Biology subjects

Bauer, K.

Publications and source records attributed to Bauer, K..

15 recordsLinked to original sources

bioRxiv2026

scIRES-seq reveals multimodal molecular heterogeneity in CTCs from small cell cervical cancer

Circulating tumor cells (CTCs) can provide a window into cellular and molecular mechanisms of cancer dissemination. However, the rarity and heterogeneity of CTCs complicate reliable identification and molecular characterization. Here, we introduce scIRES-seq, a framework linking immunophenotype, genetic variation, epigenomic profiles and gene expression within individual cells. In this proof-of-concept study, we coupled scIRES-seq to real-time imaging spectral flow cytometry and applied it to CTCs from a patient with metastatic cervical small cell neuroendocrine carcinoma. Tumor-matched copy-number alterations and targeted somatic variants established CTC identity, supported by DNA methylation profiles concordant with metastatic tissue and transcriptional features consistent with neuroendocrine differentiation. Genetic and DNA methylation analyses identified two largely concordant CTC subpopulations that were not clearly distinguished by their transcriptomes, highlighting the complementary information gained through single-cell multi-omics profiling. These findings demonstrate the feasibility of integrated CTC identification and characterization and provide a framework for investigating relationships between genetic diversity and molecular states in rare, heterogeneous cell populations.

cancer biology↗

bioRxiv2026

Engineering CAR T Cells for Hepatocellular Carcinoma Recurrence after Liver Transplantation

Background & AimsLiver transplantation improves outcomes in hepatocellular carcinoma (HCC), yet treatment options for patients with tumor recurrence remain limited to tyrosine kinase inhibitors. Glypican-3 (GPC3)-targeted CAR T cells offer a tumor-directed immune-based therapeutic strategy, but their efficacy may be limited by post-transplant immunosuppression. We developed a CAR T cell platform combining CRISPR/Cas9-mediated FKBP1A disruption to confer resistance to FKBP12-dependent immunosuppressive agents, including tacrolimus, everolimus, and sirolimus, with TRAC knockout to eliminate endogenous T cell receptor expression and reduce alloreactivity. MethodsHuman T cells were edited using Cas9 ribonucleoprotein complexes targeting FKBP1A and TRAC, expanded, and transduced with an anti-GPC3 CAR construct. Cytokine production and cytotoxicity were assessed in vitro. Antitumor activity under tacrolimus treatment was evaluated in a Hep G2 xenograft model, and xenoreactivity was assessed in a graft-versus-host disease model. FKBP1A/TRAC double-knockout T cells were enriched using mTOR inhibitor selection combined with CD3-based MACS depletion. PBMCs from liver transplant recipients were used to evaluate feasibility for clinical translation during the early post-transplant period. ResultsTacrolimus suppressed wild-type CAR T cell function but not FKBP1A/TRAC double-knockout CAR T cells, which retained cytokine production, cytotoxicity, and in vivo antitumor activity. Cyclosporine A remained suppressive, enabling its potential use as a pharmacologic control strategy. TRAC disruption reduced xenoreactivity. CD3-based MACS depletion and mTOR inhibition achieved functional double-knockout efficiencies greater than 98%, without compromising cell viability. Functional FKBP1A/TRAC knockout CAR T cells were generated from patient PBMC samples 30 days post-transplant. ConclusionsDual-edited GPC3 CAR T cells resist tacrolimus-based immunosuppression while limiting alloreactivity, supporting their use for recurrent HCC after liver transplantation. Sequential, high-viability selection in a modular cellular engineering framework enables adaptation to alternative tumor targets and next-generation CAR T cell designs. Impact and implicationsO_LIEngineering armored GPC3-targeting CAR T cells for hepatocellular carcinoma in the post-transplant setting C_LIO_LIDemonstrating safety and therapeutic efficacy in the presence of immunosuppressive drugs in preclinical models C_LIO_LILeveraging mTOR inhibitor resistance and CD3 destabilization enables high-efficiency, high-purity selection of genetically modified T cells C_LIO_LIA modular cellular engineering platform enables utilization for alternative tumor targets and next-generation CAR T cells C_LI

