Whole-exome sequencing and bioinformatic analyses revealed differences in gene mutation profiles in papillary thyroid cancer patients with and without benign thyroid goitre background

Abstract

BackgroundPapillary thyroid cancer (PTC) is the most common thyroid malignancy. Concurrent presence of cytomorphological benign thyroid goitre (BTG) and PTC lesion is often detected. Aberrant protein profiles were previously reported in patients with and without BTG cytomorphological background. This study aimed to evaluate gene mutation profiles to further understand the molecular mechanism underlying BTG, PTC without BTG background and PTC with BTG background.MethodsPatients were grouped according to the histopathological examination results: (i) BTG patients (n = 9), (ii) PTC patients without BTG background (PTCa, n = 8), and (iii) PTC patients with BTG background (PTCb, n = 5). Whole-exome sequencing (WES) was performed on genomic DNA extracted from thyroid tissue specimens. Nonsynonymous and splice-site variants with MAF of ≤ 1% in the 1000 Genomes Project were subjected to principal component analysis (PCA). PTC-specific SNVs were filtered against OncoKB and COSMIC while novel SNVs were screened through dbSNP and COSMIC databases. Functional impacts of the SNVs were predicted using PolyPhen-2 and SIFT. Protein-protein interaction (PPI) enrichment of the tumour-related genes was analysed using Metascape and MCODE algorithm.ResultsPCA plots showed distinctive SNV profiles among the three groups. OncoKB and COSMIC database screening identified 36 tumour-related genes including BRCA2 and FANCD2 in all groups. BRAF and 19 additional genes were found only in PTCa and PTCb. “Pathways in cancer”, “DNA repair” and “Fanconi anaemia pathway” were among the top networks shared by all groups. However, signalling pathways related to tyrosine kinases were the most significantly enriched in PTCa while “Jak-STAT signalling pathway” and “Notch signalling pathway” were the only significantly enriched in PTCb. Ten SNVs were PTC-specific of which two were novel; DCTN1 c.2786C>G (p.Ala929Gly) and TRRAP c.8735G>C (p.Ser2912Thr). Four out of the ten SNVs were unique to PTCa.ConclusionDistinctive gene mutation patterns detected in this study corroborated the previous protein profile findings. We hypothesised that the PTCa and PTCb subtypes differed in the underlying molecular mechanisms involving tyrosine kinase, Jak-STAT and Notch signalling pathways. The potential applications of the SNVs in differentiating the benign from the PTC subtypes requires further validation in a larger sample size.

Bayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO)

“…Previously, XIST had been observed to promote oncogenic activities in papillary thyroid carcinomas (PTC) [42]. Among genes highly targeted in males, tumor suppresor gene KDM6A is known to regulate multiple genes involved in immune response, suggesting its potential influence on the risks of developing various autoimmune conditions [43]; Among other genes highly targeted in males, PCM1 mutation has also been associated with PTC [44]; while mutation in KMT2C has been identified as a molecular marker for primary thyroid osteosarcoma [45]. Additionally, overexpression of SOS1 , which also showed higher targeting in males, have been found to promote cell proliferation and cell apoptosis in PTC cells [46].…”

Changes in antioxidant status and DNA repair capacity are corroborated with molecular alterations in malignant thyroid tissue of patients with papillary thyroid cancer

“…Earlier studies had reported significantly higher oxidative stress in a group of PTC patients compared to a group of BTG patients ( Erdamar et al, 2010 ; Ramli et al, 2017 ), suggesting the role of oxidative stress in PTC tumourigenesis. Furthermore, differences in gene alteration patterns had been detected between BTG and PTC patients ( Eng et al, 2023 ), providing insights into the molecular mechanisms underlying the benign-to-malignant transformation. However, studies evaluating and comparing oxidative stress and antioxidant capacity between benign and malignant thyroid lesions within the same patient are rarely performed.…”

“…The frequency of point mutations in DNA has been associated with its 8-oxoG content ( Kuchino et al, 1987 ; Ribeiro et al, 1994 ). DNA damage coupled with aberrant DNA repair-related pathways, has been suggested to initiate thyroid tumourigenesis and play a crucial role in PTC progression from BTG ( Ameziane El Hassani et al, 2019 ; Eng et al, 2023 ). OGG1 codes for 8-oxoguanine glycosylase (OGG1), which participates in the BER pathway for the mutagenic 8-oxoG ( Bruner et al, 2000 ; Izumi et al, 2003 ; Banerjee et al, 2005 ).…”

“…The CRAVAT filtering process identified four variants in PTC lesions, namely BRAF -rs113488022 ( BRAF V600E ), MAP2K7 -rs2145142862, BCR -rs372013175 and CD24 p.Gln23fs mutation. BRAF V600E has been widely found in various types of neoplasms, including PTC ( Nam et al, 2012 ; Silver et al, 2021 ; Eng et al, 2023 ), and its negative impact on BRAF kinase and the MAPK/ERK pathway is well-known ( Cantwell-Dorris et al, 2011 ; Cohen et al, 2021 ). The variant MAP2K7 -rs2145142862 is less commonly reported but is predicted to have a harmful effect based on in silico functional analysis.…”

“…The development of PTC had been strongly linked to the oncogenic activation of signalling pathways that contributes to deviant cellular processes, such as cell proliferation, differentiation, apoptosis, and survival (Abdullah et al, 2019). A previous study had also demonstrated the gene alterations in signalling pathways to be an important event in PTC transformation (Eng et al, 2023). Among the biological processes that differentially enriched between BTG and PTC lesions, "regulation of MAPK cascade", "positive regulation of ERK1 and ERK2 cascade" and "negative regulation of reactive oxygen species metabolic process" were the only terms that significantly enriched in PTC lesions.…”