The biological function and significance of CD74 in immune diseases

Glucosylated cholesterol accumulates in atherosclerotic lesions and impacts macrophage immune response

Atherosclerosis can be described as a local acquired lysosomal storage disorder (LSD), resulting from the build-up of undegraded material in lysosomes. Atherosclerotic foam cells accumulate cholesterol (Chol) and glycosphingolipids (GSLs) within lysosomes. This constitutes the ideal milieu for the formation of a side product of lysosomal storage: glucosylated cholesterol (GlcChol), previously found in several LSDs. Using LC-MS/MS, we demonstrated that GlcChol is abundant in atherosclerotic lesions. Patients suffering from cardiovascular diseases presented unaltered plasma GlcChol levels but slightly elevated GlcChol/Chol ratios. Furthermore, we mimicked GlcChol formation in vitro by exposing macrophages (Mφ) to a pro-atherogenic oxidized cholesteryl ester, an atherosclerosis foam cell model. Additionally, Mφ exposed to GlcChol exhibited an enlarged and multinucleated phenotype. These Mφ present signs of decreased proliferation and reduced pro-inflammatory capacity. Mechanistically the process seems to be associated with the activation of the AMPK signalling pathway and the cyclin-dependent kinase inhibitor 1 (CDKN1A/p21), in response to DNA damage inflicted by reactive oxygen species (ROS). At the organelle level, exposure to GlcChol impacted the lysosomal compartment, resulting in the activation of the mTOR signalling pathway and lysosomal biogenesis mediated by the transcription factor EB (TFEB). This suggests that high concentrations of GlcChol impact cellular homeostasis. In contrast, under this threshold GlcChol formation most likely represents a relatively innocuous compensatory mechanism to cope with Chol and GSL build-up within lesions. Our findings demonstrate that glycosidase-mediated lipid modifications may play a role in the aetiology of genetic and acquired LSDs, warranting further investigation.

A three-subtype prognostic classification based on base excision repair and oxidative stress genes in lung adenocarcinoma and its relationship with tumor microenvironment

Unrepaired DNA damage is the initiation of mutation and tumor-specific biological characteristics. Oxidative stress and base excision repair (BER) are the two main pathways to cope with oxidative DNA damage, which is closely related to the heterogeneity of Lung adenocarcinoma (LUAD), but their relationship with tumor biological characteristics is unclear, and a molecular subtyping based on comprehensive BER and oxidative stress gene expression is lacking. 501 samples from The Cancer Genome Atlas (TCGA) were classified into three subtypes based on genes related to BER and oxidative stress through hierarchical agglomerative cluster analysis. By integrating the nearest template prediction (NTP), four GEO datasets and 52 samples from our institution were analyzed for validation. Bioinformatic analysis was performed to define the diverse molecular characteristics, mutation background, tumor microenvironment, and prognosis. Three subtypes with distinct gene signatures were identified: relatively high BER and low oxidative stress gene expression (C1), low BER gene and high oxidative stress gene expression (C2), and high expression of both BER and oxidative stress genes (C3). C2 was characterized by a low mutation frequency in TP53 (29%) and a high mutation frequency in EGFR (20%), whereas a high frequency of mutation was seen in C3 in STK11 and KEAP1 genes. Additionally, differentially expressed genes among the three subtypes were particularly enriched in immune-related pathways, and the abundance of immune cells and Immunophenoscore were significantly higher in C2, while the Tumor Immune Dysfunction and Exclusion (TIDE) score was lower in C2, indicating a better response to immunotherapy. C2 was also associated with an improved survival outcome compared with C1 and C3, and this finding was validated in 978 samples from four independent GEO datasets and 52 samples at our institution by the NTP algorithm. The three-subtype classifications based on BER and oxidative stress gene expression offers potential for predicting the survival and response to immunotherapy of LUAD patients.

Single cell RNA-sequencing identified CCR7+/RELB+/IRF1+ T cell responding for juvenile idiopathic arthritis pathogenesis

Background

To further explore the disease heterogeneity of different subtypes of Juvenile idiopathic arthritis (JIA) and analyze their pathogenesis mechanisms.

Method

The single-cell RNA sequencing (scRNA-seq) analysis of peripheral blood mononuclear cells (PBMCs) was carried out to investigate the disease heterogeneity and molecular mechanisms of immune responses in immune cells in JIA.

Result

In our study, we provided a immunological landscape of HLA-B27-positive JIA and HLA-B27-negative JIA immune cells at single cell RNA-Seq resolution. We found a higher proportion of CCR7+/RELB+/IRF1+ triple positive T cells in the peripheral blood of patients with JIA, and such T cells were predominantly present in HLA-B27+ JIA patients. Furthermore, we hypothesized that CCR7+/RELB+/IRF1+ triple positive T cells were highly activated T cells capable of promoting the differentiation of osteoclasts by producing IL-17, thus causing damage to cartilage in HLA-B27+ JIA patients. Unlike JIA patients, CCR7+/RELB+/IRF1+ triple positive T cells were not found in the peripheral blood of pSS patients and SLE patients, moreover, T cells from pSS patients and SLE patients were less able to produce IL-17 than those from JIA patients.

Conclusion

Our study provided evidence of cellular and molecular levels of involvement in JIA pathogenesis and identified the critical roles for T cells in JIA pathogenesis. Furthermore, our results suggested that there were significant differences in T cell composition and gene expression between HLA-B27+ JIA patients and HLA-B27- JIA patients. Our findings indicated that CCR7+/RELB+/IRF1+ positive T cells could damage the cartilage of HLA-B27+ JIA by producing cytokines such as IL-17.

The immunosuppressive role of VSIG4 in colorectal cancer and its interaction with the tumor microenvironment

BACKGROUND

The tumor microenvironment in colorectal cancer (CRC) significantly influences disease progression and immune responses, particularly the role of macrophages in regulating immune evasion requires further investigation.

METHODS

This study integrated data from the TCGA-COAD dataset with the GEO database, along with single-cell RNA sequencing data, to systematically analyze key genes in colorectal cancer. R software was utilized for data normalization and differential analysis, with criteria set at ∣log2FoldChange ∣ > 1 and adjusted p-value < 0.05 for gene selection. The Seurat package was employed for clustering single-cell data, while the "Monocle2" algorithm was used to perform pseudo-time analysis on the differentiation trajectory of macrophages. Additionally, non-negative matrix factorization (NMF) was applied for subtype classification of CRC patients, and various machine learning algorithms (such as LASSO and random forest models) were utilized to identify key pathogenic genes. Finally, PCR was employed to validate the expression of these key genes, and immune analysis software was used to assess their impact on immune cells, alongside pathway enrichment analysis.

RESULTS

Through the integration of multi-omics data, we identified significant differential expression of VSIG4, CYBBC3AR1, and FCGR1A in CRC patients. LASSO and random forest models selected these three genes as critical pathogenic factors for CRC, with AUC values exceeding 0.8 across multiple machine learning models, demonstrating their high diagnostic efficacy. PCR validation further supported the differential expression of VSIG4 and other genes in CRC. Single-cell transcriptomic analysis revealed that VSIG4 was highly enriched in specific macrophage subpopulations and significantly influenced the tumor microenvironment by regulating CD8 + T cell immune exhaustion. Pseudo-time analysis indicated that the differentiation trajectory of macrophages during tumor progression was closely associated with VSIG4 expression. Additionally, cell communication analysis. highlighted the important role of VSIG4 in the interactions between macrophages and endothelial cells. Pathway enrichment analysis demonstrated that VSIG4 expression was closely linked to the regulation of the JAK-STAT pathway and metabolic pathways such as the TCA cycle.

CONCLUSION

This study provides the first evidence that VSIG4, CYBBC3AR1, and FCGR1A play critical roles in the immune microenvironment of colorectal cancer, particularly emphasizing the immunoregulatory function of VSIG4 in macrophage activity and CD8 + T cell immune exhaustion. PCR validation further confirmed the differential expression of these genes. These findings offer new insights into the molecular mechanisms of CRC and provide a potential theoretical basis for targeting VSIG4 in immunotherapy.

Exploring the role of the CD74+ cardiac macrophage subset in trastuzumab cardiotoxicity and its mechanisms

Trastuzumab (TRZ) is the standard treatment for human epidermal growth factor receptor 2 (HER-2) positive breast cancer, but its cardiotoxicity significantly impacts the prognosis and quality of survival of patients, and the underlying mechanism of TRZ-related cardiotoxicity remains incompletely understood. Macrophage subsets better reflect macrophage heterogeneity than the traditional macrophage M1/M2 type polarization classification. CD74, a receptor with strong binding affinity for macrophage migration inhibitory factor, plays an important role in macrophage activation. After successfully constructing a mouse TRZ cardiotoxicity model, flow cytometry indicated that CD74+ cardiac macrophages (CMφs) were significantly elevated in the TRZ group. Single-cell data were utilized to identify CD74+ CMφs, GO and KEGG analyses of the DEGs were conducted to further validate the CD74/STAT1 signaling pathway. Analyses using RT-PCR, immunofluorescence, and western blot revealed a marked increase in the expression of genes and proteins linked to this pathway in TRZ-treated group. Additionally, levels of inflammation-related factors and the expression of apoptotic proteins was elevated following TRZ treatment. CD74-knockdown RAW 264.7 macrophages cell line were constructed via Lentiviruses carrying CD74 (hU6-MCS-CBh-gcGFP-IRES-puromycin) transfection and co-cultured with HL-1 cardiomyocytes to establish an in vitro TRZ cardiotoxicity model. Western blot analysis of CD74/STAT1 signaling pathway protein levels demonstrated that CD74 knockdown rescued TRZ-induced cellular damage. These findings suggest that TRZ may promote inflammation and apoptosis in cardiomyocytes, leading to cardiotoxicity through the CD74+ CMφ subset, which regulates the CD74/STAT1 signaling pathway. CD74+ CMφs are anticipated to be a novel intervention target and therapeutic strategy for addressing TRZ-induced cardiotoxicity.

