Biology subjects

Lehmann, R.

Publications and source records attributed to Lehmann, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Mitochondrial amino acid export preserves mitochondrial volume at the egg-to-embryo transition

In animals, the transition from egg to embryo marks a rapid shift in cellular physiology, yet how mitochondria adapt to support this conversion remains poorly understood. We performed a targeted RNAi screen of conserved, nuclear-encoded mitochondrial proteins in Drosophila melanogaster to identify maternal effects. We identified distinct phenotypic classes affecting mitochondrial distribution or morphology in early embryos. We focused on Sideroflexin-1/3 (Sfxn1-3), a conserved mitochondrial inner membrane transporter, because it uniquely affects embryonic mitochondrial morphology. Maternal loss of Sfxn1-3 causes striking mitochondrial enlargement in embryos but not in oocytes, placing the trigger at the egg-to-embryo transition. Combining mitochondrial immunopurification with LC/MS-based metabolomic profiling, we show that amino acids are markedly enriched in Sfxn1-3-deficient mitochondria in both oocytes and embryos. This accumulation developmentally uncouples the metabolic and morphological phenotypes. By selectively disrupting discrete steps of egg activation, including translational activation, cell cycle re-entry, and fertilization, we demonstrate that mitochondrial swelling is independent of each, prompted instead by egg hydration. Beyond its reported role in proliferating cells as a serine importer, our data support a role for germline Sfxn1-3 in regulating inner mitochondrial membrane permeability to osmotically active amino acids. This activity is crucial for preserving organelle volume during the osmotic challenge of oocyte hydration. When this export fails, amino acid accumulation amplifies osmotic stress and drives rapid mitochondrial swelling. Together, these findings identify mitochondrial inner membrane permeability to amino acids as a key regulatory step that couples pre-established metabolite compartmentalization to osmotic adaptation at egg activation, and reveal how mitochondrial metabolic integrity and volume control are coordinated at this critical developmental transition.

developmental biology↗

bioRxiv2026

Decoupling Transcription from Cell Fate Preserves Germ Cell Totipotency

Only germ cells can give rise to a totipotent embryo, yet a conserved transcriptional program for germ cell identity remains elusive. Profiling Drosophila primordial germ cells (PGCs) across embryogenesis, we find that nascent PGCs are not silent, as previously thought, but instead transcribe the same totipotency program as the early embryo, reflecting an open chromatin state. This chromatin state, established by the pioneer factor Zelda, persists in PGCs throughout development. The associated transcriptional program normally drives somatic differentiation, but in PGCs the conserved RNA-regulator Nanos represses its translation, leaving germline chromatin uncommitted. Cells that fail to establish the totipotent state die before reaching the gonad. Thus, germ cells preserve developmental potential not by restricting transcription, but by preventing transcripts from determining cell fate.

developmental biology↗

bioRxiv2026

Co-regulatory changes in Homo sapiens prefrontal cortex shape RNA-chromatin interactions

Noncoding RNAs (ncRNAs) regulate gene expression through RNA-chromatin interactions, yet their role in human brain evolution remains unclear. To map these interactions, we integrated FANTOM6 neurogenic data with a comprehensive atlas of regulatory regions active during early cortical development. This integration effort linked ncRNAs and transcription factors (TFs) to their genomic targets, revealing functional interactions captured by RNA-DNA contact mapping, yet largely missed by chromatin conformation data. Overlaying these interactions with nearly fixed variants in Homo sapiens relative to extinct hominins uncovered widespread rewiring of TF binding, affecting genes implicated in progenitor proliferation and neuronal differentiation. Gene regulatory network reconstruction identified TEAD2 and ONECUT2 as key regulators of intermediate progenitors and migrating neurons. Functional perturbation followed by Cut&Tag and ATAC-seq linked the two TFs to disease- and evolutionarily- relevant pathways. Together, these results show how ncRNA-TF cooperation and selective cis-regulatory rewiring contributed to sapiens-specific features of cortical development.

molecular biology↗

bioRxiv2026

Synthetic germ granules reveal a direct role of Vasa/DDX4 in RNA localization and translational activation

