Spatial Transcriptomics Analysis of Tumor Microenvironment

Abstract:

1. Background and Purpose

Spatial transcriptomics is a cutting-edge technology that enables the mapping of gene expression to precise locations within tissue sections while preserving spatial context. Tumors are highly heterogeneous and composed of diverse cell populations (immune cells, fibroblasts, endothelial cells, cancer cells) whose spatial organization shapes tumor progression and therapeutic response.

This project aims to investigate the spatial architecture of the tumor microenvironment (TME) using spatial transcriptomics data, with a specific focus on cell–cell interactions, immune infiltration patterns, and molecular pathways associated with cancer progression or treatment resistance. The ultimate goal is to identify spatial biomarkers that may inform precision oncology and personalized treatment strategies.

2. Research Questions

1. How are different cell types spatially distributed within the tumor microenvironment?
2. What are the key cell–cell interaction networks that promote tumor progression or immune evasion?
3. Which spatially-resolved gene expression signatures correlate with clinical outcomes or treatment response?
4. Can spatial transcriptomics data reveal new biomarkers or therapeutic targets in cancer?

Skills and experience required for the project:

1. Background in Biomedical Sciences, Chinese Medicine, Bioinformatics, Molecular Biology, or Medicine-related disciplines
2. Basic knowledge of cancer biology or tumor microenvironment
3. Experience with transcriptomic data (RNA-seq or single-cell RNA-seq) is preferred
4. Prefer R or Python programming skills for data analysis
5. Good written and verbal communication skills in English
6. Self-motivated, responsible, and able to work independently or in a research team