Biology subjects

Becher, B.

Publications and source records attributed to Becher, B..

At least 19 recordsLinked to original sources

bioRxiv2026

GM-CSF signaling on monocytes and monocyte-derived dendritic cells is required for effective pulmonary immunity to Aspergillus fumigatus

Aspergillus fumigatus is the most common cause of invasive aspergillosis (IA), an opportunistic pulmonary infection of immunocompromised patients that can be fatal, despite treatment with modern antifungal drugs. During infection, myeloid cells, such as neutrophils, monocytes, and monocyte-derived dendritic cells (Mo-DCs) are recruited to the lung and are critical for phagocytosing and killing A. fumigatus spores. Recent evidence has shown that intracellular crosstalk between these professional immune cells and other resident pulmonary cell types is required for an effective immune response to A. fumigatus, and that signaling via the cytokine granulocyte macrophage-colony stimulating factor (GM-CSF) is part of this intracellular communication. In this study, we sought to determine a role for GM-CSF signaling on monocytes and their progeny. We harnessed a mouse model of deletion of GM-CSF receptor {beta} chain (encoded by Csf2rb) in CCR2-expressing cells. Using this model, we found that GM-CSF signaling is required on CCR2+ cells for killing of A. fumigatus and for host survival. This observation expands the importance of GM-CSF in host defense during A. fumigatus pulmonary infection and extends its role in pathways of intracellular crosstalk that mediate effective pulmonary antifungal immunity.

immunology↗

bioRxiv2026

Dendritic cell PD-L2 restrains intratumoral CD8+ T cell immunity

Blockade of inhibitory PD-1 signaling on T cells is a cornerstone of cancer immunotherapy, with current strategies targeting PD-1 or its ligand PD-L1. However, PD-1 engages an alternative ligand, PD-L2, whose role in tumor immunity remains poorly defined. Here, we show that PD-L2 is upregulated on intratumoral CCR7+ conventional dendritic cells (cDCs) in both mouse and human melanoma. Using genetic mouse models enabling selective ablation of PD-L1 or PD-L2 in cDCs, we identify a division of labor between these ligands: PD-L1 controls the size of the progenitor CD8 T cell pool in tumor-draining lymph nodes by modulating stem-like CD8 T cells, whereas PD-L2 limits progenitor exhausted CD8 T cell differentiation within the tumor microenvironment. Loss of PD-L2 in cDCs enhances cytotoxic CD8 T cell responses and suppresses tumor growth, particularly in tumors enriched for CCR7+ cDC1s. Consistent with this, increased CCR7+ cDC abundance is associated with poor prognosis in human cancers. Spatial transcriptomic analyses reveal co-localization of CCR7+ cDC1s and Tpex within CCL19hi niches, where cancer-associated fibroblasts serve as the predominant source of CCL19. Finally, intratumoral GM-CSF drives PD-L2 expression on CCR7+ cDCs, with Tpex and NK cells as major sources. Together, these findings establish cDC-associated PD-L1 and PD-L2 as spatially and functionally distinct checkpoints governing CD8 T cell differentiation. Our results suggest that the abundance of CCR7+ cDC1s may guide the choice between anti-PD-1 and anti-PD-L1 therapies and support the development of PD-L2-directed blockade.

immunology↗

bioRxiv2026

Ex vivo activation unmasks a sex-convergent, exhaustion-associated CD8+ T cell expansion in Parkinsons disease

Parkinsons disease (PD) affects an estimated 6.4 million men and 5.3 million women worldwide, and still lacks a validated peripheral biomarker. Brain tissue is inaccessible in living patients, making peripheral blood an attractive alternative, but existing studies have profiled immune cells almost exclusively as static, resting-state snapshots that cannot reveal how those cells function under challenge. A longitudinal design, following patients over time, or applying a controlled stimulus to reveal functional differences invisible at rest, offers a more sensitive window onto disease-associated dysfunction, and sex, despite differential PD incidence and progression, is rarely treated as a primary variable. Here, using ex vivo PMA/ionomycin stimulation as a controlled functional challenge, we profiled 195k PBMCs from 84 samples of 14 PD patients and 14 controls by single-cell RNA sequencing across an activation time course (0h, 2h, 4h), stratified by sex throughout. Sex explained more transcriptional variance than disease status, and male and female PD patients showed largely divergent responses at rest that converged, by peak activation, on a discrete CD8+ effector memory T cell subpopulation (Tem-CD8). This subpopulation showed an exhaustion-consistent programme, coinciding with a failure to resolve AP-1 induction and a reduction in inferred intercellular communication. The PD peripheral immune phenotype is therefore better characterised as a activation-dependent response than a fixed resting-state signature, identifying Tem-CD8 exhaustion as a disease-associated, sex-convergent candidate for further study.

