Year

2019

Degree Name

Doctor of Philosophy

Department

School of Chemistry and Molecular Bioscience

Abstract

Cutaneous squamous cell carcinoma (cSCC) is a common skin malignancy. Rates of cSCC in Australia are the highest in the world, approaching 800 cases/100 000 people per annum in North Queensland. Between 2-5% of cSCC will metastasise to regional lymph nodes, representing a higher clinical stage and requiring more aggressive and more morbid treatment, principally surgery and radiotherapy. Little is known of the molecular mechanisms of metastasis in cSCC, which makes a stratified method of appropriate surveillance challenging.

Patients with biopsy proven metastatic cSCC to lymph nodes of the head and neck were identified and recruited for fresh tumour and whole blood harvest. DNA extracted from 19 nodal metastases of cSCC was sequenced using whole genome sequencing. Following quality control, in particular verification of tumour cellularity, this number was reduced to 15 for the purposes of the study. Tumour DNA was compared to DNA from whole blood (germline) to establish the pattern of somatic variation.

Approaching 98% of the somatic short variants observed were in the noncoding regions of the genome in all samples. A mutational burden (207/Mb) greater than any other malignancy previously described underpinned the mutational landscape, characterised by UV implicated C>T single nucleotide variation in known oncogenes and tumour suppressor genes, a highly amplified genome and significant structural variation, particularly involving TTC28. Recurrent high impact short variants were seen in known cancer associated genes including TP53, CDKN2A and NOTCH1, but also in less well described but emerging genes of interest including MECOM, PTPRD, PLCB4, PCLO, CSMD3 and FAT4. Non-coding variants were particularly evident in the TERT promoter region identifying a variant pattern not previously found in cSCC. Significant amplification of microRNA miR-3147 was seen in all samples.

Prominent amplification of cancer associated long non-coding RNAs not previously identified in cSCC was observed. These included PVT1, MALAT1, HULC and NORAD. Expression changes resulting from somatic mutation were explored using co-extracted RNA on the NanoString platform. Prominent overexpression of key genes in cancer progression and metastasis was observed such as NDRG1, PIK3CA and SOX2.

This work has catalogued the extent and pattern of somatic variation in metastatic cSCC and has provided potential new targets that can now be investigated for their utility as biomarkers of progression and metastasis.

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Unless otherwise indicated, the views expressed in this thesis are those of the author and do not necessarily represent the views of the University of Wollongong.