Cell Reports

The generation of an effective T cell response against an antigen depends on the recognition of the antigen by the T cell receptor (TCR), followed by T cell priming, initiating coordinated biophysical, biochemical and proliferative changes that drive differentiation into effector and memory clones. The immunological environments in which priming occurs, such as natural infection or vaccination, influences the quality and persistence of memory T cells, but the long-term impacts remain incompletely understood. Here, we investigate how the mode of priming shapes durable antigen-specific CD4+ T cell memory, utilising two cohorts 3-4 years after initial antigen encounter: individuals recovered from SARS-CoV-2 infection and infection-naive individuals who received a SARS-CoV-2 vaccination. Using ex vivo single-cell RNA sequencing, paired TCR sequencing and in vitro functional analyses, we characterise the transcriptional, clonal and functional profile of Spike-specific CD4+ T cells. Across both cohorts, CD4+ T cell responses against spike epitopes S166-180, S751-765 and S866-880, were immunodominant, with shared public TCR clonotypes indicating conserved antigen-recognition regardless of mode of priming. Despite this shared specificity, infection-primed individuals exhibited greater TCR repertoire diversity and lower CDR3{beta} sequence convergence. Transcriptionally, infection-primed cells exhibited a more cytotoxic and effector phenotype, while vaccine-primed cells preferentially adopted T follicular helper (Tfh)- and Th1-associated phenotypes. Infection-primed individuals also displayed enrichment of cell adhesion and integrin signalling pathways, with a greater proportion of spike-specific CD4+ T cells expressing 4{beta}1 integrin subunits, consistent with enhanced migratory and effector potential. Collectively, our findings demonstrate that the mode of antigen priming may influence the long-term CD4+ T cell memory states, influencing TCR repertoire diversity, functional differentiation and tissue-homing potential, years after the initial immune response.

N-methyl-D-aspartate receptors (NMDARs) populate fast-spiking (FS)-parvalbumin-positive (PV+) GABAergic interneurons (INs), where they play a critical role in shaping circuit motifs and memory. However, it is largely unknown whether and how NMDARs at FS-PV+-INs are gated by their co-agonists and the functional relevance of such modulations for their synaptic coupling with excitatory neurons. Here, we report that FS-PV+-INs in the adolescent mouse prefrontal cortex, an area central to complex cognitive operation exhibit functional GluN2B/D containing NMDARs. These receptors contribute to the excitatory drive of FS-PV+-INs and to the feedforward inhibition, controlling short-term and long-term synaptic plasticity. While the identity of the co-agonist controlling GABAergic tone is tuned by the synaptic activity regime from D-serine to glycine, we reveal that it remains largely unchanged at the excitatory synapse with D-serine being the sole co-agonist gating NMDARs. Lastly, we show that D-serine-deficient mice, a model of NMDAR hypofunction show selective attenuation of PV+-INs excitation together with selective loss of temporal summation and long-term plasticity at the excitatory synapse. Our study reveals the segregation of pools of NMDARs at the soma and dendrites that are differently sensitive to D-serine or glycine, the existence of distinct modes of activity-dependent regulation of these NMDARs by their co-agonists at this major type of GABAergic INs, and hence the rules governing cortical inhibition by FS-PV+-INs during a critical period of late postnatal development.

