric and adult patients who were treated in France for a range of diseases that involve infection of T or NK cells. Of these 21 cases, 5 pediatric patients (21%) and 11 adult patients (52%) were of Caucasian origin. In about 30% of the cases, some of the EBV genomes contain a large deletion. The deletions are different in every patient but tend to cluster near the BART region of the viral genome. Detailed investigation of a family in which several members have persistent T or NK cell infection by EBV indicates that the virus genome deletions arise or are selected independently in each individual patient. Genome sequence polymorphisms in the EBV in these T or NK cell diseases reflect the geographic origin of the patient and not a distinct type of EBV (the 21 cases studied included examples of both type 1 and type 2 EBV infection). Using virus produced from type 1 or type 2 EBV genomes cloned in bacterial artificial chromosome (BAC) vectors, we demonstrate infection of T cells in cord blood from healthy donors. Our results are consistent with transient infection of some T cells being part of normal asymptomatic infection by EBV in young children. IMPORTANCE EBV contributes to several types of human cancer. Some cancers and nonmalignant lymphoproliferative diseases involving T or NK cells contain EBV. These diseases are relatively frequent in Japan and China and have been shown sometimes to have deletions in the EBV genome in the disease cells. We identify further examples of deletions within the EBV genome associated with T or NK cell diseases, and we provide evidence that the virus genomes with these deletions are most likely selected in the individual cases, rather than being transmitted between people during infection. We demonstrate EBV infection of cord blood T cells by highly characterized, cloned EBV genomes and suggest that transient infection of T cells may be part of normal asymptomatic infection by EBV in young children. [ABSTRACT FROM AUTHOR]

Chimeric antigen receptor (CAR)-expressing T-cells are without a doubt a breakthrough therapy for hematological malignancies. Despite their success, clinical experience has revealed several challenges, which include relapse after targeting single antigens such as CD19 in the case of B-cell acute lymphoblastic leukemia (B-ALL), and the occurrence of side effects that could be severe in some cases. Therefore, it became clear that improved safety approaches, and targeting multiple antigens, should be considered to further improve CAR T-cell therapy for B-ALL. In this paper, we address both issues by investigating the use of CD10 as a therapeutic target for B-ALL with our switchable UniCAR system. The UniCAR platform is a modular platform that depends on the presence of two elements to function. These include UniCAR T-cells and the target modules (TMs), which cross-link the T-cells to their respective targets on tumor cells. The TMs function as keys that control the switchability of UniCAR T-cells. Here, we demonstrate that UniCAR T-cells, armed with anti-CD10 TM, can efficiently kill B-ALL cell lines, as well as patient-derived B-ALL blasts, thereby highlighting the exciting possibility for using CD10 as an emerging therapeutic target for B-cell malignancies. [ABSTRACT FROM AUTHOR]

The human body generates a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design vaccines for highly mutable pathogens such as influenza and HIV. BCR diversity is induced by naturally occurring combinatorial "V(D)J" rearrangement, mutation, and selection processes. Most current methods for BCR sequence analysis focus on separately modeling the above processes. Statistical phylogenetic methods are often used to model the mutational dynamics of BCR sequence data, but these techniques do not consider all the complexities associated with B cell diversification such as the V(D)J rearrangement process. In particular, standard phylogenetic approaches assume the DNA bases of the progenitor (or "naive") sequence arise independently and according to the same distribution, ignoring the complexities of V(D)J rearrangement. In this paper, we introduce a novel approach to Bayesian phylogenetic inference for BCR sequences that is based on a phylogenetic hidden Markov model (phylo-HMM). This technique not only integrates a naive rearrangement model with a phylogenetic model for BCR sequence evolution but also naturally accounts for uncertainty in all unobserved variables, including the phylogenetic tree, via posterior distribution sampling. Author summary: Rational vaccine design efforts depend on accurate inference of full evolutionary paths from a given naive sequence to the corresponding mature B cell receptor sequences in a germinal center. Before one can perform ancestral sequence inference for clonal sequences that result from the same naive rearrangement event, one must first obtain an estimate of the clonal phylogenetic tree. Currently, standard phylogenetic inference techniques are used to model the process of sequence evolution along the tree; however, these methods do not account for all the complexities associated with this evolutionary process. In this paper, we propose a Bayesian approach to phylogenetic inference for clonal sequences that is based on a phylogenetic hidden Markov model. Our phylo-HMM models both the naive rearrangement and somatic hypermutation processes and this Bayesian framework allows us to naturally account for uncertainty in all unobserved variables, including a phylogenetic tree, via posterior distribution sampling. We perform simulation-based experiments to show that naive sequence and phylogenetic inference performed jointly provides higher-quality estimates than those obtained by considering these inferences separately. Our application to real data reveals significant uncertainty in naive and ancestral sequences, confirming the importance of a Bayesian approach. [ABSTRACT FROM AUTHOR]

