Biology subjects

Boyartchuk, V.

Publications and source records attributed to Boyartchuk, V..

5 recordsLinked to original sources

bioRxiv2026

Transcriptomic view of key events during early embryogenesis in the duplicated Atlantic salmon genome

Early embryogenesis is governed by tightly regulated transcriptional programs, including the maternal-to-zygotic transition (MZT), zygotic genome activation (ZGA), and maintenance of pluripotency. While these processes are well studied in model vertebrates, they remain poorly understood in salmonid fishes, whose genomes are shaped by a relatively recent whole genome duplication (WGD) event. Here, we present a temporally resolved transcriptomic analysis of Atlantic salmon (Salmo salar) embryogenesis using bulk RNA-seq across key stages spanning early embryogenesis. Dimensionality reduction and unsupervised clustering of gene expression revealed stage-specific transitions encompassing maternal RNA clearance, cell cycle regulation, and the onset of metabolic activity. We demonstrate that ZGA occurs early and in multiple phases, beginning soon after fertilization, accompanied by chromatin remodelling and the activation of epigenetic regulators. Duplicated gene pairs retained from the salmonid WGD frequently displayed asynchronous expression, indicative of functional divergence and the evolution of additional regulatory complexity of embryonic development. To gain insights into pluripotency, we integrated analyses of gene expression, transcription factor motifs, and chromatin accessibility, to reveal conserved regulators including genes encoding Pou5f3, Nanog, and Sox19b, alongside divergent functions of Klf family members. Our cross-stage profiling allowed us to define a novel panel of stably-expressed reference genes for normalization during quantitative PCR analyses, which were used to validate pluripotency- and differentiation-associated dynamics inferred by RNA-seq. Together, our findings delineate the transcriptional architecture of early embryogenesis in Atlantic salmon, revealing both conserved and lineage-specific features of pluripotency regulation, and providing a foundational resource for future functional genomics and stem cell applications in salmonids.

developmental biology↗

bioRxiv2026

Evaluating in vitro spermatogenesis in Atlantic salmon using single-cell transcriptomics

Understanding how to maintain and direct spermatogenesis in vitro is central to advancing reproductive biotechnologies in aquaculture species where the ability to generate gametes outside the organism could facilitate selective breeding, genetic modification, and germline preservation. However, current culture systems remain poorly defined in farmed fish species. In Atlantic salmon (Salmo salar), progress has been further limited by the absence of a comprehensive reference atlas of testicular cell types, making it difficult to determine how cells maintained in culture relate to their native counterparts. To address this, we first established a single-cell RNA atlas of the Atlantic salmon testis from freshly isolated tissue, resolving somatic and germ cell populations across all major stages of spermatogenesis. Primary testicular cells were then cultured under distinct conditions designed to promote either proliferation or differentiation for 14 days and subsequently subjected to single-cell RNA sequencing. To assign cell identities in cultured samples, the transcriptional profiles of cultured cells were computationally mapped onto the atlas, allowing direct comparison of cultured and native cell states. This approach revealed pronounced, condition-specific shifts in cellular composition. Proliferation medium supplemented with epidermal growth factors (EGF) and insulin-like growth factor (IGF) enriched spermatogonial populations, indicating preferential support of undifferentiated and actively dividing germ cells. In contrast, basal medium favoured the preferential survival of Sertoli cells in the absence of defined growth cues. A differentiation medium containing hormones that stimulate male gonad development (gonadotropins and androgens) failed to robustly promote meiotic progression. Further, comparative analysis of Sertoli cells across different conditions (in vivo and in vitro) revealed a loss of canonical identity markers and induction of stress-associated transcriptional programs in vitro compared to in vivo, indicating a shift away from specialised somatic function. Together, these findings establish the first single-cell reference atlas of Atlantic salmon testis and provide a framework for evaluating and optimising testis culture systems in salmonids. While early germ cell populations could be maintained and enriched in vitro, progression through later stages of spermatogenesis remained limited, indicating that important biological requirements of the native testicular environment are not yet fully recapitulated under current culture conditions.

