In vivo single-cell CRISPR uncovers distinct TNF programmes in tumour evolution

Area of Science:

• Cancer Biology
• Genetics
• Immunology

Background:

• Tumorigenesis involves clonal expansions driven by mutations, but mechanisms leading to malignant transformation remain unclear.
• Understanding clonal dynamics in normal tissues is crucial for deciphering early cancer development.

Purpose of the Study:

• To systematically investigate tissue-wide clonal dynamics and gene programs during tumor evolution using in vivo single-cell CRISPR.
• To uncover mechanisms driving clonal expansions and malignant transformation in squamous cell carcinoma.

Main Methods:

• Developed an in vivo single-cell CRISPR strategy coupled with ultrasound-guided in utero lentiviral microinjections.
• Utilized longitudinal monitoring via single-cell RNA sequencing and guide capture to analyze clonal expansions.
• Investigated the role of 150 frequently mutated squamous cell carcinoma genes.

Main Results:

• Identified a tumor necrosis factor (TNF) signaling module, involving TNF receptor 1 and macrophages, as a driver of clonal expansions in epithelial tissues.
• Observed downregulation of the TNF signaling module during tumorigenesis, with a switch to an autocrine TNF program in invasive cancer cells.
• Demonstrated that the autocrine TNF program mediates invasive properties and correlates with shorter patient survival.

Conclusions:

• In vivo single-cell CRISPR screening is a powerful tool for studying mammalian tissue dynamics.
• Distinct TNF signaling programs play critical roles in tumor evolution, clonal expansion, and invasion.
• Understanding the interplay between clonal expansion and tumorigenesis is vital for cancer research.