Respiratory syncytial virus (RSV) infection results in millions of hospitalizations and thousands of deaths each year. Variations in the adaptive and innate immune response appear to be associated with RSV severity. To investigate the host response to RSV infection in infants, we performed a systems-level study of RSV pathophysiology, incorporating high-throughput measurements of the peripheral innate and adaptive immune systems and the airway epithelium and microbiota. We implemented a novel multi-omic data integration method based on multilayered principal component analysis, penalized regression, and feature weight back-propagation, which enabled us to identify cellular pathways associated with RSV severity. In both airway and immune cells, we found an association between RSV severity and activation of pathways controlling Th17 and acute phase response signaling, as well as inhibition of B cell receptor signaling. Dysregulation of both the humoral and mucosal response to RSV may play a critical role in determining illness severity. Author summary: This paper presents a novel approach to understanding the localized molecular responses to respiratory syncytial virus (RSV) and the system-level correlates of clinical outcomes. To do this, we developed a novel statistical method able to integrate high dimensional molecular data characterizing the host airway microbota and immune and nasal gene expression. We show that this integrative approach facilitates superior performance in estimating clinical outcome as opposed to any single data type. Using this approach, we identified both cell type-specific and shared biomarkers and regulatory pathways associated with RSV severity. Specifically, we identified an association between RSV severity, activation of pathways controlling Th17, and inhibition of B cell receptor signaling, which were present in both the site of infection airway and in peripheral immune cells. These results can guide future efforts to identify biomarkers for identifying or predicting illness severity following infant RSV infection. They may also be useful as biomarkers to inform the efficacy of future interventions (e.g., therapies) or preventative measures to suppress the rate of severe disease (e.g., vaccines). [ABSTRACT FROM AUTHOR]

Single-cell RNA sequencing has enabled to capture the gene activities at single-cell resolution, thus allowing reconstruction of cell-type-specific gene regulatory networks (GRNs). The available algorithms for reconstructing GRNs are commonly designed for bulk RNA-seq data, and few of them are applicable to analyze scRNA-seq data by dealing with the dropout events and cellular heterogeneity. In this paper, we represent the joint gene expression distribution of a gene pair as an image and propose a novel supervised deep neural network called DeepDRIM which utilizes the image of the target TF-gene pair and the ones of the potential neighbors to reconstruct GRN from scRNA-seq data. Due to the consideration of TF-gene pair's neighborhood context, DeepDRIM can effectively eliminate the false positives caused by transitive gene–gene interactions. We compared DeepDRIM with nine GRN reconstruction algorithms designed for either bulk or single-cell RNA-seq data. It achieves evidently better performance for the scRNA-seq data collected from eight cell lines. The simulated data show that DeepDRIM is robust to the dropout rate, the cell number and the size of the training data. We further applied DeepDRIM to the scRNA-seq gene expression of B cells from the bronchoalveolar lavage fluid of the patients with mild and severe coronavirus disease 2019. We focused on the cell-type-specific GRN alteration and observed targets of TFs that were differentially expressed between the two statuses to be enriched in lysosome, apoptosis, response to decreased oxygen level and microtubule, which had been proved to be associated with coronavirus infection. [ABSTRACT FROM AUTHOR]

In primary SS (pSS), chemokines and cytokines orchestrate immunopathology driven by a complex network of interacting inflammatory cells. In recent years, the importance of chemotactic and non-chemotactic cytokines that control function, movement and placing of all cells within the inflamed exocrine glands and directing immunopathology has become increasingly clear. This paper reviews the current knowledge on chemokines and focuses on the emerging roles of novel chemotactic and non-chemotactic mediators in pSS. It highlights their contribution to pathogenic processes such as B cell hyperactivity and the formation of ectopic lymphoid structures. To this end, the role of acquired (CXCR5/CCR9 Th-cell–mediated) and innate (inflammasome/IL-1/IL-18–mediated) pathways in steering immunopathology is discussed. [ABSTRACT FROM AUTHOR]

An interesting inference drawn by some COVID-19 epidemiological models is that there exists a proportion of the population who are not susceptible to infection—even at the start of the current pandemic. This paper introduces a model of the immune response to a virus. This is based upon the same sort of mean-field dynamics as used in epidemiology. However, in place of the location, clinical status, and other attributes of people in an epidemiological model, we consider the state of a virus, B and T-lymphocytes, and the antibodies they generate. Our aim is to formalise some key hypotheses as to the mechanism of resistance. We present a series of simple simulations illustrating changes to the dynamics of the immune response under these hypotheses. These include attenuated viral cell entry, pre-existing cross-reactive humoral (antibody-mediated) immunity, and enhanced T-cell dependent immunity. Finally, we illustrate the potential application of this sort of model by illustrating variational inversion (using simulated data) of this model to illustrate its use in testing hypotheses. In principle, this furnishes a fast and efficient immunological assay—based on sequential serology—that provides a (1) quantitative measure of latent immunological responses and (2) a Bayes optimal classification of the different kinds of immunological response (c.f., glucose tolerance tests used to test for insulin resistance). This may be especially useful in assessing SARS-CoV-2 vaccines. [ABSTRACT FROM AUTHOR]

The article discusses various studies regarding the role of a certain gene in the formation of the insulin-producing cells of the pancreas. Geneticist Constantin Polychronakos of McGill University found that each pancreas of a child lacks insulin-producing cells, as though the body had no proper instructions for making them. Michael German of the University of California suggests that Rfx6 expression is one of the earliest genes to be turned on by neurogenin 3.

