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Article ; Online: A landscape of metabolic variation among clinical outcomes of peritoneal dialysis in end-stage renal disease.

Yang, Ting / Wei, Bangbang / Liu, Jing / Si, Xinxin / Wang, Lulu / Jiang, Chunming

Clinica chimica acta; international journal of clinical chemistry

2024 Volume 555, Page(s) 117826

Abstract: Background: Peritoneal dialysis (PD) helps prevent lethal complications of end-stage renal disease (ESRD). However, the clinical outcomes are affected by PD-related complications. We investigated metabolic biomarkers to estimate the clinical outcomes of ...

Abstract	Background: Peritoneal dialysis (PD) helps prevent lethal complications of end-stage renal disease (ESRD). However, the clinical outcomes are affected by PD-related complications. We investigated metabolic biomarkers to estimate the clinical outcomes of PD and identify patients at high risk of downstream complications and recurrent/relapsing infections. Methods: Metabolites of normal control and ESRD patient were compared via an untargeted metabolomic analysis. Potential metabolic biomarkers were selected and quantified using a multiple reaction monitoring-based target metabolite detection method. A nomogram was built to predict the clinical outcomes of PD patients using clinical features and potential metabolic biomarkers with the least absolute shrinkage and selection operator Cox regression model. Results: Twenty-five endogenous metabolites were identified and analyzed. ESRD-poor clinical outcome-related metabolic modules were constructed. Adenine, isoleucine, tyramine, xanthosine, phenylacetyl-L-glutamine, and cholic acid were investigated using the weighted gene correlation network analysis blue module. Potential metabolic biomarkers were differentially expressed between the NC and ESRD groups and the poor and good clinical outcomes of PD groups. A 3-metabolite fingerprint classifier of isoleucine, cholic acid, and adenine was included in a nomogram predicting the clinical outcomes of PD. Conclusion: Metabolic variations can predict the clinical outcomes of PD in ESRD patients.
MeSH term(s)	Humans ; Isoleucine ; Retrospective Studies ; Kidney Failure, Chronic/diagnosis ; Peritoneal Dialysis/adverse effects ; Peritoneal Dialysis/methods ; Adenine ; Cholic Acid ; Biomarkers ; Renal Dialysis/adverse effects
Chemical Substances	Isoleucine (04Y7590D77) ; Adenine (JAC85A2161) ; Cholic Acid (G1JO7801AE) ; Biomarkers
Language	English
Publishing date	2024-02-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	80228-1
ISSN	1873-3492 ; 0009-8981
ISSN (online)	1873-3492
ISSN	0009-8981
DOI	10.1016/j.cca.2024.117826
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Article: Rapid and accurate genotyping of human SNP rs671 in aldehyde dehydrogenase 2 gene using one-step CRISPR/Cas12b assay without DNA amplification.

Wu, Fang / Xue, Yong / Wang, Yan / Si, Xinxin / Zhang, Xinyue / Xu, Yuyang / Luo, Zhidan

Cell division

2023 Volume 18, Issue 1, Page(s) 14

Abstract: Background: The SNP rs671 of Human aldehyde dehydrogenase (ALDH) is G-A transition at 1510th nucleotides, which is an important clinical indicator of alcoholic liver disease, digestive tract cancer and some drug efficiency. The commonly used genotyping ... ...

Abstract	Background: The SNP rs671 of Human aldehyde dehydrogenase (ALDH) is G-A transition at 1510th nucleotides, which is an important clinical indicator of alcoholic liver disease, digestive tract cancer and some drug efficiency. The commonly used genotyping assay of this polymorphism is relatively time-consuming and costly. Finding: This study develops a rapid and accurate one-step CRISPR/Cas12b assay to distinguish the G1510A polymorphism of human ALDH2 free of DNA amplification. The method we established requires only one step of adding 1 μl genomic DNA sample to premixed system, and waiting for the acquisition of fluorescent signal, taking approximate 30 min. Conclusions: This method provides a potential tool for more accurate and reliable nucleic acid detection with a single base difference and supports the relevant disease diagnosis and personalized medicine.
Language	English
Publishing date	2023-08-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2236097-9
ISSN	1747-1028
ISSN	1747-1028
DOI	10.1186/s13008-023-00095-6
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Article: Biomaterial-assisted tumor therapy: A brief review of hydroxyapatite nanoparticles and its composites used in bone tumors therapy.

