SpatialTCR

An integrated platform for high-resolution spatial sequencing of T cell receptor repertoires

SpatialTCR: An integrated platform for high-resolution spatial sequencing of T cell receptor repertoires

Status: Active project, Independent Research Project

Role: Co-first author, Lead computational developer

Institution: Prof. Wanlu Liu Lab, ZJU-UoE Institute, Zhejiang University

Duration: January 2025 – Present

Project Overview

SpatialTCR represents a groundbreaking advancement in spatial immunology, combining cutting-edge wet lab techniques with sophisticated computational methods to enable high-resolution spatial sequencing of T cell receptor (TCR) repertoires. This project bridges experimental innovation with computational biology to provide unprecedented insights into immune cell organization and function within tissues.

My Responsibilities

As the lead computational developer, I am responsible for:

  • Upstream Data Processing: Developing robust pipelines for raw spatial TCR sequencing data processing
  • Algorithm Development: Creating novel computational methods for spatial TCR analysis
  • Downstream Analysis Tools: Building comprehensive analysis frameworks for TCR-omics data interpretation
  • Method Integration: Ensuring seamless integration between wet lab protocols and computational analysis

Technical Innovation

The computational framework includes:

  • Novel algorithms for spatial TCR sequence alignment and quality control
  • Advanced statistical methods for TCR repertoire diversity analysis in spatial context
  • Machine learning approaches for identifying spatially-enriched TCR clonotypes
  • Visualization tools for spatial TCR repertoire mapping

Collaborative Approach

This project exemplifies successful interdisciplinary collaboration:

  • Wet Lab Partnership: Close collaboration with experimental team members to optimize protocols
  • Method Co-development: Iterative development process ensuring computational methods align with experimental capabilities
  • Validation Studies: Comprehensive validation using both simulated and real experimental data

Impact and Significance

SpatialTCR will provide the research community with:

  • The first comprehensive platform for spatial TCR sequencing analysis
  • Novel insights into immune cell spatial organization
  • Tools for studying tissue-resident immune responses
  • Applications in cancer immunology, autoimmune diseases, and vaccine development

Recognition

Best Poster Presentation Award at GPB Omics & Bioinformatics Frontiers Symposium, Zhejiang, China (2025)

Presenters: Tian R†, Chen Y†#, Qi Y†, Xue Z, Yu Z, Liu W (†Co-first authors, #Presenting author)

References