Detecting T-cell clonal expansions and quantifying clone survival using deep profiling of immune repertoires
In this study, we report a bioinformatic method for quantifying the T-cell repertoire dynamics from TCR sequencing data. We demonstrate its utility by measuring the T-cell repertoire stability in healthy donors, by quantifying the effect of donor lymphocyte infusion (DLI), and by tracking the fate of the different T-cell subsets in HSCT patients and the expansion of pathogen-specific clones in vaccinated individuals. (Source: Frontiers in Immunology)
Source: Frontiers in Immunology - April 3, 2024 Category: Allergy & Immunology Source Type: research
Case report: EBV-related eye orbits and sinuses lymphohistiocytic infiltration responsive to rituximab in a patient with X lymphoproliferative syndrome type 1
ConclusionWe described an unusual presentation of incomplete HLH in a patient affected with XLP1: an EBV-driven infiltration of the orbits and paranasal sinuses. This led us to a challenging differential diagnosis of lymphoma-associated hemophagocytic syndrome, which can be frequently observed in patients with XLP1. Considering the extremely poor prognosis of this clinical finding, we sought for a prompt diagnosis and managed to obtain it and to immediately establish the right treatment on the basis of the pathological finding. (Source: Frontiers in Immunology)
Source: Frontiers in Immunology - April 3, 2024 Category: Allergy & Immunology Source Type: research
IMPROVE: a feature model to predict neoepitope immunogenicity through broad-scale validation of T-cell recognition
ConclusionOverall, IMPROVE was found to significantly advance the identification of neoepitopes compared to other current methods. (Source: Frontiers in Immunology)
Source: Frontiers in Immunology - April 3, 2024 Category: Allergy & Immunology Source Type: research
Diverse potential of secretome from natural killer cells and monocyte-derived macrophages in activating stellate cells
Chronic liver diseases, such as non-alcoholic steatohepatitis (NASH)-induced cirrhosis, are characterized by an increasing accumulation of stressed, damaged, or dying hepatocytes. Hepatocyte damage triggers the activation of resident immune cells, such as Kupffer cells (KC), as well as the recruitment of immune cells from the circulation toward areas of inflammation. After infiltration, monocytes differentiate into monocyte-derived macrophages (MoMF) which are functionally distinct from resident KC. We herein aim to compare the in vitro signatures of polarized macrophages and activated hepatic stellate cells (HSC) with ex ...
Source: Frontiers in Immunology - April 3, 2024 Category: Allergy & Immunology Source Type: research
The role and mechanism of TXNDC5 in disease progression
Thioredoxin domain containing protein-5 (TXNDC5), also known as endothelial protein-disulfide isomerase (Endo-PDI), is confined to the endoplasmic reticulum through the structural endoplasmic reticulum retention signal (KDEL), is a member of the PDI protein family and is highly expressed in the hypoxic state. TXNDC5 can regulate the rate of disulfide bond formation, isomerization and degradation of target proteins through its function as a protein disulfide isomerase (PDI), thereby altering protein conformation, activity and improving protein stability. Several studies have shown that there is a significant correlation bet...
Source: Frontiers in Immunology - April 2, 2024 Category: Allergy & Immunology Source Type: research
PyPop: a mature open-source software pipeline for population genomics
Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well....
Source: Frontiers in Immunology - April 2, 2024 Category: Allergy & Immunology Source Type: research
Donor KIR genotype based outcome prediction after allogeneic stem cell transplantation: no land in sight
Optimizing natural killer (NK) cell alloreactivity could further improve outcome after allogeneic hematopoietic cell transplantation (alloHCT). The donor’s Killer-cell Immunoglobulin-like Receptor (KIR) genotype may provide important information in this regard. In the past decade, different models have been proposed aiming at maximizing NK cell activation by activating KIR-ligand interactions or minimizing inhibitory KIR-ligand interactions. Alternative classifications intended predicting outcome after alloHCT by donor KIR-haplotypes. In the present study, we aimed at validating proposed models and exploring more classif...
Source: Frontiers in Immunology - April 2, 2024 Category: Allergy & Immunology Source Type: research
Multiple functions of the nonstructural protein 3D in picornavirus infection
3D polymerase, also known as RNA-dependent RNA polymerase, is encoded by all known picornaviruses, and their structures are highly conserved. In the process of picornavirus replication, 3D polymerase facilitates the assembly of replication complexes and directly catalyzes the synthesis of viral RNA. The nuclear localization signal carried by picornavirus 3D polymerase, combined with its ability to interact with other viral proteins, viral RNA and cellular proteins, indicate that its noncatalytic role is equally important in viral infections. Recent studies have shown that 3D polymerase has multiple effects on host cell bio...
