Department Molecular Genetics
Principal investigator Miao-Ping Chien
E-mail address m.p.chien@erasmusmc.nl
Website http://www.mpchienlab.org/
Development of a spatial-omics or multiplexed omics profiling technology for tumor immunology
In Dr. Chien’s lab, we develop single-cell and spatial omics technologies by combining optical imaging, biomedical techniques, and bioinformatics to address key biological questions, particularly in cancer biology and immuno-oncology. There are two potential projects: the first involves applying our microscopy-based functional single-cell sequencing method to study the effects of fibroblasts on the clonogenicity of cancer cells; the second focuses on helping to develop a spatial-omics or multiplexed omics profiling technology and applying it to investigate the interplay between cancer cells and the tumor microenvironment.
Techniques
- Advanced imaging
- Single-cell and spatial -omics technology development
- Bioinformatics
Further reading
Nature Biomedical Engineering, 2022 (https://rdcu.be/cJct9) (https://doi.org/10.1038/s41551-022-00853-x)
Functional single cell sequencing method development
Supervisor: Lars van Roemburg, l.vanroemburg@erasmusmc.nl
In our lab, we have functional single cell sequencing (FUNseq), however it has some multiplexibility and throughput limitations, to overcome these, we are developing in situ FUNseq from scratch. It is a 3′ mRNA semi-bulk sequencing method, and in this project, you would get a full understanding of the method design and dive into the optimization of its details to be able to make it functional. Having the internal drive to really understand what is happening in your experiments and questioning everything is a very good plus/pro.
Techniques
Project can consist of (but not mandatory or limited to):
- FUNseq pipeline
- Fluorescence microscopy
- Tissue immunostaining
- Cell culture
- cDNA library preparation
- Optimization experiments
- Sequencing data analysis (still limited)
Single cell sequencing approaches such as single-cell ATAC-seq, DamID-seq and a custom MUCE-seq
Supervisor: Oluwatoba (Toba) Ajani, o.ajani@erasmusmc.nl
Toba is setting up plate based single cell sequencing for epigenetics approaches such as ATAC-seq, DamID-seq and our lab’s own designed MUCE-seq. You could focus on one of the approaches and do the functional single cell pipeline of our lab coupled to this specific epigenetics approach.
Techniques
- FUNseq
- ATAC-seq
- DamID-seq
- Cell culture
- Fluorescence microscopy
- cDNA library preparation
- Sequencing data analysis
Single cell sequencing data analysis on e.g. VASA-seq data
Supervisor: Mayte Lopez Cascales, maytelopezcascales@gmail.com
Learn everything about single cell sequencing data analysis with our bioinformatician post-doc Mayte. We have VASA-seq data that needs to be analyzed to answer biological questions.
Techniques
- Single cell sequencing data analysis
- Programming
- Pathway analysis
Investigate interaction between CIN cancer cells and immune cells
Supervisor: Tsai-Ying Chen, t.chen@erasmusmc.nl
Here you would use our FUNseq pipeline to investigate how cancer cells with micronuclei communicate with immune cells and compare it to how “normal” cancer cells communicate with immune cells to see what the impact is of micronuclei in this communication. Quite a complex project only for master students.
Techniques
- FUNseq
- Cell culture
- Fluorescence microscopy
- Image analysis
- Sequencing data analysis
- Literature research on possible pathways correlated to the cancer-immune cell communication