Search

Your search keyword '"Teiichi Sugiura"' showing total 272 results
Start Over Author "Teiichi Sugiura" Database OpenAIRE
272 results on '"Teiichi Sugiura"'

2. Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Keiichi Ohshima, Takeshi Nagashima, Keiichi Fujiya, Keiichi Hatakeyama, Yuko Watanabe, Kimiko Morimoto, Fukumi Kamada, Yuji Shimoda, Sumiko Ohnami, Akane Naruoka, Masakuni Serizawa, Shumpei Ohnami, Hirotsugu Kenmotsu, Akio Shiomi, Yasuhiro Tsubosa, Etsuro Bando, Teiichi Sugiura, Takashi Sugino, Masanori Terashima, Katsuhiko Uesaka, Kenichi Urakami, Yasuto Akiyama, and Ken Yamaguchi

Abstract

Gastrointestinal stromal tumors (GIST) with KIT exon 11 deletions involving in codons 557–558 (KIT Δ557–558) exhibit higher proliferation rates and shorter disease-free survival times compared with GISTs with other KIT exon 11 mutations. We analyzed 30 GIST cases and observed genomic instability and global DNA hypomethylation only in high-risk malignant GISTs with KIT Δ557–558. Whole-genome sequencing revealed that the high-risk malignant GISTs with KIT Δ557–558 (12 cases) had more structural variations (SV), single-nucleotide variants, and insertions and deletions compared with the low-risk, less malignant GISTs with KIT Δ557–558 (six cases) and the high-risk (six cases) or low-risk (6 cases) GISTs with other KIT exon 11 mutations. The malignant GISTs with KIT Δ557–558 showed higher frequency and significance in copy number (CN) reduction on chromosome arms 9p and 22q, and 50% of them had LOH or CN-dependent expression reduction in CDKN2A. In addition, SVs with driver potential were detected in 75% of them, in which AKT3 and MGMT were recurrently identified. Genome-wide DNA methylation and gene expression analyses showed global intergenic DNA hypomethylation, SNAI2 upregulation, and higher expression signatures, including p53 inactivation and chromosomal instability, as characteristics of malignant GISTs with KIT Δ557–558 that distinguished them from other GISTs. These genomic and epigenomic profiling results revealed that KIT Δ557–558 mutations are associated with increased genomic instability in malignant GISTs. Significance: We present genomic and epigenomic insights into the malignant progression of GISTs with KIT exon 11 deletions involving in 557–558, demonstrating their unique chromosomal instability and global intergenic DNA hypomethylation.

Published
2023

3. Surgical Outcomes of Pancreatectomy with Resection of the Portal Vein and/or Superior Mesenteric Vein and Jejunal Vein for Pancreatic Head Cancer

Author

Yuichi, Nagakawa, Jin-Young, Jang, Manabu, Kawai, Song Cheol, Kim, Yosuke, Inoue, Yasuhiro, Yabushita, Jin Seok, Heo, Masayuki, Honda, Teiichi, Sugiura, Shingo, Kagawa, Aoi, Hayasaki, Wooil, Kwon, Kenichiro, Uemura, Ho-Seong, Han, Motokazu, Sugimoto, Yasuhisa, Ando, Masafumi, Nakamura, Keita, Wada, Yusuke, Kumamoto, Hiroaki, Osakae, Akihiko, Tsuchida, Yoo-Seok, Yoon, Joon Seong, Park, Hiroki, Yamaue, and Itaru, Endo