immunology↗

bioRxiv2026

Robust mammalian RNA localization elements are complex and multipartite

The subcellular localization patterns of RNAs are controlled by regulatory elements contained within them. However, for most localized RNAs, the identities of these elements remain unknown. We had previously identified several localization elements that are necessary and sufficient for robust, kinesin-dependent RNA targeting to microtubule plus ends in a variety of cell types. Yet the characteristics of these elements that are critical for function remained unclear. To address this, we systematically created tens of thousands of mutant localization elements and quantified their ability to regulate subcellular RNA localization in neuronal cells. We found that the minimally active size of these localization elements is large, approximately 200 nucleotides. These elements contain multiple important subsequences, with some being completely intolerant of any changes and others being tolerant to a shuffling of nucleotide order but not to changes in nucleotide composition. Using single molecule microscopy, we verified these findings in primary rat neurons. Together, these results demonstrate that highly active mammalian RNA localization elements are large, complex, and multipartite and lay a foundation for further mechanistic studies of their function.

molecular biology↗

bioRxiv2026

Fluoxetine for Prenatal Alcohol-Exposed Mice: Addressing Impaired Enrichment-Mediated Neurogenesis

BackgroundFetal alcohol spectrum disorder (FASD) encompasses a variety of disorders that occur after a fetus has been exposed to alcohol. Hippocampal related issues are a common neurological deficit found in FASD. The dentate gyrus within the hippocampus is a unique area of the brain that continues to generate new neurons into adulthood. This neurogenesis can be enhanced by an enriched environment (EE); however in prenatal alcohol exposed (PAE) mice this EE-mediated neurogenesis is impaired. In addition to EE, selective serotonin reuptake inhibitors (SSRIs), such as fluoxetine, also promote neurogenesis. Here we examine if fluoxetine restores the impaired EE-mediated neurogenesis of PAE mice. MethodPAE mice were generated using a voluntary limited access model where mice received a 10% ethanol (w/v) solution during gestation. To evaluate neurogenesis, we use a NestinCreT2:tdTomato transgenic mouse line in which newborn dentate granule cells (nDGCs) can be evaluated by tdTomato flourescence. PAE and saccharine control (SAC) mice were placed in either standard housing (SH) or enriched environment (EE). Subsequently, we administered fluoxetine (FLX) or vehicle (VEH) after which neurogenesis was evaluated. ResultsPAE resulted in impaired EE-mediated neurogenesis. This neurogenic impairment was not restored by FLX. Interestingly, FLX did increase neurogenesis in PAE mice while housed in SH. ConclusionThese results suggest that there is a neurogenic ceiling in PAE mice that cannot be increased by fluoxetine in EE. However, fluoxetine can increase neurogenesis while the environment is less complex.

neuroscience↗

bioRxiv2026

Inflammatory injury drives CIN and STING loss in polyploidpancreatic acinar cells

Epidemiological studies link pancreatic inflammation to increased cancer risks with elevated levels of chromosomal instability (CIN), yet the underlying cause remains unclear. The exocrine pancreas and lactating mammary gland harbor polyploid cells to boost secretory efficiency. Using organoid and in vivo models of pancreatic injury, we show that polyploid acinar cells contribute to regeneration via acinar-to-ductal metaplasia. The metaplasia induced cell size reduction is associated with crowding and spindle misorientation, leading to mitotic errors such as lagging chromosomes, chromatin bridges, and micronuclei. Micronucleated cells are not always eliminated or arrested in the cell cycle but can continue to proliferate and expand. Polyploid cells in post-lactational mammary gland organoids equally exhibited proliferation-related CIN. Single-cell proteomics of acinar cells shows STING1 loss and increased ATR levels in polyploid cells, enabling continued proliferation. These findings uncover physiological links between polyploidy, tissue repair, and CIN, offering new insights into cancer risks after tissue remodeling.

cell biology↗

bioRxiv2026

A divergent mutational and clonal landscape in aged HSCs is not linked to aging-associated clonal hematopoiesis

Somatic mutations accumulate throughout life and can serve as endogenous markers to trace cellular lineage relationships. In hematopoietic stem cells (HSCs), aging is associated with functional decline and clonal skewing, yet how somatic mutational histories shape clonal architecture at single-cell resolution remains incompletely understood. Here, we leverage single-cell RNA sequencing from murine and human long-term HSCs to identify expressed somatic single-nucleotide variants and reconstruct mutation-based genealogies. To address technical noise inherent to single-cell transcriptomes, we implement a stringent joint variant filtering strategy that exploits daughter cell relationships and probabilistic modeling to distinguish true somatic events from artifacts. Using these high-confidence variants, we infer phylogenetic and clonal relationships among individual HSCs and uncover striking age-dependent differences in lineage structure. Whereas young HSCs show little evidence of hierarchical clonal organization, aged HSCs frequently exhibit structured genealogies consistent with clonal expansion. Integration of mutational, transcriptional, and signature-based analyses further reveals that genetically distinct clones in aged samples are transcriptionally divergent and enriched for pathways linked to aging and DNA damage responses. Together, our findings demonstrate that somatic mutations recovered from single-cell transcriptomes can resolve HSC clonal evolution and reveal age-associated alterations in stem cell dynamics.

