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Article ; Online: Construction of novel lncRNA-miRNA-mRNA ceRNA networks associated with prognosis of hepatitis C virus related hepatocellular carcinoma

Lishi Shao / Lei Liang / Qixiang Fang / Jiaping Wang

Heliyon, Vol 8, Iss 10, Pp e10832- (2022)

2022

Abstract: Background: Hepatitis C virus (HCV) infection contribute to liver fibrosis and cirrhosis, which significantly increases the risk of hepatocellular carcinoma (HCC) development. Previous studies have demonstrated the pivotal role of competitive endogenous ... ...

Abstract	Background: Hepatitis C virus (HCV) infection contribute to liver fibrosis and cirrhosis, which significantly increases the risk of hepatocellular carcinoma (HCC) development. Previous studies have demonstrated the pivotal role of competitive endogenous RNA (ceRNA) networks in tumorigenesis and cancer progression. Consequently, we herein seek to identify and evaluate the prognostic relevance of a novel ceRNA network associated with HCV-related HCC. Methods: Differentially expressed genes (DEGs) in GSE140846 dataset from GEO were identified using Network Analyst, and GO, KEGG and Reactome analyses were performed. Furthermore, a protein-protein interaction network was generated, and hub genes were detected. Hub gene expression levels, as well as those of their upstream lncRNAs and miRNAs and associated survival analyses were conducted using appropriate bioinformatics databases. Predicted target relationships were used to establish putative ceRNA networks for HCV-related HCC. Results: A total of 372 and 360 up- and down-regulated DE-mRNA were identified, which were associated with nuclear division, cell cycle, and ATPase activity. A PPI network containing 704 DE-mRNAs was constructed, and the 6 hub gene with the highest degree of connectivity were selected for subsequent analysis. We discovered that 22 miRNAs and 4 lncRNAs upstream of 11 hub gene were significantly associated with poor prognosis of HCV-related HCC, and used them to constructe a prognostic ceRNA network. Further experiments confirmed the ceRNA-regulatory relationship of BUB1-hsa-miR-193a-3p-MALAT1. Conclusion: This study provides novel insights into the lncRNA-miRNA-mRNA ceRNA network, and reveals potential lncRNA biomarkers in HCV related HCC.
Keywords	Hepatitis C virus Related hepatocellular carcinoma ; Bioinformatics ; Prognosis ; Competitive endogenous RNA ; Non-coding RNA ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	570
Language	English
Publishing date	2022-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An overview on therapeutic efficacy and challenges of nanoparticles in blood cancer therapy

Jiaping Wang / Lixia Sheng / Yanli Lai / Zhijuan Xu

Journal of King Saud University: Science, Vol 34, Iss 6, Pp 102182- (2022)

2022

Abstract: Cancer is a disease with limited therapeutic options, despite tremendous improvements in medical research and technology. Cancer metastasis and recurrence are major causes of disability and death. Traditional cancer treatments have many limitations, ... ...

Abstract	Cancer is a disease with limited therapeutic options, despite tremendous improvements in medical research and technology. Cancer metastasis and recurrence are major causes of disability and death. Traditional cancer treatments have many limitations, prompting nanotechnology innovation for more precise and less harmful cancer treatment, also known as cancer nanomedicine. In recent years, novel biomolecule-stabilized nanomaterials have emerged as prominent next-generation materials. Nanoparticles, facilitated by advances in nanotechnology, provide possibilities for effective blood cancer therapy. Nanoparticles are amenable to modification. They can be designed to target and control the dose of drug that enter the target region. As a result, nanoparticles may enhance drug effectiveness while reducing negative effects. Several experimental difficulties must be overcome to get nanoparticle treatment to the bedside. Finally it is vital to develop effective formulations that can address the aforementioned concerns while also offering precision targeting of tumour areas without affecting healthy tissue survival. This review primarily focuses on the highlights of current research progress using nanoparticles to deliver various blood cancer therapeutic medicines to illustrate nanoparticles' promise in leukemia, myeloma, and lymphoma therapy. Finally, we explore prospects and possible initiatives for potential therapeutic nanomedicine research.
Keywords	Nanoparticle ; Nanomaterial ; Cancer ; Leukemia ; Myeloma ; Lymphoma ; Science (General) ; Q1-390
Subject code	610
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Mesenchymal Stem Cell Therapy in Kidney Diseases

Fukun Chen / NaNa Chen / Chunjuan Xia / Hongyue Wang / Lishi Shao / Chen Zhou / Jiaping Wang

Cell Transplantation, Vol

Potential and Challenges

2023 Volume 32

Abstract: Kidney disease (KD) is a life-threatening disease characterized by high morbidity and mortality in clinical settings, which can be caused by many reasons, and the incidence increases with age. However, supportive therapy and kidney transplantation still ... ...