Subjects
Surgery
Abstract

To investigate the safety and survival benefits of portal vein and/or superior mesenteric vein (PV/SMV) resection with jejunal vein resection (JVR) for pancreatic ductal adenocarcinoma (PDAC).Few studies have shown the surgical outcome and survival of pancreatic resection with JVR, and treatment strategies for patients with PDAC suspected of jejunal vein (JV) infiltration remain unclear.In total, 1260 patients who underwent pancreatectomy with PV/SMV resection between 2013 and 2016 at 50 facilities were included; treatment outcomes were compared between the PV/SMV group (PV/SMV resection without JVR; n = 824), PV/SMV-J1 V group (PV/SMV resection with first jejunal vein resection; n = 394), and PV/SMV-J2,3 V group (PV/SMV resection with second jejunal vein or later branch resection; n = 42).Postoperative complications and mortality did not differ between the three groups. The postoperative complication rate associated with PV/SMV reconstruction was 11.9% in PV/SMV group, 8.6% in PV/SMV-J1 V group, and 7.1% in PV/SMV-J2,3 V group; there were no significant differences among the three groups. Overall survival did not differ between PV/SMV and PV/SMV-J1 V groups (median survival; 29.2 months vs. 30.9 months. p = 0.60). Although PV/SMV-J2,3 V group had significantly shorter survival than PV/SMV group who underwent upfront surgery (p = 0.05), no significant differences in overall survival of patients who received preoperative therapy. Multivariate survival analysis revealed that adjuvant therapy and R0 resection were independent prognostic factors in all groups.PV/SMV resection with JVR can be safely performed and may provide satisfactory overall survival with the pre-and postoperative adjuvant therapy.

Published
2023

4. Clinical significance of immunocytochemical staining for peritoneal lavage cytology in pancreatic cancer

Author

Hidemasa Kubo, Katsuhisa Ohgi, Nobuyuki Ohike, Kiyoshi Tone, Tomoko Norose, Teiichi Sugiura, Ryo Ashida, Mihoko Yamada, Shimpei Otsuka, and Katsuhiko Uesaka

Subjects
Pancreatic Neoplasms, Staining and Labeling, Humans, Peritoneal Lavage, Surgery, Prognosis, Retrospective Studies, Carcinoma, Pancreatic Ductal
Abstract

Peritoneal lavage cytology for pancreatic ductal adenocarcinoma is conducted with both an intraoperative rapid diagnosis by Papanicolaou staining (cytology-rapid) and a final diagnosis by immunocytochemical staining at a later date (cytology-final) in our hospital. However, the clinical significance of cytology-final has not yet been elucidated.A total of 675 pancreatic ductal adenocarcinoma patients who underwent pancreatectomy and cytology between 2002 and 2018 were retrospectively reviewed. Diagnostic results of cytology-rapid and cytology-final and survival outcomes were analyzed.A total of 43 patients (6.4%) were diagnosed as cytology-rapid (+), and all of them were ultimately diagnosed as cytology-final (+). Among the 632 patients with cytology-rapid (-), 19 (3.0%) were eventually diagnosed as cytology-final (+). The overall survival of patients with cytology-rapid (+) and that of patients with cytology-rapid (-) did not differ to a statistically significant extent (median survival time 26.4 vs 32.9 months; P = .106). In contrast, the overall survival of patients who were diagnosed as a false-negative result by cytology-rapid was significantly worse than that of patients diagnosed as a true negative (18.7 vs 34.8 months; P = .031). The overall survival of patients with cytology-final (+) was significantly worse than that of patients with cytology-final (-) (23.6 vs 34.8 months; P = .012). A multivariate analysis showed that cytology-final (+) was an independent prognostic factor for the OS (hazard ratio = 1.43; P = .049), whereas cytology-rapid (+) was not.Immunocytochemical staining may be a useful complement to a diagnosis of cytology by conventional Papanicolaou staining in pancreatic ductal adenocarcinoma patients.

Published
2022

6. Clinical Outcomes of Inside Stents and Conventional Plastic Stents as Bridge-to-Surgery Options for Malignant Hilar Biliary Obstruction

Author

Hirotoshi Ishiwatari, Takanori Kawabata, Hiroki Kawashima, Yousuke Nakai, Shin Miura, Hironari Kato, Hideyuki Shiomi, Nao Fujimori, Takeshi Ogura, Osamu Inatomi, Kensuke Kubota, Toshio Fujisawa, Mamoru Takenaka, Hiroshi Mori, Kensaku Noguchi, Yuki Fujii, Teiichi Sugiura, Noboru Ideno, Tomoki Nakafusa, Atsushi Masamune, Hiroyuki Isayama, and Naoki Sasahira

