A1

Spatio-temporal analysis of forebrain development on a

single cell level
Institute of Anatomy and Cell Biology, University Freiburg, Germany

The Vogel lab researches the influence of epigenetic modifications of histones during central
nervous system development. We are particularly interested in the function of the histone
methyltransferase DOT1L on the specification of stem and progenitor cells during development of
the cerebral cortex. We recently showed that DOT1L has a high plasticity leading to pleiotropic
effects during specification of the cerebral neocortex layers (Franz et al, 2019), to alterations of
the enhancer landscapes (Ferrari et al, 2020), and based on single cell analyses, to an adaptation
of the metabolic program during neuronal differentiation (Appiah et al, 2022). In our MeInBio
project we now further resolve the mechanism of DOT1L-associated defects in cerebral cortex
development in mice and humans. Specifically, we aim at understanding DOT1L-mediated
transcriptional control and how it impacts chromatin properties and enhancer landscapes to
prevent neuronal differentiation and to preserve stem cell states. We therefore explore the DOT1L-
dependent transcriptome and epigenome in individual progenitor populations during cortical
differentiation. The future project shall advance our understanding on human cortical
development by exploring the DOT1L-dependent transcriptome and epigenome in single cells
during human brain organoid differentiation, with spatio-temporal resolution. We aim to resolve
the different stem cell populations, their differentiation potential and trajectories and to resolve
chromatin-mediated mechanisms of epigenetic control of gene expression networks.

Main methods: single cell RNA-seq, single cell ATAC-seq, single cell Cut&Run, spatial
transcriptomics, bioinformatics analyses, human brain organoid differentiation, iPSC, ChIP-seq,
FACS

A3

Regulation of hematopoietic stem cell dormancy

Recently, we functionally and molecularly defined multipotent progenitor 5 (MPP5) cells and other
hematopoietic stem progenitor cells (HSPC). Specifically, we aimed to address: (1) the in vivo role
of MPP5 in the hematopoietic system; (2) the molecular profile of MPP5 cells at the population
level; (3) the heterogeneity within the HSPC compartment particularly within the MPP5 population;
(4) the MPP5 regulatory mechanisms (Sommerkamp*, Mulero-Romero*, et al., Blood 2021)

The main aim of the future PhD project will be to unravel the molecular mechanisms on how MPP6
are regulated upon aging and stress- activating conditions. To do so, we will apply state-of-the-art
techniques such as single-cell RNA-seq, ATAC-seq, metabolomics, ChIP-seq combined with in
vivo functional experiments.
Main methods: ATAC-seq, HSC cultures, single cell RNA-seq, ChIP-seq
A4
Genome organization during differentiation, Deep
sequencing data analysis
Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany

The Manke group develops tools for the analysis and visualisation of deep-sequencing data. In a
long-running collaboration with the lab of Prof. Vogel, we aim at understanding the chromatin
state and genome organisation during murine neuronal differentiation at single-cell resolution.
Using advanced machine learning methods, we are integrating multi-modal data from gene
expression and chromatin accessibility to infer cell-type specific regulatory networks.

The PhD project will utilise spatial transcriptomics and place these networks into the context of a
spatially evolving brain. For candidate transcription factors, we will also use highly sensitive
assays to map their targets genome-wide. The ultimate goal is to develop a joint model for
chromatin- and sequence-dependent control of gene expression during neuronal differentiation.

Main methods: ChIP-seq/RELACS, single cell ATAC-seq, bioinformatics algorithm and tool
development, cell culture

A5

Epigenetic mechanisms controlling transition states in

neural differentiation
Institute of Biology, University Freiburg, Germany

The Driver lab has a long-standing interest in investigating signaling and transcriptional networks
that control stem cell development during embryogenesis. In MeInBio we characterise dynamic
transcriptome changes between neural stem cells, proliferating precursors, differentiating and
mature neurons in zebrafish in vivo, and identify specific epigenetic mechanisms involved in
these transitions. Currently, we aim at characterizing dopaminergic neurogenesis from neural
stem cells in the subpallial proliferation zone in zebrafish.

Main methods: FACS, single cell RNA-seq,fluorescent in situ hybridization

A7

Spatially resolved multimodal dissection of heart failure

pathogenesis
Institute of Experimental and Clinical Pharmocology and Toxicology, University Freiburg,
Germany

Our lab has a focus on regulation of transcription, including epigenetic mechanisms. We have
dissected the role of DNA methylation and histone modification in cardiac development and
disease in mouse models and human samples, and we have uncovered the dynamics of 3D
chromatin interactions and enhancer activity during differentiation of human pluripotent stem
cells to cardiomyocytes. A main objective of the lab’s research is to build a molecular framework
of how external cues are integrated to regulate gene expression and how perturbations of the
molecular networks can lead to diseases such as heart failure or atrial fibrillation.

