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Article ; Online: Characterization of Tumor Mutation Burden-Based Gene Signature and Molecular Subtypes to Assist Precision Treatment in Gastric Cancer.

Wei, Cheng / Li, Minzhe / Lin, Shaofeng / Xiao, Jun

2022 Volume 2022, Page(s) 4006507

Abstract: Objective: Tumor mutation burden (TMB) represents a useful biomarker for predicting survival outcomes and immunotherapy response. Here, we aimed to conduct TMB-based gene signature and molecular subtypes in gastric cancer.: Methods: Based on ... ...

Abstract	Objective: Tumor mutation burden (TMB) represents a useful biomarker for predicting survival outcomes and immunotherapy response. Here, we aimed to conduct TMB-based gene signature and molecular subtypes in gastric cancer. Methods: Based on differentially expressed genes (DEGs) between high- and low-TMB groups in TCGA, a LASSO model was developed for predicting overall survival (OS) and disease-free survival (DFS). The predictive performance was externally verified in the GSE84437 dataset. Molecular subtypes were conducted via consensus clustering approach based on TMB-related DEGs. The immune microenvironment was estimated by ESTIMATE and ssGSEA algorithms. Results: High-TMB patients had prolonged survival duration. TMB-related DEGs were distinctly enriched in cancer- (MAPK, P53, PI3K-Akt, and Wnt pathways) and immune-related pathways (T cell selection and differentiation). The TMB-based gene model was developed (including MATN3, UPK1B, GPX3, and RGS2), and high-risk score was predictive of poor prognosis and recurrence. ROC and multivariate analyses revealed the well predictive performance, which was confirmed in the external cohort. Furthermore, we established the nomogram containing the risk score, age, and stage for personalized prediction of OS and DFS. High-risk score was characterized by high stromal score, increased immune checkpoints, immune cell infiltrations, and enhanced sensitivity to gefitinib, vinorelbine, and gemcitabine. Three TMB-based molecular subtypes were conducted, characterized by distinct prognosis, immune microenvironment, and drug sensitivity. Conclusion: Collectively, we established a prognostic signature and three distinct molecular subtypes based on TMB features for gastric cancer, which might be beneficial for prognostic prediction and clinical decision-making.
MeSH term(s)	Biomarkers, Tumor/genetics ; Gene Expression Regulation, Neoplastic ; Humans ; Mutation/genetics ; Phosphatidylinositol 3-Kinases/genetics ; Prognosis ; Stomach Neoplasms/drug therapy ; Stomach Neoplasms/genetics ; Tumor Microenvironment/genetics
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2022-05-13
Publishing country	United States
Document type	Journal Article ; Retracted Publication
ZDB-ID	2698540-8
ISSN	2314-6141 ; 2314-6133
ISSN (online)	2314-6141
ISSN	2314-6133
DOI	10.1155/2022/4006507
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Salvage lymphadenectomy for isolated cervical lymph node recurrence after curative resection of thoracic esophageal squamous cell carcinoma.

Wang, Zhen / Lin, Shaofeng / Wang, Feng / Liu, Shuoyan

Annals of translational medicine

2019 Volume 7, Issue 11, Page(s) 238

Abstract: Background: Patients with thoracic esophageal squamous cell carcinoma (ESCC) often display recurrence in the cervical lymph nodes after surgery. The optimal treatment strategy for these patients has not been established. We retrospectively reviewed ... ...

