Non-CpG sites preference in G:C > A:T transition of TP53 in gastric cancer of Eastern Europe (Poland, Romania and Hungary) compared to East Asian countries (China and Japan)

Abstract

Aim Mutation spectrum of TP53 in gastric cancer (GC) has been investigated world-widely, but a comparison of mutation spectrum among GCs from various regions in the world are still sparsely documented. In order to identify the difference of TP53 mutation spectrum in GCs in Eastern Europe and in East Asia, we sequenced TP53 in GCs from Eastern Europe, Lujiang (China), and Yokohama, Kanagawa (Japan) and identified the feature of TP53 mutations of GC in these regions. Subjects and method In total, 689 tissue samples of GC were analyzed: 288 samples from East European populations (25 from Hungary, 71 from Poland and 192 from Romania), 268 from Yokohama, Kanagawa, Japan and 133 from Lujiang, Anhui province, China. DNA was extracted from FFPE tissue of Chinese, East European cases; and from frozen tissue of Japanese GCs. PCR products were direct-sequenced by Sanger method, and in ambiguous cases, PCR product was cloned and up to 8 clones were sequenced. We used No. NC_000017.11(hg38) as the reference sequence of TP53. Mutation patterns were categorized into nine groups: six base substitutions, insertion, deletion and deletion-insertion. Within G:C > A:T mutations the mutations in CpG and non-CpG sites were divided. The Cancer Genome Atlas data (TCGA, ver.R20, July, 2019) having somatic mutation list of GCs from Whites, Asians, and other ethnicities were used as a reference for our data. Results The most frequent base substitutions were G:C > A:T transition in all the areas investigated. The G:C > A:T transition in non-CpG sites were prominent in East European GCs, compared with Asian ones. Mutation pattern from TCGA data revealed the same trend between GCs from White (TCGA category) vs Asian countries. Chinese and Japanese GCs showed higher ratio of G:C > A:T transition in CpG sites and A:T > G:C mutation was more prevalent in Asian countries. Conclusion The divergence in mutation spectrum of GC in different areas in the world may reflect various pathogeneses and etiologies of GC, region to region. Diversified mutation spectrum in GC in Eastern Europe may suggest GC in Europe has different carcinogenic pathway of those from Asia.

Clinicopathological Characteristics and Mutational Landscape of APC, HOXB13, and KRAS among Rwandan Patients with Colorectal Cancer

“…After amplification, PCR products were purified and sequenced as described in a previous study [48]. Briefly, PCR products were purified using ExoSAP-IT (ThermoFisher Scientific).…”

“…Transformed cells were grown overnight on X-gal/IPTG LB agar plates described above, allowing the selection of blue/white colonies. White colonies (i.e., eight subclones) were then selected [48] and each cultured in 50 µL of liquid LB medium containing ampicillin at a final concentration of 100 µg/µL for 1 h and 30 min at 37 • C. The resulting cultures were centrifuged, and 1 µL of the lower phase was used for PCR in a 20 µL volume using HotStartTaq (Qiagen) polymerase enzyme and pGEM Easy V-2930F (5 -AGG CGA TTA AGT TGG GTA ACG-3 ) and pGEM Easy V-134R (5 -CAA GCT ATG CAT CCA ACG C-3 ) primers. The resulting PCR products were then purified and sequenced as described above.…”

TP53 mutations in Romanian patients with colorectal cancer

“…Our data are too small to give any insight that the mutations in CRC in Romania may reflect known or unknown specific environmental or dietary exposures, but the accumulation of the mutation spectrum would highlight the risk and the reason for the increase of CRC in Romania in the future. Recently, we observed the difference in TP53 mutation spectrum between Eastern Europe and East Asia [ 25 ], and it would be interesting to see the status of TP53 mutation in CRC in East Asia for comparison.…”

“…DNA from exons number 2 to 11 of TP53 [ 24 ] was amplified using HotStarTaq (Qiagen) and sequenced in the forward and reverse directions by the Sanger sequencing method using the BigDye Terminator Cycle Sequencing Reaction Kit, ver.3.1 and ABI 3130xL Genetic Analyzer (ThermoFisher Scientific) as described by Natsume et al [ 25 ].…”

Socioeconomic inequality in organized and opportunistic screening for gastric cancer: results from the Korean National Cancer Screening Survey 2009–2022

“…This figure was much lower in Western countries and regions where the ASR was about 7 per 100,000 in Southern Europe, Central America, and only 4.6 in Northern Europe ( 1 ). The differences are due to the various socio- demographic characteristics, dietary behaviors, prevalence of Helicobacter pylori infection, and genetic factors ( 2–4 ). Although its incidence rate has recently been decreasing, GC remains the fourth leading cause of cancer-related deaths worldwide ( 1 ).…”