SLAMF9 regulates pDC homeostasis and function in health and disease

The prognostic and immune significance of SLAMF9 in pan-cancer and validation of its role in colorectal cancer

SLAMF9, a member of the conserved lymphocyte activation molecules family (SLAMF), has been less investigated compared to other SLAMs, especially concerning its implications across various cancer types. In our systematic pan-cancer investigation, we observed elevated SLAMF9 expression in various tumor tissues, which was correlated with reduced patient survival across most malignancies. Correlation analyses further revealed significant associations between SLAMF9 expression and immune cell infiltrates, immune checkpoint inhibitors, tumor mutation load, microsatellite instability, and epithelial-mesenchymal transition (EMT) scores. Cell-based assays demonstrated that SLAMF9 knockdown attenuated the proliferative, motile, and invasive capacities of colorectal cancer (CRC) cells. In a nude mouse xenograft model, suppression of SLAMF9 expression substantially inhibited tumor growth. These findings highlight the potential of SLAMF9 as a prognostic and therapeutic biomarker across tumors, with notable implications for CRC cell proliferation and migration.

Development and function of chicken XCR1+ conventional dendritic cells

Conventional dendritic cells (cDCs) are antigen-presenting cells (APCs) that play a central role in linking innate and adaptive immunity. cDCs have been well described in a number of different mammalian species, but remain poorly characterised in the chicken. In this study, we use previously described chicken cDC specific reagents, a novel gene-edited chicken line and single-cell RNA sequencing (scRNAseq) to characterise chicken splenic cDCs. In contrast to mammals, scRNAseq analysis indicates that the chicken spleen contains a single, chemokine receptor XCR1 expressing, cDC subset. By sexual maturity the XCR1+ cDC population is the most abundant mononuclear phagocyte cell subset in the chicken spleen. scRNAseq analysis revealed substantial heterogeneity within the chicken splenic XCR1+ cDC population. Immature MHC class II (MHCII)LOW XCR1+ cDCs expressed a range of viral resistance genes. Maturation to MHCIIHIGH XCR1+ cDCs was associated with reduced expression of anti-viral gene expression and increased expression of genes related to antigen presentation via the MHCII and cross-presentation pathways. To visualise and transiently ablate chicken XCR1+ cDCs in situ, we generated XCR1-iCaspase9-RFP chickens using a CRISPR-Cas9 knockin transgenesis approach to precisely edit the XCR1 locus, replacing the XCR1 coding region with genes for a fluorescent protein (TagRFP), and inducible Caspase 9. After inducible ablation, the chicken spleen is initially repopulated by immature CD1.1+ XCR1+ cDCs. XCR1+ cDCs are abundant in the splenic red pulp, in close association with CD8+ T-cells. Knockout of XCR1 prevented this clustering of cDCs with CD8+ T-cells. Taken together these data indicate a conserved role for chicken and mammalian XCR1+ cDCs in driving CD8+ T-cells responses.

Analysis of a new therapeutic target and construction of a prognostic model for breast cancer based on ferroptosis genes

Breast cancer, which is the most common malignant tumor among women worldwide and an important cause of death in women. The existing prognostic model for patients with breast cancer is not accurate as breast cancer is resistant to commonly used antitumor drugs. Ferroptosis is a novel mechanism of programmed cell death that depends on iron accumulation and lipid peroxidation. Various studies have confirmed the role of ferroptosis in tumor regulation and ferroptosis is now considered to play an important role in breast cancer development. At present, the association between breast cancer prognosis and ferroptosis-related gene expression remains unclear. Further exploration of this research area may optimize the evaluation and prediction of prognosis of patients with breast cancer and finding of new therapeutic targets. In this study, clinical factors and the expression of multiple genes were evaluated in breast cancer samples from the Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database database. Eleven prognostication-related genes (TP63, IFNG, MT3, ANO6, FLT3, PTGS2, SLC1A4, JUN, SLC7A5, CHAC1, and TF) were identified from differentially expressed genes to construct a survival prediction model, which showed a good prediction ability. KEGG pathway analysis revealed that immune-related pathways were the primary pathways. ssGSEA analysis showed significant differences in the distribution of certain immune-related cell subsets, such as CD8+T cells and B cells, and in the expression of multiple immune genes, including type II IFN response and APC coinhibition. In addition, 10 immune targets related to ferroptosis in breast cancer were found: CD276, CD80, HHLA2, LILRA2, NCR3LG1, NECTIN3, PVR, SLAMF9,TNFSF4, and BTN1A1. Using TCGA, new ferroptosis genes related to breast cancer prognosis were identified, a new reliable and accurate prognosis model was developed, and 10 new potential therapeutic targets different from the traditional targeted drugs were identified to provide a reference for improving the poor prognosis of patients with breast cancer.