A vaccine which is effective against the HIV virus is considered to be the best solution to the ongoing global HIV/AIDS epidemic. In the past thirty years, numerous attempts to develop an effective vaccine have been made with little or no success, due, in large part, to the high mutability of the virus. More recent studies showed that a vaccine able to elicit broadly neutralizing antibodies (bnAbs), that is, antibodies that can neutralize a high fraction of global virus variants, has promise to protect against HIV. Such a vaccine has been proposed to involve at least three separate stages: First, activate the appropriate precursor B cells; second, shepherd affinity maturation along pathways toward bnAbs; and, third, polish the Ab response to bind with high affinity to diverse HIV envelopes (Env). This final stage may require immunization with a mixture of Envs. In this paper, we set up a framework based on theory and modeling to design optimal panels of antigens to use in such a mixture. The designed antigens are characterized experimentally and are shown to be stable and to be recognized by known HIV antibodies. [ABSTRACT FROM AUTHOR]

Thiopurine drugs are immunomodulatory antimetabolites relevant for pediatric patients characterized by dose-dependent adverse effects such as myelosuppression and hepatotoxicity, often related to inter-individual differences, involving the activity of important enzymes at the basis of their biotransformation, such as thiopurine S-methyltransferase (TPMT). Surface Enhanced Raman Scattering (SERS) spectroscopy is emerging as a bioanalytical tool and represents a valid alternative in terms of affordable costs, shorter analysis time and easier sample preparation in comparison to the most employed methods for pharmacokinetic analysis of drugs. The aim of this study is to investigate mercaptopurine and thioguanine pharmacokinetics by SERS in cell lysates of a B-lymphoblastoid cell line (NALM-6), that did (TPMT*1) or did not (MOCK) overexpress the wild-type form of TPMT as an in vitro cellular lymphocyte model to discriminate between cells with different levels of TPMT activity on the base of the amount of thioguanosine nucleotides (TGN) metabolites formed. SERS analysis of the cell lysates was carried out using SERS substrates constituted by Ag nanoparticles deposited on paper and parallel samples were used for quantification of thiopurine nucleotides with liquid chromatography-tandem mass spectrometry (LC-MS/MS). A direct SERS detection method has been set up that could be a tool to study thiopurine drug pharmacokinetics in in vitro cellular models to qualitatively discriminate between cells that do and do not overexpress the TPMT enzyme, as an alternative to other more laborious techniques. Results underlined decreased levels of TGN and increased levels of methylated metabolites when TPMT was overexpressed, both after mercaptopurine and thioguanine treatments. A strong positive correlation (Spearman's rank correlation coefficient rho = 0.96) exists between absolute quantification of TGMP (pmol/1 x 106 cells), obtained by LC-MS/MS, and SERS signal (intensity of TGN at 915 cm−1). In future studies, we aim to apply this method to investigate TPMT activity in pediatric patients' leukocytes. • A direct SERS method to qualitatively discriminate between cells that do and do not overexpress TPMT is discussed. • LC-MS/MS and SERS parallel analysis of cell lysate detect decreased levels of TGN when TPMT is overexpressed. • Quantification by LC-MS/MS of 12 thiopurine metabolites in human B-lymphoblastoid cell line is reported. [ABSTRACT FROM AUTHOR]

The immune system employs complex tolerance mechanisms in order to avoid harmful autoimmunity, yet autoantibodies are frequently observed in cancer. In a paper in Cell , Mazor et al. report that autoantibodies produced by tumor-infiltrating B cells in human ovarian cancer frequently recognize the self-protein matrix metalloproteinase 14 (MMP14) through two distinct mechanisms of tolerance disruption. [ABSTRACT FROM AUTHOR]