The main goal of the PhD project will be to reveal the dynamics of spatial organization of cell
types and activity patterns of transcription factors and chromatin regulators associated with heart
failure pathogenesis through integration of single cell transcriptomes, epigenomes and
subcellular spatial transcriptomes. This project will uncover molecular mechanisms, biomarkers
and potential therapeutic targets for heart failure. Detailed goals are (1) to reveal the spatial
organization of cell types and expression patterns of transcriptional regulators associated with
heart failure, (2) to elucidate the dynamics of spatio-temporal transcriptional and epigenetic
changes in a mouse model of heart failure, and (3) functional validation of transcription factors
and cell-cell interactions associated with heart failure.

Main methods: multiplexed error-robust RNA FISH (MERFISH), single nucleus multiomics, in vitro
differentiation models, CRISPR gene editing

B1

Genetic Epidemiology
Institute of Genetic Epidemiology, University Freiburg, Germany

The Kottgen lab uses data from epidemiological and clinical studies to gain insights into human
physiology and the pathophysiology of complex traits and diseases. We are especially interested
in kidney and metabolic diseases. Through the integration of genome-wide genetic and
metabolomic data, we recently showed that the levels of metabolites in urine are under strong
genetic influence and capture processes related to metabolite absorption, distribution,
metabolism and excretion. In the future, we want to use multi-Omic data from thousands of study
participants to better understand if genetic differences on metabolite levels in plasma versus
urine reflect specific metabolic functions of the kidney, and to what extent these are influence by
patient characteristics.

Main methods: genome-wide association studies, analysis of non-targeted MS-based

metabolomics, single cell RNA- and ATAC-seq, bioinformatics analyses

B2

B02 Cell death and survival

Institute of Molecular Medicine and Cell Research, University Freiburg, Germany

The Maurer group aims at understanding how growth factor availability and stress signals are
sensed by cells and integrated into cell signaling pathways, e.g. by posttranslational
modifications like phosphorylation or acetylation. In MeInBio we investigate the role of TIP60
phosphorylation in transcriptional regulation in human cancer cells. We analyse the spatial
distribution of wild-type and mutated TIP60 and their influence on transcriptional control and
chromatin properties and explore the role of GSK-3b for NF-kB activity and identify GSK-3b
dependent NF-kB target genes. The genome wide analysis of the crosstalk of PI3K and NF-kB
signaling will improve our understanding of the regulation of inflammation and cell death.
Main methods: Cut&Run, CRISPR-rAAV knock-in, RNA-seq

B03 Prof. Dr. Dr. Melanie Börries:

Systems biology
Institute of Molecular Medicine and Cell Research, University Freiburg, Germany

The group of Melanie Börries focuses on the development and verification of mathematical
models for cellular behavior and cell communication from an initial stimulus to the final
phenotype. We identify transcriptional regulation in the spatio-temporal communication between
melanoma cells (from different origin and mutation status) and fibroblasts, and relate this to
mechanisms of treatment resistance.

By using CRISPR/Cas9 gene editing to target PTEN, we are currently investigating the
contribution of the PI3K/AKT pathway to resistance mechanisms. The next PhD candidate will
investigate the role of this pathway activation in remodeling of the tumor microenvironment
(TME). The project aims to explore transcriptional changes during melanoma invasion and to
develop an integrative in silico predictive model of cell communication.

Main methods: CRISPR/Cas, RNA-seq, cell culture, in silico analysis and data integration

B05 Proteomics, Proteolytic signaling

Institute of Clinical Pathology, University Freiburg, Germany

The Schilling laboratory employs proteomics and proteogenomics to better understand disease
processes, e.g., for solid tumors. The planned project will probe the spatial proteome biology of
solid tumors using state-of-the-art methods in mass spectrometry imaging (MSI). We will advance
the bioinformatic processing of MSI data to enhance the proteome coverage in situ. Moreover, we
will integrate MSI-based, highly multiplexed immune-detection of proteins. The project aims to
understand intratumor heterogeneity of proteome biology and characterize cell-cell and cell-
matrix interactions with novel tools.

Main methods: several proteomics techniques, computational and statistical methods

Quantitative single cell biology in hematopoietic differentiation

The Grün lab investigates how gene expression programs are regulated with spatial and temporal
precision during stem cell differentiation in the presence of gene expression noise. In MeInBio we
currently study mouse hematopoiesis as a model to understand differentiation transitions in
single cells. We perform a detailed analysis of progenitor stage transitions at subsequent
timepoints of embryonic development, where hematopoiesis occurs within different tissue
contexts. By co-analyzing the hematopoietic cell populations with the endothelial niche at single-
cell resolution, we are investigating the role of the microenvironment in determining
hematopoietic cell fate. In the future project we will focus on the liver, which is an ideal model for
cellular plasticity, in order to study perturbations in liver disease and cell state changes during
liver regeneration in both, human organoids and mouse models at spatial single-cell resolution.

Main methods: seqFISH, single cell RNA-seq, computational and statistical methods, FACS