Zhang, Quan / Qiang, Lei / Liu, Yihao / Fan, Minjie / Si, Xinxin / Zheng, Pengfei

Frontiers in bioengineering and biotechnology

2023 Volume 11, Page(s) 1167474

Abstract: Malignant bone tumors can inflict significant damage to affected bones, leaving patients to contend with issues like residual tumor cells, bone defects, and bacterial infections post-surgery. However, hydroxyapatite nanoparticles (nHAp), the principal ... ...

Abstract	Malignant bone tumors can inflict significant damage to affected bones, leaving patients to contend with issues like residual tumor cells, bone defects, and bacterial infections post-surgery. However, hydroxyapatite nanoparticles (nHAp), the principal inorganic constituent of natural bone, possess numerous advantages such as high biocompatibility, bone conduction ability, and a large surface area. Moreover, nHAp's nanoscale particle size enables it to impede the growth of various tumor cells
Language	English
Publishing date	2023-04-07
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2719493-0
ISSN	2296-4185
ISSN	2296-4185
DOI	10.3389/fbioe.2023.1167474
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Article ; Online: Comprehensive bioinformatics analysis reveals the significance of forkhead box family members in pancreatic adenocarcinoma.

Hu, Wei / Li, Mingxu / Wang, Yan / Zhong, Chengcheng / Si, Xinxin / Shi, Xiao / Wang, Zhong

Aging

2023 Volume 15, Issue 1, Page(s) 92–107

Abstract: Background: Forkhead box proteins (FOXs) play important roles in multiple biological processes; while little is known regarding the role of FOX members in pancreatic adenocarcinoma (PAAD). This study aimed to comprehensively investigate the function of ... ...

Abstract	Background: Forkhead box proteins (FOXs) play important roles in multiple biological processes; while little is known regarding the role of FOX members in pancreatic adenocarcinoma (PAAD). This study aimed to comprehensively investigate the function of FOX family members in PAAD. Methods: Expression and prognostic value of FOXs were analyzed by R language and GEPIA. Genetic alteration and promoter methylation level were analyzed using CBioPortal and UALCAN. Protein-protein interactions and gene functions were analyzed using STRING and DAVID. TIMER and SENESCopedia were utilized to analyze the correlation of FOXs with immune cell infiltration or tumor senescence. Protein levels of FOXs were detected by immunohistochemistry. Results: Expression of 15 of 50 FOXs were significantly elevated in PAAD. Among these 15 differentially expressed FOXs (DE-FOXs), 4 were significantly associated with the clinical cancer stage and 4 were negatively associated with overall survival. Functions of DE-FOXs were related to epithelial tube morphogenesis, nuclear chromatin, and DNA-binding. Promoter methylation and genomic alterations were not major causes of FOX dysregulation. Most DE-FOX was correlated with diverse immune infiltration cells. Seven of the DE-FOXs were positively related to tumor senescence. The protein levels of FOXM1, FOXP1, and FOXN3 were negatively correlated with OS in the collected PAAD patients. Conclusions: FOXM1, FOXP1, and FOXN3 have prognostic value. Seven FOXs were related senescence, whereas most DE-FOXs were related to immune infiltration in PAAD. Our findings are instructive for future research on FOX family and provide novel insights into the selection of FOXs with potential prognostic or therapeutic target value.
MeSH term(s)	Humans ; Adenocarcinoma/genetics ; Pancreatic Neoplasms/genetics ; Computational Biology ; Genomics ; Prognosis ; Repressor Proteins ; Forkhead Transcription Factors/genetics ; Pancreatic Neoplasms
Chemical Substances	FOXP1 protein, human ; Repressor Proteins ; Forkhead Transcription Factors
Language	English
Publishing date	2023-01-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1945-4589
ISSN (online)	1945-4589
DOI	10.18632/aging.204455
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Article ; Online: AutoMolDesigner for Antibiotic Discovery: An AI-Based Open-Source Software for Automated Design of Small-Molecule Antibiotics.

Shen, Tao / Guo, Jiale / Han, Zunsheng / Zhang, Gao / Liu, Qingxin / Si, Xinxin / Wang, Dongmei / Wu, Song / Xia, Jie

Journal of chemical information and modeling

2024 Volume 64, Issue 3, Page(s) 575–583

Abstract: Discovery of small-molecule antibiotics with novel chemotypes serves as one of the essential strategies to address antibiotic resistance. Although a considerable number of computational tools committed to molecular design have been reported, there is a ... ...