• SHC014748M was proved to be more selective for PI3Kδ inhibition relative to other class i PI3K enzymes. • SHC014748M showed in vitro activity in most of 23 B lymphoma cell lines and primary CLL cells and also inhibited phosphorylation of AKT, targets downstream of PI3Kδ. • In vivo study revealed that SHC014748M significantly reduced lymphoma cell growth in the treatment group compared with control mice. • SHC014748M seemed to be a novel promising compound in the treatment of B cell lymphomas and CLL. PI3Kδ (phosphatidylinositol 3-kinase-δ), one of the class I PI3Ks, is found expressed primarily in leukocytes and plays an essential role in B-cell development and function. This provides a rationale for the development of small molecule inhibitors that selectively target p110δ for patients with indolent non-Hodgkin lymphomas. Here in this paper, we comprehensively evaluated the in vitro and in vivo antitumor activity of SHC014748M, an oral selective inhibitor of PI3Kδ under Phase I clinical evaluation. Biochemical and cell-based assays were used to measure compound potency and selectivity in lymphoma cell lines as well as primary chronic lymphocytic leukemia (CLL) cells. Scid mice were subcutaneously inoculated with the SU-DHL-6 cell line. SHC014748M was more selective for PI3Kδ inhibition relative to other class I PI3K enzymes and showed in vitro activity in most of 23 B lymphoma cell lines and primary CLL cells. SHC014748M also inhibited phosphorylation of AKT, targets downstream of PI3Kδ, in both lymphoma cells and primary CLL cells. In vivo study revealed that SHC014748M significantly reduced lymphoma cell growth in the treatment group compared with control mice. CCL4, CCL17, CCL22 and CXCL13 in patient serum decreased sharply after SHC014748M treatment. According to the results, SHC014748M appeared to be a novel promising compound in the treatment of B cell lymphomas and CLL. [ABSTRACT FROM AUTHOR]

CD11c is a transmembrane protein, belonging to the ß2 integrin subfamily. It is generally accepted as a marker of conventional dendritic cells, but can also be found on macrophages, neutrophils, and some B cells. The aim of this paper was to determine numerical areal density of CD11c-immunopositive cells in different morphological compartments of tonsillar tissue in recurrent tonsillitis (RT) and chronic hypertrophic tonsillitis (CHT). As a material we used tonsils which were taken after tonsillectomy, from patients of both sexes, aged 10-29 years: six tonsils with RT and nine tonsils with CHT. The quantification of the CD11c-immunopositive cells was performed on 5 µm thick serial paraffin tissue slices, which were stained immunohistochemically, by using mouse monoclonal anti-CD11c antibody. For quantification we used ImageJ software. Our results showed that CD11c-immunopositive cells were present in all morphological compartments of tonsils with RT and CHT. The higher value for numerical areal density of CD11c-immunopositive cells in RT showed statistically significant difference in crypt epithelium and subepithelial lymphoid tissue compared to CHT. There was not statistically significant difference of CD11c-immunopositive cells in lymphoid follicles and interfollicular regions between the groups. Crypt epithelium and subepithelial lymphoid tissue represent the first site of contact between antigens and tonsillar tissue, and are crucial for the initiation of the immune response. The higher number of CD11c-immunopositive cells in crypt epithelium and subepithelial lymphoid tissue in RT might be connected with more efficient immunological response of this morphological compartment, compared to CHT. [ABSTRACT FROM AUTHOR]

This study deals with 3D laser investigation on the border between the human lymph node T-zone and germinal centre. Only a few T-cells specific for antigen selected B-cells are allowed to enter germinal centres. This selection process is guided by sinus structures, chemokine gradients and inherent motility of the lymphoid cells. We measured gaps and wall-like structures manually, using IMARIS, a 3D image software for analysis and interpretation of microscopy datasets. In this paper, we describe alpha-actin positive and semipermeable walls and wall-like structures that may hinder T-cells and other cell types from entering germinal centres. Some clearly defined holes or gaps probably regulate lymphoid traffic between T- and B-cell areas. In lymphadenitis, the morphology of this border structure is clearly defined. However, in case of malignant lymphoma, the wall-like structure is disrupted. This has been demonstrated exemplarily in case of angioimmunoblastic T-cell lymphoma. We revealed significant differences of lengths of the wall-like structures in angioimmunoblastic T-cell lymphoma in comparison with wall-like structures in reactive tissue slices. The alterations of morphological structures lead to abnormal and less controlled T- and B-cell distributions probably preventing the immune defence against tumour cells and infectious agents by dysregulating immune homeostasis. [ABSTRACT FROM AUTHOR]

The trend of intellectualization and complication of mechanical equipment makes the demand for intelligent diagnostic methods more and more intense in industry. In view of the difficulty of obtaining mechanical fault samples and the requirement of clear and reliable diagnosis results, intelligent diagnosis methods need to adapt to the learning of small samples and have the interpretability of white box model. In this paper, inspired by biological immunity, an intelligent fault diagnosis method was proposed--optimizing b-cell pool clonal selection classification algorithm (OBPCSCA). The OBPCSCA provides a method to construct unique B-cell pools corresponding to specific antigen pools, and uses greedy strategy to generate memory B-cell pools. The experimental comparison with AIRS and AICSL on four UCI benchmark data sets shows that the OBPCSCA has a better balance between the number of memory cells and the accuracy of classification. In particular, compared with AIRS, the OBPCSCA can greatly reduce the number of memory B-cells on the premise of ensuring high classification accuracy. In comparison with the top general classifiers, the OBPCSCA has certain competitiveness in these four data sets. Finally, the algorithm was applied to the bearing data set of Case Western Reserve University for fault diagnosis, and the results showed effectiveness of the algorithm. [ABSTRACT FROM AUTHOR]

