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Lian B, Li Z, Wu N, Li M, Chen X, Zheng H, Gao M, Wang D, Sheng X, Tian H, Si L, Chi Z, Wang X, Lai Y, Sun T, Zhang Q, Kong Y, Long GV, Guo J, Cui C. Phase II clinical trial of neoadjuvant anti-PD-1 (toripalimab) combined with axitinib in resectable mucosal melanoma. Ann Oncol 2024; 35:211-220. [PMID: 37956739 DOI: 10.1016/j.annonc.2023.10.793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND The outcome of patients with resectable mucosal melanoma is poor. Toripalimab combined with axitinib has shown impressive results in metastatic mucosal melanoma with an objective response rate of 48.3% and a median progression-free survival of 7.5 months in a phase Ib trial. It was hypothesized that this combination administered in the neoadjuvant setting might induce a pathologic response in resectable mucosal melanoma, so we conducted this trial. PATIENTS AND METHODS This single-arm phase II trial enrolled patients with resectable mucosal melanoma. Patients received toripalimab 3 mg/kg once every 2 weeks (Q2W) plus axitinib 5 mg two times a day (b.i.d.) for 8 weeks as neoadjuvant therapy, then surgery and adjuvant toripalimab 3 mg/kg Q2W starting 2 ± 1weeks after surgery for 44 weeks. The primary endpoint was the pathologic response rate according to the International Neoadjuvant Melanoma Consortium recommendations. RESULTS Between August 2019 and October 2021, 29 patients were enrolled and received treatment, of whom 24 underwent resection. The median follow-up time was 34.2 months (95% confidence interval 20.4-48.0 months). The pathologic response rate was 33.3% (8/24; 4 pathological complete responses and 4 pathological partial responses). The median event-free survival for all patients was 11.1 months (95% confidence interval 5.3-16.9 months). The median overall survival was not reached. Neoadjuvant therapy was tolerable with 8 (27.5%) grade 3-4 treatment-related adverse events and no treatment-related deaths. Tissue samples of 17 patients at baseline and after surgery were collected (5 responders and 12 nonresponders). Multiplex immunohistochemistry demonstrated a significant increase in CD3+ (P = 0.0032) and CD3+CD8+ (P = 0.0038) tumor-infiltrating lymphocytes after neoadjuvant therapy, particularly in pathological responders. CONCLUSIONS Neoadjuvant toripalimab combined with axitinib in resectable mucosal melanoma demonstrated a promising pathologic response rate with significantly increased infiltrating CD3+ and CD3+CD8+ T cells after therapy.
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Affiliation(s)
- B Lian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital and Institute, Beijing
| | - Z Li
- Department of Pathology, Peking University Cancer Hospital and Institute, Beijing
| | - N Wu
- Department of Thoracic Surgery, Peking University Cancer Hospital and Institute, Beijing
| | - M Li
- Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing
| | - X Chen
- Department of Otorhinolaryngology, Key Laboratory of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing
| | - H Zheng
- Department of Gynecologic Oncology, Peking University Cancer Hospital and Institute, Beijing
| | - M Gao
- Department of Gynecologic Oncology, Peking University Cancer Hospital and Institute, Beijing
| | - D Wang
- Peking University School of Stomatology, Beijing
| | - X Sheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital and Institute, Beijing
| | - H Tian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital and Institute, Beijing
| | - L Si
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital and Institute, Beijing
| | - Z Chi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital and Institute, Beijing
| | - X Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital and Institute, Beijing
| | - Y Lai
- Department of Pathology, Peking University Cancer Hospital and Institute, Beijing
| | - T Sun
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Q Zhang
- The Medical Department, Jiangsu Simcere Diagnostics Co., Ltd, Nanjing, China
| | - Y Kong
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital and Institute, Beijing
| | - G V Long
- Melanoma Institute of Australia, The University of Sydney, and Royal North Shore and Mater Hospitals, Sydney, Australia
| | - J Guo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital and Institute, Beijing
| | - C Cui
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital and Institute, Beijing.
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Yang X, Lian B, Zhang N, Long J, Li Y, Xue J, Chen X, Wang Y, Wang Y, Xun Z, Piao M, Zhu C, Wang S, Sun H, Song Z, Lu L, Dong X, Wang A, Liu W, Pan J, Hou X, Guan M, Huo L, Shi J, Zhang H, Zhou J, Lu Z, Mao Y, Sang X, Wu L, Yang X, Wang K, Zhao H. Genomic characterization and immunotherapy for microsatellite instability-high in cholangiocarcinoma. BMC Med 2024; 22:42. [PMID: 38281914 PMCID: PMC10823746 DOI: 10.1186/s12916-024-03257-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/15/2024] [Indexed: 01/30/2024] Open
Abstract
BACKGROUND Microsatellite instability-high (MSI-H) is a unique genomic status in many cancers. However, its role in the genomic features and immunotherapy in cholangiocarcinoma (CCA) is unclear. This study aimed to systematically investigate the genomic characterization and immunotherapy efficacy of MSI-H patients with CCA. METHODS We enrolled 887 patients with CCA in this study. Tumor samples were collected for next-generation sequencing. Differences in genomic alterations between the MSI-H and microsatellite stability (MSS) groups were analyzed. We also investigated the survival of PD-1 inhibitor-based immunotherapy between two groups of 139 patients with advanced CCA. RESULTS Differential genetic alterations between the MSI-H and MSS groups included mutations in ARID1A, ACVR2A, TGFBR2, KMT2D, RNF43, and PBRM1 which were enriched in MSI-H groups. Patients with an MSI-H status have a significantly higher tumor mutation burden (TMB) (median 41.7 vs. 3.1 muts/Mb, P < 0.001) and more positive programmed death ligand 1 (PD-L1) expression (37.5% vs. 11.9%, P < 0.001) than those with an MSS status. Among patients receiving PD-1 inhibitor-based therapy, those with MSI-H had a longer median overall survival (OS, hazard ratio (HR) = 0.17, P = 0.001) and progression-free survival (PFS, HR = 0.14, P < 0.001) than patients with MSS. Integrating MSI-H and PD-L1 expression status (combined positive score ≥ 5) could distinguish the efficacy of immunotherapy. CONCLUSIONS MSI-H status was associated with a higher TMB value and more positive PD-L1 expression in CCA tumors. Moreover, in patients with advanced CCA who received PD-1 inhibitor-based immunotherapy, MSI-H and positive PD-L1 expression were associated with improved both OS and PFS. TRIAL REGISTRATION This study was registered on ClinicalTrials.gov on 07/01/2017 (NCT03892577).
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Affiliation(s)
- Xu Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Department of Breast Surgery, Peking, Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | | | - Nan Zhang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junyu Long
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yiran Li
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jingnan Xue
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiangqi Chen
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yunchao Wang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanyu Wang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ziyu Xun
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Mingjian Piao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chenpei Zhu
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shanshan Wang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huishan Sun
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | | | | | | | - Jie Pan
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaorong Hou
- Department of Radiotherapy, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Mei Guan
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Li Huo
- Department of Nuclear Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jie Shi
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Haohai Zhang
- Center for Inflammation Research, Department of Anesthesia, Critical Care & Pain Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jinxue Zhou
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Zhenhui Lu
- Hepatobiliary and Pancreatic Surgery, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Yilei Mao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinting Sang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liqun Wu
- Liver Disease Center, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiaobo Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Kai Wang
- OrigiMed Co., Ltd, Shanghai, China.
| | - Haitao Zhao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Chen XJ, Zhang J, Li WD, Lian B, Guo HM. [Interpretation on Expert systematic review on the choice of conduits for coronary artery bypass grafting endorsed by the European Association for Cardio-Thoracic Surgery and the Society of Thoracic Surgeons in 2023]. Zhonghua Wai Ke Za Zhi 2023; 62:45-49. [PMID: 38044607 DOI: 10.3760/cma.j.cn112139-20230917-00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Expert systematic review on the choice of conduits for coronary artery bypass grafting: endorsed by the European Association for Cardio-Thoracic Surgery and the Society of Thoracic Surgeons published in 2023 made recommendations for the selection of bypass vessels. The left internal thoracic artery-anterior descending branch anastomosis represents the accepted gold standard. Radial artery could achieve a better long-term patency rate and a reduction in adverse cardiac events compared to the great saphenous vein. Radial artery graft using an open harvesting method should be chosen to graft the target vessel with low competitive coronary flow, with the use of vasodilators for the first year. There was no clear evidence of better patency for the right internal thoracic artery compared to the great saphenous vein. The bilateral internal thoracic artery had better long-term survival compared to great saphenous vein but may be associated with a higher risk of deep sternal wound infection and should be avoided in high-risk patients. The impact of skeletonization of the internal thoracic artery on graft patency and cardiovascular outcomes was unclear. Endoscopic vein harvest reduced the risk of leg wound complications and was associated with reduced long-term patency. The patency of the no-touch great saphenous vein was significantly better than that of conventional great saphenous vein. A significantly higher risk of complications at the harvesting site and no clear evidence of better long-term clinical outcomes were found in the no-touch great saphenous vein compared to the conventional. There was limited data on the use of right gastroepiploic artery and skeletonized harvesting, which should be used to bypass target vessels in patients with low competitive flow.
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Affiliation(s)
- X J Chen
- Department of Cardiac Surgery, Wuhan First Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - J Zhang
- Department of Cardiovascular Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China
| | - W D Li
- Department of Cardiovascular Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China
| | - B Lian
- Cardiovascular Surgery, Peking University Peoples Hospital, Beijing 100044, China
| | - H M Guo
- Department of Cardiac Surgery, Guangdong Provincial People's Hospital, Guangzhou 510080, China
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Lian B, Yu PF, Yang B, Wang SQ, Li MB, Zhao QC. [Management of radiation-induced intestinal injury:from multi-disciplinary team team to holistic integrative management]. Zhonghua Wei Chang Wai Ke Za Zhi 2023; 26:922-928. [PMID: 37849261 DOI: 10.3760/cma.j.cn441530-20230709-00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Radiation-induced intestinal injury is a radiation injury of the colon and rectum after radiotherapy for pelvic malignant tumors. This condition affects multiple organs in the pelvis, making treatment challenging. In clinical practice, the most effective protocol is often determined through discussion by a multi-disciplinary team (MDT). However, due to the severity and complexity of radiation enteritis, many patients still experience poor diagnosis and treatment outcomes. Holistic integrative management (HIM) is a rapidly developing concept that has greatly enhanced clinical medicine in recent years. It improves the level of diagnosis, treatment, prevention, and rehabilitation from multiple dimensions of prevention, screening, diagnosis, treatment, and rehabilitation. In the context of radiation-induced intestinal injury, HIM also calls for the implementation of an individualized management system that focuses on the patient as a whole within the healthcare team. From the perspective of HIM, this article introduces some of the latest progress of radiation-induced intestinal injury in recent years.
