Immunology & Cell Biology

Bone marrow chimeras are widely used to study immune development and function. As the field moves from cesium-137 (137Cs)-based irradiators to X-ray irradiators for safety reasons, it is essential to determine if there are differences in immune system reconstitution after irradiating mice with one of these two radiation sources. Here, we performed a comprehensive immunological comparison of mice lethally irradiated with 137Cs or one of two different X-ray platforms and reconstituted with congenic bone marrow. Mice received 12 Gy total body radiation in two 6 Gy sessions followed by intravenous transfer of donor hematopoietic stem cells and were analyzed eight weeks post-transplant. We assessed mouse survival, donor chimerism, immune cell subset distribution, and activation states across multiple organs (bone marrow, spleen, lymph nodes, liver, and lung). All groups exhibited comparable survival and high levels of donor chimerism, with expected organ-specific reconstitution patterns. Immune lineage distributions, CD4/CD8 ratios, and activation states did not differ by irradiation type. Host-derived radioresistant cells were also similar across all irradiation groups and were predominantly composed of T cells skewed toward an activated phenotype. Overall, our data show that X-ray irradiation with proper filters and energy levels (225 KVp and 320 KVp) can yield equivalent immunological outcomes, including immune reconstitution and activation states, as compared to the same radiation dose from 137Cs-based irradiation in bone marrow chimera models. These results support the continued adoption of X-ray irradiation systems in place of 137Cs for generating bone marrow chimeras to be used across a wide range of immunologic studies.

CD8 T cells play a central role in immune responses to infection and cancer. However, the diversity of T cell receptor (TCR) specificities makes it challenging to study the mechanisms that regulate T cell activation, differentiation, and effector function. Beyond TCR transgenic mouse models, various complex genome-editing approaches have been employed to overcome this challenge. However, these strategies are often technically demanding, time-intensive, and difficult to adapt. Investigators who are interested in testing de novo TCRs under their chosen experimental conditions would benefit from a standardized and accessible method. Here, we describe a protocol that combines ribonucleoprotein (RNP)-based CRISPR-Cas9 editing with retroviral transduction to enable efficient genetic manipulation of murine CD8 T cells. We show that T cells engineered via this protocol can be generated at sufficient scale for downstream in vitro assays and in vivo adoptive transfer experiments. We expect this method will be useful for investigators who require a standardized and accessible way to study how TCR specificity impacts CD8 T cell responses.

Major histocompatibility complexes (MHC) govern antigen presentation and T cell receptor (TCR) selection. Accurate in vivo modeling of human immunity therefore requires physiological human MHC TCR interactions. Humanized NOD scid IL2null (NSG) mice engrafted with human CD34+ hematopoietic stem cells are widely used to provide preclinical platforms for the development of advanced therapies; however, interactions between murine MHC and human TCR can promote xenoreactivity and alter T cell development. Here, we investigated how elimination of murine MHC together with different conditioning regimens shapes human T cell maturation in vivo. CD34+ cells from ten cord blood donors were transplanted into conventional NSG mice or murine MHC deficient NSG derivatives (DKO) following either sublethal irradiation or myeloablative busulfan conditioning. Integrated analyses combining flow cytometry, plasma cytokine profiling, and bulk and single cell TCR sequencing revealed marked differences in T cell differentiation across models. Busulfan conditioned DKO mice developed highly proliferative, activated, and cytotoxic T cells together with clonally expanded TCR repertoires. In contrast, irradiated NSG mice preferentially accumulated naive, NKT, and regulatory T cell populations. Busulfan-conditioned DKO mice showed no evidence of xenogeneic graft versus host disease and represent a refined enabling platform for human T cell development and provide a foundation for future preclinical evaluation of advanced gene and cell therapies.

