Biology subjects

Seidel, J.

Publications and source records attributed to Seidel, J..

6 recordsLinked to original sources

bioRxiv2026

AN OPTIMIZED AND DRUGGABLE HUMAN KERATINOCYTE AND IPSC-DERIVED SENSORY NEURON CO-CULTURE SYSTEM FOR ATOPIC ITCH

Atopic dermatitis (AD) is a highly prevalent, relapse-remitting, inflammatory skin disease, the hallmark symptom of which is chronic itch. Mechanisms underlying AD itch are multifactorial, involving various cells, receptors, and mediators. Developing a physiologically relevant, human model system for AD itch research and drug development is crucial. To this end, human induced pluripotent stem cell-derived sensory neurons (iPSCSNs) were cultured with human primary keratinocytes to form deconstructed skin models. Using Ca2+-imaging in a direct contact, 2.5D co-culturing format, which mimics natural skin innervation and permits both paracrine exchange and juxtacrine signaling, iPSCSNs exhibited functional TRPA1 responses not seen in monotypic iPSCSN cultures or in iPSCSNs conditioned with keratinocyte medium. Different AD-associated cytokines were used to stimulate the co-culture systems to mimic an inflamed lesional skin environment, whereby TNF was found to increase iPSCSN chemosensitivity. Finally, both TRPA1 and JAK1/2 inhibition reduced iPSCSN responses to pruritogens (TSLP, IL-31), thus supporting TRPA1 as a therapeutic target for AD itch in humans. This study demonstrates that human deconstructed skin models can be a useful tool in AD and broader pruritus research. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/724000v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@11c0c9borg.highwire.dtl.DTLVardef@7fa518org.highwire.dtl.DTLVardef@2fe7a2org.highwire.dtl.DTLVardef@1105fa7_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

HDA19-mediated deacetylation of histone H3.3 lysine 27 and 36 regulates plant sensitivity to salt stress

Plants survive extreme environments through rapid chromatin reprogramming, yet the epigenetic marks that confer stress resilience remain poorly understood. Histone deacetylase HDA19 is a key epigenetic regulator in Arabidopsis, and hda19-deficient mutants display tolerance to multiple abiotic stresses, including drought, heat, and salinity. Using lysine acetylome profiling, we identified a non-canonical K27/K36 di-acetylation mark on histone H3.3, among nine H3 variants, as a specific substrate of HDA19. Under salinity stress, this mark decreased in wild-type plants but increased in hda19 mutants, while other known H3 modifications were similarly affected in both genotypes. Mimicking constitutive di-acetylation of H3.3 K27/K36 through lysine-to-glutamine substitutions promoted accumulation of stress-responsive late embryogenesis abundant (LEA) proteins and conferred salinity tolerance in seedlings, phenocopying hda19 mutants. Furthermore, generating the lea7-1/lea29-1/rab18-1 triple mutant abolished hda19-dependent salinity tolerance, confirming the LEA proteins role downstream of HDA19. Our findings demonstrate that H3.3 K27/K36 di-acetylation, modulated by HDA19, drives LEA protein accumulation and enables plants to withstand environmental stress, revealing a previously unknown core mechanism of plant stress resilience. Significance statementHistone acetylation is crucial for regulating chromatin states and transcription, yet the specific histone codes controlled by histone deacetylases and acetyltransferases during plant stress acclimation remain unclear. Arabidopsis mutants lacking histone deacetylase 19 show enhanced tolerance to drought, heat, and salinity. Using acetylome profiling and genetic analyses, we identify a previously unknown di-acetylation of histone H3.3 at lysines 27 and 36 as a key epigenetic switch activating late embryogenesis abundant proteins essential for salt tolerance in seedlings. This discovery reveals a novel mechanism linking histone H3.3 K27/K36 di-acetylation to stress-resilient protein accumulation, offering new insights into epigenetic control of plant stress responses and informing strategies to improve crop resilience under climate change.

plant biology↗

bioRxiv2025

nf-core/detaxizer: A Benchmarking Study for Decontamination from Human Sequences

Privacy is paramount in health data, particularly in human genetics, where information extends beyond individuals to their relatives. Metagenomic datasets contain substantial human genetic material, necessitating careful handling to mitigate data leakage risks when sharing or publishing. The same applies to genetic datasets from the environment or datasets from contaminated laboratory samples, although to a lesser extent. To address these topics, we developed nf-core/detaxizer, a nextflow-based pipeline that employs Kraken2 and bbmap/bbduk for taxonomic classification, identifying and optionally filtering Homo sapiens reads. Due to its generalized design, other taxa can also be classified and filtered. We benchmark its filtering efficacy for human reads against Hostile and CLEAN, demonstrating its utility for secure data preprocessing. The comparison revealed that the choice of tool and database can lead to an order of magnitude more human data not removed. As part of the nf-core initiative, nf-core/detaxizer adheres to best practices, leveraging containerized dependencies for streamlined installation. The source code is openly available under the MIT license: https://github.com/nf-core/detaxizer.

