Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

Deciphering immune cell heterogeneity in vascular diseases: Insights from single-cell sequencing

The complexity and diversity of vascular diseases highlight the urgent need to study their pathogenesis, particularly the key role of immune cell-mediated inflammatory responses in their development. While previous reviews have outlined the involvement of immune cells in vascular pathology, a comprehensive understanding of their dynamic changes, functional states, and intercellular interactions remains incomplete. Recent advances in single-cell sequencing (SCS) have provided unprecedented insights into immune cell heterogeneity, enabling the identification of novel subpopulations and their roles in disease progression.This review extends prior work by systematically summarizing the latest applications of SCS in vascular diseases, highlighting newly discovered immune cell subsets, their interactions, and their impact on vascular pathology. By addressing current gaps in the literature-such as the functional plasticity of immune cells and their temporal dynamics-this review offers new perspectives on immune-mediated mechanisms in vascular diseases and proposes novel therapeutic strategies for their prevention and treatment.

Effects of culture media on gene expression in reconstructed human epidermis and THP-1 monocytes for skin sensitization evaluation in co-culture systems

Co-culture with reconstituted epidermis formed by normal human epidermal keratinocytes (RhE) increases the expression of the skin sensitization markers CD54 and CD86 on the human monocytic leukemia cell line THP-1 without chemicals. Therefore, we investigated the effects of culture media [RPMI1640 for RhE; keratinization induction (KI) medium for THP-1], co-culture, and the responses to the skin sensitizer 2,4-dinitrochlorobenzene (DNCB) on gene expression in mono- and cocultures of RhE and THP-1 cells. Microarray and pathway analyses revealed that in mono-RhE, RPMI medium induced epidermal differentiation-related genes, whereas in monoculture THP-1 cells, KI medium upregulated inflammation-related genes. Surprisingly, the medium composition had a more significant impact than co-culture in both cells. However, crosstalk between RhE and THP-1 cells was observed upon DNCB exposure by comparing the differentially expressed gene sets. DNCB-treated THP-1 cells showed increased expression of NR4A1, NR4A2, NR4A3, SIK1, and HMOX1 in co-culture than in monoculture, and these gene expression patterns were confirmed by real-time RT-PCR. It has been suggested that danger signals from RhE, in response to DNCB, enhance the expression of these genes in THP-1 cells. We clarified the effects of the medium and co-culture and proposed these five genes as potential markers for skin sensitization evaluation.

scMODAL: a general deep learning framework for comprehensive single-cell multi-omics data alignment with feature links

Recent advancements in single-cell technologies have enabled comprehensive characterization of cellular states through transcriptomic, epigenomic, and proteomic profiling at single-cell resolution. These technologies have significantly deepened our understanding of cell functions and disease mechanisms from various omics perspectives. As these technologies evolve rapidly and data resources expand, there is a growing need for computational methods that can integrate information from different modalities to facilitate joint analysis of single-cell multi-omics data. However, integrating single-cell omics datasets presents unique challenges due to varied feature correlations and technology-specific limitations. To address these challenges, we introduce scMODAL, a deep learning framework tailored for single-cell multi-omics data alignment using feature links. scMODAL integrates datasets with limited known positively correlated features, leveraging neural networks and generative adversarial networks to align cell embeddings and preserve feature topology. Our experiments demonstrate scMODAL's effectiveness in removing unwanted variation, preserving biological information, and accurately identifying cell subpopulations across diverse datasets. scMODAL not only advances integration tasks but also supports downstream analyses such as feature imputation and feature relationship inference, offering a robust solution for advancing single-cell multi-omics research.

Mon4 as a novel monocyte subset with distinct profile and predictor of poor outcomes in individuals with myocardial infarction

Recently, a new monocyte subset known as Mon4, characterized by distinct gene expressions, has been identified but remains poorly characterized. In this study, our objective was to comprehensively characterise Mon4 in healthy individuals and explore its correlation with major adverse cardiovascular events (MACE) in patients with ST-elevation myocardial infarction (STEMI). Our study enrolled 20 healthy individuals and 245 STEMI patients who underwent primary percutaneous coronary intervention (PCI). We analysed monocyte subsets using flow cytometry and collected bone marrow samples from 11 healthy individuals. Cardiac function assessments were performed in STEMI patients through echocardiography within 3 days post-PCI. Mon4 displayed significant differences compared to Mon1, Mon2, and Mon3 in various parameters among healthy individuals, underscoring its distinct profile. In STEMI patients, above-median Mon4 counts were associated with a increased risk of MACE (hazard ratio [HR] 3.11, 95% confidence interval [CI] 1.55-6.24, p = 0.01) and heart failure (HR 3.25, 95% CI 1.14-9.24, p = 0.03) after adjusting for other predictive factors. This study highlights the unique characteristics of Mon4 and its clinical significance. The distinctive gene signature of Mon4, coupled with its association with MACE and heart failure, suggests its potential utility as a biomarker for risk assessment in MI patients. Further investigations are warranted to explore the therapeutic potential of targeting Mon4 in reducing cardiovascular complications following MACE.

Cutaneous lupus features specialized stromal niches and altered retroelement expression

Cutaneous Lupus is an inflammatory skin disease causing highly morbid inflamed skin and hair loss. In order to investigate the pathophysiology of cutaneous lupus, we performed single-cell RNA and spatial sequencing of lesional and non-lesional cutaneous lupus skin compared to healthy controls. Pathway enrichment analyses of lesional keratinocytes revealed elevated responses to type I interferon, type II interferon, tumor necrosis factor, and apoptotic signaling. Detailed clustering demonstrated unique fibroblasts specific to lupus skin with likely roles in inflammatory cell recruitment and fibrosis. We also evaluated the association of retroelement expression with type I interferons in the skin. We observed increased retroelement expression which correlated with interferon-stimulated genes across multiple cell types. Moreover, we saw elevated expression of genes involved in RIG-I and cGAS-STING pathways, which transduce elevated nucleic acid signals. Treatment of active cutaneous lupus with Anifrolumab reduced RIG-I and cGAS-STING pathways in addition to the most abundant retroelement family, L2b. Our studies better define type I interferon-mediated immunopathology in cutaneous lupus and identify an association between retroelement expression and interferon signatures in cutaneous lupus.

Serotonin transporter inhibits antitumor immunity through regulating the intratumoral serotonin axis

Identifying additional immune checkpoints hindering antitumor T cell responses is key to the development of next-generation cancer immunotherapies. Here, we report the induction of serotonin transporter (SERT), a regulator of serotonin levels and physiological functions in the brain and peripheral tissues, in tumor-infiltrating CD8 T cells. Inhibition of SERT using selective serotonin reuptake inhibitors (SSRIs), the most widely prescribed antidepressants, significantly suppressed tumor growth and enhanced T cell antitumor immunity in various mouse syngeneic and human xenograft tumor models. Importantly, SSRI treatment exhibited significant therapeutic synergy with programmed cell death protein 1 (PD-1) blockade, and clinical data correlation studies negatively associated intratumoral SERT expression with patient survival in a range of cancers. Mechanistically, SERT functions as a negative-feedback regulator inhibiting CD8 T cell reactivities by depleting intratumoral T cell-autocrine serotonin. These findings highlight the significance of the intratumoral serotonin axis and identify SERT as an immune checkpoint, positioning SSRIs as promising candidates for cancer immunotherapy.

Innate Immunity and Platelets: Unveiling Their Role in Chronic Pancreatitis and Pancreatic Cancer

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal forms of cancer, characterized by a highly desmoplastic tumor microenvironment. One main risk factor is chronic pancreatitis (CP). Progression of CP to PDAC is greatly influenced by persistent inflammation promoting genomic instability, acinar-ductal metaplasia, and pancreatic intraepithelial neoplasia (PanIN) formation. Components of the extracellular matrix, including immune cells, can modulate this progression phase. This includes cells of the innate immune system, such as natural killer (NK) cells, macrophages, dendritic cells, mast cells, neutrophils, and myeloid-derived suppressor cells (MDSCs), either promoting or inhibiting tumor growth. On one hand, innate immune cells can trigger inflammatory responses that support tumor progression by releasing cytokines and growth factors, fostering tumor cell proliferation, invasion, and metastasis. On the other hand, they can also activate immune surveillance mechanisms, which can limit tumor development. For example, NK cells are cytotoxic innate lymphoid cells that are able to kill tumor cells, and active dendritic cells are crucial for a functioning anti-tumor immune response. In contrast, mast cells and MDSCs rather support a pro-tumorigenic tumor microenvironment that is additionally sustained by platelets. Once thought to play a role in hemostasis only, platelets are now recognized as key players in inflammation and cancer progression. By releasing cytokines, growth factors, and pro-angiogenic mediators, platelets help shape an immunosuppressive microenvironment that promotes fibrotic remodeling, tumor initiation, progression, metastasis, and immune evasion. Neutrophils and macrophages exist in different functional subtypes that can both act pro- and anti-tumorigenic. Understanding the complex interactions between innate immune cells, platelets, and early precursor lesions, as well as PDAC cells, is crucial for developing new therapeutic approaches that can harness the immune and potentially also the coagulation system to target and eliminate tumors, offering hope for improved patient outcomes.

