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Article: Characteristics of intestinal flora in patients with cerebral infarction complicated with Type 2 diabetes mellitus.

Cheng, Xueying / Zhang, Zhengqian / Dong, Wen / Lun, Yongzhi / Liu, Ben

Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences

2024 Volume 48, Issue 8, Page(s) 1163–1175

Abstract: Objectives: The intestinal microbial characteristics of patients with simple cerebral infarction (CI) and CI complicated with Type 2 diabetes mellitus (CI-T2DM) are still not clear. This study aims to analyze the differences in the variable ... ...

Title translation	脑梗死合并2型糖尿病患者的肠道菌群特征(英文).
Abstract	Objectives: The intestinal microbial characteristics of patients with simple cerebral infarction (CI) and CI complicated with Type 2 diabetes mellitus (CI-T2DM) are still not clear. This study aims to analyze the differences in the variable characteristics of intestinal flora between patients simply with CI and CI-T2DM. Methods: This study retrospectively collected the patients who were admitted to the Affiliated Hospital of Putian University from September 2021 to September 2022. The patients were divided into a CI group ( Results: At phylum level, the average ratio of Firmicutes, Bacteroidetes, and Proteobacteria in the CI-T2DM group were 33.07%, 54.80%, and 7.00%, respectively. In the CI group, the ratios of each were 14.03%, 69.62%, and 11.13%, respectively, while in the control group, the ratios were 50.99%, 37.67%, and 5.24%, respectively. There was significant differences in the distribution of Firmicutes ( Conclusions: From phylum level to species level, the composition of intestinal flora in the patients with CI-T2DM is different from those in the patients simply with CI. The change in the proportion of
MeSH term(s)	Humans ; Gastrointestinal Microbiome/genetics ; Diabetes Mellitus, Type 2/complications ; Retrospective Studies ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing
Language	Chinese
Publishing date	2024-03-19
Publishing country	China
Document type	Journal Article
ZDB-ID	2168533-2
ISSN	1672-7347
ISSN	1672-7347
DOI	10.11817/j.issn.1672-7347.2023.220558
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Article: Transcriptome Analysis Revealed Potential Neuro-Immune Interaction in Papillary Thyroid Carcinoma Tissues.

Hu, Haibei / Chen, Qiang / Zheng, Siqi / Du, Shan / Ding, Siqin / Lun, Yongzhi

Diseases (Basel, Switzerland)

2023 Volume 11, Issue 1

Abstract: Background: A recent study reported that papillary thyroid carcinoma (PTC) was associated with increased adrenergic nerve density. Meanwhile, emerging evidence suggested that tumor-innervating nerves might play a role in shaping the tumor ... ...

Abstract	Background: A recent study reported that papillary thyroid carcinoma (PTC) was associated with increased adrenergic nerve density. Meanwhile, emerging evidence suggested that tumor-innervating nerves might play a role in shaping the tumor microenvironment. We aimed to explore the potential interaction between neuronal markers and tumor microenvironmental signatures through a transcriptomic approach. Methods: mRNA sequencing was conducted using five pairs of PTC and adjacent normal tissues. The Gene Set Variation Analysis (GSVA) was performed to calculate enrichment scores of gene sets related to tumor-infiltrating immune cells and the tumor microenvironment. The potential interaction was tested using the expression levels of a series of neuronal markers and gene set enrichment scores. Results: PTC tissues were associated with increased enrichment scores of CD8 T cells, cancer-associated fibroblasts, mast cells, and checkpoint molecules. The neuronal marker for cholinergic neurons was positively correlated with CD8 T cell activation, while markers for serotonergic and dopaminergic neurons showed an inverse correlation. Conclusion: Distinct neuronal markers exerted different correlations with tumor microenvironmental signatures. Tumor-innervating nerves might play a role in the formation of the PTC microenvironment.
Language	English
Publishing date	2023-01-04
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2720869-2
ISSN	2079-9721
ISSN	2079-9721
DOI	10.3390/diseases11010009
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Article: MicroRNA-96-5p is negatively regulating GPC3 in the metastasis of papillary thyroid cancer.

