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Article ; Online: Dear-DIA

He, Qingzu / Zhong, Chuan-Qi / Li, Xiang / Guo, Huan / Li, Yiming / Gao, Mingxuan / Yu, Rongshan / Liu, Xianming / Zhang, Fangfei / Guo, Donghui / Ye, Fangfu / Guo, Tiannan / Shuai, Jianwei / Han, Jiahuai

Research (Washington, D.C.)

2023 Volume 6, Page(s) 179

Abstract: Data-independent acquisition (DIA) technology for protein identification from mass spectrometry and related algorithms is developing rapidly. The spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition ... ...

Abstract	Data-independent acquisition (DIA) technology for protein identification from mass spectrometry and related algorithms is developing rapidly. The spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition data represents a promising direction. In this paper, we proposed an untargeted analysis method, Dear-DIA
Language	English
Publishing date	2023-06-26
Publishing country	United States
Document type	Journal Article
ISSN	2639-5274
ISSN (online)	2639-5274
DOI	10.34133/research.0179
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Article ; Online: Dear-DIAXMBD

Qingzu He / Chuan-Qi Zhong / Xiang Li / Huan Guo / Yiming Li / Mingxuan Gao / Rongshan Yu / Xianming Liu / Fangfei Zhang / Donghui Guo / Fangfu Ye / Tiannan Guo / Jianwei Shuai / Jiahuai Han

Research, Vol

Deep Autoencoder Enables Deconvolution of Data-Independent Acquisition Proteomics

2023 Volume 6

Abstract	Data-independent acquisition (DIA) technology for protein identification from mass spectrometry and related algorithms is developing rapidly. The spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition data represents a promising direction. In this paper, we proposed an untargeted analysis method, Dear-DIAXMBD, for direct analysis of DIA data. Dear-DIAXMBD first integrates the deep variational autoencoder and triplet loss to learn the representations of the extracted fragment ion chromatograms, then uses the k-means clustering algorithm to aggregate fragments with similar representations into the same classes, and finally establishes the inverted index tables to determine the precursors of fragment clusters between precursors and peptides and between fragments and peptides. We show that Dear-DIAXMBD performs superiorly with the highly complicated DIA data of different species obtained by different instrument platforms. Dear-DIAXMBD is publicly available at https://github.com/jianweishuai/Dear-DIA-XMBD.
Keywords	Science ; Q
Subject code	006
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	American Association for the Advancement of Science
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Targeting KRAS-mutant stomach/colorectal tumors by disrupting the ERK2-p53 complex.

Wang, Xiang / Xie, Qing / Ji, Yan / Yang, Jiaxin / Shen, Jiayan / Peng, Fangfei / Zhang, Yongfeng / Jiang, Feng / Kong, Xiangyin / Ma, Wenzhe / Liu, Dandan / Zheng, Leizhen / Qing, Chen / Lang, Jing-Yu

Cell reports

2023 Volume 42, Issue 1, Page(s) 111972

Abstract: KRAS is widely mutated in human cancers, resulting in unchecked tumor proliferation and metastasis, which makes identifying KRAS-targeting therapies a priority. Herein, we observe that mutant KRAS specifically promotes the formation of the ERK2-p53 ... ...

Abstract	KRAS is widely mutated in human cancers, resulting in unchecked tumor proliferation and metastasis, which makes identifying KRAS-targeting therapies a priority. Herein, we observe that mutant KRAS specifically promotes the formation of the ERK2-p53 complex in stomach/colorectal tumor cells. Disruption of this complex by applying MEK1/2 and ERK2 inhibitors elicits strong apoptotic responses in a p53-dependent manner, validated by genome-wide knockout screening. Mechanistically, p53 physically associates with phosphorylated ERK2 through a hydrophobic interaction in the presence of mutant KRAS, which suppresses p53 activation by preventing the recruitment of p300/CBP; trametinib disrupts the ERK2-p53 complex by reducing ERK2 phosphorylation, allowing the acetylation of p53 protein by recruiting p300/CBP; acetylated p53 activates PUMA transcription and thereby kills KRAS-mutant tumors. Our study shows an important role for the ERK2-p53 complex and provides a potential therapeutic strategy for treating KRAS-mutant cancer.
MeSH term(s)	Humans ; Phosphorylation ; Proto-Oncogene Proteins p21(ras)/genetics ; Proto-Oncogene Proteins p21(ras)/metabolism ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Protein p53/metabolism ; Colorectal Neoplasms/genetics ; Colorectal Neoplasms/metabolism ; Stomach
Chemical Substances	Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2) ; Tumor Suppressor Protein p53 ; KRAS protein, human
Language	English
Publishing date	2023-01-14
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2022.111972
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Article ; Online: Single-cell profile reveals the landscape of cardiac immunity and identifies a cardio-protective Ym-1