Abstract	Kidney disease (KD) is a life-threatening disease characterized by high morbidity and mortality in clinical settings, which can be caused by many reasons, and the incidence increases with age. However, supportive therapy and kidney transplantation still have limitations in alleviating KD progression. Recently, mesenchymal stem cells (MSCs) have shown great potential in repairing injury through their multidirectional differentiation and self-renewal ability. Of note, MSCs serve as a safe and effective therapeutic strategy for treating KD in preclinical and clinical trials. Functionally, MSCs ameliorate KD progression by regulating the immune response, renal tubular cell apoptosis, tubular epithelial–mesenchymal transition, oxidative stress, angiogenesis, and so on. In addition, MSCs exhibit remarkable efficacy in both acute kidney injury (AKI) and chronic kidney disease (CKD) through paracrine mechanisms. In this review, we outline the biological characteristics of MSCs, discuss the efficacy and mechanisms of MSCs-based therapy for KD, summarize the completed and ongoing clinical trials, as well as analyze limitations and new strategies, aiming to provide new ideas and approaches for the preclinical experiments and clinical trials of MSCs transplantation for KD.
Keywords	Medicine ; R
Subject code	610
Language	English
Publishing date	2023-04-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Prognostic and immunological characterization of diffuse large B-cell lymphoma evaluated by co-stimulatory molecular-related features

Lixia Sheng / Tongyu Li / Yun Li / Miao Zhou / Jiaping Wang / Yanli Lai / Yanli Zhang / Ping Yi / Qitian Mu / Guifang Ouyang

Heliyon, Vol 9, Iss 9, Pp e19342- (2023)

2023

Abstract: Background: Co-stimulatory molecules have been shown to enhance antitumor immune responses, but their role in Diffuse Large B-cell Lymphoma (DLBCL) remains unexplored. Methods: This study aimed to explore the molecular typing of DLBCL with co-stimulatory ...

Abstract	Background: Co-stimulatory molecules have been shown to enhance antitumor immune responses, but their role in Diffuse Large B-cell Lymphoma (DLBCL) remains unexplored. Methods: This study aimed to explore the molecular typing of DLBCL with co-stimulatory molecule genes and to construct a prognostic profile to improve treatment decisions and clinical outcomes. Results: We conducted the first comprehensive analysis of co-stimulatory molecules in DLBCL patients and identified five co-stimulatory molecule genes with prognostic and diagnostic values. Consensus cluster analysis based on these five co-stimulatory molecule genes revealed that the two identified clusters had different distribution patterns and prognostic differences. Co-stimulatory molecular correlation signatures were then constructed based on these five co-stimulatory molecular genes and validated in an external dataset, showing good performance in predicting patient prognosis. The signature is an independent risk factor for DLBCL patients and significantly correlates with clinical factors in patients and can be used as a complement to clinical factors. Furthermore, the signature was associated with the tumor immune microenvironment. Patients identified as being at high risk according to our signature exhibit high levels of immune cell infiltration microenvironment. Conclusions: In conclusion, our signature can provide clinicians with prognostic predictions and help guide the treatment of patients with DLBCL.
Keywords	Diffuse large B-Cell lymphoma ; Co-stimulatory molecule ; Prognosis ; Immune microenvironment ; Infiltration ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	610 ; 616
Language	English
Publishing date	2023-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Profile distribution of CO2 in an arid saline-alkali soil with gypsum and wheat straw amendments

Junyi Wang / Xiujun Wang / Jiaping Wang

Scientific Reports, Vol 8, Iss 1, Pp 1-

a two-year incubation experiment

2018 Volume 10

Abstract: Abstract Adding gypsum and/or straw is a common practice for ameliorating saline-alkali soils. However, the effect of amendment on soil CO2 is poorly known. An incubation experiment was conducted for over two years in a saline-alkali soil of Yanqi Basin, ...