Adaptive immune receptor repertoire sequencing (AIRR-Seq) offers the possibility of identifying and tracking B cell clonal expansions during adaptive immune responses. Members of a B cell clone are descended from a common ancestor and share the same initial V(D)J rearrangement, but their B cell receptore (BCR) sequence may differ due to the accumulation of somatic hypermutations (SHMs). Clonal relationships are learned from AIRR-seq data by analyzing the BCR sequence, with the most common methods focused on the highly diverse junction region. However, clonally related cells often share SHMs which have been accumulated during affinity maturation. Here, we investigate whether shared SHMs in the V and J segments of the BCR can be leveraged along with the junction sequence to improve the ability to identify clonally related sequences. We develop independent distance functions that capture junction similarity and shared mutations, and combine these in a spectral clustering framework to infer the BCR clonal relationships. Using both simulated and experimental data, we show that this model improves both the sensitivity and specificity for identifying B cell clones. Source code for this method is freely available in the SCOPer (Spectral Clustering for clOne Partitioning) R package (version 0.2 or newer) in the Immcantation framework: www.immcantation.org under the CC BY-SA 4.0 license. Author summary: B cells recognize antigens through their BCR. During adaptive immune responses, antigen-specific B cells undergo intense proliferation. This B cell clonal expansion is coupled with a process of SHM, which results in the accumulation of mutations in the DNA encoding the BCR. Within the specialized micro-environment of the germinal center, these diversified B cells compete for antigen binding and presentation to follicular helper T cells. Successful binding leads to repeated cycles of proliferation, SHM and affinity-dependent selection ultimately resulting in the generation of high-affinity memory and antibody-secreting plasma cells. Driven by dramatic improvements in high-throughput sequencing technologies, large-scale characterization of BCR repertoires is now feasible. However, a critical barrier to quantitative analysis of these large-scale BCR repertoire data is the accurate identification of B cell clones. B cells are inferred to be clonally related if the distance between their BCR sequences is close enough. This paper develops a hybrid distance function that integrates information from the V(D)J recombination process (distance between CDR3 sequences), along with information from a common history of clonal expansion (shared SHMs in the V and J segments of the BCR) to improve the ability to identify clonally related sequences. [ABSTRACT FROM AUTHOR]

Background: Regulatory T cells (Tregs) play an important role in sustaining the hepatitis B and C viruses (HBV and HCV) persistence and protecting the liver tissues from cytokine-associated detrimental effects through unclear mechanisms. This paper aims to review the frequency of Tregs during the course of HBV and HCV infection. Method: Electronic databases were searched to identify studies investigated the frequency of intrahepatic and peripheral Tregs of the patients infected with HBV and/ or HCV. Results: The majority of studies reported the increase of intrahepatic and peripheral Tregs in acute and chronic infection of HBV and HCV. The decrease of peripheral Tregs occurred in patients with chronic hepatitis B who respond to interferon a or nucleos(t)ide analogues treatment as well as those with chronic hepatitis C who were treated with interferon, ribavirin or liver transplantation. Conclusion: Infection with HBV and HCV appears to induce the production of Tregs in blood and hepatocytes whereas treatment may decrease Tregs levels. As the optimum balance between regulatory and effector T during HBV and HCV infection is crucial for preventing liver damage, further studies should be directed on the development of Tregs during HBV and HCV infection as well as their involvement in immunomodulatory strategies for combating HBV and HCV. [ABSTRACT FROM AUTHOR]

The Epstein-Barr virus (EBV) induces B-cell proliferation with high efficiency through expression of latent proteins and microRNAs. This process takes place in vivo soon after infection, presumably to expand the virus reservoir, but can also induce pathologies, e.g. an infectious mononucleosis (IM) syndrome after primary infection or a B-cell lymphoproliferation in immunosuppressed individuals. In this paper, we investigated the growth characteristics of EBV-infected B-cells isolated from transplant recipients or patients with IM. We found that these cells grew and withstood apoptosis at highly variable rates, suggesting that the expansion rate of the infected B-cells widely varies between individuals, thereby influencing the size of the B-cell reservoir and the ability to form tumors in infected individuals. All viruses investigated were type 1 and genetically close to western strains. EBV-infected B-cells expressed the transforming EBV latent genes and microRNAs (miRNAs) at variable levels. We found that the B-cell growth rates positively correlated with the BHRF1 miRNA levels. Comparative studies showed that infected B-cells derived from transplant recipients with iEBVL on average expressed higher levels of EBV miR-BHRF1 miRNAs and grew more rapidly than B-cells from IM patients, suggesting infection by more transforming viruses. Altogether, these findings suggest that EBV infection has a highly variable impact on the B-cell compartment that probably reflects the genetic diversity of both the virus and the host. It also demonstrates the unexpected finding that B-cells from different individuals can grow at different speed under the influence of the same virus infection. [ABSTRACT FROM AUTHOR]