The role of epigenetic modifiers in astrogenesis is less understood compared to neurogenesis. For example, the Disruptor of telomeric silencing 1 like, DOT1L, conferring H3K79 methylation safeguards neural progenitors from premature differentiation in various brain regions, however, its role in astrogenesis has not yet been reported. Here, we decipher its role during astrogenesis using an Emx1-cre driven DOT1L conditional knock-out during the development of mouse cerebral cortex from E12.5 till P0. We describe two astrocyte types at P0, distinguishable by expression of phagocytosis markers genes. DOT1L loss-of-function (LOF) increased the number of those astrocytes that express fewer phagocytosis marker genes, while it affects a larger number of differentially expressed genes in those astrocytes that strongly express homeostasis marker genes. Our findings establish DOT1L as a barrier between these astrocyte states, limiting differentiation of the astrocytes expressing phagocytosis marker genes. We also identify multiple developmental origins of astrocytes. In addition to apical progenitors (AP), the prevailing stem cell population considered as origin of cortical astrocytes, we identify neural stem cells (NSC) in the dorsal telencephalon differentiating towards astrocytes, and Nkx2.1-lineage derived astrocytes, originating from the ventral telencephalon. This finding refines the prevailing view that dorsal telencephalon APs are the only source of embryonic cortical astrocytes, and enter astrogliogenesis after neurogenesis. We show that the expression of Emx1 discriminates different astrocyte origins during cortical development, and we describe a new set of transcription factors (TFs) that mark the state conversion between the homeostasis or phagocytosis expression programs in astrocytes. DOT1L orchestrates different TF networks, of which Lhx2, Nfia, Sox6, and Creb5 drive astrogliogenesis, and Nfia, Nfib, and Tcf4 affect astrocyte state conversion. Importantly, our analysis also shows that NSCs, APs and astrocytes de-differentiate within this lineage trajectory, and lowering the DOT1L-mediated epigenetic barrier strongly favours appearance of astrocytes with limited phagocytosis properties and reactivation of progenitor programs.

Olfactory dysfunction is a hallmark of COVID-19, yet the mechanisms by which severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes widespread sensory impairment remain incompletely understood. We compared the olfactory epithelial tropism of multiple SARS-CoV-2 variants in a mouse model and observed that Alpha and Beta variants exhibited the greatest infectivity for the olfactory epithelium (OE), whereas Omicron rarely infected this tissue despite comparable pulmonary viral titers. We further defined the effects of SARS-CoV-2 on olfactory sensory neurons (OSNs) using immunohistochemistry, single-cell RNA sequencing, spatial gene expression characterization, and functional odor stimulation. The localized infection of sustentacular cells triggered a tissue-wide interferon-stimulated antiviral response that extended beyond infected regions for Alpha and Beta but was largely absent following Omicron infection. Mature OSNs transiently adopted an interferon-responsive state before exhibiting persistent downregulation of odorant signal transduction, mitochondrial, and activity-dependent gene pathways. Consistent with these transcriptional changes, odor stimulation failed to elicit normal activity-dependent gene expression during SARS-CoV-2 infection, indicating impaired neuronal function without widespread neuronal loss. Progressive accumulation of macrophages further indicated sustained inflammatory remodeling of the OE. Together, these findings demonstrate that SARS-CoV-2 infection initiates tissue-wide antiviral signaling in the OE that persistently disrupts OSN function, providing a mechanistic framework for COVID-19-associated anosmia.

Human CD8 T cells have traditionally been classified into naive, central memory, effector memory, and terminal effector subsets using CCR7 and CD45RA expression, a framework that has guided immunological research and clinical immune monitoring for nearly three decades. However, recent single-cell studies have revealed transcriptionally distinct CD8 T cell populations, including GZMK-, GZMB-, and central memory-like states, raising important questions regarding their relationship to canonical flow cytometric subsets. Here, we systematically integrated transcriptomic, epigenetic, and phenotypic analyses to evaluate the correspondence between these classification schemes. We demonstrate that conventional CCR7-CD45RA gating generates heterogeneous populations containing extensive mixtures of transcriptionally and epigenetically distinct CD8 T cell states, resulting in poor resolution of biologically meaningful subsets. To address this limitation, we developed a surface-marker framework based on CD55, CD319, and CX3CR1 that accurately identifies transcriptionally defined human CD8 T cell populations using standard flow cytometry. This strategy enables direct isolation of viable cells, including GZMK-expressing cells increasingly implicated in aging, chronic inflammation, autoimmunity, and cancer, which previously could only be identified using intracellular staining or single-cell sequencing. Functional characterization of purified subsets revealed marked differences in proliferative capacity, cytokine production, and cytotoxic activity, demonstrating that transcriptionally defined states possess distinct immune functions. Together, these findings establish a biologically grounded framework for CD8 T cell classification and provide a practical platform for mechanistic studies, biomarker discovery, and cellular immunotherapy applications.