Preclinical in vitro and in vivo evidence for targeting CD74 as an effective treatment strategy for cutaneous T-cell lymphomas

BACKGROUND

Prognosis and quality of life in patients with advanced cutaneous T-cell lymphoma (CTCL), particularly in those with Sézary syndrome (SS) or advanced-stage mycosis fungoides (MF), are poor. Monoclonal antibodies or antibody-drug conjugates (ADCs) have been added into CTCL treatment algorithms, but the spectrum of antibody-targetable cell surface antigens in T-cell non-Hodgkin lymphomas (T-NHLs) is limited.

OBJECTIVES

To evaluate the expression of the major histocompatibility complex class II chaperone CD74 in common subtypes of CTCL by various methods, and to explore the efficacy of targeting CD74 in CTCL cells with an anti-CD74 ADC in vitro and in vivo.

METHODS

We comprehensively investigated the expression of CD74 in well-defined CTCL cell lines by polymerase chain reaction, immunoblotting and flow cytometry. More than 140 primary CTCL samples of all common subtypes were analysed by immunohistochemistry, flow cytometry, immunofluorescence and 'co-detection by indexing' (CODEX) multiplexed tissue imaging, as well as by single-cell RNA sequencing (scRNAseq) analyses. DNA methylation of CTCL cell lines was interrogated by the generation of genome-wide methylation profiling. The effect of a maytansinoid-conjugated humanized ADC against CD74 was investigated in CTCL cell lines in vitro, alone or in combination with gemcitabine, and in vivo after xenotransplantation of CTCL cell lines in NOD-scid Il2rgnull mice.

RESULTS

We demonstrated that CD74 is widely and robustly expressed in CTCL cells. In addition, CD74 expression in SS and MF was confirmed by scRNAseq data analysis and was correlated in CTCL cell lines with CD74 DNA hypomethylation. CD74 was rapidly internalized in CTCL cells and CD74 targeting by the ADC STRO-001 efficiently killed CTCL-derived cell lines. Finally, targeting of CD74 synergized with conventional chemotherapy in vitro and eradicated murine xenotransplants of CTCL cell lines in vivo.

CONCLUSIONS

CD74 is expressed in common CTCL subtypes. Targeting CD74 efficiently killed CTCL cells in vitro and in vivo. We therefore suggest the targeting of CD74 to be a highly promising treatment strategy for CTCL.

Persistent and progressive acute lung allograft dysfunction is linked to cell compositional and transcriptional changes in small airways

BACKGROUND

Acute lung allograft dysfunction (ALAD) is a clinical syndrome of forced expiratory volume in 1-second (FEV1) decline concerning for chronic lung allograft dysfunction (CLAD) onset. Novel diagnostic tools are needed to identify those with ALAD who will progress to CLAD and to target appropriate therapies. We hypothesized that progressive ALAD would be associated with changes in small airway cell composition and cell-specific transcription.

METHODS

We prospectively identified recipients with undifferentiated ALAD and controls with stable allograft function for small airway brushing and single-cell RNA sequencing analysis. ALAD outcome group was categorized as (1) control (n = 8), or ALAD with (2) recovered (n = 4), (3) persistent (n = 5), or (4) progressive (n = 3) FEV1 decline. Cell compositional changes, pseudobulk Reactome pathways, and the AI2 score, previously linked to CLAD in airway brush transcriptomes, were assessed as a function of ALAD outcome group.

RESULTS

Across 68,140 cells, the distribution of cell composition was linked to ALAD outcome group (PERMANOVA, p = 0.004). Worse ALAD outcomes correlated with loss of basal cells, changes in club and ciliated subsets, a loss of macrophages, and expansion of cytotoxic T cells. The AI2 gene score was positively associated with ALAD outcome group, particularly in epithelial cell subsets (p < 0.001). Pathway analysis showed increased interferon signaling and inhibition of cell proliferation in epithelial cells.

CONCLUSIONS

In this pilot study, persistent and progressive ALAD was associated with changes in bronchiolar cell composition and transcriptional programs. Molecular phenotyping may help identify and characterize individuals with ALAD at increased risk for progression.

Novel Identification of CD74 as a Biomarker for Diagnosing and Prognosing Sepsis Patients

Purpose

Sepsis, a life-threatening inflammatory condition due to an imbalanced response to infections, has been a major concern. Necroptosis, a newly discovered programmed cell death form, plays a crucial role in various inflammatory diseases. Our study aims to identify necroptosis - related genes (NRGs) and explore their potential for sepsis diagnosis.

Patients and methods

We used weighted gene co-expression network analysis to identify gene modules associated with sepsis. Cox regression and Kaplan-Meier methods were employed to assess the diagnostic and prognostic value of these genes. Single-cell and immune infiltration analyses were carried out to explore the immune environment in sepsis. Plasma CD74 protein levels were quantified in our samples, and relevant clinical data from electronic patient records were analyzed for correlation.

Results

CD74 was identified through the intersection of the hub genes of sepsis and NRGs related modules. Septic patients had lower CD74 expression compared to healthy controls. The CD74-based diagnostic model showed better performance in the training dataset (AUC, 0.79 [95% CI, 0.75-0.84]), was cross-validated in external datasets, and demonstrated better performances than other published diagnostic models. Pathway analysis and single-cell profiling supported further exploration of CD74-related inflammation and immune response in sepsis.

Conclusion

This study presents the first quantitative assessment of human plasma CD74 in sepsis patients. CD74 levels were significantly lower in the sepsis cohort. CD74 warrants further exploration as a potential prognostic and therapeutic target for sepsis.

Functional analysis of yak alveolar type II epithelial cells at high and low altitudes based on single-cell sequencing

The adaptation of lung cells to high-altitude environments represents a notable gap in our understanding of how animals cope with hypoxic conditions. Alveolar epithelial cells type II (AEC II) are crucial for lung development and repair. However, their, specific role in the adaptation of yaks to high-altitude environments remains unclear. In this study, we aimed to address this gap by investigating the differential responses of AEC II in yaks at high and low altitudes (4000 m and 2600 m, respectively). We used the 10 × scRNA-seq technology to construct a comprehensive cell atlas of yak lung tissue, and identified 15 distinct cell classes. AEC II in high-altitude yaks revealed increased immunomodulatory, adhesive, and metabolic activities, which are crucial for maintaining lung tissue stability and energy supply under hypoxic conditions. Furthermore, alveolar epithelial progenitor cells within AEC II can differentiate into both Alveolar epithelial cell type I (AEC I) and AEC II. SHIP1 and other factors are promoters of AEC I transdifferentiation, whereas SFTPC and others promote AEC II transdifferentiation. This study provides new insights into the evolutionary adaptation of lung cells in plateau animals by elucidating the molecular mechanisms underlying AEC II adaptation to high-altitude environments.

Analysis of the effect of ALA-PDT on macrophages in footpad model of mice infected with Fonsecaea monophora based on single-cell sequencing

Chromoblastomycosis (CBM) is a chronic neglected fungal disease that causes serious damage to the physical and mental health of patients. 5-Aminolevulinic acid photodynamic therapy (ALA-PDT) has garnered significant attention in the recent era for the treatment of CBM and has exhibited promising effects in several clinical case reports. We established a mice footpad infection model with Fonsecaea monophora and analyzed the impact of PDT treatment on the immune response of macrophages using single-cell sequencing. The results showed that infection of the mouse footpad skin with F. monophora results in an increase in inflammatory cells, primarily mononuclear-macrophages, with the activation of complement and enhancement of cell chemotaxis, leading to upregulation of anti-infection-related pathways. After ALA-PDT treatment, the number of inflammatory cells decreased, while macrophages upregulated the expression of antigen-recognition-related genes, enhancing phagocytosis and autophagy-related biological functions.

Metabolic reprogramming and macrophage expansion define ACPA-negative rheumatoid arthritis: insights from single-cell RNA sequencing

Background

Anti-citrullinated peptide antibodies (ACPA)-negative (ACPA-) rheumatoid arthritis (RA) presents significant diagnostic and therapeutic challenges due to the absence of specific biomarkers, underscoring the need to elucidate its distinctive cellular and metabolic profiles for more targeted interventions.

Methods

Single-cell RNA sequencing data from peripheral blood mononuclear cells (PBMCs) and synovial tissues of patients with ACPA- and ACPA+ RA, as well as healthy controls, were analyzed. Immune cell populations were classified based on clustering and marker gene expression, with pseudotime trajectory analysis, weighted gene co-expression network analysis (WGCNA), and transcription factor network inference providing further insights. Cell-cell communication was explored using CellChat and MEBOCOST, while scFEA enabled metabolic flux estimation. A neural network model incorporating key genes was constructed to differentiate patients with ACPA- RA from healthy controls.

Results

Patients with ACPA- RA demonstrated a pronounced increase in classical monocytes in PBMCs and C1QChigh macrophages (p < 0.001 and p < 0.05). Synovial macrophages exhibited increased heterogeneity and were enriched in distinct metabolic pathways, including complement cascades and glutathione metabolism. The neural network model achieved reliable differentiation between patients with ACPA- RA and healthy controls (AUC = 0.81). CellChat analysis identified CD45 and CCL5 as key pathways facilitating macrophage-monocyte interactions in ACPA- RA, prominently involving iron-mediated metabolite communication. Metabolic flux analysis indicated elevated beta-alanine and glutathione metabolism in ACPA- RA macrophages.

Conclusion

These findings underscore that ACPA-negative rheumatoid arthritis is marked by elevated classical monocytes in circulation and metabolic reprogramming of synovial macrophages, particularly in complement cascade and glutathione metabolism pathways. By integrating single-cell RNA sequencing with machine learning, this study established a neural network model that robustly differentiates patients with ACPA- RA from healthy controls, highlighting promising diagnostic biomarkers and therapeutic targets centered on immune cell metabolism.