Subjects
Physiology, Gastroenterology
Abstract

The appropriate method of preoperative endoscopic biliary drainage (EBD) for cholangiocarcinoma with hilar biliary obstruction remains controversial. The inside-stent technique is a method of placing plastic stents entirely inside the bile duct. Several studies of patients with unresectable stage have reported longer stent patency compared with conventional endoscopic biliary stenting (EBS). Inside-stent techniques have been introduced as a bridge-to-surgery option and as an alternative to conventional EBS.We aimed to evaluate the clinical outcomes of inside stent use and conventional EBS.During this retrospective multicenter study, we reviewed consecutive patients with cholangiocarcinoma who underwent radical surgery after conventional EBS or inside-stent insertion. Adverse event (AE) rates after EBD and post-surgical AEs were compared. A multivariable analysis was performed to identify factors affecting cholangitis after EBD.Conventional EBS and inside-stent procedures were performed for 56 and 73 patients, respectively. Patient backgrounds were similar between groups, except for percutaneous transhepatic portal vein embolization. The waiting time before surgery was similar between groups (28.5 days vs. 30 days). There were no significant differences in the cholangitis rate (21.4% vs. 26.0%; P = 0.68) and all AEs (25.0% vs. 30.1%; P = 0.56) between groups. The post-surgical AE rate was similar between the groups. The multivariable analysis found that preprocedural cholangitis was a risk factor for cholangitis after EBD (odds ratio: 5.67; 95% confidence interval: 1.61-19.9).The outcomes of inside-stent techniques and conventional EBS for the management of preoperative EBD are comparable for patients with cholangiocarcinoma.

Published
2022

8. Converted-hepatopancreatoduodenectomy for an intraoperative positive ductal margin after pancreatoduodenectomy in distal cholangiocarcinoma

Author

Ryusei Yamamoto, Teiichi Sugiura, Ryo Ashida, Katsuhisa Ohgi, Mihoko Yamada, Shimpei Otsuka, Yukiyasu Okamura, and Katsuhiko Uesaka

Subjects
Cholangiocarcinoma, Bile Ducts, Intrahepatic, Bile Duct Neoplasms, Bile Ducts, Extrahepatic, Humans, Hepatectomy, Margins of Excision, Surgery, Pancreaticoduodenectomy, Retrospective Studies
Abstract

Pancreatoduodenectomy (PD) is the standard treatment for distal cholangiocarcinoma, and a negative ductal margin (DM0) is indispensable for the long-term survival. When intraoperative frozen sections of ductal margin after PD are positive, converted-hepatopancreatoduodenectomy (C-HPD) is the final option available to gain an additional ductal margin. However, the efficacy of C-HPD remains unclear.Patients who underwent PD or C-HPD for distal cholangiocarcinoma between 2002 and 2019 were analyzed. The type of hepatectomy in C-HPD was restricted to left hepatectomy to prevent posthepatectomy liver failure.Of 203 patients who underwent PD for distal cholangiocarcinoma, 49 patients exhibited intraoperative positive ductal margin (DM1) after PD. Eleven patients underwent C-HPD for intraoperative DM1 after PD, in which intraoperative DM1 with invasive carcinoma (DM1inv) was observed in 3 patients, and intraoperative DM1 with carcinoma in situ (DM1cis) was observed in 8 patients. The median additional ductal margin yielded by C-HPD was 9 mm (interquartile range 7-13 mm). C-HPD eradicated intraoperative DM1inv in 3 patients, with 2 patients showing DM0 and 1 patient showing DM1cis. Regarding 8 patients who underwent C-HPD for intraoperative DM1cis, 4 patients had DM0, but the others had DM1cis. C-HPD was associated with a high complication rate, but no mortality was observed. The median survival time of patients who underwent C-HPD was 48.8 months.C-HPD was able to safely eradicate intraoperative DM1inv after PD. However, the length of the resected bile duct according to C-HPD may not be sufficient to remove intraoperative DM1cis after PD.

