Characterising peripheral responses to immune checkpoint inhibitors

Thesis

The introduction of immune checkpoint blockade (ICB) therapy for metastatic melanoma (MM) has dramatically improved survival in this patient group. However, only some patients experience durable clinical response, and many will develop immune-related adverse events (irAEs). The identification of predictive biomarkers which can be assessed in a biopsy-free manner may facilitate early detection of non-responders and optimal targeting of treatment.

There is emerging evidence to show that the circulating monocyte population has a prognostic and predictive role in the context of ICB, but this has yet to be fully characterised. Circulating-cell free DNA (cfDNA) is derived predominantly from leukocytes, but in patients with cancer may comprise circulating tumour DNA (ctDNA). Assessment of epigenetic cfDNA profiles may provide tumour profiling and reflect immune responses as a ‘liquid biopsy’. Although epigenetic tumour profiles have diagnostic and prognostic utility across multiple cancer types, epigenetic cfDNA profiles in MM and following ICB are not yet characterised.

In this thesis I dissect both circulating myeloid and epigenetic cfDNA profiles in MM patients. Firstly, I explore MM-associated monocyte transcriptomic profiles with bulk RNA sequencing (RNA-seq), characterising on-treatment modulation and association with clinical response. I then use scRNA-seq to explore the transcriptional heterogeneity of the peripheral monocyte compartment, and describe monocyte subset-wise responses to ICB. Lastly, I characterise epigenetic cfDNA profiles in this cohort, revealing distinct 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) cfDNA profiles in MM and following ICB.

In this thesis I present novel findings regarding peripheral myeloid and epigenetic cfDNA responses to ICB and demonstrate that these profiles may have potential diagnostic and predictive clinical utility.

Authors: Cooper, R

• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: immune checkpoint blockade; melanoma; monocytes; circulating epigenetic cell-free DNA profiles; single-cell RNA sequencing
• Subjects: Immune response; Epigenetics; Monocytes; Melanoma