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Article: StRAB4

Li, Pan / Zhu, Hang / Wang, Chengze / Zeng, Fanli / Jia, Jingzhe / Feng, Shang / Han, Xinpeng / Shen, Shen / Wang, Yanhui / Hao, Zhimin / Dong, Jingao

Frontiers in microbiology

2024 Volume 14, Page(s) 1302081

Abstract: Setosphaeria ... ...

Abstract	Setosphaeria turcica
Language	English
Publishing date	2024-01-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2023.1302081
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Article ; Online: sc-ImmuCC: hierarchical annotation for immune cell types in single-cell RNA-seq.

Jiang, Ying / Chen, Ziyi / Han, Na / Shang, Jingzhe / Wu, Aiping

Frontiers in immunology

2023 Volume 14, Page(s) 1223471

Abstract: Accurately identifying immune cell types in single-cell RNA-sequencing (scRNA-Seq) data is critical to uncovering immune responses in health or disease conditions. However, the high heterogeneity and sparsity of scRNA-Seq data, as well as the similarity ... ...

Abstract	Accurately identifying immune cell types in single-cell RNA-sequencing (scRNA-Seq) data is critical to uncovering immune responses in health or disease conditions. However, the high heterogeneity and sparsity of scRNA-Seq data, as well as the similarity in gene expression among immune cell types, poses a great challenge for accurate identification of immune cell types in scRNA-Seq data. Here, we developed a tool named sc-ImmuCC for hierarchical annotation of immune cell types from scRNA-Seq data, based on the optimized gene sets and ssGSEA algorithm. sc-ImmuCC simulates the natural differentiation of immune cells, and the hierarchical annotation includes three layers, which can annotate nine major immune cell types and 29 cell subtypes. The test results showed its stable performance and strong consistency among different tissue datasets with average accuracy of 71-90%. In addition, the optimized gene sets and hierarchical annotation strategy could be applied to other methods to improve their annotation accuracy and the spectrum of annotated cell types and subtypes. We also applied sc-ImmuCC to a dataset composed of COVID-19, influenza, and healthy donors, and found that the proportion of monocytes in patients with COVID-19 and influenza was significantly higher than that in healthy people. The easy-to-use sc-ImmuCC tool provides a good way to comprehensively annotate immune cell types from scRNA-Seq data, and will also help study the immune mechanism underlying physiological and pathological conditions.
MeSH term(s)	Humans ; Gene Expression Profiling/methods ; Influenza, Human ; Single-Cell Gene Expression Analysis ; COVID-19/genetics ; Algorithms
Language	English
Publishing date	2023-07-20
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1223471
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Article ; Online: Bacteriophage classification for assembled contigs using graph convolutional network.

Shang, Jiayu / Jiang, Jingzhe / Sun, Yanni

Bioinformatics (Oxford, England)

2021 Volume 37, Issue Suppl_1, Page(s) i25–i33

Abstract: Motivation: Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the biology of microbes. As the most abundant biological entities on the planet, the number of discovered phages is only the tip of the iceberg. Recently, many new ... ...

Abstract	Motivation: Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the biology of microbes. As the most abundant biological entities on the planet, the number of discovered phages is only the tip of the iceberg. Recently, many new phages have been revealed using high-throughput sequencing, particularly metagenomic sequencing. Compared to the fast accumulation of phage-like sequences, there is a serious lag in taxonomic classification of phages. High diversity, abundance and limited known phages pose great challenges for taxonomic analysis. In particular, alignment-based tools have difficulty in classifying fast accumulating contigs assembled from metagenomic data. Results: In this work, we present a novel semi-supervised learning model, named PhaGCN, to conduct taxonomic classification for phage contigs. In this learning model, we construct a knowledge graph by combining the DNA sequence features learned by convolutional neural network and protein sequence similarity gained from gene-sharing network. Then we apply graph convolutional network to utilize both the labeled and unlabeled samples in training to enhance the learning ability. We tested PhaGCN on both simulated and real sequencing data. The results clearly show that our method competes favorably against available phage classification tools. Availability and implementation: The source code of PhaGCN is available via: https://github.com/KennthShang/PhaGCN.
MeSH term(s)	Bacteriophages/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics ; Software
Language	English
Publishing date	2021-07-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btab293
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Article ; Online: Suppression of the METTL3-m