Dendritic cell vaccine of gliomas: challenges from bench to bed

Gliomas account for the majority of brain malignant tumors. As the most malignant subtype of glioma, glioblastoma (GBM) is barely effectively treated by traditional therapies (surgery combined with radiochemotherapy), resulting in poor prognosis. Meanwhile, due to its "cold tumor" phenotype, GBM fails to respond to multiple immunotherapies. As its capacity to prime T cell response, dendritic cells (DCs) are essential to anti-tumor immunity. In recent years, as a therapeutic method, dendritic cell vaccine (DCV) has been immensely developed. However, there have long been obstacles that limit the use of DCV yet to be tackled. As is shown in the following review, the role of DCs in anti-tumor immunity and the inhibitory effects of tumor microenvironment (TME) on DCs are described, the previous clinical trials of DCV in the treatment of GBM are summarized, and the challenges and possible development directions of DCV are analyzed.

SLAM-family receptors come of age as a potential molecular target in cancer immunotherapy

The signaling lymphocytic activation molecule (SLAM) family receptors were discovered in immune cells for the first time. The SLAM-family receptors are a significant player in cytotoxicity, humoral immune responses, autoimmune diseases, lymphocyte development, cell survival, and cell adhesion. There is growing evidence that SLAM-family receptors have been involved in cancer progression and heralded as a novel immune checkpoint on T cells. Previous studies have reported the role of SLAMs in tumor immunity in various cancers, including chronic lymphocytic leukemia, lymphoma, multiple myeloma, acute myeloid leukemia, hepatocellular carcinoma, head and neck squamous cell carcinoma, pancreas, lung, and melanoma. Evidence has deciphered that the SLAM-family receptors may be targeted for cancer immunotherapy. However, our understanding in this regard is not complete. This review will discuss the role of SLAM-family receptors in cancer immunotherapy. It will also provide an update on recent advances in SLAM-based targeted immunotherapies.

SLAMF7 modulates B cells and adaptive immunity to regulate susceptibility to CNS autoimmunity

Background

Multiple sclerosis (MS) is a chronic, debilitating condition characterized by CNS autoimmunity stemming from a complex etiology involving both environmental and genetic factors. Our current understanding of MS points to dysregulation of the immune system as the pathogenic culprit, however, it remains unknown as to how the many genes associated with increased susceptibility to MS are involved. One such gene linked to MS susceptibility and known to regulate immune function is the self-ligand immune cell receptor SLAMF7.

Methods

We subjected WT and SLAMF7^−/− mice to multiple EAE models, compared disease severity, and comprehensively profiled the CNS immune landscape of these mice. We identified all SLAMF7-expressing CNS immune cells and compared the entire CNS immune niche between genotypes. We performed deep phenotyping and in vitro functional studies of B and T cells via spectral cytometry and BioPlex assays. Adoptive transfer studies involving the transfer of WT and SLAMF7^−/− B cells into B cell-deficient mice (μMT) were also performed. Finally, B–T cell co-culture studies were performed, and a comparative cell–cell interaction network derived from scRNA-seq data of SLAMF7⁺ vs. SLAMF7⁻ human CSF immune cells was constructed.