microbiology↗

bioRxiv2023

Metabolic and imaging phenotypes associated with RB1 loss in castrate resistant prostate cancer

Advanced prostate cancer is treated with androgen receptor (AR) signaling inhibitors, which are initially effective, but most patients eventually develop resistance and progress to castrate-resistant prostate cancer (CRPC). Loss of RB1 in CRPC tumors is correlated with rapid progression and poor patient survival and, in combination with TP53 loss, predisposes patients to the development of transitional neuroendocrine prostate cancer (NEPC). Although progressive CRPC is clinically associated with higher 18FDG-PET SUVmax values, it is unknown whether inactivation of RB1 and/or TP53 is a driver of increased glucose import. Using a cohort of patient-derived xenograft (PDX)-derived CRPC organoids, we found that NEPC could not be conclusively distinguished from adenocarcinoma by 18FDG uptake alone, and PSMA protein levels did not correlate with cancer phenotype or 18FDG uptake. Castration-resistant models showed higher 18FDG uptake, but lower pyruvate-to-lactate conversion compared to their castration-sensitive counterparts. In parallel studies using castration-sensitive prostate cancer models, RB1/TP53 knockdown did not affect 18FDG uptake, but increased basal respiration and glycolytic activity, with combined depletion leading to glucose diversion into glycogenesis. These metabolic changes were reflected in increased lactate dehydrogenase flux detected by 13C-hyperpolarized magnetic resonance spectroscopy upon RB1 loss, but not in 18FDG uptake. The metabolic heterogeneity revealed here suggests that a multimodal molecular imaging approach can improve tumor characterization, potentially leading to a better prognosis in cancer treatment.

cancer biology↗

bioRxiv2023

Spontaneous onset of cellular markers of inflammation and genome instability during aging in the immune niche of the naturally short-lived turquoise killifish (Nothobranchius furzeri)

Turquoise killifish (Nothobranchius furzeri) are naturally short-lived vertebrates, recapitulating several aspects of human aging, including protein aggregation, telomere shortening, cellular senescence, and declined antibody diversity. The mechanistic causes of systemic aging in killifish are still poorly understood. Here we ask whether killifish undergo significant age-dependent changes in the main hematopoietic organ, which together could contribute to systemic aging. To characterize immune aging in killifish, we employed single-cell RNA sequencing, proteomics, cytometry and a functional in vitro assay. Our data indicate how old killifish display increased inflammatory markers, and while immune cells from adult killifish display increased markers of proliferation and replication-independent DNA repair in progenitor-like cell clusters, progenitors from old killifish display extensive markers of DNA double-strand breaks. In less than 10 weeks, killifish undergo several dramatic spontaneous aging-related changes in the immune niche, which could be functionally linked with its extensive systemic aging and serve as targets for anti-aging interventions.

immunology↗

bioRxiv2017

Placental gene expression mediates the interaction between obstetrical history and genetic risk for schizophrenia

Defining the environmental context in which genes enhance susceptibility can provide insight into the pathogenesis of complex disorders, like schizophrenia. Here we show that the intrauterine and perinatal environment modulates the association of schizophrenia with genomic risk, as measured with polygenic risk scores (PRS) based primarily on GWAS significant variants. Genomic risk interacts with intrauterine and perinatal complications (Early Life Complications, ELCs) in each of three independent samples from USA, Italy and Germany (overall n= 1693, p= 6e-05). In each sample, the liability of schizophrenia explained by PRS is nominally more than five times greater in the presence of a history of ELCs compared with its absence. In each sample, patients with positive ELC histories have higher PRS than patients without ELCs, which is further confirmed in two additional patient samples from Germany and Japan (overall n=2038, p= 1e-04). The gene set based on the schizophrenia loci interacting with ELCs is highly expressed in multiple placental compartments and dynamically regulated in placenta from complicated in comparison with normal pregnancies. The same genes are differentially up-regulated in placentae from male compared with female offspring. The interaction between genomic risk and ELCs is mainly driven by GWAS significant loci enriched for genes highly expressed in the various placenta samples. Molecular pathway analyses based on the genes not driving this interaction reflect previous analyses about schizophrenia risk-genes, while genes highly and differentially expressed in placentae implicate an orthogonal biology involving cellular stress. These results suggest that the most significant genetic variants detected by current schizophrenia GWAS contribute to risk in part by converging on a developmental trajectory sensitive to events affecting placentation, which may underlie the male preponderance of schizophrenia and offer new insights into primary prevention.

genetics↗