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Affiliation(s)
- B Lian
- Department of Clinical Nutrition, First Affiliated Hospital of Air Force Military Medical University, Xi'an 710032, China
| | - P F Yu
- Department of Digestive Surgery, First Affiliated Hospital of Air Force Military Medical University, Xi'an 710032, China
| | - B Yang
- Department of Digestive Surgery, First Affiliated Hospital of Air Force Military Medical University, Xi'an 710032, China
| | - S Q Wang
- Department of Digestive Surgery, First Affiliated Hospital of Air Force Military Medical University, Xi'an 710032, China
| | - M B Li
- Department of Digestive Surgery, First Affiliated Hospital of Air Force Military Medical University, Xi'an 710032, China
| | - Q C Zhao
- Department of Digestive Surgery, First Affiliated Hospital of Air Force Military Medical University, Xi'an 710032, China
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Yang Y, Lian B, Si L, Chi Z, Sheng X, Kong Y, Cui CL, Guo J. 851P Frequency and clinical significance of homologous recombination deficiency gene mutations in non-cutaneous melanoma. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Lian B, Yang Y, Si L, Zhou L, Chi Z, Sheng X, Mao L, Wang X, Cui CL, Zheng B, Guo J. 808P Postoperative adjuvant radiotherapy can reduce the local recurrence of nasal cavity and paranasal sinus mucosal melanoma: A prospective design, retrospective analysis and case–control study. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Wei X, Wang X, Bai X, Li C, Mao L, Chi Z, Lian B, Bixia T, Kong Y, Dai J, Andtbacka R, Guo J, Cui CL, Si L. 795P A phase Ib trial of neoadjuvant oncolytic virus OrienX010 (ori) and anti-PD-1 toripalimab (tori) combo in patients (pts) with resectable stage IIIb-IV (M1a) acral melanoma. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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8
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Cui CL, Li Z, Wu N, Li M, Chen X, Zheng H, Gao M, Wang D, Lian B, Wang X, Tian H, Si L, Chi Z, Sheng X, Lai Y, Sun T, Zhang Q, Kong Y, Guo J. 796P Neoadjuvant toripalimab plus axitinib in patients (pts) with resectable mucosal melanoma (MuM): Updated findings of a single-arm, phase II trial. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Si L, Qi Z, Dai J, Bai X, Mao L, Li C, Wei X, Cui CL, Chi Z, Sheng X, Kong Y, Bixia T, Zhou L, Lian B, Wang X, Duan R, Guo J. 815P A single-arm, phase II clinical study of imatinib mesylate/toripalimab combo in patients (pts) with advanced melanoma harboring c-Kit mutation or amplification. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Wang X, Wu W, Wu X, Si L, Chi Z, Sheng X, Li L, Han W, Li H, Lian B, Zhou L, Mao L, Bai X, Bixia T, Wei X, Cui CL, Kong Y, Guo J. 879P Whole-genome landscape of head and neck melanomas in East Asia (China). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Wang SQ, Lian B, Guo M, Huang W, Li Q, Wang M, Lu J, Liu Y, Ji G, Zhao QC. [Patient experience in the implementation of enhanced recovery after surgery strategy after radical gastric cancer surgery]. Zhonghua Wei Chang Wai Ke Za Zhi 2022; 25:582-589. [PMID: 35844120 DOI: 10.3760/cma.j.cn441530-20211115-00463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Objective: To investigate the experience of patients in the implementation of enhanced recovery after surgery (ERAS) strategy after radical gastrectomy and the factors affecting the treatment experience. Methods: A prospective cohort study was carried out. Patients who were diagnosed with gastric cancer by pathology and underwent radical gastrectomy at the Xijing Digestive Disease Hospital from December 2019 to December 2020 were consecutively enrolled. Those who received emergency surgery, residual gastric cancer surgery, preoperative neoadjuvant chemotherapy, non-curative tumor resection, intraperitoneal metastasis, or other malignant tumors were excluded. Patients' expectation and experience during implementation were investigated by questionnaires. The questionnaire included three main parts: patients' expectation for ERAS, patients' experience during the ERAS implementation, and patients' outcomes within 30 days after discharge. The items on the expectation and experience were ranked from 0 to 10 by patients, which indicated to be unsatisfied/unimportant and satisfied/important respectively. According to their attitudes towards the ERAS strategy, patients were divided into the support group and the reject group. Patients' expectation and experience of hospital stay, and the clinical outcomes within 30 days after discharge were compared between the two groups. Categorical data were reported as number with percentage and the quantitative data were reported as mean with standard deviation, or where appropriate, as the median with interquartile range (Q1, Q3). Categorical data were compared using the Chi-squared test or Fisher's exact test, where appropriate. For continuous data, Student's t test or Mann-Whitney U test were used. Complication was classified according to Clavien-Dindo classification. Results: Of the included 112 patients (88 males and 24 females), aged (57.8±10.0) years, 35 patients (31.3%) were in the support group and 77 (68.7%) in the reject group. Anxiety was detected in 56.2% (63/112) of the patients with score >8. The admission education during the ERAS implementation improved the patients' cognitions of the ERAS strategy [M(Q1, Q3) score: 8 (4, 10) vs. 2 (0, 5), Z=-7.130, P<0.001]. The expected hospital stay of patients was longer than the actual stay [7 (7, 10) days vs. 6 (6, 7) days, Z=-4.800, P<0.001]. During the ERAS implementation, patients had low score in early mobilization [3 (1, 6)] and early oral intake [5 (2.25, 8)]. Fifty-eight (51.8%) patients planned the ERAS implementation at home after discharge, while 32.1% (36/112) preferred to stay in hospital until they felt totally recovered. Compared with the reject group, the support group had shorter expected hospital stay [7 (6, 10) days vs. 10 (7, 15) days, Z=-2.607, P=0.009], and higher expected recovery-efficiency score [9 (8, 10) vs. 7(5, 9), Z=-3.078, P=0.002], lower expected less-pain score [8 (6, 10) vs. 6 (5, 9) days, Z=-1.996, P=0.046], expected faster recovery of physical strength score [8 (6, 10) vs. 6 (4, 9), Z=-2.200, P=0.028] and expected less drainage tube score [8 (8, 10) vs. 8 (5, 10), Z=-2.075, P=0.038]. Worrying about complications (49.1%) and self-recognition of not recovery (46.4%) were the major concerns when assessing the experience toward ERAS. During the follow-up, 105 patients received follow-up calls. There were 57.1% (60/105) of patients who experienced a variety of discomforts after discharge, including pain (28.6%), bloating (20.0%), nausea (12.4%), fatigue (7.6%), and fever (2.9%). Within 30 days after discharge, 6.7% (7/105) of patients developed Clavien-Dindo level I and II operation-associated complications, including poor wound healing, intestinal obstruction, intraperitoneal bleeding, and wound infection, all of which were cured by conservative treatment. There were no complications of level III or above in the whole group after surgery. Compared with the support group, more patients in the reject group reported that they had not yet achieved self-expected recovery when discharged [57.1% (44/77) vs. 22.9% (8/35), χ2=11.372, P<0.001], and expected to return to their daily lives [39.0% (30/77) vs. 8.6% (3/35), χ2=10.693, P<0.001], with statistically significant differences (all P<0.05). Only 52.4% (55/105) of patients returned home to continue rehabilitation, and the remaining patients chose to go to other hospitals to continue their hospitalization after discharge, with a median length of stay of 7 (7, 9) days. Compared with the reject group, the support group had a higher proportion of home rehabilitation [59.7% (12/33) vs. 36.4% (43/72), χ2=4.950, P=0.026], and shorter time of self-perceived postoperative full recovery [14 (10, 20) days vs. 15 (14, 20) days, Z=2.100, P=0.036], with statistically significant differences (all P<0.05). Conclusions: Although ERAS has promoted postoperative rehabilitation while ensuring surgical safety, it has not been unanimously recognized by patients. Adequate rehabilitation education, good analgesia, good physical recovery, and early removal of drainage tubes may improve the patient's experience of ERAS.
