Biology subjects

Vrljicak, P.

Publications and source records attributed to Vrljicak, P..

9 recordsLinked to original sources

bioRxiv2026

Multi-Objective Bayesian Optimization for Data-Efficient Bioprocess Development

Process optimization for Chinese hamster ovary (CHO) cell culture remains a challenge in biopharmaceutical development because multiple interacting parameters jointly influence productivity and product quality attributes. Traditional design-of-experiments (DoE) methods, while systematic, become impractically expensive when extended across multiple parameters and clones. To address this challenge, we developed a multi-objective Bayesian Optimization (BO) framework that identifies optimal process conditions efficiently in grouped recommendations, which is well suited for experimental workflows in bioprocess development. The model integrates continuous variables such as pH, DO, temperature, and feed rate with categorical identifiers to enable knowledge transfer across clones and scales, optimizing titer, glycan profile, and charge variants. We validated the framework through in-silico benchmarks on analytic functions, retrospective cross-validation on historical CHO datasets, and forward experimental validation in small-scale bioreactors. Across these tests, our algorithm consistently outperformed Latin Hypercube Sampling (LHS) and Random Search baselines, achieving superior performance under a limited experimental budget. The framework improved titer by up to 37% under single-objective optimization. In the multi-objective setting, it increased titer by 25% while simultaneously reducing overall glycan-profile error by a factor of seven, demonstrating the ability to optimize multiple biologically coupled objectives simultaneously. Through comprehensive in-silico and experimental validation, this study establishes a framework that enables adaptive, AI-guided process development and improves decision-making across multiple objectives, clones, and scales while minimizing experimental runs in process development and optimization workflows.

bioengineering↗

bioRxiv2025

In toto imaging of germ plasm dynamics reveals an essential role for early distribution of germ granules in germline development

A fundamental question in developmental biology is how the fertilized egg gives rise to all the different cell types of an organism. The traditional view is that the different cell types are specified either by intrinsic factors such as cell fate determinants or via intercellular signaling. In some animals a cytoplasmic determinant-like substance called germplasm specifies the germline. In zebrafish eggs, germplasm is dispersed in form of mRNP complexes called germ granules, which are enriched at the animal pole. After fertilization the distribution of germ granules changes dramatically. The germ granules accumulate in the corners of the first two cleavage furrows of the embryo, to form four large masses that are essential for germline development. Although germ granule movement has been linked to the network dynamics of the microtubular and actin cytoskeleton, a clear mechanistic understanding of the process is currently lacking. Fundamental questions about germplasm dynamics, including "What is the main driving force?" have not been answered yet. To address this gap, we performed careful quantitative analysis of germ granule dynamics relative to dynamic cytoskeletal reorganization in early zebrafish embryos by live-imaging. We identified stereotypic signatures of germ granule dynamics across different regions of the early embryo. Interestingly, we find that the timing of large-scale germ granule movements contrasts prevailing models for the mechanism of germ granule aggregation during cleavage divisions, and rather points to cytokinetic apparatus itself. Using zebrafish mutants affecting the RNA-binding protein Ybx1 (Y-box binding-protein 1), we show that the timing and dynamics of germ granule accumulation in the blastodisc is a crucial factor for appropriate later aggregation into cleavage furrows and eventual distribution to PGCs. Germplasm accumulation in the cleavage furrows is reduced and ectopic aggregates form at the blastoderm margin of ybx1 mutant embryos. Our work establishes Ybx1 as a novel factor with crucial functions in germplasm distribution and suggests that additional factors drive normal germplasm dynamics.

developmental biology↗

bioRxiv2024

Stalling of the endometrial decidual reaction determines the recurrence risk of miscarriage risk

In each menstrual cycle, progesterone acting on estrogen-primed endometrium elicits an inflammatory decidual reaction, rendering it poised for embryo implantation and transformation into the decidua of pregnancy. Here, we show that the sequential functions of the decidual reaction - implantation and decidualization - pivot on the time-sensitive loss of progesterone-resistant stromal cells that form a transient implantation niche and reciprocal expansion of progesterone-responsive pre-decidual cells. In parallel, proliferation and differentiation increase the abundance of immunotolerant uterine natural killer (uNK) cells. Examination of pre-pregnancy endometrial biopsies from 924 women revealed that the frequency of cycles culminating in a blunted or stalled decidual reaction closely aligns with the age-independent recurrence risk of miscarriage. Further, analysis of 632 biopsies obtained in different cycles from 316 women indicated that prior miscarriages disrupt intercycle endometrial homeostasis, an observation supported by modelling the impacts of prolonged decidual inflammation in three-dimensional endometrial assembloids. Although stalling of the decidual reaction is often accompanied by a poor expansion of immunotolerant uNK cells, miscarriages do not impact intercycle uNK cell dynamics. Our findings indicate that intrinsic uterine mechanisms hardwire the recurrence risk of miscarriage, underscoring the need for pre-pregnancy diagnostics and therapeutics. One Sentence SummaryThe frequency of menstrual cycles culminating in a suboptimal decidual reaction determines the recurrence risk of miscarriage.

