Biology subjects

Kappes, F.

Publications and source records attributed to Kappes, F..

9 recordsLinked to original sources

bioRxiv2026

SELECTIVE TRANSCRIPTOMIC VULNERABILITY OF MEMBRANE-INTEGRATED ARCHITECTURES DURING NEURAL TISSUE VITRIFICATION

Cryopreservation is essential for long-term storage of biological tissues. Yet, surprisingly, the precise molecular impact of cryopreservation on tissue transcriptomes remains poorly defined. This study provides the first resource of whole-genome transcriptomic changes following cryopreservation. This study used bulk RNA sequencing to examine how preservation method (snap freezing or vitrification) affects transcriptomes in mouse cerebral cortex and hippocampus. This allowed us to separate cryoprotectant-specific changes from cold induced-changes via snap freezing. In a subset of genes, tissues processed under vitrification conditions showed selective under-representation of a small but structurally coherent group of transcripts, with the hippocampus exhibiting greater vulnerability than the cortex. UniProt annotation revealed that affected transcripts were strongly enriched for proteins with membrane-associated, secretory-pathway, and multi-pass topologies, indicating that structurally complex membrane-integrated architectures are disproportionately sensitive to vitrification. Pathway-level analysis using iPANDA further showed that negative preservation scores in vitrified tissue clustered primarily within signal transduction and metabolic pathways, suggesting coordinated pathway-level disruption rather than global transcript loss. Together, these results demonstrate that vitrification conditions induce selective and structured molecular perturbations in neural tissue, defined by the under-recovery of transcripts associated with membrane and secretory pathway organization. This work highlights molecular vulnerability during vitrification and emphasizes the need for transcript-level evaluation when optimizing cryopreservation approaches for neural systems.

molecular biology↗

bioRxiv2026

Phosphorylation of serines 287/288 in DEK regulates cell-type-specific chromatin occupancy and compaction

The conserved multifunctional chromatin modulator and oncogene DEK exhibits context-dependent genomic binding and function, but how these activities are regulated in cancer remains poorly understood. Using multi-omics and biochemical approaches, we find that while DEK predominantly occupies promoter-proximal regions in HeLa cells and primary melanocytes, its chromatin binding is dramatically reduced in melanoma cell lines--despite DEK overexpression. We attributed this to CK2-mediated phosphorylation, which governs DEK chromatin association and transcriptional output in a cell-type-specific manner. Phosphoproteomics identified 34 phosphorylation sites, including S287 and S288 within the DEK C-terminal DNA-binding domain. Strikingly, CK2 inhibition and concomitant loss of phosphorylation at S287/S288 triggered DEK redistribution to promoter regions, coinciding with transcriptional repression of oncogenic pathways and global chromatin compaction. Melanoma subtypes showed divergent responses: NRAS-mutant cells displayed dynamic, phosphorylation-dependent DEK redistribution, whereas BRAF-mutant cells lacked detectable DEK binding. Our work establishes DEK as a phosphorylation-sensitive regulator of chromatin states, with CK2-mediated modification orchestrating its tumor-specific regulatory functions. These findings nominate phospho-DEK as a potential biomarker and therapeutic target in melanoma and possibly other cancers.

biochemistry↗

bioRxiv2025

Exposure to per- and polyfluoroalkyl substances elicits cell type-specific impacts on p53 and TGF-β signaling pathways

Per- and polyfluoroalkyl substances (PFAS) are a class of synthetic chemicals extensively used as plastic additives. Their environmental persistence and potential for bioaccumulation have raised significant toxicological concerns. This study evaluates the cytotoxic and molecular effects of Perfluorooctanoic acid (PFOA) and its replacement compound, Perfluoro(2-methyl-3-oxohexanoic) acid (GenX), in human-derived skin (A375), liver (HepG2), kidney (SN12C), and colon (SW620) cell lines. The experimental design assessed cell viability, gene expression, and perturbations in key cellular stress pathways, with a particular focus on TGF-{beta}/SMAD-mediated inflammation and the p53-driven DNA damage response. Our results demonstrate compound- and cell-type-specific toxicity, with GenX displaying reduced cytotoxicity compared to PFOA across all cell types. Molecular analyses revealed that both PFAS compounds induced alterations in the TGF-{beta}/SMAD pathway, consistent with a pro-inflammatory cellular state. Additionally, we observed activation of the DNA damage response, as evidenced by increased expression of ATM, ATR, and p53, alongside ribosomal stress-related changes in RPL5 and RPL11. Notably, while skin and liver cells exhibited similar response profiles, kidney and colon cells showed divergent modulation of SMAD signaling, suggesting tissue-specific susceptibility and mechanistic differences. These findings contribute to a deeper understanding of the differential toxicological profiles of legacy and replacement PFAS, with implications for health risk assessment and regulatory policy. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/652004v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@ce20aaorg.highwire.dtl.DTLVardef@c29608org.highwire.dtl.DTLVardef@1081ae6org.highwire.dtl.DTLVardef@11e0401_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