Single-Cell RNA Sequencing of Ewing Sarcoma Tumors Demonstrates Transcriptional Heterogeneity and Clonal Evolution

PURPOSE

Ewing sarcoma is the second most common bone cancer in children, accounting for 2% of pediatric cancer diagnoses. Patients who present with metastatic disease at the time of diagnosis have a dismal prognosis compared with the >70% 5-year survival of those with localized disease. Novel therapeutic approaches that can impact metastatic disease are desperately needed, as well as a deeper understanding of the heterogeneity of Ewing sarcoma tumors.

EXPERIMENTAL DESIGN

In this study, we utilized single-cell RNA sequencing to characterize the transcriptional landscape of primary Ewing sarcoma tumors and the surrounding tumor microenvironment in a cohort of seven untreated patients with Ewing sarcoma, as well as in circulating tumor cells (CTC). A potential CTC therapeutic target was evaluated through immunofluorescence of fixed CTCs from a separate cohort.

RESULTS

Primary tumor samples demonstrate a heterogeneous transcriptional landscape with several conserved gene expression programs, including those composed of genes related to proliferation and Ewing sarcoma gene targets, which were found to correlate with overall survival. Copy-number analysis identified subclonal evolution within patients prior to treatment. Analyses of the immune microenvironment reveal an immunosuppressive microenvironment with complex intercellular communication among the tumor and immune cells. Single-cell RNA sequencing and immunofluorescence of CTCs at the time of diagnosis identified TSPAN8 as a potential therapeutic target.

CONCLUSIONS

Ewing sarcoma tumors demonstrate significant transcriptional heterogeneity as well as a complex immunosuppressive microenvironment. This work evaluates several proposed targets that warrant further exploration as novel therapeutic strategies.

Interferon-induced activation of dendritic cells and monocytes by yellow fever vaccination correlates with early antibody responses

Yellow fever vaccination provides long-lasting protection and is a unique model for studying the immune response to an acute RNA virus infection in humans. To elucidate the early innate immune events preceding the rapid generation of protective immunity, we performed transcriptome analysis of human blood dendritic cell (DC) and monocyte subpopulations before and 3, 7, 14, and 28 d after vaccination. We detected temporary upregulation of IFN-stimulated genes (ISG) in all DC and monocyte subsets on days 3 and 7 after vaccination as well as cell type-specific responses and response kinetics. Single-cell RNA sequencing revealed rapid appearance of activated DC and monocyte clusters dominated by ISGs, inflammatory chemokines, and genes involved in antigen processing and presentation. This was confirmed by flow cytometric analysis in a large cohort of vaccinees. We identified SIGLEC1/CD169 upregulation as a sensitive indicator of the transient IFN-induced activation state elicited in DCs and monocytes by YF17D vaccination correlating with early protective IgM antibody responses.

Extracellular vesicles from human semen induce unique tolerogenic phenotypes in vaginal dendritic cells and regulatory T lymphocytes

Introduction

The regulation of immune responses to promote tolerance to the fetus is critical for successful pregnancy. An understudied aspect of this process is the initiation of regulation pre-conception via exposure to semen. Our study aimed to understand how semen impacts recipient dendritic cells (DCs) and their subsequent role in shaping CD4 T cell differentiation.

Methods

Monocyte-derived DCs (MoDCs) were exposed to semen extracellular vesicles (SEV) or vesicle-depleted semen plasma (VDSP). Phenotypic and functional markers were analyzed using flow cytometry. We also exposed epithelial sheets from vaginal tissue to SEV and VDSP, and measured the number and marker expression of emigrating cells. Finally, we tested how SEV- or VDSP-exposed DCs altered CD4 T cell differentiation by co-culturing exposed MoDCs or tissue emigrated cells with autologous naïve CD4 T cells.

Results

MoDCs exhibited a significant increase of CD141, CD1a, CD38, and ILT4 expression when exposed to SEV or VDSP. A unique feature of semen-treated MoDCs was expression of indoleamine 2,3-dioxygenase (IDO), a potent contributor to the induction of regulatory T cells (Tregs). SEV but not VDSP significantly increased the emigration of intraepithelial DCs. Additionally, SEV significantly enhanced the expression of multiple immunoregulatory markers in the emigrated DCs. After co-culture, we observed significantly more FOXP3+ Tregs expressing high levels of TIGIT in the groups that were initially exposed to SEV.

Discussion

These findings indicate that exposure to SEV induces a tolerogenic program in DCs that can direct differentiation of a unique memory Treg subset, primed for expansion and presumably destined to support a successful pregnancy.

Multi-dimensional characterization of cellular states reveals clinically relevant immunological subtypes and therapeutic vulnerabilities in ovarian cancer

BACKGROUND

Diverse cell types and cellular states in the tumor microenvironment (TME) are drivers of biological and therapeutic heterogeneity in ovarian cancer (OV). Characterization of the diverse malignant and immunology cellular states that make up the TME and their associations with clinical outcomes are critical for cancer therapy. However, we are still lack of knowledge about the cellular states and their clinical relevance in OV.

METHODS

We manually collected the comprehensive transcriptomes of OV samples and characterized the cellular states and ecotypes based on a machine-learning framework. The robustness of the cellular states was validated in independent cohorts and single-cell transcriptomes. The functions and regulators of cellular states were investigated. Meanwhile, we thoroughly examined the associations between cellular states and various clinical factors, including clinical prognosis and drug responses.

RESULTS

We depicted and characterized an immunophenotypic landscape of 3,099 OV samples and 80,044 cells based on a machine learning framework. We identified and validated 32 distinct transcriptionally defined cellular states from 12 cell types and three cellular communities or ecotypes, extending the current immunological subtypes in OV. Functional enrichment and upstream transcriptional regulator analyses revealed cancer hallmark-related pathways and potential immunological biomarkers. We further investigated the spatial patterns of identified cellular states by integrating the spatially resolved transcriptomes. Moreover, prognostic landscape and drug sensitivity analysis exhibited clinically relevant immunological subtypes and therapeutic vulnerabilities.

CONCLUSION

Our comprehensive analysis of TME helps leveraging various immunological subtypes to highlight new directions and targets for the treatment of cancer.

Decoding the Resistin-CAP1 Pathway in Intermediate Monocytes Mediating Liver Allograft Rejection

BACKGROUND & AIMS

Lymphocytes are widely recognized as the primary mediators of cellular rejection post-liver transplantation. However, conventional immunosuppressive regimens that target lymphocytes, such as calcineurin phosphatase inhibitors, corticosteroids, or lymphocyte-depleting antibodies, can only partially mitigate rejection while inducing severe adverse effects. This necessitates the search for novel immunotherapeutic targets.

METHODS

We harnessed the power of single-cell RNA sequencing and spatial transcriptome in 24 rat transplanted liver and peripheral blood single nucleated cells (PBMCs) samples to derive gene expression signatures recapitulating 13 cell phenotypes. We used flow cytometry, multifactor assays and multiple recombinant assays to validate in vitro and in vivo the role of the target protein Resistin on human T-cell function, as well as the Resistin-CAP1 interaction. Gold nanoparticles were used to package Retn siRNA sequences to validate the role of Retn knockdown on acute rejection after liver transplantation.

RESULTS

By distinguishing between donor and recipient cells, we delineate the dynamic landscape of immune cells during allograft rejection and their spatial distributions across donors and recipients. Our findings underscore the pivotal role of recipient derived intermediate monocytes in cellular rejection. Using CellChat ligand-receptor analysis, we identify the Resistin-CAP1 pathway as a key mechanism by which intermediate monocytes participate in T cell-mediated rejection reactions. We confirm that Resistin knockdown significantly alleviates acute rejection after rat liver transplantation, markedly extending the survival of recipients using innovative nanogold technology.

CONCLUSION

These findings offer insights into the dynamic changes in the alloimmune microenvironment, pinpointing intermediate monocytes as potential diagnostic and immunotherapeutic targets during allograft rejection. This study holds significant importance in advancing non-invasive diagnostic technologies and immunotherapeutic strategies for allogeneic rejection.

