Single-Cell Analysis of Different Stages of Oral Cancer Carcinogenesis in a Mouse Model

Oral carcinogenesis involves the progression of the normal mucosa into potentially malignant disorders and finally into cancer. Tumors are heterogeneous, with different clusters of cells expressing different genes and exhibiting different behaviors. 4-nitroquinoline 1-oxide (4-NQO) and arecoline were used to induce oral cancer in mice, and the main factors for gene expression influencing carcinogenesis were identified through single-cell RNA sequencing analysis. Male C57BL/6J mice were divided into two groups: a control group (receiving normal drinking water) and treatment group (receiving drinking water containing 4-NQO (200 mg/L) and arecoline (500 mg/L)) to induce the malignant development of oral cancer. Mice were sacrificed at 8, 16, 20, and 29 weeks. Except for mice sacrificed at 8 weeks, all mice were treated for 16 weeks and then either sacrificed or given normal drinking water for the remaining weeks. Tongue lesions were excised, and all cells obtained from mice in the 29- and 16-week treatment groups were clustered into 17 groups by using the Louvain algorithm. Cells in subtypes 7 (stem cells) and 9 (keratinocytes) were analyzed through gene set enrichment analysis. Results indicated that their genes were associated with the MYC_targets_v1 pathway, and this finding was confirmed by the presence of cisplatin-resistant nasopharyngeal carcinoma cell lines. These cell subtype biomarkers can be applied for the detection of patients with precancerous lesions, the identification of high-risk populations, and as a treatment target.

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Role of Chemokine and TNF signaling pathway in oral squamous cell carcinoma: A RNA deep sequencing analysis of oral buccal mucosa squamous carcinoma model of Chinese hamster

10.1101/778399 ◽

2019 ◽

Author(s):

Guoqiang Xu ◽

Jianing Wei ◽

Bing Huangfu ◽

Jiping Gao ◽

Xiaotang Wang ◽

...

Keyword(s):

Oral Cancer ◽

Signaling Pathway ◽

Rna Sequencing ◽

Squamous Cell ◽

Buccal Mucosa ◽

Chinese Hamster ◽

Squamous Carcinoma ◽

Enrichment Analysis ◽

Control Group ◽

Sequencing Analysis

AbstractOral cancer is one of the most common cancers in the world, meanwhile, differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas (OSCC). In this study we screened RNA transcripts from the oral buccal mucosa of healthy male Chinese hamster, divided into 3 groups: a control group with no disposal, a solvent control group coated with acetone solvent, and an experimental group coated with 0.5% DMBA acetone solution by high-throughput RNA sequencing. Tophat and Bowtie were used to align the high-quality reads into transcripts, DEseq was used to analysis the expression of differential gene. Then, the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted. The chemokine and TNF signaling pathway were differentially expression and the mRNA expression of CXCL1, CXCL2, CXCL3, CCL7, MMP9, monitored by qRT-PCR, increased remarkably in the cancer group and coincided with the result of RNA-Sequencing. Meanwhile, the CXCL1, CXCL2, CXCL3, and CCL7 are significantly enriched in the chemokine signaling pathway, and CXCL1, CXCL2, CXCL3, and MMP9 are significantly enriched in the tumor necrosis factor (TNF) signaling pathway. The differentially expression of the chemokine and TNF signaling pathway was a response to the invasion of the organism immune system due to oral buccal mucosa squamous carcinoma. All the findings provided novel insights for further molecular researches of oral cancer.

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Integrated network analysis identifying potential novel drug candidates and targets for Parkinson's disease

Scientific Reports ◽

10.1038/s41598-021-92701-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Pusheng Quan ◽

Kai Wang ◽

Shi Yan ◽

Shirong Wen ◽

Chengqun Wei ◽

...