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Affiliation(s)
- S Q Wang
- Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - B Lian
- Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - M Guo
- Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - W Huang
- Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Q Li
- Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - M Wang
- Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - J Lu
- Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Y Liu
- Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - G Ji
- Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Q C Zhao
- Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
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Zhu M, Chen E, Yu S, Xu C, Yu Y, Cao X, Li W, Zhang P, Wang Y, Lian B, Zhang S, Qu Y, Huang L, Shi W, Cui Y, Qian L, Liu T. Genomic profiling and the impact of MUC19 mutation in hepatoid adenocarcinoma of the stomach. Cancer Commun (Lond) 2022; 42:1032-1035. [PMID: 35851588 PMCID: PMC9558685 DOI: 10.1002/cac2.12336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/22/2022] [Accepted: 07/04/2022] [Indexed: 12/04/2022] Open
Affiliation(s)
- Mengxuan Zhu
- Department of Medical Oncology, Zhongshan Hospital Fudan University Shanghai 20032 P. R. China
- Center of Evidence‐based medicine Fudan University Shanghai 20032 P. R. China
| | - Erbao Chen
- Hepato‐Pancreato‐Biliary Surgery Peking University Shenzhen Hospital Shenzhen Guangdong 518036 P. R. China
| | - Shan Yu
- Department of Medical Oncology, Zhongshan Hospital Fudan University Shanghai 20032 P. R. China
- Center of Evidence‐based medicine Fudan University Shanghai 20032 P. R. China
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital Fudan University Shanghai 20032 P. R. China
| | - Yiyi Yu
- Department of Medical Oncology, Zhongshan Hospital Fudan University Shanghai 20032 P. R. China
| | - Xin Cao
- Institute of Clinical Science, Zhongshan Hospital Fudan University Shanghai 20032 P. R. China
| | - Wei Li
- Department of Medical Oncology, Zhongshan Hospital Fudan University Shanghai 20032 P. R. China
| | - Pengfei Zhang
- Department of Medical Oncology, Zhongshan Hospital Fudan University Shanghai 20032 P. R. China
| | - Yan Wang
- Department of Medical Oncology, Zhongshan Hospital Fudan University Shanghai 20032 P. R. China
| | | | | | - Yueting Qu
- Origimed Co. Ltd Shanghai 20032 P. R. China
| | | | - Weiwei Shi
- Origimed Co. Ltd Shanghai 20032 P. R. China
| | - Yuehong Cui
- Department of Medical Oncology, Zhongshan Hospital Fudan University Shanghai 20032 P. R. China
- Center of Evidence‐based medicine Fudan University Shanghai 20032 P. R. China
| | - Li Qian
- Department of Medical Oncology, Zhongshan Hospital Fudan University Shanghai 20032 P. R. China
- Center of Evidence‐based medicine Fudan University Shanghai 20032 P. R. China
- Cancer center Zhongshan hospital Fudan University Shanghai 20032 P. R. China
| | - Tianshu Liu
- Department of Medical Oncology, Zhongshan Hospital Fudan University Shanghai 20032 P. R. China
- Center of Evidence‐based medicine Fudan University Shanghai 20032 P. R. China
- Cancer center Zhongshan hospital Fudan University Shanghai 20032 P. R. China
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13
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Lian B, Si L, Chi ZH, Sheng XN, Kong Y, Wang X, Tian H, Li K, Mao LL, Bai X, Tang BX, Yan XQ, Li SM, Zhou L, Dai J, Tang XW, Ran FW, Yao S, Guo J, Cui CL. Toripalimab (anti-PD-1) versus High-Dose Interferon-α2b as Adjuvant Therapy in Resected Mucosal Melanoma: A Phase II Randomized Trial. Ann Oncol 2022; 33:1061-1070. [PMID: 35842199 DOI: 10.1016/j.annonc.2022.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/25/2022] [Accepted: 07/06/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND No standard of care for mucosal melanoma (MM) in the adjuvant setting has been established. Meanwhile, relapse-free survival (RFS) is only about five months after surgery alone. This phase II trial aimed to compare toripalimab vs. high-dose interferon-α2b (HDI) as an adjuvant therapy for resected MM. PATIENTS AND METHODS From July 2017 to May 2019, 145 patients with resected MM were randomized (1:1) to receive HDI (N = 72) or toripalimab (N = 73) for one year until disease relapse/distant metastasis, unacceptable toxicity, or withdrawal of consent. The primary endpoint was RFS. The secondary endpoints included distant metastasis-free survival (DMFS), overall survival (OS), and safety. RESULTS After a median follow-up of 26.3 months, the numbers of RFS, OS, and DMFS events were 51 vs. 46, 33 vs. 29, and 49 vs. 44 in the toripalimab arm and the HDI arm, respectively. The median RFS were 13.6 (95%CI: 8.31-19.02) months and 13.9 (95%CI: 8.28-19.61) months in the toripalimab arm and HDI arm, respectively. The DMFS was not significantly different between the two arms (HR: 1.00, 95%CI: 0.65-1.54). The median OS was 35.1 months (95%CI: 27.93-NR) in the toripalimab arm, with no significant difference in all-cause death (HR: 1.11, 95% CI: 0.66-1.84) for the two arms. The median sums of the patients' actual infusion doses were 3672 mg and 1054.5 MIU in the toripalimab arm and HDI arm, respectively. The incidence of treatment-emergent adverse events with a grade ≥ 3 was much higher in the HDI arm than in the toripalimab arm (87.5% vs. 27.4%). CONCLUSION Toripalimab showed a similar RFS and a more favorable safety profile than HDI, both better than historical data, suggesting that toripalimab might be the better treatment option. However, additional translational studies and better treatment regimens are still warranted to improve the clinical outcome of MM.
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Affiliation(s)
- B Lian
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - L Si
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Z H Chi
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - X N Sheng
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Y Kong
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - X Wang
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - H Tian
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - K Li
- Department of Cancer Biotherapy Center, Yunnan Cancer Hospital, Kunming, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - L L Mao
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - X Bai
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - B X Tang
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - X Q Yan
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - S M Li
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - L Zhou
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - J Dai
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - X W Tang
- Shanghai Junshi Biosciences, Shanghai, China
| | - F W Ran
- Shanghai Junshi Biosciences, Shanghai, China
| | - S Yao
- Shanghai Junshi Biosciences, Shanghai, China
| | - J Guo
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - C L Cui
- Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing, China.
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14
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Yang X, Lian B, Li Y, Xue J, Wang Y, Wang Y, Xun Z, Zhang N, Sun H, Long J, Song Z, Lu L, Pan J, Zhao L, Guan M, Yang X, Mao Y, Sang X, Wang K, Zhao HT. Genomic characterization and translational immunotherapy of microsatellite instability-high (MSI-H) in cholangiocarcinoma. J Clin Oncol 2022. [DOI: 10.1200/jco.2022.40.16_suppl.4101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
4101 Background: Microsatellite instability-high (MSI-H) status is a unique genomic state with encouraging effects of PD-1-based therapy in patients with advanced cancer. Cholangiocarcinoma is often driven by genetic mutations. However, the genomic characterization and translational medicine of MSI-H are not clear. Methods: In this study, 881 Chinese patients with cholangiocarcinoma (582 intrahepatic cholangiocarcinoma and 299 extrahepatic cholangiocarcinoma) were enrolled and their genomes were investigated using panel sequencing or whole-exome sequencing. Clinicopathological and genomic features as well as PD-1 inhibitor-based immunotherapy were analyzed by MSI status in patients with cholangiocarcinoma. Results: Overall, 47 (5.3%) cholangiocarcinoma patients were identified as MSI-H patients after enrichment enrollment. Intrahepatic cholangiocarcinoma (ICC) accounted for 74.47% (35/47) of MSI-H patients. Clinicopathological parameters showed younger, ICC-dominated, and more positive PD-L1 expression in MSI-H patients. In the genome of MSI-H cholangiocarcinoma, ACVR2A (75.00%), ARID1A (75.0%), KMT2D (72.2%), TGFBR2 (63.9%), PBRM1 (58.3%), RNF43 (55.6%), TP53 (52.8%) ), ARID1B (47.2%) had a higher mutation frequency. Comparing the SNV and INDEL mutation in the genome, the differential genes between MSI-H and MSS were ARID1A, ACVR2A, KMT2D, TGFBR2, PBRM1, RNF43, LRP1B, ARID1B, etc., respectively. In addition, the differential mutation pathways of MSI-H showed that the mutation rate of DDR, SWI/SNF CellCycle, HRD and other pathways was significantly higher than that of MSS samples. The tumor mutation burden (TMB) in MSI-H patients was significantly higher than that in MSS (P<0.001). In a cohort of 151 CCA patients who received PD-1 inhibitor-based immunotherapy, 19 patients with MSI-H cholangiocarcinoma were found to have a favorable prognosis (1-year survival rate 68.4%). Compared with 132 MSS cholangiocarcinoma patients, Patients with MSI-H cholangiocarcinoma had significantly prolonged OS (Not reach vs. 13.4m, P<0.001, HR=0.17, P <0.001) and high clinical benefit (CBR) (OR=8.16, P <0.001). In this immunotherapy cohort, ≥2 DDR pathway genes and ≥2 SWI/SNF pathway genes mutations, positive PD-L1 expression and TMB-H were also associated with better OS and CBR (both P<0.05). Conclusions: MSI-H cholangiocarcinoma has distinct genomic features, and the effect of PD-1 inhibitors immunotherapy is excellent to these patients. Clinical trial information: NCT03892577.
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Affiliation(s)
- Xu Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Yiran Li
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinnan Xue
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yunchao Wang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanyu Wang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ziyu Xun
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Zhang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huishan Sun
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junyu Long
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Leilei Lu
- Shanghai OrigiMed Co., Ltd, Shanghai, China
| | - Jie Pan
- Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Lin Zhao
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Mei Guan
- Department of Medical Oncology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaobo Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yilei Mao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinting Sang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kai Wang
- Shanghai OrigiMed Co., Ltd, Shanghai, China
| | - Hai-Tao Zhao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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15
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Lian B, Cao XP, Deng HJ, Jiang J, Jiang KW, Li XX, Li YS, Lin GL, Liu JH, Bai SM, Wang F, Wang ZQ, Wu AW, Xiao Y, Yao HW, Yuan WT, Zhang W, Zhang Z, Zhou YB, Ma TH, Zhao QC. [Questionnaire investigation of radiation rectal injury with anxiety, depression and somatic disorder]. Zhonghua Wei Chang Wai Ke Za Zhi 2021; 24:984-990. [PMID: 34823299 DOI: 10.3760/cma.j.cn441530-20210804-00308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Objective: To observe the incidence and treatment of radiation rectal injury complicated with anxiety, depression and somatic symptom disorder. Methods: A cross-sectional survey research method was carried out. Patients with radiation rectal injury managed by members of the editorial board of Chinese Journal of Gastrointestinal Surgery were the subjects of investigation. The inclusion criteria of the survey subjects: (1) patients suffered from pelvic tumors and received pelvic radiotherapy; (2) colonoscopy showed inflammatory reaction or ulcer in the rectum. Exclusion criteria: (1) patient had a history of psycho-somatic disease before radiotherapy; (2) patient was unable to use a smart phone, unable to read and understand the questions in the questionnaire displayed on the phone; (3) patient refused to sign an informed consent form. According to the SOMA self-rating scale, PHQ-15 self-rating scale, GAD-7 and PHQ-9 self-rating scale, the electronic questionnaire of "Psychological Survey of Radiation Proctitis" was designed. The questionnaire was sent to patients with radiation rectal injury managed by the committee through the WeChat group. Observational indicators: (1) radiation rectal injury symptom assessment: using SOMA self-rating scale, radiation rectal injury symptom classification: mild group (≤3 points), moderate group (4-6 points) and severe group (> 6 points); (2) incidence of anxiety, depression and physical disorder: using GAD-7, PHQ-9 and PHQ-15 self-rating scales respectively for assessment; (3) correlation of radiation rectal injury symptom grading with anxiety, depression, and somatic symptom disorder. Results: Seventy-one qualified questionnaires were collected, of which 41 (56.9%) were from Guangzhou. Among the 71 patients, 6 were males and 65 were females; the mean age was (55.7±9.3) years old and 48 patients (67.6%) were less than 60 years old; the median confirmed duration of radiation rectal injury was 2.0 (1.0, 5.0) years. (1) Evaluation of symptoms of radiation rectal injury: 18 cases of mild (25.4%), 27 cases of moderate (38.0%), and 26 cases of severe (36.6%). (2) Incidence of anxiety, depression and somatic disorder: 12 patients (16.9%) without comorbidities; 59 patients (83.1%) with anxiety, depression, or somatic disorder, of whom 2 patients only had anxiety, 1 patient only had depression, 9 only had somatic disorder, 2 had anxiety plus depression, 4 had anxiety plus somatic disorder, 2 had depression plus somatic disorder, and 40 had all three symptoms. (3) correlation of radiation rectal injury grading with anxiety, depression, and somatic symptom disorder: as compared to patients in mild group and moderate group, those in severe group had higher severity of anxiety and somatic symptom disorder (Z=-2.143, P=0.032; Z=-2.045, P=0.041), while there was no statistically significant difference of depression between mild group and moderate group (Z=-1.176, P=0.240). Pearson correlation analysis revealed that radiation rectal injury symptom score was positively correlated with anxiety (r=0.300, P=0.013), depression (r=0.287, P=0.015) and somatic symptom disorder (r=0.344, P=0.003). Conclusions: The incidence of anxiety, depression, and somatic symptom disorder in patients with radiation rectal injury is extremely high. It is necessary to strengthen the diagnosis and treatment of somatic symptom disorder, so as to alleviate the symptoms of patients with pelvic perineum pain and improve the quality of life.