Results

We found SLAMF7^−/− mice to be more susceptible to EAE compared to WT mice and found SLAMF7 to be expressed on numerous CNS immune cell subsets. Absence of SLAMF7 did not grossly alter the CNS immune landscape, but allowed for altered immune cell subset infiltration during EAE in a model-dependent manner. Global lack of SLAMF7 expression increased myeloid cell activation states along with augmented T cell anti-MOG immunity. B cell profiling studies revealed increased activation states of specific plasma and B cell subsets in SLAMF7^−/− mice during EAE, and functional co-culture studies determined that SLAMF7^−/− B cells induce exaggerated T cell activation. Adoptive transfer studies revealed that the increased susceptibility of SLAMF7^−/− mice to EAE is partly B cell dependent and reconstruction of the human CSF SLAMF7-interactome found B cells to be critical to cell–cell communication between SLAMF7-expressing cells.

Conclusions

Our studies have identified novel roles for SLAMF7 in CNS immune regulation and B cell function, and illuminate underpinnings of the genetic association between SLAMF7 and MS.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12974-022-02594-9.

Human M1 macrophages express unique innate immune response genes after mycobacterial infection to defend against tuberculosis

Mycobacterium tuberculosis (Mtb) is responsible for approximately 1.5 million deaths each year. Though 10% of patients develop tuberculosis (TB) after infection, 90% of these infections are latent. Further, mice are nearly uniformly susceptible to Mtb but their M1-polarized macrophages (M1-MΦs) can inhibit Mtb in vitro, suggesting that M1-MΦs may be able to regulate anti-TB immunity. We sought to determine whether human MΦ heterogeneity contributes to TB immunity. Here we show that IFN-γ-programmed M1-MΦs degrade Mtb through increased expression of innate immunity regulatory genes (Inregs). In contrast, IL-4-programmed M2-polarized MΦs (M2-MΦs) are permissive for Mtb proliferation and exhibit reduced Inregs expression. M1-MΦs and M2-MΦs express pro- and anti-inflammatory cytokine-chemokines, respectively, and M1-MΦs show nitric oxide and autophagy-dependent degradation of Mtb, leading to increased antigen presentation to T cells through an ATG-RAB7-cathepsin pathway. Despite Mtb infection, M1-MΦs show increased histone acetylation at the ATG5 promoter and pro-autophagy phenotypes, while increased histone deacetylases lead to decreased autophagy in M2-MΦs. Finally, Mtb-infected neonatal macaques express human Inregs in their lymph nodes and macrophages, suggesting that M1 and M2 phenotypes can mediate immunity to TB in both humans and macaques. We conclude that human MФ subsets show unique patterns of gene expression that enable differential control of TB after infection. These genes could serve as targets for diagnosis and immunotherapy of TB.

SLAMF1 Is Dispensable for Vaccine-Induced T Cell Development but Required for Resistance to Fungal Infection

Homotypic signaling lymphocyte activation molecule (SLAM) receptor-ligand cell surface interactions between myeloid and lymphoid cells regulate innate and adaptive immune responses. In this article, we report that SLAMF1 is indispensable for host resistance to primary and vaccine-induced protection against fungal infection. Because vaccine immunity is dependent on cell-mediated immunity, we investigated the development of Ag-specific T cells. We studied the T cell-intrinsic and -extrinsic role of SLAMF1. We generated SLAMF1^-/- TCR transgenic mice and analyzed the responses of adoptively transferred T cells. We also tracked endogenous Ag-specific T cells by using a tetramer. Intrinsic and extrinsic SLAMF1 signaling was dispensable for the development of antifungal Th1 and Th17 cells, which are requisite for the acquisition of vaccine-induced immunity. Despite intact T cell development, vaccinated SLAMF1^-/- mice failed to control fungal infection. Failed accumulation of Ag-specific T cells in the lung on infection of vaccinated mice was due to uncontrolled early infection and inflammation, revealing a role for SLAMF1 in innate host immunity.

