Genetic analysis of Anaplastic Thyroid Cancer

Popular Abstract

Anaplastic thyroid cancer is one of the most fatal endocrine malignancies. The tumour is highly invasive and show aggressive growth patterns with poor prognosis. Thyroid tumourgenesis is poorly understood. Thyroid malignancy incidences are higher in women than men with a ratio of 2:1, the average age at diagnosis is 60, tumour size ranging between 6 cm to 9 cm, highly infiltrative on presentation and median survival of 5 months. The incidences of ATC has drastically reduced in the past decade, mainly due to the better management of well differentiated tumours of the thyroid gland.

Thyroid tumours can arise from follicular epithelial cells or para follicular cells. The well differentiated tumours, namely papillary thyroid cancer (PTC) and follicular thyroid cancer (FTC) are the common subtypes with excellent prognosis, whereas the poorly differentiated (PDTC) and the undifferentiated anaplastic variant are highly aggressive subtypes with poor prognosis, arising from follicular epithelial cells.

The genetic aberrations leading to this aggressive tumor subtype is unclear. To date, only 8 karyotypes from primary tumors and 8 from cell lines of ATC have been published. RET-PTC and PAX8-PPARγ are the common genetic rearrangements detected in thyroid malignancies; apart from these fusions identified, nothing much is known regarding the gene fusions in ATC. In this study, we have sequenced the transcriptome of 8 ATC cell lines, 3 PTC cell lines and 1 normal thyroid sample to find the genetic aberrations in ATC.

Fusion genes

Using the paired end RNA-Seq data, fusion genes were detected using ChimeraScan and SOAPFuse. The list probable fusions were filtered for pseudogenes, read through fusions, unannotated genes and the genes were selected on the criteria that they possess at least one spanning read or more than 10 flanking reads. The downsized list of workable fusion were tested and validated using RT-PCR and Sanger sequencing.

Primers were designed for each partner of the fusion gene, tested using RT-PCR and validated using Sanger sequencing. 24 out of 51 fusion transcripts tested were positive. No reciprocal fusion were detected. Most of the fusions were unique to specific sample; with one fusion C15ORF57-CBX3 was recurrent in 3 samples TC2, TC4 and TC12. FISH was performed to validate the findings. Even though were not able to validate the fusion using FISH, this approach was not sufficient to recognize it as an artefact.

Supervised hierarchal clustering was performed using Qlucore. 49 Genes were differentially expressed between ATC and PTC (Figure 1). Gene set enrichment analysis was also performed to find the pathways that were deregulated in ATC. KRAS and MAPK pathway signalling were upregulated, as ATC frequently harbour mutations which deregulate these pathways. Other pathways also found to be deregulated were cell cycle deregulation, regulation of apoptosis and regulation of gene expression. Our findings has helped us to achieve a better understanding of the complex acquired genetic aberrations in ATC.

Supervisor: Kajsa Paulsson
Master’s Degree Project in Molecular Biology 60 credits 2015
Department of Biology, Lund University

• author: Ravi, Naveen
• supervisor: Kajsa Paulsson
• organization: Degree Projects in Molecular Biology
• course: MOBT01 20142
• year: 2015
• type: H2 - Master's Degree (Two Years)
• subject: Biology and Life Sciences
• language: English
• id: 7441173
• date added to LUP: 2015-08-14 11:25:44
• date last changed: 2015-08-14 11:25:44