physiology↗

bioRxiv2024

Spatial targeting of the prostaglandin receptor EP2 to very early endosomes co-ordinates PGE2-mediated cAMP signaling in decidualizing human endometrium

Decidualization denotes the differentiation of endometrial stromal cells into specialized decidual cells, essential for embryo implantation and pregnancy. The process requires coordinated activation of both progesterone and cAMP signaling pathways, which converge on downstream transcription factors. PGE2 and relaxin, acting respectively through their Gs-coupled GPCRs EP2 and RXFP1, are putative candidates responsible for generating cAMP in differentiating stromal cells. Here, we show that PGE2 is less efficacious than relaxin in elevating intracellular cAMP levels in primary stromal cells but more effective at driving the expression of canonical decidual genes. Both PGE2- and relaxin-induced cAMP generation involves receptor internalization, but EP2 is endocytosed into very early endosomes (VEEs). Perturbation of the VEE machinery dysregulates PGE2-dependent cAMP profiles and disrupts key decidual signaling pathways, resulting in a disordered differentiation response. We demonstrate that the spatial location of EP2 is essential for coordinated activation of the downstream signaling cascades that govern decidualization.

cell biology↗

bioRxiv2023

Dynamic chromatin remodeling in cycling human endometrium at single cell level

Estrogen-dependent proliferation followed by progesterone-dependent differentiation of the endometrium culminates in a short implantation window. We performed single cell ATAC-seq on endometrial samples obtained across the menstrual cycle to investigate the regulation of temporal gene networks that control embryo implantation. We identified uniquely accessible chromatin regions in all major cellular constituents of the endometrium, delineated temporal patterns of coordinated chromatin remodeling in epithelial and stromal cells, and gained mechanistic insights into the emergence of a receptive state through integrated analysis of enriched transcription factor (TF) binding sites in dynamic chromatin regions, ChIP-seq analyses, and gene expression data. We demonstrate that the implantation window coincides with pervasive cooption of transposable elements (TE) into the regulatory chromatin landscape of decidualizing cells and expression of TE-derived transcripts in a spatially defined manner. Our data constitute the first comprehensive map of the chromatin changes that control TF activities in cycling endometrium at cellular resolution.

genomics↗

bioRxiv2021

Gata2a maintains cebpa and npm1a in haematopoietic stem cells to sustain lineage differentiation and genome stability

The transcription factor Gata2 is required to produce and maintain haematopoietic stem and progenitor cells (HSPCs) in development and adult haematopoiesis. Mutations in GATA2 lead to GATA2 deficiency syndrome and predispose patients to acquire leukaemia. Here we use zebrafish gata2a enhancer deletion mutants and single cell transcriptomics to understand how GATA2 mediates survival and differentiation of haematopoietic stem cells in GATA2 deficiency. Gata2a mutants show marrow failure, neutropenia, B-lymphopenia and erythrocytosis from 6 months post-fertilization (mpf). Single cell transcriptional profiling of the adult kidney marrow demonstrated that HSPCs express elevated expression of erythroid- and decreased expression of myeloid genes, including cebpa. This is associated with a lineage skewing towards the erythroid fate at the expense of the myeloid fate. Thus, Gata2a is required to initiate and maintain lineage priming in HSPCs, favouring myeloid differentiation. Gata2a regulates expression of multiple targets associated with replication and DNA damage repair (DDR), including npm1a, a zebrafish NPM1 orthologue. Accordingly, mutant marrow cells show increased DNA damage associated with progressive loss of npm1a expression with age. This effect was replicated by inhibiting NPM1 activity in murine HPC7 progenitor cells. We propose that the impaired DDR leads to marrow failure in GATA2 deficiency. This leads to increased genomic instability in the surviving HSPCs, favouring acquisition of secondary leukaemogenic mutations.