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Affiliation(s)
- B Lian
- Department of Digestive Surgery, the First Affiliated Hospital of Air Force Military Medical University, Xi'an 710000, China
| | - X P Cao
- Department of Radiotherapy, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China
| | - H J Deng
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - J Jiang
- Research Institute of General Surgery, Jinling Hospital, Nanjing 210002, China
| | - K W Jiang
- Department of Gastrointestinal Surgery, Peking University People's Hospital, Beijing 100044, China
| | - X X Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Y S Li
- Department of General Surgery, Shanghai Ninth People's Hospital, Medical School of Shanghai Jiaotong University, Shanghai 200011, China
| | - G L Lin
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - J H Liu
- Department of Radiotherapy, Sun Yat-Sen University Cancer Center, Guangzhou 510060, China
| | - S M Bai
- Department of Radiology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510199, China
| | - F Wang
- Department of Gastroenterology, Beijing Tsinghua Changgung Hospital, School of Clinical Medical, Tsinghua University, Beijing 102218, China
| | - Z Q Wang
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - A W Wu
- Department of Gastrointestinal Cancer, Unit III, Peking University Cancer Hospital & Institute, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Bejing 100142, China
| | - Y Xiao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - H W Yao
- Department of General Surgery, Beijing Friendship Hospital, Capital Medical University & National Clinical Research Center for Digestive Diseases, Beijing 100050, China
| | - W T Yuan
- Department of Colorectal and Anal Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - W Zhang
- Department of Colorectal Surgery, Changhai Hospital, the Navy Medical University, Shanghai 200433, China
| | - Z Zhang
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Y B Zhou
- Department of Gastrointestinal Surgery, the Affiliated Hospital of Qingdao University, Qingdao 266003, China
| | - T H Ma
- Department of Colorectal Surgery, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, Guangzhou 510655, China
| | - Q C Zhao
- Department of Digestive Surgery, the First Affiliated Hospital of Air Force Military Medical University, Xi'an 710000, China
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16
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Lian B, Cui C, Si L, Chi Z, Sheng X, Mao L, Wang X, Tang B, Bai X, Yan X, Li S, Zhou L, Zhou H, Wang Y, Hou QS, Guo J. 1086P IBI310 alone or in combination with sintilimab for advanced melanoma: Updated results of a phase Ia/Ib study. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.1471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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17
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Song R, Cheng X, Lian B, Zhang X, Zhang J, Li K, Fu W. P33.05 Identifying Biomarkers of Immune Signature Related to Smoking and Overall Survival in NSCLC on Gene Co-Expression Network. J Thorac Oncol 2021. [DOI: 10.1016/j.jtho.2021.01.674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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Huang W, Zhao S, Zhang C, Li Z, Ge S, Lian B, Feng H, Wang K, Xu R, Ji J, Gao J, Shi W, Shen L. Identification of "regulation of RhoA activity panel" as a prognostic and predictive biomarker for gastric cancer. Aging (Albany NY) 2020; 13:714-734. [PMID: 33288739 PMCID: PMC7835016 DOI: 10.18632/aging.202179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/14/2020] [Indexed: 11/29/2022]
Abstract
RhoA is a member of the RHO family GTPases and is associated with essential functions in gastric cancer. In this study, we identified a gastric cancer biomarker, termed the “regulation of RhoA activity panel” (RRAP). Patients with gastric cancer from The Cancer Genome Atlas database were divided into training (N=160) and validation (N=155) cohorts. A cohort of 109 Chinese gastric cancer patients was utilized as an independent validation. Patients with mutated RRAP showed significantly better overall survival than patients with wild type RRAP. We also analyzed the association between RRAP and the migration capacity, immune-related signatures, and the tumor microenvironment. RRAP-mutant tumors had a significantly lower degree of lymph node metastasis and lower activities of migration-related pathways. These tumors also showed significantly increased immune cell infiltration and cytotoxic activity. Furthermore, two independent patient cohorts who received immune checkpoint blockade therapy were assessed for RRAP mutant status. As expected, for both immunotherapy cohorts, higher response rates to immune checkpoint blockade therapy were observed in patients with RRAP-mutant tumors than in patients with wild type RRAP tumors. Overall, this study indicates that the RRAP gene set is a potential biomarker for gastric cancer prognosis and therapeutic selection.
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Affiliation(s)
- Wenwen Huang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | | | - Cheng Zhang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Zhongwu Li
- Department of Pathology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Sai Ge
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | | | - Hui Feng
- Shanghai Junshi Biosciences Co., Ltd, Shanghai 201203, China
| | - Kai Wang
- OrigiMed Inc., Shanghai 201112, China
| | - Ruihua Xu
- State Key Laboratory of Oncology in South China, Department of Medical Oncology, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jiafu Ji
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Jing Gao
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen 518116, China
| | - Weiwei Shi
- OrigiMed Inc., Shanghai 201112, China.,Department of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
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Liu T, Chen E, Xu C, Li W, Li Q, Cui Y, Yu Y, Shi W, Lian B, Qu YT. Genomic alterations and clinical correlations of Chinese patients with hepatoid adenocarcinoma of the stomach/alpha-fetoprotein gastric cancer. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.e13514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e13514 Background: Hepatoid adenocarcinoma of stomach (HAS) is a rare subtype of gastric cancer (GC) with poor prognosis due to frequent liver metastasis. HAS, recognized as an extrahepatic cancer that resembles hepatocellular carcinoma (HCC), is characterized by solid sheet-like growth structures with hepatoid differentiation and excessive production of alpha-fetoprotein (AFP). This HAS subtype of GC (AFPGC) is genetically distinct compared to other common GC but requires more evidences for better characterization. Methods: Formalin-fixed, paraffin-embedded (FFPE) tumor tissues were collected from 25 HAS and 9 AFPGC patients at Zhongshan Hospital from July 2013 to August 2017 for whole exome sequencing (WES) test. The testing was carried out by a College of American Pathologists (CAP) accredited and Clinical Laboratory Improvement Amendments (CLIA) certified laboratory. Results: Our cohort included 25 males and 9 females who had undergone surgical treatment. The 25 HAS patients had a median age of 66.5 years (range 48-82) and the 9 AFPGC patients had a median age of 64 years (range 52-76). Patients with AFP>20 had a significantly better overall survival (OS) compared with patients with AFP≤20. The most frequently mutated genes were TP53 (44%), TTN (44%), and MUC19 (30%) in HAS tumor samples and CDC27 (44%), NKX2-3 (44%), and TTN (44%) in AFPGC samples. Patients with URI1 or POP4 alterations had a significantly poorer OS than patients without those genes mutations (7.6 months vs. 19.8 months, p = 0.016, and 10.9 months vs. 19.7 months, p = 0.038, respectively). However, patients with SPTA1 alterations had a significantly better OS compared to patients without SPTA1 alterations (27.6 months vs. 15.8 months, p = 0.042). Patients with higher tumor mutational burden (TMB) (≥3.9 muts/Mb) had a significantly better OS compared with patients with lower TMB (<3.9 muts/Mb), which indicated TMB may be an independent prognostic factor (HR: 0.032, 95%CI: 0.003-0.33, p = 0.004). Conclusions: Our study revealed the genomic profile of HAS/AFPGC patients. The most frequently mutated genes in HAS and AFPGC were different, which helps to better characterize these tumors. AFP and TMB may be potential biomarkers for predicting patients’ prognosis.
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Affiliation(s)
- Tianshu Liu
- Zhongshan Hospital, Fudan University, Shanghai, China
| | - Erbao Chen
- Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chen Xu
- Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei Li
- Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qian Li
- Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yuehong Cui
- Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yiyi Yu
- Zhongshan Hospital, Fudan University, Shanghai, China
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Si L, Mao L, Zhou L, Li C, Wang X, Cui C, Sheng X, Chi Z, Lian B, Tang B, Yan X, Li S, Bai X, Dai J, Kong Y, Lin L, Zhang J, Wu Z, Hui A, Guo J. A phase Ia/Ib clinical study to evaluate the safety, pharmacokinetics (PK) and preliminary anti-tumour activity of FCN-159 in patients with advanced melanoma harboring NRAS-aberrant (Ia) and NRAS-mutation (Ib). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz255.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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21
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Dai J, Si L, Cui C, Sheng X, Kong Y, Chi Z, Mao L, Wang X, Lian B, Li S, Yan X, Tang B, Bai X, Zhou L, Guo J. Genomic landscape of primary malignant melanoma of esophagus. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz255.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Wang G, Ouyang J, Li S, Wang H, Lian B, Liu Z, Xie L. The analysis of risk factors for diabetic nephropathy progression and the construction of a prognostic database for chronic kidney diseases. J Transl Med 2019; 17:264. [PMID: 31409386 PMCID: PMC6693179 DOI: 10.1186/s12967-019-2016-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/05/2019] [Indexed: 12/12/2022] Open
Abstract
Background Diabetic nephropathy (DN) affects about 40% of diabetes mellitus (DM) patients and is the leading cause of chronic kidney disease (CKD) and end-stage renal disease (ESRD) all over the world, especially in high- and middle-income countries. Most DN has been present for years before it is diagnosed. Currently, the treatment of DN is mainly to prevent or delay disease progression. Although many important molecules have been discovered in hypothesis-driven research over the past two decades, advances in DN management and new drug development have been very limited. Moreover, current animal/cell models could not replicate all the features of human DN, while the development of Epigenetics further demonstrates the complexity of the mechanism of DN progression. To capture the key pathways and molecules that actually affect DN progression from numerous published studies, we collected and analyzed human DN prognostic markers (independent risk factors for DN progression). Methods One hundred and fifty-one DN prognostic markers were collected manually by reading 2365 papers published between 01/01/2002 and 12/15/2018. One hundred and fifteen prognostic markers of other four common CKDs were also collected. GO and KEGG enrichment analysis was done using g:Profiler, and a relationship network was built based on the KEGG database. Tissue origin distribution was derived mainly from The Human Protein Atlas (HPA), and a database of these prognostic markers was constructed using PHP Version 5.5.15 and HTML5. Results Several pathways were significantly enriched corresponding to different end point events. It is shown that the TNF signaling pathway plays a role through the process of DN progression and adipocytokine signaling pathway is uniquely enriched in ESRD. Molecules, such as TNF, IL6, SOD2, etc. are very important for DN progression, among which, it seems that “AGER” plays a pivotal role in the mechanism. A database, dbPKD, was constructed containing all the collected prognostic markers. Conclusions This study developed a database for all prognostic markers of five common CKDs, offering some bioinformatics analyses of DN prognostic markers, and providing useful insights towards understanding the fundamental mechanism of human DN progression and for identifying new therapeutic targets. Electronic supplementary material The online version of this article (10.1186/s12967-019-2016-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gang Wang
- Division of Nephrology, Jinling Hospital, Southern Medical University, Nanjing, 210016, China.,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Jian Ouyang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Shen Li
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Hui Wang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China
| | - Baofeng Lian
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Zhihong Liu
- Division of Nephrology, Jinling Hospital, Southern Medical University, Nanjing, 210016, China. .,National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, 210016, China.