Abstract	Abstract Adding gypsum and/or straw is a common practice for ameliorating saline-alkali soils. However, the effect of amendment on soil CO2 is poorly known. An incubation experiment was conducted for over two years in a saline-alkali soil of Yanqi Basin, which included four treatments: control, gypsum addition (Ca), wheat straw addition (S) and gypsum-wheat straw combination (Ca+S). We continuously monitored soil CO2 concentration, temperature and moisture at 15, 30, 45 and 60 cm. There was a clear seasonality in soil CO2 under all four treatments, which was generally similar to those in soil temperature and moisture. Straw addition led to a significant increase in soil CO2 over 0–60 cm in summer. While there was a significant increase of soil CO2 with gypsum addition only, soil CO2 significantly decreased with the addition of gypsum and straw (relative to straw addition only) during autumn and winter in 2014. Interestingly, integrated soil CO2 was lowest in soil profile under the Ca+S treatment during winter and spring. Our study implies that different amendments of organic matter and gypsum may result in various responses and interactions of biological, chemical and physical processes, with implications for the carbon cycle in saline-alkaline soils of arid region.
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2018-08-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: An Aerosol Optical Module With Observation‐Constrained Black Carbon Properties for Global Climate Models

Ganzhen Chen / Jiandong Wang / Yuan Wang / Jiaping Wang / Yuzhi Jin / Yueyue Cheng / Yan Yin / Hong Liao / Aijun Ding / Shuxiao Wang / Jiming Hao / Chao Liu

Journal of Advances in Modeling Earth Systems, Vol 15, Iss 10, Pp n/a-n/a (2023)

2023

Abstract: Abstract Atmospheric black carbon (BC) aerosols have been long‐lasting uncertain components in environmental and climate studies. Global climate models (GCMs) potentially overestimate BC absorption efficiency due to a lack of consideration of complex BC ... ...

Abstract	Abstract Atmospheric black carbon (BC) aerosols have been long‐lasting uncertain components in environmental and climate studies. Global climate models (GCMs) potentially overestimate BC absorption efficiency due to a lack of consideration of complex BC microphysical and mixing properties. We extract multiple BC properties from observations and develop an aerosol optical module known as Advanced Black Carbon (ABC) in the framework of the Modal Aerosol Model version 4 (MAM4). The ABC module is implemented in the Community Atmosphere Model version 6 (CAM6) and evaluated by in situ and remote sensing observations. CAM6‐ABC addresses the shortcomings of CAM6‐MAM4 in terms of BC microphysical and mixing properties, particularly their size, mixing state and optical simulations. Sensitivity simulations show that the global BC absorption aerosol optical depth at 550 nm simulated by CAM6‐ABC is reduced by ∼29% compared with that in CAM6‐MAM4. The BC absorption enhancement simulated by CAM6‐ABC is reduced from ∼2.6 of the default MAM4 to ∼1.4, which is closer to the observed values (mostly less than 1.5). With improved BC absorption estimation, the biases of aerosol single‐scattering coalbedo simulations are reduced by 18%–69% compared with global Aerosol Robotic Network observations. Moreover, the globally averaged BC direct radiative effect is reduced from 0.37 to 0.28 W/m2 at the top of the atmosphere. Our new scheme alleviates the overestimation of BC absorption in GCMs by constraining BC microphysical and mixing properties when assessing aerosol radiative and climate effects, and it can be easily implemented in most modal‐based aerosol modules of climate models.
Keywords	black carbon ; CAM6 ; optical properties ; absorption enhancement ; radiative effects ; mixing states ; Physical geography ; GB3-5030 ; Oceanography ; GC1-1581
Subject code	551
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	American Geophysical Union (AGU)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Data-Driven Learning for Data Rights, Data Pricing, and Privacy Computing

Jimin Xu / Nuanxin Hong / Zhening Xu / Zhou Zhao / Chao Wu / Kun Kuang / Jiaping Wang / Mingjie Zhu / Jingren Zhou / Kui Ren / Xiaohu Yang / Cewu Lu / Jian Pei / Harry Shum

Engineering, Vol 25, Iss , Pp 66-

2023 Volume 76

Abstract: In recent years, data has become one of the most important resources in the digital economy. Unlike traditional resources, the digital nature of data makes it difficult to value and contract. Therefore, establishing an efficient and standard data- ... ...