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Drug Target ◽

Target Genes ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Functional Enrichment ◽

Control Group ◽

Drug Candidates ◽

Novel Drug

AbstractThis study aimed to identify potential novel drug candidates and targets for Parkinson’s disease. First, 970 genes that have been reported to be related to PD were collected from five databases, and functional enrichment analysis of these genes was conducted to investigate their potential mechanisms. Then, we collected drugs and related targets from DrugBank, narrowed the list by proximity scores and Inverted Gene Set Enrichment analysis of drug targets, and identified potential drug candidates for PD treatment. Finally, we compared the expression distribution of the candidate drug-target genes between the PD group and the control group in the public dataset with the largest sample size (GSE99039) in Gene Expression Omnibus. Ten drugs with an FDR < 0.1 and their corresponding targets were identified. Some target genes of the ten drugs significantly overlapped with PD-related genes or already known therapeutic targets for PD. Nine differentially expressed drug-target genes with p < 0.05 were screened. This work will facilitate further research into the possible efficacy of new drugs for PD and will provide valuable clues for drug design.

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Age-Dependent Transcriptional Alterations in Cardiac Endothelial Cells

Physiological Genomics ◽

10.1152/physiolgenomics.00037.2021 ◽

2021 ◽

Author(s):

Uchenna Emechebe ◽

Jonathan William Nelson ◽

Nabil J. Alkayed ◽

Sanjiv Kaul ◽

Andrew C Adey ◽

...

Keyword(s):

Endothelial Cells ◽

Endothelial Cell ◽

Single Cell ◽

Significant Risk ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Mouse Heart ◽

Age Related ◽

Organ Systems ◽

Transcriptional Alterations

Aging is a significant risk factor for cardiovascular disease. Despite the fact that endothelial cells play critical roles in cardiovascular function and disease, the molecular impact of aging on this cell population in many organ systems remains unknown. In this study, we sought to determine age-associated transcriptional alterations in cardiac endothelial cells. Highly enriched populations of endothelial cells (ECs) isolated from the heart, brain and kidney of young (3 months) and aged (24 months) C57/BL6 mice were profiled for RNA expression via bulk RNA sequencing. Approximately 700 cardiac endothelial transcripts significantly differ by age. Gene set enrichment analysis indicated similar patterns for cellular pathway perturbations. Receptor-ligand comparisons indicated parallel alterations in age-affected circulating factors and cardiac endothelial-expressed receptors. Single-cell RNA-seq analysis identified 9 distinct endothelial cell subtypes in the heart with an age-associated population shift observed for the Aplnr-enriched endothelial cell clusters. Gene and pathway enrichment analyses show that age-related transcriptional response of cardiac endothelial cells is distinct from that of endothelial cells derived from the brain or kidney vascular bed. Furthermore, single-cell analysis identified 9 distinct EC subtypes, and shows that the Aplnr-enriched subtype is reduced with age in mouse heart. Finally, we identify age-dysregulated genes in specific aged cardiac endothelial subtypes.

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Expression Signatures of Long Noncoding RNAs in Left Ventricular Noncompaction

Frontiers in Cardiovascular Medicine ◽

10.3389/fcvm.2021.763858 ◽

2021 ◽

Vol 8 ◽

Author(s):

Qingshan Tian ◽

Hanxiao Niu ◽

Dingyang Liu ◽

Na Ta ◽

Qing Yang ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Noncoding Rnas ◽

Enrichment Analysis ◽

Left Ventricular ◽

Long Noncoding Rnas ◽

Gene Set Enrichment Analysis ◽

Differentially Expressed ◽

Control Group ◽

Left Ventricular Noncompaction ◽

Ventricular Noncompaction

Long noncoding RNAs have gained widespread attention in recent years for their crucial role in biological regulation. They have been implicated in a range of developmental processes and diseases including cancer, cardiovascular, and neuronal diseases. However, the role of long noncoding RNAs (lncRNAs) in left ventricular noncompaction (LVNC) has not been explored. In this study, we investigated the expression levels of lncRNAs in the blood of LVNC patients and healthy subjects to identify differentially expressed lncRNA that develop LVNC specific biomarkers and targets for developing therapies using biological pathways. We used Agilent Human lncRNA array that contains both updated lncRNAs and mRNAs probes. We identified 1,568 upregulated and 1,141 downregulated (log fold-change > 2.0) lncRNAs that are differentially expressed between LVNC and the control group. Among them, RP11-1100L3.7 and XLOC_002730 are the most upregulated and downregulated lncRNAs. Using quantitative real-time reverse transcription polymerase chain reaction (RT-QPCR), we confirmed the differential expression of three top upregulated and downregulated lncRNAs along with two other randomly picked lncRNAs. Gene Ontology (GO) and KEGG pathways analysis with these differentially expressed lncRNAs provide insight into the cellular pathway leading to LVNC pathogenesis. We also identified 1,066 upregulated and 1,017 downregulated mRNAs. Gene set enrichment analysis (GSEA) showed that G2M, Estrogen, and inflammatory pathways are enriched in differentially expressed genes (DEG). We also identified miRNA targets for these differentially expressed genes. In this study, we first report the use of LncRNA microarray to understand the pathogenesis of LVNC and to identify several lncRNA and genes and their targets as potential biomarkers.