IMPACT AND IMPLICATIONS

This study pioneers the application of spatial transcriptomics in liver transplantation, providing a comprehensive analysis of immune cell spatial distribution, complemented by Souporcell-based chimerism assessment. We demonstrate that intermediate monocytes play a pivotal role in T cell-mediated acute rejection via the Resistin-CAP1 signaling axis. Targeting this pathway using nanogold-siRNA technology effectively mitigates rejection and enhances graft survival. These findings contribute novel insights into the mechanisms of transplant rejection and present promising avenues for the development of targeted therapeutic and diagnostic strategies in liver transplantation.

Identification of leukemia-enriched signature through the development of a comprehensive pediatric single-cell atlas

Single-cell transcriptome profiling enables unparalleled characterization of the heterogeneous microenvironment of pediatric leukemias. To facilitate comparative analyses and generate pediatric leukemia signatures, we collect, process, and annotate single-cell data comprising over 540,000 cells from 159 different pediatric acute leukemia (myeloid, lymphoid, mixed phenotype lineages) and healthy bone marrow (BM) samples, profiled in our lab and curated from publicly available studies. The analysis identifies a leukemia-enriched signature of nine genes with over-expression in leukemic blast compared to healthy BM cells. This signature is also consistently over-expressed in leukemia samples compared to normal BM in bulk RNA-seq datasets (over 2000 samples). Outcome-based analysis on diagnosis samples using measurable residual disease (MRD) status depicts a significant association of oncogene-induced senescence and g-protein activation pathways with MRD positivity. MRD positivity across pediatric leukemias is also correlated with significant depletion of CD8+ and CD4+ naïve T-cells and M1-macrophages at diagnosis. To enable easy access to this comprehensive pediatric leukemia single-cell atlas, we develop the Pediatric Single-cell Cancer Atlas (PedSCAtlas, https://bhasinlab.bmi.emory.edu/PediatricSCAtlas/ ). The atlas allows for quick exploration of single-cell data based on genes, cell type composition, and clinical outcomes to understand the cellular landscape of pediatric leukemias.

Cystatin A promotes the antitumor activity of T helper type 1 cells and dendritic cells in murine models of pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is a disease with poor prognosis due to diagnostic and therapeutic limitations. We previously identified cystatin A (CSTA) as a PDAC biomarker and have conducted the present study to investigate the antitumor effects of CSTA. PDAC murine models were established with genetically modified PAN02 tumor cell lines to evaluate the antitumor immune response. PDAC mouse survival was significantly longer with CSTA, and its antitumor effect was mediated mainly by CD4+ cells and partly by CD8+ cells. We also observed an increased infiltration of CD4+ and CD8+ cells in tumors of mice overexpressing CSTA. Phenotypically, we confirmed higher T helper type 1 (Th1) cell activity and increased frequency and activity of M1 macrophages and dendritic cells (DCs) in CSTA-overexpressing mice. Gene expression analysis highlighted pathways related to interferon gamma (IFN-γ) induction and Th1 lymphocyte activation that were induced by CSTA. Macrophages and DCs shifted toward proinflammatory antitumor phenotypes. Furthermore, activated splenocytes of PDAC model mice expressing CSTA had increased proapoptotic activity. CSTA also promoted the selective migration of CD4+ and CD11c+ immune cells in an in vitro migration assay. In conclusion, CSTA exerts antitumor effects by enhancing Th1-mediated antitumor effects through promotion of DC and M1 macrophage activity, thereby increasing immune cell chemotaxis. CSTA could be a novel therapeutic candidate for PDAC.

Deciphering Immunosenescence From Child to Frailty: Transcriptional Changes, Inflammation Dynamics, and Adaptive Immune Alterations

Aging induces significant alterations in the immune system, with immunosenescence contributing to age-related diseases. Peripheral blood mononuclear cells (PBMCs) offer a convenient and comprehensive snapshot of the body's immune status. In this study, we performed an integrated analysis of PBMCs using both bulk-cell and single-cell RNA-seq data, spanning from children to frail elderlies, to investigate age-related changes. We observed dynamic changes in the PBMC transcriptome during healthy aging, including dramatic shifts in inflammation, myeloid cells, and lymphocyte features during early life, followed by relative stability in later stages. Conversely, frail elderly individuals exhibited notable disruptions in peripheral immune cells, including an increased senescent phenotype in monocytes with elevated inflammatory cytokine expression, heightened effector activation in regulatory T cells, and functional impairment of cytotoxic lymphocytes. Overall, this study provides valuable insights into the complex dynamics of immunosenescence, elucidating the mechanisms driving abnormal inflammation and immunosuppression in frailty.

Bioinformatic analysis and experimental verification reveal expansion of monocyte subsets with an interferon signature in systemic lupus erythematosus patients

BACKGROUND

Systemic lupus erythematosus (SLE) is a complex autoimmune disorder characterized by chronic inflammation and multi-organ damage. A central factor in SLE pathogenesis is the excessive production of type I interferon (IFN-I), which drives immune dysregulation. Monocytes, key components of the immune system, significantly contribute to IFN-I production. However, their specific roles in SLE remain incompletely understood.

METHODS

This study utilized bioinformatics and statistical analyses, including robust rank aggregation (RRA), DESeq2, and limma, to analyze transcriptome data from peripheral blood mononuclear cells (PBMCs) and monocytes of SLE patients and healthy controls. Single-cell RNA sequencing (scRNA-seq) data were processed using the Seurat R package to identify and characterize monocyte subsets with a strong IFN-driven gene signature. Flow cytometry was employed to validate key findings, using markers such as CD14, SIGLEC1, and IRF7 to confirm monocyte subset composition.

RESULTS

Our research has found that monocytes in SLE undergo IFN-driven transcriptional reprogramming, with the upregulation of key interferon signature genes (ISGs), forming the SLE-Related Monocyte Signature (SLERRAsignature). Moreover, the composition of mononuclear phagocyte subsets in SLE patients changes, with an increase trend in the proportion of the CD14Mono8 subset in the flare group. The differentially expressed genes (DEGs) in 13 mononuclear phagocyte subsets of SLE are mainly ISGs, and the expression of ISGs is higher in severe patients. We identified SIGLEC1+IRF7+ monocytes among these subsets and for the first time discovered this group of cells in the peripheral blood of healthy individuals. In SLE, the enrichment score of the gene set representing SIGLEC1+IRF7+ monocytes is positively correlated with the severity of SLE. Finally, flow cytometry confirmed that the frequency of CD14+SIGLEC1+IRF7+ monocytes in PBMCs was higher in SLE compared with healthy controls.

CONCLUSIONS

Our study found that the expansion of IFN-I-producing monocyte subsets, particularly the CD14+SIGLEC1+IRF7+ subset, plays a crucial role in SLE pathogenesis. This subset may serve as a potential biomarker and therapeutic target for managing SLE.

Single-cell RNA sequencing dissects the immunosuppressive signatures in Helicobacter pylori-infected human gastric ecosystem

Helicobacter pylori (H. pylori) manipulates the host immune system to establish a persistent colonization, posing a serious threat to human health, but the mechanisms remain poorly understood. Here we integrate single-cell RNA sequencing and TCR profiling for analyzing 187,192 cells from 11 H. pylori-negative and 12 H. pylori-positive individuals to describe the human gastric ecosystem reprogrammed by H. pylori infection, as manifested by impaired antigen presentation and phagocytosis function. We further delineate a monocyte-to-C1QC+ macrophage differentiation trajectory driven by H. pylori infection, while T cell responses exhibit broad functional impairment and hyporesponsiveness with restricted clonal expansion capacity. We also identify an HLA-DRs- and CTLA4-expressing T cell population residing in H. pylori-inhabited stomach that potentially contribute to immune evasion. Together, our findings provide single-cell resolution information into the immunosuppressive microenvironment shaped by H. pylori infection, offering critical insights for developing novel therapeutic approaches to eliminate this globally prevalent pathogen.

Human type 1 conventional dendritic cells contribute to skin transplant rejection

The skin is the most immunogenic tissue in transplantation and the most difficult tissue in which to induce immune modulation. Batf3-dependent type 1 conventional dendritic cells (cDC1s) are important in initiating rejection in murine skin transplantation. In humans, the CD141+ cDC1 subset is the functional counterpart of the murine Batf3-dependent cDC1s. However, their contribution to the rejection of human skin allografts remains unknown. Using samples from human face and upper extremity transplant recipients, we demonstrated that CD141+ cDC1s are increased and more activated in human skin grafts than native skin tissue from the same individual. Moreover, circulating and tissue CD141+ cDC1s were elevated at rejection time points. Local modulation of graft CD141+ cDC1s decreased HLA-DR expression and increased regulatory T cells, which correlated with a decreased presence of skin allogeneic T cells in a humanized transplantation model. Thus, CD141+ cDC1s play an important role in rejecting human skin allografts, and their local modulation is a promising therapeutic approach.