The long non-coding RNA Negative Regulator of Antiviral Response (NRAV) is known to suppress antiviral immunity by regulating interferon response, but its functional role in tumor immunology remains poorly understood. We examined the relevance of NRAV in melanoma and found that high NRAV expression was associated with poor survival, reduced inflammatory pathway activation, and resistance to immune checkpoint blockade. Bulk and single-cell transcriptomic profiling indicates that NRAV expression is selectively enriched in malignant cells suggesting a potential cancer cell-intrinsic function. To examine whether NRAV can regulate inflammatory responses in melanoma cells, we manipulated the levels of NRAV in the BRAF-mutant A375 melanoma model and characterized the expression of key interferon-stimulated genes (ISGs) following type-I and type-II interferon stimulation. Our findings reveal that the stable NRAV overexpression blunts the induction of key ISGs, whereas NRAV knockdown reciprocally amplifies their transcription. Subcellular fractionation revealed that NRAV is predominantly localized to the nuclear compartment of melanoma cells and the overexpression of NRAV altered regulatory histone marks on the target ISG promoters including MX1 and IFITM3. Collectively, these findings establish NRAV as a tumor-intrinsic epigenetic regulator of interferon signaling, highlighting its potential contribution to melanoma immune evasion.

Physical exertion at high-altitude imposes a dual stress of hypoxia and mechanical load, yet the underlying immune adaptations remain poorly understood. Plasma proteomics and single-cell RNA sequencing were performed in 46 healthy men undergoing standardized exercise at low and high altitudes, and the findings were validated in mice exposed to chronic extreme hypoxia (simulated 5,800 m) combined with exhaustive exercise. Whereas broad immune activation was induced by low-altitude exercise, cytotoxic and innate effector programs in CD8 T cells, natural killer cells, monocytes, and dendritic cells were broadly suppressed following high-altitude exercise. In contrast, humoral immunity was enhanced, as indicated by the activation of plasmablasts and CD4 memory and proliferating T cells. Mature neutrophils were functionally reprogrammed toward phagocytosis and degranulation, accompanied by an expansion of activated circulating neutrophils. A high-altitude-specific program involving chemotaxis and vascular extravasation was further identified by plasma proteomic and murine muscle transcriptomic analyses. These adaptations were associated with enhanced APRIL, MIF, and Annexin A1 signaling and attenuated CCL-chemokine and complement pathways. Collectively, high-altitude exercise was shown to induce coordinated immune reconfiguration characterized by cellular immunosuppression, selective humoral enhancement, and neutrophil-mediated tissue infiltration.

Efficient myelin regeneration requires coordinated signaling between oligodendrocyte progenitor cells (OPCs) and the extracellular matrix, yet how specific heparan sulfate sulfation patterns regulate this process remains poorly understood. The extracellular endosulfatases Sulf1 and Sulf2 selectively remove 6-O-sulfate groups from heparan sulfate proteoglycans (HSPGs). We previously demonstrated that these enzymes are highly expressed by OPCs following demyelination and inhibit OPC recruitment, differentiation, and remyelination through activation of BMP and WNT signaling. We investigated whether sulfotransferases that establish 2-O and 6-O sulfation during HSPG biosynthesis regulate remyelination. Using OPC-specific conditional knockout models, deletion of the 2-O sulfotransferase Hs2st1 enhanced OPC recruitment, oligodendrocyte differentiation, and remyelination through suppression of BMP and WNT signaling. Loss of 2-O sulfation induced compensatory remodeling of the heparan sulfate glycome, with a marked enrichment of 6-O-sulfated HS species. Conversely, deletion of 6-O sulfotransferases impaired OPC recruitment and differentiation and reversed the Hs2st1 phenotype, identifying 6-O sulfation as the dominant functional determinant of remyelination. Together, these findings establish hierarchical control of remyelination by heparan sulfate sulfation, demonstrating that compensatory remodeling of the heparan sulfate glycome governs regenerative signaling following demyelination.