AbstractCytoplasmic RNA granules, including stress granules, P bodies, neuronal RNA granules, and germ granules, are essential for RNA storage and regulation across a wide range of organisms. However, dissecting the contributions of individual factors to granule function is challenging because of the interdependence of components in vivo. This is especially true for DEAD-box helicases, common regulators of mRNA granules, whose specific contributions remain unclear. In this study, we developed a synthetic approach to de novo generate germ granules, enabling us to identify the minimal machinery needed for RNA localization and translational activation. Using a self-assembling PopTag-based scaffold derived from Caulobacter fused to the RNA-binding domain (RBD) of the germplasm organizer Oskar, we found that the recruitment of endogenous germ granule mRNAs (nanos and pgc) depended on the DDX4 protein Vasa. By employing orthogonal RNA tethering approaches, we demonstrate that Vasa is both necessary and sufficient for localized mRNA translation. Consistent with these findings, acute depletion of Vasa from endogenous germ granules specifically reduced Nanos translation without affecting mRNA localization, confirming Vasa as a core factor linking RNA recruitment to localized translational activation. These in vivo reconstitution experiments reveal a two-component module in which a scaffold RBD and the Vasa helicase, but not other DEAD-box helicases, enable RNP condensates to accumulate specific RNAs and promote their translation. Overall, our study uncovers previously unrecognized functions of an RNA helicase within ribonucleoprotein condensates and demonstrates the power of synthetic biology to analyze complex biomolecular condensates in living organisms.

developmental biology↗

bioRxiv2025

GCL pruning of PIP3 establishes the soma-germline boundary

Primordial germ cells (PGCs) are the first cells specified in the Drosophila embryo and serve as precursors to the germline. Their formation requires suppression of somatic fates, a process achieved by excluding the receptor tyrosine kinase Torso from the posterior pole through degradation mediated by the ubiquitin ligase adaptor Germ Cell-Less (GCL). Although Torso is known to antagonize PGC formation, the underlying mechanism has remained unclear. Here, we combine optogenetic Ras activation and Ras effector loop mutants to show that Ras signaling suppresses PGC formation independently of the canonical Raf/MEK/ERK pathway. We identify an unexpected early role for Torso in activating phosphoinositide 3-kinase (PI3K), generating posterior membrane domains enriched in phosphatidylinositol (3,4,5)-trisphosphate (PIP3). Elevated PI3K activity disrupts PGC formation, while reduced PI3K activity leads to ectopic PGCs. We further demonstrate that GCL remodels the posterior pole membrane by suppressing Torso-dependent PI3K activation. Clearing PIP3 enables Myosin II enrichment, thereby constricting the pole bud for PGC formation. Together, our findings reveal how antagonistic Torso and GCL activities establish the soma-germline boundary by regulating cortical lipid organization. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/697122v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1efe138org.highwire.dtl.DTLVardef@1ab3b17org.highwire.dtl.DTLVardef@b49412org.highwire.dtl.DTLVardef@1655c5e_HPS_FORMAT_FIGEXP M_FIG Graphical AbstractO_LIMembrane domains with high Torso activity (purple) in the early embryo have a higher PIP3 content. C_LIO_LIAt the posterior pole, GCL-containing germplasm (green) degrades Torso, resulting in a PIP3-low membrane. C_LIO_LIClearing PIP3 enables Myosin II pole bud constriction required for PGC formation. C_LI C_FIG

cell biology↗

bioRxiv2025

Charting the single cell transcriptional landscape governing visual imprinting.

Memory-related transcriptional events in brain remain poorly understood. Visual imprinting is a form of learning in which young animals develop preferences through early exposure to specific stimuli. In chicks, visual imprinting memory is stored in the intermediate medial mesopallium (IMM) of the forebrain. To investigate learning-associated molecular changes, we performed single-nucleus RNA sequencing of the left IMM in strongly imprinted chicks and untrained controls. This analysis generated the first classification of cells composing the IMM, identifying as a result over 30 cell clusters with distinct transcriptional differences putatively linked to memory formation, nearly half of them in long non-coding RNAs (lncRNAs). Follow-up analysis on selected genes, confirmed that the gene expression levels of two lncRNAs and protein levels of FOXP2, RORA (transcription factors), LUC7L (splicing factor), and ROBO1 (axon guidance molecule) correlate with memory strength, reflecting either innate learning potential or imprinting experience. Additionally, among the confirmed lncRNAs, the brain- and avian-specific lncRNA ENSGALG00010007489 is enriched in the nuclei of specific glutamatergic clusters and its association with imprinting was further confirmed through quantitative multi-probe in situ hybridization. These findings offer the first single-cell resolution map of transcriptional changes underlying memory formation in the avian brain.