Immunoregulatory iPSC-derived non-lymphoid progeny in autoimmunity and GVHD alloimmunity

Non-lymphoid immunoregulatory cells, including mesenchymal stem cells (MSCs), myeloid-derived suppressor cells (MDSCs), regulatory macrophages (Mregs), and tolerogenic dendritic cells (Tol-DCs), play critical roles in maintaining immune homeostasis. However, their therapeutic application in autoimmune diseases and graft-versus-host disease (GVHD) has received comparatively less attention. Induced pluripotent stem cells (iPSCs) offer a promising platform for cell engineering, enabling superior quality control, scalable production, and large-scale in vitro expansion of iPSC-derived non-lymphoid immunoregulatory cells. These advances pave the way for their broader application in autoimmune disease and GVHD therapy. Recent innovations in iPSC differentiation protocols have facilitated the generation of these cell types with functional characteristics akin to their primary counterparts. This review explores the unique features and generation processes of iPSC-derived non-lymphoid immunoregulatory cells, their therapeutic potential in GVHD and autoimmune disease, and their progress toward clinical translation. It emphasizes the phenotypic and functional diversity within each cell type and their distinct effects on disease modulation. Despite these advancements, challenges persist in optimizing differentiation efficiency, ensuring functional stability, and bridging the gap to clinical application. By synthesizing current methodologies, preclinical findings, and translational efforts, this review underscores the transformative potential of iPSC-derived non-lymphoid immunoregulatory cells in advancing cell-based therapies for alloimmune and autoimmune diseases.

Highly immunogenic DNA/LION nanocarrier vaccine potently activates lymph nodes inducing long-lasting immunity in macaques

A SARS-CoV-2 spike DNA vaccine formulated with a cationic nanoparticle emulsion (LION) was tested in Rhesus macaques. It induced robust, long-lasting (>2 years) cellular and humoral immunity, including increased neutralization breadth. T cell responses were predominantly CD8+, in contrast to other DNA vaccines. A rapid transient cytokine/chemokine response was associated with expansion and trafficking of myeloid cells and lymphocytes. Increased proliferation and dynamic changes between blood and lymph node (LN) were found for monocyte-derived cells, dendritic cells, and B and T cells, resulting in activation of LN and expansion of germinal centers (GCs), likely critical in shaping long-lasting adaptive immunity. Significant GC expansion of B, CD4-, and CD8- cells, including the Tfc3 subset, reflects a balanced immune response, including antibody (Ab) development. DNA/LION vaccination activates myeloid and lymphoid cells in blood and LN and promotes effective antigen presentation, resulting in sustained antigen-specific cellular and humoral responses, emerging as an effective DNA vaccine delivery platform.

Single-cell RNA sequencing reveals important role of monocytes and macrophages during mucopolysaccharidosis treatment

Mucopolysaccharidosis (MPS) encompasses a heterogeneous group of lysosomal storage diseases resulting from mutations in genes encoding lysosomal enzymes responsible for the degradation of mucopolysaccharides, also known as glycosaminoglycans (GAGs). Current therapeutic strategies for MPS include hematopoietic stem cell transplantation (HSCT), enzyme replacement therapy (ERT), and symptomatic therapy. This study investigated dynamic changes in MPS type II (MPS-II) through genomic and single-cell sequencing in a patient undergoing ERT. Analysis of peripheral blood mononuclear cells (PBMCs) from one MPS-II patient of 10 year old at different disease stages through scRNA-seq identified various immune cell types, including natural killer (NK) cells, NKT cells, CD4 + and CD8 + T cells, CD14 + and CD16 + monocytes, and B cells. Monocytes and macrophages were significantly reduced during the severe stage of MPS-II but increased during the recovery stage following ERT. Notably, monocyte subtype mono3 was exclusively expressed in the severe stage, while mono1_2, a subtype of mono1, was absent during the severe stage and exhibited distinct biological functions. These findings suggest that monocytes and macrophages play critical roles in the pathogenesis of MPS-II and in the response to ERT. Pseudotime, Gene Ontology, and cell-communication analyses revealed unique functions for the different cellular subtypes. Notably, key molecules mediating cellular interactions during ERT in MPS-II included CXCR3, PF4, APP, and C5AR1 in macrophages, RPS19 in T cells, HLA-DPB1 in B cells, ADRB2 in NK cells, and IL1B, C5AR1, RPS19, and TNFSF13B in monocytes. Overall, integrative analysis delineated the expression dynamics of various cell types and identified mutations in MPS-II, providing a comprehensive atlas of transcriptional programs, cellular characterizations, and genomic variation profiles in MPS-II. This dataset, along with advanced integrative analysis, represents a valuable resource for the discovery of drug targets and the improvement of therapeutic strategies for MPS-II.

Are We There Yet? Assessing the Readiness of Single-Cell Proteomics to Answer Biological Hypotheses

Single-cell analysis is an active area of research in many fields of biology. Measurements at single-cell resolution allow researchers to study diverse populations without losing biologically meaningful information to sample averages. Many technologies have been used to study single cells, including mass spectrometry-based single-cell proteomics (SCP). SCP has seen a lot of growth over the past couple of years through improvements in data acquisition and analysis, leading to greater proteomic depth. Because method development has been the main focus in SCP, biological applications have been sprinkled in only as proof-of-concept. However, SCP methods now provide significant coverage of the proteome and have been implemented in many laboratories. Thus, a primary question to address in our community is whether the current state of technology is ready for widespread adoption for biological inquiry. In this Perspective, we examine the potential for SCP in three thematic areas of biological investigation: cell annotation, developmental trajectories, and spatial mapping. We identify that the primary limitation of SCP is sample throughput. As proteome depth has been the primary target for method development to date, we advocate for a change in focus to facilitate measuring tens of thousands of single-cell proteomes to enable biological applications beyond proof-of-concept.

Immune-parenchymal multicellular niches are shared across distinct thyroid autoimmune diseases

Thyroid hormone, produced in the thyroid gland, regulates metabolism, development, and cardiac function. The thyroid is susceptible to autoimmune attack by both cellular and humoral immunity exemplified by Hashimoto's thyroiditis (HT) and Graves' Disease (GD), respectively. In HT, immune-mediated destruction impairs thyroid hormone production, while in GD, stimulating autoantibodies promote over-production. Here, we generated a multi-modal atlas of 604,076 human thyroid and blood cells from HT, GD, and control patients. We found that, despite markedly different clinical presentations and distinct antigenic triggers, HT and GD exhibit convergent cellular dynamics resulting in a shared continuum of immune infiltration. Along this continuum, a key feature is a thyrocyte niche containing CD8 + T cells that may segregate pathogenic T cells from regions with preserved thyroid hormone production. These findings of a shared disease continuum characterized by spatially defined immune niches provide a new framework for understanding tissue homeostasis in human autoimmune disease.

Aging immunity: unraveling the complex nexus of diet, gut microbiome, and immune function

Aging is associated with immune senescence and gut dysbiosis, both of which are heavily influenced by the diet. In this review, we summarize current knowledge regarding the impact of diets high in fiber, protein, or fat, as well as different dietary components (tryptophan, omega-3 fatty acids, and galacto-oligosaccharides) on the immune system and the gut microbiome in aging. Additionally, this review discusses how aging alters tryptophan metabolism, contributing to changes in immune function and the gut microbiome. Understanding the relationship between diet, the gut microbiome, and immune function in the context of aging is critical to formulate sound dietary recommendations for older individuals, and these personalized nutritional practices will ultimately improve the health and longevity of the elderly.

TNF/TNFR Superfamily Members in Costimulation of T Cell Responses-Revisited

Prosurvival tumor necrosis factor receptor (TNFR) superfamily (TNFRSF) members on T cells, including 4-1BB, CD27, GITR, and OX40, support T cell accumulation during clonal expansion, contributing to T cell memory. During viral infection, tumor necrosis factor superfamily (TNFSF) members on inflammatory monocyte-derived antigen-presenting cells (APCs) provide a postpriming signal (signal 4) for T cell accumulation, particularly in the tissues. Patients with loss-of-function mutations in TNFR/TNFSF members reveal a critical role for 4-1BB and CD27 in CD8 T cell control of Epstein-Barr virus and other childhood infections and of OX40 in CD4 T cell responses. Here, on the 20th anniversary of a previous Annual Review of Immunology article about TNFRSF signaling in T cells, we discuss the effects of endogenous TNFRSF signals in T cells upon recognition of TNFSF members on APCs; the role of TNFRSF members, including TNFR2, on regulatory T cells; and recent advances in the incorporation of TNFRSF signaling in T cells into immunotherapeutic strategies for cancer.

The tumor microenvironment and dendritic cells: Developers of pioneering strategies in colorectal cancer immunotherapy?