Abstract	Discovery of small-molecule antibiotics with novel chemotypes serves as one of the essential strategies to address antibiotic resistance. Although a considerable number of computational tools committed to molecular design have been reported, there is a deficit in holistic and efficient tools specifically developed for small-molecule antibiotic discovery. To address this issue, we report AutoMolDesigner, a computational modeling software dedicated to small-molecule antibiotic design. It is a generalized framework comprising two functional modules, i.e., generative-deep-learning-enabled molecular generation and automated machine-learning-based antibacterial activity/property prediction, wherein individually trained models and curated datasets are out-of-the-box for whole-cell-based antibiotic screening and design. It is open-source, thus allowing for the incorporation of new features for flexible use. Unlike most software programs based on Linux and command lines, this application equipped with a Qt-based graphical user interface can be run on personal computers with multiple operating systems, making it much easier to use for experimental scientists. The software and related materials are freely available at GitHub (https://github.com/taoshen99/AutoMolDesigner) and Zenodo (https://zenodo.org/record/10097899).
MeSH term(s)	Software ; Computer Simulation ; Artificial Intelligence
Language	English
Publishing date	2024-01-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	190019-5
ISSN	1549-960X ; 0095-2338
ISSN (online)	1549-960X
ISSN	0095-2338
DOI	10.1021/acs.jcim.3c01562
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Article ; Online: Combined transcriptome and proteome analysis reveals MSN and ARFIP2 as biomarkers for trastuzumab resistance of breast cancer.

Shi, Xiao / Sheng, Yuan / Fei, Haoran / Wei, Bangbang / Zhang, Zhenyu / Xia, Xinyu / Mao, Changfei / Si, Xinxin

Breast cancer research and treatment

2024

Abstract: Purpose: HER2-positive breast cancer (BC) accounts for 20-30% of all BC subtypes and is linked to poor prognosis. Trastuzumab (Tz), a humanized anti-HER2 monoclonal antibody, is a first-line treatment for HER2-positive breast cancer which faces ... ...

Abstract	Purpose: HER2-positive breast cancer (BC) accounts for 20-30% of all BC subtypes and is linked to poor prognosis. Trastuzumab (Tz), a humanized anti-HER2 monoclonal antibody, is a first-line treatment for HER2-positive breast cancer which faces resistance challenges. This study aimed to identify the biomarkers driving trastuzumab resistance. Methods: Differential expression analysis of genes and proteins between trastuzumab-sensitive (TS) and trastuzumab-resistant (TR) cells was conducted using RNA-seq and iTRAQ. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were used to study their functions. The prognostic significance and protein levels of ARFIP2 and MSN were evaluated using online tools and immunohistochemistry. Sensitivity of MSN and ARFIP2 to other therapies was assessed using public pharmacogenomics databases and the R language. Results: Five genes were up-regulated, and nine genes were down-regulated in TR cells at both transcriptional and protein levels. Low ARFIP2 and high MSN expression linked to poor BC prognosis. MSN increased and ARFIP2 decreased in TR patients, correlating with shorter OS. MSN negatively impacted fulvestrant and immunotherapy sensitivity, while ARFIP2 had a positive impact. Conclusion: Our findings suggest that MSN and ARFIP2 could serve as promising biomarkers for predicting response to Tz, offering valuable insights for future research in the identification of diagnostic and therapeutic targets for BC patients with Tz resistance.
Language	English
Publishing date	2024-05-15
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	604563-7
ISSN	1573-7217 ; 0167-6806
ISSN (online)	1573-7217
ISSN	0167-6806
DOI	10.1007/s10549-024-07355-1
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Article: Preparation, characterization, and properties of wampee seed antioxidant peptides‐iron chelate

Liu, Yong / Ma, Xiu‐Yun / Si, Xin‐Xin / Lai, Wen‐Feng

Journal of food processing and preservation. 2022 May, v. 46, no. 5

2022

Abstract: The chelation process of antioxidant peptides with iron was optimized by response surface methodology with iron chelation percentage as a response. The optimum process was chelation time of 38 min, chelation temperature of 31°C, chelation pH of 5.2, and ... ...