Abstract	In recent years, data has become one of the most important resources in the digital economy. Unlike traditional resources, the digital nature of data makes it difficult to value and contract. Therefore, establishing an efficient and standard data-transaction market system would be beneficial for lowering cost and improving productivity among the parties in this industry. Although numerous studies have been dedicated to the issue of complying with data regulations and other data-transaction issues such as privacy and pricing, little work has been done to provide a comprehensive review of these studies in the fields of machine learning and data science. To provide a complete and up-to-date understanding of this topic, this review covers the three key issues of data transaction: data rights, data pricing, and privacy computing. By connecting these topics, this paper provides a big picture of a data ecosystem in which data is generated by data subjects such as individuals, research agencies, and governments, while data processors acquire data for innovational or operational purposes, and benefits are allocated according to the data’s respective ownership via an appropriate price. With the long-term goal of making artificial intelligence (AI) beneficial to human society, AI algorithms will then be assessed by data protection regulations (i.e., privacy protection regulations) to help build trustworthy AI systems for daily life.
Keywords	Data science ; Artificial intelligence ; Data rights ; Data pricing ; Privacy computing ; Engineering (General). Civil engineering (General) ; TA1-2040
Subject code	330
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Investigation on Intestinal Proteins and Drug Metabolizing Enzymes in Simulated Microgravity Rats by a Proteomics Method

Huayan Liu / Jingjing Guo / Yujuan Li / Yushi Zhang / Jiaping Wang / Jianyi Gao / Yulin Deng / Yongzhi Li

Molecules, Vol 25, Iss 4391, p

2020 Volume 4391

Abstract: The present study aimed to investigate the change of intestinal mucosa proteins, especially the alteration of intestinal drug metabolizing enzymes (IDMEs) following 14-day simulated microgravity. Morey–Holton tail-suspension analog was used to simulate ... ...

Abstract	The present study aimed to investigate the change of intestinal mucosa proteins, especially the alteration of intestinal drug metabolizing enzymes (IDMEs) following 14-day simulated microgravity. Morey–Holton tail-suspension analog was used to simulate microgravity. Intestinal mucosa proteins of rats were determined by label-free quantitative proteomic strategy. A total of 335 differentially expressed proteins (DEPs) were identified, 190 DEPs were upregulated, and 145 DEPs were downregulated. According to bioinformatic analysis, most of DEPs exhibited hydrolase, oxidoreductase, transferase, ligase, or lyase catalytic activity. DEPs were mainly enriched in metabolic pathways, including metabolism of amino acid, glucose, and carbon. Moreover, 11 of DEPs were involved in exogenous drug and xenobiotics metabolism. Owing to the importance of IDMEs for the efficacy and safety of oral drugs, the expression of cytochrome P450 1A2 (CYP1A2), CYP2D1, CYP3A2, CYP2E1, alcohol dehydrogenase 1 (ADH1), and glutathione S-transferase mu 5 (GSTM5) in rat intestine mucosa was determined by Western-blot. The activity of ADH, aldehyde dehydrogenase (ALDH) and GST was evaluated. Compared with control rats, the expression of CYP1A2, CYP2D1, CYP3A2, and ADH1 in the simulated microgravity (SMG) group of rats were dramatically decreased by 33.16%, 21.93%, 48.49%, and 22.83%, respectively. GSTM5 was significantly upregulated by 53.14% and CYP2E1 expression did not show a dramatical change in SMG group rats. Moreover, 14-day SMG reduced ADH activity, while ALDH and GST activities was not altered remarkably. It could be concluded that SMG dramatically affected the expression and activity of some IDMEs, which might alter the efficacy or safety of their substrate drugs under microgravity. The present study provided some preliminary information on IDMEs under microgravity. It revealed the potential effect of SMG on intestinal metabolism, which may be helpful to understand the intestinal health of astronauts and medication use.
Keywords	simulated microgravity ; intestinal mucosa ; proteomics ; metabolic pathways ; intestinal drug metabolic enzymes ; Organic chemistry ; QD241-441
Subject code	570
Language	English
Publishing date	2020-09-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Novel MEF2C point mutations in Chinese patients with Rett (−like) syndrome or non-syndromic intellectual disability

Jiaping Wang / Qingping Zhang / Yan Chen / Shujie Yu / Xiru Wu / Xinhua Bao / Yongxin Wen

BMC Medical Genetics, Vol 19, Iss 1, Pp 1-

insights into genotype-phenotype correlation

2018 Volume 6

Abstract: Abstract Background MEF2C (Myocyte-specific enhancer factor 2C) has been associated with neurodevelopmental disorders. This study aimed at delineating the clinical profiles of MEF2C gene mutations. Methods In total, 112 Chinese patients with intellectual ...