cancer biology↗

bioRxiv2020

Impact of sustained TGFβ receptor inhibition on chromatin accessibility and gene expression in cultured human endometrial MSC

Endometrial mesenchymal stem cells (eMSC) drive the extraordinary regenerative capacity of the human endometrium. Clinical application of eMSC for therapeutic purposes is hampered by spontaneous differentiation and cellular senescence upon large-scale expansion in vitro. A83-01, a selective transforming growth factor-{beta} receptor (TGF{beta}-R) inhibitor, promotes pharmacological expansion of eMSC in culture by blocking differentiation and senescence, but the underlying mechanisms are incompletely understood. In this study, we combined RNA-seq and ATAC-seq to study the impact of sustained TGF{beta}-R inhibition on gene expression and chromatin architecture of eMSC. Treatment of primary eMSC with A83-01 for 5 weeks resulted in differential expression of 1,463 genes. Gene ontology analysis showed enrichment of genes implicated in cell growth whereas extracellular matrix genes and genes involved in cell fate commitment were downregulated. ATAC-seq analysis demonstrated that sustained TGF{beta}-R inhibition results in opening and closure of 3,555 and 2,412 chromatin loci, respectively. Motif analysis revealed marked enrichment of retinoic acid receptor (RAR) binding sites, which was paralleled by the induction of RARB, encoding retinoic acid receptor beta (RAR{beta}). Selective RAR{beta} inhibition attenuated proliferation and clonogenicity of A83-01 treated eMSC. Taken together, our study provides new insights into the gene networks and genome-wide chromatin changes that underpin maintenance of an undifferentiated phenotype of eMSC in prolonged culture. Significance statementCycling human endometrium is a rich source of adult stem/progenitor cells that could be exploited for clinical purposes. Small molecules, such as A83-01, that modulate cell identity may open new avenues to maintain the functional properties of eMSC upon expansion in culture. By integrating complementary genome-wide profiling techniques, we mapped the dynamic changes in chromatin landscape and gene expression in response to prolonged A83-01 treatment of eMSC. Our findings provide new insights into the mechanisms of action of TGF{beta}-R inhibition that may lead to the development of more targeted pharmacological approaches for MSC expansion.

cell biology↗

bioRxiv2018

Reconstruction of the Decidual Pathways in Human Endometrial Cells Using Single-Cell RNA-Seq

Breakdown of the feto-maternal interface in early pregnancy causes miscarriage. The cycling endometrium becomes poised to transition to a pregnant state during the midluteal implantation window, coinciding with differentiation of stromal cells into decidual cells (DC) and emergence of senescent decidual cells (snDC). Emerging evidence suggests that DC engage uterine natural killer cells to eliminate their senescent counterparts, thus enabling formation of a robust decidual matrix in pregnancy. To examine if failure to constrain snDC during the peri-implantation window increases the risk of miscarriage, we reconstructed the decidual pathway at single-cell level in vitro and demonstrated that, without immune surveillance, secondary senescence rapidly transforms DC into progesterone-resistant cells that abundantly express extracellular matrix remodelling factors. Additional single-cell analysis of midluteal endometrium identified DIO2 and SCARA5 as marker genes of a diverging decidual response in vivo. Finally, we report a conspicuous link between a pro-senescent decidual response in luteal phase endometrium and recurrent pregnancy loss, suggesting that pre-pregnancy screening and intervention may reduce the burden of miscarriage.

systems biology↗

bioRxiv2017

Clearance of senescent decidual cells by uterine natural killer cells drives endometrial remodeling during the window of implantation

In cycling human endometrium, menstruation is followed by rapid estrogen-dependent growth. Upon ovulation, progesterone and rising cellular cAMP levels activate the transcription factor Forkhead box O1 (FOXO1) in endometrial stromal cells (EnSCs), leading to cell cycle exit and differentiation into decidual cells that control embryo implantation. Here we show that FOXO1 also causes acute senescence of a subpopulation of decidualizing EnSCs in an IL-8 dependent manner. Selective depletion or enrichment of this subpopulation revealed that decidual senescence drives the transient inflammatory response associated with endometrial receptivity. Further, senescent cells prevent differentiation of endometrial mesenchymal stem cells in decidualizing cultures. As the cycle progresses, IL-15 activated uterine natural killer (uNK) cells selectively target and clear senescent decidual cells through granule exocytosis. Our findings reveal that acute decidual senescence governs endometrial rejuvenation and remodeling at embryo implantation, and suggest a critical role for uNK cells in maintaining homeostasis in cycling endometrium.

cell biology↗