Science bulletin

2024 Volume 69, Issue 7, Page(s) 949–967

Abstract: Myocardial ischemia-reperfusion injury (MIRI) is a major hindrance to the success of cardiac reperfusion therapy. Although increased neutrophil infiltration is a hallmark of MIRI, the subtypes and alterations of neutrophils in this process remain unclear. ...

Abstract	Myocardial ischemia-reperfusion injury (MIRI) is a major hindrance to the success of cardiac reperfusion therapy. Although increased neutrophil infiltration is a hallmark of MIRI, the subtypes and alterations of neutrophils in this process remain unclear. Here, we performed single-cell sequencing of cardiac CD45
MeSH term(s)	Animals ; Mice ; Intercellular Adhesion Molecule-1/genetics ; Myocardial Reperfusion Injury/metabolism ; Myocardium ; Neutrophils
Chemical Substances	Intercellular Adhesion Molecule-1 (126547-89-5)
Language	English
Publishing date	2024-02-07
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2816140-3
ISSN	2095-9281 ; 2095-9273
ISSN (online)	2095-9281
ISSN	2095-9273
DOI	10.1016/j.scib.2024.02.003
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Article ; Online: Immune response to hepatitis B vaccination in human immunodeficiency virus-positive patients in China: A 2-year retrospective study.

Deng, Haohui / Feng, Qianchang / Wu, Yue / Lin, Haowei / Cao, Xin / Xiang, Fangfei / Li, Linghua / Yu, Weihua

Journal of medical virology

2021 Volume 94, Issue 6, Page(s) 2684–2693

Abstract: Currently, the studies focused on the immune response to hepatitis B vaccination in Chinese human immunodeficiency virus (HIV)-positive patients are limited. In this study, the participants with an initial hepatitis B surface antibody (HBsAb) titer <10 ... ...

Abstract	Currently, the studies focused on the immune response to hepatitis B vaccination in Chinese human immunodeficiency virus (HIV)-positive patients are limited. In this study, the participants with an initial hepatitis B surface antibody (HBsAb) titer <10 mIU/ml were assigned to Cohort 1 to receive a standard dose of recombinant hepatitis B vaccine, and participants with an initial HBsAb titer between 10 and 100 mIU/ml were assigned to Cohort 2 to receive a single reinforced recombinant vaccine. In Cohort 1, the immune and high response rates in HIV-positive patients were 93.4%/81.4%, 87.4%/51.5%, and 83.2%/40.7% at 1-3 months, 1 year, and 2 years postvaccination. Multivariate analysis showed that only age and HIV RNA status at baseline were independent factors related to sustained immune response at 2 years postvaccination. In Cohort 2, the high immune response rates in HIV-positive patients were 78.8%, 60.6%, and 51.5% at 1-3 months, 1 year, and 2 years postvaccination. The immune or high response rates did not differ between HIV-positive patients and healthy controls at 1-3 months postvaccination in these two cohorts; however, HBsAb titers were significantly lower in HIV-positive patients. This study summarized the 2-year data of immune response to hepatitis B vaccination and analyzed the factors related to sustained immune response at 2 years postvaccination in Chinese HIV-positive patients.
MeSH term(s)	HIV ; HIV Seropositivity ; Hepatitis B/prevention & control ; Hepatitis B Antibodies ; Hepatitis B Vaccines ; Humans ; Immunity ; Retrospective Studies ; Vaccination
Chemical Substances	Hepatitis B Antibodies ; Hepatitis B Vaccines
Language	English
Publishing date	2021-12-21
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.27523
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Article ; Online: Early Elevation of Fibrosis-4 Liver Fibrosis Score Is Associated With Adverse Outcomes Among Patients With Coronavirus Disease 2019.