Wildfire smoke is an escalating global public health threat exposing millions of people, including children, to hazardous air pollution each year. Although wildfire smoke toxicants have been linked to a range of adverse health outcomes, including immune dysregulation, the long-term consequences of real-world pediatric wildfire smoke exposure on health and development remain largely unknown. To investigate the persistent effects of early-life exposure on immune health, here we leveraged a cohort of rhesus macaques that experienced nine consecutive days of hazardous wildfire smoke exposure in infancy during the 2020 Oregon Labor Day wildfires. By integrating ex vivo immune stimulations, multiplex cytokine profiling, single-cell transcriptomics, and genome-wide DNA methylation profiling, we identified persistent immunological consequences across molecular and functional levels. We found that a single severe postnatal exposure, in the first three months of life, was associated with persistent change in the innate immune response, including reduced pro-inflammatory cytokine response to a bacterial endotoxin, with subtle but consistent transcriptional changes in myeloid cells, particularly among males. Wildfire smoke exposure was also associated with changes in proportion of B and T/NK cells, and within the T/NK cell compartment, exposed animals exhibited an expansion of cytotoxic cells. Consistent with this, CD8+ T cells displayed extensive transcriptional remodeling and shifted toward more differentiated effector states, with the greatest differentiation observed in animals exposed at the youngest ages. Genome-wide DNA methylation profiling identified smoke-associated methylation changes consistent with acceleration of epigenetic aging, as well as persistent epigenetic alterations impacting genes involved in oxidative stress responses, innate immunity, T cell differentiation, and hematopoiesis. These findings demonstrate that a single severe wildfire smoke exposure during a critical developmental window is associated with extensive immune and epigenetic remodeling that persist years after exposure, providing new insight into the long-term biological consequences of early-life wildfire smoke exposure.

While professional antigen-presenting cells drive adaptive immunity, atypical cell types can fulfill this role in the bone marrow. Megakaryocytes (MKs) are canonically recognized for platelet production, but recent studies indicate functional heterogeneity and immune potential. We found that ~20% of bone marrow MKs express Major Histocompatibility Complex (MHC) II and co-stimulatory receptors CD80, CD86, CD40, and CD83. These MKs process and present antigen to activate T cells ex vivo in an MHC II-dependent manner. MK/T cell interactions induced TGF-{beta}1 secretion and promoted induced Treg differentiation. Prior stimulation of MKs with LPS or Poly I:C was associated with modest Th1-associated CD4+ T cell responses, including IFN-{gamma} and TNF- production, without robust Th17 differentiation. Immunopeptidomics of the murine MK MHC II receptor confirmed occupancy by exogenous peptides, suggesting in vivo functionality. Using a murine model with MK-targeted deletion of MHC II (Pf4-MHC{Delta}/{Delta}), we observed altered TLR signaling and reduced bone marrow TGF-{beta}1. Together, these findings identify MHC II+ MKs as noncanonical antigen-presenting cells with the potential to modulate CD4 T cell responses as part of the immune regulation of the bone marrow niche.

Current vaccines for respiratory viruses are primarily administered intramuscularly. Messenger RNA-lipid nanoparticle (LNP)-based intramuscular vaccination for respiratory coronaviruses induces strong systemic IgG antibody responses; they do not consistently elicit IgA in the upper and lower respiratory tracts. Using a synthetic consensus spike protein aimed to broadening immunity against SARS-like viruses, SarbConS, coupled to ferritin nanoparticles co-delivered with mastoparan-7 and an FDA-approved CpG adjuvant, we intranasally boost SARS-CoV-2-immune animals. This intranasal boosting strategy elicits durable mucosal IgA responses in the respiratory tract, along with robust systemic IgG responses, and demonstrates durable protection against SARS-CoV-2 and zoonotic SARS-like viruses from bats and pangolins. Intranasal delivery of mastoparan-7 and CpG with MERS-CoV spike protein similarly elicits MERS-CoV-specific mucosal IgA and protects against MERS-CoV challenge in mice. Moreover, we observe durable protection against these genetically divergent zoonotic SARS-like viral challenges compared to intramuscular mRNA-LNP or unadjuvanted intranasal spike boosters. Intranasal SarbConS-ferritin nanoparticle intranasal vaccination similarly elicited durable mucosal IgA and antigen-specific memory B cell responses in the airways. The protective efficacy of M7-CpG adjuvanted SarbConS ferritin nanoparticle intranasal boosters was abolished in IgA knockout mice, suggesting a requirement for IgA in mediating respiratory mucosal vaccine-mediated protection against coronavirus infection. Altogether, our results demonstrate that respiratory mucosal vaccination can elicit durable and cross-protective mucosal IgA responses against genetically diverse zoonotic coronaviruses with implications for improved mucosal vaccines for highly transmissible respiratory viral pathogens.