Source: Frontiers in Immunology - April 2, 2024 Category: Allergy & Immunology Source Type: research
Clonal structure and the specificity of vaccine-induced T cell response to SARS-CoV-2 Spike protein
In conclusion, our study demonstrates the immunogenicity of the Ad5-nCoV adenoviral vaccine and highlights its ability to induce robust and durable T cell responses. These findings provide valuable insight into the efficacy of the vaccine against COVID-19 and provide critical information for ongoing efforts to control infectious diseases. (Source: Frontiers in Immunology)
Source: Frontiers in Immunology - April 2, 2024 Category: Allergy & Immunology Source Type: research
Single-cell RNA-seq reveals T cell exhaustion and immune response landscape in osteosarcoma
ConclusionIn summary, our research elucidates the role of T cell exhaustion in the immunotherapy and progression of OS, the prognostic model constructed based on T cell exhaustion-related genes holds promise as a potential method for prognostication in the management and treatment of OS patients. (Source: Frontiers in Immunology)
Source: Frontiers in Immunology - April 2, 2024 Category: Allergy & Immunology Source Type: research
Higher odds of periodontitis in systemic lupus erythematosus compared to controls and rheumatoid arthritis: a systematic review, meta-analysis and network meta-analysis
DiscussionGiven that RA is the autoimmune disease classically associated with periodontal disease, the higher odds of having periodontitis in SLE are striking. These results highlight the importance of addressing the dental health needs of patients with SLE.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/ identifier CRD42021272876. (Source: Frontiers in Immunology)
Source: Frontiers in Immunology - April 2, 2024 Category: Allergy & Immunology Source Type: research
Neoadjuvant chemotherapy is associated with suppression of the B cell-centered immune landscape in pancreatic ductal adenocarcinoma
Pancreatic ductal adenocarcinoma (PDAC) is typically diagnosed at advanced stages and associated with early distant metastasis and poor survival. Besides clinical factors, the tumor microenvironment (TME) emerged as a crucial determinant of patient survival and therapy response in many tumors, including PDAC. Thus, the presence of tumor-infiltrating lymphocytes and the formation of tertiary lymphoid structures (TLS) is associated with longer survival in PDAC. Although neoadjuvant therapy (NeoTx) has improved the management of locally advanced tumors, detailed insight into its effect on various TME components is limited. Wh...
Source: Frontiers in Immunology - April 2, 2024 Category: Allergy & Immunology Source Type: research
TGF- β, IL-1β, IL-6 levels and TGF-β/Smad pathway reactivity regulate the link between allergic diseases, cancer risk, and metabolic dysregulations
This study offers a potential explanation for these observations, proposing that the premalignant levels of circulating transforming growth factor-β (TGF-β), IL-1β, and IL-6 as well as the reactivity of the TGF-β/Smad signaling pathway at the specific cancer site, are crucial factors contributing to the observed disparities. Circulating TGF-β, IL- β and IL-6 levels also help clarify why asthma is positively associated with obesity, Type 2 diabetes, hypertension, and insulin resistance, whereas allergic rhinitis is negatively linked to these conditions. Furthermore, TGF-β/Smad pathway reactivity explains the dual imp...
Source: Frontiers in Immunology - April 2, 2024 Category: Allergy & Immunology Source Type: research
A novel flow cytometry panel to identify prognostic markers for steroid-sensitive forms of idiopathic nephrotic syndrome in childhood
ConclusionWe have set up a novel, reproducible, disease-specific flow cytometry panel that allows a comprehensive characterization of circulating lymphocytes. We found that, at disease onset, relapsing patients had significantly more transitional, CD19+CD27+ memory and unswitched memory B cells and those who are at higher risk of relapse had increased circulating levels of unswitched memory B cells, independently of age. This approach can allow prediction of clinical evolution, monitoring of immunosuppression and tailored treatment in different forms of INS. (Source: Frontiers in Immunology)
Source: Frontiers in Immunology - April 2, 2024 Category: Allergy & Immunology Source Type: research
The role of B-1 cells in cancer progression and anti-tumor immunity
In recent years, in addition to the well-established role of T cells in controlling or promoting tumor growth, a new wave of research has demonstrated the active involvement of B cells in tumor immunity. B-cell subsets with distinct phenotypes and functions play various roles in tumor progression. Plasma cells and activated B cells have been linked to improved clinical outcomes in several types of cancer, whereas regulatory B cells have been associated with disease progression. However, we are only beginning to understand the role of a particular innate subset of B cells, referred to as B-1 cells, in cancer. Here, we summa...
Source: Frontiers in Immunology - April 2, 2024 Category: Allergy & Immunology Source Type: research
