Biology subjects

Balounova, J.

Publications and source records attributed to Balounova, J..

4 recordsLinked to original sources

bioRxiv2026

FAM83H couples keratin organization to Notch signaling during epidermal morphogenesis

Keratin intermediate filaments are essential for epidermal integrity, yet how keratin organization is coupled to the cell fate signaling that coordinates keratinocyte differentiation during epidermal morphogenesis remains poorly understood. Here, we identify FAM83H as a previously unrecognized regulator that links keratin cytoskeletal organization to epidermal cell fate decisions. Using mouse models and a human 3D microphysiological epidermis model, we show that loss of FAM83H disrupts epidermal architecture by impairing basal keratinocyte differentiation, organization, and cell-cell adhesion. Single-cell transcriptomic analysis of 3D epidermal tissues identified Notch signaling as prominently associated with cell populations lost upon FAM83H depletion. Mechanistically, FAM83H localizes to cell-cell junctions, where it organizes keratin filaments and desmosome integrity. Loss of FAM83H disrupts a desmoplakin-keratin-Notch1 complex at junctions, impairing Notch1 proteolytic activation and proper keratinocyte differentiation. Together, our work identifies FAM83H as a key regulator of epidermal morphogenesis that couples keratin cytoskeletal architecture to Notch1 signaling, and positions keratin-associated proteins as active participants in the epithelial fate decisions that govern epidermal homeostasis.

cell biology↗

bioRxiv2026

Adeno-Associated Virus Co-Precipitation with Extracellular Vesicles for Genome Editing in Rodent Embryo

Adeno-associated virus purification by density-gradient ultracentrifugation is labor-intensive and often results in substantial titer loss due to particle aggregation. Here, we present a scalable co-isolation strategy in which AAV is precipitated together with extracellular vesicles secreted by the producer cell line, completely bypassing density-gradient separation. The resulting AAV-EV preparations comprise free AAV, free EVs, and EV-associated AAV. Functionally, AAV-EV vectors (AAV2/1 serotype) support efficient ex vivo genome editing across multiple independent loci in mouse and rat zygotes, achieving a mean targeting efficiency of approximately 26%. Compared with gradient-purified AAV administered at matched doses, AAV-EV formulations yielded 2.34-fold higher embryo viability while maintaining equivalent transgene copy numbers. By leveraging EVs as a biological matrix, this approach enables ultracentrifugation-free AAV isolation without compromising vector functionality. Overall, AAV-EV represents an accessible and embryo-tolerant platform for rodent genome engineering that aligns with the principles of Replacement, Reduction, and Refinement (3R) principles.

bioengineering↗

bioRxiv2025

FAM83H regulates postnatal T cell development through thymic stroma organization

Family of Sequence Similarity 83H (FAM83H/ SACK1H) is primarily expressed in epithelial cells, where it interacts with casein kinase 1 (CK1) and keratins to regulate cytoskeletal organization, cell proliferation, and vesicular trafficking. Mutations in FAM83H are known to cause amelogenesis imperfecta, highlighting its critical role in enamel formation. We generated Fam83h-deficient mice (Fam83hem2(IMPC)Ccpcz, Fam83h-/-) and mice lacking a part of the N-terminal CK1-binding domain (Fam83h{Delta}87/{Delta}87). Consistent with other Fam83h-deficient models, these mice are subviable, smaller in size, and exhibit a sparse, scruffy coat, scaly skin, general weakness, and hypoactivity. Notably, both strains show impaired lymphoid cell development in early postnatal life. In the thymus, Fam83h expression is confined to thymic epithelial cells (TECs), and its deficiency in stromal cells results in disrupted thymic architecture and severe block in the expansion of DN3 (double-negative stage 3) T cells, ultimately leading to insufficient T cell production. Single-cell transcriptomic analysis reveals that Fam83h-/- cortical TECs (cTECs) express reduced levels of the TEC master regulator Foxn1, and its multiple downstream target genes, suggesting a critical role for FAM83H likely in coordination with CK1in cTEC maturation. HighlightsFam83h-deficient mice exhibit multiple epithelial defects, but no obvious enamel defects Fam83h deficiency disrupts lymphocyte development Fam83h deficiency impairs thymic epithelial cell maturation and thymus function

immunology↗

bioRxiv2018

Rapid single-cell cytometry data visualization with EmbedSOM

Efficient unbiased data analysis is a major challenge for laboratories handling large cytometry datasets. We present EmbedSOM, a non-linear embedding algorithm based on FlowSOM that improves the analyses by providing high-performance visualization of complex single cell distributions within cellular populations and their transition states. The algorithm is designed for linear scaling and speed suitable for interactive analyses of millions of cells without downsampling. At the same time, the visualization quality is competitive with current state-of-art algorithms. We demonstrate the properties of EmbedSOM on workflows that improve two essential types of analyses: The native ability of EmbedSOM to align population positions in embedding is used for comparative analysis of multi-sample data, and the connection to FlowSOM is exploited for simplifying the supervised hierarchical dissection of cell populations. Additionally, we discuss the visualization of the trajectories between cellular states facilitated by the local linearity of the embedding.

bioinformatics↗