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Article: Screening and identification of key candidate genes and pathways in myelodysplastic syndrome by bioinformatic analysis.

Le, Ying

2019 Volume 7, Page(s) e8162

Abstract: Myelodysplastic syndrome (MDS) is a heterogeneous hematologic malignancy derived from hematopoietic stem cells and the molecular mechanism of MDS remains unclear. This study aimed to elucidate potential markers of diagnosis and prognosis of MDS. The gene ...

Abstract	Myelodysplastic syndrome (MDS) is a heterogeneous hematologic malignancy derived from hematopoietic stem cells and the molecular mechanism of MDS remains unclear. This study aimed to elucidate potential markers of diagnosis and prognosis of MDS. The gene expression profiles GSE19429 and GSE58831 were obtained and downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in MDS were screened using GEO2R and overlapped DEGs were obtained with Venn Diagrams. Then, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway functional enrichment analyses, protein-protein interaction network establishment and survival analyses were performed. Functional enrichment analysis indicated that these DEGs were significantly enriched in the interferon signaling pathway, immune response, hematopoietic cell lineage and the FOXO signaling pathway. Four hub genes and four significant modules including 25 module genes were obtained via Cytoscape MCODE. Survival analysis showed that the overall survival of MDS patients having BLNK, IRF4, IFITM1, IFIT1, ISG20, IFI44L alterations were worse than that without alterations. In conclusion, the identification of these genes and pathways helps understand the underlying molecular mechanisms of MDS and provides candidate targets for the diagnosis and prognosis of MDS.
Language	English
Publishing date	2019-11-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	2703241-3
ISSN	2167-8359
ISSN	2167-8359
DOI	10.7717/peerj.8162
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Article ; Online: Coexistence of type 2 diabetes mellitus, arginine vasopressin deficiency, and Marfan syndrome: A case report.

Le, Yunyi / Zhang, Jingjing / Hong, Tianpei / Yang, Jin

Journal of diabetes investigation

2024

Abstract: Diabetes mellitus (DM) and arginine vasopressin deficiency (AVP-D) are characterized by polyuria. Marfan syndrome is an autosomal dominant disorder caused by pathogenetic variants in FBN1. Here, we report a patient with type 2 diabetes mellitus, AVP-D, ... ...

Abstract	Diabetes mellitus (DM) and arginine vasopressin deficiency (AVP-D) are characterized by polyuria. Marfan syndrome is an autosomal dominant disorder caused by pathogenetic variants in FBN1. Here, we report a patient with type 2 diabetes mellitus, AVP-D, and Marfan syndrome. Although the coexistence of type 2 diabetes mellitus and AVP-D is rare, for those patients with type 2 diabetes mellitus, the existence of AVP-D should be considered when polyuria is not in accordance with the blood glucose levels, especially for those with a low urine specific gravity. Specific symptoms or signs help to identify Marfan syndrome early, and genetic testing of the FBN1 pathogenetic variant helps to make a definitive diagnosis.
Language	English
Publishing date	2024-03-02
Publishing country	Japan
Document type	Case Reports
ZDB-ID	2625840-7
ISSN	2040-1124 ; 2040-1116
ISSN (online)	2040-1124
ISSN	2040-1116
DOI	10.1111/jdi.14169
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Article ; Online: Signaling pathways and potential therapeutic targets in acute respiratory distress syndrome (ARDS).

Huang, Qianrui / Le, Yue / Li, Shusheng / Bian, Yi

Respiratory research

2024 Volume 25, Issue 1, Page(s) 30

Abstract: Acute respiratory distress syndrome (ARDS) is a common condition associated with critically ill patients, characterized by bilateral chest radiographical opacities with refractory hypoxemia due to noncardiogenic pulmonary edema. Despite significant ... ...