Xiang, Fangfei / Sun, Jing / Chen, Po-Hung / Han, Peijin / Zheng, Haipeng / Cai, Shuijiang / Kirk, Gregory D

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2021 Volume 73, Issue 3, Page(s) e594–e601

Abstract: Background: Limited prior data suggest that preexisting liver disease is associated with adverse outcomes among patients with coronavirus disease 2019 (COVID-19). Fibrosis-4 (FIB-4) is a noninvasive index of readily available laboratory measurements ... ...

Abstract	Background: Limited prior data suggest that preexisting liver disease is associated with adverse outcomes among patients with coronavirus disease 2019 (COVID-19). Fibrosis-4 (FIB-4) is a noninvasive index of readily available laboratory measurements that represents hepatic fibrosis. We evaluated the association between FIB-4 at the early stage of infection and COVID-19 outcomes. Methods: FIB-4 was evaluated at admission in a cohort of 267 patients admitted with early-stage COVID-19 confirmed through reverse-transcription polymerase chain reaction assay. Hazard of ventilator use and of high-flow oxygen was estimated using Cox regression models controlled for covariates. Risks of progression to severe disease and of death/prolonged hospitalization were estimated using multivariable logistic regression models. Results: Forty-one (15%) patients progressed to severe disease, 36 (14%) required high-flow oxygen support, 10 (4%) required mechanical ventilator support, and 1 died. FIB-4 between 1.45 and 3.25 was associated with a greater than 5-fold (95% confidence interval [CI], 1.2-28) increased hazard of high-flow oxygen use, a greater than 4-fold (95% CI, 1.5-14.6) increased odds of progression to severe disease, and an over 3-fold (95% CI, 1.4-7.7) increased odds of death or prolonged hospitalization. FIB-4 >3.25 was associated with a greater than 12-fold (95% CI, 2.3-68. 7) increased hazard of high-flow oxygen use and an over 11-fold (95% CI, 3.1-45) increased risk of progression to severe disease. All associations were independent of sex, number of comorbidities, and inflammatory markers (D-dimer, C-reactive protein). Conclusions: FIB-4 at the early-stage of COVID-19 had an independent and dose-dependent association with adverse outcomes during hospitalization. FIB-4 provided significant prognostic value for estimating adverse outcomes among COVID-19 patients.
MeSH term(s)	COVID-19 ; Hospitalization ; Humans ; Liver Cirrhosis/epidemiology ; Liver Diseases ; SARS-CoV-2
Language	English
Publishing date	2021-05-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciaa1710
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Zs.A 1505: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: DNA Framework-Based Topological Cell Sorters.

Yin, Fangfei / Li, Min / Mao, Xiuhai / Li, Fan / Xiang, Xuelin / Li, Qian / Wang, Lihua / Zuo, Xiaolei / Fan, Chunhai / Zhu, Ying

Angewandte Chemie (International ed. in English)

2020 Volume 59, Issue 26, Page(s) 10406–10410

Abstract: Molecular recognition in cell biological process is characterized with specific locks-and-keys interactions between ligands and receptors, which are ubiquitously distributed on cell membrane with topological clustering. Few topologically-engineered ... ...

Abstract	Molecular recognition in cell biological process is characterized with specific locks-and-keys interactions between ligands and receptors, which are ubiquitously distributed on cell membrane with topological clustering. Few topologically-engineered ligand systems enable the exploration of the binding strength between ligand-receptor topological organization. Herein, we generate topologically controlled ligands by developing a family of tetrahedral DNA frameworks (TDFs), so the multiple ligands are stoichiometrically and topologically arranged. This topological control of multiple ligands changes the nature of the molecular recognition by inducing the receptor clustering, so the binding strength is significantly improved (ca. 10-fold). The precise engineering of topological complexes formed by the TDFs are readily translated into effective binding control for cell patterning and binding strength control of cells for cell sorting. This work paves the way for the development of versatile design of topological ligands.
MeSH term(s)	Aptamers, Nucleotide/chemistry ; Cell Line, Tumor ; Cell Separation/methods ; DNA/chemistry ; Humans ; Ligands ; Nucleic Acid Conformation
Chemical Substances	Aptamers, Nucleotide ; Ligands ; DNA (9007-49-2)
Language	English
Publishing date	2020-04-08
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202002020
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Article ; Online: Different clinical characteristics and survival between surgically resected pure and combined small cell lung cancer.