SLAMF8 Downregulates Mouse Macrophage Microbicidal Mechanisms via PI3K Pathways

Signaling lymphocytic activation molecule family 8 (SLAMF8) is involved in the negative modulation of NADPH oxidase activation. However, the impact of SLAMF8 downregulation on macrophage functionality and the microbicide mechanism remains elusive. To study this in depth, we first analyzed NADPH oxidase activation pathways in wild-type and SLAMF8-deficient macrophages upon different stimulus. Herein, we describe increased phosphorylation of the Erk1/2 and p38 MAP kinases, as well as increased phosphorylation of NADPH oxidase subunits in SLAMF8-deficient macrophages. Furthermore, using specific inhibitors, we observed that specific PI3K inhibition decreased the differences observed between wild-type and SLAMF8-deficient macrophages, stimulated with either PMA, LPS, or Salmonella typhimurium infection. Consequently, SLAMF8-deficient macrophages also showed increased recruitment of small GTPases such as Rab5 and Rab7, and the p47^phox subunit to cytoplasmic Salmonella, suggesting an impairment of Salmonella-containing vacuole (SCV) progression in SLAMF8-deficient macrophages. Enhanced iNOS activation, NO production, and IL-6 expression were also observed in the absence of SLAMF8 upon Salmonella infection, either in vivo or in vitro, while overexpression of SLAMF8 in RAW264.7 macrophages showed the opposite phenotype. In addition, SLAMF8-deficient macrophages showed increased activation of Src kinases and reduced SHP-1 phosphate levels upon IFNγ and Salmonella stimuli in comparison to wild-type macrophages. In agreement with in vitro results, Salmonella clearance was augmented in SLAMF8-deficient mice compared to that in wild-type mice. Therefore, in conclusion, SLAMF8 intervention upon bacterial infection downregulates mouse macrophage activation, and confirmed that SLAMF8 receptor could be a potential therapeutic target for the treatment of severe or unresolved inflammatory conditions.

Single-cell transcriptomic landscapes of a rare human laryngeal chondrosarcoma

Propose

Laryngeal chondrosarcoma is a rare non-epithelial malignant tumor. At present, the cell type composition and molecular mechanism of laryngeal chondrosarcoma have not been systematically studied.

Methods

This study focused on the histopathological and imaging features of a rare primary laryngeal chondrosarcoma in a 74-year-old male. The tumor and its paracancerous cartilage tissue were single-cell sequenced and analyzed and a total of 5455 single cells were obtained. Immunohistochemical levels were also verified.

Results

In total five cell types were identified, including chondrocytes, myeloid cells, fibroblasts, lymphocytes, and endothelial cells. We carried out further subgroup analysis, focusing on the classification and differentiation of chondrocytes, functional enrichment analysis, and cellular communication analysis of all cell types, and explored the tumor microenvironment (TME) of laryngeal chondrosarcoma. Immunohistochemistry revealed the SLAMF9 gene was specifically expressed in non-immune cells of chondrosarcoma, but was barely expressed in the normal cartilage tissues adjacent to chondrosarcomas.

Conclusion

This single-cell sequencing approach provides clues for deciphering the potential mechanisms of tumor heterogeneity and TME composition in laryngeal chondrosarcoma, and represents an important step towards the treatment of laryngeal chondrosarcoma.

A simplified method for separating renal MPCs using SLAMF9

Mononuclear phagocytes comprise an array of tissue-resident and monocyte-derived cells with important roles in tissue homeostasis and resistance to infection. Their diverse phenotypes make functional characterization within tissues challenging, because multiple surface markers are typically required for subset identification and isolation by cell sorting methods. Analysis of SLAMF9 expression within renal mononuclear phagocyte populations by multi-parametric flow cytometry indicates that SLAMF9 is a specific marker for identification of kidney-resident CD45⁺ CD11c⁺  MHC-II⁺ cells corresponding to prominent tissue-resident MPC populations derived from dendritic cell progenitors in adult mice. High SLAMF9 expression was sufficient to identify and sort these cells from disaggregated tissue using a user-operated cell sorter. The population can be further subdivided according to expression of CD11b and CD14 to identify IRF8^high cDC1 cells and cleanly separate the CD11b^high F4/80^low and CD11b^int F4/80^high CD11c⁺ MPC subsets. Therefore, SLAMF9 expression allows for the identification and sorting of kidney-resident CD11b⁺ CD11c⁺ CD64⁺ F4/80⁺ CX₃ CR1⁺ MHC-II⁺ MPCs without the need for complex antibody panels or reporter mice, simplifying isolation of these cells for study ex vivo.