Abstract	Abstract Background MEF2C (Myocyte-specific enhancer factor 2C) has been associated with neurodevelopmental disorders. This study aimed at delineating the clinical profiles of MEF2C gene mutations. Methods In total, 112 Chinese patients with intellectual disability (ID) were recruited, including 44 patients presented with Rett syndrome (RTT) or RTT-like syndrome, and 68 patients with non-syndromic ID. Targeted next-generation sequencing (NGS) was performed. Detailed clinical information was collected. Results Five heterozygous MEF2C gene mutations were identified, of which three were novel. The MEF2C mutant rate was 4.5% (5/112) in total, and 6.8% (3/44) in the RTT (−like) cohort. All patients with MEF2C gene mutation presented with cognitive impairment, gross motor delay, speech disorder and autistic features. Four patients had epilepsy, which responded well to antiepileptic drugs. One female was diagnosed with classical RTT, two females with RTT-like syndrome, and two males with non-syndromic ID. Generally, the phenotype of two males with relatively downstream mutations (c.565C > T, p.Arg 189; c.766C > T, p.Arg 256) was milder than that of three females with upstream mutations (c.48C > G, p.Asn16Lys; c.334G > T, p.Glu112* and c.403-1G > T). Conclusions Our findings expanded the current understanding of the consequences of MEF2C dysfunctions, especially MEF2C point mutations. MEF2C mutations are associated with a broad clinical spectrum, ranged from classical RTT to non-syndromic ID. Through our study, it can be inferred that there is correlation between the phenotype and MEF2C-genotype, the mutation site. Overall, the MEF2C gene mutational analysis should be performed in ID cohort, especially in patients with features overlapped with RTT.
Keywords	MEF2C ; Rett (−like) syndrome ; Non-syndromic intellectual disability ; Genotype-phenotype correlation ; Internal medicine ; RC31-1245 ; Genetics ; QH426-470
Subject code	616 ; 610
Language	English
Publishing date	2018-10-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effects of Acanthopanax senticosus on Brain Injury Induced by Simulated Spatial Radiation in Mouse Model Based on Pharmacokinetics and Comparative Proteomics

Yingyu Zhou / Cuilin Cheng / Denis Baranenko / Jiaping Wang / Yongzhi Li / Weihong Lu

International Journal of Molecular Sciences, Vol 19, Iss 1, p

2018 Volume 159

Abstract: The active compounds in Acanthopanax senticosus (AS) have different pharmacokinetic characteristics in mouse models. Cmax and AUC of Acanthopanax senticosus polysaccharides (ASPS) were significantly reduced in radiation-injured mice, suggesting that the ... ...

Abstract	The active compounds in Acanthopanax senticosus (AS) have different pharmacokinetic characteristics in mouse models. Cmax and AUC of Acanthopanax senticosus polysaccharides (ASPS) were significantly reduced in radiation-injured mice, suggesting that the blood flow of mouse was blocked or slowed, due to the pathological state of ischemia and hypoxia, which are caused by radiation. In contrast, the ability of various metabolizing enzymes to inactivate, capacity of biofilm transport decrease, and lessening of renal blood flow accounts for radiation, resulting in the accumulation of syringin and eleutheroside E in the irradiated mouse. Therefore, there were higher pharmacokinetic parameters—AUC, MRT, and t1/2 of the two compounds in radiation-injured mouse, when compared with normal mouse. In order to investigate the intrinsic mechanism of AS on radiation injury, AS extract’s protective effects on brain, the main part of mouse that suffered from radiation, were explored. The function of AS extract in repressing expression changes of radiation response proteins in prefrontal cortex (PFC) of mouse brain included tubulin protein family (α-, β-tubulin subunits), dihydropyrimidinase-related protein 2 (CRMP2), γ-actin, 14-3-3 protein family (14-3-3ζ, ε), heat shock protein 90β (HSP90β), and enolase 2. The results demonstrated the AS extract had positive effects on nerve cells’ structure, adhesion, locomotion, fission, and phagocytosis, through regulating various action pathways, such as Hippo, phagosome, PI3K/Akt (phosphatidylinositol 3 kinase/protein kinase B), Neurotrophin, Rap1 (Ras-related protein RAP-1A), gap junction glycolysis/gluconeogenesis, and HIF-1 (Hypoxia-inducible factor 1) signaling pathways to maintain normal mouse neurological activity. All of the results indicated that AS may be a promising alternative medicine for the treatment of radiation injury in mouse brain. It would be tested that whether the bioactive ingredients of AS could be effective through the blood–brain barrier in the future.
Keywords	Acanthopanax senticosus (AS) ; brain injury ; pharmacokinetic ; proteomics ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	616
Language	English
Publishing date	2018-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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