genomics↗

bioRxiv2025

Identification of pseudotetraivprolide from Pseudomonas entomophila give novel insights into the biosynthesis of detoxin/rimosamide-like anti-antibiotics

Novel variants of known natural product (NP) classes might guide our understanding of biosynthesis, mode of action and potential application as drugs for all members of such NP classes. Here we describe a novel member of the widespread detoxine/rimosamide-like (DRL) natural products named pseudotetraivprolide from Pseudomonas strains, which has the characteristic DRL-activity of protecting Bacillus cereus against the antibiotic blasticidin S. The generation of several deletion and complemented mutants, heterologous expression experiments, identification and structure elucidation of several derivatives, chemical synthesis of main derivatives, enzymatic characterization of individual biochemical steps and detailed homology modelling of enzyme complexes were performed. This allowed us to show the primary metabolism-derived malonyl CoA-ACP transacylase (AT) FabD acting as trans-AT in the biosynthesis, suggest an order for all late-stage modifications and provide a function for the three conserved hypothetical proteins PipDFG acting as last-step acetylation complex thereby stabilizing the final product.

microbiology↗

bioRxiv2025

Single-cell chromatin landscape and DNA methylation patterns reveal shared molecular programs in human tumor and non-tumor tissue CCR8+ Treg cells

Regulatory T (Treg) cells, a subset of CD4+ T cells, play a crucial role in immunoregulation. Notably, CCR8-expressing Treg cells in tissues also contribute to organ homeostasis and repair. To determine whether these tissue-regenerative programs are active in the tumor microenvironment, we employed single-cell chromatin accessibility and genome-wide DNA methylation analyses to investigate CCR8+ tissue Treg cells isolated from human tumor and adjacent tumor-free tissues. Our findings indicate that CCR8+ tissue Treg cells from tumor and corresponding tumor-free tissues exhibit a high degree of similarity, suggesting that the tumor microenvironment may harbor highly activated tissue Treg cells. This observation was consistent across various tumor types and origins, including primary tumors and metastases. Using quantitative proteomics, we identified several candidate factors associated with the regenerative and suppressive programs of Treg cells, which may serve as potential reservoir of druggable targets for future therapeutic interventions.

immunology↗

bioRxiv2023

Oncogenic RAS-Pathway Activation Drives Oncofetal Reprogramming and Creates Therapeutic Vulnerabilities in Juvenile Myelomonocytic Leukemia

Aberrant fetal gene expression facilitates tumor-specific cellular plasticity by hijacking molecular programs of embryogenesis1. Persistent fetal gene signatures in childhood malignancies are typically explained by their prenatal origins2-6. In contrast, reactivation of fetal gene expression is considered a consequence of oncofetal reprogramming (OFR) in adult malignancies and is associated with aggressive disease7-10. To date, OFR has not been described in the context of childhood malignancies. Here, we performed a comprehensive multi-layered molecular characterization of juvenile myelomonocytic leukemia (JMML) and identified OFR as a hallmark of aggressive JMML. We observed that hematopoietic stem cells (HSCs) aberrantly express mixed developmental programs in JMML. Expression of fetal gene signatures combined with a postnatal epigenetic landscape suggested OFR, which was validated in a JMML mouse model, demonstrating that postnatal activation of RAS signaling is sufficient to induce fetal gene signatures. Integrative analysis identified the fetal HSC maturation marker CD52 as a novel therapeutic target for aggressive JMML. Anti-CD52 treatment depleted human JMML HSCs and disrupted disease propagation in vivo. In summary, this study implicates OFR, defined as postnatal acquisition of fetal transcription signatures, in the pathobiology of a childhood malignancy. We provide evidence for the direct involvement of oncogenic RAS signaling in OFR. Finally, we demonstrate how OFR can be leveraged for the development of novel treatment strategies. Highlights{blacksquare} Epigenomic and transcriptomic landscape of juvenile myelomonocytic leukemia (JMML) in the context of hematopoietic development. {blacksquare}The presence of fetal transcription signatures in childhood malignancies is not indicative of a developmental maturation block. {blacksquare}High-risk JMML is characterized by oncofetal reprogramming of postnatal hematopoietic stem cells (HSCs). {blacksquare}RAS-pathway mutations induce fetal-like gene expression signatures in murine postnatal HSCs. {blacksquare}The fetal maturation marker CD52 is a novel therapeutic target in high-risk JMML.