Antibiotic use attenuates response to immune checkpoint blockade in urothelial carcinoma via inhibiting CD74-MIF/COPA: revealing cross-talk between anti-bacterial immunity and ant-itumor immunity

BACKGROUND

Immune checkpoint blockade (ICB) has emerged as a promising therapy for both resectable urothelial carcinoma (UC) patients preparing for radical surgery and unresectable UC patients, whereas the objective response rate of ICB remains unsatisfactory due to various factors. Antibiotic (ATB) use can influence intratumoral bacteria, which may further reduce ICB efficacy. The study aims to evaluate the effects of ATB use on prognosis and response in UC patients undergoing ICB, and explore potential molecular mechanisms of ATBs and intratumoral bacteria impacting UC immune microenvironment.

MATERIALS AND METHODS

Pooled analyses, synthesizing evidence from 3496 UC patients with ICB treatment, were conducted. In addition, single-cell RNA and single-cell microbiome data were analyzed based on eight UC samples and 63 185 single cells. Bulk RNA sequencing and clinical data from a single-arm, multicenter, atezolizumab-treated, phase 2 trial, IMvigor210, were used for validation.

RESULTS

ATB use exhibited worse overall survival (HR=1.46, 95% CI=[1.20-1.77], P <0.001 and lower objective response (OR=0.43, 95% CI=[0.27-0.68], P <0.001 in UC patients receiving ICB. Single-cell transcriptome and single-cell microbiome analyses identified the presence of intratumoral bacteria was obviously related to elevated antibacterial immune functions; and antibacterial immunity was positively correlated to antitumor immunity in UC immune microenvironment. Intratumoral bacteria could up-regulate CD74-MIF/COPA signaling of immune cells and activation of CD74-MIF/COPA mediated the promotion of T cell antitumor function induced by antibacterial immune cells. UC patients with higher CD74-MIF/COPA signaling carried better overall survival (HR=1.60, 95% CI=[1.19-2.15], P =0.002) in immunotherapy cohort.

CONCLUSION

ATB use reduces overall survival and objective response to ICB in UC patients. Antibacterial immune cell functions induced by intracellular bacteria in the UC microenvironment might up-regulate the function of antitumor T immune cells via activating CD74-MIF/COPA , whereas ATB could inhibit the above process through killing intracellular bacteria and result in poorer clinical benefit of ICB. The use of ATB should be considered carefully during the neoadjuvant immunotherapy period for resectable UC patients preparing for radical surgery and during the immunotherapy period for unresectable UC patients.

PPARα agonist ameliorates cholestatic liver injury by regulating hepatic macrophage homeostasis

Inflammatory response plays an essential role in the pathogenesis of cholestatic liver injury. PPARα agonists have been shown to regulate bile acid homeostasis and hepatic inflammation. However, the immunoregulatory mechanisms through which PPARα agonists ameliorate cholestatic liver injury remain unclear. In this study, surgical bile duct ligation was performed to establish a mouse model of cholestasis. Our study revealed that PPARα agonist alleviated cholestatic liver injury in mice by suppressing inflammatory response, reducing neutrophil infiltration, and promoting M2-like macrophage polarization. CyTOF analysis showed that PPARα agonist increased the proportion of anti-inflammatory F4/80hiCD44+MHCII- M2-like macrophages while decreasing the proportion of pro-inflammatory CD64+CX3CR1+CCR2hiVISTAhiCD172a+CD44hi M1-like MoMFs. Additionally, scRNA-seq indicated that PPARα agonist regulated the developmental trajectory and homeostasis of hepatic macrophages. Mechanistically, PPARα agonist may influence the expression of immune regulators in heterogeneous macrophages to exert protective effects against cholestasis. In addition, the CCL and MIF signaling pathways may participate in the communication among hepatic immune cells, including macrophages, neutrophils, natural killer cells, and dendritic cells, in response to the PPARα agonist. In conclusions, PPARα agonist alleviated cholestatic liver injury by attenuating the inflammatory response and restoring hepatic macrophage homeostasis. This study might enhance the understanding of the immunoregulatory mechanisms of PPARα agonists, providing promising therapeutic targets for cholestatic liver diseases.

A dynamic peripheral immune landscape during human pregnancy

Extensive immune adaptations occur during pregnancy to ensure successful delivery. However, these changes can increase the risk of disease in the mother. Here, we conducted single-cell RNA sequencing on peripheral blood mononuclear cells from pregnant women at different stages of pregnancy to elucidate the dynamic transcriptional changes in the maternal immune system. Gradual reduced cytotoxicity phenotype in highly variable cytotoxic T and natural killer cell types were observed during pregnancy. Reduced T- and B-cell response-related MHC-II and CD40 signaling as well as enhanced protolerance inducible costimulator and activin signaling may underlie the pregnancy-related weakening of adaptive immunity. Conversely, pro-inflammatory genes and pathways were upregulated in monocytes, possibly to compensate for the reduced T-cell response. Moreover, the transition from adaptive immune reduction to activation in late pregnancy in dendritic cells and CD4+ T cells was also detected. Notably, we proposed a novel view of the pro-aging effect of pregnancy from the perspective of immunity, and this effect may be restored postpartum. This work expands our knowledge of pregnancy immunity and may provide insights into the altered disease risks during pregnancy.

Exosomes derived from microRNA-540-3p overexpressing mesenchymal stem cells promote immune tolerance via the CD74/nuclear factor-kappaB pathway in cardiac allograft

BACKGROUND

Heart transplantation is a crucial intervention for severe heart failure, yet the challenge of organ rejection is significant. Bone marrow mesenchymal stem cells (BMSCs) and their exosomes have demonstrated potential in modulating T cells, dendtitic cells (DCs), and cytokines to achieve immunomodulatory effects. DCs, as key antigen-presenting cells, play a critical role in shaping immune responses by influencing T-cell activation and cytokine production. Through this modulation, BMSCs and their exosomes enhance graft tolerance and prolonging survival.

AIM

To explore the immunomodulatory effects of exosomes derived from BMSCs overexpressing microRNA-540-3p (miR-540-3p) on cardiac allograft tolerance, focusing on how these exosomes modulating DCs and T cells activity through the CD74/nuclear factor-kappaB (NF-κB) pathway.

METHODS

Rat models were used to assess the impact of miR-540-3p-enhanced exosomes on immune tolerance in cardiac allografts. MiR-540-3p expression was manipulated in BMSCs, and derived exosomes were collected and administered to the rat models post-heart transplantation. The study monitored expression levels of major histocompatibility complex II, CD80, CD86, and CD274 in DCs, and quantified CD4+ and CD8+ T cells, T regulatory cells, and cytokine profiles.

RESULTS

Exosomes from miR-540-3p-overexpressing BMSCs lead to reduced expression of immune activation markers CD74 and NF-κB p65 in DCs and T cells. Rats treated with these exosomes showed decreased inflammation and improved cardiac function, indicated by lower levels of pro-inflammatory cytokines (interleukin-1β, interferon-γ) and higher levels of anti-inflammatory cytokines (interleukin-10, transforming growth factor β1). Additionally, miR-540-3p skewed the profiles of DCs and T cells towards immune tolerance, increasing the ratio of T regulatory cells and shifting cytokine secretion to favor graft acceptance.

CONCLUSION

Exosomes derived from BMSCs overexpressing miR-540-3p significantly enhance immune tolerance and prolong cardiac allograft survival by modulating the CD74/NF-κB pathway, which regulates activities of DCs and T cells. These findings highlight a promising therapeutic strategy to improve heart transplantation outcomes and potentially reduce the need for prolonged immunosuppression.

Lethal COVID-19 associates with RAAS-induced inflammation for multiple organ damage including mediastinal lymph nodes

Lethal COVID-19 outcomes are attributed to classic cytokine storm. We revisit this using RNA sequencing of nasopharyngeal and 40 autopsy samples from patients dying of SARS-CoV-2. Subsets of the 100 top-upregulated genes in nasal swabs are upregulated in the heart, lung, kidney, and liver, but not mediastinal lymph nodes. Twenty-two of these are "noncanonical" immune genes, which we link to components of the renin-angiotensin-activation-system that manifest as increased fibrin deposition, leaky vessels, thrombotic tendency, PANoptosis, and mitochondrial dysfunction. Immunohistochemistry of mediastinal lymph nodes reveals altered architecture, excess collagen deposition, and pathogenic fibroblast infiltration. Many of the above findings are paralleled in animal models of SARS-CoV-2 infection and human peripheral blood mononuclear and whole blood samples from individuals with early and later SARS-CoV-2 variants. We then redefine cytokine storm in lethal COVID-19 as driven by upstream immune gene and mitochondrial signaling producing downstream RAAS (renin-angiotensin-aldosterone system) overactivation and organ damage, including compromised mediastinal lymph node function.

Single-cell RNA sequencing reveals heterogeneity and differential expression of the maternal-fetal interface during ICP and normal pregnancy

OBJECTIVE

Intrahepatic cholestasis of pregnancy (ICP) can cause adverse perinatal outcomes. Previous studies have demonstrated that the placenta of an ICP pregnancy differs in morphology and gene expression from the placenta of a normal pregnancy. To date, however, the genetic mechanism by which ICP affects the placenta is poorly understood. Therefore, the aim of this study was to investigate the differences in main cell types, gene signatures, cell ratio, and functional changes in the placenta between ICP and normal pregnancy.

METHODS

Single-cell RNA sequencing (scRNA-seq) technology was used to detect the gene expression of all cells at the placental maternal-fetal interface. Two individuals were analyzed - one with ICP and one without ICP. The classification of cell types was determined by a graph-based clustering algorithm. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the R software phyper () function and DAVID website. The differentially expressed genes (DEGs) encoding transcription factors (TFs) were identified using getorf and DIAMOND software.

