Biology subjects

Simunovic, M.

Publications and source records attributed to Simunovic, M..

3 recordsLinked to original sources

bioRxiv2025

Reconstructing the emergence of the human chorion via HIPPO-mediated trophoblast induction

The first lineage decision in the mammalian blastocyst commits outer cells to the trophectoderm and initiates the trajectory that gives rise to the placental chorion. The molecular sequence that unfolds downstream of HIPPO pathway inactivation, linking human trophectoderm specification to the early organization of the chorion, has remained unknown. Here, we establish a developmentally informed model that leverages HIPPO pathway modulation to induce the native trophectoderm trajectory in the absence of exogenous BMP or WNT signaling. We first transiently reset primed human pluripotent stem cells into a trophectoderm-competent ground state, followed by LATS kinase inhibition to set the trajectory in motion. To benchmark fidelity, we built an embryo-chorion single-cell reference integrating published early human and placental transcriptomes and applied a computational stage-matching tool to align our cultures to natural development. Stage matching revealed an ordered progression along the trophectoderm trajectory from early TE to post-implantation trophoblast. With extended culture, all major cell types of the nascent chorion emerged, encompassing both trophoblast and chorionic mesoderm lineages. Within the trophoblast, we identified proliferative and non-cycling villous cytotrophoblast, a columnar population connecting villous and extravillous domains, as well as syncytia and extravillous subtypes. When cultured in suspension, these lineages self-organized into three-dimensional organoids that recapitulated the stromal-epithelial architecture and proliferative-syncytial polarity of the emergent chorion. We identified CLDN6 as a defining surface marker of columnar trophoblast, the population that bridges villous and extravillous compartments. Prospective isolation of living CLDN6+ trophoblast revealed their capacity to reacquire a proliferative villous state and, under directed cues, generate both syncytial and extravillous fates, confirming their proposed dual developmental potential within the chorion. Together, these findings establish a developmentally informed framework that connects human trophectoderm specification to the emergent chorion and provides a dynamic platform for investigating the earliest steps of placental specification and the origins of implantation disorders.

cell biology↗

bioRxiv2025

GnnDebugger: GNN based error correction in De Bruijn Graphs

MotivationModern sequencing technologies have enabled the reconstruction of complete mammalian genomes from telomere to telomere. However, scaling this achievement to thousands of species and population-level studies remains a challenge. Key bottlenecks include the low quality of the draft assemblies and the high coverage requirements. In particular, reconstructing complete and accurate sequences of both haplotypes in diploid genomes is especially difficult since the sequencing depth is not always sufficient to properly reconstruct diverged regions. Inspired by the success of neural networks in extracting patterns from the data on a massive scale, we introduce a method for correcting errors in De Bruijn Graphs using Graph Neural Networks. ResultsOur model provides a reliable classification of edges into correct and erroneous, especially for diploid genomes with coverage depth 35 and lower. We demonstrate that these predictions can guide the downstream read error correction algorithm and genome assembly, ultimately allowing for more accurate genome assembly. Availability and implementationBoth GnnDebugger (https://github.com/m5imunovic/gnndebugger) and LJA (https://github.com/AntonBankevich/LJA/tree/gnndebugger) are available on GitHub. Datasets used for training and testing of ML model are available at Zenodo: https://doi.org/10.5281/zenodo.15073168. HG002 reference and reads are available at https://github.com/marbl/HG002. Primates references and reads are available at https://github.com/marbl/Primates.

bioinformatics↗

bioRxiv2018

Molecular mechanism of symmetry breaking in a 3D model of a human epiblast

Breaking the anterior-posterior (AP) symmetry in mammals takes place at gastrulation. Much of the signaling network underlying this process has been elucidated in the mouse, however there is no direct molecular evidence of events driving axis formation in humans. Here, we use human embryonic stem cells to generate an in vitro 3D model of a human epiblast whose size, cell polarity, and gene expression are similar to a 10-day human epiblast. A defined dose of bone mor-phogenetic protein 4 (BMP4) spontaneously breaks axial symmetry, and induces markers of the primitive streak and epithelial to mesenchymal transition. By gene knockouts and live-cell imaging we show that, downstream of BMP4, WNT3 and its inhibitor DKK1 play key roles in this process. Our work demonstrates that a model human epiblast can break axial symmetry despite no asymmetry in the initial signal and in the absence of extraembryonic tissues or maternal cues. Our 3D model opens routes to capturing molecular events underlying axial symmetry breaking phenomena, which have largely been unexplored in model human systems.

developmental biology↗