Wang, Zhe / Shang, Jingzhe / Qiu, Yajing / Cheng, Hongcheng / Tao, Mengyuan / Xie, Ermei / Pei, Xin / Li, Wenhui / Zhang, Lianjun / Wu, Aiping / Li, Guideng

Cell reports

2024 Volume 43, Issue 2, Page(s) 113796

Abstract: The acidic metabolic byproducts within the tumor microenvironment (TME) hinder T cell effector functions. However, their effects on T cell infiltration remain largely unexplored. Leveraging the comprehensive The Cancer Genome Atlas dataset, we pinpoint ... ...

Abstract	The acidic metabolic byproducts within the tumor microenvironment (TME) hinder T cell effector functions. However, their effects on T cell infiltration remain largely unexplored. Leveraging the comprehensive The Cancer Genome Atlas dataset, we pinpoint 16 genes that correlate with extracellular acidification and establish a metric known as the "tumor acidity (TuAci) score" for individual patients. We consistently observe a negative association between the TuAci score and T lymphocyte score (T score) across various human cancer types. Mechanistically, extracellular acidification significantly impedes T cell motility by suppressing podosome formation. This phenomenon can be attributed to the reduced expression of methyltransferase-like 3 (METTL3) and the modification of RNA N
MeSH term(s)	Humans ; Cell- and Tissue-Based Therapy ; Hydrogen-Ion Concentration ; Integrin beta1/genetics ; Methyltransferases/genetics ; Neoplasms ; T-Lymphocytes ; Tumor Microenvironment
Chemical Substances	Integrin beta1 ; Methyltransferases (EC 2.1.1.-) ; METTL3 protein, human (EC 2.1.1.62) ; Itgb1 protein, human
Language	English
Publishing date	2024-02-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2024.113796
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Article: Insight into the Molecular Characteristics of Langhans Giant Cell by Combination of Laser Capture Microdissection and RNA Sequencing.

Chen, Yanqing / Jiang, Haiqin / Xiong, Jingshu / Shang, Jingzhe / Chen, Zhiming / Wu, Aiping / Wang, Hongsheng

Journal of inflammation research

2022 Volume 15, Page(s) 621–634

Abstract: Purpose: The presence of Langhans giant cell (LGC) is a hallmark of mycobacterium-induced granuloma. The molecular characteristics and functions of LGC remain unclear to date. The study aimed to systematically characterize the molecular characteristics ... ...

Abstract	Purpose: The presence of Langhans giant cell (LGC) is a hallmark of mycobacterium-induced granuloma. The molecular characteristics and functions of LGC remain unclear to date. The study aimed to systematically characterize the molecular characteristics of LGC and reveal the potential functions. Methods: Human LGCs were purified through laser capture microdissection (LCM) in vitro. RNA sequencing and in-depth transcriptome analysis were performed for purified LGCs and macrophages in the same system. Skin samples from mycobacterial infection patients were used to confirm some of the transcriptional expression. Results: Human LGCs have different expression pattern from macrophages in the same in vitro system. A total of 967 differentially expressed genes were found. Bioinformatics analysis showed that LGCs are is characterized by active cell shape regulation, increased cytoskeletal components, weakened energy metabolism level, and reduced immune response. CCL7 may be a specific molecular for LGC to communicate with CCR1-expression cells in granuloma. Conclusion: LGCs have unique molecular characteristics different from that of macrophages. They may play a role in maintaining the hemostasis in granuloma.
Language	English
Publishing date	2022-02-02
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2494878-0
ISSN	1178-7031
ISSN	1178-7031
DOI	10.2147/JIR.S337241
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Article: Psoriasis and Leprosy: An Arcane Relationship.

Ge, Gai / Shang, Jingzhe / Gan, Tian / Chen, Zhiming / Pan, Chun / Mei, Youming / Long, Siyu / Wu, Aiping / Wang, Hongsheng

Journal of inflammation research

2023 Volume 16, Page(s) 2521–2533

Abstract: Purpose: Psoriasis (Ps) and leprosy are chronic inflammatory skin disorders, characterised by enhanced innate and adaptive immunity. Ps and leprosy rarely coexist. The molecular immune mechanism of the Ps and leprosy rarely coexistence is unclear.: ... ...