Abstract	Acute respiratory distress syndrome (ARDS) is a common condition associated with critically ill patients, characterized by bilateral chest radiographical opacities with refractory hypoxemia due to noncardiogenic pulmonary edema. Despite significant advances, the mortality of ARDS remains unacceptably high, and there are still no effective targeted pharmacotherapeutic agents. With the outbreak of coronavirus disease 19 worldwide, the mortality of ARDS has increased correspondingly. Comprehending the pathophysiology and the underlying molecular mechanisms of ARDS may thus be essential to developing effective therapeutic strategies and reducing mortality. To facilitate further understanding of its pathogenesis and exploring novel therapeutics, this review provides comprehensive information of ARDS from pathophysiology to molecular mechanisms and presents targeted therapeutics. We first describe the pathogenesis and pathophysiology of ARDS that involve dysregulated inflammation, alveolar-capillary barrier dysfunction, impaired alveolar fluid clearance and oxidative stress. Next, we summarize the molecular mechanisms and signaling pathways related to the above four aspects of ARDS pathophysiology, along with the latest research progress. Finally, we discuss the emerging therapeutic strategies that show exciting promise in ARDS, including several pharmacologic therapies, microRNA-based therapies and mesenchymal stromal cell therapies, highlighting the pathophysiological basis and the influences on signal transduction pathways for their use.
MeSH term(s)	Humans ; Respiratory Distress Syndrome ; Lung ; MicroRNAs/genetics ; Signal Transduction ; Pulmonary Edema
Chemical Substances	MicroRNAs
Language	English
Publishing date	2024-01-13
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2041675-1
ISSN	1465-993X ; 1465-993X
ISSN (online)	1465-993X
ISSN	1465-993X
DOI	10.1186/s12931-024-02678-5
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Article ; Online: MYB/LINC00092 regulatory axis promotes the progression of papillary thyroid carcinoma.

Cheng, Lian / Deng, Xian / Le, Yuan

Endokrynologia Polska

2024 Volume 75, Issue 1, Page(s) 27–34

Abstract: Introduction: Thyroid carcinoma is the most frequent malignancy in different endocrine-related tumours. In this study, we demonstrated a long non-coding RNA LINC00092-associated molecular mechanism in promoting the progression of papillary thyroid ... ...

Abstract	Introduction: Thyroid carcinoma is the most frequent malignancy in different endocrine-related tumours. In this study, we demonstrated a long non-coding RNA LINC00092-associated molecular mechanism in promoting the progression of papillary thyroid carcinoma (PTC). Material and methods: The expression of LINC00092 was analysed in the The Cancer Genome Atlas Thyroid Cancer (TCGA-THCA) patient cohorts and further determined by q-PCR. (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) (MTT) assay, and wound healing assay confirmed the function of LINC00092 in migration and proliferation. Q-ChIP validated the transcriptional target. Luciferase reporter assay validated the miRNA-mRNA target. Results: The analysis in patient cohorts and in PTC TPC-1 cells showed that the expression of LINC00092 was repressed in thyroid carcinoma. In addition, the expression of LINC00092 was negatively associated with the advanced thyroid TNM stages. LINC00092 repressed epithelial-mesenchymal transition (EMT), migration, and proliferation of TPC-1 cells. Interestingly, we identified that MYB, a well-studied tumour promoter, is a transcription factor of LINC00092, thereby the expression of LINC00092 was directly repressed by MYB. Furthermore, miR-4741 was also validated as a direct target of MYB and was induced by MYB. Notably, LINC00092 was repressed by miR-4741 through the direct 3'-untranslational region (3'-UTR) target. Therefore, MYB induced EMT of TPC-1 cells by repressing LINC00092 directly or indirectly via miR-4741. Conclusions: Our study validated that LINC00092 is a tumour suppressor lncRNA in PTC. MYB directly or indirectly represses LINC00092, which contributes to the PTC progression. MYB, LINC00092, and miR-4741 form a coherent feed forward loop. The axis of MYB-LINC00092 promotes progression of PTC.
MeSH term(s)	Humans ; Cell Line, Tumor ; Cell Proliferation ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Thyroid Cancer, Papillary/pathology ; Thyroid Neoplasms/pathology ; RNA, Long Noncoding
Chemical Substances	MicroRNAs ; MYB protein, human ; RNA, Long Noncoding
Language	English
Publishing date	2024-03-18
Publishing country	Poland
Document type	Journal Article
ZDB-ID	419270-9
ISSN	2299-8306 ; 0423-104X
ISSN (online)	2299-8306
ISSN	0423-104X
DOI	10.5603/ep.98120
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Article: (1-