neuroscience↗

bioRxiv2026

Altered follicular immunity in secondary lymphoid organs is associated with interferon hyperactivity in Down syndrome

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.

immunology↗

bioRxiv2026

Leishmaniamajor co-opts IL-7 feedback in monocytes to suppress CD4⁺ T-cell immunity

During immune responses, pro-and anti-inflammatory mechanisms must be balanced to ensure pathogen clearance while limiting tissue damage. Monocyte-derived cells contribute to both processes, yet the underlying regulatory circuits remain incompletely defined. Here, we show that a subset of PDPN+IL-7R+ monocyte-derived cells that impair effector CD4 T cell-mediated control of intracellular pathogens, and thus perpetuate the infection. Fibroblast-derived IL-7 drives this immunosuppressive program, which is up-regulated in response to IFN{gamma}. We thus uncover a cytokine-dependent feedback circuit in which elevated IFN{gamma} induces IL-7 production by fibroblasts, licensing immunosuppressive monocyte-derived cells that restrain CD4 T cell responses. This mechanism links excessive inflammation to immune suppression at the expense of pathogen control. Targeting this feedback loop may enable therapeutic strategies that enhance antimicrobial immunity while preserving tissue integrity.

immunology↗

bioRxiv2026

IL-12R signaling promotes type 1 regulatory T cell specialization by sustaining T-bet

Elucidating how regulatory T (Treg) cells specialize and acquire specific suppressive capacities is key for understanding immune regulation in autoimmunity and cancer. Although IL-12 is a key driver of Th1 differentiation, its role in Treg cells remains poorly defined. Here, we investigated whether IL-12R signaling contributes to Treg cell specialization during Th1 immune responses. We show that IL-12R{beta}2 KO Treg cells display reduced type 1 specialization following LCMV infection, resulting in impaired suppressive capacity. Mechanistically, IFN-{gamma} induces a first peak of T-bet, whereas IL-12 acts downstream to sustain T-bet through a positive feedback loop. The decreased suppressive function of IL-12R{beta}2 KO Treg cells alters effector T cell responses during both acute and chronic infections. Importantly, human Treg cells also respond to IL-12, promoting enhanced type 1 specialization. Together, these findings establish IL-12 as a critical regulator of type 1 Treg specialization and highlight the therapeutic potential of targeting this pathway. TeaserIL-12R signaling in Treg cells enables sustained T-bet expression, programing type 1 Tregs for suppression of Th1 responses.

immunology↗

bioRxiv2025

Characterization of Chemoresistant Cell Populations Improves Risk Stratification and Therapy Prediction in Pediatric AML

Most pediatric acute myeloid leukemia (pAML) patients achieve complete remission after chemotherapy, yet relapse is common, with nearly 40% ultimately dying of the disease. Prognosis is currently assessed using cytogenetic biomarkers and measurable residual disease after the first chemotherapy cycle, with the highest risk patients referred for stem cell transplantation (SCT) at first remission. Because aggressive therapies such as SCT are highly toxic, yet cures after relapse are rare, accurate early risk prediction is essential for improving outcomes. To address this need, we analyzed paired diagnosis-relapse samples from 33 pAML patients at single-cell resolution and identified chemoresistant cell populations whose abundance at diagnosis significantly improved risk prediction. Incorporating the detection of these cell populations into our risk model revealed a previously unrecognized patient subgroup with a 5-year event-free survival rate below 40%. Although this subgroup represents only 20% of pAML cases, it accounted for half of the deaths among patients who do not receive SCT at first remission. Moreover, molecular characterization of these chemoresistant cell populations uncovered potential therapeutic targets and candidate interventions relevant to most high-risk patients, paving the way for more effective targeted treatments for high-risk pAML patients.

