Biology subjects

Brehm, M.

Publications and source records attributed to Brehm, M..

10 recordsLinked to original sources

bioRxiv2026

Phosphorylation of Z granule components regulates germ granule organization and RNAi inheritance

Small RNAs represent important carriers of epigenetic information in nematodes, and factors involved in their biogenesis reside within perinuclear germ granules. Among these condensates, Z granules are essential for the inheritance of RNA interference (RNAi). The mechanisms by which Z granules form and promote this process remain unclear. We show that Casein kinase I alpha (KIN-19) is present in Z granules and associated with DEPS-1 and HERD-1 phosphorylation. In the absence of DEPS-1 and HERD-1 phosphorylation, animals have enlarged Z granules and enhanced RNAi inheritance. We propose that DEPS-1 acts as a phosphorylation-regulated scaffold that bridges ZNFX-1 and HERD-1 proteins. Our study demonstrates that Casein kinase I alpha-mediated phosphorylation is an important factor in germ granule modulation and RNAi inheritance, and additionally provides a novel molecular scaffold for understanding germ granule complexity in C. elegans.

molecular biology↗

bioRxiv2026

A pseudohelicase-centered complex couples assembly-dependent RNA cleavage to poly(UG)ylation

Robust RNA interference in Caenorhabditis elegans requires Argonaute targeted RNAs to be cleaved by RDE 8 and poly(UG)ylated by MUT 2, generating templates for RNA dependent RNA polymerases that synthesize secondary small RNAs. RDE 8 and MUT 2 are physically coupled within the cleavage and poly(UG)ylation (CPUG) complex, together with the pseudonuclease NYN 1 and MUT 15, but how their activities are controlled and coordinated is unknown. Structural and biochemical analyses reveal that the RDE 8/NYN 1 nuclease module is autoinhibited, restricting cleavage outside CPUG. We identify MUT 15, the CPUG scaffold linking this nuclease module to MUT 2, as a pseudohelicase. MUT 15 remodels the nuclease module, licensing RDE 8 activity upon complex assembly. Reconstituted CPUG synthesizes long poly(UG) tails, with the substrate 3' end determining tailing efficiency and register. Within CPUG, RNA engagement by MUT 2 limits RDE 8 access, while poly(UG) tails themselves are not cleaved by RDE 8, preventing re cleavage. Together, CPUG couples assembly dependent RNA cleavage to downstream processing, imposing safety and directionality.

biochemistry↗

bioRxiv2026

INHIBITION OF LIGAND-DEPENDENT BMP SIGNALING BLUNTS MELANOMA GROWTH

Treatments for advanced melanoma have markedly improved, but a significant proportion of patients still receive little to no survival benefit with standard-of-care therapies due to resistance and relapse1-5. The discovery and development of novel targets and therapies are needed to continue to improve patient outcomes in advanced melanoma. The identification of ligand-dependent BMP signaling that inhibits differentiation and promotes survival of melanoma cells suggests it is a potential therapeutic target that could complement current therapies6. Expression of the BMP ligand GDF6 (a.k.a BMP13) is responsible for this activity, and its expression is correlated with poor outcomes for melanoma patients. Here, we describe a novel monoclonal antibody targeting GDF6 that causes melanoma cell differentiation and death and blunts tumor growth in vivo. Together, these results indicate BMP-directed therapy has significant potential as a novel therapy for patients with advanced melanoma.

Cancer Biology↗

bioRxiv2026

Magnetic Tweezers Experiments Reveal Increased Mechanical Sensitivity of the F2561Y Mutant in Von Willebrand Factor

The large glycoprotein von Willebrand factor (VWF) is essential for primary hemostasis. By sensing hydrodynamic forces in the bloodstream, VWF elongates under elevated shear, increasing its adhesiveness to platelets. This mechanosensitive behavior arises from its multidomain architecture, where distinct structural elements respond at different force scales. The stem, formed by interactions between C-domains of adjacent monomers in VWF dimers, opens at relatively low forces (~1 pN), representing an early step in force activation. The F2561Y mutation in the C4 domain is a gain-of-function mutation associated with increased shear sensitivity and myocardial infarction, yet its effect on VWF mechanics in the physiologically relevant low-force regime remains unresolved. Here, we combine single-molecule magnetic tweezers with AFM imaging to investigate how F2561Y alters VWF stem dynamics. Magnetic tweezers measurements reveal that A2 domain unfolding remains unchanged in the mutant, whereas stem opening transitions occur at significantly lower forces compared to wildtype. The midpoint force for stem opening is reduced by approximately one order of magnitude, indicating a pronounced destabilization of the compact stem conformation. AFM imaging independently confirms a higher population of open stem states in the mutant, even without applied force. Our findings demonstrate that F2561Y selectively destabilizes the VWF stem and increases its force sensitivity without perturbing global domain stability, providing a direct molecular explanation for its enhanced shear responsiveness and prothrombotic phenotype. More broadly, our work establishes magnetic tweezers as a powerful approach to resolve low-force conformational equilibria in mechanosensitive proteins and to dissect the mechanical impact of disease-associated mutations. HighlightsO_LIThe F2561Y mutation lowers the force required to open the VWF stem. C_LIO_LIF2561Y mutant VWF dimers exhibit more open conformations compared to wildtype. C_LIO_LIForce sensitivity provides a mechanism for the prothrombic phenotype of F2561Y. C_LI