Osteoarthritis (OA) is characterized by cartilage breakdown, extracellular matrix remodeling, and synovial inflammation. Dysregulated integrin 5{beta}1 signaling and fibronectin fragmentation are key drivers of OA progression. We found that in ihMSC, LNA043, Full length ANGPTL3 (FL-ANGPTL3, and C-terminal fibronogen-tlike domain of ANGPTL3 (C-ANGPTL3) interacted with both integrin 5{beta}1 and fibronectin, consistent with a multivalent binding mode supported by AlphaFold based structural predictions. FL-ANGPTL3 supported ihMSC adhesion and induced human monocyte migration, with both effects being dependent on integrin {beta}1. C-ANGPTL3 alone was sufficient to mediate these effects, although with reduced efficacy compared to the full-length protein. In contrast, LNA043 did not support ihMSC adhesion but retained integrin {beta}1-dependent monocyte migratory activity, defining a more selective functional profile and indicating that further truncation modulates downstream responses without abolishing integrin engagement. To further explore the biology of ANGPTL3 and the mechanism of action of LNA043 we employed a targeted RASL Seq profiling. We found that both FL- and C-ANGPTL3, but not LNA043, induced broad transcriptional reprogramming and counter regulated fibronectin fragment-driven inflammatory signaling in monocytes. We uncovered a role for ANGPTL3 in fibronectin-integrin 5{beta}1 signaling and showed that LNA043 preserves this interaction while uncoupling it from strong immune responses.

Acquired resistance to mitogen-activated protein kinase (MAPK) pathway inhibitors remains a major barrier to durable control of BRAF-mutant melanoma. Although resistance mechanisms are heterogeneous, they converge on adaptive programs that support survival, phenotypic plasticity, and metabolic fitness. We asked whether eukaryotic translation initiation factor 4A (eIF4A)-dependent mRNA translation represents a shared vulnerability of kinase inhibitor-resistant melanoma. Using matched BRAFV600E A375 and BRAF inhibitor-resistant A375R cells together with additional melanoma models, we integrated pharmacological and functional assays with polysome-associated RNA sequencing, quantitative proteomics, bioenergetic profiling, metabolomics, [U-13C5]glutamine tracing, and xenograft studies. Melanoma cells remained sensitive to multiple eIF4A inhibitors regardless of their responsiveness to BRAF inhibition. The eIF4A inhibitor CR-1-31-B rapidly reduced nascent protein synthesis when used alone in A375 cells and when added to the BRAF inhibitor PLX4032 in A375R cells; it also reduced BCL-2, CDK4, and cyclin D3 abundance, suppressed clonogenic growth, and induced apoptosis. Integrated analysis showed that acquired resistance involved broad RNA-abundance remodeling with superimposed changes in translational efficiency and buffering, affecting survival, extracellular-matrix and plasticity programs, and mitochondrial and metabolic functions. In resistant cells, CR-1-31-B induced early transcript-selective translational changes, accompanied at later time points by RNA-abundance and proteome remodeling. Publicly annotated 5' untranslated regions (5'UTRs) of CR-1-31-B-sensitive transcripts were enriched for purine-rich sequence architecture and local structural complexity. eIF4A inhibition preferentially attenuated the expression of proteins acquired during resistance and imposed a lower-output metabolic state in sensitive and resistant cells, reducing tricarboxylic-acid-cycle and pentose-phosphate-pathway metabolite pools and restricting intracellular glutamine-carbon transfer downstream of uptake. In A375 xenografts, CR-1-31-B delayed tumor growth, while its combination with PLX4720 produced deeper and more sustained tumor control and prolonged tumor endpoint-free survival compared with PLX4720 alone. These findings show that multiple resistance-associated programs spanning signaling, cell survival, and metabolism share a dependency on eIF4A-dependent translation and provide a preclinical rationale to test whether adding eIF4A inhibition can prolong responses to MAPK-targeted therapy in melanoma.

Metabolic pathways support biomass synthesis and provide substrates for epigenetic modifications of histones and DNA. These findings are particularly relevant for adult stem cells, where metabolic changes significantly impact functional behavior. However, assessing the metabolism of these cells in their native microenvironment is challenging as this typically necessitates dissociation prior to metabolic analysis. In this study, we focus on muscle stem cells (MuSCs) and show that removing these cells from the niche significantly alters their metabolic profile. To overcome this issue, we developed a novel enzymatic staining method for in situ metabolic profiling at a single-cell resolution. This approach reveals unexpected metabolic heterogeneity of MuSCs, identifying oxidative and glycolytic subsets, and demonstrates that their metabolism is directly modulated by adjacent myofibers. Accordingly, perturbing myofiber metabolism remodels the MuSC niche and drives metabolic adaptation in MuSCs. Finally, we define the kinetics by which myofiber-dependent metabolic regulation of MuSCs is re-established during muscle regeneration, thereby revealing how niche-imposed metabolic cues shape stem cell identity in vivo.