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Influence of Estrogen Treatment on ESR1+ and ESR1− Cells in ER+ Breast Cancer: Insights from Single-Cell Analysis of Patient-Derived Xenograft Models

Cancers ◽

10.3390/cancers13246375 ◽

2021 ◽

Vol 13 (24) ◽

pp. 6375

Author(s):

Hitomi Mori ◽

Kohei Saeki ◽

Gregory Chang ◽

Jinhui Wang ◽

Xiwei Wu ◽

...

Keyword(s):

Breast Cancer ◽

Cell Cycle ◽

Single Cell ◽

Single Cell Analysis ◽

Therapy Response ◽

Sequencing Analysis ◽

Gene Set ◽

Patient Derived Xenograft ◽

Potential Marker ◽

The Impact

A 100% ER positivity is not required for an endocrine therapy response. Furthermore, while estrogen typically promotes the progression of hormone-dependent breast cancer via the activation of estrogen receptor (ER)-α, estrogen-induced tumor suppression in ER+ breast cancer has been clinically observed. With the success in establishing estrogen-stimulated (SC31) and estrogen-suppressed (GS3) patient-derived xenograft (PDX) models, single-cell RNA sequencing analysis was performed to determine the impact of estrogen on ESR1+ and ESR1– tumor cells. We found that 17β-estradiol (E2)-induced suppression of GS3 transpired through wild-type and unamplified ERα. E2 upregulated the expression of estrogen-dependent genes in both SC31 and GS3; however, E2 induced cell cycle advance in SC31, while it resulted in cell cycle arrest in GS3. Importantly, these gene expression changes occurred in both ESR1+ and ESR1– cells within the same breast tumors, demonstrating for the first time a differential effect of estrogen on ESR1– cells. E2 also upregulated a tumor-suppressor gene, IL-24, in GS3. The apoptosis gene set was upregulated and the G2M checkpoint gene set was downregulated in most IL-24+ cells after E2 treatment. In summary, estrogen affected pathologically defined ER+ tumors differently, influencing both ESR1+ and ESR1– cells. Our results also suggest IL-24 to be a potential marker of estrogen-suppressed tumors.

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Single-cell RNA-seq Analysis Reveals That Prenatal Arsenic Exposure Results in Long-term, Adverse Effects on Immune Gene Expression in Response to Influenza A Infection

Toxicological Sciences ◽

10.1093/toxsci/kfaa080 ◽

2020 ◽

Vol 176 (2) ◽

pp. 312-328 ◽

Cited By ~ 1

Author(s):

Kevin S Hsu ◽

Britton C Goodale ◽

Kenneth H Ely ◽

Thomas H Hampton ◽

Bruce A Stanton ◽

...

Keyword(s):