Background: The systemic immune responses associated with persistent respiratory symptoms (PRS) after exposure to airborne environmental pollutants remain poorly understood. Objective: To identify immune disturbances associated with PRS, defined as persistent wheeze, cough, or breathlessness, we examined systemic immune responses and airway function in a cross-sectional cohort with detailed histories of airborne pollutant exposure. Methods: Never-smoking post-deployment Veterans with PRS (n=16) or without PRS (n=24) underwent chest computed tomography, pulmonary function testing, and oscillometry to assess structural and functional airway abnormalities. Peripheral blood mononuclear cells (PBMCs) were stimulated with anti-CD3/CD28 antibodies, lipopolysaccharide, or {beta}-glucan, and cytokine production was measured. Correlation analyses evaluated associations between cytokine responses and physiological measures of airway function. Results: Oscillometry, but not conventional pulmonary function testing or chest computed tomography, detected small-airway abnormalities in participants with PRS, including significantly greater frequency dependence of resistance and higher resonant frequency. Baseline PBMC cytokine concentrations were similar between groups. After stimulation, however, PBMCs from participants with PRS showed increased IL-17A production consistent with a type 17 (T17) response; innate stimulation also increased the type 2 (T2) cytokines IL-33 and IL-4. T2/T17 cytokine responses correlated positively with oscillometric measures of small-airway dysfunction. Conclusion: Individuals with PRS exhibited a stimulus-dependent systemic T2/T17 immune signature that was associated with early small-airway dysfunction. Clinical Implication: Stimulus-dependent systemic immune profiling, combined with oscillometry, may help identify early respiratory abnormalities in pollutant-exposed individuals whose conventional pulmonary tests remain normal.

T cell repertoire sequencing has unveiled a vast, complex array of T cells responsible for the human immune responses. Traditional analytic methodology fails to fully characterize and quantify the diversity of T cell receptors constituting the T cell repertoire. T cell receptor clonal frequency measured in terms of T cell receptor beta (TRB) V gene segment usage when arrayed in correspondence with the respective V gene segment positions on the TRB loci yields a periodic, undulating curve in the spatial domain of the TRB genomic locus. Using the genomic distance from the TRB-D1 segment to the TRB-V1-29 segments, Fourier analysis was performed utilizing Lomb-Scargle periodogram to obtain Spectral Power curves quantifying the TRB V clonal frequencies from 6 allogeneic stem cell transplant donors (baseline) and recipients (>/=100 days) using a variety of analytic software. Spectral Power curves revealed dominant spectral peaks at wavelengths ranging from 4-9 kb (113-252 millicycles/kb) in the six donors, with consistent frequency domain spectral patterns. This is consistent with similar use of V segments across healthy individuals. Recipients on the other hand demonstrated more dispersed spectra, with a spectral centroid shifted towards higher frequencies compared to donors (260 vs. 247 millicycles/kb). Consistent with this observation, the Low Frequency Index was lower in the recipients (0.18 vs 0.20). Power was concentrated in the <3 kb and 3-12 kb wavelengths in both groups. The analyses reported here demonstrate that the healthy SCT donors have a remarkably similar spectral signature occupying short to intermediate wavelegnths in the frequency domain, whereas recipients tend to shift towards higher frequencies. These findings are consistent with a normal organized distribution of TRB V segment usage in healthy individuals (by analogy other loci), and a more diffuse and disorderly usage in recipients, consistent with the notion of T cell responses constituting a dynamical system which evolves as a function of time. Fourier analysis of TRB (and potentially TRA) sequencing data provides a repertoire wide summary of T cell clonal distribution.

Down syndrome, caused by trisomy 21, is characterized by chronic interferon-associated inflammation and immune dysregulation, yet the contribution of human secondary lymphoid organs to shaping this immune landscape remains unclear. Using multimodal single-cell and spatial profiling of human tonsils, we identify extensive remodeling of immune organization in trisomy 21. CD4 T cells are skewed away from canonical follicular helper (TFH) programs toward inflammatory TFH1-like and cytotoxic helper states enriched for interferon-responsive transcriptional programs. Tonsillar TFH cells exhibit increased interferon-{gamma} and interleukin-21 production, indicating inflammatory skewing toward type 1 helper immunity. These alterations are accompanied by changes in dendritic cell and CD8 T-cell compartments, reduced follicular size, increased extrafollicular TFH1-B-cell proximity and altered B-cell differentiation trajectories. Together, our findings identify trisomy 21 as a unique human context to investigate how chronic interferon-associated inflammation reshapes lymphoid tissue organization and adaptive immune cell fate decisions.