neuroscience↗

bioRxiv2025

A genome-wide, machine learning-guided exploration of the cis-regulatory code involved in neuronal differentiation

Gene expression is controlled by proximal and distal cis-regulatory elements (CREs), containing DNA motifs bound by various transcription factors (TFs). Other sequence features, such as specific k-mers or low complexity regions, have also been implicated [1-3]. However, in a dynamic biological process such as cell differentiation, we lack an understanding of how the transcriptional activity of CREs progressively change and what sequence features underlie these transitions, which may reflect common and/or coordinated regulatory processes. Here, we use single-cell ATAC-seq and RNA-seq to follow, at a genome scale, CREs along differentiation of induced pluripotent stem cells into cortical neurons and develop a method to automatically identify the diversity of CRE profiles and their underlying sequence features. We propose a machine-learning guided clustering algorithm, STOIC (Statistical learning TO Inform Clustering), that jointly learns an unsupervised clustering of the CREs in the space of the activity profiles and a supervised predictor associated with each cluster in the DNA-sequence space. STOIC is specifically designed to provide readily interpretable results. We show that the method identifies CRE profiles associated with highly predictive sequence features and outperforms methods solely concerned with co-activity clustering on this task. Orthogonal data collected in the same settings link the inferred CRE clusters to specific enhancer or promoter signatures. Furthermore, we show that the DNA features unveiled by STOIC reflect biologically relevant regulators and offer a valuable basis to dissect elements of the cisregulatory grammar. Finally, we demonstrate the general applicability of STOIC by analyzing five bulk CAGE datasets of human cells responding to various treatments.

bioinformatics↗

bioRxiv2025

GMCL1 Controls 53BP1 Stability and Modulates Paclitaxel Sensitivity in Cancer

Mitotic surveillance pathways monitor the duration of mitosis (M phase) in the cell cycle. Prolonged M phase, caused by spindle attachment defects or microtubule-targeting drugs triggers formation of the ternary "mitotic stopwatch pathway" complex (MSP) consisting of 53BP1, USP28, and p53. This complex stabilizes p53, leading to cell cycle arrest or apoptosis in daughter cells. In cancers that are resistant to paclitaxel, a microtubule-targeting agent, cells bypass mitotic surveillance activation, allowing unchecked proliferation, although the underlying mechanisms remain poorly understood. Here, we identify GMCL1 as a key negative regulator of MSP signaling. We show that 53BP1 physically interacts with GMCL1, but not its paralog GMCL2, and we map their interaction domains. CRL3GMCL1 functions as a ubiquitin ligase that targets 53BP1 for degradation during the M phase, thereby reducing p53 accumulation in daughter cells. Depletion of GMCL1 inhibits cell cycle progression upon release from prolonged mitotic arrest, a defect that is rescued by co-silencing 53BP1 or USP28. Moreover, GMCL1 depletion sensitizes cancer cells to paclitaxel in a p53-dependent manner. Together, our findings support a model in which dysregulated CRL3GMCL1-mediated degradation of 53BP1 prevents proper MSP function, leading to p53 degradation and continued proliferation. Targeting GMCL1 may therefore represent one possible avenue for addressing paclitaxel resistance in cancer cells with functional p53.

cell biology↗

bioRxiv2025

Balancing Act: Groundwater microbiome''s resilience and vulnerability to hydroclimatic extremes

Groundwater health is increasingly threatened by climate change, which alters precipitation patterns, leading to groundwater recharge shifts. These shifts impact subsurface microbial communities, crucial for maintaining ecosystem functions. In this decade-long study of carbonate aquifers, we analyzed 815 bacterial 16S rRNA gene datasets, 226 dissolved organic matter (DOM) profiles, 387 metabolomic datasets, and 174 seepage microbiome sequences. Our findings reveal distinct short- and long-term temporal patterns of groundwater microbiomes driven by environmental fluctuations. Microbiomes of hydrologically connected aquifers exhibit lower temporal stability due to stochastic processes and greater susceptibility to surface disturbances, yet they demonstrate remarkable resilience. Conversely, isolated aquifer microbiomes show resistance to short-term changes, governed by deterministic processes, but exhibit reduced stability under prolonged stress. Variability in seepage-associated microorganisms, DOM, and metabolic diversity further drive microbiome dynamics. These findings highlight the dual vulnerability of groundwater systems to acute and chronic pressures, emphasizing the critical need for sustainable management strategies to mitigate the impacts of hydroclimatic extremes.

