Gaeklrr: A Novel Clustering Method of the Low-Rank Represent Based on Graph Auto-Encoder and Relaxed K-Means for Single Cell Type Identification DOI

Linping Wang,

Jin‐Xing Liu, Junliang Shang

et al.

Published: Jan. 1, 2023

With the rapid advancement of single-cell RNA sequencing (scRNA-seq) technology, disease mechanism research has advanced to a new level. Clustering is critical for scRNA-seq because it reveals similarity expression patterns. However, data contains numerous noises and outliers. Traditional clustering algorithms may fail capture accurate information. In this study, we propose GAEKLRR method type identification, which low-rank representation (LRR) based on graph auto-encoder (GAE) relaxed k-means. consists gedLRR Among them, LRR algorithm GAE. made up an encoder decoder. Firstly, reduce impact noise outliers mapping benchmark, generates robust embedding dictionary using gedLRR. by GAE structural information node features. Due reconstruction inner product distance, interpretability. Secondly, information, utilizes seek matrix while k-means update centroid. It worth noting that indication captured labels, can be used directly tasks. Finally, experiments real datasets demonstrate significant advantages clustering.

Language: Английский

Can invariant Natural Killer T cells drive B cell fate? a look at the humoral response DOI Creative Commons
Pablo A. Palacios, Álvaro Santibáñez, Fernanda Aguirre-Muñoz

et al.

Frontiers in Immunology, Journal Year: 2025, Volume and Issue: 16

Published: Feb. 18, 2025

Invariant Natural Killer T (NKT) cells represent a unique subset of innate-like that express both NK cell and receptors. These are rapidly activated by glycolipid antigens presented via CD1d molecules on antigen-presenting (APCs), including B cells, dendritic (DCs), macrophages, or through cytokine-dependent mechanisms. Their ability to produce wide range cytokines costimulatory underscores their critical role in bridging innate adaptive immunity. traditionally recognized for antibody production, also act as potent APCs due high expression CD1d, enabling direct interactions with iNKT cells. This interaction has significant implications humoral immunity, influencing activation, class-switch recombination (CSR), germinal center formation, memory differentiation, thus expanding the conventional paradigm cell-B interactions. While influence biology responses is well-supported, many aspects remain unresolved. Key questions include roles different subsets, diversity APCs, spatiotemporal dynamics these interactions, especially during early potential distinct ligands modulate immune outcomes. Understanding factors could provide valuable insights into how regulate cell-mediated immunity offer opportunities harness immunotherapeutic applications, such vaccine development. In this review, we examine unresolved propose novel perspective regulatory emphasizing promise target innovative strategies.

Language: Английский

Citations

1
Target tumor microenvironment by innate T cells DOI Creative Commons
Yan-Ruide Li, Matthew Wilson, Lili Yang

et al.

Frontiers in Immunology, Journal Year: 2022, Volume and Issue: 13

Published: Oct. 6, 2022

The immunosuppressive tumor microenvironment (TME) remains one of the most prevailing barriers obstructing implementation effective immunotherapy against solid-state cancers. Eminently composed associated macrophages (TAMs) and myeloid-derived suppressor cells (MDSCs) among others, TME attenuates effects immune checkpoint blockade adoptive cell therapies, mandating a novel therapy capable remediation. In this review we explore potential three innate-like T subsets, invariant natural killer (iNKT), mucosal-associated (MAIT) cells, gamma delta (γδT) that display an intrinsic anti-TAM/MDSC capacity. Exhibiting both innate adaptive properties, types express subset-specific TCR with distinct recombination, morphology, target recognition, further supplemented by variety NK activating receptors. Both receptor activation result in effector cytotoxicity targeted for addition, showcase moderate levels killing, providing dual antitumor function. This latent capacity can be bolstered chimeric antigen (CAR) engineering recognition specific antigens to enhance targeting. contrast established CAR-T adoption these provides enhanced safety profile without risk graft versus host disease (GvHD), due their non-recognition mismatched major histocompatibility complex (MHC) molecules, use as widely accessible, allogeneic “off-the-shelf” cancer immunotherapy.

Language: Английский

Citations

27
Invariant natural killer T cells in lung diseases DOI Creative Commons
Dongjin Jeong, Yeon Duk Woo, Doo Hyun Chung

et al.

Experimental & Molecular Medicine, Journal Year: 2023, Volume and Issue: 55(9), P. 1885 - 1894

Published: Sept. 11, 2023

Invariant natural killer T (iNKT) cells are a subset of that characterized by restricted T-cell receptor (TCR) repertoire and unique ability to recognize glycolipid antigens. These found in all tissues, evidence date suggests they play many immunological roles both homeostasis inflammatory conditions. The latter include lung diseases such as asthma infections: the lung-resident iNKT these have been extensively researched. Here, we provide insights into biology health disease, with particular focus on role pulmonary airway inflammation other diseases.

Language: Английский

Citations

14
Unconventional T cells in brain homeostasis, injury and neurodegeneration DOI Creative Commons

Mengfei Lv,

Zhaolong Zhang, Yu Cui

et al.