biophysics↗

bioRxiv2026

SLBP-independent control of maternal histone mRNA

Replication-dependent (RD) histones are crucial for packaging newly replicated DNA into chromatin, ensuring genome stability. In metazoans, the mRNA of RD histones is uniquely regulated through a conserved 3' stem-loop bound by stem-loop binding protein (SLBP). This allows cell cycle-coupled regulation of these important transcripts. However, oocytes must stabilise histone mRNAs independently of the cell cycle to ensure maternal loading to support the first embryonic divisions. Using Caenorhabditis elegans as a model system, we discovered an SLBP-independent mechanism that ensures RD histone transcript stability during oogenesis. This is mediated by the protein complex PETISCO, bound to the effector protein TOST-1, which directly binds the histone stem-loop region and maintains maternal histone mRNA levels during oogenesis and early embryogenesis. Loss of this mechanism disrupts histone homeostasis, leading to premature genome activation, mitotic defects, and embryonic lethality. Interestingly, the same complex, PETISCO, acts in piRNA biogenesis when bound to the effector PID-1, revealing an intriguing co-option of this histone mRNA homeostasis mechanism by the piRNA pathway. Our findings reveal a unique SLBP-independent mechanism of histone mRNA regulation, that served as a basis for the evolution of a novel piRNA biogenesis mechanism.

molecular biology↗

bioRxiv2025

Murine Toll-like receptor 8 is a nucleic acid multi-sensor detecting 2',3'-cyclic monophosphate guanosine as well as combinations of ribo-, deoxy-, cyclic nucleotides, and nucleosides

Toll-like receptor 8 (TLR8) in humans senses RNA degradation products and elicits an inflammatory immune response. In contrast, the ligand specificity and function of its murine counterpart mTLR8, long considered non-functional, remain poorly defined. Here, we established an agonist combination model of poly-deoxythymidine (poly-dT) DNA and TLR7/8 binding site 1 agonists such as uridine or the benzazepine compound TL8-506, which activates mTLR8, while suppressing mTLR7 signaling. Extensive agonist analysis based on this model revealed that 2,3-cyclic guanosine monophosphate (2,3-cGMP) serves as a natural ligand for mTLR8, suggesting functionality of its binding site 1 without engagement of site 2. In addition, 2,3-cyclic uridine monophosphate, bacterial single-stranded (ss) DNA, double-stranded (ds) DNA fragments, microRNAs, ssRNA derived from HIV1, SARS-CoV-2, or bacterial sources all potentiate mTLR8 sensing of site 1 agonists. All these stimuli induce distinct inflammatory responses from murine macrophages and microglia via TLR8. In vivo, intrathecal administration of TL8-506 and poly-dT led to microglial accumulation and neuronal injury in the murine cerebral cortex through TLR8, highlighting the potential neuropathological consequences of mTLR8 activation. Taken together, our study defines mTLR8 as a nucleic acid sensor detecting 2,3-cGMP as well as combinations of ssDNA, dsDNA, ssRNA fragments, 2,3-cyclic nucleotide monophosphates, and nucleosides, with implications for host defense and neuroinflammation.

immunology↗

bioRxiv2025

Bacterial population dynamics during colonization of solid tumors

Bacterial colonization of tumors is widespread, yet the dynamics during colonization remain underexplored. Here we discover strong variability in the sizes of intratumor bacterial clones and use this variability to infer the mechanisms of colonization. We monitored bacterial population dynamics in murine tumors after introducing millions of genetically barcoded Escherichia coli cells. Results from intravenous injection revealed that roughly a hundred bacteria seeded a tumor and that colonizers underwent rapid, yet highly nonuniform growth. Within a day, bacteria reached a steady-state and then sustained load and clone diversity. Intratumor injections, circumventing infection bottlenecks, revealed that the nonuniformity persists and that the sizes of bacterial progenies followed a scale-free distribution. Theory suggested that our observations are compatible with a growth model constrained by a local niche load, global resource competition, and noise. Our work provides the first dynamical model of tumor colonization and may allow distinguishing genuine tumor microbiomes from contamination.