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China.
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Bai X, Mao LL, Chi ZH, Sheng XN, Cui CL, Kong Y, Dai J, Wang X, Li SM, Tang BX, Lian B, Zhou L, Yan XQ, Guo J, Si L. BRAF inhibitors: efficacious and tolerable in BRAF-mutant acral and mucosal melanoma. Neoplasma 2019; 64:626-632. [PMID: 28485171 DOI: 10.4149/neo_2017_419] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BRAF inhibitors substantially have impressive clinical efficacy in cutaneous melanoma. However, their role in acral and mucosal melanoma remains unclear. Records were reviewed of patients with metastatic or unresectable BRAF-mutant acral and mucosal melanoma hospitalized and administrated BRAF inhibitors during January 2011 and March 2016. Clinical data were collected to determine PFS, ORR, DCR, OS, and safety. Among 28 acral and 12 mucosal melanoma patients treated with BRAF inhibitors, median PFS were 3.6 (95%CI 3.0-6.4) and 4.4 (95%CI 0.8-12.7) months, median OS were 6.2 (95%CI 6.1-12.1) and 8.2 (95%CI 6.6-19.9) months; ORRs were 38.1% and 20.0%, DCRs were 81.0% and 70.0% in acral and mucosal melanoma, respectively. BRAF inhibitors were well tolerated. The most common adverse effects (AEs) were cutaneous and hematological. Grade 3/4 AEs were relatively rare. In conclusion, BRAF inhibitors have acceptable efficacy and good tolerance in BRAF mutant acral and mucosal melanoma.
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Wang Y, Liu Z, Lian B, Liu L, Xie L. Integrative Analysis of Dysfunctional Modules Driven by Genomic Alterations at System Level Across 11 Cancer Types. Comb Chem High Throughput Screen 2019; 21:771-783. [DOI: 10.2174/1386207322666190122110726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/15/2018] [Accepted: 11/09/2018] [Indexed: 01/05/2023]
Abstract
Aim and Objective:
Integrating multi-omics data to identify driver genes and key
biological functions for tumorigenesis remains a major challenge.
Method:
A new computational pipeline was developed to identify the Driver Mutation-Differential
Co-Expression (DM-DCE) modules based on dysfunctional networks across 11 TCGA cancers.
Results:
Functional analyses provided insight into the properties of various cancers, and found
common cellular signals / pathways of cancers. Furthermore, the corresponding network analysis
identified conservations or interactions across different types of cancers, thus the crosstalk between
the key signaling pathways, immunity and cancers was found. Clinical analysis also identified key
prognostic / survival patterns.
Conclusion:
Taken together, our study sheds light on both cancer-specific and cross-cancer
characteristics systematically.
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Affiliation(s)
- Yin Wang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
| | - Zhenhao Liu
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
| | - Baofeng Lian
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
| | - Lei Liu
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
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Crowther MR, Ford CD, Lian B, Mitchell Q. A COMPARISON OF CUSTODIAL AND NON-CUSTODIAL RURAL AFRICAN AMERICAN GRANDPARENTS ON EMOTIONAL HEALTH AND WELL-BEING. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.2260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- M R Crowther
- The University of Alabama, Tuscaloosa, Alabama, United States
| | - C D Ford
- The University of Alabama Tuscaloosa,AL
| | - B Lian
- Mercer University Macon, GA
| | - Q Mitchell
- The University of Alabama Tuscaloosa, AL
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Cui C, Yan X, Liu S, Deitz A, Si L, Chi Z, Sheng X, Lian B, Li J, Ge J, Wang X, Mao L, Tang B, Zhou L, Bai X, Li S, Li B, Wu H, Guo J. Treatment pattern and clinical outcomes of patients with locally advanced and metastatic melanoma in a real-world setting in China. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy289.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Wang X, Cui C, Yu J, Kong Y, Si L, Chi Z, Sheng X, Mao L, Lian B, Tang B, Yan X, Guo J. Soluble PD-L1 as a prognostic factor in advanced acral and mucosal melanoma. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy289.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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28
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Mao L, Wang X, Si L, Kong Y, Chi Z, Sheng X, Cui C, Lian B, Tang B, Yan X, Guo J. The use of PD-1 inhibitors for the advanced melanoma of esophagus. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy289.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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29
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Li X, Sheng XN, Chi ZH, Cui CL, Si L, Mao LL, Tang BX, Lian B, Wang X, Yan XQ, Li SM, Bai X, Zhou L, Kong Y, Dai J, Guo J. [Impact of first-line chemotherapy on renal function in patients with advanced upper tract urothelial carcinoma]. Zhonghua Yi Xue Za Zhi 2018; 98:2574-2578. [PMID: 30220142 DOI: 10.3760/cma.j.issn.0376-2491.2018.32.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To observe the impact of first-line chemotherapy on renal function in patients with unresectable/metastatic upper tract urothelial carcinoma(UTUC). Methods: A total of 222 (130 males and 92 females) unresectable/metastatic upper tract urothelial carcinoma patients were included in the study between January 2005 and May 2017, with age of 29 to 87 (62.4±10.1) years old. The serum creatinine level and estimated glomerular filtration rate (eGFR) were compared before and after first-line chemotherapy. And predictive factors for decreased renal function were analyzed in logistic regression model. Results: After the first-line chemotherapy, the average serum creatinine level increased, with a median changing value of 1.5 μmol/L. Howerver, the eGFR improved, with a median changing value of 0.5 ml·min-1· (1.73 m2)-1, but the differences were not statistically significant (all P>0.05). In 149 patients who were treated with cisplatin-based chemotherapy, the average serum creatinine level increased by 1.31 μmol/L and eGFR improved by 0.14 ml·min-1·(1.73 m2)-1, but the differences were not statistically significant (P>0.05). In multivariate logistic regression model, age more than and equal to 60 years old (OR=0.88, P=0.745) and cisplatin-based chemotherapy (OR=0.95, P=0.893) did not increase the risk of renal dysfunction after first-line chemotherapy. If the time interval between surgery and first-line chemotherapy was more than 1 year, the risk of renal dysfunction due to chemotherapy decreased (OR=0.54, P=0.196). Eastern Cooperative Oncology Group Performance Status (ECOG PS) Scale≥1 (OR=1.81, P=0.131), anemia before treatment (OR=1.14, P=0.764), the cycles of first-line chemotherapy (OR=1.41, P=0.398) may lead to increase the risk of renal dysfunction, but the differences were not statistically significant. However in the patients who accepted nephrectomy, the risk of renal dysfunction after chemotherapy increased, but the difference was still not statistically significant (OR=3.06, P=0.089). Conclusions: First-line chemotherapy, especially the cisplatin-based regimen, had no significant impact on renal function in the patients with UTUC. Nephrectomy maybe a predictive risk factor for decreased renal function after chemotherapy. Adequate assessment of renal function before treatment, hydration and close monitoring during chemotherapy can effectively protect renal function of the patients.
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Affiliation(s)
- X Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Renal Cancer and Melanoma, Peking University Cancer Hospital & Institute, Beijing 100142, China
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Lian B, De Luca S, You Y, Alwarappan S, Yoshimura M, Sahajwalla V, Smith SC, Leslie G, Joshi RK. Extraordinary water adsorption characteristics of graphene oxide. Chem Sci 2018; 9:5106-5111. [PMID: 29938042 PMCID: PMC5994872 DOI: 10.1039/c8sc00545a] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/16/2018] [Indexed: 11/21/2022] Open
Abstract
The laminated structure of graphene oxide (GO) confers unique interactions with water molecules which may be utilised in a range of applications that require materials with tuneable hygroscopic properties. The precise role of the expandable interlayer spacing and functional groups in GO laminates has not completely been understood to date. Herein, we report the experimental and theoretical investigations on the adsorption and desorption behaviour of water in GO laminates as a function of relative pressure. We observed that GO imparts high water uptake capacity of up to 0.58 gram of water per gram of GO (g g-1), which is significantly higher than silica gel as a conventional desiccant material. More interestingly, the adsorption and desorption kinetics of GO is five times higher than silica gel. The observed extraordinary adsorption/desorption rate can be attributed to the high capillary pressure in GO laminates as well as micro meter sized tunnel-like wrinkles located at the surface.
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Affiliation(s)
- B Lian
- School of Chemical Engineering , University of New South Wales Sydney , Australia
| | - S De Luca
- School of Chemical Engineering , University of New South Wales Sydney , Australia
| | - Y You
- School of Materials Science and Engineering , University of New South Wales , Sydney , Australia .
| | - S Alwarappan
- CSIR - Central Electrochemical Research Institute , Karaikudi 630003 , Tamilnadu , India
| | - M Yoshimura
- Surface Science Laboratory , Toyota Technological Institute , Nagoya , Japan
| | - V Sahajwalla
- School of Materials Science and Engineering , University of New South Wales , Sydney , Australia .
| | - S C Smith
- School of Chemical Engineering , University of New South Wales Sydney , Australia
| | - G Leslie
- School of Chemical Engineering , University of New South Wales Sydney , Australia
| | - R K Joshi
- School of Materials Science and Engineering , University of New South Wales , Sydney , Australia .