Hu, Haibei / Quan, Guangqian / Yang, Feng / Du, Shan / Ding, Siqin / Lun, Yongzhi / Chen, Qiang

SAGE open medicine

2023 Volume 11, Page(s) 20503121231205710

Abstract: Backgrounds: Papillary thyroid cancer is the most common pathological type of thyroid cancer. miR-96-5p, a member of the miR-183 family, constitute a polycistronic miRNA cluster. In breast cancer, miR-96-5p promotes cell invasion, migration, and ... ...

Abstract	Backgrounds: Papillary thyroid cancer is the most common pathological type of thyroid cancer. miR-96-5p, a member of the miR-183 family, constitute a polycistronic miRNA cluster. In breast cancer, miR-96-5p promotes cell invasion, migration, and proliferation in vitro by inhibiting PTPN9. Moreover, miR-96-5p was reported to function as an oncogene in many cancers. However, whether miR-96-5p is involved in the development of papillary thyroid cancers and its potential mechanism is still unknown. The present study aims to explore the relationship between miR-96-5p and GPC3 expression in the development of papillary thyroid cancers. Methods: Transcriptomic sequencing was carried out using six pairs of papillary thyroid cancer and adjacent normal tissues. Quantitative real-time polymerase chain reaction (PCR) experiments were performed to examine the expression of genes. Results: In total, there were 1588 up-regulated and 1803 down-regulated differentially expressed genes between papillary thyroid cancer and normal tissues. Gene ontology and Kyoto encyclopedia of genes and genomes analysis revealed that extracellular matrix structure and proteoglycans were mainly involved in papillary thyroid cancer. Among the cluster of proteoglycans, GPC3 was significantly down-regulated in papillary thyroid cancer and is a target of miR-96. Conclusion: miR-96-5p participates in the development of papillary thyroid cancer by regulating the expression of GPC3. Thus, targeting miR-96-5p may be a potential therapeutic approach for preventing and treating papillary thyroid cancer.
Language	English
Publishing date	2023-10-29
Publishing country	England
Document type	Journal Article
ZDB-ID	2735399-0
ISSN	2050-3121
ISSN	2050-3121
DOI	10.1177/20503121231205710
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Article ; Online: MicroRNA-96-5p is negatively regulating GPC3 in the metastasis of papillary thyroid cancer

Haibei Hu / Guangqian Quan / Feng Yang / Shan Du / Siqin Ding / Yongzhi Lun / Qiang Chen

SAGE Open Medicine, Vol

2023 Volume 11

Abstract	Backgrounds: Papillary thyroid cancer is the most common pathological type of thyroid cancer. miR-96-5p, a member of the miR-183 family, constitute a polycistronic miRNA cluster. In breast cancer, miR-96-5p promotes cell invasion, migration, and proliferation in vitro by inhibiting PTPN9. Moreover, miR-96-5p was reported to function as an oncogene in many cancers. However, whether miR-96-5p is involved in the development of papillary thyroid cancers and its potential mechanism is still unknown. The present study aims to explore the relationship between miR-96-5p and GPC3 expression in the development of papillary thyroid cancers. Methods: Transcriptomic sequencing was carried out using six pairs of papillary thyroid cancer and adjacent normal tissues. Quantitative real-time polymerase chain reaction (PCR) experiments were performed to examine the expression of genes. Results: In total, there were 1588 up-regulated and 1803 down-regulated differentially expressed genes between papillary thyroid cancer and normal tissues. Gene ontology and Kyoto encyclopedia of genes and genomes analysis revealed that extracellular matrix structure and proteoglycans were mainly involved in papillary thyroid cancer. Among the cluster of proteoglycans, GPC3 was significantly down-regulated in papillary thyroid cancer and is a target of miR-96. Conclusion: miR-96-5p participates in the development of papillary thyroid cancer by regulating the expression of GPC3. Thus, targeting miR-96-5p may be a potential therapeutic approach for preventing and treating papillary thyroid cancer.
Keywords	Medicine (General) ; R5-920
Subject code	610
Language	English
Publishing date	2023-10-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Transcriptome Analysis Revealed Potential Neuro-Immune Interaction in Papillary Thyroid Carcinoma Tissues