Li, Yujing / Wang, Yanan / Zhou, Wensheng / Chen, Ya / Lou, Yuqing / Qian, Fangfei / Lu, Jun / Jiang, Haohua / Xiang, Biao / Zhang, Yanwei / Han, Baohui / Zhang, Wei

Thoracic cancer

2022 Volume 13, Issue 19, Page(s) 2711–2722

Abstract: Background: Small cell lung cancer (SCLC) is the most malignant and common form of neuroendocrine lung cancer with pure (P-SCLC) and combined subtypes (C-SCLC). However, little is known about the differences between these two groups and in this study we ...

Abstract	Background: Small cell lung cancer (SCLC) is the most malignant and common form of neuroendocrine lung cancer with pure (P-SCLC) and combined subtypes (C-SCLC). However, little is known about the differences between these two groups and in this study we aimed to provide a more comprehensive insight into SCLC. Methods: Data from 580 postoperative patients with pathologically confirmed SCLC in Shanghai Chest Hospital from January 2010 to December 2020 were collected retrospectively. The clinical characteristics and prognosis were analyzed. Results: A total of 357 P-SCLC patients and 223 C-SCLC patients were included. The results indicated that P-SCLC appeared to have a higher proportion of being located in the middle lobe than C-SCLC. The incidences of P-SCLC in patients with visceral pleural invasion (VPI) and in stage II were higher than C-SCLC, while C-SCLC was more likely to be accompanied by higher incidences of epidermal growth factor receptor (EGFR) mutation, anaplastic lymphoma kinase (ALK) rearrangement, and higher levels of CEA, SCCA and CYFRA21-1 than P-SCLC. The most common were SCLC combined with large cell neuroendocrine components among 223 C-SCLCs. Survival analysis confirmed a more favorable disease-free survival (DFS) (p = 0.016) and overall survival (OS) (p = 0.024) in patients with P-SCLCs compared with C-SCLCs. Histological type, tumor location, pN stage, adjuvant chemotherapy, serum NSE and CA125 levels were independent risk factors for survival rate in SCLC. In addition, adjuvant chemotherapy was beneficial in improving stage I P-SCLC and C-SCLC DFS and OS rates, and similar results were not seen in adjuvant radiation therapy. Conclusions: Patients with C-SCLC have a poorer prognosis than P-SCLC patients. We determined that large cell neuroendocrine carcinoma was the most common additional component of C-SCLC, and patients with this component appeared to have a longer DFS and OS than other combined components.
MeSH term(s)	Anaplastic Lymphoma Kinase ; Antigens, Neoplasm ; Carcinoembryonic Antigen ; Carcinoma, Large Cell/pathology ; Carcinoma, Small Cell ; China ; ErbB Receptors ; Humans ; Keratin-19 ; Lung Neoplasms/genetics ; Prognosis ; Retrospective Studies ; Small Cell Lung Carcinoma
Chemical Substances	Antigens, Neoplasm ; Carcinoembryonic Antigen ; Keratin-19 ; antigen CYFRA21.1 ; Anaplastic Lymphoma Kinase (EC 2.7.10.1) ; ErbB Receptors (EC 2.7.10.1)
Language	English
Publishing date	2022-08-29
Publishing country	Singapore
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2625856-0
ISSN	1759-7714 ; 1759-7706
ISSN (online)	1759-7714
ISSN	1759-7706
DOI	10.1111/1759-7714.14604
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Article ; Online: DPHL v.2: An updated and comprehensive DIA pan-human assay library for quantifying more than 14,000 proteins.

