Biology subjects

Holcik, L.

Publications and source records attributed to Holcik, L..

4 recordsLinked to original sources

bioRxiv2024

Reconstitution of Human Brain Cell Diversity in Organoids via Four Protocols

Human brain organoids are powerful in vitro models for brain development and disease. However, their variability can complicate use in biomedical research and drug discovery. Both the specific protocol as well as the pluripotent starting cell line influence organoid variability and can result in incomplete representation of brain cell types in an organoid experiment. Here, we systematically analyze the cellular and transcriptional landscape of brain organoids grown from multiple cell lines using four different protocols recapitulating dorsal and ventral forebrain, midbrain, and striatum. We establish the NEST-Score as a quantitative readout for cell line-driven and protocol-driven differentiation propensities by comparing cellular states across multiple cell lines and to in vivo reference data sets. Thereby, we establish a set of organoid protocols that together recreate the vast majority of cell types in the developing human brain and provide a reference for how well cell types are recapitulated across cell lines in each protocol. Additionally, we survey factors contributing to variability during organoid development and identify early gene expression signatures predicting protocol-driven organoid generation at later stages. We provide easy online access to our data through a web-based analysis tool, creating a reference for brain organoid research that allows rapid, straightforward validation of protocol and cell line performance.

developmental biology↗

bioRxiv2024

GuaCAMOLE: GC-bias aware estimation improves the accuracy of metagenomic species abundances

Metagenomic sequencing measures the species composition of microbial communities, and has revealed the crucial role of microbiomes in the etiology of a range of diseases such as colorectal cancer. Quantitative comparisons of microbial communities are, however, affected by GC-content dependent biases. Here, we present GuaCAMOLE, a computational method to detect and remove GC bias from meta-genomic sequencing data. The algorithm relies on comparisons between individual species in a single sample to estimates the sequencing efficiency at levels of GC content, and outputs unbiased species abundances. GuaCAMOLE thus works regardless of the specific amount or direction of GC-bias present in the data and does not rely on calibration experiments or multiple samples. Applying our algorithm to 3435 gut microbiomes of colorectal cancer patients from 33 individual studies reveals that the type and severity of GC bias varies considerably between studies. In many studies we observe a clear bias against GC-poor species in the abundances reported by existing methods. GuaCAMOLE successfully removes this bias and corrects the abundance of clinically relevant GC-poor species such as F. nucleatum (28% GC) by up to a factor of two. GuaCAMOLE thus contributes to a better quantitative understanding of microbial communities by improving the accuracy and comparability of species abundances across experimental setups.

bioinformatics↗

bioRxiv2022

Molecular characteristics of diel rhythmic diversity reveal disconnection between different levels of organismal rhythmicity

The circadian clock controls behavior and metabolism in various organisms. However, the exact timing and strength of rhythmic phenotypes can vary significantly between individuals of the same species. This is highly relevant for the rhythmically complex marine environments where organismal rhythmic diversity likely permits the occupation of different microenvironments. When investigating circadian locomotor behavior of Platynereis dumerilii, a model system for marine molecular chronobiology, we found strain-specific, high variability between individual worms. The individual patterns were reproducibly maintained for several weeks independent of basic culture conditions, such as population density or feeding. A diel head transcriptome comparison of behaviorally rhythmic versus arrhythmic wildtype worms showed that 24h cycling of core circadian clock transcripts is identical between both behavioral phenotypes. While behaviorally arrhythmic worms showed a similar total number of cycling transcripts compared to their behaviorally rhythmic counterparts, the annotation categories of their transcripts, however, differed substantially. Consistent with their locomotor phenotype, behaviorally rhythmic worms exhibit an enrichment of cycling transcripts related to neuronal/behavioral processes. In contrast, behaviorally arrhythmic worms showed significantly increased diel cycling for metabolism- and physiology-related transcripts. Phenotype-specific cycling of distinct matrix metalloproteinase transcripts, encoding extracellular enzymes that modulate synaptic circuit function and neuropeptide signaling, like pigment dispersing factor (PDF), prompted us to functionally investigate Platynereis pdf. Differing from its role in Drosophila, loss of pdf impacts on overall activity levels, but shows only indirect effects on rhythmicity. Our results show that individuals arrhythmic in a given process can show increased rhythmicity in others. Across the Platynereis population, variations of this exist as a reproducible continuum. We hypothesize that such diel rhythm breadth is an important biodiversity resource enabling the species to quickly adapt to heterogeneous marine environments and potentially also to the effects of climate change, which is however endangered with shrinking population sizes and hence diversity.

animal behavior and cognition↗

bioRxiv2020

NMD is required for timely cell fate transitions by fine-tuning gene expression and controlling translation

Cell fate transitions depend on balanced rewiring of transcription and translation programmes to mediate ordered developmental progression. Here we identify a feedback loop between nonsense-mediated mRNA decay (NMD) and translation initiation. We show that NMD controls the translation initiation factor Eif4a2 and its premature termination codon encoding isoform (Eif4a2PTC). NMD deficiency leads to translation of a specific truncated Eif4a2 protein, which elicits increased translation rates and is causative for significant delays in mouse embryonic stem cell (ESC) differentiation. Our results show identical mRNA targets for Smg5, Smg6 and Smg7, but illustrate a clear hierarchy between KOs in amplitude of target deregulation and differentiation phenotype (Smg5 > Smg6 > Smg7). This hierarchy highlights heterodimer independent functions for Smg5 and Smg7. Together, our findings expose an intricate link between mRNA stability and translation initiation control, that must be maintained for normal dynamics of cell state transitions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

cell biology↗