Haibei Hu / Qiang Chen / Siqi Zheng / Shan Du / Siqin Ding / Yongzhi Lun

Diseases, Vol 11, Iss 9, p

2023 Volume 9

Abstract	Background: A recent study reported that papillary thyroid carcinoma (PTC) was associated with increased adrenergic nerve density. Meanwhile, emerging evidence suggested that tumor-innervating nerves might play a role in shaping the tumor microenvironment. We aimed to explore the potential interaction between neuronal markers and tumor microenvironmental signatures through a transcriptomic approach. Methods: mRNA sequencing was conducted using five pairs of PTC and adjacent normal tissues. The Gene Set Variation Analysis (GSVA) was performed to calculate enrichment scores of gene sets related to tumor-infiltrating immune cells and the tumor microenvironment. The potential interaction was tested using the expression levels of a series of neuronal markers and gene set enrichment scores. Results: PTC tissues were associated with increased enrichment scores of CD8 T cells, cancer-associated fibroblasts, mast cells, and checkpoint molecules. The neuronal marker for cholinergic neurons was positively correlated with CD8 T cell activation, while markers for serotonergic and dopaminergic neurons showed an inverse correlation. Conclusion: Distinct neuronal markers exerted different correlations with tumor microenvironmental signatures. Tumor-innervating nerves might play a role in the formation of the PTC microenvironment.
Keywords	papillary thyroid carcinoma ; GSVA ; neurons ; tumor microenvironment ; Medicine ; R
Subject code	616
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article: A Case of Rare Complex Translocation of four Chromosomes with Primary Infertility.

Wang, Kangying / Tu, Haijian / Lin, Hua / Xu, Guanghui / Lun, Yongzhi

Clinical laboratory

2022 Volume 68, Issue 11

Abstract: Background: Complex translocation of chromosomes often causes mental retardation, dysplasia, and a variety of abnormalities in patients, which can easily lead to sperm disorders in men, and carriers are often at high risk of adverse pregnancy.: ... ...

Abstract	Background: Complex translocation of chromosomes often causes mental retardation, dysplasia, and a variety of abnormalities in patients, which can easily lead to sperm disorders in men, and carriers are often at high risk of adverse pregnancy. Methods: The chromosome karyotypes of the patients were analyzed by collecting peripheral blood for lymphocyte culture, chromosome harvest, section and G-banding staining. Results: The results of chromosome karyotype analysis in the patient were 46,XY, T (4; 11. 6; 8)(q33; p15; p12; Q22), the translocation occurred on chromosome 4, 11, 6 and 8, and the break points were q33, p15, p12 and q22, respectively. Conclusions: Translocation occurred in 4 chromosomes of the patient, which was a complex translocation and was rare in clinic. The meiosis of the germ cells can interfere with the normal pairing and distribution of chromosomes, resulting in a high probability of abnormal gamete formation. Therefore, patients are advised to avoid natural conception, or use other people's sperm to obtain normal offspring through artificial insemination, or adopt children to achieve a successful family combination.
MeSH term(s)	Pregnancy ; Female ; Child ; Humans ; Male ; Semen ; Translocation, Genetic ; Karyotyping ; Karyotype ; Infertility, Male/diagnosis ; Infertility, Male/genetics
Language	English
Publishing date	2022-11-15
Publishing country	Germany
Document type	Case Reports
ZDB-ID	1307629-2
ISSN	1433-6510 ; 0941-2131
ISSN	1433-6510 ; 0941-2131
DOI	10.7754/Clin.Lab.2022.220127
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Article: [Identification of differentially expressed genes in peripheral blood mononuclear cells of patients with hepatocellular carcinoma and its regulatory network analysis].

Lun, Yongzhi / Sun, Jie

Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences

2019 Volume 48, Issue 2, Page(s) 148–157

Abstract: Objective: To identify the differentially expressed genes (DEGs) in peripheral blood mononuclear cells (PBMC) of patients with hepatocellular carcinoma (HCC) and to analyze their regulatory network.: Methods: The DEGs in PBMCs of HCC patients were ... ...

