Biology subjects

Budjan, C.

Publications and source records attributed to Budjan, C..

4 recordsLinked to original sources

bioRxiv2025

Cooperative short- and long-range interactions enable robust symmetry breaking and axis formation

Establishing the anterior-posterior (A-P) axis is a key symmetry-breaking event in mammalian development. Gastruloids, aggregates of embryonic stem cells, undergo a similar process, forming a single posterior pole from an initially spherical aggregate. This requires the aggregate to convert an inside-outside difference in cell state into one A-P axis. We asked what cell-cell interactions can make this transition robust. We built an agent-based coarse-grained model with an outer cell population and an inner cell population. Cells interacted through short-range adhesion and, in some simulations, through an effective long-range attraction. Adhesion alone rarely produced a single stable axis, often leaving weakly separated or unstable clusters. Adding long-range attraction between outer cells changed this behavior. The outer cells collected into one pole, the inner cells remained in the opposite domain, and most cells stayed in one aggregate. This occurred across a broad range of adhesion strengths. The model also made a simple prediction. If two polarized gastruloids merge in opposite orientations, the two posterior poles should move around the fused aggregate and join into one pole. Human gastruloid merging experiments showed this behavior. Same-orientation pairs fused rapidly. Opposite-orientation pairs fused more slowly as their posterior poles moved around the aggregate and converged. Finally, we built a minimal gene-regulatory model that generated inner and outer states and turned on the same mechanical interactions. In this model, an initially uniform cell population formed one polarized axis. Together, these results suggest that short-range adhesion and long-range attraction can work together to convert radial patterning into one body axis. They also suggest a design principle for synthetic developmental biology: adhesion can sort cells locally, but building one reproducible axis may require interactions that act beyond direct cell-cell contact.

systems biology↗

bioRxiv2025

Discovery of A Small Molecule non-IMiD Degrader of ZBTB7A for the Treatment of β-hemoglobinopathies

Sickle cell disease and {beta}-thalassemia, two major {beta}-hemoglobinopathies, pose significant clinical challenges globally. Current treatments often face limitations in efficacy and tolerability. The transcription factor ZBTB7A has emerged as a promising therapeutic target for reactivating fetal hemoglobin expression. Here, we report the discovery and characterization of SH6, a small molecule non-IMiD degrader of ZBTB7A. SH6 induces fetal hemoglobin in erythroid cell lines in a CRBN and ZBTB7A-dependent manner, and it is capable of inducing fetal hemoglobin expression in healthy donor, SCD and {beta}-thalassemia patient CD34+ cell derived erythroid cells. The efficacy of SH6 is confirmed in a xenotransplantation humanized mouse model. SH6 outperforms currently available therapeutic agents in vitro, and shows synergy with hypomethylating agents. SH6 exhibits a favorable in vivo toxicity profile. Our findings establish SH6 as a promising therapeutic lead candidate for further optimization towards clinical development for treatment of sickle cell disease and {beta}-thalassemia.

cell biology↗

bioRxiv2021

Paraxial mesoderm organoids model development of human somites

During the development of the vertebrate embryo, segmented structures called somites are periodically formed from the presomitic mesoderm (PSM), and give rise to the vertebral column. While somite formation has been studied in several animal models, it is less clear how well this process is conserved in humans. Recent progress has made it possible to study aspects of human paraxial mesoderm development such as the human segmentation clock in vitro using human pluripotent stem cells (hPSCs), however, somite formation has not been observed in these monolayer cultures. Here, we describe the generation of human paraxial mesoderm (PM) organoids from hPSCs (termed Somitoids), which recapitulate the molecular, morphological and functional features of paraxial mesoderm development, including formation of somite-like structures in vitro. Using a quantitative image-based screen, we identify critical parameters such as initial cell number and signaling modulations that reproducibly yielded somite formation in our organoid system. In addition, using single-cell RNA sequencing and 3D imaging, we show that PM organoids both transcriptionally and morphologically resemble their in vivo counterparts and can be differentiated into somite derivatives. Our organoid system is reproducible and scalable, allowing for the systematic and quantitative analysis of human spinal cord development and disease in vitro.

developmental biology↗

bioRxiv2018

In vitro characterization of the human segmentation clock

The vertebral column is characterized by the periodic arrangement of vertebrae along the anterior-posterior (AP) axis. This segmental or metameric organization is established early in embryogenesis when pairs of embryonic segments called somites are rhythmically produced by the presomitic mesoderm (PSM). The tempo of somite formation is controlled by a molecular oscillator known as the segmentation clock 1,2. While this oscillator has been well characterized in model organisms 1,2, whether a similar oscillator exists in humans remains unknown. We have previously shown that human embryonic stem (ES) cells or induced pluripotent stem (iPS) cells can differentiate in vitro into PSM upon activation of the Wnt signaling pathway combined with BMP inhibition3. Here, we show that these human PSM cells exhibit Notch and YAP-dependent oscillations4 of the cyclic gene HES7 with a 5-hour period. Single cell RNA-sequencing comparison of the differentiating iPS cells with mouse PSM reveals that human PSM cells follow a similar differentiation path and exhibit a remarkably coordinated differentiation sequence. We also demonstrate that FGF signaling controls the phase and period of the oscillator. This contrasts with classical segmentation models such as the \"Clock and Wavefront\" 1,2,5, where FGF merely implements a signaling threshold specifying where oscillations stop. Overall, our work identifying the human segmentation clock represents an important breakthrough for human developmental biology.

developmental biology↗