Abstract	Background: Patients with thoracic esophageal squamous cell carcinoma (ESCC) often display recurrence in the cervical lymph nodes after surgery. The optimal treatment strategy for these patients has not been established. We retrospectively reviewed patients who underwent salvage lymphadenectomy plus adjuvant radiotherapy/chemotherapy for recurrence limited to the cervical lymph nodes to explore whether salvage treatment could provide an opportunity for curing these patients and to observe the prognostic factors for the patients after salvage treatment. Methods: All patients with ESCC who underwent esophagectomy with lymphadenectomy and who were diagnosed with a relapse in the cervical nodes between 2007 to 2014. All cases received salvage lymphadenectomy plus adjuvant radiotherapy/chemotherapy. Their clinical characteristics and outcomes were analysed. Results: A total of 66 patients were diagnosed with recurrence in the cervical nodes after esophagectomy. Among these patients, 21 (31.8%) relapsed 6 months after esophagectomy and 45 (68.2%) recurrences were found 6 months later. Solitary cervical node recurrence was found in 31 (47.0%) patients while 35 (53.0%) cases showed multiple node relapse. Fifty-four (81.8%) patients underwent radical resection while 12 (18.2%) received reduction surgery. The univariate survival analysis showed that patients with solitary cervical node relapse had a better prognosis than patients with multiple node relapse (P=0.001). Patients who were diagnosed with a recurrence in 6 months after esophagectomy had worse outcomes than patients who relapsed 6 months later (P=0.007). Patients who underwent radical salvage lymphadenectomy had better survival than patients who underwent reduction dissection (P=0.004). The number of positive nodes at esophagectomy (3 or more/2 or less) and surgical treatment for recurrence (reduction/radical surgery) were found to have independent prognostic values by multivariate analysis, whereas the other two factors were not statistically significant. Conclusions: Salvage cervical lymphadenectomy plus adjuvant radiotherapy/chemotherapy is an effective and safe treatment for ESCC patients who develop cervical lymph node recurrence after curative esophagectomy. A lower primary N stage and radical resection of recurrent nodes were found to have independent prognostic values for these patients.
Language	English
Publishing date	2019-06-25
Publishing country	China
Document type	Journal Article
ZDB-ID	2893931-1
ISSN	2305-5847 ; 2305-5839
ISSN (online)	2305-5847
ISSN	2305-5839
DOI	10.21037/atm.2019.04.64
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Article: Facile Synthesis of Sandwich-Like rGO/CuS/Polypyrrole Nanoarchitectures for Efficient Electromagnetic Absorption.

Zhang, Bing / Lin, Shaofeng / Zhang, Jingjing / Li, Xiaopeng / Sun, Xiaodong

Materials (Basel, Switzerland)

2020 Volume 13, Issue 2

Abstract: Currently, electromagnetic pollution management has gained much attention due to the various harmful effects on wildlife and human beings. Electromagnetic absorbers can convert energy from electromagnetic waves into thermal energy. Previous reports have ... ...

Abstract	Currently, electromagnetic pollution management has gained much attention due to the various harmful effects on wildlife and human beings. Electromagnetic absorbers can convert energy from electromagnetic waves into thermal energy. Previous reports have demonstrated that reduced graphene oxide (rGO) makes progress in the electromagnetic absorption (EA) field. But the high value of permittivity of rGO always mismatches the impedance which results in more electromagnetic wave reflection on the surface. In this work, sandwich-like rGO/CuS/polypyrrole (PPy) nanoarchitectures have been synthesized by a facile two-step method. The experimental result has shown that a paraffin composite containing 10 wt.% of rGO/CuS/PPy could achieve an enhanced EA performance both in bandwidth and intensity. The minimum reflection loss (RL) value of -49.11 dB can be reached. Furthermore, the effective bandwidth can cover 4.88 GHz. The result shows that the as-prepared rGO/CuS/PPy nanoarchitectures will be a promising EA material.
Language	English
Publishing date	2020-01-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2487261-1
ISSN	1996-1944
ISSN	1996-1944
DOI	10.3390/ma13020446
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Article: Comparison of a modified one-piece mechanical and double-layer hand-sewn anastomosis in McKeown esophagogastrectomy: A single-institute retrospective study.

Zhu, Kunshou / Zhang, Jiulong / Chen, Xiaohui / Deng, Yujie / Lin, Shaofeng / Cai, Yibin / Weng, Guibin

Molecular and clinical oncology

2021 Volume 15, Issue 1, Page(s) 134

Abstract: The present study aimed to introduce a novel method of cervical esophagogastric anastomosis, so-called 'modified one-piece mechanical anastomosis' (MOMA) in McKeown esophagogastrectomy and to compare its feasibility, efficacy and safety with those of ' ... ...