Xue, Zhangzhi / Zhu, Tiansheng / Zhang, Fangfei / Zhang, Cheng / Xiang, Nan / Qian, Liujia / Yi, Xiao / Sun, Yaoting / Liu, Wei / Cai, Xue / Wang, Linyan / Dai, Xizhe / Yue, Liang / Li, Lu / Pham, Thang V / Piersma, Sander R / Xiao, Qi / Luo, Meng / Lu, Cong /

Zhu, Jiang / Zhao, Yongfu / Wang, Guangzhi / Xiao, Junhong / Liu, Tong / Liu, Zhiyu / He, Yi / Wu, Qijun / Gong, Tingting / Zhu, Jianqin / Zheng, Zhiguo / Ye, Juan / Li, Yan / Jimenez, Connie R / A, Jun / Guo, Tiannan

Patterns (New York, N.Y.)

2023 Volume 4, Issue 7, Page(s) 100792

Abstract: A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS)-based proteomics. DPHL v.1, a previous pan-human library built from 1,096 data-dependent acquisition (DDA) MS data of 16 human tissue types, ... ...

Abstract	A comprehensive pan-human spectral library is critical for biomarker discovery using mass spectrometry (MS)-based proteomics. DPHL v.1, a previous pan-human library built from 1,096 data-dependent acquisition (DDA) MS data of 16 human tissue types, allows quantifying of 10,943 proteins. Here, we generated DPHL v.2 from 1,608 DDA-MS data. The data included 586 DDA-MS data acquired from 18 tissue types, while 1,022 files were derived from DPHL v.1. DPHL v.2 thus comprises data from 24 sample types, including several cancer types (lung, breast, kidney, and prostate cancer, among others). We generated four variants of DPHL v.2 to include semi-tryptic peptides and protein isoforms. DPHL v.2 was then applied to two colorectal cancer cohorts. The numbers of identified and significantly dysregulated proteins increased by at least 21.7% and 14.2%, respectively, compared with DPHL v.1. Our findings show that the increased human proteome coverage of DPHL v.2 provides larger pools of potential protein biomarkers.
Language	English
Publishing date	2023-07-05
Publishing country	United States
Document type	Journal Article
ISSN	2666-3899
ISSN (online)	2666-3899
DOI	10.1016/j.patter.2023.100792
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Article ; Online: Brca2 deficiency drives gastrointestinal tumor formation and is selectively inhibited by mitomycin C.

Chen, Xiaomin / Peng, Fangfei / Ji, Yan / Xiang, Honggang / Wang, Xiang / Liu, Tingting / Wang, Heng / Han, Yumin / Wang, Changxu / Zhang, Yongfeng / Kong, Xiangyin / Lang, Jing-Yu

Cell death & disease

2020 Volume 11, Issue 9, Page(s) 812

Abstract: BRCA2 is crucial for repairing DNA double-strand breaks with high fidelity, and loss of BRCA2 increases the risks of developing breast and ovarian cancers. Herein, we show that BRCA2 is inactively mutated in 10% of gastric and 7% of colorectal ... ...

Abstract	BRCA2 is crucial for repairing DNA double-strand breaks with high fidelity, and loss of BRCA2 increases the risks of developing breast and ovarian cancers. Herein, we show that BRCA2 is inactively mutated in 10% of gastric and 7% of colorectal adenocarcinomas, and that this inactivation is significantly correlated with microsatellite instability. Villin-driven Brca2 depletion promotes mouse gastrointestinal tumor formation when genome instability is increased. Whole-genome screening data showed that these BRCA2 monoallelic and biallelic mutant tumors were selectively inhibited by mitomycin C. Mechanistically, mitomycin C provoked double-strand breaks in cancer cells that often recruit wild-type BRCA2 for repair; the failure to repair double-strand breaks caused cell-cycle arrest at the S phase and p53-mediated cell apoptosis of BRCA2 monoallelic and biallelic mutant tumor cells. Our study unveils the role of BRCA2 loss in the development of gastrointestinal tumors and provides a potential therapeutic strategy to eliminate BRCA2 monoallelic and biallelic mutant tumors through mitomycin C.
MeSH term(s)	Animals ; BRCA2 Protein/deficiency ; Gastrointestinal Neoplasms/genetics ; Humans ; Mice ; Mitomycin/metabolism
Chemical Substances	BRCA2 Protein ; BRCA2 protein, mouse ; Mitomycin (50SG953SK6)
Language	English
Publishing date	2020-09-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2541626-1
ISSN	2041-4889 ; 2041-4889
ISSN (online)	2041-4889
ISSN	2041-4889
DOI	10.1038/s41419-020-03013-8
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