Abstract	The chelation process of antioxidant peptides with iron was optimized by response surface methodology with iron chelation percentage as a response. The optimum process was chelation time of 38 min, chelation temperature of 31°C, chelation pH of 5.2, and peptides‐to‐iron mass ratio of 3.4:1. Scanning electron microscopy observation showed the chelate was a smooth and dense granular aggregate morphology. Fourier transform infrared spectroscopy analysis indicated the chelate's characteristic peaks shifted significantly compared with the antioxidant peptides. The α‐helix and random coil contents decreased from the peptides of 60.86% to the chelate of 43.74%. However, the β‐structure contents increased from the peptides of 39.14% to the chelate of 56.26%. The in vitro digestion test suggested the chelate had 97.37% bioaccessibility and 58.53% DPPH radical scavenging effect in gastric digestion. But those in intestinal digestion remained 50.02% and 41.02%, respectively. The chelate can be used as a new iron supplement. NOVELTY IMPACT STATEMENT: The preparation process of wampee seed antioxidant peptides‐iron chelate was optimized by response surface methodology. Iron ions binding to the peptides was through carboxyl oxygen and amino nitrogen atoms. Chelate showed good antioxidant activity and bioaccessibility during gastrointestinal digestion.
Keywords	Clausena lansium ; Fourier transform infrared spectroscopy ; amino nitrogen ; antioxidant activity ; antioxidants ; bioavailability ; chelation ; intestines ; iron ; oxygen ; pH ; peptides ; response surface methodology ; temperature
Language	English
Dates of publication	2022-05
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	243448-9
ISSN	1745-4549 ; 0145-8892
ISSN (online)	1745-4549
ISSN	0145-8892
DOI	10.1111/jfpp.16513
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Article ; Online: LncRNA DDX11-AS1 Promotes Chemoresistance through LIN28A-Mediated ATG12 mRNA Stabilization in Breast Cancer.

Si, Xinxin / Zhang, Gongming / Li, Mingyuan / Yao, Mingli / Shi, Xiao / Dong, Zibo / Gao, Song

Pharmacology

2022 , Page(s) 1–13

Abstract: Introduction: During breast cancer chemotherapy, the chemoresistance that frequently accompanies the treatment has become a big challenge. Long noncoding RNAs (LncRNAs) have been related to the development of chemoresistance in multiple cancer types. ... ...

Abstract	Introduction: During breast cancer chemotherapy, the chemoresistance that frequently accompanies the treatment has become a big challenge. Long noncoding RNAs (LncRNAs) have been related to the development of chemoresistance in multiple cancer types. LncRNA DDX11-AS1 has shown a carcinogenic role in lung and colorectal cancer and was reported to enhance oxaliplatin resistance in gastric cancer and Taxol insensitivity in esophageal cancer. But its role in breast cancer chemotherapy drug resistance remains unknown. This study aimed to investigate the function and mechanism of lncRNA DDX11-AS1 in breast cancer chemoresistance. Methods: The relationship between DDX11-AS1 and adriamycin (ADR) resistance was confirmed by qPCR, cell viability tests, and survival analysis. Then, RNA immunoprecipitation was conducted to evaluate the interaction between DDX11-AS1 and RNA-binding protein LIN28A. The regulation effect of LIN28A on autophagy-related genes ATG7 or ATG12 was detected by RNA stability assay and Western blot. Their correlation analysis was evaluated in GEO datasets and further validated by immunohistochemical results. The clinical significance of DDX11-AS1, ATG7, or ATG12 was evaluated by Kaplan-Meier Plotter analysis. Results: Here, we reported DDX11-AS1 was significantly upregulated in chemoresistant breast cancer cells and overexpression of DDX11-AS1 promoted ADR resistance in breast cancer. LIN28A could interact with DDX11-AS1 and was involved in DDX11-AS1-mediated ADR resistance. Interfering with LIN28A reversed DDX11-AS1-induced ADR resistance. LIN28A could increase the protein level of ATG7 and ATG12 by increasing their mRNA stability. Survival analysis showed that ATG12 expression level was negatively correlated with the prognosis of breast cancer patients. Conclusion: This study clarifies the role of DDX11-AS1 in breast cancer chemoresistance and revealed a new mechanism, that is, interacting with LIN28A to stabilize ATG7 and ATG12 and jointly promote chemorefractory. These findings warrant further in vivo investigations to study DDX11-AS1 as a potential target to overcome chemoresistance.
Language	English
Publishing date	2022-11-16
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	206671-3
ISSN	1423-0313 ; 0031-7012
ISSN (online)	1423-0313
ISSN	0031-7012
DOI	10.1159/000527222
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Zs.A 332: Show issues

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Article ; Online: Identification of a 2-phenylthiazole derivative acetylcholinesterase modulator with in vitro antitumor activity in breast cancer cells.

Shi, Xiao / Liu, Peng / Ma, Yanyan / Li, Mingyuan / Zhang, Zhenyu / Zhang, Xinyue / Shi, Dahua / Si, Xinxin

Chemical biology & drug design

2023 Volume 103, Issue 1, Page(s) e14402

Abstract: Acetylcholinesterase (AchE) is a serine hydrolase with classical function to degrade acetylcholine and terminate neurotransmission. While "nonclassical" functions of AchE were involved in cell growth, death, invasion, etc. The expression and activity of ... ...