Abstract	The present study aimed to introduce a novel method of cervical esophagogastric anastomosis, so-called 'modified one-piece mechanical anastomosis' (MOMA) in McKeown esophagogastrectomy and to compare its feasibility, efficacy and safety with those of 'conventionally double-layer hand-sewn anastomosis' (CDHA). Between March 2016 and March 2018, 80 consecutive patients with thoracic esophageal squamous cell carcinoma undergoing McKeown esophagogastrectomy with a curative intent were included in the present study. Among them, 40 received MOMA and the other 40 received CDHA. Their medical records, including operation time, anastomotic time, estimated blood loss, postoperative complications within 30 days, as well as survival rate, were retrospectively reviewed, analyzed and compared. Total operation time, anastomotic time and estimated blood loss in the MOMA group were significantly decreased compared with those in the CDHA group (207.73±2.66 vs. 225.40±3.43 min; 10.95±0.44 vs. 23.03±0.47 min; 144.50±21.14 vs. 241.75±23.75 ml; all P<0.01). Anastomotic leakage was present in 1 patient in the CDHA group, but no patients in the MOMA group (P=1.000). Anastomotic stenosis was documented in 4 and 2 patients in the MOMA and CDHA group, respectively (P=0.392). The 30-day operative mortality was 0% and no significant difference was demonstrated in postoperative complications within groups (P>0.05). Furthermore, the disease-free and overall survival was compared by means of Kaplan-Meier survival estimates and log-rank tests and no statistical difference was determined (P=0.5114 and P=0.7875, respectively). McKeown esophagogastrectomy with MOMA may be a feasible, effective and reproducible alternative with relatively satisfactory postoperative outcomes for the treatment of TE-SCC, providing shorter operation and anastomosis times, and less estimated intraoperative blood loss.
Language	English
Publishing date	2021-05-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2796865-0
ISSN	2049-9469 ; 2049-9450
ISSN (online)	2049-9469
ISSN	2049-9450
DOI	10.3892/mco.2021.2296
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Article: Multi-Region Genomic Landscape Analysis for the Preoperative Prediction of Lymph Node Metastasis in Esophageal Carcinoma.

Lin, Shaofeng / Chen, Yanping / Wang, Jianchao / Cai, Yibin / Chen, Xiaohui / Chen, Yuanmei / Shi, Yi / Chen, Gang / Zhu, Kunshou

Frontiers in genetics

2022 Volume 13, Page(s) 830601

Abstract: Objective: ...

Abstract	Objective:
Language	English
Publishing date	2022-03-23
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.830601
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Article ; Online: iPCD: A Comprehensive Data Resource of Regulatory Proteins in Programmed Cell Death.

Tang, Dachao / Han, Cheng / Lin, Shaofeng / Tan, Xiaodan / Zhang, Weizhi / Peng, Di / Wang, Chenwei / Xue, Yu

Cells

2022 Volume 11, Issue 13

Abstract: Programmed cell death (PCD) is an essential biological process involved in many human pathologies. According to the continuous discovery of new PCD forms, a large number of proteins have been found to regulate PCD. Notably, post-translational ... ...

Abstract	Programmed cell death (PCD) is an essential biological process involved in many human pathologies. According to the continuous discovery of new PCD forms, a large number of proteins have been found to regulate PCD. Notably, post-translational modifications play critical roles in PCD process and the rapid advances in proteomics have facilitated the discovery of new PCD proteins. However, an integrative resource has yet to be established for maintaining these regulatory proteins. Here, we briefly summarize the mainstream PCD forms, as well as the current progress in the development of public databases to collect, curate and annotate PCD proteins. Further, we developed a comprehensive database, with integrated annotations for programmed cell death (iPCD), which contained 1,091,014 regulatory proteins involved in 30 PCD forms across 562 eukaryotic species. From the scientific literature, we manually collected 6493 experimentally identified PCD proteins, and an orthologous search was then conducted to computationally identify more potential PCD proteins. Additionally, we provided an in-depth annotation of PCD proteins in eight model organisms, by integrating the knowledge from 102 additional resources that covered 16 aspects, including post-translational modification, protein expression/proteomics, genetic variation and mutation, functional annotation, structural annotation, physicochemical property, functional domain, disease-associated information, protein-protein interaction, drug-target relation, orthologous information, biological pathway, transcriptional regulator, mRNA expression, subcellular localization and DNA and RNA element. With a data volume of 125 GB, we anticipate that iPCD can serve as a highly useful resource for further analysis of PCD in eukaryotes.
MeSH term(s)	Apoptosis/genetics ; Apoptosis Regulatory Proteins/metabolism ; Eukaryota/metabolism ; Eukaryotic Cells/metabolism ; Humans ; Protein Processing, Post-Translational ; Transcription Factors/metabolism
Chemical Substances	Apoptosis Regulatory Proteins ; Transcription Factors
Language	English
Publishing date	2022-06-24
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells11132018
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Article: Combination of neutrophil-to-lymphocyte ratio and albumin concentration to predict the prognosis of esophageal squamous cell cancer patients undergoing esophagectomy.