Inflammation is essential for regeneration yet can also drive fibroinflammatory remodeling; what determines these opposing outcomes remains unclear. Comparative transcriptomic analyses revealed that injured mouse hearts activated a broad inflammatory program, whereas zebrafish hearts mounted a restricted response characterized by selective il11 induction. This divergence extended across tissues and species: the non-regenerative mammalian injuries examined shared an inflammatory signature distinct from regenerative vertebrate contexts. We identified the AP-1 transcription factor Junb as an Il-11-Stat3-dependent regulator that restrains inflammation during fin fold regeneration. Combined loss of junba and junbb amplified a mammalian-like inflammatory program, increased neutrophil recruitment and fibroinflammatory gene expression, and reduced proliferation and regenerative outgrowth. Strikingly, dexamethasone or ibuprofen substantially restored regeneration in Junb deficient zebrafish larvae, demonstrating that hyperinflammation is a major determinant of regenerative failure. Thus, the Il-11-Stat3-Junb axis maintains a regeneration permissive inflammatory state preventing a regenerative response from shifting toward mammalian-like fibroinflammation.

Life-long production of blood requires the preservation of hematopoietic stem cell (HSCs) regenerative capacity during inflammation. The cytokine, Thrombopoietin (THPO), is essential for HSC maintenance yet its role during inflammatory stress remains incompletely understood. Long-term repopulating potential was rapidly depleted in THPO-deficient HSCs upon poly(I:C) administration through inflammatory pyroptosis. Transcriptomic and chromatin accessibility analyses revealed constitutive interferon (IFN) pathway activation in THPO-deficient HSCs, characterized by enhanced STAT1 signaling, increased accessibility of STAT and IRF motifs, and elevated expression of IFN-stimulated genes. Lipidomic profiling further identified selective shifts in sphingomyelin (SM) species and enrichment of features associated with increased bilayer rigidity. THPO-deficient HSCs displayed elevated membrane SM incorporation, impaired membrane fluidity and altered membrane ultrastructure. Genetic ablation of Stat1 normalized membrane lipid abnormalities and reduced pyroptotic activation and restored HSC survival and regenerative function under inflammatory stress. Together, these findings identify a STAT1 and SM metabolism as critical THPO downstream to protect HSCs from inflammatory pyroptosis. Our results reveal membrane lipid homeostasis as a fundamental mechanism through which cytokine signaling safeguards HSC function during stress.

Group 2 innate lymphoid cells (ILC2s) regulate type 2 immune responses partly by recruiting eosinophils, but the mechanisms underlying this process remain incompletely understood. Although both ILC2s and type 2 T helper (Th2) cells are capable of expressing IL-5, a cytokine critical for recruiting eosinophils, ILC2s are more potent than Th2 cells in this process. Here, we show that the transcription factor Bhlhe40 promotes GM-CSF production in ILC2s, and Bhlhe40 expression in ILC2s is required for efficient eosinophil recruitment during both papain- and helminth-induced type 2 immune responses. However, Bhlhe40 deficiency in ILC2s had no effect on the production of classical type 2 cytokines, including IL-4, IL-5 and IL-13, despite Bhlhe40 being required for type 2 cytokine production by Th2 cells. Furthermore, in contrast to ILC2s, Th2 cells produced little GM-CSF and administration of GM-CSF rescued eosinophil recruitment in ILC2-specific Bhlhe40-deficient mice. In addition to promoting GM-CSF expression, Bhlhe40 repressed IL-10 production in ILC2s as it did in Th2 cells, particularly during chronic inflammation. Single-cell transcriptomic analyses further supported this regulatory network, and the ChIP-Seq data revealed direct binding of Bhlhe40 to the enhancer and promoter regions within the Il10 and Csf2 loci. Collectively, our findings show that Bhlhe40 exerts distinct gene regulatory functions in ILC2s and Th2 cells, and Bhlhe40 modulates the inflammatory and anti-inflammatory functions of ILC2s by promoting GM-CSF while suppressing IL-10 production.