Transcriptome-wide analysis reveals core sets of transcriptional regulators of sensome and inflammation genes in retinal microglia

BACKGROUND

Retinal microglial cells (RMCs) play crucial roles in maintaining normal visual functions in a healthy eye. However, the underlying mechanisms of RMCs over-activation manifesting the alterations of sensome profile and inflammation state, which contribute to various retinal neurodegenerative diseases, remain elusive. Here, we aimed to identify the core set of sensome and pro-inflammatory genes and their regulators using transcriptome and data mining approaches.

METHODS

We performed paired-end RNA-sequencing in primary microglial cell cultures treated with TNFα/IFNϒ (10 ng/ml for 12 h) and PBS as a control. Gene enrichment analysis and hierarchical clustering for the differentially expressed transcripts highlight functional pathways and network perturbations. We examined overlaps of the mouse microglial gene expression profiles with the data-mined human sensome and pro-inflammatory marker genes. The core sets of sensome and pro-inflammatory genes were selected and predicted for transcription factors (TFs). The identified TFs in RNA-Seq are validated by the quantitative PCR method.

RESULTS

TNFα/IFNϒ induced 668 differentially expressed transcripts in retinal microglial cells relative to the control. Furthermore, gene enrichment analysis and the gene expression network revealed activated microglial genes, biological, molecular and inflammatory pathways. The overlapping analysis of the TNFα/IFNϒ-activated microglia genes and the data-mined human gene sets revealed 22 sensome and 61 pro-inflammatory genes. Based on network analysis, we determined 10 genes as the core sets of sensome and pro-inflammatory genes and predicted the top ten TFs that regulate them. The SP110, IRF1, FLI1, SP140 (sensome) and RELB, BATF2, NFKB2, TRAFD1, SP100, NFKB1 (inflammation) are differentially expressed between the TNFα/IFNϒ activated and the non-activated microglia which were validated by quantitative PCR. The outcomes indicate that these transcriptional regulators are highly expressed and may regulate the sensome and inflammatory genes of RMCs and switch them to over-activation.

CONCLUSION

Our results comprise a powerful, cross-species functional genomics resource for sensome and inflammation of RMCs, which may provide novel therapeutic approaches to prevent retinal neurodegenerative diseases.

Type I Interferon Production of Plasmacytoid Dendritic Cells under Control

One of the most powerful and multifaceted cytokines produced by immune cells are type I interferons (IFNs), the basal secretion of which contributes to the maintenance of immune homeostasis, while their activation-induced production is essential to effective immune responses. Although, each cell is capable of producing type I IFNs, plasmacytoid dendritic cells (pDCs) possess a unique ability to rapidly produce large amounts of them. Importantly, type I IFNs have a prominent role in the pathomechanism of various pDC-associated diseases. Deficiency in type I IFN production increases the risk of more severe viral infections and the development of certain allergic reactions, and supports tumor resistance; nevertheless, its overproduction promotes autoimmune reactions. Therefore, the tight regulation of type I IFN responses of pDCs is essential to maintain an adequate level of immune response without causing adverse effects. Here, our goal was to summarize those endogenous factors that can influence the type I IFN responses of pDCs, and thus might serve as possible therapeutic targets in pDC-associated diseases. Furthermore, we briefly discuss the current therapeutic approaches targeting the pDC-type I IFN axis in viral infections, cancer, autoimmunity, and allergy, together with their limitations defined by the Janus-faced nature of pDC-derived type I IFNs.

HDAC9 deficiency promotes tumor progression by decreasing the CD8+ dendritic cell infiltration of the tumor microenvironment

BACKGROUND

The tumor microenvironment (TME) contains a variety of immune cells, which play critical roles during the multistep development of tumors. Histone deacetylase 9 (HDAC9) has been reported to have either proinflammatory or anti-inflammatory effects, depending on the immune environment. In this study, we investigated whether HDAC9 in the tumor stroma regulated inflammation and antitumor immunity.

METHODS

Hdac9 knockout mice were generated to analyze the HDAC9-associated inflammation and tumor progression. Immune cells and cytokines in TME or draining lymph nodes were quantified by flow cytometry and quantitative reverse transcription-PCR. The antigen presentation and CD8⁺ T cell priming by tumor-infiltrating dendritic cells (DCs) were evaluated in vitro and in vivo. HDAC9-associated inflammation was investigated in a mouse model with dextran sulfate sodium-induced colitis. Correlation of HDAC9 with CD8⁺ expression was assessed in tissue sections from patients with non-small cell lung cancer.