Published
2022

9. The clinical benefits of performing staging laparoscopy for pancreatic cancer treatment

Author

Taisuke Imamura, Katsuhisa Ohgi, Yukiyasu Okamura, Teiichi Sugiura, Takaaki Ito, Yusuke Yamamoto, Ryo Ashida, Shimpei Otsuka, Shunsuke Tamura, and Katsuhiko Uesaka

Subjects
Pancreatic Neoplasms, Hepatology, Endocrinology, Diabetes and Metabolism, Gastroenterology, Humans, Reproducibility of Results, Laparoscopy, Pancreatic Hormones, Neoplasm Staging
Abstract

The indications and benefits derived from staging laparoscopy (SL) for pancreatic cancer (PC) remain controversial.This study involved PC patients in whom resection had been considered possible between 2009 and 2020. We classified the patients into before 2014 (training set) and 2014 and later (validation set) groups, as SL was introduced in 2014, in our institution. In the training set, the predictors of non-curative factors were investigated, and reproducibility was confirmed in the validation set. In addition, the outcomes were compared between the datasets.A total of 802 patients were classified into the training set (n = 241) and validation set (n = 561). In the training set, pancreatic body or tail tumors (odds ratio [OR]: 2.62: P = 0.039), CA19-9 88 U/ml (OR: 3.21: P = 0.018) and a tumor diameter36 mm (OR: 6.07; P 0.001) were independent predictors of non-curative factors. The increased rate of non-curative factors was confirmed as the number of predictors increased in the validation set. The curative resection (CR) rate was significantly higher in the validation set than in the training set (P = 0.035). Although there was no significant difference in the OS in the not-resected group (P = 0.895), the OS in the CR and non-CR group was significantly better in the validation set than in the training set (CR, P 0.001; non-CR, P 0.001).The findings suggest potential candidates for SL and revealed improved outcomes by the advent of treatment strategies including SL.

Published
2022

12. Acquired hemophilia A developing in the perioperative period of pancreatoduodenectomy: a report of two cases

Author

Hidemasa Kubo, Ryo Ashida, Katsuhisa Ohgi, Masafumi Fukaya, Naoki Umezaki, Mihoko Yamada, Shimpei Otsuka, Katsuhiko Uesaka, and Teiichi Sugiura

Subjects
General Economics, Econometrics and Finance
Abstract

Background Acquired hemophilia A (AHA) is a rare disease characterized by a prolonged activated partial thromboplastin time (aPTT) and the production of coagulation factor VIII inhibitors. We encountered two cases of AHA in the perioperative period of pancreatoduodenectomy (PD). Case presentation Case 1: A 76-year-old woman with intraductal papillary mucinous carcinoma developed acute cholecystitis 5 days before PD. Despite immediate improvement in her acute cholecystitis with biliary drainage and antibiotics, her aPTT level was prolonged (55.9 s). PD was performed as scheduled. On postoperative day (POD) 2, she developed intra-abdominal hemorrhaging that required reoperation. However, intra-abdominal bleeding and concomitant anemia persisted after reoperation. On POD 13, she was diagnosed with AHA based on the detection of an inhibitor of coagulation factor VIII. Despite hemostatic and immunosuppressive treatment, including massive blood transfusion, her general condition gradually worsened due to continuous bleeding and secondary infections. She ultimately died of multiple organ failure on POD 71. Case 2: An 82-year-old man received PD for distal cholangiocarcinoma. On POD 3, a small amount of blood via abdominal drainage was observed. On POD 4, his aPTT level was prolonged (61.5 s). On POD 8, subcutaneous hemorrhaging of the median wound was observed, and corticosteroids were administered under suspicion of AHA on POD 9. On POD 15, an inhibitor of FVIII was detected, and he was diagnosed with AHA. On POD 17, the aPTT level had normalized, and an inhibitor of FVIII was undetectable. On POD 41, he was discharged without any serious hemorrhagic events. Conclusions AHA may be more frequent than previously reported. When unexplained prolonged aPTT or bleeding symptoms are observed, it is important to keep AHA in mind during the perioperative period of invasive surgery.

