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 an...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-01-01
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| Series: | Genes and Environment |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s41021-022-00257-y |
| _version_ | 1828069445102206976 |
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| author | Hiroko Natsume Kinga Szczepaniak Hidetaka Yamada Yuji Iwashita Marta Gędek Jelena Šuto Keiko Ishino Rika Kasajima Tomonari Matsuda Felix Manirakiza Augustin Nzitakera Yijia Wu Nong Xiao Qiong He Wenwen Guo Zhenming Cai Tsutomu Ohta Tıberiu Szekely Zoltan Kadar Akiko Sekiyama Takashi Oshima Takaki Yoshikawa Akira Tsuburaya Nobuhito Kurono Yaping Wang Yohei Miyagi Simona Gurzu Haruhiko Sugimura |
| author_facet | Hiroko Natsume Kinga Szczepaniak Hidetaka Yamada Yuji Iwashita Marta Gędek Jelena Šuto Keiko Ishino Rika Kasajima Tomonari Matsuda Felix Manirakiza Augustin Nzitakera Yijia Wu Nong Xiao Qiong He Wenwen Guo Zhenming Cai Tsutomu Ohta Tıberiu Szekely Zoltan Kadar Akiko Sekiyama Takashi Oshima Takaki Yoshikawa Akira Tsuburaya Nobuhito Kurono Yaping Wang Yohei Miyagi Simona Gurzu Haruhiko Sugimura |
| author_sort | Hiroko Natsume |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T00:20:08Z |
| format | Article |
| id | doaj.art-cbf4ee58a8bd45a5ab90f396841a9a36 |
| institution | Directory Open Access Journal |
| issn | 1880-7062 |
| language | English |
| last_indexed | 2024-04-11T00:20:08Z |
| publishDate | 2023-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Genes and Environment |
| spelling | doaj.art-cbf4ee58a8bd45a5ab90f396841a9a362023-01-08T12:20:55ZengBMCGenes and Environment1880-70622023-01-0145111310.1186/s41021-022-00257-yNon-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)Hiroko Natsume0Kinga Szczepaniak1Hidetaka Yamada2Yuji Iwashita3Marta Gędek4Jelena Šuto5Keiko Ishino6Rika Kasajima7Tomonari Matsuda8Felix Manirakiza9Augustin Nzitakera10Yijia Wu11Nong Xiao12Qiong He13Wenwen Guo14Zhenming Cai15Tsutomu Ohta16Tıberiu Szekely17Zoltan Kadar18Akiko Sekiyama19Takashi Oshima20Takaki Yoshikawa21Akira Tsuburaya22Nobuhito Kurono23Yaping Wang24Yohei Miyagi25Simona Gurzu26Haruhiko Sugimura27Department of Tumor Pathology, Hamamatsu University School of MedicineDepartment of Tumor Pathology, Hamamatsu University School of MedicineDepartment of Tumor Pathology, Hamamatsu University School of MedicineDepartment of Tumor Pathology, Hamamatsu University School of MedicineDepartment of Tumor Pathology, Hamamatsu University School of MedicineDepartment of Tumor Pathology, Hamamatsu University School of MedicineDepartment of Tumor Pathology, Hamamatsu University School of MedicineThe Center for Cancer Genome Medicine, Kanagawa Cancer CenterResearch Center for Environmental Quality Management, Kyoto UniversityDepartment of Tumor Pathology, Hamamatsu University School of MedicineDepartment of Tumor Pathology, Hamamatsu University School of MedicineLujiang People HospitalJiangsu Key Laboratory of Molecular Medicine, Nanjing University School of MedicineDepartment of Pathology, The Second Affiliated Hospital of Nanjing Medical UniversityJiangsu Key Laboratory of Molecular Medicine, Nanjing University School of MedicineJiangsu Key Laboratory of Molecular Medicine, Nanjing University School of MedicineDepartment of Tumor Pathology, Hamamatsu University School of MedicineDepartment of Pathology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, Targu MuresDepartment of Oncology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, Targu MuresDepartment of Clinical Laboratory, Kanagawa Cancer CenterDepartment of Gastrointestinal Surgery, Kanagawa Cancer CenterDepartment of Gastric Surgery, National Cancer Center HospitalDepartment of Surgery, Ozawa HospitalDepartment of Chemistry, Hamamatsu University School of MedicineJiangsu Key Laboratory of Molecular Medicine, Nanjing University School of MedicineMolecular Pathology and Genetics Division, Kanagawa Cancer Center Research InstituteDepartment of Pathology, George Emil Palade University of Medicine, Pharmacy, Sciences and Technology, Targu MuresDepartment of Tumor Pathology, Hamamatsu University School of MedicineAbstract 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.https://doi.org/10.1186/s41021-022-00257-yGastric cancerTP53Molecular epidemiologyMutation spectrumMutation signatureGene-environmental interaction |
| spellingShingle | Hiroko Natsume Kinga Szczepaniak Hidetaka Yamada Yuji Iwashita Marta Gędek Jelena Šuto Keiko Ishino Rika Kasajima Tomonari Matsuda Felix Manirakiza Augustin Nzitakera Yijia Wu Nong Xiao Qiong He Wenwen Guo Zhenming Cai Tsutomu Ohta Tıberiu Szekely Zoltan Kadar Akiko Sekiyama Takashi Oshima Takaki Yoshikawa Akira Tsuburaya Nobuhito Kurono Yaping Wang Yohei Miyagi Simona Gurzu Haruhiko Sugimura 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) Genes and Environment Gastric cancer TP53 Molecular epidemiology Mutation spectrum Mutation signature Gene-environmental interaction |
| title | 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) |
| title_full | 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) |
| title_fullStr | 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) |
| title_full_unstemmed | 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) |
| title_short | 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) |
| title_sort | 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 |
| topic | Gastric cancer TP53 Molecular epidemiology Mutation spectrum Mutation signature Gene-environmental interaction |
| url | https://doi.org/10.1186/s41021-022-00257-y |
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