Mesrar, M / Majdoubi, H / Le, Yan

Heliyon

2024 Volume 10, Issue 5, Page(s) e26463

Abstract: 1- ...

Abstract	(1-
Language	English
Publishing date	2024-02-23
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2024.e26463
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Article: CRISPR/Cas genome editing systems in thermophiles: Current status, associated challenges, and future perspectives.

Le, Yilin / Sun, Jianzhong

Advances in applied microbiology

2022 Volume 118, Page(s) 1–30

Abstract: Thermophiles, offering an attractive and unique platform for a broad range of applications in biofuels and environment protections, have received a significant attention and growing interest from academy and industry. However, the exploration and ... ...

Abstract	Thermophiles, offering an attractive and unique platform for a broad range of applications in biofuels and environment protections, have received a significant attention and growing interest from academy and industry. However, the exploration and exploitation of thermophilic organisms have been hampered by the lack of a powerful genome manipulation tool to improve production efficiency. At current, the clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR associated (Cas) system has been successfully exploited as a competent, simplistic, and powerful tool for genome engineering both in eukaryotes and prokaryotes. Indeed, with the significant efforts made in recent years, some thermostable Cas9 proteins have been well identified and characterized and further, some thermostable Cas9-based editing tools have been successfully established in some representative obligate thermophiles. In this regard, we reviewed the current status and its progress in CRISPR/Cas-based genome editing system towards a variety of thermophilic organisms. Despite the potentials of these progresses, multiple factors/barriers still have to be overcome and optimized for improving its editing efficiency in thermophiles. Some insights into the roles of thermostable CRISPR/Cas technologies for the metabolic engineering of thermophiles as a thermophilic microbial cell factory were also fully analyzed and discussed.
MeSH term(s)	CRISPR-Associated Protein 9/genetics ; CRISPR-Cas Systems ; Gene Editing ; Metabolic Engineering
Chemical Substances	CRISPR-Associated Protein 9 (EC 3.1.-)
Language	English
Publishing date	2022-02-25
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	160-0
ISSN	0065-2164
ISSN	0065-2164
DOI	10.1016/bs.aambs.2022.02.001
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Article ; Online: Xanthan gum modified fish gelatin and binary culture modulates the metabolism of probiotics in fermented milk mainly via amino acid metabolism pathways.

Le, Yi / Yang, Hongshun

Food research international (Ottawa, Ont.)

2022 Volume 161, Page(s) 111844

Abstract: ... ...

Abstract	1
MeSH term(s)	Amino Acids/analysis ; Animals ; Bifidobacterium animalis ; Gelatin ; Lactobacillus acidophilus/metabolism ; Milk/chemistry ; Polysaccharides, Bacterial ; Probiotics ; Sugars/analysis
Chemical Substances	Amino Acids ; Polysaccharides, Bacterial ; Sugars ; Gelatin (9000-70-8) ; xanthan gum (TTV12P4NEE)
Language	English
Publishing date	2022-08-25
Publishing country	Canada
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1111695-x
ISSN	1873-7145 ; 0963-9969
ISSN (online)	1873-7145
ISSN	0963-9969
DOI	10.1016/j.foodres.2022.111844
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Article ; Online: MALAT1 regulates PCT expression in sepsis patients through the miR-125b/STAT3 axis.

Le, Yuanjie / Shi, Yongwei

Journal of clinical laboratory analysis

2022 Volume 36, Issue 5, Page(s) e24428

Abstract: Background: Procalcitonin (PCT) is an important marker in diagnosing sepsis. However, some other diseases can also cause an increase in PCT. PCT still has some limitations in the clinical application of diagnosing sepsis. Therefore, it is of great ... ...