Published
2023

13. Surgical outcomes of gallbladder cancer: the OMEGA retrospective, multicentre, international cohort study

Author

Anita Balakrishnan, Petros Barmpounakis, Nikolaos Demiris, Asif Jah, Harry V.M. Spiers, Shibojit Talukder, Jack L. Martin, Paul Gibbs, Simon J.F. Harper, Emmanuel L. Huguet, Vasilis Kosmoliaptsis, Siong S. Liau, Raaj K. Praseedom, Bristi Basu, Xavier de Aretxabala, Javier Lendoire, Shishir Maithel, Alejandro Branes, Bodil Andersson, Alejandro Serrablo, Volkan Adsay, Tomoyuki Abe, Moh'd Abu Hilal, Maria del Mar Achalandabaso Boira, Mustapha Adham, Mohamed Adam, Maryam Ahmad, Bilal Al-Sarireh, Maite Albiol, Nassir Alhaboob, Adnan Alseidi, Houssem Ammar, Akshay Anand, Pantelis Antonakis, Veronica Araya, Stanley W. Ashley, Georgi Atanasov, Fabio Ausania, Ricardo Balestri, Abhirup Banerjee, Sudeep Banerjee, Simon Banting, Giedrius Barauskas, Fabian Bartsch, Andrea Belli, Simona Beretta, Frederik Berrevoet, Ramesh Singh Bhandari, Gerardo Blanco Fernandez, Louisa Bolm, Mathieu Bonal, Emre Bozkurt, Andries E. Braat, Luke Bradshaw, Konstantinos Bramis, Lyle Burdine, Matthew Byrne, Maria Caceres, Maria Jesus Castro Santiago, Benjamin Chan, Lynn Chong, Ahmet Çoker, Maria Conde Rodriguez, Daniel Croagh, Alyn Crutchley, Carmen Cutolo, Mathieu D'Hondt, Daniel D'Souza, Freek Daams, Raffaele Dalla Valle, José Davide, Mario de Bellis, Marieke de Boer, Celine de Meyere, Philip de Reuver, Matthew Dixon, Panagiotis Dorovinis, Gabriela Echeverría Bauer, Maria Eduarda, Hasan Eker, Joris Erdmann, Mert Erkan, Evangelos Felekouras, Emanuele Felli, Eduardo Fernandes, Eduardo Figueroa Rivera, Andras Fulop, Daniel Galun, Michael Gerhards, Poya Ghorbani, Fabio Giannone, Luis Gil, Emmanouil Giorgakis, Mario Giuffrida, Felice Giuliante, Ioannis Gkekas, Miguel Gomez Bravo, Bas Groot Koerkamp, Oscar Guevara, Alfredo Guglielmi, Aiste Gulla, Rahul Gupta, Amit Gupta, Marta Gutiérrez, Abu Bakar Hafeez Bhatti, Jeroen Hagendoorn, Zain Hajee, Abdul Rahman Hakeem, Hytham Hamid, Sayed Hassen, Stefan Heinrich, Ryota Higuchi, Daniel Hoffman, David Holroyd, Daniel Hughes, Arpad Ivanecz, Satheesh Iype, Isabel Jaen Torrejimeno, Shantanu Joglekar, Robert Jones, Klaus Kaczirek, Harsh Kanhere, Ambareen Kausar, Zhanyi Kee, Jessica Keilson, Jorg Kleef, Johannes Klose, Brett Knowles, Jun Kit Koong, Nagappan Kumar, Supreeth Kunnuru, Paleswan Joshi Lakhey, Andrea Laurenzi, Yeong Sing Lee, Felipe Leon, Voon Meng Leow, Jean-Baptiste Lequeu, Mickael Lesurtel, Elisabeth Lo, Stefan Löb, Elizabeth Lockie, Peter Lodge, Dolores López Garnica, Victor Lopez Lopez, Linda Lundgren, Nikolaos Machairas, Dhiresh Maharjan, Deep Malde, Guillaume Martel, Julie Martin, Michele Mazzola, Arianeb Mehrabi, Ricardo Memeo, Flavio Milana, George Molina, Leah Monette, Haluk Morgul, Dimitrios Moris, Antonios Morsi-Yeroyannis, Nicholas Mowbray, Francesk Mulita, Edoardo Maria Muttillo, Malith Nandasena, Pueya Rashid Nashidengo, Arash Nickkholgh, Colin Byron Noel, Masayuki Ohtsuka, Arturs Ozolins, Sanjay Pandanaboyana, Nikolaos Pararas, Alessandro Parente, June Peng, Arkaitz Perfecto Valero, Julie Perinel, Konstatinos Perivoliotis, Teresa Perra, Patrick Pessaux, Natalie Petruch, Gaetano Piccolo, Laszlo Piros, Alberto Porcu, Viswakumar Prabakaran, Raj Prasad, Mikel Prieto Calvo, Florian Primavesi, Eva Maria Pueyo Periz, Alberto Quaglia, Jose M. Ramia Angel, Ashwin Rammohan, Francesco Razionale, Ricardo Robles Campos, Manas Roy, Sophie Rozwadowski, Luis Ruffolo, Natalia Ruiz, Andrea Ruzzenante, Lily Saadat, Mohamed Amine Said, Edoardo Saladino, Gabriel Saliba, Per Sandstrom, Carlo Alberto Schena, Anthony Scholer, Christoph Schwarz, Lorenzo Serafini, Pablo E. Serrano, Deepak Sharma, Aali Sheen, Vishwanath Siddagangaiah, Michael Silva, Saurabh Singh, Ajith Siriwardena, Michal Skalski, Mante Smig, Faris Soliman, Abhinav Arun Sonkar, Donzília Sousa Silva, Ernesto Sparrelid, Parthi Srinivasan, Malin Sternby Eilard, Oliver Strobel, Urban Stupan, Miguel Angel Suarez-Munoz, Manisekar Subramaniam, Teiichi Sugiura, Robert Sutcliffe, Hilko Swank, Lillian Taylor, Prabin Bikram Thapa, Catherine The, Asara Thepbunchonchai, Caman Thieu, Navneet Tiwari, Guido Torzilli, Chutwichai Tovikkai, Blaz Trotovsek, Savvas Tsaramanidis, Georgios Tsoulfas, Katsuhiko Uesaka, Garzali Umar, Lucio Urbani, Michail Vailas, Ronald van Dam, Peter van de Boezem, Stijn van Laarhoven, Tomas Vanagas, Mike Van Dooren, Manon Viennet, Luca Vigano, Aarathi Vijayashanker, Celia Villodre, Toshifumi Wakai, Aklile Workneh, Li Xu, Masakazu Yamamoto, Zhiying Yang, Robert Young, Marko Zivanovic, Surgery, CCA - Cancer Treatment and quality of life, and Amsterdam Gastroenterology Endocrinology Metabolism