Colorectal cancer (CRC) is the world's third most frequent cancer, and both its incidence and fatality rates are rising. Despite various therapeutic approaches, neither its mortality rate nor its recurrence frequency has decreased significantly. Additionally, conventional treatment approaches, such as chemotherapy and radiotherapy, have several side effects and risks for patients with CRC. Accordingly, the need for alternative and effective treatments for CRC patients is critical. Immunotherapy that utilizes dendritic cells (DCs) harnesses the patient's immune system to combat cancer cells effectively. DCs are the most potent antigen-presenting cells (APCs), which play a vital role in generating anti-cancer T cell responses. A significant barrier to the immune system's ability to eliminate CRC is the establishment of a potent immunosuppressive tumor milieu by malignant cells. Since DCs are frequently defective in this milieu, the tumor setting significantly reduces the effectiveness of DC-based therapy. Determining central mechanisms contributing to tumor growth by unraveling and comprehending the interaction between CRC tumor milieu and DCs may lead to new therapeutic approaches. This study aims to review DC biology and discuss its role in T-cell-mediated anti-tumor immunity, as well as to highlight the immunosuppressive effects of the CRC tumor milieu on the function of DCs. We will also highlight the tumor microenvironment (TME)-related factors that interfere with DC function as a possible therapeutic target to enhance DC-based cell therapy efficacy.

Adoptively transferred tumor-specific IL-9-producing cytotoxic CD8+ T cells activate host CD4+ T cells to control tumors with antigen loss

Host effector CD4+ T cells emerge as critical mediators for tumor regression but whether they can be activated by adoptively transferred CD8+ T cells remains unknown. We previously reported that adoptive transfer of interleukin 9 (IL-9)-producing cytotoxic CD8+ T (Tc9) cells achieved long-term control of tumor growth. Here, we demonstrate that murine tumor-specific Tc9 cells control the outgrowth of antigen-loss relapsed tumors by recruiting and activating host effector CD4+ T cells. Tc9 cells secreted IL-24 and recruited CCR7-expressing conventional type 2 dendritic cells (cDC2 cells) into tumor-draining lymph nodes to prime host CD4+ T cells against relapsed tumors. Host CD4+ T cell or cDC2 deficiency impaired the ability of Tc9 cells to control relapsed tumor outgrowth. Additionally, intratumoral IL24 expression correlates with cDC2 and CD4+ T cell gene signatures in human cancers and their expression is associated with better patient survival. This study reports a mechanism for activation of tumor-specific CD4+ T cells in vivo.

Distinctive CD8+ T cell activation by antigen-presenting plasmacytoid dendritic cells compared to conventional dendritic cells

Plasmacytoid dendritic cells (pDCs) play a pivotal role in immune responses, particularly against viral infections. pDCs exhibit diverse functions, including interferon production, cytokine secretion, and antigen presentation. Here, we investigate the antigen cross-presentation capacity of pDCs and their role in CD8+ T cell activation. Utilizing a culturing system with CD8+ T cells and autologous pDCs derived from circulating CD34+ hematopoietic stem and progenitor cells, we demonstrate that pDCs efficiently activate CD8+ T cells via cross-presentation, promoting T cell expansion and cytotoxic activity. The antigen presentation capacity of pDCs is comparable to that of monocyte-derived dendritic cells (moDCs) and myeloid dendritic cells, which are known for their efficient antigen-presentation capacity. Transcriptomic analysis reveals genetic signatures in CD8+ T cells activated by pDCs distinct from moDCs, suggesting different activation mechanisms. These findings underscore the importance of pDCs in antigen presentation and their contribution to CD8+ T cell activation.

Tissue-specific properties of type 1 dendritic cells in lung cancer: implications for immunotherapy

Checkpoint inhibitors have led to remarkable benefits in non-small cell lung cancer (NSCLC), yet response rates remain below expectations. High-dimensional analysis and mechanistic experiments in clinical samples and relevant NSCLC models uncovered the immune composition of lung cancer tissues, providing invaluable insights into the functional properties of tumor-infiltrating T cells and myeloid cells. Among myeloid cells, type 1 conventional dendritic cells (cDC1s) stand out for their unique ability to induce effector CD8 T cells against neoantigens and coordinate antitumoral immunity. Notably, lung resident cDC1 are particularly abundant and long-lived and express a unique tissue-specific gene program, underscoring their central role in lung immunity. Here, we discuss recent insights on the induction and regulation of antitumoral T cell responses in lung cancer, separating it from the tissue-agnostic knowledge generated from heterogeneous tumor models. We focus on the most recent studies dissecting functional states and spatial distribution of lung cDC1 across tumor stages and their impact on T cell responses to neoantigens. Finally, we highlight relevant gaps and emerging strategies to harness lung cDC1 immunostimulatory potential.

The role of monocytes and macrophages in idiopathic inflammatory myopathies: insights into pathogenesis and potential targets

Idiopathic inflammatory myopathies (IIMs) are heterogeneous autoimmune disorders characterized by muscle inflammation, weakness, and extramuscular manifestations such as interstitial lung disease, skin rash, arthritis, dysphagia, myocarditis and other systemic organ involvement. Although T and B cells have historically been central to the understanding of IIM immunopathology, monocytes and their differentiated progenitor cells, macrophages, are increasingly being recognized as critical mediators of both tissue damage and repair. In subtypes such as dermatomyositis, immune-mediated necrotizing myopathy and antisynthetase syndrome, macrophages infiltrate skeletal muscle and other affected tissues, contributing to inflammation via production of pro-inflammatory cytokines, chemokines, and reactive oxygen species. Dysregulated interferon signaling, mitochondrial stress, and aberrant metabolic states in these cells further perpetuate tissue injury in IIMs. Conversely, certain macrophage subsets can support muscle fiber regeneration and dampen inflammation, underscoring the dual roles these cells can play. Future research into the heterogeneity of monocytes and macrophages, including single-cell transcriptomic and metabolomic approaches, will help clarify disease mechanisms, identify biomarkers of disease activity and prognosis, and guide novel therapeutic strategies targeting these innate immune cells in IIM.

Oropharyngeal carcinomas induce circulating monocytes to express a TAM-like pro-tumor expression profile that suppresses T-cell proliferation

Introduction

Tumor-associated macrophages (TAMs) recruited from circulating monocytes drive tumor-growth and establish an immunosuppressive tumor microenvironment (TME). Initial events in transition from resting monocytes to TAMs are poorly understood. Here, we report that monocytes from oropharyngeal cancer (OPC) patients and control monocytes treated with OPC-conditioned media (CM) express a repertoire of pro-tumor mediators that is characteristic of TAMs.

Methods

Monocytes were stimulated with OPC cell line CM, analyzed by single-cell RNAseq. Results of select genes were confirmed by qPCR with monocytes and analyzed in OPC tumors vs. clinically normal tissue. OPC spheroids containing control monocytes and T-cells were established, TAM phenotype characterized by flow analysis and qPCR, and T-cell proliferation assessed by flow.

Results

OPC-conditioned media induced multiple pro-tumor genes including CXCL1, CXCL5, CXCL8, SPP1, IL1B, GPNMB, and FABP5. Patient monocytes had higher baseline levels or achieved higher levels after stimulation than control monocytes. A subset of patient monocytes had high baseline levels of CXCL9/-10/-11 expression that resisted downregulation in response to stimulation, a potential sign of a more favorable TME. CXCL9/-10/-11 expression in OPC tumor biopsies compared to clinically normal tissue correlated with patient outcome. Spheroid TAMs derived from control monocytes maintained the pro-tumor repertoire seen with monocytes stimulated by tumor line conditioned media. These TAMs suppress T-cell proliferation. Inhibition of COX-2 or IL1 signaling during differentiation into TAMs partially blocked the suppression of T-cell proliferation.

Conclusion

Targeting the early transition of monocytes into pro-tumor TAMs could be used to develop new therapies for OPC.

Single-cell atlas of the pregnant equine endometrium before and after implantation†

Embryo implantation in the mare occurs just over one month after fertilization, coinciding with the production of chorionic gonadotropin. The factors that regulate this late implantation in the mare, and whether they are unique to horses or shared with more invasive embryo implantation in other species, remain poorly understood. This study aimed to determine and compare the transcriptome and subpopulations of endometrial cells before and after embryo implantation in the horse. Single-cell RNA sequencing was used to characterize the transcriptome of nearly 97,000 endometrial cells collected from biopsies of the endometrium at the beginning (day 33 of gestation) and after embryo implantation (day 42 of gestation) in mares. Sixteen immune and 24 non-immune cell clusters were identified, representing known major cell populations as well as novel subpopulations of horse immune cells such as resident innate lymphoid cells and mucosal-associated invariant T cells. Contrary to current knowledge, endometrial natural killer (eNK) cells were the most abundant endometrial leukocyte population during implantation in horses. Moreover, eNK cells not only expressed genes that may interact with fetal MHC I, such as LY49F, but also exert immunoregulatory functions independent of MHC I expression, such as CD96/TIGIT. Analogous to other species studied, upregulation of CXCR4 was found in several subpopulations of immune cells. Our results suggest that despite distinctive and later placentation compared with humans, horses share some key similarities in the mechanisms of embryo implantation.