Abstract	Acetylcholinesterase (AchE) is a serine hydrolase with classical function to degrade acetylcholine and terminate neurotransmission. While "nonclassical" functions of AchE were involved in cell growth, death, invasion, etc. The expression and activity of AchE is changed in tumors, suggesting AChE inhibitors (AchEIs) may serve as potential antitumor drugs. In this study, the antitumor activity of a series of 2-phenylthiazole derivatives originally designed and synthesized as AchEIs were investigated. One compound named A6, was screened out with superior antitumor efficacy, especially against breast cancer MCF-7 cells. A6 significantly disrupted the amino acid metabolism and inhibited migration of MCF-7. In addition, A6 induced apoptosis of MCF-7 cells. To clarify how A6 affected on MCF-7 cells, RNA-seq analysis was conducted to evaluate the whole genome effect of A6 on gene expression. A total of 153 genes were increased, and the expression of 81 genes was decreased. GO and KEGG enrichment analysis showed A6 treatment mainly disrupted sterol/cholesterol pathway, Ras signaling pathway, VEGF signaling pathway, etc. Moreover, bioinformatic analysis and cell viability test showed A6 plays anticancer role by regulating Best1 and HIST1H2BJ. These results indicate that AchEI A6 could be a potential antitumor agent for breast cancer patients and could help the development of novel therapies.
MeSH term(s)	Humans ; Female ; Acetylcholinesterase/metabolism ; Breast Neoplasms/drug therapy ; Breast Neoplasms/pathology ; Antineoplastic Agents/chemistry ; Apoptosis ; MCF-7 Cells
Chemical Substances	Acetylcholinesterase (EC 3.1.1.7) ; Antineoplastic Agents
Language	English
Publishing date	2023-11-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2216600-2
ISSN	1747-0285 ; 1747-0277
ISSN (online)	1747-0285
ISSN	1747-0277
DOI	10.1111/cbdd.14402
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Article ; Online: Discovery of a novel chemotype as DYRK1A inhibitors against Alzheimer's disease: Computational modeling and biological evaluation.

Qiu, Nianzhuang / Qian, Chenliang / Guo, Tingting / Wang, Yaling / Jin, Hongwei / Yao, Mingli / Li, Mei / Guo, Tianyang / Lv, Yuli / Si, Xinxin / Wu, Song / Wang, Hao / Zhang, Xuehui / Xia, Jie

International journal of biological macromolecules

2024 Volume 269, Issue Pt 1, Page(s) 132024

Abstract: Dual-specificity tyrosine phosphorylation-regulated kinase 1 A (DYRK1A) plays an essential role in Tau and Aβ pathology closely related to Alzheimer's disease (AD). Accumulative evidence has demonstrated DYRK1A inhibition is able to reduce the ... ...

Abstract	Dual-specificity tyrosine phosphorylation-regulated kinase 1 A (DYRK1A) plays an essential role in Tau and Aβ pathology closely related to Alzheimer's disease (AD). Accumulative evidence has demonstrated DYRK1A inhibition is able to reduce the pathological features of AD. Nevertheless, there is no approved DYRK1A inhibitor for clinical use as anti-AD therapy. This is somewhat due to the lack of effective and safe chemotypes of DYRK1A inhibitors. To address this issue, we carried out in silico screening, in vitro assays and in vivo efficacy evaluation with the aim to discover a new class of DYRK1A inhibitors for potential treatment of AD. By in silico screening, we selected and purchased 16 potential DYRK1A inhibitors from the Specs chemical library. Among them, compound Q17 (Specs ID: AO-476/40829177) potently inhibited DYRK1A. The hydrogen bonds between compound Q17 and two amino acid residues named GLU239 and LYS188, were uncovered by molecular docking and molecular dynamics simulation. The cell-based assays showed that compound Q17 could protect the SH-SY5Y human neuroblastoma cell line from okadaic acid (OA)-induced injury by targeting DYRK1A. More importantly, compound Q17 significantly improved cognitive dysfunction of 3 × Tg-AD mice, ameliorated pathological changes, and attenuated Tau hyperphosphorylation as well as Aβ deposition. In summary, our computational modeling strategy is effective to identify novel chemotypes of DYRK1A inhibitors with great potential to treat AD, and the identified compound Q17 in this study is worthy of further study.
Language	English
Publishing date	2024-05-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.132024
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