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Höfer, T.

Publications and source records attributed to Höfer, T..

11 recordsLinked to original sources
bioRxiv2026

Clonal selection of somatic mutations shapes NK cell memory

Adaptive immune memory relies on selective clonal expansion and persistence of lymphocyte populations. Whether and how clonal selection occurs in innate lymphocytes that lack rearranged antigen receptors remains poorly understood. Here, we used somatic genetics to reconstruct the natural history of human natural killer (NK) cell responses to cytomegalovirus infection. Across a large cohort of healthy seropositive individuals, we found strong clonal dominance in memory NK cells consistent with clonal selection. Dominant memory NK cell clones were marked by coherent receptor and chromatin configurations, emerged early in life and diversified into genetically related subclones. Both an excess of coding mutations, and the reconstructed population dynamics of the dominant clones, provided evidence for positive selection acting on somatic genetic variation. We identified somatic loss-of-function mutations in the chromatin modifier KMT2D, and showed in a mouse model that Kmt2d deletion alters NK-cell fitness depending on timing and environmental context. Together, these findings establish clonal selection as an organizing principle of human NK-cell memory and support a model in which heritable cell states and acquired genetic variation contribute to shape clonal competition.

immunology↗
bioRxiv2025

Recurrent DNA Break Clusters Regulated by Polymerase Theta Are Essential for Replication Stress Induced Copy Number Variation

Copy number variations (CNVs) are a form of genetic alteration strongly implicated in numerous neurological and psychiatric disorders, as well as brain cancer. Replication stress is a common cause of CNVs. Despite the prevailing model that CNVs arise from DNA double strand breaks (DSBs), there has been no assay that directly perturbs presumed DSB sources and measures CNV output. Here, we identified a subset of recurrent DNA break clusters (RDCs) as a causal factor for CNV formation. In murine neural progenitor cells under replication stress, mapping the formation of CNVs revealed their location in RDC regions that contain actively transcribed genes. CRISPR/Cas9-mediated transcriptional suppression abrogated both RDC and CNV formation, but does not alter their replication timing. We found that DNA polymerase theta (Pol {theta}), a protector against CNV formation, plays a critical but context dependent role upstream of RDC formation. Chemically inhibiting the activity of Pol {theta} reduced end filling and micro-homology-mediated end joining in XRCC4/P53-deficient cells. Conversely, Pol {theta} inhibition led to elevated DSB density detection at RDC-containing loci in wild-type neural stem and progenitor cells, suggesting its role in preventing transcription-replication conflicts. Our data identify RDCs as contributors to genomic heterogeneity with plausible downstream effects on brain disorders and malignancy.

molecular biology↗
bioRxiv2025

Clonal Dynamics in the Male Germline from Development to Next Generation

Germ cells secure the continuity and evolutionary potential of species. Yet how reproductive success is allocated among the founder cells of the mammalian male germline, the primordial germ cells (PGCs), remains unknown. Here, we quantitatively traced individual PGCs, non-invasively barcoded in mouse embryos, across their establishment, lifelong maintenance within the testis, spermatogenesis, and transmission to the next generation. We found that highly skewed clonal contributions arise from a very early stochastic bottleneck during migration to the developing testes and remain stable throughout adult reproductive life. Reproductive success during adulthood was proportional to the embryonically established PGC clone size. Mathematical modeling shows that the patchy compartmentalization of PGC clones within the extended thin seminiferous tubules maintain clonal diversity and safeguard against the expansion of clones that gain a selective advantage. These findings uncover fundamental principles governing the development, stability, and evolutionary transmission of the mammalian germline.

developmental biology↗
bioRxiv2025

Competitive resource allocation drives asynchronous and rapid nuclear multiplication in the malaria parasite

The unicellular malaria parasite Plasmodium falciparum proliferates within the red blood cells of its human host, where it generates approximately 20 new parasites within an infection cycle of two days. Proliferation proceeds by nuclear divisions in a shared cytoplasm, followed by cellularization. In stark contrast to the highly synchronized nuclear division cycles in many eukaryotes, Plasmodium nuclear cycles desynchronize rapidly. Here, we elucidate the mechanism of desynchronization and study its impact on parasite fitness by combining live-cell imaging of DNA replication with biophysical modeling. We find that the standard model of independent nuclear cycles with transgenerational inheritance cannot account for the experimental data, and therefore desynchronization requires nuclear coupling. Competition for a limiting pool of a replication resource explains the data, provided that the resource is allocated sequentially to individual nuclei. Sequential allocation can be achieved by stable but reversible loading of a replication component to DNA, for example proliferating cell nuclear antigen (PCNA). Remarkably, the resultant asynchronous nuclear cycles accelerate parasite proliferation by minimizing idling times of resources. Indeed, we predict theoretically that this mechanism maximizes overall proliferation rate with limited resource availability. Thus, our findings identify nuclear cycle asynchrony as a resource-efficient means to achieve rapid proliferation.