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31
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Lian B, Xin H, Zhimin S. Abstract P4-03-07: Combined genome-scale CRISPR-Cas9 knockout screening with transcriptome sequencing to identify paclitaxel related drivers in triple negative breast cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p4-03-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background. Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancers, for which the only standard therapeutics is chemotherapy containing Taxol. However, quite a number of TNBC patients cannot get the expected drug response after paclitaxel treatment and the resistant mechanism has not been clear yet. Other than the traditional “genotype-to-phenotype” means, the high-throughput functional screening, such as CRISPR-CAS9 library, selects genes with the phenotype of interest. Here, we combine the novel screening model with the drug-resistant genotype to explore the decisive role in paclitaxel effect.
Methods. Breast cancer cell line MDA-MB-231(231WT) was treated by paclitaxel from 1ug/ml to 5ug/ml to establish a paclitaxel-resistant cell type (231PTX) for transcriptome sequencing. Genome-scale CRISPR-Cas9 sgRNA library was made into lentivirus to affect MDA-MB-231 cells expressed Cas9 protein (231cas9). Then 231cas9-sgRNA was treated by low dose of paclitaxel for 14 days and was read by next generation sequencing. RNA sequencing data was processed to TPM values and sgRNA data to gene ranking and p value. The threshold of “231PTX TPM/231WT TPM” was above 2 or below 1/2 and the gene p value was smaller than 0.05. Biological technology applied in this study includes western blot (WB), immunofluorescence (IF), real time PCR and cell proliferation assay. In vivo, 20 balb/c mouse were injected MDA-MB-231 in situ for tumor formation and were treated with paclitaxel/normal saline for six times.
Results. Crosstalk between these two sequencing data had result of 124 genes related to paclitaxel resistance (fold change> 2 and p value<0.05 compared Day 14 treated group to Day 14 untreated group) and 18 genes related to paclitaxel sensitivity (fold change< 1/2 and p value<0.05 compared Day 14 untreated group to Day 14 treated group). Considering clinical prognosis and gene information, six paclitaxel resistant candidates and four paclitaxel sensitive candidates were chosen for further research. Eight (STRA6, BIRC3, MTUS1, HDAC9, ADAM28, S1PR5, TNNC1, ZKSCAN7) of ten candidates displayed consistent phenotypes with sequencing results including mRNA expression and the cellular proliferation in paclitaxel treatment. HDAC9 is a histone deacetylation gene that is likely to be a paclitaxel resistant gene. Knockout HDAC9 (231H9 KO) contributed to nearly 2-fold decrease IC50 value (1.7nM versus 3.7nM, p value<0.01). Confocal microscopy observed the formation of multiple spindle foci in the paclitaxel treated 231H9 KO cells. After treatment with paclitaxel, the mark of polymerized tubulin, acetylation tubulin and the mark of cell cycle G2/M, cyclin B1 were notably increased when HDAC9 knockout in both MD-MB1-231 and BT-100 cell lines. In vivo assays found that HDAC9 knockout induced the declined tumorigenesis and more sensitive breast tumors to paclitaxel.
Conclusions.Combined Genome-scale CRISPR-Cas9 knockout screening with transcriptome sequencing is efficient to investigate potent drug targets. In vitro assays suggest that HDAC9 is conductive to paclitaxel resistance in TNBC cells. In vivo results imply inhibition HDAC9 may beneficial to paclitaxel therapeutic response.
Citation Format: Lian B, Xin H, Zhimin S. Combined genome-scale CRISPR-Cas9 knockout screening with transcriptome sequencing to identify paclitaxel related drivers in triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P4-03-07.
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Affiliation(s)
- B Lian
- Fudan University Shanghai Cancer Center, China; Shanghai Medical College, Fudan University, China
| | - H Xin
- Fudan University Shanghai Cancer Center, China; Shanghai Medical College, Fudan University, China
| | - S Zhimin
- Fudan University Shanghai Cancer Center, China; Shanghai Medical College, Fudan University, China
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Li X, Xu Y, Cui H, Huang T, Wang D, Lian B, Li W, Qin G, Chen L, Xie L. Prediction of synergistic anti-cancer drug combinations based on drug target network and drug induced gene expression profiles. Artif Intell Med 2017; 83:35-43. [DOI: 10.1016/j.artmed.2017.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 04/18/2017] [Accepted: 05/11/2017] [Indexed: 12/12/2022]
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Cui C, Lian B, Chi Z, Si L, Sheng X, Bixia T, Mao L, Wang X, Yan X, Li S, Zhou L, Bai X, Guo J. Phase Ic trial of intralesional OrienX010 oncolytic viral therapy into liver metastases among melanoma patients. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx667.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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34
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Mao L, Si L, Bai X, Chi Z, Cui C, Sheng X, Lian B, Bixia T, Yan X, Guo J. Choice of adjuvant therapy in uveal melanoma: A retrospective analysis in China. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx667.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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35
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Lian B, Cui C, Zhou L, Song X, Zhang X, Wu D, Si L, Chi Z, Sheng X, Balch C, Guo J. 404O The natural history and patterns of metastases from mucosal melanoma: an analysis of 706 prospectively-followed patients from china. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw589.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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36
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Wang HY, Jia HY, Lin XX, Lian B, Zhang T. [The surrounding radiation dose of iodine-125 seeds on normal larynx tissue in rabbits]. Lin Chung Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2016; 30:1957-1959. [PMID: 29798274 DOI: 10.13201/j.issn.1001-1781.2016.24.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Indexed: 11/12/2022]
Abstract
Objective:To monitor the change of the radiation dose of the rabbits which were implanted rasioactive 125I seed into the normal laryngeal tiseue at different time,and to evaluate the safety of radiation protection. Method:Sixty New Zwaland rabbits, weighing 2.15-2.30 kg,were randomly divided into 5 groups:7 d,1month,2 month,4 month group and the control group, 12 rabbits in each group Iodine-125 of 0.8 mCi were implanted into the right side of the first trachea ring. At the different time and different distance, the surrounding radiation dose was measured after 4 months of implanting. The results were analyzed in statistics. Result:With the increase of the distance and the prolong of the time, the radiation dose was decreasing,and with the increase of distance,the radiation dose decreased slowly. At the site of 1 meter from the seeds, the detected dose is close to the natural background radiation dose. Conclusion:The clinical application of radioactive 125I seed interstitial implant is easy to protected,the surrounding close contacts is satety.
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Affiliation(s)
- H Y Wang
- Department of Otolaryngology,the First Affiliated Hospital of Ji'nan University,Guangzhou
| | - H Y Jia
- Department of Otolaryngology,the First Affiliated Hospital of Ji'nan University,Guangzhou
| | - X X Lin
- Department of Otolaryngology,the First Affiliated Hospital of Ji'nan University,Guangzhou
| | - B Lian
- Department of Otolaryngology,the First Affiliated Hospital of Ji'nan University,Guangzhou
| | - T Zhang
- Department of Otolaryngology,the First Affiliated Hospital of Ji'nan University,Guangzhou
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37
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Liu X, Lian B, Lin Y. [Gene regulatory network of hepatocellular carcinoma: a review]. Sheng Wu Gong Cheng Xue Bao 2016; 32:1322-1331. [PMID: 29027443 DOI: 10.13345/j.cjb.160045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the common malignant tumors. HCC gene regulatory network (HCC GRN), whose nodes consist of genes, miRNAs or TFs and whose edges consist of interaction relationships of nodes, is one of the important ways to study molecular mechanism of HCC. Based on various experimental data, types of HCC GRNs could be conducted such as TF-miRNA regulatory network. Integrating the studies of HCC GRN, TF-miRNA transcriptional regulatory network performs better in identifying core genes which play important roles in network disturbances. It is a trend that gene variations and transcriptional regulatory networks should be combined, however the corresponding research is almost blank. This review summarizes the source of HCC data sources, the classification, character, and research program of HCC GRN. Finally, according to present analysis and discussion of progress and research status of HCC GRN, we provide a useful reference for researchers.
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Affiliation(s)
- Xiangqiong Liu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.,Shanghai Center for Bioinformation Technology, Shanghai 201203, China
| | - Baofeng Lian
- Affiliated First People's Hospital, Shanghai Jiaotong University, Shanghai 200240, China.,Shanghai Center for Bioinformation Technology, Shanghai 201203, China
| | - Yong Lin
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
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Yi FX, Yu YH, Wei CY, Yang WP, Qin QH, Tan QX, Mo QG, Huang Z, Lian B. [Efficacy observation of (125)I seed implantation therapy for locoregional recurrent and metastatic breast cancer]. Zhonghua Zhong Liu Za Zhi 2016; 38:472-5. [PMID: 27346407 DOI: 10.3760/cma.j.issn.0253-3766.2016.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE To assess the efficacy and side effects of (125)I seed implantation for locoregional recurrent and metastatic breast cancer, and to discuss its role in the comprehensive therapy of breast cancer. METHODS Forty-three patients with locoregional recurrent or metastatic breast cancer were included in this study. They received (125)I seed implantation and were followed up to evaluate the efficacy and adverse reactions of the treatment. RESULTS Among 54 lesions in the 43 cases, there were complete response (CR) in 39, partial response (PR) in 13, stable disease (SD) in 2 patients, with a response rate of 96.3%. All 17 cases with local pain achieved pain relief. With a median follow up of 36 months (range 14 to 60 months), the 1-, 3-, and 5-year local control rate was 85.2%, 53.7% and 1.9%, and the 1-, 3-, and 5-year survival rate was 95.3%, 67.4% and 37.2%, respectively. No serious radiotherapy side effect was observed. CONCLUSION In patients with unresectable locoregional recurrent or metastatic breast cancer, (125)I seed implantation shows proved efficacy and few complications, and can be an important treatment option.
