Biology subjects

van Oudenaarden, A.

Publications and source records attributed to van Oudenaarden, A..

6 recordsLinked to original sources

bioRxiv2018

Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells.

Environmental stimuli often lead to heterogeneous cellular responses and transcriptional output. We developed single-cell RNA and Immunodetection (RAID) to allow combined analysis the transcriptome and intracellular (phospho-)proteins from fixed single cells. RAID successfully recapitulated differentiation-state changes at the protein and mRNA level in human keratinocytes. Furthermore, we show that differentiated keratinocytes that retain high phosphorylated FAK levels, a feature associated with stem cells, also express a selection of stem cell associated transcripts. Our data demonstrates that RAID allows investigation of heterogenenous cellular responses to environmental signals at the mRNA and phospho-proteome level.

genomics↗

bioRxiv2018

Spatial transcriptomics of C. elegans males and hermaphrodites identifies novel fertility genes

To advance our understanding of the genetic programs that drive cell and tissue specialization, it is necessary to obtain a comprehensive overview of gene expression patterns. Here, we have used RNA tomography to generate the first high-resolution, anteroposterior gene expression maps of C. elegans males and hermaphrodites. To explore these maps, we have developed computational methods for discovering region and tissue-specific genes. Moreover, by combining pattern-based analysis with differential gene expression analysis, we have found extensive sex-specific gene expression differences in the germline and sperm. We have also identified genes that are specifically expressed in the male reproductive tract, including a group of uncharacterized genes that encode small secreted proteins that are required for male fertility. We conclude that spatial gene expression maps provide a powerful resource for identifying novel tissue-specific gene functions in C. elegans. Importantly, we found that expression maps from different animals can be precisely aligned, which opens up new possibilities for transcriptome-wide comparisons of gene expression patterns.

genomics↗

bioRxiv2018

Long-term expanding human airway organoids for disease modelling.

Organoids are self-organizing 3D structures grown from stem cells that recapitulate essential aspects of organ structure and function. Here we describe a method to establish long-term-expanding human airway organoids from broncho-alveolar biopsies or lavage material. The pseudostratified airway organoid epithelium consists of basal cells, functional multi-ciliated cells, mucus-producing goblet cells, and CC10-secreting club cells. Airway organoids derived from cystic fibrosis (CF) patients allow assessment of CFTR function in an organoid swelling assay. Organoid culture conditions also allow gene editing as well as the derivation of various types of lung cancer organoids. Respiratory syncytial virus (RSV) infection recapitulated central disease features and dramatically increases organoid cell motility, found to be driven by the non-structural viral NS2 protein. We conclude that human airway organoids represent versatile models for the in vitro study of hereditary, malignant, and infectious pulmonary disease.

cell biology↗

bioRxiv2018

Neuromesodermal Progenitors are a Conserved Source of Spinal Cord with Divergent Growth Dynamics

During gastrulation, embryonic cells become specified into distinct germ layers. In mouse, this continues throughout somitogenesis from a population of bipotent stem cells called neuromesodermal progenitors (NMps). However, the degree self-renewal is associated with NMps in the fast-developing zebrafish embryo is unclear. With a genetic clone tracing method, we labelled early embryonic progenitors and find a strong clonal similarity between spinal cord and mesoderm tissues. We then followed individual cell lineages by light-sheet imaging and reveal a common neuromesodermal lineage contribution to a subset of spinal cord tissue across the anterior-posterior body axis. An initial population subdivides at mid gastrula stages and is directly allocated to neural and mesodermal compartments during gastrulation. A second population in the tailbud undergoes delayed allocation to contribute to the neural and mesodermal compartment only at late somitogenesis. We suggest that NMps undergo vastly different rates of differentiation and growth in a species-specific manner.

developmental biology↗

bioRxiv2018

Tdrd6a regulates the aggregation of Buc into functional subcellular compartments that drive germ cell specification

In recent years, it has become clear that phase separation represents an important class of subcellular compartmentalization. However, relatively little is known about how the formation or disassembly of such compartments is regulated. In zebrafish, the Balbiani body (Bb) and the germ plasm (Gp) are phase-separated structures essential for germ cell specification and home to many germ cell-specific mRNAs and proteins. Throughout development, these structures range from a single large aggregate (Bb), to a dispersed state and back to relatively large assemblies (Gp). Formation of the Bb requires Bucky ball (Buc), a protein with prion-like properties. We found that the multi-tudor domain-containing protein Tdrd6a interacts directly with Buc, affecting its mobility and aggregation properties. Importantly, lack of this regulatory interaction leads to significant defects in germ cell development. Our work presents a new mechanism for how prion-like protein-aggregations can be regulated and highlights the biological relevance of such regulatory events.

molecular biology↗

bioRxiv2018

Sharq, a versatile preprocessing and QC pipeline for Single Cell RNA-seq

Despite the meteoric rise of single cell RNA-seq, only a few preprocessing pipelines exist that are able to perform all steps from the original fastq files to a gene expression table ready for further analysis. Here we present Sharq, a versatile preprocessing pipeline designed to work with plate-based 3-end protocols that include Unique Molecular Identifiers (UMIs). Sharq performs stringent step-wise trimming of reads, assigns them to features according to a flexible hierarchical model, and uses the barcode and UMI information to avoid amplification biases and produce gene expression tables. Additionally, Sharq provides an extensive plate diagnostics report for quality control and troubleshooting, including that of spatial artefacts. The diagnostics report includes measures of the quality of the individual plate wells as well as a robust assessment which of them contain material from live cells. Collectively, the innovative approaches presented here provide a valuable tool for processing and quality control of single cell RNA-seq data.

bioinformatics↗