The chromatin remodeler DEK promotes proliferation of mammary epithelium and is associated with H3K27me3 epigenetic modifications

The DEK chromatin remodeling protein was previously shown to confer oncogenic phenotypes to human and mouse mammary epithelial cells using in vitro and knockout mouse models. However, its functional role in normal mammary gland epithelium remained unexplored. We developed two novel mouse models to study the role of Dek in normal mammary gland biology in vivo. Mammary gland-specific Dek over-expression in mice resulted in hyperproliferation of cells that visually resembled alveolar cells, and a transcriptional profile that indicated increased expression of cell cycle, mammary stem/progenitor, and lactation-associated genes. Conversely, Dek knockout mice exhibited an alveologenesis or lactation defect, resulting in dramatically reduced pup survival. Analysis of previously published single-cell RNA-sequencing of mouse mammary glands revealed that Dek is most highly expressed in mammary stem cells and alveolar progenitor cells, and to a lesser extent in basal epithelial cells, supporting the observed phenotypes. Mechanistically, we discovered that Dek is a modifier of Ezh2 methyltransferase activity, upregulating the levels of histone H3 trimethylation on lysine 27 (H3K27me3) to control gene transcription. Combined, this work indicates that Dek promotes proliferation of mammary epithelial cells via cell cycle deregulation. Furthermore, we report a novel function for Dek in alveologenesis and histone H3 K27 trimethylation.

developmental biology↗

bioRxiv2024

DEK-rRNA interactions regulate ribosome biogenesis and stress response

DNA/chromatin-based functions of the DEK oncogene, a unique nucleic acid-interacting factor in metazoans, have been widely investigated, yet its role in cellular RNA biology is under-studied. Herein we employed CLIP-seq alongside mutational, biochemical, and cellular approaches to gain deeper insights into the cellular DEK-RNA interplay. We confirm interaction of DEK with coding RNA, yet also report association with ribosomal RNA (rRNA) and thereby establishing a robust link between DEK and ribosome biology. Indeed, cells lacking DEK showed marked deficits in cytoplasmic ribosome quality and function. This phenotype was exclusively rescued by C-terminal DEK, harboring two RNA interaction domains, but not by an rRNA-binding deficient mutant. Mechanistically, we uncovered pleiotropic involvement of DEK in RNA polymerase I-mediated rRNA transcription and processing pathways. More specifically, we found direct interaction of DEK with RNA polymerase III-transcribed 5S rRNA and identified DEK as a regulator of the Impaired Ribosome Biogenesis Checkpoint (IRBC). Within this ribosomal stress pathway, DEK depletion results in free 5S RNP, triggering stabilization of p53 via inhibition of MDM2. In summary, our multilayer analysis revealed DEK as a potent cellular RNA binding protein and provides first evidence of DEK as a regulator of ribosome biogenesis and stress response via the 5S RNP-MDM2-p53 axis.

biochemistry↗

bioRxiv2024

Upregulation of DEK Expression in Uterine Myomas and Cervical Cancer as a Potential Prognostic Factor

The aim of this pilot study is to investigate the role of the DEK protein as a potential prognostic marker in gynecological tumors, specifically focusing on uterine myomas and cervical cancer. The study cohort comprised Chinese female patients manifesting with menorrhagia and pelvisalgia, from whom neoplastic and adjacent non-neoplastic tissue specimens were procured during surgical intervention for either leiomyomas or cervical carcinoma. DEK protein and messenger RNA (mRNA) levels were measured across normal uterine tissue, uterine myomas, and cervical cancer tissues using Western blotting, immunohistochemistry, and quantitative real time polymerase chain reaction (qRT-PCR). Results revealed a marked increase in DEK protein expression in cervical cancer tissues, moderate expression in uterine myomas, and minimal levels in normal uterine tissues. Statistical analyses confirmed significant differences in DEK protein expression between tissue types, though mRNA expression differences did not reach statistical significance. These findings suggest DEKs involvement in tumor development and suppression, making it a promising biomarker for early detection in gynecological tumors. Further research is needed to elucidate DEKs mechanisms in gynecological tumorigenesis and its potential as an early biomarker, addressing critical need in womens health.

cancer biology↗

bioRxiv2024

Detection of Nontoxic BoNT/A Levels in Post-Facial Botox Injection Breastmilk using a Multi-technique Approach