The present paper reports the case of a 3 years old, female Bearded Dragon (Pogona vitticeps) presenting lethargy, anorexia,weight loss, and anemia and marked leukocytosis at CBC. The majority of leukocytes were lymphocytic/lymphoblastic cells (97%). Immunocytochemical staining of blood smears marked for CD3 (neg) and CD79a (pos) suggested immunophenotype B. The patient died after one month from diagnosis. Histology evidenced lymphoid infi ltration in the heart, spleen, liver, kidneys and gut. In addition, in the bone marrow a massive infi ltration of lymphoid cells confi rmed the diagnosis of leukemia. Immunohistochemistry confi rmed the CD79a positivity of a large part of infi ltrating lymphoid cells indicating a B cells immunophenotype of the neoplastic population. The presence of lymphocytosis and multiorgan infi ltration supported the diagnosis of lymphocytic leukemia. Finally, a revision of the literature has also been made. [ABSTRACT FROM AUTHOR]

Diffuse large B cell lymphoma (DLBCL) is an aggressive non-Hodgkin lymphoma, accounting for approximately 30% of lymphoma cases in Canada. Although most patients will achieve a cure, up to 40% will experience refractory disease after initial treatment, or relapse after a period of remission. In eligible patients, salvage therapy followed by high-dose therapy and autologous stem-cell transplantation (ASCT) is the standard of care. However, many patients are transplant-ineligible, and more than half of those undergoing asct will subsequently relapse. For those patients, outcomes are dismal, and novel treatment approaches are a critical unmet need. In this paper, we present available data about emerging treatment approaches in the latter setting and provide a perspective about the potential use of those approaches in Canada. [ABSTRACT FROM AUTHOR]

The importance of B cells and their critical role in the maintenance of health through generation of antibody-mediated immune protection is undoubted. However, the differences between the responses of B cells with different surface phenotypes in different microanatomical sites as well as diversity in B-cell function outside antibody production are just starting to be acknowledged and resolved. This series of reviews and papers that focus on human B cells will be divided across two issues. The first part of the review series in this issue captures practical information on identifying B-cell subtypes in blood in health and inflammatory diseases as well as describing aspects of B-cell diversity depending on immunoglobulin isotype and microanatomical context. It also explores our current understanding of cytokine production by human B cells and the effect of obesity on the B-cell response. The last review in this issue will reflect on the important lessons learned from the SARS-CoV-2 pandemic; in particular the role of antigen availability and its effect on B-cell memory and antibody production. [ABSTRACT FROM AUTHOR]

The presence or absence of terminal sialic acid residues in the sugar moiety attached to the Fc-domain of IgG molecules modulates IgG activity and is associated with autoimmune or infection related inflammation. In a recent paper, Oswald and colleagues suggest that IgG sialylation may occur post IgG secretion from plasma cells, which would be a major issue for therapeutic antibodies injected into patients. In contrast, we argue that previous work rather demonstrates that IgG sialylation occurs within B cells and that the experimental system used by the authors is not suitable to address this critical question. [ABSTRACT FROM AUTHOR]

Due to the rapid development of DNA microarray technology, a large number of microarray data come into being and classifying these data has been verified useful for cancer diagnosis, treatment and prevention. However, microarray data classification is still a challenging task since there are often a huge number of genes but a small number of samples in gene expression data. As a result, a computational method for reducing the dimension of microarray data is necessary. In this paper, we introduce a computational gene selection model for microarray data classification via adaptive hypergraph embedded dictionary learning (AHEDL). Specifically, a dictionary is learned from the feature space of original high dimensional microarray data, and this learned dictionary is used to represent original genes with a reconstruction coefficient matrix. Then we use a l 2, 1 -norm regularization to impose the row sparsity on the coefficient matrix for selecting discriminate genes. Meanwhile, in order to capture the localmanifold geometrical structure of original microarray data in a high-order manner, a hypergraph is adaptively learned and embedded into the model. An iterative updating algorithm is designed for solving the optimization problem. In order to validate the efficacy of the proposed model, we have conducted experiments on six publicly available microarray data sets and the results demonstrate that AHEDL outperforms other state-of-the-art methods in terms of microarray data classification. Unlabelled Table AHEDL Adaptive Hypergraph Embedded Dictionary Learning ADMM Alternating Direction method of Multipliers SVM Support Vector Machine RF Random Forest k-NN k-Nearest Neighbor CV cross validation MSVM-RF Multiclass Support Vector Machine-Recursive Feature Elimination KernelPLS Kernel Partial Least Squares WLMGS Weight Local Modularity based Gene Selection GRSL-GS Gene Selection via Subspace Learning and Manifold Regularization LNNFW Local-Nearest-Neighbors-based Feature Weighting for Gene Selection RLR Regularized Logistic Regression ACC accuracy SD standard deviations ANOVA Analysis of Variance DF Degrees of Freedom SS Sum-of-Square MS Mean Sum-of-Square F F-value Sig statistical significance SRBCT Small Round Blue Cell Tumors GCM Global Cancer Map CLL_SUB_111 B-cell chronic lymphocytic leukemia • We introduce a new gene selection model for microarray data classification. • A dictionary is learned to reconstruct original genes. • A hypergraph is adaptively learned and embedded into the model. • The hypergraph is used to capture the high-order locality of microarray data. • Experiments on six data sets validate the efficacy of the proposed model. [ABSTRACT FROM AUTHOR]