Multi-Targeting CAR-T Cell Strategies to Overcome Immune Evasion in Lymphoid and Myeloid Malignancies

BACKGROUND

Chimeric antigen receptor (CAR)-T cell therapy has become a groundbreaking treatment for hematological malignancies, particularly lymphomas and multiple myeloma, with high remission rates in refractory and relapsed patients. However, most CAR-T therapies target a single antigen, such as CD19, which can result in immune evasion through antigen escape. This mechanism describes the downregulation or complete loss of the targeted antigen by the tumor cells, eventually leading to relapse. To address this issue, multi-targeting strategies like logic-gated CARs, adapter CARs, or combination therapies can increase the potency of CAR-T cells. These approaches aim to minimize immune evasion by targeting multiple antigens simultaneously, thereby increasing treatment durability. Additionally, advanced tools such as next-generation sequencing (NGS), direct stochastic optical reconstruction microscopy (dSTORM), or multiparametric flow cytometry are helping to identify novel tumor-specific targets and improve therapy designs.

SUMMARY

This review explores the current landscape of CAR-T cell therapies in lymphoid and myeloid malignancies, highlights ongoing clinical trials, and discusses the future of these innovative multi-targeting approaches to improve patient outcome.

KEY MESSAGES

Antigen escape limits CAR-T cell therapy success, but multi-targeting strategies like logic gates and adapter CARs offer solutions. Optimizing antigen selection and CAR design, along with larger clinical trials, is essential for improving patient outcomes. Personalization using advanced technologies like CRISPR screening and single-cell RNA sequencing can enhance durability and effectiveness of treatments for heavily pretreated patients.

From Gene to Intervention: NLRC4 and WIPI1 Regulate Septic Acute Lung Injury Through Autophagy

Background

Septic Acute Lung Injury (SALI)-induced severe respiratory dysfunction has been established to significantly increase patient mortality rates and socioeconomic costs. To mitigate cellular damage, autophagy -a conserved biological process in organisms -degrades damaged cellular components, such as proteins and organelles. Although autophagy is crucially involved in the inflammatory response, its precise molecular mechanisms in SALI remain unclear, forming the basis of this study.

Methods

Herein, two microarray datasets (GSE33118 and GSE131761) and three single-cell sequencing datasets (SCP43, SCP548, and SCP2156) derived from human samples were used to ascertain the interrelationship between Differentially Expressed Autophagy-Related Genes (DEARGs) and SALI. The relationship between key DEARGs and SALI was validated both in vitro and in vivo using various techniques, including flow cytometry, Immunofluorescence (IF), Quantitative Polymerase Chain Reaction (qPCR), Western Blotting (WB), and small interfering RNA (siRNA).

Results

Herein, we found that autophagy activation attenuated SALI, with NLRC4 and WIPI1 as the two key DEARGs involved. Specifically, NLRC4 and WIPI1 downregulation mitigated SALI via autophagy activation. Compared to NLRC4, WIPI1 was more closely associated with noncanonical autophagic flux in SALI. Furthermore, immune infiltration analysis and single-cell data showed a close relationship between NLRC4, WIPI1, and immune cells.

Conclusion

Our findings revealed that SALI correlated strongly with autophagy, with the downregulation of the two key DEARGs, NLRC4 and WIPI1, attenuating sepsis lung injury via autophagy regulation, highlighting their therapeutic significance in SALI.

Altered X-chromosome inactivation of the TLR7/8 locus and heterogeneity of pDCs in systemic sclerosis

Systemic sclerosis (SSc) is an autoimmune disease that has a strong female predominance. Both the X-linked TLR7 and TLR8 can induce type I IFN (IFN-I) by plasmacytoid DCs (pDCs), which can promote fibrosis. We identified five subclusters of pDCs, including ISGhigh clusters that were over-represented in SSc patients. We observed that both TLR7 and TLR8 genes escape from X chromosome inactivation (XCI) at higher frequency in pDCs of SSc patients, which was associated with changes in TLR7 protein profile. Combined DNA/RNA FISH analysis revealed that the TLR7/8 locus is preferentially located outside of the inactive X (Xi) territory when TLR7 is expressed, suggesting that higher-order loop formation is linked to TLR7/8 expression from the Xi. Furthermore, the expression levels of XIST and the transcriptional repressor SPEN were reduced in SSc pDCs. Hence, our data revealed the heterogeneity of pDCs in SSc and suggested that altered XCI at the TLR7/8 locus may contribute to the chronic IFN-I activity of pDCs in female SSc patients.

A Phase I Clinical Trial Adding OX40 Agonism to In Situ Therapeutic Cancer Vaccination in Patients with Low-Grade B-cell Lymphoma Highlights Challenges in Translation from Mouse to Human Studies

PURPOSE

Activating T-cell costimulatory receptors is a promising approach for cancer immunotherapy. In preclinical work, adding an OX40 agonist to in situ vaccination with SD101, a TLR9 agonist, was curative in a mouse model of lymphoma. We sought to test this combination in a phase I clinical trial for patients with low-grade B-cell lymphoma.

PATIENTS AND METHODS

We treated 14 patients with low-dose radiation, intratumoral SD101, and intratumoral and intravenous BMS986178, an agonistic anti-OX40 antibody. The primary outcome was safety. Secondary outcomes included overall response rate and progression-free survival.

RESULTS

Adverse events were consistent with prior experience with low-dose radiation and SD101. No synergistic or dose-limiting toxicities were observed. One patient had a partial response, and nine patients had stable disease, a result inferior to our experience with TLR9 agonism and low-dose radiation alone. Flow cytometry and single-cell RNA sequencing of serial tumor biopsies revealed that T and NK cells were activated after treatment. However, high baseline OX40 expression in T follicular helper and T regulatory type 1 cells, as well as high posttreatment soluble OX40, shed from these T cells upon activation, associated with progression-free survival of less than 6 months.

CONCLUSIONS

Clinical results of T-cell costimulatory receptor agonism have now repeatedly been inferior to the motivating preclinical results. Our study highlights potential barriers to clinical translation, particularly differences in preclinical and clinical reagents and the complex biology of these coreceptors in heterogeneous T cell subpopulations, some of which may antagonize immunotherapy.

Chenodeoxycholic acid modulates cholestatic niche through FXR/Myc/P-selectin axis in liver endothelial cells

Cholestatic liver diseases are characterized by excessive bile acid accumulation in the liver. Endothelial cells (ECs) shape the local microenvironment in both normal conditions and liver injury, yet their role in cholestasis is unclear. Through a comparative analysis of single-cell RNA sequencing data from various murine models of liver injury, we identify distinctive Myc activation within ECs during obstructive cholestasis resulting from bile duct ligation (BDL). Myc overexpression in ECs significantly upregulates P-selectin, increasing neutrophil infiltration and worsening cholestatic liver injury. This process occurs through the FXR, activated by chenodeoxycholic acid (CDCA) and its conjugate TCDCA. Inhibiting P-selectin with PSI-697 reduces neutrophil recruitment and alleviates injury. Cholestatic patient liver samples also show elevated Myc and P-selectin in ECs, along with increased neutrophils. The findings identify ECs as key drivers of cholestatic liver injury through a Myc-driven program and suggest that targeting the CDCA/FXR/Myc/P-selectin axis may offer a therapeutic approach.

Bidirectional epigenetic editing reveals hierarchies in gene regulation

CRISPR perturbation methods are limited in their ability to study non-coding elements and genetic interactions. In this study, we developed a system for bidirectional epigenetic editing, called CRISPRai, in which we apply activating (CRISPRa) and repressive (CRISPRi) perturbations to two loci simultaneously in the same cell. We developed CRISPRai Perturb-seq by coupling dual perturbation gRNA detection with single-cell RNA sequencing, enabling study of pooled perturbations in a mixed single-cell population. We applied this platform to study the genetic interaction between two hematopoietic lineage transcription factors, SPI1 and GATA1, and discovered novel characteristics of their co-regulation on downstream target genes, including differences in SPI1 and GATA1 occupancy at genes that are regulated through different modes. We also studied the regulatory landscape of IL2 (interleukin-2) in Jurkat T cells, primary T cells and chimeric antigen receptor (CAR) T cells and elucidated mechanisms of enhancer-mediated IL2 gene regulation. CRISPRai facilitates investigation of context-specific genetic interactions, provides new insights into gene regulation and will enable exploration of non-coding disease-associated variants.