Brain capillary pericytes are essential components of the neurovascular unit, yet the extent of their molecular heterogeneity within intact vascular networks remains poorly understood. Here, we combined spatial imaging with reanalysis of independent single-cell transcriptomic datasets to investigate the molecular organization of adult mouse brain pericytes. We identified spatial organization of pericyte molecular heterogeneity associated with anatomical region and position within the vascular network, including recurrent differences in ACE2, CASQ2, Igf2, and OPN expression. Moreover, pericyte molecular phenotypes varied with aging, acute ischemia, and circadian phase. Notably, light-dark phase emerged as a major axis of transcriptional variation, with pericytes exhibiting distinct circadian phase-associated molecular states. Together, these data demonstrate that adult brain pericytes exhibit spatially organized and dynamically regulated molecular heterogeneity associated with vascular and physiological context.

Cognitive flexibility (CF) declines during aging and is further impaired in neurodegenerative diseases such as Huntingtons disease (HD), yet the molecular mechanisms underlying these deficits remain poorly understood. Thalamostriatal (T-S) synapses are critical for CF, and we previously identified Heat Shock Factor 1 (HSF1) as a regulator of T-S density in HD. However, how HSF1 regulates T-S synapses and whether it modulates cognitive flexibility (CF) remained unclear. Here, we combined HSF1 ChIP-seq, transcriptomics, synapto-proteomics, targeted genetic manipulations and behavioral analyses to study how HSF1 regulates T-S synapses and CF. We found HSF1 directly controls a transcriptional program governing postsynaptic architecture and actin cytoskeletal dynamics, which are disrupted in aging and HD. Loss of HSF1 drives selective destabilization of actin patches at T-S shaft synapses and impaired CF decline. Our results underscore a novel function for HSF1 in the regulation of striatal neural circuits with essential implications in the neurobiology of cognitive flexibility.

The tumor suppressor p53 and the transcription factors estrogen receptor and androgen receptor regulate growth in a sex-dependent hormone-responsive manner, as in breast and prostate tumors and muscle tissue. Using a model of transcriptional regulation, we investigated co-regulation between p53 and hormone receptors in different cellular contexts and highlight an enrichment in mammary and muscle cell types. Sequence, structural and epigenomic evidence demonstrate a broadly distributed functional 73-bp p53-estrogen receptor grammar spanning nucleosome entry/exit to dyad, while p53-androgen receptor grammar spans 146 bp. At a functional breast cancer enhancer regulating Cyclin D, varied spacing led to lower predicted p53 binding. Genome-wide analysis found a major role of Alu sequences in distributing this grammar, in particular in mTORC1 pathway genes, with an evolutionary association of primate body-size sexual dimorphism and muscle aging.

Germinal center (GC) B-cells give rise to the majority of non-Hodgkin lymphomas, underscoring the need to pinpoint critical processes that initiate and drive lymphomagenesis. Lymphoma driver mutations can alter GC B cell functions and B cell fate decisions. Here, we studied how EZH2 oncogenic mutation in GC B cells alters cellular motility and interactions with T follicular helper (Tfh) cells and follicular dendritic cells (FDCs) to determine B cell fate. By combining intravital imaging, single-cell behavior analyses, and RNA sequencing, we uncover how lymphoma-associated EZH2 mutations reprogram the behaviors of GC B cells in vivo. We found that EZH2 mutations increased single-cell motility speeds and morphological plasticity of GC B cells, redirecting migration toward the FDC-rich light zone subregions rather than to the dark zone. Although mutant EZH2 GC B cells exhibited normal engagement quality with FDCs, they showed shorter interaction times and reduced surface engagement with Tfh cells. Notably, EZH2 mutant B cells required prior contact with FDC before engaging with Tfh cells, thus impairing DZ recycling. This motility phenotype scaled with local mutant clone abundance, suggesting a behavioral strategy underlying how mutant cells outcompete WT cells. Lastly, we developed scMOTIPh, a computational framework that integrates single-cell behavioral features with transcriptomic profiles. Applying scMOTIPh to mutant GC B cells within the FDC-rich zone revealed enhanced ATP production, metabolic and antigen-presentation programs, and suppression of cell-death pathways, which is consistent with a tendency for malignant transformation and survival fitness. These findings provide an in vivo, single-cell view of how an epigenetic lesion rewires the local microenvironment by modulating single-cell behaviors within native GCs, revealing a dynamic mechanism for early lymphomagenesis.

