The identification of novel therapy options in difficult to treat non-small cell Lung cancer

Robbins, Helen Louise ORCID: 0000-0001-8283-0830 (2024). The identification of novel therapy options in difficult to treat non-small cell Lung cancer. University of Birmingham. Ph.D.

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Abstract

Overview:
There is a lack of treatment options for smoking related lung cancer. It is important to explore reasons for failure of apparently rational targeted therapies and to identify new avenues for treatment. This thesis focuses on three common subsets of smoking related lung cancer: STK11-mutant lung adenocarcinoma, KRAS-mutant lung adenocarcinoma and 3q amplified squamous cell lung cancer. In STK11-mutant lung cancer, this thesis seeks to explore resistance to mTORC1/2 inhibition. In KRAS-mutant lung cancer, this thesis seeks to identify predictors of sensitivity to CDK4/6 inhibition. In 3q-amplified squamous cell lung cancer, this thesis seeks to identify key driver (or drivers) within the 3q amplicon, and to identify potential targeting options for this driver through both supervised and unsupervised approaches.

Methods:
Serial ctDNA samples were analysed from patients treated in the National Lung Matrix Trial from STK11-mutant lung adenocarcinoma patients treated with vistusertib (mTORC1/2 inhibition) and KRAS-mutant lung adenocarcinoma treated with palbociclib (CDK4/6 inhibition). Reactivation of PI3K/Akt signalling following prolonged treatment with mTORC1/2 inhibition in vitro was assessed using western blotting. Critical drivers on the 3q amplicon were identified using genome-wide CRISPR knockout data from DepMap, with validation using siRNA. Western blotting was used to assess the impact of drugs on SOX2 protein expression in squamous cell lung cancer cells, with parallel assessment of the impact on drugs viability. Finally, novel strategies to modulate SOX2 expression in 3q amplified squamous cell lung cancer was explored using a FACS assisted genome wide CRISPR knockout screen.

Key Results:
SMARCA4 and FOXP1 mutations become enriched following treatment with vistusertib in patients with STK11-mutant lung adenocarcinoma, potentially reflecting a novel resistance mechanism. Analysis of KRAS-mutant lung adenocarcinoma treated with palbociclib suggests that absence of KDR variants, and presence of MTOR or CHEK2 mutations may predict better prognosis, potentially reflecting a new cohort of patients who may benefit from CDK4/6 inhibitor therapy. In 3q amplified squamous cell lung cancer, SOX2 was identified as a critical driver within 3q. BRD4 inhibition and CDK7 inhibition represent potential strategies to modulate SOX2 protein expression in the context of 3q amplification. The FACS-assisted genome wide CRISPR knockout screen identifies PCNA as an important regulator of SOX2, therefore targeting PCNA is a potential additional strategy for indirect targeting of SOX2.

Conclusions:
Smoking related lung cancer remains a challenge for personalised medicine. SOX2 is a crucial component of the 3q amplicon and represents a candidate for targeted therapies. Identification of co-mutations that may drive resistance and sensitivity to CDK4/6 and mTORC1/2 inhibition may allow better selection of patients who may benefit from these targeted therapies.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

Supervisor(s):