cancer biology↗

bioRxiv2023

Multifactorial approach is needed to unravel the maturation phases of human neurons derived from induced pluripotent stem cells

Neurons derived from induced pluripotent stem cells (h-iPSC-Ns) provide an invaluable model for studying the physiological aspects of neuronal development and diseases. However, multiple studies have also demonstrated that h-iPSC-Ns exhibit a high degree of functional and epigenetic diversity. Due to the imprecise characterization and significant variation among the currently available maturation protocols, it is essential to establish a set of criteria to standardize models and accurately characterize and define the developmental properties of neurons derived from iPSCs. In this study, we conducted a comprehensive analysis of the h-iPSC-Ns via electrophysiological and microscopic techniques to follow their functional development at the cellular and network levels. This enabled us to provide a thorough description of the maturation process of h-iPSC-Ns over a 10-week period in vitro. Specifically, we have used conventional whole-cell patch-clamp and dynamic clamp techniques, alongside morphometry, to assess the characteristics of maturing h-iPSC-Ns. Additionally, we utilized calcium imaging to monitor the progression of synaptic activity and network communication. At the single cell level, human neurons exhibited gradually decreasing membrane resistance in parallel with improved excitability by 5 weeks of maturation. Their firing profiles were consistent with those of mature regular firing type of neurons. At the network level we observed the development of abundant fast glutamatergic and depolarizing GABAergic synaptic connections together with synchronized network activity. The identified sequence of differentiation events are consistent and offers a robust framework for developing targeted experiments at varying stages of neuronal maturation. This framework allows for the use of different, age-related methodologies or a singular set of experiments for a cultures maturation.

neuroscience↗

bioRxiv2023

Enhancing sensitivity and versatility of Tn5 based single cell omics

The analysis of chromatin features in single cells centers around Tn5 transposase and exploits its activity to simultaneously fragment target DNA and integrate adapter sequences of choice. This reaction provides a direct readout in the assay for transposase-accessible chromatin in single cells (scATAC-seq) to map open chromatin regions. However, a current limitation is the sparse coverage of open chromatin loci that are detected in a given single cell by droplet-based methods. Thus, enhancing Tn5 activity to improve genomic coverage of scATAC-seq or facilitating multi-omics readouts of chromatin features via Tn5 together with the transcriptome is of great interest. Here, we address these issues by optimizing scATAC-seq for an increased number of integrations per cell. In addition, we provide a protocol that combines mapping of histone modification with scRNA-seq from the same cell by targeting Tn5 to antibody-bound chromatin epitopes. Our experimental workflows improve the results obtained from the downstream data analysis and serve to better resolve epigenetic heterogeneity and transcription regulation in single cells.

molecular biology↗

bioRxiv2023

Clec12a tempers inflammation while restricting expansion of a colitogenic commensal

SUMMARYRegulation of the microbiota is critical to intestinal health yet the mechanisms employed by innate immunity remain unclear. Here we show that mice deficient in the C-Type-lectin receptor, Clec12a developed severe colitis, which was dependent on the microbiota. Fecal-microbiota-transplantation (FMT) studies into germfree mice revealed a colitogenic microbiota formed within Clec12a-/- mice that was marked by expansion of the gram-positive organism, Faecalibaculum rodentium. Treatment with F. rodentium was sufficient to worsen colitis in wild-type mice. Macrophages within the gut express the highest levels of Clec12a. Cytokine and sequencing analysis in Clec12a-/- macrophages revealed heighten inflammation but marked reduction in genes associated with phagocytosis. Indeed, Clec12a-/- macrophages are impaired in their ability to uptake F. rodentium. Purified Clec12a had higher binding to gram-positive organisms such as F. rodentium. Thus, our data identifies Clec12a as an innate immune surveillance mechanism to control expansion of potentially harmful commensals without overt inflammation.