cancer biology↗

bioRxiv2025

RIPPLET: Mutation-Only Gene and Pathway Profiling for Precision Oncology

Clinical implementation of comprehensive genomic profiling, via whole-genome (WGS) or whole-exome sequencing (WES), is constrained by sparse mutation burdens and analytic pipelines reliant on matched transcriptomes. Currently, gene-centric analysis prevails, but overlooks the complex, multigene and pathway perturbations shaping tumor biology. We introduce RIPPLET, a DNA-only framework converting somatic variants into quantitative gene-impact scores and topology-aware pathway-perturbation profiles. By integrating tissue-specific protein-protein interaction networks with cohort-informed reweighting, RIPPLET prioritizes likely functionally relevant alterations. Applied across 33 TCGA cancer types, RIPPLET surpasses four state-of-the-art multi-omic driver-prioritization tools in recovering cancer type-specific drivers. In a cohort of metastatic cutaneous melanomas, it identifies pathway signatures that predict drug response, provide prognostic insight and distinguish immune-infiltration phenotypes without RNA data, independently validated on an in-house cohort. RIPPLET enables DNA-only inference of tumor-specific gene and pathway dysregulation, aligning with clinical sequencing workflows and offering a scalable precision-oncology strategy in transcriptome-limited settings.

bioinformatics↗

bioRxiv2025

Mapping Leukocyte Dynamics during Neuroinflammation Identifies Meningeal Monocyte-Derived Macrophages as Drivers of Progressive Disease

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) characterized by increasing disability. The cellular and molecular drivers of clinical transition towards progressive disease are poorly understood. Here, we combine single-cell profiling technologies with genetic and pharmacological perturbations across the course of murine CNS inflammation to dissect the role of the local immune landscape in disease progression. We uncover a chronic monocyte-to-phagocyte transition as a hallmark of progressive disease, characterized by the emergence of maladaptive, lipid-associated macrophages (LAMs) marked by lysosomal activation and fibrotic features. Spatial transcriptomics and multiplexed imaging revealed that these LAMs localized to the leptomeninges in close proximity to parenchymal colony-stimulating factor (CSF)-1 producing disease-associated microglia (DAMs) and meningeal granulocyte-macrophage (GM)-CSF-expressing T helper cells that license their differentiation. Interference with this local cytokine network revealed a protective role for resident microglia and implicated monocyte-derived phagocytes as key drivers of progressive neuroinflammation. Notably, LAM-like macrophages could also be identified in the meninges of people with MS, indicating a homology to human disease. By elucidating their ontogeny, spatial niche, and regulatory cytokine milieu, we provide a mechanistic framework for targeting harmful myeloid states while preserving reparative CNS immunity in progressive MS.

immunology↗

bioRxiv2025

Tissue imprinting defines functional mosaic of dermal macrophages

Dermal macrophages (macs) protect the skin from invading pathogens. They are derived from embryonic as well as hematopoietic progenitors. However, the functional impact of their diverse origin and the control networks defining different subsets remain unclear. Here, using multidimensional analysis of dermal macs, we reveal that the absence of circulating monocytes in interferon regulatory factor 8 (Irf8) deficient mice delays mac renewal during the steady state. Yet, the functional mosaic of dermal macs remains largely intact, i.e., major dermal mac subsets develop independently of monocyte replenishment. Thus, the tissue microenvironment is sufficient to induce alternative differentiation pathways and functional specialization of resident cells. Mycobacterial skin infection induces a steep increase in mac density due to monocyte-derived macs which execute urgent antibacterial functions and differentiate into site-adapted mac subsets in wildtype but not Irf8-/-mice, while long-term resident macs are required to initiate a tissue repair program already in early stages of infection. In summary, we introduce a model, where an intricate network of specialized mac subsets develops to meet microanatomical needs and external cellular input is required only during immunological emergency situations. HighlightsO_LIIrf8-/--driven monocytopenia has negligible impact on homeostatic dermal macrophage diversity. C_LIO_LIResident dermal macrophages have diverse specializations but remain flexible to adapt to challenges such as lacking monocyte influx C_LIO_LIBone marrow-derived macrophages differentiate into specialized resident cells, with microenvironmental cues overriding origin-dependent programming. C_LIO_LIIn chronic bacterial infections, distinct specialized bone-marrow-derived macrophages mount the defense, while resident macrophages activate a tissue-modifying program from early on. C_LI

immunology↗

bioRxiv2024

Unveiling a unique macrophage population in exocrine glands sustained by ILC2-derived GM-CSF

Granulocyte-macrophage colony-stimulating factor (GM-CSF) has a non-redundant role in the emergence and maintenance of alveolar macrophages (AMs). However, its role in developmental and steady-state myelopoiesis outside the lung is largely unexplored. Scanning through developing tissues using a Fate-map and reporter of GM-CSF mouse strain, we discovered that GM-CSF was produced by type 2 innate lymphoid cells (ILC2s) in the submandibular and sublingual salivary gland (SG) during postnatal development. GM-CSF producing ILC2s foster the development of a hitherto undescribed phagocyte subset, which we named adenophages. Detailed analysis focusing on phenotypic and transcriptional profiling revealed that adenophages display shared aspects of both, macrophages and dendritic cells (DCs). We found them to be homogenously distributed across the SG, but always in close proximity to GM-CSF producing ILC2s and myoepithelial cells. Importantly, adenophages were present throughout all analyzed exocrine glands such as lacrimal glands and mammary glands, and were also identified in human SG sections, indicating a conserved role in exocrine glands across species.

