[Stellenangebote] Master’s Thesis: Mapping tumor subtypes and immune infiltrate in liposarcoma

[Münch, Amos]

Master’s Thesis at the Institute of Pathology, Charité Berlin

As part a collaborative research project, we offer a Master’s thesis on:
Mapping tumor subtypes and immune infiltrate in liposarcoma
This project focuses on the computational analysis of spatial transcriptomics datasets of liposarcoma, a soft tissue tumor that arises from fat tissue progenitor cells [1]. Treatment options for liposarcoma are limited and recurrence rates reach up to 80% after surgical resection. Different subtypes of the tumor exist, but their distinction currently relies on subjective assessments of routine histopathology images while specific molecular biomarkers are lacking. Infiltration of immune cells into the tumor is observed in a subset of liposarcomas, but its significance and whether it could be used therapeutically is unknown [2].
Spatial transcriptomics is a recent technology that allows us to spatially resolve gene expression at the single-cell level [3]. We have generated two datasets of spatial gene expression in human liposarcoma samples, using two different experimental technologies (Nanostring CosMx and 10x Xenium).
You will address the following questions:

  1.  How does gene expression correlate with morphological differences between liposarcoma subtypes?
  2.  What are the interactions of liposarcoma cells with infiltrating immune cells?
  3.  How do results compare between the two experimental technologies?
You will implement and adapt existing analysis frameworks [4] and combine them into a computational pipeline that will be applied to additional tumor samples in the future.

Requirements:

  *   Enrolment as a master’s student in bioinformatics, computer science, molecular biology, genetics or a related field
  *   Proficient in at least one programming language (e.g. Python, R) and experienced in data analysis
We are looking forward to your application! An immediate start is possible.
If you have any questions, please don’t hesitate to contact us:
frank.dubois at charite.de<mailto:frank.dubois at charite.de>                  teresa.krieger at charite.de<mailto:teresa.krieger at charite.de>
duboislab.org<http://duboislab.org/>                                   kriegerlab.org<https://www.kriegerlab.org/>
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References:
[1] https://ascopubs.org/doi/10.1200/JCO.2017.74.9598
[2] https://www.mdpi.com/2072-6694/14/19/4578
[3] https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-022-01075-1
[4] https://www.sciencedirect.com/science/article/pii/S2001037022003786


Amos Münch
PhD student
Computational Oncology - Krieger Lab
Institute of Pathology
Charité - Universitätsmedizin Berlin
amos.muench at charite.de