microbiology↗

bioRxiv2025

Single-cell transcriptional profiling reveals a novel RAB13+ endothelial subpopulation and profibrotic mesenchymal cells in the aged human bone marrow

The bone marrow (BM) microenvironment plays a crucial role in regulating hematopoiesis, yet the molecular changes associated with aging in humans remain poorly understood. Using single-cell RNA sequencing, we uncovered transcriptional shifts in BM endothelial cells (EC) and mesenchymal stem cells (MSC) during aging. Aged sinusoidal EC exhibited a prothrombotic phenotype with compromised mitochondrial and vascular function. Additionally, we identified a novel arterial EC subset, emerging in aged individuals, characterized by RAB13 expression and associated with transcriptional regulatory processes. MSC from aged subjects displayed impaired matrix remodeling and epithelial-mesenchymal transition, driven partly by a subpopulation of THY1+ profibrotic cells absent in younger individuals. Finally, immunofluorescent imaging and spatial transcriptomics confirmed the presence of these aging-associated cells in BM samples from aged individuals. In summary, this work provides a comprehensive view of the transcriptional landscape, cellular interactions, and spatial organization of aged EC and MSC, offering novel insights and potential targets that could be exploited for preventing age-associated changes in humans. TeaserAging reshapes the bone marrow with emergence of RAB13+ endothelial cells and profibrotic stromal cells altering tissue function.

molecular biology↗

bioRxiv2024

PrePR-CT: Predicting Perturbation Responses in Unseen Cell Types Using Cell-Type-Specific Graphs

Predicting the transcriptional response of chemical perturbations is crucial to understanding gene function and developing drug candidates, promising a streamlined drug development process. Single-cell sequencing has provided an ideal data basis for training machine learning models for this task. Recent advances in deep learning have led to significant improvements in predictions of chemical as well as genetic perturbations at the single cell level. Experiments have shown that different cell types exhibit distinct transcriptional patterns and responses to perturbation. This poses a fundamental problem for predicting transcriptional responses of drugs or cell types outside the training data. Accordingly, existing methods lack cell-type-specific modeling or do not explicitly provide an interpretable mechanism for the gene features. In this study, we introduce a novel approach that employs a network representation of various cell types as an inductive bias, improving prediction performance in scenarios with limited data while acknowledging cellular differences. We applied our framework to four small-scale single-cell perturbation datasets and one large-scale screening experiment, demonstrating that this representation can inherently generalize to previously unseen cell types. Furthermore, our method outperforms the state-of-the-art methods in predicting the post-perturbation response in unobserved cell types.

bioinformatics↗

bioRxiv2024

Current-use and legacy contaminants evidence dissolved organic matter transfer and dynamics across a fractured-rock groundwater recharge area