Abstract	Background: Procalcitonin (PCT) is an important marker in diagnosing sepsis. However, some other diseases can also cause an increase in PCT. PCT still has some limitations in the clinical application of diagnosing sepsis. Therefore, it is of great significance to clarify the regulatory mechanism of PCT expression in sepsis and provide new therapeutic targets for sepsis. Methods: Blood samples from clinical patients were collected, and peripheral blood monocytes were isolated. Bioinformatics was performed to find the ceRNA regulatory network of STAT3/PCT. MALAT1 and miR-125b were detected by qRT-PCR. MALAT1 was located by fluorescence in situ hybridization (FISH) in U937 cells, and the regulatory relationship between MALAT1, miR-125b, and STAT3 was verified by double luciferase activity report and RNA pull-down assay. U937 cells were transfected with miR-125b, and the effects of the MALAT1/miR-125b/STAT3 pathway on gene and protein secretion levels of PCT were verified by qRT-PCR, western blot, and ELISA. Results: In the serum of sepsis patients and lipopolysaccharide(LPS)-induced U937 cells, MALAT1, STAT3, and PCT gene expression levels were significantly increased, while miR-125b expression level was decreased. FISH results showed that the MALAT1 transcript was mainly located in the nucleus. The double luciferase activity report and RNA pull-down assay results suggested a targeted regulatory relationship between MALAT1, miR-125b, and STAT3. LPS-induced U937 cells transfection with MALAT1 siRNA decreased STAT3 protein expression and phosphorylation level and the expression of PCT. Co-transfection with miR-125b inhibitor effectively reversed this phenomenon. Conclusions: MALAT1 could upregulate the expressions of STAT3 and PCT by targeted adsorption of miR-125b.
MeSH term(s)	Humans ; In Situ Hybridization, Fluorescence ; Lipopolysaccharides ; MicroRNAs/genetics ; Procalcitonin/metabolism ; RNA, Long Noncoding/genetics ; STAT3 Transcription Factor/genetics ; STAT3 Transcription Factor/metabolism ; Sepsis/genetics
Chemical Substances	Lipopolysaccharides ; MALAT1 long non-coding RNA, human ; MIRN125 microRNA, human ; MicroRNAs ; Procalcitonin ; RNA, Long Noncoding ; STAT3 Transcription Factor ; STAT3 protein, human
Language	English
Publishing date	2022-04-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	645095-7
ISSN	1098-2825 ; 0887-8013
ISSN (online)	1098-2825
ISSN	0887-8013
DOI	10.1002/jcla.24428
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Article ; Online: Pericoronary adipose tissue attenuation predicts outcome of percutaneous intervention for chronic total occlusion.

Le, Y / Wang, R / Xing, H / Chen, H / Song, X / He, Y

Clinical radiology

2023 Volume 79, Issue 2, Page(s) e232–e238

Abstract: Aim: To investigate the association between pericoronary adipose tissue (PCAT) attenuation (PCATA) and outcomes of chronic total occlusion (CTO) after percutaneous coronary intervention (PCI), and to establish a clinical model that can be easily ... ...