biophysics↗
bioRxiv2024

Holistic genetic barcoding reveals a lineage tree of tissue macrophage development

Tissue macrophages are crucial for organ development and homeostasis, yet the developmental routes leading to tissue macrophages remain controversial. By combining unbiased Polylox barcoding with computational inference, we comprehensively mapped tissue macrophage ontogeny in mice from gastrulation to adult organs. Our data reveal a lineage tree of all tissue macrophages. This tree originates from a pan-hematopoietic progenitor at embryonic day (E)6.5 and branches, via oligolineage progenitors (E7.5-E9.5), into organ-specific macrophage lineages by E10.5. Barcode analysis in embryonic tissues and adult organ fragments suggests that local macrophage colonies, formed by organ-specific progenitors, persist into adulthood. Indeed, spatial fate mapping with Polytope barcoding detects local Kupffer cell colonies of the size predicted by the lineage tree model. Our findings uncover the origin of tissue-resident macrophages from a lineage tree, and show how holistic barcoding can comprehensively map complex cellular lineage specification. One-Sentence SummaryHolistic, time- and space-resolved barcoding in the embryo reveals a unified lineage tree for all tissue macrophages, generating local macrophage colonies persisting in adult organs.

developmental biology↗
bioRxiv2024

Quantitative analysis of MHC class II peptide exchange reveals pivotal role of peptide association rate

MHC-II presents antigenic peptides to T helper cells, thus shaping adaptive immune responses. Peptide loading of MHC-II in endosomes is shaped by the susceptibility of the peptide-MHC-II complex to dissociation by the catalyst HLA-DM. For a given MHC-II allotype, experimental data reveal an enormous range of HLA-DM susceptibilities of different peptides - more than five orders of magnitude. To understand the underlying mechanisms, we develop a coarse-grained kinetic model and confront it with experimental data. The model explains the observed variation of HLA-DM susceptibility with the peptide-MHC-II binding energy by an allosteric competition mechanism. Paradoxically, however, certain peptides are resistant to dissociation by HLA-DM regardless of their binding energy. Our model predicts that this resistance is linked with fast peptide association to MHC-II in the absence of HLA-DM. In sum, our data-based theoretical analysis identifies two distinct molecular mechanisms that shape antigen presentation by MHC-II.

systems biology↗
bioRxiv2022

Temporal control of the integrated stress response by a stochastic molecular switch

Stress granules (SGs) are formed in the cytosol as an acute response to environmental cues and activation of the integrated stress response (ISR), a central signaling pathway controlling protein synthesis. Using chronic virus infection as stress model, we previously uncovered a unique temporal control of the ISR resulting in recurrent phases of SG assembly and disassembly. Here, we elucidate the molecular network generating this fluctuating stress response, by integrating quantitative experiments with mathematical modeling, and find that the ISR operates as a stochastic switch. Key elements controlling this switch are the cooperative activation of the stress-sensing kinase PKR, the ultrasensitive response of SG formation to the phosphorylation of the translation initiation factor eIF2, and negative feedback via GADD34, a stress-induced subunit of protein phosphatase 1. We identify GADD34 mRNA levels as the molecular memory of the ISR that plays a central role in cell adaptation to acute and chronic stress.

cell biology↗
bioRxiv2020

Adaptation to host cell environment during experimental evolution of Zika virus

Zika virus (ZIKV) infection can cause important developmental and neurological defects in Humans. Type I/III interferon responses control ZIKV infection and pathological processes, yet the virus has evolved various mechanisms to defeat these host responses. Here, we established a pipeline to delineate at high-resolution the genetic evolution of ZIKV in a controlled host cell environment. We uncovered that serially passaged ZIKV acquired increased infectivity and simultaneously developed a resistance to TLR3-induced restriction. We built a mathematical model that suggests that the increased infectivity is due to a reduced time-lag between infection and viral replication. We found that this adaptation is cell-type specific, suggesting that different cell environments may drive viral evolution along different routes. Deep-sequencing of ZIKV populations pinpointed mutations whose increased frequencies temporally coincide with the acquisition of the adapted phenotype. We functionally validated S455L, a substitution in ZIKV envelope (E) protein, recapitulating the adapted phenotype. Its positioning on the E structure suggests a putative function in protein refolding/stability. Taken together, our results uncovered ZIKV adaptations to the cellular environment leading to accelerated replication onset coupled with resistance to TLR3-induced antiviral response. Our work provides insights into Zika virus adaptation to host cells and immune escape mechanisms.