RESULTS

We identified 14 cell types and 22 distinct cell subtypes that showed unique functional properties. Additionally, we found differences in the proportions of fibroblasts 1, helper T (Th) cells, extravillous trophoblasts, and villous cytotrophoblasts, and we observed heterogeneity of gene expression between ICP and control placentas. Furthermore, we identified 263 DEGs that belonged to TF families, including zf-C2H2, HMGI/HMGY, and Homeobox. In addition, 28 imprinted genes were preferentially expressed in specific cell types, such as PEG3 and PEG10 in trophoblasts as well as DLK1 and DIO3 in fibroblasts.

CONCLUSIONS

Our results revealed the differences in cell-type ratios, gene expression, and functional changes between ICP and normal placentas, and heterogeneity was found among cell subgroups. Hence, the imbalance of various cell types affects placental activity to varying degrees, indicating the complexity of the cell networks that form the placental tissue system, and this alteration of placental function is associated with adverse events in the perinatal period.

Microglia and monocyte-derived macrophages drive progression of pediatric high-grade gliomas and are transcriptionally shaped by histone mutations

Pediatric high-grade gliomas (pHGGs), including hemispheric pHGGs and diffuse midline gliomas (DMGs), harbor mutually exclusive tumor location-specific histone mutations. Using immunocompetent de novo mouse models of pHGGs, we demonstrated that myeloid cells were the predominant infiltrating non-neoplastic cell population. Single-cell RNA sequencing (scRNA-seq), flow cytometry, and immunohistochemistry illustrated the presence of heterogeneous myeloid cell populations shaped by histone mutations and tumor location. Disease-associated myeloid (DAM) cell phenotypes demonstrating immune permissive characteristics were identified in murine and human pHGG samples. H3.3K27M DMGs, the most aggressive DMG, demonstrated enrichment of DAMs. Genetic ablation of chemokines Ccl8 and Ccl12 resulted in a reduction of DAMs and an increase in lymphocyte infiltration, leading to increased survival of tumor-bearing mice. Pharmacologic inhibition of chemokine receptors CCR1 and CCR5 resulted in extended survival and decreased myeloid cell infiltration. This work establishes the tumor-promoting role of myeloid cells in DMG and the potential therapeutic opportunities for targeting them.

Dissecting L-glutamine metabolism in acute myeloid leukemia: single-cell insights and therapeutic implications

BACKGROUND

Acute myeloid leukemia (AML) is a rapidly progressing blood cancer. The prognosis of AML can be challenging, emphasizing the need for ongoing research and innovative approaches to improve outcomes in individuals affected by this formidable hematologic malignancy.

METHODS

In this study, we used single-cell RNA sequencing (scRNA-seq) from AML patients to investigate the impact of L-glutamine metabolism-related genes on disease progression.

RESULTS

Our analysis revealed increased glutamine-related activity in CD34 + pre-B cells, suggesting a potential regulatory role in tumorigenesis and AML progression. Furthermore, intercellular communication analysis revealed a significant signaling pathway involving macrophage migration inhibitory factor signaling through CD74 + CD44 within CD34 + pre-B cells, which transmit signals to pre-dendritic cells and monocytes. Ligands for this pathway were predominantly expressed in stromal cells, naïve T cells, and CD34 + pre-B cells. CD74, the pertinent receptor, was predominantly detected in a variety of cellular components, including stromal cells, pre-dendritic cells, plasmacytoid dendritic cells, and hematopoietic progenitors. The study's results provide insights into the possible interplay among these cell types and their collective contribution to the pathogenesis of AML. Moreover, we identified 10 genes associated with AML prognosis, including CCL5, CD52, CFD, FABP5, LGALS1, NUCB2, PSAP, S100A4, SPINK2, and VCAN. Among these, CCL5 and CD52 have been implicated in AML progression and are potential therapeutic targets.

CONCLUSIONS

This thorough examination of AML biology significantly deepens our grasp of the disease and presents pivotal information that could guide the creation of innovative treatment strategies for AML patients.

Single-cell sequencing technology to characterize stem T-cell subpopulations in acute T-lymphoblastic leukemia and the role of stem T-cells in the disease process

BACKGROUND

Precursor T-cell acute lymphoblastic leukemia (Pre-T ALL) is a malignant neoplastic disease in which T-cells proliferate in the bone marrow. Single-cell sequencing technology could identify characteristic cell types, facilitating the study of the therapeutic mechanisms in Pre-T ALL.

METHODS

The single-cell sequencing data (scRNA-seq) of Pre-T ALL were obtained from public databases. Key immune cell subpopulations involved in the progression of Pre-T ALL were identified by clustering and annotating the cellular data using AUCell. Next, pseudo-temporal analysis was performed to identify the differentiation trajectories of immune cell subpopulations using Monocle. Copy number mutation landscape of cell subpopulations was characterized by inferCNV. Finally, cellphoneDB was used to analyze intercellular communication relationships.

RESULTS

A total of 10 cellular subpopulations were classified, with Pre-T ALL showing a higher proportion of NK/T cells. NK/T cells were further clustered into two subpopulations. Stem T cells showed a high expression of marker genes related to hematopoietic stem cells, Naive T cells had a high expression of CCR7, CCR7, RCAN3, and NK cells high-expressed KLRD1, TRDC. The cell proliferation was reduced and the activation of T cell was increased during the differentiation of stem T cells to Naive T cells. We observed interaction between stem T cells with dendritic cells such as CD74-COPA, CD74-MIF as well as co-inhibition-related interactions such as LGALS9-HAVCR2, TGFB1-TGFBR3.

CONCLUSION

Stem T cells were involved in the development of Pre-T-ALL through the regulatory effects of transcription factors (TFs) KLF2 and FOS and multiple ligand-receptor pairs.

Identification of immune microenvironment subtypes and clinical risk biomarkers for osteoarthritis based on a machine learning model

Background

Osteoarthritis (OA) is a degenerative disease with a high incidence worldwide. Most affected patients do not exhibit obvious discomfort symptoms or imaging findings until OA progresses, leading to irreversible destruction of articular cartilage and bone. Therefore, developing new diagnostic biomarkers that can reflect articular cartilage injury is crucial for the early diagnosis of OA. This study aims to explore biomarkers related to the immune microenvironment of OA, providing a new research direction for the early diagnosis and identification of risk factors for OA.

Methods

We screened and downloaded relevant data from the Gene Expression Omnibus (GEO) database, and the immune microenvironment-related genes (Imr-DEGs) were identified using the ImmPort data set by combining weighted coexpression analysis (WGCNA). Functional enrichment of GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) were conducted to explore the correlation of Imr-DEGs. A random forest machine learning model was constructed to analyze the characteristic genes of OA, and the diagnostic significance was determined by the Receiver Operating Characteristic Curve (ROC) curve, with external datasets used to verify the diagnostic ability. Different immune subtypes of OA were identified by unsupervised clustering, and the function of these subtypes was analyzed by gene set enrichment analysis (GSVA). The Drug-Gene Interaction Database was used to explore the relationship between characteristic genes and drugs.

Results

Single sample gene set enrichment analysis (ssGSEA) revealed that 16 of 28 immune cell subsets in the dataset significantly differed between OA and normal groups. There were 26 Imr-DEGs identified by WGCNA, showing that functional enrichment was related to immune response. Using the random forest machine learning model algorithm, nine characteristic genes were obtained: BLNK (AUC = 0.809), CCL18 (AUC = 0.692), CD74 (AUC = 0.794), CSF1R (AUC = 0.835), RAC2 (AUC = 0.792), INSR (AUC = 0.765), IL11 (AUC = 0.662), IL18 (AUC = 0.699), and TLR7 (AUC = 0.807). A nomogram was constructed to predict the occurrence and development of OA, and the calibration curve confirmed the accuracy of these 9 genes in OA diagnosis.

Conclusion

This study identified characteristic genes related to the immune microenvironment in OA, providing new insight into the risk factors of OA.

Identification of crucial genes and possible molecular pathways associated with active vitamin D intervention in diabetic kidney disease

Background

A significant cause of advanced renal failure is diabetic nephropathy (DKD), with few treatment options available. Calcitriol shows potential in addressing fibrosis related to DKD, though its molecular mechanisms remain poorly understood. This research seeks to pinpoint the crucial genes and pathways influenced by calcitriol within the scope of DKD-related fibrosis.

Methods

Single-cell gene expression profiling of calcitriol treated DKD rat kidney tissue and screening of fibrosis-associated cell subsets. Mendelian randomization and enrichment analyses (CIBERSORT, GSVA, GSEA, Motif Enrichment) were used to explore gene-immune cell interactions and signaling pathways. Key findings were validated using independent datasets and protein expression data from the Human Protein Atlas.

Results

Calcitriol treatment reduced proliferative cell populations and highlighted the FoxO signaling pathway's role in DKD. SUMO3 and CD74 were identified as key markers linked to immune infiltration and renal function. These genes were significantly associated with creatinine levels and eGFR, indicating their potential role in DKD progression.

Conclusion

Our results suggest that calcitriol modulates DKD fibrosis through the FoxO pathway, with SUMO3 and CD74 serving as potential biomarkers for kidney protection. These results provide fresh insights into strategies for treating DKD.

CD74 is a potential biomarker predicting the response to immune checkpoint blockade

BACKGROUND

Immune checkpoint blockade (ICB) has been improving the patient outcome in multiple cancer types. However, not all patients respond to ICB. Biomarkers are needed for selecting appropriate patients to receive ICB. CD74 is an important chaperone that regulates antigen presentation for immune response. However, the relationship between CD74 expression and ICB response remains elusive.

METHODS

The unified normalized pan-cancer dataset was downloaded from the UCSC database. Wilcoxon Rank Sum Rank Tests were used to analyze the expression differences between normal and tumor samples in each tumor type. Then, the prognostic value of CD74 was determined using univariable Cox proportional hazards regression analysis. The STRING database was utilized to construct the protein-protein interaction (PPI) network of CD74 and the signal pathways were analyzed as well. The correlation of CD74 expression with immune cells and immune regulating genes was investigated in the TIMER database. The TIDE framework was utilized to evaluate the relationship between CD74 expression and the response to immunotherapy. Moreover, the localization of CD74 in the tumor immune microenvironment was verified using multiplex immunohistochemistry. Clinically annotated samples from 38 patients with esophageal cancer treated with neoadjuvant chemotherapy combined with ICB were analyzed for CD74 expression using immunohistochemistry.