Abstract	Objective: To identify the differentially expressed genes (DEGs) in peripheral blood mononuclear cells (PBMC) of patients with hepatocellular carcinoma (HCC) and to analyze their regulatory network. Methods: The DEGs in PBMCs of HCC patients were screened based on GEO database. The functional enrichment analysis and interaction analysis were carried out for DEGs. MCODE algorithm was used to screen core genes of DEGs, and the mirDIP and starBase online tools were used to predict upstream miRNAs and lncRNAs of the core genes. Results: A total of 265 DEGs with a high credibility were identified, which were mainly enriched in the biological activity, such as regulation of cell proliferation, metabolic regulation, cell communication and signaling, and inflammatory diseases according to Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and the two analyses were correlated. Four diagnostic candidate genes were identified, including FUS RNA binding protein, C-X-C motif chemokine ligand 8, cullin 1 and RNA polymerase Ⅱ subunit H. Subsequently, 10 miRNAs, 1 lncRNAs and 38 circRNAs were predicted, and finally a lncRNA/circRNA-miRNA-mRNA-pathway regulatory networks was constructed. Conclusions: The diagnostic candidate genes and its regulatory network in HCC PBMC have been identified based on data mining, which could provide potential tumor biomarkers for early diagnosis and treatment of HCC.
MeSH term(s)	Carcinoma, Hepatocellular/physiopathology ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Humans ; Leukocytes, Mononuclear/metabolism ; Liver Neoplasms/physiopathology
Language	Chinese
Publishing date	2019-07-10
Publishing country	China
Document type	Journal Article
ISSN	1008-9292
ISSN	1008-9292
DOI	10.3785/j.issn.1008-9292.2019.04.05
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Article ; Online: Transcriptome analysis of the effect of a novel human serine protease inhibitor SPINK13 on gene expression in MHCC97-H cells.

Wei, Ling / An, Tao / An, Yunhe / He, Zheng / Jia, Tingting / Li, Baoming / Lun, Yongzhi

Translational cancer research

2022 Volume 10, Issue 10, Page(s) 4464–4477

Abstract: Background: Serine peptidase inhibitor, Kazal type 13 (SPINK13) (also known as hespinter) is a low-molecular-weight inhibitor of uPA that was discovered in 2006. It was detected in prokaryotic cells in 2013 for the first time and preliminarily shown to ... ...

Abstract	Background: Serine peptidase inhibitor, Kazal type 13 (SPINK13) (also known as hespinter) is a low-molecular-weight inhibitor of uPA that was discovered in 2006. It was detected in prokaryotic cells in 2013 for the first time and preliminarily shown to inhibit hepG2 liver cancer cells growth Methods: Preliminary study of the molecular mechanism of SPINK13's anti-cancer effect was performed by identifying potential target sites and signal pathways of SPINK13 through transcriptomics and bioinformatics analysis. Results: The results of the transcriptome study showed that there were 446 significantly differentially expressed genes between the experimental group and the blank control group, of which 347 genes were up-regulated and 99 genes were down-regulated. The Gene Ontology (GO) analysis showed that differentially expressed genes were enriched in cell growth regulation and cell division. They were enriched in the signal pathways of tumor transcription and cell cycle by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis; there were 6 classical tumor signaling pathways (P<0.001): MAPK, apoptosis, tumor necrosis factor (TNF), cell cycle, p53, and transcriptional misregulation in cancer. There were 8 genes in 2 or more classical tumor signaling pathways at the same time: Conclusions: This study showed that SPINK13 inhibits hepatocellular carcinoma cell development by regulating the JNK, p53, and the IKK/NF-κB pathways, its potential targets for antitumor drugs may be J
Language	English
Publishing date	2022-01-15
Publishing country	China
Document type	Journal Article
ZDB-ID	2901601-0
ISSN	2219-6803 ; 2218-676X
ISSN (online)	2219-6803
ISSN	2218-676X
DOI	10.21037/tcr-21-1928
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Book ; Online: BEVPlace

Luo, Lun / Zheng, Shuhang / Li, Yixuan / Fan, Yongzhi / Yu, Beinan / Cao, Siyuan / Shen, Huiliang

Learning LiDAR-based Place Recognition using Bird's Eye View Images

2023

Abstract: Place recognition is a key module for long-term SLAM systems. Current LiDAR-based place recognition methods are usually based on representations of point clouds such as unordered points or range images. These methods achieve high recall rates of ... ...