immunology↗

bioRxiv2023

HEATR5B associates with dynein-dynactin and selectively promotes motility of AP1-bound endosomal membranes

The dynein motor complex mediates polarised trafficking of a wide variety of organelles, intracellular vesicles and macromolecules. These functions are dependent on the dynactin complex, which helps recruit cargoes to dyneins tail region and activates motor movement. How dynein and dynactin orchestrate trafficking of diverse cargoes is unclear. Here, we identify HEATR5B, an interactor of the AP1 clathrin adaptor complex, as a novel player in dynein-dynactin function. HEATR5B is one of several proteins recovered in a biochemical screen for proteins whose association with the human dynein tail complex is augmented by dynactin. We show that HEATR5B binds directly to the dynein tail and dynactin and stimulates motility of AP1-associated endosomal membranes in human cells. We also demonstrate that the HEATR5B homologue in Drosophila is an essential gene that promotes dynein-based transport of AP1-bound membranes to the Golgi apparatus. As HEATR5B lacks the coiled-coil architecture typical of dynein adaptors, our data point to a non-canonical process orchestrating motor function on a specific cargo. We additionally show that HEATR5B promotes association of AP1 with endosomal membranes in a dynein-independent manner. Thus, HEATR5B co-ordinates multiple events in AP1-based trafficking.

cell biology↗

bioRxiv2022

Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage

Medulloblastoma with extensive nodularity (MBEN) are cerebellar tumors with two histologically distinct compartments and varying disease course. In some children MBEN progresses, while others show spontaneous differentiation into more benign tumors. However, the mechanisms that control the tug-of-war between proliferation and differentiation are not well understood. Here, we dissected this process with a multi-modal single cell transcriptome analysis. We found that the internodular MBEN compartment comprised proliferating early cerebellar granular neuronal precursors (CGNP)-like tumor cells as well as stromal, vascular, and immune cells. In contrast, the nodular compartment consisted of postmitotic, neuronally differentiated MBEN cells. Both compartments were connected through an intermediate cell stage of actively migrating CGNPs. Furthermore, astrocyte-like tumor cells were identified that had branched off the main CGNP developmental trajectory. Cells with an astroglial phenotype were found in close proximity to migrating, late CGNP-like and postmitotic neuronally differentiated cells. Our study reveals how the spatial tissue organization is linked to the developmental trajectory of proliferating tumor cells through a migrating precursor stage into differentiated tumor cells with a more benign phenotype. We anticipate that our framework for integrating single nucleus RNA-sequencing and spatial transcriptomics will help to uncover intercompartmental interactions also in other cancers with varying histology.

cancer biology↗

bioRxiv2019

The cell-wall-localised BETA-XYLOSIDASE 4 contributes to immunity of Arabidopsis against Botrytis cinerea

Plant cell walls constitute physical barriers that restrict access of microbial pathogens to the contents of plant cells. The primary cell wall of multicellular plants predominantly consists of cellulose, hemicellulose and pectin. In Arabidopsis, a cell wall-localised protein, BETA-XYLOSIDASE 4 (BXL4) that belongs to a seven-member BETA-XYLOSIDASE (BXL) gene family was induced upon infection with the necrotrophic fungal pathogen Botrytis cinerea and mechanical wounding in a jasmonoyl isoleucine (JA-Ile) dependent manner. Ectopic expression of the BXL4 gene in Arabidopsis seed coat epidermal cells was able to rescue a bxl1 mutant phenotype suggesting that like BXL1, BXL4, had both xylosidase and arabinosidase activity and acts in mura on cell wall polysaccharides. bxl4 mutants show a compromised resistance to B. cinerea. Upon infection, bxl4 mutants accumulated reduced levels of JA-Ile and camalexin. Conditional overexpression of BXL4 resulted in enhanced expression of PDF1.2 and PAD3 transcripts both before and after B. cinerea infection. This was associated with reduced susceptibility of the transgenic lines to B. cinerea. These data suggest that remodelling or degradation of one or more cell wall polysaccharides is important for plant immunity against B. cinerea and plays a role in pathogen-induced JA-Ile and camalexin accumulation. One-sentence summaryBXL4 is a putative bifunctional xylosidase/arabinofuranisodase localising to the apoplast, important for immunity against the necrotrphic pathogen B. cinerea.

plant biology↗