Lin, Shaofeng / Lin, Jingping / Weng, Jinsen / Su, Weikun / Weng, Guibin / Chen, Yuanmei / Hirahara, Noriyuki / Min, Yang Won / Chen, Xiaohui / Zhu, Kunshou / Lin, Kangni

Journal of thoracic disease

2023 Volume 15, Issue 4, Page(s) 2224–2232

Abstract: Background: Esophageal squamous cell cancer (ESCC) is an aggressive cancer with high incidence and mortality. It is crucial to predict prognosis of these patients individually. Neutrophil-to-lymphocyte ratio (NLR) has been reported as a prognostic ... ...

Abstract	Background: Esophageal squamous cell cancer (ESCC) is an aggressive cancer with high incidence and mortality. It is crucial to predict prognosis of these patients individually. Neutrophil-to-lymphocyte ratio (NLR) has been reported as a prognostic indicator in several tumors, including esophageal cancer. Besides inflammatory factors, nutritional status can impact survival of cancer patients. Albumin (Alb) concentration is an easily obtained indicator to reflect nutritional status. Methods: In this study, we retrospectively collected the data of patients with ESCC and used univariate and multivariate analysis to investigate the relationship between combination of NLR and Alb (NLR-Alb) and survival. Meanwhile, we compared clinical features among NLR-Alb cohorts. Results: Univariate analysis showed that age (P=0.013), gender (P=0.021), surgical type (P=0.031), preoperative therapy (P=0.007), NLR-Alb (P=0.001), and tumor-node-metastasis (TNM) status (P<0.001) were associated with 5-year overall survival (OS). In multivariate analysis, NLR-Alb [hazard ratio (HR) =2.53, 95% confidence interval (95% CI): 1.38-4.63, P=0.003] and TNM status (HR =4.76, 95% CI: 3.09-7.33, P<0.001) were independent predictive factors for 5-year OS. The 5-year OS rates were 83%, 62%, and 55% for NLR-Alb 1, NLR-Alb 2, and NLR-Alb 3, respectively (P=0.001). Conclusions: In summary, pre-operative NLR-Alb is a favorable and cost-effective index to predict prognosis of patients with ESCC individually.
Language	English
Publishing date	2023-04-12
Publishing country	China
Document type	Journal Article
ZDB-ID	2573571-8
ISSN	2077-6624 ; 2072-1439
ISSN (online)	2077-6624
ISSN	2072-1439
DOI	10.21037/jtd-23-333
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Article ; Online: dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes.

Shi, Ying / Zhang, Ying / Lin, Shaofeng / Wang, Chenwei / Zhou, Jiaqi / Peng, Di / Xue, Yu

Scientific data

2020 Volume 7, Issue 1, Page(s) 164

Abstract: In prokaryotes, protein phosphorylation plays a critical role in regulating a broad spectrum of biological processes and occurs mainly on various amino acids, including serine (S), threonine (T), tyrosine (Y), arginine (R), aspartic acid (D), histidine ( ... ...

Abstract	In prokaryotes, protein phosphorylation plays a critical role in regulating a broad spectrum of biological processes and occurs mainly on various amino acids, including serine (S), threonine (T), tyrosine (Y), arginine (R), aspartic acid (D), histidine (H) and cysteine (C) residues of protein substrates. Through literature curation and public database integration, here we reported an updated database of phosphorylation sites (p-sites) in prokaryotes (dbPSP 2.0) that contains 19,296 experimentally identified p-sites in 8,586 proteins from 200 prokaryotic organisms, which belong to 12 phyla of two kingdoms, bacteria and archaea. To carefully annotate these phosphoproteins and p-sites, we integrated the knowledge from 88 publicly available resources that covers 9 aspects, namely, taxonomy annotation, genome annotation, function annotation, transcriptional regulation, sequence and structure information, family and domain annotation, interaction, orthologous information and biological pathway. In contrast to version 1.0 (~30 MB), dbPSP 2.0 contains ~9 GB of data, with a 300-fold increased volume. We anticipate that dbPSP 2.0 can serve as a useful data resource for further investigating phosphorylation events in prokaryotes. dbPSP 2.0 is free for all users to access at: http://dbpsp.biocuckoo.cn.
MeSH term(s)	Archaea/chemistry ; Archaeal Proteins/chemistry ; Bacteria/chemistry ; Bacterial Proteins/chemistry ; Databases, Protein ; Datasets as Topic ; Phosphoproteins/chemistry ; Phosphorylation
Chemical Substances	Archaeal Proteins ; Bacterial Proteins ; Phosphoproteins
Language	English
Publishing date	2020-05-29
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2775191-0
ISSN	2052-4463 ; 2052-4463
ISSN (online)	2052-4463
ISSN	2052-4463
DOI	10.1038/s41597-020-0506-7
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Article: Ultrathin nitrogen-doping graphene films for flexible and stretchable EMI shielding materials

Lin, Shaofeng / He, Yonglyu / Jiang, Dazhi / Ju, Su / Shi, Gang / Zhang, Jianwei

Journal of materials science. 2019 May, v. 54, no. 9

2019

Abstract: Ultrathin, flexible and highly conductive materials that possess excellent electromagnetic interference (EMI) shielding performance are greatly needed, especially for the fabrication of stretchable shielding materials in practical applications such as ... ...