The mammalian BRG-/BRM-associated factor (BAF) chromatin remodeling complexes are crucial regulators of hematopoietic stem and progenitor cell (HSPC) fate. Expression of the ncBAF subcomponent, BRD9, is altered in both normal aging and myeloid malignancies. We find that in adult human HSPC, BRD9 regulates the differentiation of myeloid progenitors. Upon degradation of BRD9 in these cells, ncBAF is displaced from the chromatin, leading in turn to enhanced recruitment of cBAF to bona fide CEBPA target sites. With the shift from ncBAF to cBAF, HSPC differentiation results in increased generation of myeloid-derived suppressor cells (MDSC) that secrete elevated levels of IL-8. Soluble factors from these myeloid cells, which have lost BRD9, enhance the stemness of breast cancer cells in vitro. In contrast, bromodomain inhibition of BRD9 results in minimal alterations of ncBAF binding and myeloid differentiation, indicating that BRD9 acts as a barrier to human MDSC differentiation in a bromodomain-independent manner.

The digestive tract is a major site of nutrient absorption. It also harbors the densest microbial communities in our body. It is well known that the brain perceives ingested nutrient information through the intestinal epithelium enteroendocrine cell (EEC)-vagal pathway. Little is known about how the brain senses gut bacteria that reside in the intestinal lumen. In this study, we combined novel in vivo EEC calcium imaging, EEC optochemical stimulation, and vagal sensory neuron calcium imaging in the zebrafish model, and revealed that segregated pathways mediated by different EEC and vagal sensory neuron subtypes differentially perceive beneficial nutrient information and harmful irritant pathogenic bacterial information. Our study revealed that a group of EECs that express the nociceptive receptor Transient receptor potential ankyrin A1 (Trpa1) can be activated by the pathogenic bacterium Edwardsiella tarda (E. tarda) or E. tarda-produced irritant metabolites. These Trpa1+EECs do not sense nutrients. Trpa1+EECs, but not other EECs, uniquely and highly express both Serotonin and the neuronal peptide Pituitary adenylate cyclase-activating polypeptide (Pacap). Using pharmaceutical and genetic approaches, our data showed that Pacap synergizes with Serotonin and is required for Trpa1+EEC-induced vagal activation. Stimulating the Trpa1+EEC-vagal sensory pathway potently inhibits a group of vagal motor neurons that innervate visceral organs in the caudal dorsal motor nucleus of the vagus (cDMV). However, the same group of cDMV neurons is activated by nutrients. Microbially induced cDMV inhibition enhances liver gluconeogenesis and promotes intestinal neutrophil recruitment. Inhibiting glucose metabolism, disrupting Trpa1+EEC-vagal sensory pathway, or optogenetically activating cDMV neurons in E. tarda colonized zebrafish induces intestinal E. tarda to switch from an aggregated phenotype to a diffused phenotype and hinders E. tarda clearance. Furthermore, our data show that disrupting the Trpa1+EEC-vagal sensory pathway impairs intestinal neutrophil recruitment and hinders survival, suggesting a protective role of the Trpa1+EEC-vagal microbial sensing pathway in pathogen defense. Together, our data revealed that a distinct non-nutrient-sensing Trpa1+EEC-vagal circuit senses gut microbial irritants, coordinating neuronal, metabolic, and immune responses to enhance host defense and pathogen clearance.