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Affiliation(s)
- F X Yi
- Department of Breast Surgery, Tumor Hospital Affiliated to Guangxi Medical University, Nanning 530021, China
| | - Y H Yu
- Department of Breast Surgery, Tumor Hospital Affiliated to Guangxi Medical University, Nanning 530021, China
| | - C Y Wei
- Department of Breast Surgery, Tumor Hospital Affiliated to Guangxi Medical University, Nanning 530021, China
| | - W P Yang
- Department of Ultrasound Diagnosis, Tumor Hospital Affiliated to Guangxi Medical University, Nanning 530021, China
| | - Q H Qin
- Department of Breast Surgery, Tumor Hospital Affiliated to Guangxi Medical University, Nanning 530021, China
| | - Q X Tan
- Department of Breast Surgery, Tumor Hospital Affiliated to Guangxi Medical University, Nanning 530021, China
| | - Q G Mo
- Department of Breast Surgery, Tumor Hospital Affiliated to Guangxi Medical University, Nanning 530021, China
| | - Z Huang
- Department of Breast Surgery, Tumor Hospital Affiliated to Guangxi Medical University, Nanning 530021, China
| | - B Lian
- Department of Breast Surgery, Tumor Hospital Affiliated to Guangxi Medical University, Nanning 530021, China
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Ouyang J, Sun Y, Li W, Zhang W, Wang D, Liu X, Lin Y, Lian B, Xie L. dbPHCC: a database of prognostic biomarkers for hepatocellular carcinoma that provides online prognostic modeling. Biochim Biophys Acta Gen Subj 2016; 1860:2688-95. [PMID: 26940364 DOI: 10.1016/j.bbagen.2016.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/27/2016] [Accepted: 02/26/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common malignant cancers with a poor prognosis. For decades, more and more biomarkers were found to effect on HCC prognosis, but these studies were scattered and there were no unified identifiers. Therefore, we built the database of prognostic biomarkers and models for hepatocellular carcinoma (dbPHCC). METHODS dbPHCC focuses on biomarkers which were related to HCC prognosis by traditional experiments rather than high-throughput technology. All of the prognostic biomarkers came from literatures issued during 2002 to 2014 in PubMed and were manually selected. dbPHCC collects comprehensive information of candidate biomarkers and HCC prognosis. RESULTS dbPHCC mainly contains 567 biomarkers: 323 proteins, 154 genes, and 90 microRNAs. For each biomarker, the reference information, experimental conditions, and prognostic information are shown. Based on two available patient cohort data sets, an exemplified prognostic model was constructed using 15 phosphotransferases in dbPHCC. The web interface does not only provide a full range of browsing and searching, but also provides online analysis tools. dbPHCC is available at http://lifecenter.sgst.cn/dbphcc/ CONCLUSIONS dbPHCC provides a comprehensive and convenient search and analysis platform for HCC prognosis research. GENERAL SIGNIFICANCE dbPHCC is the first database to focus on experimentally verified individual biomarkers, which are related to HCC prognosis. Prognostic markers in dbPHCC have the potential to be therapeutic drug targets and may help in designing new treatments to improve survival of HCC patients. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.
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Affiliation(s)
- Jian Ouyang
- Biomedical Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Ying Sun
- Biomedical Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Wei Li
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China
| | - Wen Zhang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of People Libration Army General Hospital, Beijing 100048, China
| | - Dandan Wang
- Biomedical Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Xiangqiong Liu
- Biomedical Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yong Lin
- Biomedical Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Baofeng Lian
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China; Shanghai Jiaotong University Affiliated First People's Hospital, Shanghai 200240, China.
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai 201203, China.
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Yu X, Lian B, Wang L, Zhang Y, Dai E, Meng F, Liu D, Wang S, Liu X, Wang J, Li X, Jiang W. The pan-cancer analysis of gene expression patterns in the context of inflammation. Mol Biosyst 2015; 10:2270-6. [PMID: 24958091 DOI: 10.1039/c4mb00258j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Although several studies have investigated the essential roles of inflammation in tumor progression, not many have systematically analyzed gene expression patterns across diverse cancers in the context of inflammation. In this study, in order to better understand the inflammatory scenario, we initially constructed the inflammatory timeline (IT) based on two gene expression profiles during inflammatory progression (inflammatory bowel disease and Helicobacter pylori infection). Then, we separately identified the differentially expressed genes (DEGs) from 25 cancer-related microarray data. By comparing the distributions of DEGs in the IT, we identified three novel pan-cancer gene expression patterns. In the first pattern, the up-regulated genes in cancers were over-expressed in the early phase of inflammation, while the down-regulated genes were over-expressed in the late phase of inflammation. The second pattern was the opposite of the first one. The third pattern appeared to be transitional between the first and second patterns. We found that some cancers with different tissue origins have similar gene expression patterns. Finally, we identified two sets of tissue-independent inflammatory signatures that were over-expressed in early and late phases of inflammation, respectively. The dominant biological processes of early inflammatory signatures were cell proliferation, DNA replication, and DNA repair, whereas the late inflammatory signatures were reflective of innate immune response, neutrophil migration, and antigen processing. These inflammatory signatures may be useful to predict gene expression patterns in human cancers. Therefore, the pan-cancer analysis of gene expression patterns in the context of inflammation provides a novel insight into cancers and an unprecedented opportunity to develop new therapies.
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Affiliation(s)
- Xuexin Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, China.
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Wang S, Li W, Lian B, Liu X, Zhang Y, Dai E, Yu X, Meng F, Jiang W, Li X. TMREC: A Database of Transcription Factor and MiRNA Regulatory Cascades in Human Diseases. PLoS One 2015; 10:e0125222. [PMID: 25932650 PMCID: PMC4416930 DOI: 10.1371/journal.pone.0125222] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 03/22/2015] [Indexed: 11/18/2022] Open
Abstract
Over the past decades, studies have reported that the combinatorial regulation of transcription factors (TFs) and microRNAs (miRNAs) is essential for the appropriate execution of biological events and developmental processes. Dysregulations of these regulators often cause diseases. However, there are no available resources on the regulatory cascades of TFs and miRNAs in the context of human diseases. To fulfill this vacancy, we established the TMREC database in this study. First, we integrated curated transcriptional and post-transcriptional regulations to construct the TF and miRNA regulatory network. Next, we identified all linear paths using the Breadth First Search traversal method. Finally, we used known disease-related genes and miRNAs to measure the strength of association between cascades and diseases. Currently, TMREC consists of 74,248 cascades and 25,194 cascade clusters, involving in 412 TFs, 266 miRNAs and 545 diseases. With the expanding of experimental support regulation data, we will regularly update the database. TMREC aims to help experimental biologists to comprehensively analyse gene expression regulation, to understand the aetiology and to predict novel therapeutic targets.TMREC is freely available at http://bioinfo.hrbmu.edu.cn/TMREC/.
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Affiliation(s)
- Shuyuan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
| | - Wei Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
- EpiRNA Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Baofeng Lian
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, P. R. China
- Shanghai Center for Bioinformation Technology, Shanghai, 201203, P. R. China
| | - Xinyi Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
| | - Enyu Dai
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
| | - Xuexin Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
| | - Fanlin Meng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
| | - Wei Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
- * E-mail: (XL); (WJ)
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, P. R. China
- * E-mail: (XL); (WJ)
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Sun H, Chen C, Lian B, Zhang M, Wang X, Zhang B, Li Y, Yang P, Xie L. Identification of HPV Integration and Gene Mutation in HeLa Cell Line by Integrated Analysis of RNA-Seq and MS/MS Data. J Proteome Res 2015; 14:1678-86. [PMID: 25698088 DOI: 10.1021/pr500944c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Han Sun
- Shanghai
Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Ke Yuan Road, Shanghai 201203, China
- Key
Laboratory of Systems Biology, Shanghai Institutes for Biological
Science, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Chen Chen
- Department
of Chemistry, Institutes of Biomedical Sciences, Fudan University, 138
Yixueyuan Road, Shanghai, 200433, China
| | - Baofeng Lian
- Shanghai
Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Ke Yuan Road, Shanghai 201203, China
| | - Menghuan Zhang
- Shanghai
Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Ke Yuan Road, Shanghai 201203, China
| | - Xiaojing Wang
- Department
of Biomedical Informatics, Vanderbilt University School of Medicine, 2525
West End Avenue, Nashville, Tennessee 37232, United States
| | - Bing Zhang
- Department
of Biomedical Informatics, Vanderbilt University School of Medicine, 2525
West End Avenue, Nashville, Tennessee 37232, United States
| | - Yixue Li
- Shanghai
Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Ke Yuan Road, Shanghai 201203, China
- Key
Laboratory of Systems Biology, Shanghai Institutes for Biological
Science, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Pengyuan Yang
- Department
of Chemistry, Institutes of Biomedical Sciences, Fudan University, 138
Yixueyuan Road, Shanghai, 200433, China
| | - Lu Xie
- Shanghai
Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 1278 Ke Yuan Road, Shanghai 201203, China
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Li W, Yu J, Lian B, Sun H, Li J, Zhang M, Li L, Li Y, Liu Q, Xie L. Identifying prognostic features by bottom-up approach and correlating to drug repositioning. PLoS One 2015; 10:e0118672. [PMID: 25738841 PMCID: PMC4349868 DOI: 10.1371/journal.pone.0118672] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/22/2015] [Indexed: 12/31/2022] Open
Abstract
Background Traditionally top-down method was used to identify prognostic features in cancer research. That is to say, differentially expressed genes usually in cancer versus normal were identified to see if they possess survival prediction power. The problem is that prognostic features identified from one set of patient samples can rarely be transferred to other datasets. We apply bottom-up approach in this study: survival correlated or clinical stage correlated genes were selected first and prioritized by their network topology additionally, then a small set of features can be used as a prognostic signature. Methods Gene expression profiles of a cohort of 221 hepatocellular carcinoma (HCC) patients were used as a training set, ‘bottom-up’ approach was applied to discover gene-expression signatures associated with survival in both tumor and adjacent non-tumor tissues, and compared with ‘top-down’ approach. The results were validated in a second cohort of 82 patients which was used as a testing set. Results Two sets of gene signatures separately identified in tumor and adjacent non-tumor tissues by bottom-up approach were developed in the training cohort. These two signatures were associated with overall survival times of HCC patients and the robustness of each was validated in the testing set, and each predictive performance was better than gene expression signatures reported previously. Moreover, genes in these two prognosis signature gave some indications for drug-repositioning on HCC. Some approved drugs targeting these markers have the alternative indications on hepatocellular carcinoma. Conclusion Using the bottom-up approach, we have developed two prognostic gene signatures with a limited number of genes that associated with overall survival times of patients with HCC. Furthermore, prognostic markers in these two signatures have the potential to be therapeutic targets.