RESULTS

In this study, we investigated the prognostic and predictive value of CD74 in different types of cancer. Compared with normal tissue, the expression of CD74 was higher in tumor tissue in various cancers. High expression of CD74 was associated with improved patient prognosis in the majority of cancers. CD74 and its interacting proteins were mainly enriched in the immune-related pathways. The expression of CD74 was significantly positively correlated with B cells, CD4 T-cells, CD8 T-cells, neutrophils, macrophages and dendritic cells. TIDE analysis showed that tumors with high CD74 expression may have better responses to immunotherapy and improved patient survival. In patients with esophageal cancer who had received ICB, higher intratumoral CD74 expression was associated with improved response to ICB.

CONCLUSIONS

The findings of this study suggest that the high expression of CD74 may be a potential predictive biomarker of response to ICB.

MATES: a deep learning-based model for locus-specific quantification of transposable elements in single cell

Transposable elements (TEs) are crucial for genetic diversity and gene regulation. Current single-cell quantification methods often align multi-mapping reads to either 'best-mapped' or 'random-mapped' locations and categorize them at the subfamily levels, overlooking the biological necessity for accurate, locus-specific TE quantification. Moreover, these existing methods are primarily designed for and focused on transcriptomics data, which restricts their adaptability to single-cell data of other modalities. To address these challenges, here we introduce MATES, a deep-learning approach that accurately allocates multi-mapping reads to specific loci of TEs, utilizing context from adjacent read alignments flanking the TE locus. When applied to diverse single-cell omics datasets, MATES shows improved performance over existing methods, enhancing the accuracy of TE quantification and aiding in the identification of marker TEs for identified cell populations. This development facilitates the exploration of single-cell heterogeneity and gene regulation through the lens of TEs, offering an effective transposon quantification tool for the single-cell genomics community.

Host derived macrophage migration inhibitory factor expression attenuates anti-tumoral immune cell accumulation and promotes immunosuppression in the tumor microenvironment of head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a significant public health concern worldwide. Immunomodulatory targets in the HNSCC tumor microenvironment are crucial to enhance the efficacy of HNSCC immunotherapy. Macrophage migration inhibitory factor (MIF) is a pro-inflammatory cytokine that has been linked to poor prognosis in many cancers, but the mechanistic role of MIF in HNSCC remains unclear. Using a murine orthotopic oral cancer model in Mif+/+ or Mif-/- mice, we determined the function of host derived MIF in HNSCC tumor development, metastasis as well as localized and systemic tumor immune responses. We observed that Mif-/- mice have decreased tumor growth and tumor burden compared to their wild-type counterparts. Flow cytometric analysis of immune populations within the primary tumor site revealed increased Th1 and cytotoxic T cell recruitment to the HNSCC tumor microenvironment. Within the tumors of Mif-/- mice, MIF deletion also enhanced the effector function of anti-tumoral effector CD8+ T cells as well as Th1 cells and decreased the accumulation of granulocytic myeloid derived suppressor cells (g-MDSCs) in the tumor microenvironment. Furthermore, MDSCs isolated from tumor bearing mice chemotactically respond to MIF in a dose dependent manner. Taken together, our results demonstrate a chemotactic and immunomodulatory role for host derived MIF in promoting HNSCC and suggest that MIF targeted immunomodulation is a promising approach for HNSCC treatment.

Single-cell RNA Sequencing Identifies a Novel Subtype of Microglia with High Cd74 Expression that Facilitates White Matter Inflammation During Chronic Cerebral Hypoperfusion

Vascular dementia (VaD) causes progressive cognitive decline in the elderly population, but there is short of available therapeutic measures. Microglia-mediated neuroinflammation is vigorously involved in the pathogenesis of VaD, but the traditional classification of microglial M1/M2 phenotypes remains restrictive and controversial. This study aims to investigate whether microglia transform into novel subtypes in VaD. Chronic cerebral hypoperfusion (CCH) rat model was constructed to mimic VaD. Microglia were isolated via magnetic-activated cell sorting and analyzed by single-cell RNA sequencing (scRNA-seq) and bioinformatics. The findings inferred from scRNA-seq and bioinformatics were further validated through in vivo experiments. In this study, microglia were divided into eight clusters. The proportion of MG5 cluster was significantly increased in the white matter of the CCH group compared with the Sham group and was named chronic ischemia-associated microglia (CIAM). Immunity- and inflammation-related genes, including RT1-Db1, RT1-Da, RT1-Ba, Cd74, Spp1, C3, and Cd68, were markedly upregulated in CIAM. Enrichment analysis illustrated that CIAM possessed the function of evoking neuroinflammation. Further studies unveiled that Cd74 is associated with the most abundant GO terms involved in inflammation as well as cell proliferation and differentiation. In addition, microglia-specific Cd74 knockdown mediated by adeno-associated virus decreased the abundance of CIAM in the white matter, thereby mitigating inflammatory cytokine levels, alleviating white matter lesions, and improving cognitive impairment for CCH rats. These findings indicate that Cd74 is the core molecule of CIAM to trigger neuroinflammation and induce microglial differentiation to CIAM, suggesting that Cd74 may be a potential therapeutic target for VaD.

APP-CD74 axis mediates endothelial cell-macrophage communication to promote kidney injury and fibrosis

Background

Kidney injuries often carry a grim prognosis, marked by fibrosis development, renal function loss, and macrophage involvement. Despite extensive research on macrophage polarization and its effects on other cells, like fibroblasts, limited attention has been paid to the influence of non-immune cells on macrophages. This study aims to address this gap by shedding light on the intricate dynamics and diversity of macrophages during renal injury and repair.

Methods

During the initial research phase, the complexity of intercellular communication in the context of kidney injury was revealed using a publicly available single-cell RNA sequencing library of the unilateral ureteral obstruction (UUO) model. Subsequently, we confirmed our findings using an independent dataset from a renal ischemia-reperfusion injury (IRI) model. We treated two different types of endothelial cells with TGF-β and co-cultured their supernatants with macrophages, establishing an endothelial cell and macrophage co-culture system. We also established a UUO and an IRI mouse model. Western blot analysis, flow cytometry, immunohistochemistry and immunofluorescence staining were used to validate our results at multiple levels.

Results

Our analysis revealed significant changes in the heterogeneity of macrophage subsets during both injury processes. Amyloid β precursor protein (APP)-CD74 axis mediated endothelial-macrophage intercellular communication plays a dominant role. In the in vitro co-culture system, TGF-β triggers endothelial APP expression, which subsequently enhances CD74 expression in macrophages. Flow cytometry corroborated these findings. Additionally, APP and CD74 expression were significantly increased in the UUO and IRI mouse models. Immunofluorescence techniques demonstrated the co-localization of F4/80 and CD74 in vivo.

Conclusion

Our study unravels a compelling molecular mechanism, elucidating how endothelium-mediated regulation shapes macrophage function during renal repair. The identified APP-CD74 signaling axis emerges as a promising target for optimizing renal recovery post-injury and preventing the progression of chronic kidney disease.

Histopathology and transcriptome profiling reveal features of immune responses in gills and intestine induced by Spring viremia of carp virus

The immune system of bony fish closely resembles that of mammals, comprising both specific (adaptive) and non-specific (innate) components. Notably, the mucosa-associated lymphoid tissue (MALT) serves as the first line of defense within the non-specific immune system, playing a critical role in protecting these aquatic organisms against invading pathogens. MALT encompasses a network of immune cells strategically distributed throughout the gills and intestines, forming an integral part of the mucosal barrier that interfaces directly with the surrounding aquatic environment. Spring Viremia of Carp Virus（SVCV）, a highly pathogenic agent causing substantial harm to common carp populations, has been designated as a Class 2 animal disease by the Ministry of Agriculture and Rural Affairs of China. Utilizing a comprehensive array of research techniques, including Hematoxylin and Eosin (HE)、Alcian Blue Periodic Acid-Schiff (AB-PAS)、transcriptome analysis for global gene expression profiling and Reverse Transcription-Polymerase Chain Reaction (RT-qPCR), this study uncovered several key findings: SVCV is capable of compromising the mucosal architecture in the gill and intestinal tissues of carp, and stimulate the proliferation of mucous cells both in gill and intestinal tissues. Critically, the study revealed that SVCV's invasion elicits a robust response from the carp's mucosal immune system, demonstrating the organism's capacity to resist SVCV invasion despite the challenges posed by the pathogen.

Cancer-associated fibroblasts: a versatile mediator in tumor progression, metastasis, and targeted therapy

Tumor microenvironment (TME) has been demonstrated to play a significant role in tumor initiation, progression, and metastasis. Cancer-associated fibroblasts (CAFs) are the major component of TME and exhibit heterogeneous properties in their communication with tumor cells. This heterogeneity of CAFs can be attributed to various origins, including quiescent fibroblasts, mesenchymal stem cells (MSCs), adipocytes, pericytes, endothelial cells, and mesothelial cells. Moreover, single-cell RNA sequencing has identified diverse phenotypes of CAFs, with myofibroblastic CAFs (myCAFs) and inflammatory CAFs (iCAFs) being the most acknowledged, alongside newly discovered subtypes like antigen-presenting CAFs (apCAFs). Due to these heterogeneities, CAFs exert multiple functions in tumorigenesis, cancer stemness, angiogenesis, immunosuppression, metabolism, and metastasis. As a result, targeted therapies aimed at the TME, particularly focusing on CAFs, are rapidly developing, fueling the promising future of advanced tumor-targeted therapy.