In TLR7-driven macrophage activation syndrome (MAS), inflammatory hemophagocytes (iHPCs) differentiate from Ly6CHI monocytes, phagocytose red blood cells and promote disease, including anemia and thrombocytopenia. We demonstrate here that IRF5 is required for iHPC differentiation and MAS in TLR7-overexpressing (TLR7.1) mice. Both constitutive and myeloid-specific Irf5 deletion reduced iHPCs and improved anemia, thrombocytopenia and survival. Furthermore, therapeutic inhibition of IRF5 ameliorated MAS features and reduced splenic and circulating iHPCs. While cell-intrinsic IRF5 expression was required for iHPC differentiation, it was not required for TLR7.1 Ly6CHI monocyte differentiation and monocyte transcriptional programs. We further show that the transcriptome and chromatin landscape changed dramatically as iHPCs differentiated from TLR7.1 Ly6CHI monocytes. Many transcriptional programs gained in iHPCs were enriched in genes associated with IRF5-binding accessible chromatin regions, including those associated with NF-kB signaling, cytokine and chemokine production, and complement activation. Our data suggest that IRF5 collaborates with other transcription factor families, including NF-kB, ETS and AP1 members, to regulate iHPC gene programs. Together, our findings demonstrate that expression of IRF5 in myeloid cells is critical for MAS, for iHPC differentiation, and acts broadly across iHPC-specific gene programs in TLR7-driven inflammation.

Myeloid bias is a hallmark of aging and genotoxic stress, yet the mechanisms underlying the preferential suppression of lymphopoiesis and the resulting predominance of myeloid cells following DNA damage remain incompletely understood. Here, we systematically characterized the acute hematopoietic response to a clinically relevant 2 Gy dose of ionizing radiation in young adult mice. Forty-eight hours after irradiation, overall bone marrow cellularity was reduced by [~]50-60%, with hematopoietic stem and progenitor cells (HSPCs) and myeloid populations declining proportionally. Strikingly, immature and naive B cells in the bone marrow and developing T cells in the thymus exhibited profound hypersensitivity, declining by [~]90%, thereby recapitulating the preferential vulnerability of lymphocytes to DNA damage. Single-cell RNA sequencing mapped this vulnerability to cells undergoing programmed clonal expansion associated with V(D)J recombination. Specifically, B and T lymphocytes immediately following productive V(D)J recombination at the immunoglobulin heavy-chain (IgH) and T-cell receptor {beta} (TCR{beta}) loci were the most radiosensitive, resulting in the marked depletion of the immediately downstream small pre-B and CD4CD8 double-positive (DP) thymocyte populations. Mechanistically, this stage-specific radiosensitivity was mediated by ATM-dependent DNA damage responses, as Atm deficiency selectively rescued the hypersensitivity of clonally expanding lymphoid progenitors while leaving the global reduction of HSPCs and myeloid cells largely unchanged. Rapidly proliferating S3 erythroblasts also exhibited a similar ATM-dependent hypersensitivity, suggesting that programmed proliferative bursts may represent a general determinant of radiation sensitivity. Together, these findings identify programmed clonal expansion associated with V(D)J recombination as an intrinsic developmental vulnerability that underlies the preferential suppression of lymphopoiesis following DNA damage and provides a mechanistic explanation for the emergence of myeloid bias. Key PointsO_LI2 Gy irradiation preferentially depletes developing mouse B and T cells beyond global hematopoietic loss C_LIO_LIProgrammed clonal expansion drives ATM-dependent DNA damage sensitivity in developing lymphocytes. C_LI