Abstract	Purpose: Psoriasis (Ps) and leprosy are chronic inflammatory skin disorders, characterised by enhanced innate and adaptive immunity. Ps and leprosy rarely coexist. The molecular immune mechanism of the Ps and leprosy rarely coexistence is unclear. Patients and methods: RNA-sequencing (RNA-seq) was performed on 20 patients with Ps, 5 adults with lepromatous leprosy (L-lep), and 5 patients with tuberculoid leprosy (T-lep) to analyse the differentially expressed genes (DEGs) between them. Moreover, the biological mechanism of Ps and leprosy was explored by Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, Gene Ontology (GO) analysis, Gene Set Enrichment Analysis analysis, and protein-protein interaction (PPI) analyses. Finally, 13 DEGs of 10 skin biopsies of Ps patients, 6 samples of L-lep patients, 6 samples of T-lep patients and 5 healthy controls were confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). Results: The PPI network was constructed and primarily associated with immune response, IL-17 signalling, and Toll-like receptor pathway between Ps and leprosy. Th17 markers (interleukin ( Conclusion: To put it simply, Ps patients with
Language	English
Publishing date	2023-06-14
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2494878-0
ISSN	1178-7031
ISSN	1178-7031
DOI	10.2147/JIR.S407650
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Article ; Online: Genetic differentiation and diversity of SARS-CoV-2 Omicron variant in its early outbreak.

Weng, Shenghui / Shang, Jingzhe / Cheng, Yexiao / Zhou, Hangyu / Ji, Chengyang / Yang, Rong / Wu, Aiping

Biosafety and health

2022 Volume 4, Issue 3, Page(s) 171–178

Abstract: The recently emerged Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has quickly spread around the world. Although many consensus mutations of the Omicron variant have been recognized, little is known about its genetic ... ...

Abstract	The recently emerged Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has quickly spread around the world. Although many consensus mutations of the Omicron variant have been recognized, little is known about its genetic variation during its transmission in the population. Here, we comprehensively analyzed the genetic differentiation and diversity of the Omicron variant during its early outbreak. We found that Omicron achieved more structural variations, especially deletions, on the SARS-CoV-2 genome than the other four variants of concern (Alpha, Beta, Gamma, and Delta) in the same timescale. In addition, the Omicron variant acquired, except for 50 consensus mutations, seven great new non-synonymous nucleotide substitutions during its spread. Three of them are on the S protein, including S_A701V, S_L1081V, and S_R346K, which belong to the receptor-binding domain (RBD). The Omicron BA.1 branch could be divided into five divergent groups spreading across different countries and regions based on these seven novel mutations. Furthermore, we found that the Omicron variant possesses more mutations related to a faster transmission rate than the other SARS-CoV-2 variants by assessing the relationship between the genetic diversity and transmission rate. The findings indicated that more attention should be paid to the significant genetic differentiation and diversity of the Omicron variant for better disease prevention and control.
Language	English
Publishing date	2022-04-25
Publishing country	Netherlands
Document type	Journal Article
ISSN	2590-0536
ISSN (online)	2590-0536
DOI	10.1016/j.bsheal.2022.04.004
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Article ; Online: Genetic differentiation and diversity of SARS-CoV-2 Omicron variant in its early outbreak

Shenghui Weng / Jingzhe Shang / Yexiao Cheng / Hangyu Zhou / Chengyang Ji / Rong Yang / Aiping Wu