The collection of immunoglobulin genes in an individual’s germline, which gives rise to B cell receptors via recombination, is known to vary significantly across individuals. In humans, for example, each individual has only a fraction of the several hundred known V alleles. Furthermore, the currently-accepted set of known V alleles is both incomplete (particularly for non-European samples), and contains a significant number of spurious alleles. The resulting uncertainty as to which immunoglobulin alleles are present in any given sample results in inaccurate B cell receptor sequence annotations, and in particular inaccurate inferred naive ancestors. In this paper we first show that the currently widespread practice of aligning each sequence to its closest match in the full set of IMGT alleles results in a very large number of spurious alleles that are not in the sample’s true set of germline V alleles. We then describe a new method for inferring each individual’s germline gene set from deep sequencing data, and show that it improves upon existing methods by making a detailed comparison on a variety of simulated and real data samples. This new method has been integrated into the partis annotation and clonal family inference package, available at , and is run by default without affecting overall run time. [ABSTRACT FROM AUTHOR]

The subset of pro-inflammatory B cells, called late memory, tissue-like or double negative (DN), accumulates in the blood of elderly individuals. Here we show that DN B cells do not proliferate and do not make antibodies to influenza antigens, but they secrete antibodies with autoimmune reactivity, in agreement with their membrane phenotype (CD95+CD21-CD11c+) and their spontaneous expression of the transcription factor T-bet. These cells also increase in the blood of individuals with obesity and autoimmune diseases, but causative mechanisms and signaling pathways involved are known only in part. In the present paper we compare frequencies and metabolic requirements of these cells in the blood of healthy individuals of different ages and in the blood and the subcutaneous adipose tissue (SAT) of individuals with obesity. Results show that DN B cells from young individuals have minimal metabolic requirements, DN B cells from elderly and obese individuals utilize higher amounts of glucose to perform autoimmune antibody production and enroll in aerobic glycolysis to support their function. DN B cells from the SAT have the highest metabolic requirements as they activate oxidative phosphorylation, aerobic glycolysis and fatty acid oxidation. DN B cells from the SAT also show the highest levels of ROS and the highest levels of phosphorylated AMPK (5’-AMP activated kinase) and Sestrin 1, both able to mitigate stress and cell death. This metabolic advantage drives DN B cell survival and function (secretion of autoimmune antibodies). [ABSTRACT FROM AUTHOR]

Humanized mouse models can well be modified to study specific aspects of Graft-versus-Host Disease (GvHD). This paper shows the results of both macrophage depletion and (early) B-cell depletion in a humanized mouse model using RAG2-/-γc-/- mice injected with HuPBMCs. Macrophage depletion showed a significant decrease in survival and also lead to a change in the histomorphology of the xenogeneic reaction. Higher levels of infiltrating B-cells were observed in various organs of mice depleted for macrophages. With (early) B-cell depletion using Rituximab, a clear improvement on clinical symptoms was observed, even when probably only inactivated B-cells were deleted. However, the histological examinations only showed a significant morphological effect on liver fibrosis. This may be related to a difference in the mRNA levels of TGF-β. Also, lower mRNA levels of Tregs in some organs were observed after Rituximab treatment, which contradicts that a higher number of Tregs would always be related to less severe GvHD. Our data show that both macrophage depletion and (early) B-cell depletion in a xenogeneic mouse model can influence the clinical, histological, and cytokine production of a GvHD response. [ABSTRACT FROM AUTHOR]