Subjects
General Medicine
Abstract

Background: Gallbladder cancer (GBC) is rare but aggressive. The extent of surgical intervention for different GBC stages is non-uniform, ranging from cholecystectomy alone to extended resections including major hepatectomy, resection of adjacent organs and routine extrahepatic bile duct resection (EBDR). Robust evidence here is lacking, however, and survival benefit poorly defined. This study assesses factors associated with recurrence-free survival (RFS), overall survival (OS) and morbidity and mortality following GBC surgery in high income countries (HIC) and low and middle income countries (LMIC). Methods: The multicentre, retrospective Operative Management of Gallbladder Cancer (OMEGA) cohort study included all patients who underwent GBC resection across 133 centres between 1st January 2010 and 31st December 2020. Regression analyses assessed factors associated with OS, RFS and morbidity. Findings: On multivariable analysis of all 3676 patients, wedge resection and segment IVb/V resection failed to improve RFS (HR 1.04 [0.84–1.29], p = 0.711 and HR 1.18 [0.95–1.46], p = 0.13 respectively) or OS (HR 0.96 [0.79–1.17], p = 0.67 and HR 1.48 [1.16–1.88], p = 0.49 respectively), while major hepatectomy was associated with worse RFS (HR 1.33 [1.02–1.74], p = 0.037) and OS (HR 1.26 [1.03–1.53], p = 0.022). Furthermore, EBDR (OR 2.86 [2.3–3.52], p < 0.0010), resection of additional organs (OR 2.22 [1.62–3.02], p < 0.0010) and major hepatectomy (OR 3.81 [2.55–5.73], p < 0.0010) were all associated with increased morbidity and mortality. Compared to LMIC, patients in HIC were associated with poorer RFS (HR 1.18 [1.02–1.37], p = 0.031) but not OS (HR 1.05 [0.91–1.22], p = 0.48). Adjuvant and neoadjuvant treatments were infrequently used. Interpretation: In this large, multicentre analysis of GBC surgical outcomes, liver resection was not conclusively associated with improved survival, and extended resections were associated with greater morbidity and mortality without oncological benefit. Aggressive upfront resections do not benefit higher stage GBC, and international collaborations are needed to develop evidence-based neoadjuvant and adjuvant treatment strategies to minimise surgical morbidity and prioritise prognostic benefit. Funding:Cambridge Hepatopancreatobiliary Department Research Fund.