Biosafety and Health, Vol 4, Iss 3, Pp 171-

2022 Volume 178

Abstract	The recently emerged Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has quickly spread around the world. Although many consensus mutations of the Omicron variant have been recognized, little is known about its genetic variation during its transmission in the population. Here, we comprehensively analyzed the genetic differentiation and diversity of the Omicron variant during its early outbreak. We found that Omicron achieved more structural variations, especially deletions, on the SARS-CoV-2 genome than the other four variants of concern (Alpha, Beta, Gamma, and Delta) in the same timescale. In addition, the Omicron variant acquired, except for 50 consensus mutations, seven great new non-synonymous nucleotide substitutions during its spread. Three of them are on the S protein, including S_A701V, S_L1081V, and S_R346K, which belong to the receptor-binding domain (RBD). The Omicron BA.1 branch could be divided into five divergent groups spreading across different countries and regions based on these seven novel mutations. Furthermore, we found that the Omicron variant possesses more mutations related to a faster transmission rate than the other SARS-CoV-2 variants by assessing the relationship between the genetic diversity and transmission rate. The findings indicated that more attention should be paid to the significant genetic differentiation and diversity of the Omicron variant for better disease prevention and control.
Keywords	SARS-CoV-2 ; Omicron ; Genetic diversity ; Infectious and parasitic diseases ; RC109-216 ; Public aspects of medicine ; RA1-1270
Subject code	572
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Bacteriophage classification for assembled contigs using Graph Convolutional Network

Shang, Jiayu / Jiang, Jingzhe / Sun, Yanni

2021

Abstract	Motivation: Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the biology of microbes. As the most abundant biological entities on the planet, the number of discovered phages is only the tip of the iceberg. Recently, many new phages have been revealed using high throughput sequencing, particularly metagenomic sequencing. Compared to the fast accumulation of phage-like sequences, there is a serious lag in taxonomic classification of phages. High diversity, abundance, and limited known phages pose great challenges for taxonomic analysis. In particular, alignment-based tools have difficulty in classifying fast accumulating contigs assembled from metagenomic data. Results: In this work, we present a novel semi-supervised learning model, named PhaGCN, to conduct taxonomic classification for phage contigs. In this learning model, we construct a knowledge graph by combining the DNA sequence features learned by convolutional neural network (CNN) and protein sequence similarity gained from gene-sharing network. Then we apply graph convolutional network (GCN) to utilize both the labeled and unlabeled samples in training to enhance the learning ability. We tested PhaGCN on both simulated and real sequencing data. The results clearly show that our method competes favorably against available phage classification tools. Comment: 15 pages, 10 figures
Keywords	Quantitative Biology - Genomics ; Computer Science - Machine Learning
Subject code	006
Publishing date	2021-02-07
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genomic annotation and molecular evolution of monkeypox virus outbreak in 2022.

Wang, Lulan / Shang, Jingzhe / Weng, Shenghui / Aliyari, Saba R / Ji, Chengyang / Cheng, Genhong / Wu, Aiping

Journal of medical virology

2022 Volume 95, Issue 1, Page(s) e28036

Abstract: Monkeypox virus (MPXV) has generally circulated in West and Central Africa since its emergence. Recently, sporadic MPXV infections in several nonendemic countries have attracted widespread attention. Here, we conducted a systematic analysis of the recent ...

Abstract	Monkeypox virus (MPXV) has generally circulated in West and Central Africa since its emergence. Recently, sporadic MPXV infections in several nonendemic countries have attracted widespread attention. Here, we conducted a systematic analysis of the recent outbreak of MPXV-2022, including its genomic annotation and molecular evolution. The phylogenetic analysis indicated that the MPXV-2022 strains belong to the same lineage of the MPXV strain isolated in 2018. However, compared with the MPXV strain in 2018, in total 46 new consensus mutations were observed in the MPXV-2022 strains, including 24 nonsynonymous mutations. By assigning mutations to 187 proteins encoded by the MPXV genome, we found that 10 proteins in the MPXV are more prone to mutation, including D2L-like, OPG023, OPG047, OPG071, OPG105, OPG109, A27L-like, OPG153, OPG188, and OPG210 proteins. In the MPXV-2022 strains, four and three nucleotide substitutions are observed in OPG105 and OPG210, respectively. Overall, our studies illustrated the genome evolution of the ongoing MPXV outbreak and pointed out novel mutations as a reference for further studies.
MeSH term(s)	Humans ; Monkeypox virus/genetics ; Mpox (monkeypox) ; Phylogeny ; Genomics ; Evolution, Molecular
Language	English
Publishing date	2022-08-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	752392-0
ISSN	1096-9071 ; 0146-6615
ISSN (online)	1096-9071
ISSN	0146-6615
DOI	10.1002/jmv.28036
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