Melanomacrophages (MMs) are phagocytizing cells with high amounts of pigments including melanin which can be found in a number of cold-blooded species. In Osteichthyes, these cells cluster to form so-called melanomacrophage centres (MMCs), which are predominantly present in the stroma of hematopoietic and lymphoid tissues, that is, in the kidney and spleen. The functionality of MMs and MMCs results from their involvement and role in the defence reactions, related to both the innate and the adaptive immune mechanisms, and in processes unrelated to defence functions as well. There is evidence that MMCs are structurally and functionally similar to mammals' germinal centres (GCs). It appears that mature IgM+ B cells in Osteichthyes can be the equivalent of mIgM+ centrocytes in mammals, whereas MMs can be, in terms of the function, the equivalent of follicular dendritic cells (FDCs), and MMCs can be, in terms of clustered specific cells, the equivalent of GCs. This paper presents selected facts about the structural and functional similarity between GCs and MMCs and about the involvement and role of MMCs and MMs in the immune response. The facts help get a proper picture of the location of MMs and MMCs within the structure of the fish immune system, also in the context of their evolutionary relationship with GCs and of the possibility of pointing out the evolutionary closeness between MMCs in Osteichthyes and GCs in mammals. [ABSTRACT FROM AUTHOR]

Aberrant expression of CD5 (as a T-cell marker) is seen in some leukemia and lymphoma of B lineage origin. Given that the signaling resulting from the expression of this marker plays an essential role in the development of leukemia and lymphoma, evaluating the expression of this marker is of paramount importance. Therefore, our goal in this study was to investigate the prognostic importance of CD5 expression in B-cell leukemia and lymphoma. We evaluate CD5 expression in normal and leukemic B-cells by identifying relevant literature through a PubMed search (1998-2018) of English language papers using the terms: 'CD5,' 'B-cell,' 'Leukemia,' and 'Lymphoma.' We are doing this thorough comparison of results from CD5 positive and negative cases to make a correct decision about prognostic importance of CD5 expression in these malignancies. In a number of B-cell malignancies, CD5 is expressed in varying degrees. Due to the different origins and characteristics of these malignancies, the results of CD5 expression evaluations are heterogeneous and impossible to generalize. However, CD5 expression is sometimes associated with clinicopathologic findings, more invasive clinical course, and even resistance to treatment (specifically in DLBCL) among CD5- positive patients, which appears to be a function of CD5 signaling and its downstream factors such as STAT3. Depending on the type of malignancy, CD5 expression is associated with good or bad prognosis, which can be used as an auxiliary prognostic factor to assess the clinical course of B-cell malignancies. Moreover, the difference in expression levels of CD5 in a variety of B-cell malignancies allows for differential diagnosis of these malignancies, which can be helpful when diagnosis is difficult. [ABSTRACT FROM AUTHOR]

B cells develop high affinity receptors during the course of affinity maturation, a cyclic process of mutation and selection. At the end of affinity maturation, a number of cells sharing the same ancestor (i.e. in the same “clonal family”) are released from the germinal center; their amino acid frequency profile reflects the allowed and disallowed substitutions at each position. These clonal-family-specific frequency profiles, called “substitution profiles”, are useful for studying the course of affinity maturation as well as for antibody engineering purposes. However, most often only a single sequence is recovered from each clonal family in a sequencing experiment, making it impossible to construct a clonal-family-specific substitution profile. Given the public release of many high-quality large B cell receptor datasets, one may ask whether it is possible to use such data in a prediction model for clonal-family-specific substitution profiles. In this paper, we present the method “Substitution Profiles Using Related Families” (SPURF), a penalized tensor regression framework that integrates information from a rich assemblage of datasets to predict the clonal-family-specific substitution profile for any single input sequence. Using this framework, we show that substitution profiles from similar clonal families can be leveraged together with simulated substitution profiles and germline gene sequence information to improve prediction. We fit this model on a large public dataset and validate the robustness of our approach on two external datasets. Furthermore, we provide a command-line tool in an open-source software package () implementing these ideas and providing easy prediction using our pre-fit models. [ABSTRACT FROM AUTHOR]

Objective: The objective of this paper was to reveal hub pathways in primary mediastinal B-cell lymphoma (PMBL) based on multiple pathway crosstalk networks (PCNs) and give insight for its pathological mechanism.Materials and Methods: Based on gene expression data, pathway data and protein-protein interaction data, background PCN (BPCN) and tumor PCN (TPCN) of PMBL were constructed. The rank product algorithm was implemented to identify hub pathways of BPCN and TPCN. Finally, topological properties (degree, closeness, betweenness, and transitivity) of hub pathways were analyzed.Results: For BPCN, there were three hundred nodes and 42,239 edges, and the pathway pairs had great overlaps. TPCN was composed of 281 nodes and 12,700 cross-talks. A total of five hub pathways were identified, nonalcoholic fatty liver disease (NAFLD), tuberculosis, human T-lymphotropic virus type-I (HTLV-I) infection, hepatitis B, and Epstein-Barr virus infection. The topological properties for them were different from each other, further between PMBL and normal controls.Conclusion: We have identified five hub pathways for PMBL, such as NAFLD, HTLV-I infection, and Hepatitis B, which might be potential biomarkers for target therapy for PMBL. [ABSTRACT FROM AUTHOR]