cell biology↗

bioRxiv2026

Whole genome screening defines a key role of autophagy in resistance of bovine cells to BVDV infection

Bovine viral diarrhea virus (BVDV, genus Pestivirus, family Flaviviridae) is a notifiable pathogen of cattle which significantly impacts animal health, welfare, and the economy. Several cellular factors important for BVDV infection, such as Jiv, CD46 and ADAM17, have already been identified providing new targets development of effective defense strategies. However, our knowledge about BVDV host factor requirements remains limited, as no genome-wide studies of BVDV host resistance factors were performed to date, in part due to lack of accessible whole genome libraries. To close this gap, we have designed a novel bovine whole genome knockout library and successfully used it to identify a set of BVDV host resistance factors. The validity of our approach is highlighted by the strong selection of cells with inactivated ADAM17 and TMEM41B, which have both been described to be of pivotal importance for BVDV infection. In addition, guides targeting VMP1, recently identified as an important factor for flavivirus infection, were also significantly enriched in our screen. Furthermore, we found differential selection of several proteins essential for triggering autophagy, providing additional strong evidence of this process underlying key cellular functions involved in resistance to BVDV.

cell biology↗

bioRxiv2025

SLAMF1-peptide mediated epigenetic priming reprograms innate immune responses in sepsis

Sepsis is characterized by profound immune dysregulation, including impaired innate immune responses and epigenetic reprogramming of monocytes. However, strategies to therapeutically restore immune function remain limited. Here, we identify a cell-penetrating peptide, P7-Pen, as a modulator of monocyte epigenetic state and inflammatory responsiveness. Using primary human monocytes and peripheral blood mononuclear cells (PBMCs) from healthy donors and sepsis patients, we demonstrate that P7-Pen enhances cytokine production in response to Toll-like receptor stimulation while having minimal effects under basal conditions. P7-Pen treatment increased global histone acetylation, particularly H3 acetylation, and prevented the development of endotoxin tolerance. Transcriptomic and functional analyses revealed restoration of inflammatory gene expression, including TNF, IL6, and IFNB1, in otherwise hyporesponsive cells. Mechanistically, we identified the lysine deacetylase ABHD14B as a direct binding partner of P7-Pen. Silencing of ABHD14B recapitulated the effects of P7-Pen, leading to enhanced histone acetylation and cytokine production. Importantly, P7-Pen selectively potentiated responses to TLR ligands without inducing basal hyperinflammation. Collectively, our findings identify ABHD14B-dependent epigenetic regulation as a key checkpoint in innate immune tolerance and establish P7-Pen as a novel tool to restore immune responsiveness in sepsis.

immunology↗

bioRxiv2025

Genome-wide CRISPR knockout screen reveals the landscape of essential genes across the porcine genome

1Characterization of essential genes across the genome is fundamental to understanding cellular functions at a molecular level. While significant progress has been made in characterizing essential genes in human and mouse models, relatively little is known about essential genes in the porcine genome. Pigs are an important production species and are now emerging as valuable models for studying human diseases due to their physiological similarities to humans. To map essential genes across the porcine genome, we have developed a novel porcine genome-wide CRISPR knockout screening library (pGeCKO) and applied it to two porcine cell lines, PK15 and IPEC-J2. We identified 2,245 essential genes in PK15 cells and 919 essential genes in IPEC-J2 cells, with 683 of these shared between both cell lines. Functional analyses revealed that most essential genes are involved in core cellular processes such as cell cycle regulation, DNA replication, transcription, and translation. Comparative analysis with human essential genes from the DepMap project revealed that over half of the genes are shared with humans and the rest are porcine-specific. These porcine-specific essential genes included genes in core functional pathways related to protein and RNA processing as well as many related to N-glycan biosynthesis, signal transduction, and several long-noncoding RNAs. This work provides a new resource for leveraging porcine models in disease research, enhancing our understanding of porcine genetics and its implications for human health.

genomics↗