Frontiers in Immunology, Journal Year: 2023, Volume and Issue: 14

Published: Oct. 3, 2023

The interaction between peripheral immune cells and the brain is an important component of neuroimmune axis. Unconventional T cells, which include natural killer (NKT) mucosal-associated invariant (MAIT) γδ other poorly defined subsets, are a special group lymphocytes that recognize wide range nonpolymorphic ligands connection adaptive innate immunity. Recently, increasing number complex functions these unconventional in homeostasis various disorders have been revealed. In this review, we describe classification effector function review evidence for involvement regulation homeostasis, summarize roles mechanisms injury neurodegeneration, discuss immunotherapeutic potential as well future research goals. Insight processes can shed light on cell immunity diseases provide new clues therapeutic approaches targeting neurodegeneration.

Language: Английский

Citations

14
Genetic engineering strategies to enhance antitumor reactivity and reduce alloreactivity for allogeneic cell-based cancer therapy DOI Creative Commons
Yuning Chen, Yichen Zhu, Adam Kramer

et al.

Frontiers in Medicine, Journal Year: 2023, Volume and Issue: 10

Published: March 29, 2023

The realm of cell-based immunotherapy holds untapped potential for the development next-generation cancer treatment through genetic engineering chimeric antigen receptor (CAR)-engineered T (CAR-T) cell therapies targeted eradication cancerous malignancies. Such allogeneic “off-the-shelf” products can be advantageously manufactured in large quantities, stored extended periods, and easily distributed to treat an exponential number patients. At current, patient risk graft-versus-host disease (GvHD) host-versus-graft (HvG) allorejection severely restrict CAR-T products. To address these limitations, a variety strategies have been implemented enhance antitumor efficacy, reduce GvHD HvG onset, improve overall safety profile T-cell based immunotherapies. In this review, we summarize discuss challenges prospects approaches provide expedite progression translational clinical studies adoption universal immunotherapy.

Language: Английский

Citations

10
Tissue-resident immune cells: from defining characteristics to roles in diseases DOI Creative Commons
Jia Li, Xiao Chu, Chunxiang Li

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2025, Volume and Issue: 10(1)

Published: Jan. 16, 2025

Tissue-resident immune cells (TRICs) are a highly heterogeneous and plastic subpopulation of that reside in lymphoid or peripheral tissues without recirculation. These endowed with notably distinct capabilities, setting them apart from their circulating leukocyte counterparts. Many studies demonstrate complex roles both health disease, involving the regulation homeostasis, protection, destruction. The advancement tissue-resolution technologies, such as single-cell sequencing spatiotemporal omics, provides deeper insights into cell morphology, characteristic markers, dynamic transcriptional profiles TRICs. Currently, reported TRIC population includes tissue-resident T cells, memory B (BRM) innate lymphocytes, macrophages, neutrophils (TRNs), mast but unignorably existence TRNs is controversial. Previous focus on one specific diseases, however, origins, developmental trajectories, intercellular cross-talks every type not fully summarized. In addition, systemic overview TRICs disease progression development parallel therapeutic strategies lacking. Here, we describe function characteristics all types major diseases. We shed light how to harness offer new targets present burning questions this field.

Language: Английский

Citations

0
Single-cell transcriptomic profiling reveals diversity in human iNKT cells across hematologic tissues DOI Creative Commons
Reyka G. Jayasinghe,

Derek Hollingsworth,

Nathan C. Schedler

et al.

Cell Reports, Journal Year: 2025, Volume and Issue: 44(5), P. 115587 - 115587

Published: April 29, 2025

Language: Английский

Citations

0
Markers and makers of NKT17 cells DOI Creative Commons
Nurçin Liman, Jung‐Hyun Park

Experimental & Molecular Medicine, Journal Year: 2023, Volume and Issue: 55(6), P. 1090 - 1098

Published: June 1, 2023

Abstract Invariant natural killer T ( i NKT) cells are thymus-generated innate-like αβ that undergo terminal differentiation in the thymus. Such a developmental pathway differs from of conventional cells, which generated thymus but complete their functional maturation peripheral tissues. Multiple subsets NKT have been described, among IL-17-producing commonly referred to as NKT17 cells. IL-17 is considered proinflammatory cytokine can play both protective and pathogenic roles has implicated key regulatory factor many disease settings. Akin other subsets, acquire effector function during thymic development. However, cellular mechanisms drive subset specification, how general prior antigen encounter, remain largely unknown. Considering all express canonical Vα14-Jα18 TCRα chain display same ligand specificity, i.e., glycolipid antigens context nonclassical MHC-I molecule CD1d, conundrum explaining cell specification determined. Mapping molecular circuitry differentiation, combined with discovery markers identify provided new insights into The current review aims highlight recent advances our understanding development place these findings larger differentiation.

Language: Английский

Citations

9
Unraveling the phenotypic states of human innate-like T cells: Comparative insights with conventional T cells and mouse models DOI Creative Commons
Liyen Loh, Salomé Carcy, S. Harsha Krovi

et al.

Cell Reports, Journal Year: 2024, Volume and Issue: 43(9), P. 114705 - 114705

Published: Sept. 1, 2024

Language: Английский

Citations

3
Current insights in mouse iNKT and MAIT cell development using single cell transcriptomics data DOI Creative Commons
S. Harsha Krovi, Liyen Loh,

Andrea Spengler

et al.

Seminars in Immunology, Journal Year: 2022, Volume and Issue: 60, P. 101658 - 101658

Published: March 1, 2022

Language: Английский

Citations

12