BackgroundThe use of cosmetic Botox (Botulinum Neurotoxin Type A, BoNT/A ) has become increasingly prevalent. Particularly after pregnancy, postpartum depression represents one major factor motivating women to use Botox even during the lactation and breastfeeding period. Currently, there is limited understanding of the impact of Botox on lactation and the potential of its active component passing into breastmilk and affecting the infant. MethodsBreastmilk samples were acquired from five women aged between 28 - 45 through a clinic in Suzhou, Jiangsu, P.R. China. Three sample sets ranged from 1 hour to 1 year after facial Botox treatments (64 U), whereas the remaining two sample sets were from women who never received Botox treatment. BoNT/A concentrations in samples were detected using standard Enzyme-Linked Immunosorbent Assay (ELISA), unreduced and reduced Western Blotting, confocal micro-Raman Spectroscopy, and Mass Spectrometry(LC-MS). FindingsFrom ELISA, breastmilk BoNT/A concentrations peaked at 33.4 pg/mL 4 days after Botox injection. BoNT/A concentrations were highest overall in the first week and around two months after injection. While non-reducing polyacrylamide gel electrophoresis (PAGE) showed a protein band of 150 kDa peaking at 48 hours, reduced SDS-PAGE detected a 100 kDa protein first peaking at 72 hours, then re-emerging after 7 days, respectively, and in line with previous observations by others. Interestingly, micro-Raman spectroscopy indicated additional Raman peaks at 6 hours and 48 hours that were not present in other breastmilk samples which were evaluated in this study. However, no clear indication of BoNT/A was detected in Mass Spectrometry (LC-MS). InterpretationThe amount of BoNT/A in breastmilk peaks around 48 hours, and at 2 months after facial injection. Even over a year after injection, BoNT/A can be detected. However, all quantities of BoNT/A detected in this study are highly likely to be safe for infants. Additionally, our study suggests that alternative methods, besides ELISA, may be utilized for the rapid detection of low concentrations of BoNT/A in body fluid samples. FundingDuke Kunshan University Start-Up funds, Duke Kunshan University Undergraduate Studies Signature Work Research Grant, Synear and Wang-Cai Biochemistry grants, and Kunshan Municipal Government research funding. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/595434v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@fcdd11org.highwire.dtl.DTLVardef@11591daorg.highwire.dtl.DTLVardef@11ab30eorg.highwire.dtl.DTLVardef@1e19311_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIBoNT/A was detected in the breastmilk of 3 women after facial Botox injections of 64 U. C_LIO_LIToxin levels peaked in the first week and at around 2 months after injection. C_LIO_LIAll detected levels (up to 33.40 pg/mL) were significantly below the lethal dose for newborns. C_LI

molecular biology↗

bioRxiv2023

DEK oncoprotein participates in heterochromatin replication via SUMO-dependent nuclear bodies

The correct inheritance of chromatin structure is key for maintaining genome function and preventing cellular transformation. DEK, a conserved chromatin protein, has recognized tumor-promoting properties, its overexpression being associated with poor prognosis in various cancer types. At the cellular level, DEK displays pleiotropic functions, influencing differentiation, apoptosis, and stemness, but a characteristic oncogenic mechanism remains elusive. Here, we report the identification of DEK bodies, focal assemblies of DEK occurring at specific, yet unidentified sites of heterochromatin replication. In these bodies, DEK localizes in direct proximity to active replisomes suggesting a function in the early maturation of heterochromatin. A high-throughput siRNA screen identifies SUMO as a major regulator of DEK body formation, linking DEK to the SUMO network that controls chromatin states and cell fate. This work combines and refines our previous data on DEK as a factor essential for heterochromatin integrity and facilitating replication under stress and delineates an avenue of further study for unraveling DEKs contribution to cancer development.

cell biology↗

bioRxiv2019

The oncoprotein DEK affects the outcome of PARP1/2 inhibition during replication stress

DNA replication stress is a major source of genomic instability and is closely linked to tumor formation and progression. Poly(ADP-ribose)polymerases1/2 (PARP1/2) enzymes are activated in response to replication stress resulting in poly(ADP-ribose) (PAR) synthesis. PARylation plays an important role in the remodelling and repair of impaired replication forks, providing a rationale for targeting highly replicative cancer cells with PARP1/2 inhibitors. The human oncoprotein DEK is a unique, non-histone chromatin architectural protein whose deregulated expression is associated with the development of a wide variety of human cancers. Recently, we showed that DEK is a high-affinity target of PARylation and that it promotes the progression of impaired replication forks. Here, we investigated a potential functional link between PAR and DEK in the context of replication stress. Under conditions of mild replication stress induced either by topoisomerase1 inhibition with camptothecin or nucleotide depletion by hydroxyurea, we found that the effect of acute PARP1/2 inhibition on replication fork progression is dependent on DEK expression. Reducing DEK protein levels also overcomes the restart impairment of stalled forks provoked by blocking PARylation. Non-covalent DEK-PAR interaction via the central PAR-binding domain of DEK is crucial for counteracting PARP1/2 inhibition as shown for the formation of RPA positive foci in hydroxyurea treated cells. Finally, we show by iPOND and super resolved microscopy that DEK is not directly associated with the replisome since it binds to DNA at the stage of chromatin formation. Our report sheds new light on the still enigmatic molecular functions of DEK and suggests that DEK expression levels may influence the sensitivity of cancer cells to PARP1/2 inhibitors.

cancer biology↗