RESULTS

HDAC9 deficiency promoted tumor progression by decreasing the CD8⁺ DC infiltration of the TME. Compared with wild-type mice, the tumor-infiltrating DCs of Hdac9^-/- mice displayed impaired cross-presentation of tumor antigens and cross-priming of CD8⁺ T cells. Moreover, HDAC9 expression was significantly positively correlated with CD8⁺ cell counts in human lung cancer stroma samples.

CONCLUSIONS

HDAC9 deficiency decreased inflammation and promoted tumor progression by decreasing CD8⁺ DC infiltration of the TME. HDAC9 expression in the tumor stroma may represent a promising biomarker to predict the therapeutic responses of patients receiving CD8⁺ T cell-dependent immune treatment regimens.

Evidence for the loss and recovery of SLAMF9 during human evolution: implications on Dollo's law

Signaling lymphocyte activation molecule family member 9 (SLAMF9) is a cell surface protein of the CD2/SLAM family of leukocyte surface receptors. It is conserved throughout mammals and has roles in the initiation of inflammatory responses and regulation of plasmacytoid dendritic cell function. Through comparison of reference sequences encoding SLAMF9 in human, mouse, and primate sequences, we have determined that the SLAMF9 gene underwent successive mutation events, resulting in the loss of the protein and subsequent recovery of a less stable version. The mutations included a single base pair deletion in the second exon and a change in the splice acceptor site of that same exon. These changes would have had the effect of creating and later repairing a frameshift in the coding sequence. These events took place since the divergence of the human lineage from the chimpanzee-human last common ancestor and represent the first known case of the functional loss and recovery of a gene within the human lineage.

Signalling lymphocyte activation molecule family member 9 is found on select subsets of antigen-presenting cells and promotes resistance to Salmonella infection

Signalling lymphocyte activation molecule family member 9 (SLAMF9) is an orphan receptor of the CD2/SLAM family of leucocyte surface proteins. Examination of SLAMF9 expression and function indicates that SLAMF9 promotes inflammation by specialized subsets of antigen‐presenting cells. Within healthy liver and circulating mouse peripheral blood mononuclear cells, SLAMF9 is expressed on CD11b⁺, Ly6C⁻, CD11c^low, F4/80^low, MHC‐II⁺, CX₃CR1⁺ mononuclear phagocytes as well as plasmacytoid dendritic cells. In addition, SLAMF9 can be found on peritoneal B1 cells and small (F4/80^low), but not large (F4/80^high), peritoneal macrophages. Upon systemic challenge with Salmonella enterica Typhimurium, Slamf9^−/− mice were impaired in their ability to clear the infection from the liver. In humans, SLAMF9 is up‐regulated upon differentiation of monocytes into macrophages, and lipopolysaccharide stimulation of PMA‐differentiated, SLAMF9 knockdown THP‐1 cells showed an essential role of SLAMF9 in production of granulocyte–macrophage colony‐stimulating factor, tumour necrosis factor‐α, and interleukin‐1β. Taken together, these data implicate SLAMF9 in the initiation of inflammation and clearance of bacterial infection.

SLAM Family Receptor Signaling in Viral Infections: HIV and Beyond

The signaling lymphocytic activation molecule (SLAM) family of receptors are expressed on the majority of immune cells. These receptors often serve as self-ligands, and play important roles in cellular communication and adhesion, thus modulating immune responses. SLAM family receptor signaling is differentially regulated in various immune cell types, with responses generally being determined by the presence or absence of two SLAM family adaptor proteins-Ewing's sarcoma-associated transcript 2 (EAT-2) and SLAM-associated adaptor protein (SAP). In addition to serving as direct regulators of the immune system, certain SLAM family members have also been identified as direct targets for specific microbes and viruses. Here, we will discuss the known roles for these receptors in the setting of viral infection, with special emphasis placed on HIV infection. Because HIV causes such complex dysregulation of the immune system, studies of the roles for SLAM family receptors in this context are particularly exciting.