microbiology↗
bioRxiv2020

CycleFlow quantifies cell-cycle heterogeneity in vivo

While the average cell-cycle length in a cell population can be derived from pulse-chase experiments, proliferative heterogeneity has been difficult to quantify. Here we describe CO_SCPLOWYCLEC_SCPLOWFO_SCPLOWLOWC_SCPLOW, a broadly applicable method that applies Bayesian inference to combined measurements of EdU incorporation and DNA content. CO_SCPLOWYCLEC_SCPLOWFO_SCPLOWLOWC_SCPLOW accurately quantifies the fraction of proliferating versus quiescent cells and the durations of cell-cycle phases of the proliferating cells in vitro and in vivo.

cell biology↗
bioRxiv2019

Exponential Growth of Glioblastoma In Vivo Driven by Rapidly Dividing and Outwardly Migrating Cancer Stem Cells

How overall tumor growth emerges from the properties of functionally heterogeneous tumor cell subpopulations is a fundamental question of cancer biology. Here we combined lineage tracing, continuous monitoring of tumor mass, proliferation assays and transcriptomics with mathematical modeling and statistical inference to dissect the growth of glioblastoma in mice. We found that tumors grow exponentially at the rate of symmetric divisions of brain tumor stem cells (BTSCs). Spatial modeling predicts, and data show, that BTSCs accumulate at the tumor rim rather than in the core. The physiological differentiation hierarchy downstream of BTSCs is preserved in mice and humans: transit amplifying progenitors give rise to terminally differentiated cells. Consistent with our quantification of the mechanisms underlying tumor growth, molecular data show elevated expression of cell cycle-and migration-related genes in BTSCs. Our systematic approach reveals fundamental properties of glioblastoma and may be transferable to the study of other animal models of cancer.

cancer biology↗
bioRxiv2018

Differential induction of interferon stimulated genes between type I and type III interferons is independent of interferon receptor abundance

It is currently believed that type I and III interferons (IFNs) have redundant functions. However, the preferential distribution of type III IFN receptor on epithelial cells suggests functional differences at epithelial surfaces. Here, using human intestinal epithelial cells we could show that although both type I and type III IFNs confer an antiviral state to the cells, they do so with distinct kinetics. Type I IFN signaling is characterized by an acute strong induction of interferon stimulated genes (ISGs) and confers fast antiviral protection. On the contrary, the slow acting type III IFN mediated antiviral protection is characterized by a weaker induction of ISGs in a delayed manner compared to type I IFN. Moreover, while transcript profiling revealed that both IFNs induced a similar set of ISGs, their temporal expression strictly depended on the IFNs, thereby leading to unique antiviral environments. Using a combination of data-driven mathematical modeling and experimental validation, we addressed the molecular reason for this differential kinetic of ISG expression. We could demonstrate that these kinetic differences are intrinsic to each signaling pathway and not due to different expression levels of the corresponding IFN receptors. We report that type III IFN is specifically tailored to act in specific cell types not only due to the restriction of its receptor but also by providing target cells with a distinct antiviral environment compared to type I IFN. We propose that this specific environment is key at surfaces that are often challenged with the extracellular environment.\n\nAuthor summaryThe human intestinal tract plays two important roles in the body: first it is responsible for nutrient absorption and second it is the primary barrier which protects the human body from the outside environment. This complex tissue is constantly exposed to commensal bacteria and is often exposed to both bacterial and viral pathogens. To protect itself, the gut produces, among others, secreted agents called interferons which help to fight against pathogen attacks. There are several varieties (type I, II, and III) of interferons and our work aims at understanding how type I and III interferon act to protect human intestinal epithelial cells (hIECs) during viral infection. In this study, we confirmed that both interferons can protect hIECs against viral infection but with different kinetics. We determined that type I confer an antiviral state to hIECs faster than type III interferons. We uncovered that these differences were intrinsic to each pathway and not the result of differential abundance of the respective interferon receptors. The results of this study suggest that type III interferon may provide a different antiviral environment to the epithelium target cells which is likely critical for maintaining gut homeostasis. Our findings will also help us to design therapies to aid in controlling and eliminating viral infections of the gut.

immunology↗