Anthropogenic activities cause the release of vast amounts of contaminants into the environment which eventually reach even groundwater resources. With usually sparse regulatory monitoring of limited priority compounds, the large spectrum of contaminants, and the intricacies of intra- and inter-annual contaminant dynamics, such as the emergence and mobilisation of contaminants, are easily overlooked. Utilizing an 6-year record of untargeted LC-MS assessment of dissolved organic, we report the detection and tracing of selected environmental chemicals in the Hainich Critical Zone Exploratory (central Germany), representing a model groundwater flow system under different land use. The insect repellent DEET (N,N-diethyl-m-toluamide) and the coniferous resin acid 7-ODAA (7-oxodehydroabietic acids) show phases of seasonal dynamics in line with their expected periods of release. The legacy herbicides simazine, the triazine transformation product hydroxypropazine, and the flame retardant/plasticiser TPP (triphenyl phosphate) occurred episodically at various locations in the fractured sedimentary bedrock. Within the period of monitoring, extreme weather events (i.e., the severe 2018 drought) and extreme subsurface responses (i.e., 5-year groundwater highstand 2018) likely contributed to long-term organic matter dynamics, potentially causing re-emergence of legacy agrochemicals. This investigation points to the persistence and mobilisation of anthropogenic contaminants, and highlights the importance of long-term combined untargeted and targeted analysis of the groundwater dissolved organic matter for understanding subsurface ecosystems processes. The results add a note of caution for regulatory monitoring since also legacy contaminant levels may considerably vary over time. HighlightsO_LI6 years of monitoring with non-target LC-MS screenings; 4-weekly samplings C_LIO_LI5 current-use and legacy compounds that evidence dissolved organic matter transfer C_LIO_LICompounds comprise regularly targeted and non-monitored features in groundwater C_LIO_LIPronounced phases of non-detects help to further investigate surface-subsurface coupling C_LIO_LIThis illustrates the need for spatiotemporally highly resolved non-target monitoring C_LI

biochemistry↗

bioRxiv2024

Predictive biomarkers of breast ductal carcinoma in situ may underestimate the risk of recurrence due to de novo ipsilateral breast carcinoma development

Development of ipsilateral breast carcinoma following diagnosis of breast ductal carcinoma in situ (DCIS) has been assumed to represent recurrence of the primary tumour. However, this may not be the case and it is important to know how often recurrences are new tumours. Ipsilateral primary-recurrence pairs (n=78) were sequenced to test their clonal relatedness. Shared genetic events were identified from whole exome sequencing (n=54 pairs) using haplotype-specific copy number and phylogenetic analysis. The remaining pairs were sequenced by a targeted panel or low-coverage whole genome sequencing. We included 32 non-recurrent DCIS to compare recurrent and non-recurrent disease. We found that 7% of DCIS recurrences were non-clonal by whole exome sequencing, indicative of a new breast carcinoma. Lower resolution methods detected a higher non-clonality rate (29%). Comparing primary DCIS with their recurrences found that evolution of DCIS to invasive disease was associated with increased ploidy and copy number events. TP53 mutations were enriched in DCIS with clonal recurrence compared with non-recurrent DCIS. Our results verify that de novo "recurrent tumours" of independent origin occur in patients who may be at high risk.

cancer biology↗

bioRxiv2024

SpatialDiffusion: Predicting Spatial Transcriptomics with DenoisingDiffusion Probabilistic Models

Spatial Transcriptomics (ST) allows deep characterization of the 2D organization of expression data within tissue slices. The ST technology provides a tissue contextualization of deep single-cell profiles. Recently, numerous computational and machine learning methods have addressed challenges such as data quality, augmentation, annotation, and the development of integrative platforms for data analysis. In contrast, here we ask whether unseen spatial transcriptomics data can be predicted and if we can interpolate novel transcriptomic slices. To this end, we adopt a denoising diffusion probabilistic-based model (DDPM) to demonstrate the learning of generative ST models for several tissues. Furthermore, our generative diffusion model interpolates (predicts) unseen slices located "between" the collected finite number of ST slices. This methodology set the stage for learning predictive deep 3D models of tissues from a finite number of spatial transcriptomics slices, thus harboring the advent of AI-augmented spatial transcriptomics.

bioinformatics↗

bioRxiv2023

Teaching transposon classification as a means to crowd source the curation of repeat annotation - a tardigrade perspective

The advancement of sequencing technologies results in the rapid release of hundreds of new genome assemblies a year providing unprecedented resources for the study of genome evolution. Within this context, the significance of in-depth analyses of repetitive elements, transposable elements (TEs) in particular, is increasingly recognized in understanding genome evolution. Despite the plethora of available bioinformatic tools for identifying and annotating TEs, the phylogenetic distance of the target species from a curated and classified database of repetitive element sequences constrains any automated annotation effort. Manual curation of raw repeat libraries is deemed essential due to the frequent incompleteness of automatically generated consensus sequences. However, manual curation and classification are time-consuming processes that offer limited short-term academic rewards and are typically confined to a few research groups where methods are taught through hands-on experience. Crowd sourcing efforts could offer a significant opportunity to bridge the gap between learning the methods of curation effectively and empowering the scientific community with high-quality, reusable repeat libraries. Here, we present an example of such crowd sourcing effort developed through both in-person and online courses built around a collaborative peer-reviewed teaching process that can be used as teaching reference guide for similar projects. The collaborative manual curation of TEs from two tardigrade species, for which there were no TE libraries available, resulted in the successful characterization of hundreds of new and diverse TEs: A hidden treasure awaits discovery within non-model organisms.