Innate Immunity and Asthma Exacerbations: Insights From Human Models

Asthma is a common chronic respiratory disease characterized by the presence of airway inflammation, airway hyperresponsiveness, and mucus hypersecretion. Repeated asthma exacerbations can lead to progressive airway remodeling and irreversible airflow obstruction. Thus, understanding and preventing asthma exacerbations are of paramount importance. Although multiple endotypes exist, asthma is most often driven by type 2 airway inflammation. New therapies that target specific type 2 mediators have been shown to reduce the frequency of asthma exacerbations but are incompletely effective in a significant number of asthmatics. Furthermore, it remains unknown whether current treatments lead to sustained changes in the airway or if targeting additional pathways may be necessary to achieve asthma remission. Activation of innate immunity is the initial event in the inflammatory sequence that occurs during an asthma exacerbation. However, there continue to be critical gaps in our understanding of the innate immune response to asthma exacerbating factors. In this review, we summarize the current understanding of the role of innate immunity in asthma exacerbations and the methods used to study them. We also identify potential novel therapeutic targets for asthma and future areas for investigation.

Two distinct fetal-type signatures characterize juvenile myelomonocytic leukemia

Juvenile myelomonocytic leukemia (JMML) is an aggressive clonal myeloproliferative neoplasm that affects infants and young children. The narrow window of onset suggests that age-related factors are involved in leukemogenesis. To investigate whether ontogeny-related features are involved in JMML oncogenesis, we compared the gene expression profile of hematopoietic progenitor cells isolated from JMML patients with that of healthy individuals at different stages of ontogeny. This analysis identified two main groups of JMML patients. In the first group, JMML progenitors exhibited a gene expression profile similar to that of embryo-fetal progenitors. Progenitors showed a strong monocytic identity as evidenced by the overexpression of monocytic/dendritic, inflammasome, and innate immune markers. This resembled the monocyte-predominant myelopoiesis characteristic of normal fetal hematopoiesis. However, in the second group, despite evidence of developmental dysregulation as indicated by the aberrant signature of the master oncofetal regulator LIN28B, JMML clustered separately from healthy prenatal and postnatal fractions. These findings highlight the intricate relationship between JMML and development, which will help inform future therapeutic approaches for this rare but severe form of leukemia.

Recent advances on immunity and hypertension: the new cells on the kidney block

Over the past 50 years, the contribution of the immune system has been identified in the development of hypertension and renal injury. Both human and experimental animal models of hypertension have demonstrated that innate and adaptive immune cells, along with their cytokines and chemokines, modulate blood pressure fluctuations and end organ renal damage. Numerous cell types of the innate immune system, specifically monocytes, macrophages, and dendritic cells, present antigenic peptides to T cells, promoting inflammation and the elevation of blood pressure. These T cells and other adaptive immune cells migrate to vascular and tubular cells of the kidney and promote end-organ fibrosis, damage, and ultimately hypertensive injury. Through the development of high-throughput screening, novel renal and immune cell subsets have been identified as possible contributors and regulators of renal injury and hypertension. In this review, we will consider classical immunological cells and their contribution to renal inflammation, and novel cell subsets, including renal stromal cells, that could potentially shed new light on renal injury and hypertension. Finally, we will discuss how interorgan inflammation contributes to the development of hypertension and hypertension-related multiorgan damage, and explore the clinical implications of the immunological components of renal injury and hypertension.

Single-Cell Transcriptomic Profile of Innate Cell Populations in Mesenteric Lymph Nodes of Inflammatory Bowel Disease Patients

BACKGROUND AND AIMS

Innate immune cells, including dendritic cells (DCs), monocytes (Mono), macrophages (Mac), natural killer (NK), and innate lymphoid cells (ILC), contribute to chronic inflammation in lymphoid tissues. Here, we characterized the innate immune cell landscape in inflamed mesenteric lymph nodes (MLNs) of patients with inflammatory bowel diseases (IBD) at the single-cell level.

METHODS

Surgically resected colonic MLNs were obtained from patients with Crohn's disease (CD; n = 3), ulcerative colitis (UC; n = 3), non-inflamed UC (n = 1), and non-IBD (n = 2). CD45+CD3-CD19- non-T/non-B cells were FACS-sorted to capture rare innate immune cells. Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) was performed on the BD Rhapsody platform alongside multiparameter flow cytometry staining.

RESULTS

CITE-seq analysis unveiled the molecular signature of 11 Mono/Mac/DC (MMDC) and 7 NK/ILC enriched clusters in human MLNs. DC clusters included 3 newly characterized DC clusters such as CD1c/CD163/VCAN/CD64-expressing DC3; AXL-expressing DCs; and a CD103+ DC subset, expressing LTB, S100B, and IL22RA2 (encoding IL22BP). Mono/Mac clusters comprised inflammatory monocytes, which accumulated in IBD compared to non-IBD MLNs. Among NK/ILC clusters, we identified a cytotoxic ILC subset (IL7R, KLRD1, GNLY), previously not reported in MLNs, reminiscent of cytotoxic ILC1-like cells found in inflamed gut mucosa.

CONCLUSION

CITE-seq and flow-cytometry analyses of colonic MLNs from patients with active IBD reveal the molecular signature and cell distribution of previously uncharacterized DC and ILC subpopulations in human MLNs. These findings expand our understanding of immune responses during chronic inflammation in IBD.

Single-cell analysis of CD14+CD16+ monocytes identifies a subpopulation with an enhanced migratory and inflammatory phenotype

Monocytes in the central nervous system (CNS) play a pivotal role in surveillance and homeostasis, and can exacerbate pathogenic processes during injury, infection, or inflammation. CD14+CD16+ monocytes exhibit diverse functions and contribute to neuroinflammatory diseases, including HIV-associated neurocognitive impairment (HIV-NCI). Analysis of human CD14+CD16+ monocytes matured in vitro by single-cell RNA sequencing identified a heterogenous population of nine clusters. Ingenuity pathway analysis of differentially expressed genes in each cluster identified increased migratory and inflammatory pathways for a group of clusters, which we termed Group 1 monocytes. Group 1 monocytes, distinguished by increased ALCAM, CD52, CD63, and SDC2, exhibited gene expression signatures implicated in CNS inflammatory diseases, produced higher levels of CXCL12, IL-1Ra, IL-6, IL-10, TNFα, and ROS, and preferentially transmigrated across a human in vitro blood-brain barrier model. Thus, Group 1 cells within the CD14+CD16+ monocyte subset are likely to be major contributors to neuroinflammatory diseases.

Ebola Virus Infection of Flt3-Dependent, Conventional Dendritic Cells and Antigen Cross-presentation Leads to High Levels of T-Cell Activation

BACKGROUND

Previous studies have described that Ebola virus (EBOV) infection of human monocyte-derived dendritic cells (moDCs) inhibits dendritic cell (DC) maturation, resulting in poor T-cell activation. However, it is unknown how other DC subsets distinct from moDCs respond to EBOV infection.

METHODS

To better understand how DCs initiate T-cell activation during EBOV infection, we assessed the response of conventional mouse DCs (cDCs) to EBOV infection utilizing a recombinant EBOV expressing the model antigen ovalbumin.

RESULTS

In contrast to moDCs, mouse cDC2s and cDC1s were poorly infected with EBOV but were highly activated. DCs were able to prime CD8 T cells via cross-presentation of antigens obtained from cell debris of EBOV-infected cells. EBOV infection further enhanced DC cross-presentation.

CONCLUSIONS

Our findings indicate that EBOV infection of cDCs results in activation rather than inhibition, leading to high levels of T-cell activation. With that we propose a mechanistic explanation for the excess T-cell activation observed in human Ebola virus disease.

scCobra allows contrastive cell embedding learning with domain adaptation for single cell data integration and harmonization

The rapid advancement of single-cell technologies has created an urgent need for effective methods to integrate and harmonize single-cell data. Technical and biological variations across studies complicate data integration, while conventional tools often struggle with reliance on gene expression distribution assumptions and over-correction. Here, we present scCobra, a deep generative neural network designed to overcome these challenges through contrastive learning with domain adaptation. scCobra effectively mitigates batch effects, minimizes over-correction, and ensures biologically meaningful data integration without assuming specific gene expression distributions. It enables online label transfer across datasets with batch effects, allowing continuous integration of new data without retraining. Additionally, scCobra supports batch effect simulation, advanced multi-omic integration, and scalable processing of large datasets. By integrating and harmonizing datasets from similar studies, scCobra expands the available data for investigating specific biological problems, improving cross-study comparability, and revealing insights that may be obscured in isolated datasets.