Abstract	Place recognition is a key module for long-term SLAM systems. Current LiDAR-based place recognition methods are usually based on representations of point clouds such as unordered points or range images. These methods achieve high recall rates of retrieval, but their performance may degrade in the case of view variation or scene changes. In this work, we explore the potential of a different representation in place recognition, i.e. bird's eye view (BEV) images. We observe that the structural contents of BEV images are less influenced by rotations and translations of point clouds. We validate that, without any delicate design, a simple VGGNet trained on BEV images achieves comparable performance with the state-of-the-art place recognition methods in scenes of slight viewpoint changes. For more robust place recognition, we design a rotation-invariant network called BEVPlace. We use group convolution to extract rotation-equivariant local features from the images and NetVLAD for global feature aggregation. In addition, we observe that the distance between BEV features is correlated with the geometry distance of point clouds. Based on the observation, we develop a method to estimate the position of the query cloud, extending the usage of place recognition. The experiments conducted on large-scale public datasets show that our method 1) achieves state-of-the-art performance in terms of recall rates, 2) is robust to view changes, 3) shows strong generalization ability, and 4) can estimate the positions of query point clouds. Source code will be made publicly available at https://github.com/zjuluolun/BEVPlace.
Keywords	Computer Science - Computer Vision and Pattern Recognition ; Computer Science - Robotics
Subject code	006
Publishing date	2023-02-28
Publishing country	us
Document type	Book ; Online
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Article: [Comparative analysis of structural characteristics and epitopes in S proteins between SARS-CoV-2 and SARS-CoV].

Lun, Yongzhi / Liu, Ben / Dong, Wen / Sun, Jie / Pan, Linghong

Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences

2020 Volume 49, Issue 3, Page(s) 315–323

Abstract: Objective: To provide data support for the study of pathogenic mechanism of SARS-CoV-2 at the molecular level, and provide suitable candidate targets for vaccine, antibody and drug research and development through comparative analysis for structural ... ...

Abstract	Objective: To provide data support for the study of pathogenic mechanism of SARS-CoV-2 at the molecular level, and provide suitable candidate targets for vaccine, antibody and drug research and development through comparative analysis for structural characteristics and epitopes of S protein of SARS-CoV-2 and SARS-CoV. Methods: Based on the reference sequences of S protein, physical and chemical properties, hydrophobicity, signal peptide, transmembrane region, domain, secondary structure, tertiary structure analysis and antigenic epitopes prediction were carried out. Meanwhile, the tissue expression, related pathways and reactome pathways of angiotensis Ⅰ converting enzyme 2 (ACE2) and C-type lectin domain family 4 member M (CLEC4M) receptors were analyzed. Results: The amino acid sequence of S protein of SARS-CoV-2 and SARS-CoV has a 75.80% consistency. The structural characteristics of the two coronaviruses are highly consistent, but the secondary structure and tertiary structure of SARS-CoV-2 is not as obvious as SARS-CoV. ACE2 and CLEC4M are expressed in alimentary system, heart, kidney, lung and placenta. The main related the pathways of renin-angiotensin system, protein digestion and absorption pathway, and the reactome pathways of metabolism of angiotensinogen to angiotensins, GPCR ligand binding, are related to typical symptoms of coronavirus disease 2019 induced by SARS-CoV-2. Three pairs of highly or completely homologous epitopes of S protein were obtained. The 600-605, 695-703 and 888-896 amino acid residues in SARS-CoV-2 were highly homologous with 586-591, 677-685 and 870-878 amino acid residues in SARS-CoV, respectively. Conclusions: The similarity of S protein of SARS-CoV-2 and SARS-CoV determines that they have similar infection patterns and clinical manifestations. The candidate epitopes with high reliability can provide reference for virus diagnosis and vaccine development.
MeSH term(s)	Betacoronavirus ; COVID-19 ; Cell Adhesion Molecules ; Coronavirus Infections ; Epitopes ; Humans ; Lectins, C-Type ; Ligands ; Pandemics ; Peptidyl-Dipeptidase A ; Pneumonia, Viral ; Receptors, Cell Surface ; Receptors, Virus ; Reproducibility of Results ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus
Chemical Substances	CLEC4M protein, human ; Cell Adhesion Molecules ; Epitopes ; Lectins, C-Type ; Ligands ; Receptors, Cell Surface ; Receptors, Virus ; Spike Glycoprotein, Coronavirus ; Peptidyl-Dipeptidase A (EC 3.4.15.1)
Keywords	covid19
Language	Chinese
Publishing date	2020-08-05
Publishing country	China
Document type	Comparative Study ; Journal Article
ISSN	1008-9292
ISSN	1008-9292
DOI	10.3785/j.issn.1008-9292.2020.06.06
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