Identification of key genes and pathways in duck fatty liver syndrome using gene set enrichment analysis

High-laying ducks are often fed high-energy, nutritious feeds to maintain high productivity, which predisposes them to lipid metabolism disorders and the development of fatty liver syndrome (FLS), which seriously affects production performance and has a substantial economic impact on the poultry industry. Therefore, it is necessary to elucidate the mechanisms underlying the development of fatty liver syndrome. In this study, seven Shan Partridge ducks, each with fatty liver syndrome and normal laying ducks, were selected, and Hematoxylin Eosin staining (HE staining), Masson staining, and transcriptome sequencing were performed on liver tissue. In addition to exploring key genes and pathways using conventional analysis methods, we constructed the first Kyoto Encyclopedia of Genes and Genomes (KEGG) database-based predefined gene set containing 12,764 pathways and 16,836 genes and further performed gene set enrichment analysis (GSEA) on the liver transcriptome data. Finally, key nodes and biological processes were identified via the protein-protein interaction (PPI) network. The results showed that the liver in the FL group exhibited steatosis and fibrosis, and a total of 3,663 genes with upregulated expression versus 2,296 downregulated genes were screened by conventional analysis. GSEA analysis and PPI network analysis revealed that the liver in the FL group exhibited disruption of the mitochondrial electron transport chain, leading to decreased oxidative phosphorylation and the secretion of excessive proinflammatory factors amid the continuous accumulation of lipids. Under continuous chronic inflammation, cell cycle arrest triggers apoptosis, while fibrosis becomes more severe, and procarcinogenic genes are activated, leading to the continuous development and deterioration of the liver. In conclusion, the predefined gene set constructed in this study can be used for GSEA, and the identified hub genes provide useful reference data and a solid foundation for the study of the genetic regulatory mechanism of fatty liver syndrome in ducks.

Host-pathogen interactions in the Plasmodium-infected mouse liver at spatial and single-cell resolution

Upon infecting its vertebrate host, the malaria parasite initially invades the liver where it undergoes massive replication, whilst remaining clinically silent. The coordination of host responses across the complex liver tissue during malaria infection remains unexplored. Here, we perform spatial transcriptomics in combination with single-nuclei RNA sequencing over multiple time points to delineate host-pathogen interactions across Plasmodium berghei-infected liver tissues. Our data reveals significant changes in spatial gene expression in the malaria-infected tissues. These include changes related to lipid metabolism in the proximity to sites of Plasmodium infection, distinct inflammation programs between lobular zones, and regions with enrichment of different inflammatory cells, which we term 'inflammatory hotspots'. We also observe significant upregulation of genes involved in inflammation in the control liver tissues of mice injected with mosquito salivary gland components. However, this response is considerably delayed compared to that observed in P. berghei-infected mice. Our study establishes a benchmark for investigating transcriptome changes during host-parasite interactions in tissues, it provides informative insights regarding in vivo study design linked to infection and offers a useful tool for the discovery and validation of de novo intervention strategies aimed at malaria liver stage infection.

Sex Differences in Doxorubicin‐Induced Cardiotoxicity: Insights from Transcriptome Analysis

Male patients have a higher risk of cardiotoxicity following doxorubicin (DOX) treatment than female patients. However, how this difference occurs at the transcriptome level remains unclear, and the mechanisms underlying these differences are understudied. This study aimed to describe the transcriptional patterns of males and females after DOX treatment and explore the possible mechanisms of sexual differences in DOX‐induced cardiotoxicity. Following DOX treatment, male mice exhibit more severe heart damage than female mice. Transcriptome analysis of mice with and without DOX treatment showed that differentially expressed genes (DEGs) are significantly different between males and females. The majority of DEGs are sex‐specific, and more DEGs are identified in males than females. A number of genes, including the oxidation‐related genes Gdf15 and Rbm3, exhibited altered expression either in males or females. Some other genes, including the ferroptosis‐related gene Cd74, changed their expression levels in both sexes, but at different scales. Biochemical experiments suggested that cardiomyocyte oxidation and ferroptosis may contribute to the sexual dimorphism of DOX‐induced cardiotoxicity. In summary, this study shows that, after exposure to DOX, males and females respond differently regarding the expression of hundreds of genes, including Gdf15, Rbm3, and Cd74, possibly explaining the sexual differences in DOX‐induced cardiotoxicity.

Unveiling major histocompatibility complex-mediated pan-cancer immune features by integrated single-cell and bulk RNA sequencing

Immune checkpoint inhibitors (ICIs) have transformed cancer therapy, yet persistent challenges such as low response rate and significant heterogeneity necessitate attention. The pivotal role of the major histocompatibility complex (MHC) in ICI efficacy, its intricate impacts and potentials as a prognostic marker, warrants comprehensive exploration. This study integrates single-cell RNA sequencing (scRNA-seq), bulk RNA-seq, and spatial transcriptomic analyses to unveil pan-cancer immune characteristics governed by the MHC transcriptional feature (MHC.sig). Developed through scRNA-seq analysis of 663,760 cells across diverse cohorts and validated in 30 solid cancer types, the MHC.sig demonstrates a robust correlation between immune-related genes and infiltrating immune cells, highlighting its potential as a universal pan-cancer marker for anti-tumor immunity. Screening the MHC.sig for therapeutic targets using CRISPR data identifies potential genes for immune therapy synergy and validates its predictive efficacy for ICIs responsiveness across diverse datasets and cancer types. Finally, analysis of cellular communication patterns reveals interactions between C1QC+macrophages and malignant cells, providing insights into potential therapeutic agents and their sensitivity characteristics. This comprehensive analysis positions the MHC.sig as a promising marker for predicting immune therapy outcomes and guiding combinatorial therapeutic strategies.

CD74 facilitates immunotherapy response by shaping the tumor microenvironment of hepatocellular carcinoma

BACKGROUND

CD74 is ectopically expressed in many tumors and can regulate tumor immunity. However, there are many gaps in the study of the prognostic value of CD74 expression and immune infiltration in hepatocellular carcinoma (HCC).

METHODS

An online tumor database was searched to obtain data on gene/protein expression. Immune infiltration analysis was performed using the Tumor Immune Estimation Resource and Comprehensive Analysis on Multi-Omics of Immunotherapy in Pan-cancer databases. Single-cell data were obtained from the Tissue-specific Gene Expression and Regulation, Single-cell Transcriptomes of Tumor Immune Microenvironment and Tumor Immune Single-cell Hub 2 databases.

RESULTS

CD74 was highly expressed in HCC patients. HCC patients with high CD74 expression who consumed alcohol or were negative for hepatitis virus had a better prognosis than patients with low CD74 expression. CD74 was mainly enriched in immune response regulation pathways. Both copy number variations in CD74 and CD74 expression patterns affected the infiltration levels of immune cells. Interestingly, CD74 regulated the differentiation of myeloid cells. CD74 in macrophages and dendritic cells (DCs) forms complex networks with malignant cells and hepatic progenitor cell (HPC)-like cells, respectively. High CD74 expression in HPC-like cells and malignant cells significantly decreased the fraction of C-type lectin domain family 9 A (CLEC9A)-cDC1+ DCs and IL-1B+ macrophages, respectively. Their crosstalk subsequently shaped the tumor microenvironment of HCC, possibly through the CD74-MIF axis. Importantly, patients with high CD74 expression presented higher immune scores and achieved good outcomes after receiving immunotherapy.

CONCLUSION

High CD74 expression is associated with the abundance of a variety of immune cell types, mediating interactions among tumor and immune cells and shaping the malignant behavior of HCC. In summary, CD74 may be a hallmark for determining the prognosis and immune cell infiltration levels of HCC patients.

Deciphering the interplay of HPV infection, MHC-II expression, and CXCL13+ CD4+ T cell activation in oropharyngeal cancer: implications for immunotherapy

BACKGROUND

Human papillomavirus (HPV) infection has become an important etiological driver of oropharyngeal squamous cell carcinoma (OPSCC), leading to unique tumor characteristics. However, the interplay between HPV-associated tumor cells and tumor microenvironment (TME) remains an enigma.

METHODS

We performed a single-cell RNA-sequencing (scRNA-seq) on HPV-positive (HPV+) and HPV-negative (HPV‒) OPSCC tumors, each for three samples, and one normal tonsil tissue. Ex vivo validation assays including immunofluorescence staining, cell line co-culture, and flow cytometry analysis were used to test specific subtypes of HPV+ tumor cells and their communications with T cells.

RESULTS

Through a comprehensive single-cell transcriptome analysis, we uncover the distinct transcriptional signatures between HPV+ and HPV‒ OPSCC. Specifically, HPV+ OPSCC tumor cells manifest an enhanced interferon response and elevated expression of the major histocompatibility complex II (MHC-II), potentially bolstering tumor recognition and immune response. Furthermore, we identify a CXCL13+CD4+ T cell subset that exhibits dual features of both follicular and pro-inflammatory helper T cells. Noteworthily, HPV+ OPSCC tumor cells embrace extensive intercellular communications with CXCL13+CD4+ T cells. Interaction with HPV+ OPSCC tumor cells amplifies CXCL13 and IFNγ release in CD4+T cells, fostering a pro-inflammatory TME. Additionally, HPV+ tumor cells expressing high MHC-II and CXCL13+CD4+ T cell prevalence are indicative of favorable overall survival rates in OPSCC patients.

CONCLUSIONS

Together, our study underscores a synergistic inflammatory immune response orchestrated by highly immunogenic tumor cells and CXCL13+CD4+ T cells in HPV+ OPSCC, offering useful insights into strategy development for patient stratification and effective immunotherapy in OPSCC.

Genome-wide CRISPR screening identifies tyrosylprotein sulfotransferase-2 as a target for augmenting anti-PD1 efficacy

BACKGROUND

Immune checkpoint therapy (ICT) provides durable responses in select cancer patients, yet resistance remains a significant challenge, prompting the exploration of underlying molecular mechanisms. Tyrosylprotein sulfotransferase-2 (TPST2), known for its role in protein tyrosine O-sulfation, has been suggested to modulate the extracellular protein-protein interactions, but its specific role in cancer immunity remains largely unexplored.