Advancements in single-cell RNA sequencing and spatial transcriptomics: transforming biomedical research

In recent years, significant advancements in biochemistry, materials science, engineering, and computer-aided testing have driven the development of high-throughput tools for profiling genetic information. Single-cell RNA sequencing (scRNA-seq) technologies have established themselves as key tools for dissecting genetic sequences at the level of single cells. These technologies reveal cellular diversity and allow for the exploration of cell states and transformations with exceptional resolution. Unlike bulk sequencing, which provides population-averaged data, scRNA-seq can detect cell subtypes or gene expression variations that would otherwise be overlooked. However, a key limitation of scRNA-seq is its inability to preserve spatial information about the RNA transcriptome, as the process requires tissue dissociation and cell isolation. Spatial transcriptomics is a pivotal advancement in medical biotechnology, facilitating the identification of molecules such as RNA in their original spatial context within tissue sections at the single-cell level. This capability offers a substantial advantage over traditional single-cell sequencing techniques. Spatial transcriptomics offers valuable insights into a wide range of biomedical fields, including neurology, embryology, cancer research, immunology, and histology. This review highlights single-cell sequencing approaches, recent technological developments, associated challenges, various techniques for expression data analysis, and their applications in disciplines such as cancer research, microbiology, neuroscience, reproductive biology, and immunology. It highlights the critical role of single-cell sequencing tools in characterizing the dynamic nature of individual cells.

scHNTL: single-cell RNA-seq data clustering augmented by high-order neighbors and triplet loss

MOTIVATION

The rapid development of single-cell RNA sequencing (scRNA-seq) has significantly advanced biomedical research. Clustering analysis, crucial for scRNA-seq data, faces challenges including data sparsity, high dimensionality, and variable gene expressions. Better low-dimensional embeddings for these complex data should maintain intrinsic information while making similar data close and dissimilar data distant. However, existing methods utilizing neural networks typically focus on minimizing reconstruction loss and maintaining similarity in embeddings of directly related cells, but fail to consider dissimilarity, thus lacking separability and limiting the performance of clustering.

RESULTS

We propose a novel clustering algorithm, called scHNTL (scRNA-seq data clustering augmented by high-order neighbors and triplet loss). It first constructs an auxiliary similarity graph and uses a Graph Attentional Autoencoder to learn initial embeddings of cells. Then it identifies similar and dissimilar cells by exploring high-order structures of the similarity graph and exploits a triplet loss of contrastive learning, to improve the embeddings in preserving structural information by separating dissimilar pairs. Finally, this improvement for embedding and the target of clustering are fused in a self-optimizing clustering framework to obtain the clusters. Experimental evaluations on 16 real-world datasets demonstrate the superiority of scHNTL in clustering over the state-of-the-arts single-cell clustering algorithms.

AVAILABILITY AND IMPLEMENTATION

Python implementation of scHNTL is available at Figshare (https://doi.org/10.6084/m9.figshare.27001090) and Github (https://github.com/SWJTU-ML/scHNTL-code).

Characteristics of a CCL21 Gene-Modified Dendritic Cell Vaccine Utilized for a Clinical Trial in Non-Small Cell Lung Cancer

The treatment of non-small cell lung cancer has made major strides with the use of immune checkpoint inhibitors; however, there remains a significant need for therapies that can overcome immunotherapy resistance. Dendritic cell (DC) vaccines have been proposed as a therapy that can potentially enhance the antitumor immune response. We have embarked on a phase I clinical trial of a vaccine consisting of monocyte-derived DCs (moDC) modified to express the chemokine C-C motif chemokine ligand 21 (CCL21-DC) given in combination with pembrolizumab. In this study, we report a comprehensive characterization of this CCL21-DC vaccine and interrogate the effects of multiple factors in the manufacturing process. We show that the cellular makeup of the CCL21-DC vaccine is heterogeneous because of the presence of passenger lymphocytes at a proportion that is highly variable among patients. Single-cell RNA sequencing of vaccines revealed further heterogeneity within the moDC compartment, with cells spanning a spectrum of DC phenotypes. Transduction with a CCL21-containing adenoviral vector augmented CCL21 secretion by moDCs, but otherwise had a minimal effect on vaccine characteristics. A single freeze-thaw cycle for stored vaccines was associated with minor alterations to the DC phenotype, as was the use of healthy donors rather than patient autologous blood. Our results highlight important considerations for the production of DC vaccines and identify underexplored factors that may affect their efficacy and immunologic impact.

Altered Monocyte Populations and Activation Marker Expression in Children with Autism and Co-Occurring Gastrointestinal Symptoms

Autism spectrum disorder (ASD) is an early-onset neurodevelopmental condition that now impacts 1 in 36 children in the United States and is characterized by deficits in social communication, repetitive behaviors, and restricted interests. Children with ASD also frequently experience co-morbidities including anxiety and ADHD, and up to 80% experience gastrointestinal (GI) symptoms such as constipation, diarrhea, and/or abdominal pain. Systemic immune activation and dysregulation, including increased pro-inflammatory cytokines, are frequently observed in ASD. Evidence has shown that the innate immune system may be impacted in ASD, as altered monocyte gene expression profiles and cytokine responses to pattern recognition ligands have been observed compared to typically developing (TD) children. In humans, circulating monocytes are often categorized into three subpopulations-classical, transitional (or "intermediate"), and nonclassical monocytes, which can vary in functions, including archetypal inflammatory and/or reparative functions, as well as their effector locations. The potential for monocytes to contribute to immune dysregulation in ASD and its comorbidities has so far not been extensively studied. This study aims to determine whether these monocyte subsets differ in frequency in children with ASD and if the presence of GI symptoms alters subset distribution, as has been seen for T cell subsets. Whole blood from ASD children with (ASD+GI+) and without gastrointestinal symptoms (ASD+GI-) and their TD counterparts was collected from children enrolled in the Childhood Autism Risk from Genetics and Environment (CHARGE) study. Peripheral blood mononuclear cells were isolated and stained for commonly used subset identifiers CD14 and CD16 as well as activation state markers CCR2, HLA-DR, PD-1, and PD-L1 for flow cytometry analysis. We identified changes in monocyte subpopulations and their expression of surface markers in children with ASD compared to TD children. These differences in ASD appear to be dependent on the presence or absence of GI symptoms. We found that the ASD+GI+ group have a different monocyte composition, evident in their classical, transitional, and nonclassical populations, compared to the ASD+GI- and TD groups. Both the ASD+GI+ and ASD+GI- groups exhibited greater frequencies of classical monocytes compared to the TD group. However, the ASD+GI+ group demonstrated lower frequencies of transitional and nonclassical monocytes than their ASD+GI- and TD counterparts. CCR2+ classical monocyte frequencies were highest in the ASD+GI- group. HLA-DR+ classical, transitional, and nonclassical monocytes were statistically comparable between groups, however, HLA-DR- nonclassical monocyte frequencies were lower in both ASD groups compared to TD. The frequency of classical monocytes displaying exhaustion markers PD-1 and PD-L1 were increased in the ASD+GI+ group compared to ASD+GI- and TD, suggesting potentially impaired ability for clearance of foreign pathogens or debris, typically associated with worsened inflammation. Taken together, the findings of differential proportions of the monocyte subpopulations and altered surface markers may explain some of the characteristics of immune dysregulation, such as in the gastrointestinal tract, observed in ASD.

Towards the Next Generation of Data-Driven Therapeutics Using Spatially Resolved Single-Cell Technologies and Generative AI

Recent advances in multi-omics and spatially resolved single-cell technologies have revolutionised our ability to profile millions of cellular states, offering unprecedented opportunities to understand the complex molecular landscapes of human tissues in both health and disease. These developments hold immense potential for precision medicine, particularly in the rational design of novel therapeutics for treating inflammatory and autoimmune diseases. However, the vast, high-dimensional data generated by these technologies present significant analytical challenges, such as distinguishing technical variation from biological variation or defining relevant questions that leverage the added spatial dimension to improve our understanding of tissue organisation. Generative artificial intelligence (AI), specifically variational autoencoder- or transformer-based latent variable models, provides a powerful and flexible approach to addressing these challenges. These models make inferences about a cell's intrinsic state by effectively identifying complex patterns, reducing data dimensionality and modelling the biological variability in single-cell datasets. This review explores the current landscape of single-cell and spatial multi-omics technologies, the application of generative AI in data analysis and modelling and their transformative impact on our understanding of autoimmune diseases. By combining spatial and single-cell data with advanced AI methodologies, we highlight novel insights into the pathogenesis of autoimmune disorders and outline future directions for leveraging these technologies to achieve the goal of AI-powered personalised medicine.