Published
2023

15. Supplementary Table S1 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Genes for expression signatures.

Published
2023

16. Supplementary Data S1 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

SVs identified in the 30 GIST cases in our study cohort.

Published
2023

17. Supplementary Figure S2 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

KIT exon 11 mutations detected in 30 GIST samples.

Published
2023

18. Supplementary Data S3 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

CNAs identified in the 30 GIST cases in our study cohort.

Published
2023

19. Supplementary Data S2 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

SNVs/Indels identified in the 30 GIST cases in our study cohort.

Published
2023

20. Supplementary Data S4 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Data for gene expression signatures.

Published
2023

21. Supplementary Figure S3 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Kaplan-Meier curves.

Published
2023

22. Supplementary Figure S6 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Visualization of methylation status in GISTs.

Published
2023

23. Supplementary Figure S7 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

DNA methylation in each autosome of GISTs. Genome-wide DNA methylation sites are shown in 300-kb bins.

Published
2023

24. Supplementary Figure S1 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Circos plots of the 30 GIST genomes in our study cohort.

Published
2023

25. Supplementary Figure S10 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Expression levels for genes involved in recurrently detected SVs.

Published
2023

26. Supplementary Figure S8 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Functional enrichment analysis of the differentially expressed genes in malignant GISTs with KIT Δ557–558.

Published
2023

27. Supplementary Table S2 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Summary of WGS, methylation and expression data.

Published
2023

28. Supplementary Table S3 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Probes for genes with specific expression alterations in malignant GISTs with KIT Δ557–558.

Published
2023

29. Supplementary Figure S9 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Genome-wide relationship between DNA methylation and gene expression in malignant GISTs with KIT Δ557–558.

Published
2023

30. Data from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Gastrointestinal stromal tumors (GIST) with KIT exon 11 deletions involving in codons 557–558 (KIT Δ557–558) exhibit higher proliferation rates and shorter disease-free survival times compared with GISTs with other KIT exon 11 mutations. We analyzed 30 GIST cases and observed genomic instability and global DNA hypomethylation only in high-risk malignant GISTs with KIT Δ557–558. Whole-genome sequencing revealed that the high-risk malignant GISTs with KIT Δ557–558 (12 cases) had more structural variations (SV), single-nucleotide variants, and insertions and deletions compared with the low-risk, less malignant GISTs with KIT Δ557–558 (six cases) and the high-risk (six cases) or low-risk (6 cases) GISTs with other KIT exon 11 mutations. The malignant GISTs with KIT Δ557–558 showed higher frequency and significance in copy number (CN) reduction on chromosome arms 9p and 22q, and 50% of them had LOH or CN-dependent expression reduction in CDKN2A. In addition, SVs with driver potential were detected in 75% of them, in which AKT3 and MGMT were recurrently identified. Genome-wide DNA methylation and gene expression analyses showed global intergenic DNA hypomethylation, SNAI2 upregulation, and higher expression signatures, including p53 inactivation and chromosomal instability, as characteristics of malignant GISTs with KIT Δ557–558 that distinguished them from other GISTs. These genomic and epigenomic profiling results revealed that KIT Δ557–558 mutations are associated with increased genomic instability in malignant GISTs.Significance:We present genomic and epigenomic insights into the malignant progression of GISTs with KIT exon 11 deletions involving in 557–558, demonstrating their unique chromosomal instability and global intergenic DNA hypomethylation.

Published
2023

31. Supplementary Figure S4 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Comparison of somatic mutational landscape between malignant and less malignant GISTs with and without KIT Δ557–558.

Published
2023

32. Supplementary Data S5 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Expression data of probes used for the volcano plot comparing between malignant GISTs carrying KIT Δ557–558 and other GISTs.

Published
2023

33. Supplementary Figure S5 from Whole-genome and Epigenomic Landscapes of Malignant Gastrointestinal Stromal Tumors Harboring KIT Exon 11 557–558 Deletion Mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

SVs and expression levels of DMD in 30 GIST samples.

Published
2023

34. Supplementary Figure S6 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Visualization of methylation status in GISTs.

