Maurits Unkel

Background: High-throughput genomic and proteomic technologies are used to study biological systems by performing differential expression analysis across various experimental conditions. Geneset Ordinal Association Test (GOAT) is an analytic method recently introduced to statistically evaluate the differential expression of a defined set of genes or proteins. Despite the availability of numerous enrichment tools, many lack accessibility for users without programming expertise, provide limited continuation beyond listing top enriched terms, and offer little support for interactive visual exploration or hypothesis generation. Moreover, existing web-based platforms rarely support multi-contrast comparisons and generally omit gene-level or network-based context for pathway analysis. Results: To address these limitations, we present Geneset Ordinal Association Test Enrichment Analysis (GOATEA), an R/Shiny application that implements and extends the GOAT algorithm with interactive visualization, multi-contrast comparison, and integrated gene- and network-based context for bottom-up pathway analysis, enabling comprehensive enrichment analysis. GOATEA supports independent analysis of transcriptomic and proteomic data. To demonstrate its capability to integrate matched modalities, we applied it to the Colameo dataset containing paired mass spectrometry and RNA sequencing data. This proof-of-concept example highlights the tool’s strength in enabling multi-omics analyses and simultaneous comparison of multiple contrasts. An interactive overlap analysis identified 458 shared genes for focused enrichment and network exploration. By integrating these results in a gene- and network-based context for bottom-up pathway analysis, GOATEA applies a stringent interaction confidence threshold to emphasize qualitative protein–protein interactions, highlighting topic-relevant associations for further hypothesis generation. Conclusions: GOATEA streamlines enrichment analysis workflows by combining the GOAT algorithm with interactive visualizations in a user-friendly graphical interface. It facilitates exploratory analysis and hypothesis generation for researchers with or without programming expertise. GOATEA is available as an open-source tool, with full documentation, including usage vignettes ( https://mauritsunkel.github.io/goatea/ ).

In the growing diversity of human induced pluripotent stem cell (iPSC)-derived models of brain development, we present here a novel method that exhibits 3D cortical layer formation in a reproducible topography of minimal dimensions. The resulting adherent cortical organoids (ACOs) develop by self-organization after seeding frontal cortex-patterned iPSC-derived neural progenitor cells in 384-well plates during 8 weeks of differentiation. The organoids have stereotypical dimensions of 3 × 3 × 0.2 mm, contain multiple subtypes of neurons, astrocytes, and oligodendrocyte lineage cells, and are amenable to extended culture for at least 10 months. Longitudinal imaging revealed morphologically mature dendritic spines, axonal myelination, and robust neuronal activity. Moreover, ACOs compare favorably to existing free-floating brain organoid models on the basis of robust reproducibility in obtaining topographically standardized radial cortical structures and circumventing internal necrosis. Adherent human cortical organoids hold considerable potential for high-throughput drug discovery applications, neurotoxicological screening, and mechanistic pathophysiological studies of brain disorders.

The rising popularity of wearable devices allows for extensive and unobtrusive collection of personal health data for extended periods of time. Recent studies have used machine learning to create predictive algorithms to assess symptoms of major depressive disorder (MDD) based on these data. This review evaluates the clinical relevance of these models. Studies were selected to represent the range of methodologies and applications of wearables for MDD algorithms, with a focus on wrist-worn devices. The reviewed studies demonstrated that wearable-based algorithms were able to predict symptoms of MDD with considerable accuracy. These models may be used in the clinic to complement the monitoring of treatments or to facilitate early intervention in high-risk populations. In a preventative context, they could prompt users to seek help for earlier intervention and better clinical outcomes. However, the lack of standardized methodologies and variation in which performance metrics are reported complicates direct comparisons between studies. Issues with reproducibility, overfitting, small sample sizes, and limited population demographics also limit the generalizability of findings. As such, wearable-based algorithms show considerable promise for predicting and monitoring MDD, but there is significant room for improvement before this promise can be fulfilled.

Astrocytes are essential for the formation and maintenance of neural networks. However, a major technical challenge for investigating astrocyte function and disease-related pathophysiology has been the limited ability to obtain functional human astrocytes. Despite recent advances in human pluripotent stem cell (hPSC) techniques, primary rodent astrocytes remain the gold standard in coculture with human neurons. We demonstrate that a combination of leukemia inhibitory factor (LIF) and bone morphogenetic protein-4 (BMP4) directs hPSC-derived neural precursor cells to a highly pure population of astroglia in 28 d. Using single-cell RNA sequencing, we confirm the astroglial identity of these cells and highlight profound transcriptional adaptations in cocultured hPSC-derived astrocytes and neurons, consistent with their further maturation. In coculture with human neurons, multielectrode array recordings revealed robust network activity of human neurons in a coculture with hPSC-derived or rat astrocytes [3.63 ± 0.44 min⁻¹(hPSC-derived), 2.86 ± 0.64 min⁻¹(rat);p = 0.19]. In comparison, we found increased spike frequency within network bursts of human neurons cocultured with hPSC-derived astrocytes [56.31 ± 8.56 Hz (hPSC-derived), 24.77 ± 4.04 Hz (rat);p < 0.01], and whole-cell patch-clamp recordings revealed an increase of postsynaptic currents [2.76 ± 0.39 Hz (hPSC-derived), 1.07 ± 0.14 Hz (rat);p < 0.001], consistent with a corresponding increase in synapse density [14.90 ± 1.27/100 μm²(hPSC-derived), 8.39 ± 0.63/100 μm²(rat);p < 0.001]. Taken together, we show that hPSC-derived astrocytes compare favorably with rat astrocytes in supporting human neural network activity and maturation, providing a fully human platform for investigating astrocyte function and neuronal-glial interactions.