Aging and tobacco exposure are major determinants of risk and outcome in HPV-negative oral cavity squamous cell carcinoma (OSCC), yet the cellular programs linking host factors to tumor immunity remain poorly defined. We reprocessed and reanalyzed previously published single-cell RNA-seq data from 19 HPV-negative OSCC tumors and we identified a robust age- and smoking-associated expansion of SPP1high tumor-associated macrophages (TAMs), accompanied by a shift toward a myeloid-dominant and lymphocyte-reduced tumor microenvironment. SPP1high TAMs exhibit a distinct transcriptional state enriched for extracellular-matrix remodeling and metabolic programs and reduced antigen-presentation pathways. They also express inflammatory chemokines such as CXCL2 and CXCL3 and down-regulate the cytotoxic mediator TNFSF10, suggesting a broadly protumor TAM phenotype. Ligand-receptor modeling suggests that SPP1high TAMs act as key communication hubs, with dominant SPP1-CD44 signaling to T-cell subsets. Transcription-factor analysis further implicates a POU2F1/POU2F2/SP1 module in maintaining this state. In the TCGA HNSCC cohort, the association between SPP1 expression and overall survival did not reach statistical significance after adjustment for age and tumor purity. These findings demonstrate that aging and tobacco exposure converge to expand an SPP1high TAM population that remodels the extracellular matrix and suppresses antitumor immunity, highlighting the SPP1-CD44 axis and its upstream regulators as potential therapeutic targets in high-risk OSCC.

RTTN (rotatin) is a centrosomal protein mutated in severe malformations of cortical development, yet how its dysfunction disrupts human corticogenesis has remained unclear. Here, we show that RTTN has an unrecognized function at the core of the translation machinery. Using human telencephalic and hippocampal organoids carrying distinct RTTN alleles, together with single-cell and bulk transcriptomics, polysome profiling, and tRNA pseudouridine sequencing, we find that RTTN is enriched in cycling first-trimester neural progenitors and physically associates with ribosome-biogenesis and RNA-processing factors. RTTN mutations impair rRNA biogenesis and polysome assembly, reduce cytoplasmic ribosome density and nascent protein synthesis, and remodel the tRNA pseudouridylation landscape through both a PUS7L-dependent variable-arm signature and a broader RTTN-specific defect. These translational deficits are accompanied by prolonged mitosis, reduced entry into S-phase, and impaired interkinetic nuclear migration in mutant progenitors. Our findings redefine RTTN as a regulator of ribosome homeostasis and mRNA translation and implicate defective translational capacity as a driver of RTTN-associated microcephaly. Graphical AbstractRTTN sustains ribosome and tRNA homeostasis in human neural progenitors; its mutation disrupts mRNA translation, stalling progenitor proliferation and interkinetic nuclear migration, and driving cortical malformation and growth failure. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/744412v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@193ebb1org.highwire.dtl.DTLVardef@56c7d0org.highwire.dtl.DTLVardef@1586876org.highwire.dtl.DTLVardef@1322e21_HPS_FORMAT_FIGEXP M_FIG C_FIG

B cell-derived IgG in the dorsal root ganglia (DRG) drives neuropathic pain after peripheral nerve injury (PNI), but the site of B cell organization is unclear. Here, PNI induced leukocyte clusters in the DRG meninges, enveloped by lymphatic endothelium and apposed to high endothelial venules. These clusters resemble tertiary lymphoid structures (TLSs) with germinal center-like features, including germinal center B cells and plasma cells, and follicular dendritic and follicular helper T cells. Single-cell RNA sequencing revealed enrichment of germinal center B cells in the DRG meninges after PNI. Germinal center B cells regulate TLS organization: TLSs were absent after deletion of Ezh2 from germinal center-experienced B cells. Intrathecal CD20 monoclonal antibody to locally deplete B cells also disrupted TLS organization. Conversely, intrathecal B cell transfer to B cell-deficient (muMT) mice was sufficient for TLS organization after PNI. Allodynia did not develop when TLS organization was disordered. Similar TLSs formed in pig DRG after tail docking and in human donors with chronic pain, where B cell receptor clonotype analysis confirmed functional maturity. Together, these data establish that germinal center B cells are required for TLS organization, and that disrupting this process abolishes the development of neuropathic pain after PNI.