Published
2023

35. Supplementary Data S5 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Expression data of probes used for the volcano plot comparing between malignant GISTs carrying KIT Δ557–558 and other GISTs.

Published
2023

36. Supplementary Data S4 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Data for gene expression signatures.

Published
2023

37. Supplementary Figure S7 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

DNA methylation in each autosome of GISTs. Genome-wide DNA methylation sites are shown in 300-kb bins.

Published
2023

38. Supplementary Figure S9 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Genome-wide relationship between DNA methylation and gene expression in malignant GISTs with KIT Δ557–558.

Published
2023

39. Supplementary Table S1 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Genes for expression signatures.

Published
2023

40. Supplementary Figure S8 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Functional enrichment analysis of the differentially expressed genes in malignant GISTs with KIT Δ557–558.

Published
2023

41. Supplementary Figure S1 (continued) from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Circos plots of the 30 GIST genomes in our study cohort.

Published
2023

42. Supplementary Data S2 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

SNVs/Indels identified in the 30 GIST cases in our study cohort.

Published
2023

43. Supplementary Figure S2 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

KIT exon 11 mutations detected in 30 GIST samples.

Published
2023

44. Supplementary Figure S4 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Comparison of somatic mutational landscape between malignant and less malignant GISTs with and without KIT Δ557–558.

Published
2023

45. Supplementary Figure S3 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Kaplan-Meier curves.

Published
2023

46. Supplementary Table S2 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Summary of WGS, methylation and expression data.

Published
2023

47. Supplementary Figure S10 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Expression levels for genes involved in recurrently detected SVs.

Published
2023

48. Data from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Gastrointestinal stromal tumors (GISTs) with KIT exon 11 deletions involving in codons 557–558 (KIT Δ557–558) exhibit higher proliferation rates and shorter disease-free survival times compared with GISTs with other KIT exon 11 mutations. We analyzed 30 GIST cases and observed genomic instability and global DNA hypomethylation only in high-risk malignant GISTs with KIT Δ557–558. Whole-genome sequencing revealed that the high-risk malignant GISTs with KIT Δ557–558 (12 cases) had more structural variations (SVs), single nucleotide variants, and insertions and deletions compared with the low-risk, less malignant GISTs with KIT Δ557–558 (6 cases) and the high- (6 cases) or low-risk (6 cases) GISTs with other KIT exon 11 mutations. The malignant GISTs with KIT Δ557–558 showed higher frequency and significance in copy number (CN) reduction on chromosome arms 9p and 22q, and 50% of them had loss of heterozygosity or CN-dependent expression reduction in CDKN2A. Additionally, SVs with driver potential were detected in 75% of them, in which AKT3 and MGMT were recurrently identified. Genome-wide DNA methylation and gene expression analyses showed global intergenic DNA hypomethylation, SNAI2 upregulation, and higher expression signatures, including p53 inactivation and chromosomal instability, as characteristics of malignant GISTs with KIT Δ557–558 that distinguished them from other GISTs. These genomic and epigenomic profiling results revealed that KIT Δ557–558 mutations are associated with increased genomic instability in malignant GISTs.

Published
2023

49. Supplementary Table S3 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

Probes for genes with specific expression alterations in malignant GISTs with KIT Δ557–558.

Published
2023

50. Supplementary Data S3 from Whole-genome and epigenomic landscapes of malignant gastrointestinal stromal tumors harboring KIT exon 11 557–558 deletion mutations

Author

Ken Yamaguchi, Yasuto Akiyama, Kenichi Urakami, Katsuhiko Uesaka, Masanori Terashima, Takashi Sugino, Teiichi Sugiura, Etsuro Bando, Yasuhiro Tsubosa, Akio Shiomi, Hirotsugu Kenmotsu, Shumpei Ohnami, Masakuni Serizawa, Akane Naruoka, Sumiko Ohnami, Yuji Shimoda, Fukumi Kamada, Kimiko Morimoto, Yuko Watanabe, Keiichi Hatakeyama, Keiichi Fujiya, Takeshi Nagashima, and Keiichi Ohshima

Abstract

CNAs identified in the 30 GIST cases in our study cohort.

Published
2023

Catalog

Books, media, physical & digital resources
See catalog results