immunology↗

bioRxiv2024

Monocyte-derived cells but not Microglia cause Oxidative Tissue Damage in Neuroinflammation

Multiple sclerosis (MS) is characterized by neuroinflammation, oxidative stress, iron toxicity and mitochondrial dysfunction. Reactive oxygen species (ROS) produced by mononuclear phagocytes (MPs) are widely held to drive tissue damage, yet the specific roles of central nervous system (CNS)- resident versus CNS-invading MPs remain unclear. Here, by combining single-cell profiling with conditional gene targeting, we systematically dissected and interfered with ROS production across CNS MPs in a preclinical model for neuroinflammation. We show that CNS-invading monocyte derived cells (MdCs) exhibit a higher oxidative stress gene signature and produce more ROS compared to CNS-resident microglia. While NADPH oxidase 2 (NOX2), a phagocytic source of ROS, proved redundant, our findings underscore the critical role of mitochondrial ROS (mtROS) in driving oxidative tissue damage. Quenching mtROS through mitocatalase overexpression in MdCs, but not microglia, significantly alleviated neuroinflammation in mice. Thus, our study resolves a longstanding controversy, identifying MdCs as the primary driver of ROS-mediated neuropathology.

immunology↗

bioRxiv2024

Early precursor-derived pituitary gland tissue-resident macrophages play a pivotal role in modulating hormonal balance

The pituitary gland is the central endocrine regulatory organ underneath the brain, producing and releasing a variety of hormones that coordinate major body functions. The physical location of the pituitary gland underneath the brain, though outside the protective blood-brain barrier, leads to a unique immune environment of the pituitary that has not been studied. Here, we defined the development, diversity, spatial niche, and origin of the pituitary gland macrophage subsets using single cell transcriptomics, fate mapping, and imaging. We identified early yolk sac precursors solely seeding pituitary gland macrophages which are maintained by proliferation. Macrophage depletion experiments unveiled the essential contribution of early macrophages in the pituitary glands hormonal production and in modulating the post-pubertal expression of genes related to the sexually dimorphic processes regulated by the pituitary gland. Altogether, these findings provide novel information on pituitary gland macrophages and advance our understanding of immune-endocrine system crosstalk.

immunology↗

bioRxiv2024

Regulatory T cells control type 1-driven immunopathology restraining GM-CSF-producing helper T cells

Regulatory T (Treg) cells are critical for maintaining peripheral tolerance and preventing autoimmunity. Treg cell depletion or dysfunction rapidly results in fatal multiorgan inflammation linked to unrestrained effector T cell expansion, but the cytokine network underlying immunopathology, and its direct cellular mediators, remain elusive. Here, we combined gene targeting, fate-mapping tools, and high-dimensional cytometry to identify the T helper (TH) cell-derived cytokines and responding cells that execute inflammatory tissue damage upon global loss of peripheral tolerance in mice. We found that TH cell-derived GM-CSF, but not IL-17A, directed the ensuing immunopathology and thereby mortality through recruitment of tissue-invading phagocytes and granulocytes, and enhancement of their reactive oxygen species production and phagocytic proficiency. Our study highlights the critical role of Treg cells in controlling GM-CSF- producing TH cells and type 1-responses to restrain phagocyte-mediated tissue destruction and provides a framework for the use of anti-GM-CSF therapies in patients with chronic inflammatory disorders.

immunology↗

bioRxiv2024

Targeted CRISPR-Cas9 screening identifies transcription factor network controlling murine haemato-endothelial fate commitment

Haematopoiesis is a tightly coordinated process that forms and maintains all blood cells. During development blood generation begins in the yolk sac with the differentiation of haemato-endothelial mesoderm giving rise to haematopoietic progenitors. Which molecular regulators are crucial for haemato-endothelial mesoderm formation remains unclear and has not been studied in an unbiased way. Here we employ a mouse embryonic stem cell model that recapitulates embryonic blood development and perform targeted CRISPR-Cas9 knock out screens focusing on transcription factors and chromatin regulators. Focusing on the transition of primitive towards haematoendothelial mesoderm we identified the known master regulator Etv2 and novel transcription factors including Smad1, Ldb1, Six4 and Zbtb7b acting as crucial drivers or repressors of mesodermal commitment. Our transcriptome analysis highlights that each factor has a precise impact on the gene expression signature of the developing mesoderm resulting in the formation of mesodermal subsets with a defined lineage differentiation bias. Our study reveals novel molecular pathways governing mesodermal development crucial to allow endothelial and haematopoietic lineage specification.