systems biology↗

bioRxiv2023

Physical activity regulates the immune response to breast cancer by a hematopoietic stem cell-autonomous mechanism

Physical activity is a modifiable lifestyle factor that is associated with a decreased risk for the development of breast cancer. While the exact mechanisms for the reduction in cancer risk due to physical activity are largely unknown, it is postulated that the biological reduction in cancer risk is driven by improvements in inflammation and immune function with exercise. Hematopoietic stem cells (HSCs) are the progenitor for all of the cells of the immune system and are involved in cancer immunosurveillance through differentiation into cytotoxic cell population. In this study, we investigate the role of physical activity (PA) in a spontaneously occurring model of breast cancer over time, with a focus on tumor incidence, circulating and tumor-infiltrating immune cells as well gene expression profiles of tumors and hematopoietic stem cells. Furthermore, we show that, in addition to a direct effect of PA on the immune cells of tumor-bearing mice, PA reduces the oxidative stress in HSCs of wildtype and tumor-bearing mice, and by doing so, alters the differentiation of the HSCs towards T cells in order to enhance cancer immunosurveillance.

cancer biology↗

bioRxiv2023

A distinct class of hematopoietic stem cells develop from the human yellow bone marrow

During aging, adipose tissue within the bone marrow expands while the trabecular red marrow contracts. The impact of these changes on blood cell formation remains unclear. To address this question, we performed single-cell and single-nuclei transcriptomic analysis on adipose-rich yellow bone marrow (BMY) and adipose-poor trabecular red marrow (BMR) from human subjects undergoing lower limb amputations. Surprisingly, we discovered two distinct hematopoietic niches, in which BMY contains a higher number of monocytes and progenitor cells expressing genes associated with inflammation. To further investigate these niches, we developed an in-vitro organoid system that maintains features of the human bone marrow. We find cells from BMY are distinct in their expression of the leptin receptor, and respond to leptin stimulation with enhanced proliferation, leading to increased monocyte production. These findings suggest that the age-associated expansion of bone marrow adipose tissue drives a pro-inflammatory state by stimulating monocyte production from a spatially distinct, leptin-responsive hematopoietic stem/progenitor cell population. SignificanceThis study reveals that adipose tissue within the human bone marrow is a niche for hematopoietic stem and progenitor cells that can give rise to pro-inflammatory monocytes through leptin signaling. Expansion of bone marrow adipose tissue with age and stress may thus underlie inflammageing.

developmental biology↗

bioRxiv2021

Global mRNA and chromatin accessibility profiling elucidate how HIV-1 perturbs ILC and NK cell subsets

The interrelatedness of human blood innate lymphoid cell (ILC) subsets, and how they are perturbed by HIV-1, remains unclear. Transcriptional and chromatin profiling separated blood ILCs into ILC2s, ILCPs, one cluster that included CD56dim and CD56-NK cells, and CD56hiNK cells that have features of both CD56dim/-NK cells and ILCs. In contrast to mice, human NK cells expressed tissue repair protein amphiregulin (AREG), with greater production by CD56hiNK cells than by ILCs. AREG was induced by TCF7/WNT signaling, IL-2, or IL-15, but not by inflammatory cytokines, and was inhibited by TGFB1, a cytokine elevated in people living with HIV-1. NK cell knockout of the TGFB1-stimulated WNT antagonist RUNX3 increased AREG production. In people living with HIV-1, AREG+NK cell percentage correlated with numbers of ILCs and CD4+T cells, and correlated inversely with inflammatory cytokine IL-6. RNA-Seq showed increased antiviral gene expression in all ILC subsets from people who were HIV-1 viremic, and increased expression of anti-inflammatory gene MYDGF in CD56hiNK cells from elite controllers. Functionally-defective CD56-NK cells were increased in people living with HIV-1 in inverse correlation with CD56dimNK cells, ILCs, and CD4+T cells. Experiments with human PBMCs ex vivo and in humanized mice revealed that CD4+T cells and their production of IL-2 prevented CD56dim transition to CD56-NK cells by activating mTOR, and, in people living with HIV-1, plasma IL-2 correlated with CD4+T cell number but not with CD8+T cells. These studies clarify how ILC subsets are interrelated and provide insight into how HIV-1 infection disrupts NK cells, including homeostatic functions of NK cells discovered here. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/440368v3_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@9d6be2org.highwire.dtl.DTLVardef@115f0e8org.highwire.dtl.DTLVardef@17b1a28org.highwire.dtl.DTLVardef@f262e9_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