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Affiliation(s)
- Wei Li
- Key Laboratory of Biomedical Photonics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Jian Yu
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
| | - Baofeng Lian
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai, 200240, P. R. China
| | - Han Sun
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, 200031, P. R. China
| | - Jing Li
- Key Laboratory of Biomedical Photonics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Menghuan Zhang
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai, 200240, P. R. China
| | - Ling Li
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
| | - Yixue Li
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai, 200240, P. R. China
- Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, 200031, P. R. China
| | - Qian Liu
- Key Laboratory of Biomedical Photonics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
- * E-mail: (LX); (QL)
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai, 201203, P. R. China
- * E-mail: (LX); (QL)
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Zhang Y, Qiu Z, Wei L, Tang R, Lian B, Zhao Y, He X, Xie L. Integrated analysis of mutation data from various sources identifies key genes and signaling pathways in hepatocellular carcinoma. PLoS One 2014; 9:e100854. [PMID: 24988079 PMCID: PMC4079600 DOI: 10.1371/journal.pone.0100854] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/28/2014] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Recently, a number of studies have performed genome or exome sequencing of hepatocellular carcinoma (HCC) and identified hundreds or even thousands of mutations in protein-coding genes. However, these studies have only focused on a limited number of candidate genes, and many important mutation resources remain to be explored. PRINCIPAL FINDINGS In this study, we integrated mutation data obtained from various sources and performed pathway and network analysis. We identified 113 pathways that were significantly mutated in HCC samples and found that the mutated genes included in these pathways contained high percentages of known cancer genes, and damaging genes and also demonstrated high conservation scores, indicating their important roles in liver tumorigenesis. Five classes of pathways that were mutated most frequently included (a) proliferation and apoptosis related pathways, (b) tumor microenvironment related pathways, (c) neural signaling related pathways, (d) metabolic related pathways, and (e) circadian related pathways. Network analysis further revealed that the mutated genes with the highest betweenness coefficients, such as the well-known cancer genes TP53, CTNNB1 and recently identified novel mutated genes GNAL and the ADCY family, may play key roles in these significantly mutated pathways. Finally, we highlight several key genes (e.g., RPS6KA3 and PCLO) and pathways (e.g., axon guidance) in which the mutations were associated with clinical features. CONCLUSIONS Our workflow illustrates the increased statistical power of integrating multiple studies of the same subject, which can provide biological insights that would otherwise be masked under individual sample sets. This type of bioinformatics approach is consistent with the necessity of making the best use of the ever increasing data provided in valuable databases, such as TCGA, to enhance the speed of deciphering human cancers.
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Affiliation(s)
- Yuannv Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaoping Qiu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin Wei
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ruqi Tang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Baofeng Lian
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China
| | - Yingjun Zhao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xianghuo He
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- * E-mail: (XH); (LX)
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China
- * E-mail: (XH); (LX)
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Li L, Lian B, Li C, Li W, Li J, Zhang Y, He X, Li Y, Xie L. Integrative analysis of transcriptional regulatory network and copy number variation in intrahepatic cholangiocarcinoma. PLoS One 2014; 9:e98653. [PMID: 24897108 PMCID: PMC4045758 DOI: 10.1371/journal.pone.0098653] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 05/06/2014] [Indexed: 01/02/2023] Open
Abstract
Background Transcriptional regulatory network (TRN) is used to study conditional regulatory relationships between transcriptional factors and genes. However few studies have tried to integrate genomic variation information such as copy number variation (CNV) with TRN to find causal disturbances in a network. Intrahepatic cholangiocarcinoma (ICC) is the second most common hepatic carcinoma with high malignancy and poor prognosis. Research about ICC is relatively limited comparing to hepatocellular carcinoma, and there are no approved gene therapeutic targets yet. Method We first constructed TRN of ICC (ICC-TRN) using forward-and-reverse combined engineering method, and then integrated copy number variation information with ICC-TRN to select CNV-related modules and constructed CNV-ICC-TRN. We also integrated CNV-ICC-TRN with KEGG signaling pathways to investigate how CNV genes disturb signaling pathways. At last, unsupervised clustering method was applied to classify samples into distinct classes. Result We obtained CNV-ICC-TRN containing 33 modules which were enriched in ICC-related signaling pathways. Integrated analysis of the regulatory network and signaling pathways illustrated that CNV might interrupt signaling through locating on either genomic sites of nodes or regulators of nodes in a signaling pathway. In the end, expression profiles of nodes in CNV-ICC-TRN were used to cluster the ICC patients into two robust groups with distinct biological function features. Conclusion Our work represents a primary effort to construct TRN in ICC, also a primary effort to try to identify key transcriptional modules based on their involvement of genetic variations shown by gene copy number variations (CNV). This kind of approach may bring the traditional studies of TRN based only on expression data one step further to genetic disturbance. Such kind of approach can easily be extended to other disease samples with appropriate data.
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Affiliation(s)
- Ling Li
- School of Life Sciences and Technology, Tongji University, Shanghai, P.R.China
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
| | - Baofeng Lian
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
- School of Life Sciences and Technology, Shanghai Jiaotong University, Shanghai, P.R.China
| | - Chao Li
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
| | - Wei Li
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
| | - Jing Li
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
| | - Yuannv Zhang
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
| | - Xianghuo He
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
| | - Yixue Li
- School of Life Sciences and Technology, Tongji University, Shanghai, P.R.China
- School of Life Sciences and Technology, Shanghai Jiaotong University, Shanghai, P.R.China
- Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China
- * E-mail: (LX); (YL)
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China
- * E-mail: (LX); (YL)
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Wei L, Lian B, Zhang Y, Li W, Gu J, He X, Xie L. Application of microRNA and mRNA expression profiling on prognostic biomarker discovery for hepatocellular carcinoma. BMC Genomics 2014; 15 Suppl 1:S13. [PMID: 24564407 PMCID: PMC4046763 DOI: 10.1186/1471-2164-15-s1-s13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most highly malignant and lethal cancers of the world. Its pathogenesis has been reported to be multi-factorial, and the molecular carcinogenesis of HCC can not be attributed to just a few individual genes. Based on the microRNA and mRNA expression profiling of normal liver tissues, pericancerous hepatocellular tissues and hepatocellular carcinoma tissues, we attempted to find prognosis related gene sets for HCC patients. Results We identified differentially expressed genes (DEG) from three comparisons: Cancer/Normal, Cancer/Pericancerous and Pericancerous/Normal. GSEA (gene set enrichment analysis) were performed. Based on the enriched gene sets of GO terms, pathways and transcription factor targets, it was found that the genome instability and cell proliferation increased while the metabolism and differentiation decreased in HCC tissues. The expression profile of DEGs in each enriched gene set was used to correlate to the postoperative survival time of HCC patients. Nine gene sets were found to prognostic correlation. Furthermore, after substituting DEG-targeting-microRNA for DEG members of each gene set, two gene sets with the microRNA expression profiles were obtained that had prognostic potential. Conclusions The malignancy of HCC could be represented by gene sets, and pericancerous liver exhibits important characteristics of liver cancer. The expression level of gene sets not only in HCC but also in the pericancerous liver showed potential for prognosis implying an option for HCC prognosis at an early stage. Additionally, the gene-targeting-microRNA expression profiles also showed prognostic potential, demonstrating that the multi-factorial molecular pathogenesis of HCC is contributed by various genes and microRNAs. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-S1-S13) contains supplementary material, which is available to authorized users.
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Jiang W, Zhang Y, Meng F, Lian B, Chen X, Yu X, Dai E, Wang S, Liu X, Li X, Wang L, Li X. Identification of active transcription factor and miRNA regulatory pathways in Alzheimer’s disease. Bioinformatics 2013; 29:2596-602. [DOI: 10.1093/bioinformatics/btt423] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Yuan W, Huang T, Yu J, Zeng L, Lian B, He Q, Li Y, Zhang X, Zhou F, Xie L. Comparative analysis of viral protein interaction networks in Hepatitis B virus and Hepatitis C virus infected HCC. Biochim Biophys Acta 2013; 1844:271-9. [PMID: 23774196 DOI: 10.1016/j.bbapap.2013.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 05/09/2013] [Accepted: 06/04/2013] [Indexed: 02/07/2023]
Abstract
Previously, the different mechanisms of HBV infection and HCV infection were studied experimentally. Multiple studies also compared the differential network between HBV induced HCC and HCV induced HCC based on gene expression data. However network level comparison combining viral-human interaction network and dysfunctional protein interaction network for HBV and HCV-HCC has rarely been done before. In this work we did some pioneer job in construction of HBV/HCV viral dysfunctional network in HCC, in hope of investigating viral infection impact on the change of genome expression and eventually, the development of HCC. We found that HBx, the main HBV viral protein, directly acted on the gene groups of cell cycle, which could perfectly explain the dominant cell proliferation effect shown in the dysfunctional network of HBV-HCC. On the other hand, multiple important HCV viral proteins including CORE, NS3 and NS5A were found to target very important cancer related proteins such as TP53 and SMAD3, but no direct targeting to major immune response or inflammation related proteins. Therefore the dominant activation of immune response and inflammation related pathways shown in dysfunctional network of HCV-HCC might not be a direct effect of HCV infection. They might have been an indirect demonstration of activated cancer promoting pathways. Similar approaches may as well be applied to other important virus infection caused human diseases to help elucidate the mechanisms of virus-host interaction, and even help with investigations on anti-virus based therapies. This article is part of a Special Issue entitled: Computational Proteomics, Systems Biology & Clinical Implications.
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Affiliation(s)
- Weilan Yuan
- School of Life Sciences and Technology, Tongji University, Shanghai 200092, PR China; Shanghai Center for Bioinformation Technology, Shanghai 201203, PR China.
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Cheng S, Lian B, Liang J, Shi T, Xie L, Zhao YL. Site selectivity for protein tyrosine nitration: insights from features of structure and topological network. Mol BioSyst 2013; 9:2860-8. [DOI: 10.1039/c3mb70260j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Li X, Jiang W, Li W, Lian B, Wang S, Liao M, Chen X, Wang Y, Lv Y, Wang S, Yang L. Dissection of human MiRNA regulatory influence to subpathway. Brief Bioinform 2011; 13:175-86. [PMID: 21908864 DOI: 10.1093/bib/bbr043] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The global insight into the relationships between miRNAs and their regulatory influences remains poorly understood. And most of complex diseases may be attributed to certain local areas of pathway (subpathway) instead of the entire pathway. Here, we reviewed the studies on miRNA regulations to pathways and constructed a bipartite miRNAs and subpathways network for systematic analyzing the miRNA regulatory influences to subpathways. We found that a small fraction of miRNAs were global regulators, environmental information processing pathways were preferentially regulated by miRNAs, and miRNAs had synergistic effect on regulating group of subpathways with similar function. Integrating the disease states of miRNAs, we also found that disease miRNAs regulated more subpathways than nondisease miRNAs, and for all miRNAs, the number of regulated subpathways was not in proportion to the number of the related diseases. Therefore, the study not only provided a global view on the relationships among disease, miRNA and subpathway, but also uncovered the function aspects of miRNA regulations and potential pathogenesis of complex diseases. A web server to query, visualize and download for all the data can be freely accessed at http://bioinfo.hrbmu.edu.cn/miR2Subpath.
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Affiliation(s)
- Xia Li
- College of Bioinformatics Science and Technology and Bio-pharmaceutical Key Laboratory of Heilongjiang Province, Harbin Medical University, Harbin 150081, P. R. China.
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