developmental biology↗

bioRxiv2024

GM-CSF-mediated epithelial-immune cell crosstalk orchestrates pulmonary immunity to Aspergillus fumigatus

Aspergillus fumigatus causes life-threatening mold pneumonia in immune compromised patients, particularly in those with quantitative or qualitative defects in neutrophils. While innate immune cell crosstalk licenses neutrophil antifungal activity in the lung, the role of epithelial cells in this process is unknown. Here, we find that that surfactant protein C (SPC)-expressing lung epithelial cells integrate infection-induced IL-1 and type III interferon signaling to produce granulocyte-macrophage colony-stimulating factor (GM-CSF) preferentially at local sites of fungal infection and neutrophil influx. Using in vivo models that distinguish the role of GM-CSF during acute infection from its homeostatic function in alveolar macrophage survival and surfactant catabolism, we demonstrate that epithelial-derived GM-CSF increases the accumulation and fungicidal activity of GM-CSF-responsive neutrophils, with the latter being essential for host survival. Our findings establish SPC+ epithelial cells as a central player in regulating the quality and strength of neutrophil-dependent immunity against inhaled mold pathogens. HIGHLIGHTSO_LIGM-CSF is essential for host defense against A. fumigatus in the lung C_LIO_LIIL-1 and IFN-{lambda} promote GM-CSF production by lung epithelial cells in parallel C_LIO_LIEpithelial cell-derived GM-CSF increases neutrophil accumulation and fungal killing capacity C_LIO_LIEpithelial cells preferentially upregulate GM-CSF in local sites of inflammation C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/574062v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@708497org.highwire.dtl.DTLVardef@11106f7org.highwire.dtl.DTLVardef@e08140org.highwire.dtl.DTLVardef@1459e89_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Cell-binding IgM in CSF is distinctive of multiple sclerosis and targets the iron transporter SCARA5

Intrathecal IgM production in multiple sclerosis (MS) is associated with a worse disease course. To investigate pathogenic relevance of autoreactive IgM in MS, CSF from two independent cohorts, including MS patients and controls, were screened for antibody binding to induced pluripotent stem cell-derived neurons and astrocytes, and a panel of CNS-related cell lines. IgM binding to a primitive neuro-ectodermal tumour cell line discriminated 10% of MS donors from controls. Transcriptomes of single IgM producing CSF B cells from patients with cell-binding IgM were sequenced and used to produce recombinant monoclonal antibodies for characterisation and antigen identification. We produced 5 cell-binding recombinant IgM antibodies, of which one, cloned from an HLA-DR+ plasma-like B cell, mediated antigen-dependent complement activation. Immunoprecipitation and mass spectrometry, and biochemical and transcriptome analysis of the target cells identified the iron transport scavenger protein SCARA5 as the antigen target of this antibody. Intrathecal injection of a SCARA5 antibody led to an increased T cell infiltration in an EAE model. CSF IgM might contribute to CNS inflammation in MS by binding to cell surface antigens like SCARA5 and activating complement, or by facilitating immune cell migration into the brain.

immunology↗

bioRxiv2023

Epidermal barrier dysregulation in atopic skin predisposes for excessive growth of the allergy-associated yeast Malassezia

The skin barrier is vital for protection against environmental threats including insults caused by skin-resident microbes. Dysregulation of the barrier is a hallmark of atopic dermatitis (AD) and ichthyosis, with variable consequences for host immune control of colonizing commensals and opportunistic pathogens. While sensitisation to Malassezia, the most abundant commensal fungus of the skin, is common in AD, its relevance for pathogenesis remains unclear. Here we show that in barrier-disrupted skin, Malassezia acquires enhanced fitness. This is not a consequence of the dysregulated allergic immune status characteristic for AD but is rather explained by structural and metabolic changes in the cutaneous niche that provide increased accessibility and a favourable lipid profile, to which the lipid-dependent yeast adapts for enhanced nutrient assimilation. These findings reveal fundamental insights into the role of the mycobiota in the pathogenesis of common skin barrier disorders.

microbiology↗