Advances in immunophenotyping of tumour-infiltrating lymphocytes (TILs) have improved our understanding of prognostic biomarkers and immune targets in human melanoma. However, whether the tumour-immune landscape in canine oral malignant melanoma (COMM) is concordant with that of human melanoma has not been properly defined. To address this gap, we developed a 16-colour spectral flow cytometry panel to characterise TIL phenotypic and functional profiles in COMM. Validation using mitogen-stimulated peripheral blood mononuclear cells from healthy dogs (n = 5) demonstrated robust identification of major T cell lineages, including regulatory T cells (Tregs) and memory subsets, and reliable evaluation of their activation and exhaustion status. COMM patients (n = 8) displayed a distinct protumour microenvironment, characterised by an increased proportion of Tregs, enrichment of tumour-specific exhausted-like T cells co-expressing programmed cell death protein 1 (PD-1) and tumour necrosis factor receptor 2 (TNFR2), and a reduction in cytotoxic CD8 and natural killer T (NKT) cell populations compared with tissue-resident (n = 4) and circulating (n = 8) lymphocytes. Analysis of additional solid tumours, including a mast cell tumour, nerve sheath tumour and adrenal cortical carcinoma, further supported the capability of the panel to identify similar patterns of immune dysregulation across diverse canine tumour landscapes. Collectively, this work describes the first detailed evaluation of canine TIL immunophenotyping using spectral flow cytometry and provides insights into the immunosuppressive mechanisms shaping the tumour microenvironment in COMM. These findings not only increase our understanding of canine tumour immunology but also identify potential immune targets and support ongoing comparative immuno-oncology efforts.

Chronic inflammation disrupts hormonal balance in the Hypothalamic-Pituitary-Gonadal (HPG) axis, contributing to reproductive disorders. While immune cells in the hypothalamus and ovaries have been extensively studied, their impact on the pituitary remains largely unexplored. Our research identifies pituitary macrophages (PitMacs) as the dominant pituitary immune cell population with a role in regulating reproductive gonadotropin secretion both in vitro and in vivo. Using a targeted AAV-based depletion strategy, we demonstrate that a reduction of PitMacs decreases serum gonadotropins, luteinizing hormone (LH) and follicle-stimulating hormone (FSH), in female mice. PitMacs are transcriptomically distinct from other tissue-resident macrophages and harbor a unique translational program that reflects the pituitarys endocrine identity, including active translation of growth hormone (Gh) and prolactin (Prl). Cytokine profiling identified CXCL5 and IFN-{gamma} as key PitMac-derived mediators of gonadotropin regulation. Mechanistically, CXCL5 signals through CXCR2 to activate the MAPK pathway, converging with Gonadotropin-Releasing Hormone (GnRH) signaling in a time-dependent manner to regulate LH secretion and GnRH receptor surface expression. These findings establish PitMacs as essential endocrine-immune integrators, opening new avenues for understanding inflammation-driven reproductive disorders. One Sentence SummaryPituitary macrophages are unique hormone-producing immune cells that regulate hormone secretion via cytokine signaling.

NKG2D (encoded by KLRK1 in humans and Klrk1 in mice) is an activating receptor expressed by cytotoxic lymphocytes. In humans, NKG2D signaling is regulated post-transcriptionally: activated T cells retain intron 4 of KLRK1 to generate NKG2D-TR, a truncated dominant-negative isoform that limits receptor signaling. Whether mice, the principal preclinical model for NKG2D-directed therapies, possess an analogous regulatory mechanism remains unknown. Across four murine RNA-seq datasets comprising 50 samples and spanning T-cell differentiation, graft-versus-host disease, and acute and chronic LCMV infection, we examined the retained-intron isoform Klrk1-203. The transcript retains the canonical start codon, while its predicted stop codon lies within the terminal exon downstream of the final exon-exon junction, suggesting that it may escape nonsense-mediated decay. If translated, Klrk1-203 is predicted to encode a truncated product that retains the cytoplasmic and transmembrane domains but lacks most of the ligand-binding ectodomain. This predicted architecture resembles human NKG2D-TR, although the murine product contains a short C-terminal sequence encoded by the retained intron. Klrk1-203 was below the detection limit in unchallenged naive and early-effector T cells but was induced in differentiated effector and memory populations, reaching approximately one-fifth of total Klrk1 transcripts in one effector-memory sample. Read-level analyses independently demonstrated increased intron 4 retention with differentiation; however, short-read sequencing cannot fully distinguish Klrk1-203 from the co-retained Klrk1-204 transcript, making isoform-specific abundance dependent on model-based quantification. An independent coding-potential algorithm classified Klrk1-203 as non-coding, providing an important counterpoint to the structural predictions. Together, these findings identify Klrk1-203 as a candidate NMD-resistant, differentiation-associated regulator of murine NKG2D and a potential counterpart of human NKG2D-TR that warrants experimental validation.