Abstract	Aim: To investigate the association between pericoronary adipose tissue (PCAT) attenuation (PCATA) and outcomes of chronic total occlusion (CTO) after percutaneous coronary intervention (PCI), and to establish a clinical model that can be easily generalised to predict the outcomes of PCI-CTO. Materials and methods: Between September 2015 and September 2019, patients from two centres were enrolled retrospectively. The primary endpoint was a procedural success (defined as achieving residual stenosis of <30% and a grade 3 thrombolysis in myocardial infarction [TIMI] flow). The new predictive model was generated by factors that were determined by multivariate analysis. The PCATA of CTO (PCATA-CTO) score was developed by assigning 1 point for each independent predictor, and then summing all points accrued. In addition, the predictive efficacy and interobserver and intraobserver agreement of PCATA-CTO and other scoring systems based on coronary computed tomography angiography (CCTA) were compared. Results: A total of 201 patients (mean age 58.9 ± 10.8 years, 85% male) were enrolled. The PCI success was achieved in 76% of the lesions. PCAT was higher in the PCI success group (-72.44 ± 10.45HU versus -76.76 ± 10.54 HU, p<0.05). Multivariable analysis yielded severe calcification, lesion length ≥15 mm, and perivascular fat attenuation index (FAI) ≤-69.5HU as independent negative predictors for procedural success. The area under the receiver operating characteristic curves for the PCATA-CTO score was 0.72. Comparing the PCATA-CTO score with other predictive scores, the PCATA-CTO score showed the highest interobserver (kappa = 0.74) and intraobserver agreement (kappa = 0.90, all p<0.01). Conclusion: FAI ≤-69.5HU is an independent negative predictor of procedural success. The PCATA-CTO score improved the reliability of the prediction model. Its potential for clinical implementation requires evaluation.
MeSH term(s)	Humans ; Male ; Middle Aged ; Aged ; Female ; Percutaneous Coronary Intervention/methods ; Coronary Angiography/methods ; Coronary Occlusion/diagnostic imaging ; Coronary Occlusion/surgery ; Reproducibility of Results ; Retrospective Studies ; Epicardial Adipose Tissue ; Treatment Outcome ; Chronic Disease ; Risk Factors ; Registries
Language	English
Publishing date	2023-10-29
Publishing country	England
Document type	Journal Article
ZDB-ID	391227-9
ISSN	1365-229X ; 0009-9260
ISSN (online)	1365-229X
ISSN	0009-9260
DOI	10.1016/j.crad.2023.10.012
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Article ; Online: Xanthan gum modified fish gelatin and binary culture modulates the metabolism of probiotics in fermented milk mainly via amino acid metabolism pathways

Le, Yi / Yang, Hongshun

Food Research International. 2022 Nov., v. 161 p.111844-

2022

Abstract: H NMR combined with multivariate data analysis were applied to investigate the effects of fish gelatin (FG) addition and co-culture of Lactobacillus acidophilus LA-5 (La-5) and Bifidobacterium lactis BB-12 (Bb-12) on the growth and metabolic pathways of ...

Abstract	¹H NMR combined with multivariate data analysis were applied to investigate the effects of fish gelatin (FG) addition and co-culture of Lactobacillus acidophilus LA-5 (La-5) and Bifidobacterium lactis BB-12 (Bb-12) on the growth and metabolic pathways of the probiotics themselves. The results showed that the addition of FG had no significant effects on the growth of probiotics, but co-culture did promote the growth of probiotics, especially for Bb-12 (up to 2 log CFU/mL). FG addition inhibited amino acids synthesis and TCA cycling in Lacticaseibacillus paracasei subsp. paracasei CASEI 431 (L431) to some extent. However, for the single La-5 strain, these pathways were promoted. As for mixed bacterial cultures, Bb-12 promoted amino acids metabolism, sugar transport and energy metabolism in La-5. These findings suggested that the metabolic profile of probiotic bacteria can be adequately explained by metabolic pathway analysis, which also provides theoretical guidance for the industrialization of functional fermented milk.
Keywords	Bifidobacterium animalis subsp. lactis ; Lactobacillus acidophilus ; amino acid metabolism ; biochemical pathways ; coculture ; energy metabolism ; fermented milk ; fish ; food research ; gelatin ; industrialization ; multivariate analysis ; probiotics ; sugars ; xanthan gum ; Fish gelatin ; Binary ; Metabolic pathway ; NMR ; Food metabolomics ; Foodomics
Language	English
Dates of publication	2022-11
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	1111695-x
ISSN	1873-7145 ; 0963-9969
ISSN (online)	1873-7145
ISSN	0963-9969
DOI	10.1016/j.foodres.2022.111844
Database	NAL-Catalogue (AGRICOLA)

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