Biology subjects

Tanis, S. E. J.

Publications and source records attributed to Tanis, S. E. J..

4 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

Single-cell ID-seq identifies BMP signaling as a driver of a late stage epidermal differentiation program.

AbstractEpidermal homeostasis requires balanced and coordinated adult stem cell renewal and differentiation. These processes are controlled by both extracellular signaling and by cell intrinsic transcription regulatory networks, yet how these control mechanisms are integrated to achieve this unclear. Here, we developed single-cell ID-seq and measured 69 antibody-DNA conjugates (including 34 phospho-specific epitopes) to study the activation state of signaling pathways during epidermal differentiation at the single-cell level. Computational pseudo-timing inference revealed activation of the JAK-STAT, WNT and BMP pathways along the epidermal differentiation trajectory. During differentiation, cells start producing BMP2 ligands and activate the canonical intracellular effectors SMAD1/5/9. Mechanistically, the BMP pathway is responsible for directly activating a specific transcription program that includes the key differentiation transcription factors MAF and MAFB to allow terminal differentiation. We propose that incorporating autocrine signaling pathway activation into a transcription regulatory network enables regional coordination of transcription programs during epidermal differentiation.

developmental biology↗

bioRxiv2018

Splicing and epigenetic factors jointly regulate epidermal differentiation

Epidermal homeostasis requires a continuous balance between progenitor cell proliferation and loss of differentiated cells from its surface. During this process cells undergo major changes in their transcriptional programs to accommodate new cellular functions. We found that transcriptional and post-transcriptional mechanisms underlying these changes are functionally connected and jointly control genes involved in cell adhesion, a key process in epidermal maintenance. Using siRNA-based perturbation screens, we identified novel DNA/RNA binding regulators of epidermal differentiation. Computational modeling and experimental validation identified functional interactions between the matrin-type 2 zinc-finger protein ZMAT2 and the epigenetic modifiers ING5, SMARCA5, BRD1, UHRF1, BPTF, SMARCC2. ZMAT2 is required to keep cells in an undifferentiated, proliferative state and quantitative proteomics identified ZMAT2 as an interactor of the pre-spliceosome. RNA-Immunoprecipitation and transcriptome-wide RNA splicing analysis showed that ZMAT2 associates with and regulates transcripts involved in cell adhesion in conjuction with ING5. Thus, joint control by post-transcriptional and epigenetic mechanisms is important to maintain epidermal cells in an undifferentiated state.\n\nHighlights- Gene-perturbation screens identify a role for ZMAT2 in the control of human epidermal differentiation.\n- ZMAT2 functionally interacts with known epigenetic regulators of epidermal differentiation.\n- ZMAT2 interacts with the pre-spliceosome and transcripts involved in cell adhesion.\n- ZMAT2 mediated splicing and epigenetic control jointly target an adhesion related transcriptional program in human epidermal stem cells.

systems biology↗

bioRxiv2017

Immuno-Detection by sequencing (ID-seq) enables large-scale high-dimensional phenotyping in cells.

Cell-based small molecule screening is an effective strategy leading to new medicines. Scientists in the pharmaceutical industry as well as in academia have made tremendous progress in developing both large-scale and smaller-scale screening assays. However, an accessible and universal technology for measuring large numbers of molecular and cellular phenotypes in many samples in parallel is not available. Here, we present the Immuno-Detection by sequencing (ID-seq) technology that combines antibody-based protein detection and DNA-sequencing via DNA-tagged antibodies. We used ID-seq to simultaneously measure 84 (phospho-)proteins in hundreds of samples and screen the effects of ~300 kinase inhibitor probes on primary human epidermal stem cells to characterise the role of 225 kinases. Our work highlighted a previously unrecognized downregulation of mTOR signaling during differentiation and uncovered 13 kinases regulating epidermal renewal through distinct mechanisms.

genomics↗