Abstract	Ultrathin, flexible and highly conductive materials that possess excellent electromagnetic interference (EMI) shielding performance are greatly needed, especially for the fabrication of stretchable shielding materials in practical applications such as wearable and foldable electronics. Graphene oxide (GO) sheets are modified with ethylenediamine to prepare cross-linked graphene films using a pressure-assisted self-assembly technique. FTIR and XPS results demonstrate that amine monomers are chemically bonded to GO sheets, with simultaneous reduction of GO sheets. After thermal annealing and followed with compression, the 6.6-μm-thick nitrogen-doping graphene film (rGO-EDA-2) is obtained with ultrahigh electrical conductivity of 8796 S cm−1. The excellent electrical conductivity is mainly attributed to nitrogen-doping effect, defects repair during chemical functionalization and removal of oxygenated groups. Ultrahigh electrical conductivity, multilayer structure and modified electronic structure with nitrogen doping lead to outstanding shielding performance for the rGO-EDA-2 film, with excellent shielding effectiveness (SE) of 58.5 dB and the specific SE/thickness of 43902 dB cm2 g−1, respectively. By fixing the rGO-EDA-2 film on the pre-stretched wavy substrate, the stretchable shielding composite is obtained, with constant EMI SE of 56.3 dB after repeated stretching. The pre-stretched wavy substrate allows the multilayer graphene film to achieve wavy structure after strain release, which is capable of bearing tensile strain up to 32.6%. This study could be significant in the applications of stretchable and wearable electronic devices.
Keywords	annealing ; crosslinking ; electrical conductivity ; electromagnetic interference ; electronic equipment ; electronics ; ethylenediamines ; Fourier transform infrared spectroscopy ; graphene ; graphene oxide ; nitrogen ; tensile strength ; X-ray photoelectron spectroscopy
Language	English
Dates of publication	2019-05
Size	p. 7165-7179.
Publishing place	Springer US
Document type	Article
ZDB-ID	2015305-3
ISSN	1573-4803 ; 0022-2461
ISSN (online)	1573-4803
ISSN	0022-2461
DOI	10.1007/s10853-019-03372-4
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Hypoxia-inducible factor-1α cooperates with histone Lys methylation to predict prognosis in esophageal squamous cell carcinoma.

Shen, Xiaohui / Li, Yiping / Xu, Ying / Liu, Min / Zhang, Qin / Yin, Rong / Zhou, Menghan / Lin, Shaofeng / Fan, Hong

Biomarkers in medicine

2021 Volume 15, Issue 7, Page(s) 509–522

Abstract: Aim: ...

Abstract	Aim:
MeSH term(s)	Adult ; Aged ; Biomarkers, Tumor/metabolism ; Esophageal Neoplasms/genetics ; Esophageal Neoplasms/metabolism ; Esophageal Neoplasms/pathology ; Esophageal Squamous Cell Carcinoma/genetics ; Esophageal Squamous Cell Carcinoma/metabolism ; Esophageal Squamous Cell Carcinoma/pathology ; Female ; Histones/metabolism ; Humans ; Hypoxia-Inducible Factor 1, alpha Subunit/chemistry ; Hypoxia-Inducible Factor 1, alpha Subunit/genetics ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism ; Male ; Methylation ; Middle Aged ; Prognosis ; Survival Rate
Chemical Substances	Biomarkers, Tumor ; HIF1A protein, human ; Histones ; Hypoxia-Inducible Factor 1, alpha Subunit ; histone H3 trimethyl Lys4
Language	English
Publishing date	2021-04-15
Publishing country	England
Document type	Journal Article
ZDB-ID	2481014-9
ISSN	1752-0371 ; 1752-0363
ISSN (online)	1752-0371
ISSN	1752-0363
DOI	10.2217/bmm-2020-0256
Database	MEDical Literature Analysis and Retrieval System OnLINE

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