METHODS

To explore tumor cell-intrinsic factors influencing anti-PD1 responsiveness, we conducted a pooled loss-of-function genetic screen in humanized mice engrafted with human immune cells. The responsiveness of cancer cells to interferon-γ (IFNγ) was estimated by evaluating IFNγ-mediated induction of target genes, STAT1 phosphorylation, HLA expression, and cell growth suppression. The sulfotyrosine-modified target gene of TPST2 was identified by co-immunoprecipitation and mass spectrometry. The in vivo effects of TPST2 inhibition were evaluated using mouse syngeneic tumor models and corroborated by bulk and single-cell RNA sequencing analyses.

RESULTS

Through in vivo genome-wide CRISPR screening, TPST2 loss-of-function emerged as a potential enhancer of anti-PD1 treatment efficacy. TPST2 suppressed IFNγ signaling by sulfating IFNγ receptor 1 at Y397 residue, while its downregulation boosted IFNγ-mediated signaling and antigen presentation. Depletion of TPST2 in cancer cells augmented anti-PD1 antibody efficacy in syngeneic mouse tumor models by enhancing tumor-infiltrating lymphocytes. RNA sequencing data revealed TPST2's inverse correlation with antigen presentation, and increased TPST2 expression is associated with poor prognosis and altered cancer immunity across cancer types.

CONCLUSIONS

We propose TPST2's novel role as a suppressor of cancer immunity and advocate for its consideration as a therapeutic target in ICT-based treatments.

Prognostic and therapeutic insights into MIF, DDT, and CD74 in melanoma

Macrophage Migration Inhibitory Factor (MIF) and its homolog D-dopachrome Tautomerase (DDT) have been implicated as drivers of tumor progression across a variety of cancers. Recent evidence suggests MIF as a therapeutic target in immune checkpoint inhibition (ICI) resistant melanomas, however clinical evidence of MIF and particularly of DDT remain limited. This retrospective study analyzed 97 patients treated at Yale for melanoma between 2002-2020. Bulk-RNA sequencing of patient tumor samples from the Skin Cancer SPORE Biorepository was used to evaluate for differential gene expression of MIF, DDT, CD74, and selected inflammatory markers, and gene expression was correlated with patient survival outcomes. Our findings revealed a strong correlation between MIF and DDT levels, with no statistically significant difference across common melanoma mutations and subtypes. Improved survival was associated with lower MIF and DDT levels and higher CD74:MIF and CD74:DDT levels. High CD74:DDT and CD74:MIF levels were also associated with enrichment of infiltrating inflammatory cell markers. These data suggest DDT as a novel target in immune therapy. Dual MIF and DDT blockade may provide synergistic responses in patients with melanoma, irrespective of common mutations, and may overcome ICI resistance. These markers may also provide prognostic value for further biomarker development.

Single-cell landscape of functionally cured chronic hepatitis B patients reveals activation of innate and altered CD4-CTL-driven adaptive immunity

BACKGROUND & AIMS

Hepatitis B surface antigen (HBsAg) loss or functional cure (FC) is considered the optimal therapeutic outcome for patients with chronic hepatitis B (CHB). However, the immune-pathological biomarkers and underlying mechanisms of FC remain unclear. In this study we comprehensively interrogate disease-associated cell states identified within intrahepatic tissue and matched PBMCs (peripheral blood mononuclear cells) from patients with CHB or after FC, at the resolution of single cells, to provide novel insights into putative mechanisms underlying FC.

METHODS

We combined single-cell transcriptomics (single-cell RNA sequencing) with multiparametric flow cytometry-based immune phenotyping, and multiplexed immunofluorescence to elucidate the immunopathological cell states associated with CHB vs. FC.

RESULTS

We found that the intrahepatic environment in CHB and FC displays specific cell identities and molecular signatures that are distinct from those found in matched PBMCs. FC is associated with the emergence of an altered adaptive immune response marked by CD4 cytotoxic T lymphocytes, and an activated innate response represented by liver-resident natural killer cells, specific Kupffer cell subtypes and marginated neutrophils. Surprisingly, we found MHC class II-expressing hepatocytes in patients achieving FC, as well as low but persistent levels of covalently closed circular DNA and pregenomic RNA, which may play an important role in FC.

CONCLUSIONS

Our study provides conceptually novel insights into the immuno-pathological control of HBV cure, and opens exciting new avenues for clinical management, biomarker discovery and therapeutic development. We believe that the discoveries from this study, as it relates to the activation of an innate and altered immune response that may facilitate sustained, low-grade inflammation, may have broader implications in the resolution of chronic viral hepatitis.

IMPACT AND IMPLICATIONS

This study dissects the immuno-pathological cell states associated with functionally cured chronic hepatitis B (defined by the loss of HBV surface antigen or HBsAg). We identified the sustained presence of very low viral load, accessory antigen-presenting hepatocytes, adaptive-memory-like natural killer cells, and the emergence of helper CD4 T cells with cytotoxic or effector-like signatures associated with functional cure, suggesting previously unsuspected alterations in the adaptive immune response, as well as a key role for the innate immune response in achieving or maintaining functional cure. Overall, the insights generated from this study may provide new avenues for the development of alternative therapies as well as patient surveillance for better clinical management of chronic hepatitis B.

Spatial multiomics of arterial regions from cardiac allograft vasculopathy rejected grafts reveal novel insights into the pathogenesis of chronic antibody-mediated rejection

Cardiac allograft vasculopathy (CAV) causes late graft failure and mortality after heart transplantation. Donor-specific antibodies (DSAs) lead to chronic endothelial cell injury, inflammation, and arterial intimal thickening. In this study, GeoMx digital spatial profiling was used to analyze arterial areas of interest (AOIs) from CAV+DSA+ rejected cardiac allografts (N = 3; 22 AOIs total). AOIs were categorized based on CAV neointimal thickening and underwent whole transcriptome and protein profiling. By comparing our transcriptomic data with that of healthy control vessels of rapid autopsy myocardial tissue, we pinpointed specific pathways and transcripts indicative of heightened inflammatory profiles in CAV lesions. Moreover, we identified protein and transcriptomic signatures distinguishing CAV lesions exhibiting low and high neointimal lesions. AOIs with low neointima showed increased markers for activated inflammatory infiltrates, endothelial cell activation transcripts, and gene modules involved in metalloproteinase activation and TP53 regulation of caspases. Inflammatory and apoptotic proteins correlated with inflammatory modules in low neointima AOIs. High neointima AOIs exhibited elevated TGFβ-regulated transcripts and modules enriched for platelet activation/aggregation. Proteins associated with growth factors/survival correlated with modules enriched for proliferation/repair in high neointima AOIs. Our findings reveal novel insight into immunological mechanisms mediating CAV pathogenesis.

Traumatic brain injury alters the effects of class II invariant peptide (CLIP) antagonism on chronic meningeal CLIP + B cells, neuropathology, and neurobehavioral impairment in 5xFAD mice

BACKGROUND

Traumatic brain injury (TBI) is a significant risk factor for Alzheimer's disease (AD), and accumulating evidence supports a role for adaptive immune B and T cells in both TBI and AD pathogenesis. We previously identified B cell and major histocompatibility complex class II (MHCII)-associated invariant chain peptide (CLIP)-positive B cell expansion after TBI. We also showed that antagonizing CLIP binding to the antigen presenting groove of MHCII after TBI acutely reduced CLIP + splenic B cells and was neuroprotective. The current study investigated the chronic effects of antagonizing CLIP in the 5xFAD Alzheimer's mouse model, with and without TBI.

METHODS

12-week-old male wild type (WT) and 5xFAD mice were administered either CLIP antagonist peptide (CAP) or vehicle, once at 30 min after either sham or a lateral fluid percussion injury (FPI). Analyses included flow cytometric analysis of immune cells in dural meninges and spleen, histopathological analysis of the brain, magnetic resonance diffusion tensor imaging, cerebrovascular analysis, and assessment of motor and neurobehavioral function over the ensuing 6 months.

RESULTS

9-month-old 5xFAD mice had significantly more CLIP + B cells in the meninges compared to age-matched WT mice. A one-time treatment with CAP significantly reduced this population in 5xFAD mice. Importantly, CAP also improved some of the immune, histopathological, and neurobehavioral impairments in 5xFAD mice over the ensuing six months. Although FPI did not further elevate meningeal CLIP + B cells, it did negate the ability of CAP to reduce meningeal CLIP + B cells in the 5xFAD mice. FPI at 3 months of age exacerbated some aspects of AD pathology in 5xFAD mice, including further reducing hippocampal neurogenesis, increasing plaque deposition in CA3, altering microgliosis, and disrupting the cerebrovascular structure. CAP treatment after injury ameliorated some but not all of these FPI effects.

Elevated phagocytic capacity directs innate spinal cord repair

Immune cells elicit a continuum of transcriptional and functional states after spinal cord injury (SCI). In mammals, inefficient debris clearance and chronic inflammation impede recovery and overshadow pro-regenerative immune functions. We found that, unlike mammals, zebrafish SCI elicits transient immune activation and efficient debris clearance, without causing chronic inflammation. Single-cell transcriptomics and inducible genetic ablation showed zebrafish macrophages are highly phagocytic and required for regeneration. Cross-species comparisons between zebrafish and mammalian macrophages identified transcription and immune response regulator ( tcim ) as a macrophage-enriched zebrafish gene. Genetic deletion of zebrafish tcim impairs phagocytosis and regeneration, causes aberrant and chronic immune activation, and can be rescued by transplanting wild-type immune precursors into tcim mutants. Conversely, genetic expression of human TCIM accelerates debris clearance and regeneration by reprogramming myeloid precursors into activated phagocytes. This study establishes a central requirement for elevated phagocytic capacity to achieve innate spinal cord repair.