BCMA-directed chimeric antigen receptor T cells induce deep responses in multiple myeloma, yet the immune ecology accompanying early response remains incompletely resolved. We reanalysed 171,971 single-cell transcriptomes from 25 peripheral-blood and bone-marrow specimens from ten patients. At day 30, responders showed concordant enrichment of C1Q and IFN-{gamma} programmes in blood and marrow myeloid pseudobulk profiles. Antigen-presentation genes were enriched in blood, whereas TGF-{beta} and hypoxia programmes were depleted in responding marrow. Cholesterol-efflux genes were not enriched in responders or after treatment. A composite C1Q-cholesterol score showed nominal associations with response and CD8 dysfunction in selected compartments, but none survived study-wide correction. The pathway results support an adaptive, antigen-presenting C1Q-associated programme rather than a uniformly suppressive C1Q macrophage model. This state-contingent interpretation of early myeloid remodelling requires prospective, patient-level validation before biomarker or causal claims are warranted.

Tumor infiltrating CD8+ T cells (TILs) progress to a state of terminal exhaustion (Ttex) which have impaired functionality and are nonrenewable. However their precursors (Tpex) are renewable and can generate efficient effector cells. We started from the observation that melanoma patients undergoing therapy with checkpoint inhibitors show increased survival when their T cells have low BCL11B mRNA. In line with this, ablation of Bcl11b in CD8+ TILs conferred a superior anti-tumor response in murine melanoma and ovarian cancer models. Bcl11b KO TILs failed to progress to the Ttex state and retained elevated stemness. Bcl11b exerted its role by repressing expression of essential transcription factors (TF) controlling stemness, and conversely by promoting expression of exhaustion-associated TFs and inhibitory receptor genes, through complex epigenetic control. In addition, Bcl11b KO CD8+ T cells showed increased Ag-specific cytolytic activity and elevated Gzmb and Prf1 proteins, but no increase in their mRNAs, however presented higher expression of genes with role in translation. Furthermore, CRISPR-CAS9-mediated deletion of BCL11B in human TILs from a patient with poor response to adoptive cell therapy with autologous TILs, improved their cytolytic activity and promoted expression of the stemness-associated TF TCF1, underlying its potential therapeutic use. HIGHLIGHTS- Adoptive transfer of Bcl11b KO CD8+ TILs surpasses WT in tumor burden reduction - Bcl11b ablation reprograms TILs and impairs the progression to Ttex state - Bcl11b KO CD8+ T cells have elevated cytotoxicity and kill only Ag-MHCI targets - BCL11B deletion in nonresponder ACT-TIL improves cytolytic activity and elevates TCF1 GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/742578v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@10040d4org.highwire.dtl.DTLVardef@1a045caorg.highwire.dtl.DTLVardef@145f790org.highwire.dtl.DTLVardef@8012ab_HPS_FORMAT_FIGEXP M_FIG C_FIG

Ubiquitin-dependent regulation of NF-{kappa}B signaling is essential for B-cell homeostasis and fate decisions, yet the contribution of specific deubiquitinating enzymes remains incompletely defined. OTUB1, a lysine-48-specific deubiquitinase, has been broadly implicated in immune regulation, including control of NF-{kappa}B signaling and prevention of immune hyperactivation. Previous studies have demonstrated that B cell-specific deletion of OTUB1 leads to B cell hyperplasia, increased antibody production, and lupus-like autoimmunity, highlighting its importance in maintaining B cell tolerance and immune homeostasis. Using B cell-specific OTUB1-deficient mice, we show that loss of OTUB1 leads to a marked expansion of marginal zone (MZ) B cells and their precursor populations in the spleen, accompanied by an activated phenotype and enhanced proliferative responses, particularly upon CD40 stimulation. OTUB1 deficiency results in altered CD40-induced NF-{kappa}B signaling, characterized by enhanced I{kappa}B degradation and increased nuclear accumulation of p50-containing NF-{kappa}B complexes, despite reduced RelA stability. Mechanistically, we show that OTUB1 interacts with RelA, restricting its lysine-48-linked ubiquitination and proteasomal degradation, thereby stabilizing this key transcription factor. Collectively, these findings identify RelA as a novel OTUB1 target and uncover an additional layer of ubiquitin-dependent control of NF-{kappa}B signaling that governs splenic B-cell homeostasis and marginal zone B-cell development.