evolutionary biology↗

bioRxiv2023

Repressor sequestration activates translation of germ granule localized mRNA

Biomolecular condensates organize and compartmentalize biochemical processes within cells1. Among these, ribonucleoprotein (RNP) granules are characterized as storage depots for translationally repressed mRNA2-8. Whether RNP granules can also activate translation and how such translation is achieved remains unclear9. This question is particularly relevant for embryonic germ granules, whose activity has been linked to germ cell fate10-13. Here, we use single-molecule imaging to show that embryonic germ cell RNP granules in Drosophila are the sites of active translation for nanos mRNA. Translating nanos mRNA is oriented with the 5end preferentially at the germ granule surface while the 3UTR is buried within the granule. Untranslated nanos mRNAs remain internal within the granule. Quantitative analysis of translational kinetics demonstrates that germ granules activate translation by antagonizing translational repression rather than changing the rate or efficiency of translation. We generated separation-of-function mutations in the disordered linker region of the scaffold protein Oskar that specifically impede nanos translation without affecting germ granule morphology or RNA localization. These mutations reveal that nanos translation is dependent on the sequestration of translational repressors within germ granules. Together, our findings show that RNP granules regulate localized protein synthesis through compartmentalized relief of translational repression raising the possibility that similar repressor-activator switches control translation in other condensates.

cell biology↗

bioRxiv2023

Integrator-mediated clustering of poised RNA polymerase II synchronizes histone transcription

Numerous components of the transcription machinery, including RNA polymerase II (Pol II), accumulate in high-concentration clusters at promoters. Whether these clusters assemble on demand during transcription or constitute regulatory units remains unclear. Examining the Drosophila histone locus--where histone genes are transcribed exclusively during S phase--we unexpectedly found large clusters containing non-chromatin-bound Pol II and elongation factors outside S phase. When transcription is activated during S phase, P-TEFb drives accelerated turnover of cluster components. Dispersion of clusters through depletion of the Integrator complex endonuclease module causes histone transcription to have a diminished S-phase peak and instead occur ectopically throughout the cell cycle. We propose that clusters act as gatekeeping hubs by maintaining a poised machinery pool, thereby restricting gene activation to defined temporal windows.

genetics↗

bioRxiv2023

HLA-Based Banking of Human Induced Pluripotent Stem Cells in Saudi Arabia

Human iPSCs derivation and use in clinical studies are transforming medicine. Yet, there is a high cost and long waiting time for autologous iPS-based cellular therapy, and the genetic engineering of hypo-immunogenic iPS cell lines is hampered with numerous hurdles. Therefore, it is increasingly interesting to create cell stocks based on HLA haplotype distribution in a given population. In this study, we assessed the potential of HLA-based iPS banking for the Saudi population. First, we analyzed the HLA database of the Saudi Stem Cell Donor Registry (SSCDR), which contains high-resolution HLA genotype data of 64,315 registered Saudi donors at the time of analysis. We found that only 13 iPS lines would be required to cover 30% of the Saudi population, 39 iPS lines would offer 50% coverage and 596 for more than 90% coverage. Next, As a proof-of-concept, we launched the first HLA-based banking of iPSCs in Saudi Arabia. Using clinically relevant methods, we generated the first iPSC line from a homozygous donor for the most common HLA haplotype in Saudi. The two generated clones expressed pluripotency markers, could be differentiated into all three germ layers, beating cardiomyocytes and neuronal progenitors. To ensure that our reprogramming method generates genetically stable iPSCs, we assessed the mutational burden in the generated clones and the original blood sample from which the iPSCs were derived using whole-genome sequencing. All detected variants were found in the original donor sample and were classified as benign according to current guidelines of the American College of Medical Genetics and Genomics (ACMG). This study sets a road map for introducing iPS-based cell therapy in the Kingdom of Saudi Arabia.

genetics↗