Insights into the prognostic value and immunological role of CD74 in pan-cancer

BACKGROUND

CD74 is a non-polymorphic type II transmembrane glycoprotein. It is involved in the regulation of T and B cell development, and dendritic cell (DC) motility. Numerous studies have found that CD74 exerts an essential role in tumor immunity, but the expression profile of CD74 is still not systematically reported, and its value in human pan-cancer analysis is unknown. In this study, we analyzed the expression pattern of CD74 in 33 cancers, and evaluated the significance of CD74 in prognosis prediction and cancer immunity.

METHODS

Pan-cancer dataset from UCSC Xena.We used the Sangerbox website combined with R software' Timer, CIBERSORT method and IOBR package to analyze and plot the data. Survival was assessed using the Kaplan-Meier method and log-rank test for 33 cancer types (p < 0.05). In addition, to explore the relationship between CD74 expression and immune checkpoints, immune cell infiltration, tumor mutational burden (TMB) and microsatellite instability (MSI), Spearman correlation analysis was performed.

RESULTS

This study comprehensively analyzed CD74 expression in 33 different tumor types, revealing that CD74 play an crucial role in cancer formation and development.

CONCLUSIONS

CD74 gene expression in different cancers is associated with immune cell infiltration and immunomodulators and may provide a promising target for survival and immunotherapy. Our study shows that CD74 has an essential role as a biomarker of prognosis during tumor development, which highlights the possibility of new targeted therapies.

A novel gain-of-function phosphorylation site modulates PTPN22 inhibition of TCR signaling

Protein tyrosine phosphatase nonreceptor type 22 (PTPN22) is encoded by a major autoimmunity gene and is a known inhibitor of T cell receptor (TCR) signaling and drug target for cancer immunotherapy. However, little is known about PTPN22 posttranslational regulation. Here, we characterize a phosphorylation site at Ser325 situated C terminal to the catalytic domain of PTPN22 and its roles in altering protein function. In human T cells, Ser325 is phosphorylated by glycogen synthase kinase-3 (GSK3) following TCR stimulation, which promotes its TCR-inhibitory activity. Signaling through the major TCR-dependent pathway under PTPN22 control was enhanced by CRISPR/Cas9-mediated suppression of Ser325 phosphorylation and inhibited by mimicking it via glutamic acid substitution. Global phospho-mass spectrometry showed Ser325 phosphorylation state alters downstream transcriptional activity through enrichment of Swi3p, Rsc8p, and Moira domain binding proteins, and next-generation sequencing revealed it differentially regulates the expression of chemokines and T cell activation pathways. Moreover, in vitro kinetic data suggest the modulation of activity depends on a cellular context. Finally, we begin to address the structural and mechanistic basis for the influence of Ser325 phosphorylation on the protein's properties by deuterium exchange mass spectrometry and NMR spectroscopy. In conclusion, this study explores the function of a novel phosphorylation site of PTPN22 that is involved in complex regulation of TCR signaling and provides details that might inform the future development of allosteric modulators of PTPN22.

Macrophage migration inhibitor factor (MIF): Potential role in cognitive impairment disorders

Macrophage migration inhibitory factor (MIF) is a cytokine in the immune system, participated in both innate and adaptive immune responses. Except from immune cells, MIF is also secreted by a variety of non-immune cells, including hematopoietic cells, endothelial cells (ECs), and neurons. MIF plays a crucial role in various diseases, such as sepsis, rheumatoid arthritis, acute kidney injury, and neurodegenerative diseases. The role of MIF in the neuropathogenesis of cognitive impairment disorders is emphasized, as it recruits multiple inflammatory mediators, leading to activating microglia or astrocyte-derived neuroinflammation. Furthermore, it contributes to the cell death of neurons and ECs with the binding of apoptosis-inducing factor (AIF) through parthanatos-associated apoptosis-inducing factor nuclease (PAAN) / MIF pathway. This review comprehensively delves into the relationship between MIF and the neuropathogenesis of cognitive impairment disorders, providing a series of emerging MIF-targeted pharmaceuticals as potential treatments for cognitive impairment disorders.

Molecular Responses of the Eukaryotic Cell Line INT407 on the Internalized Campylobacter jejuni-The Other Side of the Coin

Campylobacter jejuni is a zoonotic bacterium with the capacity to invade the epithelial cells during the pathogenic process. Several bacterial factors have been identified to contribute to this process, but our knowledge is still very limited about the response of the host. To reveal the major routes of this response, a whole-transcriptome analysis (WTA) was performed where gene expressions were compared between the 1st and the 3rd hours of internalization in INT407 epithelial cells. From the 41,769 human genes tested, altogether, 19,060 genes were shown through WTA to be influenced to different extents. The genes and regulation factors of transcription (296/1052; 28%), signal transduction (215/1052; 21%), apoptosis (153/1052; 15%), immune responses (97/1052; 9%), transmembrane transport (64/1052; 6%), cell-cell signaling (32/1052; 3%), cell-cell adhesions (29/1052; 3%), and carbohydrate metabolism (28/1052; 3%) were the most affected biological functions. A striking feature of the gene expression of this stage of the internalization process is the activation of both immune functions and apoptosis, which convincingly outlines that the invaded cell faces a choice between death and survival. The seemingly balanced status quo between the invader and the host is the result of a complex process that also affects genes known to be associated with postinfectious pathological conditions. The upregulation of TLR3 (3.79×) and CD36 (2.73×), two general tumor markers, and SERPINEB9 (11.37×), FNDC1 (7.58×), and TACR2 (8.84×), three factors of tumorigenesis, confirms the wider pathological significance of this bacterium.

Blocking the MIF-CD74 axis augments radiotherapy efficacy for brain metastasis in NSCLC via synergistically promoting microglia M1 polarization

BACKGROUND

Brain metastasis is one of the main causes of recurrence and death in non-small cell lung cancer (NSCLC). Although radiotherapy is the main local therapy for brain metastasis, it is inevitable that some cancer cells become resistant to radiation. Microglia, as macrophages colonized in the brain, play an important role in the tumor microenvironment. Radiotherapy could activate microglia to polarize into both the M1 and M2 phenotypes. Therefore, searching for crosstalk molecules within the microenvironment that can specifically regulate the polarization of microglia is a potential strategy for improving radiation resistance.

METHODS

We used databases to detect the expression of MIF in NSCLC and its relationship with prognosis. We analyzed the effects of targeted blockade of the MIF/CD74 axis on the polarization and function of microglia during radiotherapy using flow cytometry. The mouse model of brain metastasis was used to assess the effect of targeted blockade of MIF/CD74 axis on the growth of brain metastasis.

RESULT

Our findings reveals that the macrophage migration inhibitory factor (MIF) was highly expressed in NSCLC and is associated with the prognosis of NSCLC. Mechanistically, we demonstrated CD74 inhibition reversed radiation-induced AKT phosphorylation in microglia and promoted the M1 polarization in combination of radiation. Additionally, blocking the MIF-CD74 interaction between NSCLC and microglia promoted microglia M1 polarization. Furthermore, radiation improved tumor hypoxia to decrease HIF-1α dependent MIF secretion by NSCLC. MIF inhibition enhanced radiosensitivity for brain metastasis via synergistically promoting microglia M1 polarization in vivo.

CONCLUSIONS

Our study revealed that targeting the MIF-CD74 axis promoted microglia M1 polarization and synergized with radiotherapy for brain metastasis in NSCLC.

Revealing Genetic Dynamics: scRNA-seq Unravels Modifications in Human PDL Cells across In Vivo and In Vitro Environments

The periodontal ligament (PDL) is a highly specialized fibrous tissue comprising heterogeneous cell populations of an intricate nature. These complexities, along with challenges due to cell culture, impede a comprehensive understanding of periodontal pathophysiology. This study aims to address this gap, employing single-cell RNA sequencing (scRNA-seq) technology to analyze the genetic intricacies of PDL both in vivo and in vitro. Primary human PDL samples (n = 7) were split for direct in vivo analysis and cell culture under serum-containing and serum-free conditions. Cell hashing and sorting, scRNA-seq library preparation using the 10x Genomics protocol, and Illumina sequencing were conducted. Primary analysis was performed using Cellranger, with downstream analysis via the R packages Seurat and SCORPIUS. Seven distinct PDL cell clusters were identified comprising different cellular subsets, each characterized by unique genetic profiles, with some showing donor-specific patterns in representation and distribution. Formation of these cellular clusters was influenced by culture conditions, particularly serum presence. Furthermore, certain cell populations were found to be inherent to the PDL tissue, while others exhibited variability across donors. This study elucidates specific genes and cell clusters within the PDL, revealing both inherent and context-driven subpopulations. The impact of culture conditions-notably the presence of serum-on cell cluster formation highlights the critical need for refining culture protocols, as comprehending these influences can drive the creation of superior culture systems vital for advancing research in PDL biology and regenerative therapies. These discoveries not only deepen our comprehension of PDL biology but also open avenues for future investigations into uncovering underlying mechanisms.

Phenotypic switching as a non-genetic mechanism of resistance predicts antibody therapy regimens

Despite the specificity and effectiveness of antibody therapy, resistance to treatment remains a major barrier for their broad clinical applications. While genetic mutations are known to be critical, the impact of non-genetic mechanisms, such as epigenetic changes and phenotypic adaptations, on resistance to antibody-dependent cellular cytotoxicity (ADCC) is not fully understood. Our study investigated the non-genetic resistance mechanisms that colorectal cancer cells develop against cetuximab and the resulting ADCC pressure. Resistance clones exhibited decreased EGFR/HER2 expressions, enriched interferon-related pathways, and lower NK cell activation. Interestingly, these resistance clones regained sensitivity upon the withdrawal of therapeutic pressure, implying phenotypic plasticity and reversibility. To counter resistance, we developed a mathematical model recapitulating the phenotypic switching dynamics. The model predicted that intermittent dosing strategy outperforms continuous regimen in delaying treatment resistance. Our findings have implications for improving efficacy and circumventing resistance to targeted antibody therapies.