Massively parallel interrogation of human functional variants modulating cancer immunosurveillance

Area of Science:

• Cancer immunology
• Genomics
• Molecular biology

Background:

• Immune checkpoint blockade (ICB) therapy, targeting PD-1/PD-L1, has transformed cancer treatment.
• Tumor cell expression of PD-L1 and HLA-I critically influences ICB efficacy.
• Somatic mutations impacting these regulators are linked to tumor progression and treatment response, yet a comprehensive understanding is lacking.

Purpose of the Study:

• To systematically identify and characterize cancer mutations that modulate PD-L1 and HLA-I expression.
• To explore the functional impact of these mutations on cancer immunosurveillance and ICB response.
• To provide a resource for guiding clinical diagnosis and developing novel cancer therapies.

Main Methods:

• Utilized the ABEmax system to create a large-scale sgRNA library (approx. 820,000 sgRNAs) targeting genome-wide serine, threonine, and tyrosine residues.
• Conducted systematic screens to identify mutations affecting PD-L1 or HLA-I expression.
• Investigated functional mechanisms including effects on mRNA/protein stability, DNA binding, protein interactions, and enzymatic activity.

Main Results:

• Discovered thousands of novel mutations that decrease or increase PD-L1 or HLA-I expression.
• Identified mutations impacting diverse cellular processes beyond phosphorylation, such as gene regulation and protein stability.
• Uncovered mutations concurrently modulating both PD-L1 and HLA-I, exemplified by SETD2_Y1666.
• Demonstrated that SETD2_Y1666 induces consistent phenotypic effects and enhances immunotherapy efficacy in preclinical models.

Conclusions:

• This research provides an extensive catalog of functional residues regulating cancer immune evasion.
• The findings offer valuable insights for improving clinical diagnosis and patient stratification for ICB therapy.
• The identified mutations and mechanisms pave the way for developing targeted cancer immunotherapies.