Immune Response ◽

Drinking Water ◽

Single Cell ◽

Influenza A ◽

Arsenic Exposure ◽

Innate Immune ◽

Lung Damage ◽

Health Concern ◽

Immune Gene ◽

Sequencing Analysis

Abstract Arsenic exposure via drinking water is a serious environmental health concern. Epidemiological studies suggest a strong association between prenatal arsenic exposure and subsequent childhood respiratory infections, as well as morbidity from respiratory diseases in adulthood, long after systemic clearance of arsenic. We investigated the impact of exclusive prenatal arsenic exposure on the inflammatory immune response and respiratory health after an adult influenza A virus (IAV) lung infection. C57BL/6J mice were exposed to 100 ppb sodium arsenite in utero, and subsequently infected with IAV (H1N1) after maturation to adulthood. Assessment of lung tissue and bronchoalveolar lavage fluid at various time points post-IAV infection reveals greater lung damage and inflammation in arsenic-exposed mice versus control mice. Single-cell RNA sequencing analysis of immune cells harvested from IAV-infected lungs suggests that the enhanced inflammatory response is mediated by dysregulation of innate immune function of monocyte-derived macrophages, neutrophils, natural killer cells, and alveolar macrophages. Our results suggest that prenatal arsenic exposure results in lasting effects on the adult host innate immune response to IAV infection, long after exposure to arsenic, leading to greater immunopathology. This study provides the first direct evidence that exclusive prenatal exposure to arsenic in drinking water causes predisposition to a hyperinflammatory response to IAV infection in adult mice, which is associated with significant lung damage.

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Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data

Nature Communications ◽

10.1038/s41467-021-25534-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Yifan Zhao ◽

Huiyu Cai ◽

Zuobai Zhang ◽

Jian Tang ◽

Yue Li

Keyword(s):

Single Cell ◽

Large Scale ◽

Topic Model ◽

Enrichment Analysis ◽

Gene Signature ◽

Gene Set Enrichment Analysis ◽

Learning Performance ◽

Cell Type ◽

Gene Set Enrichment ◽

Gene Sets

AbstractThe advent of single-cell RNA sequencing (scRNA-seq) technologies has revolutionized transcriptomic studies. However, large-scale integrative analysis of scRNA-seq data remains a challenge largely due to unwanted batch effects and the limited transferabilty, interpretability, and scalability of the existing computational methods. We present single-cell Embedded Topic Model (scETM). Our key contribution is the utilization of a transferable neural-network-based encoder while having an interpretable linear decoder via a matrix tri-factorization. In particular, scETM simultaneously learns an encoder network to infer cell type mixture and a set of highly interpretable gene embeddings, topic embeddings, and batch-effect linear intercepts from multiple scRNA-seq datasets. scETM is scalable to over 106 cells and confers remarkable cross-tissue and cross-species zero-shot transfer-learning performance. Using gene set enrichment analysis, we find that scETM-learned topics are enriched in biologically meaningful and disease-related pathways. Lastly, scETM enables the incorporation of known gene sets into the gene embeddings, thereby directly learning the associations between pathways and topics via the topic embeddings.

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A single-cell analysis of the molecular lineage of chordate embryogenesis

Science Advances ◽

10.1126/sciadv.abc4773 ◽

2020 ◽

Vol 6 (45) ◽

pp. eabc4773

Author(s):

Tengjiao Zhang ◽

Yichi Xu ◽

Kaoru Imai ◽

Teng Fei ◽

Guilin Wang ◽

...

Keyword(s):

Single Cell ◽

Single Cell Analysis ◽

Cell Lineage ◽

Cell Types ◽

Gene Signature ◽

Mouse Cell ◽

Embryonic Cell ◽

Sequencing Analysis ◽

Lineage Differentiation ◽

In The Wild

Progressive unfolding of gene expression cascades underlies diverse embryonic lineage development. Here, we report a single-cell RNA sequencing analysis of the complete and invariant embryonic cell lineage of the tunicate Ciona savignyi from fertilization to the onset of gastrulation. We reconstructed a developmental landscape of 47 cell types over eight cell cycles in the wild-type embryo and identified eight fate transformations upon fibroblast growth factor (FGF) inhibition. For most FGF-dependent asymmetric cell divisions, the bipotent mother cell displays the gene signature of the default daughter fate. In convergent differentiation of the two notochord lineages, we identified additional gene pathways parallel to the master regulator T/Brachyury. Last, we showed that the defined Ciona cell types can be matched to E6.5-E8.5 stage mouse cell types and display conserved expression of limited number of transcription factors. This study provides a high-resolution single-cell dataset to understand chordate early embryogenesis and cell lineage differentiation.

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Cytokine/Chemokine Release Patterns and Transcriptomic Profiles of LPS/IFNγ-Activated Human Macrophages Differentiated with Heat-Killed Mycobacterium obuense, M-CSF, or GM-CSF

International Journal of Molecular Sciences ◽

10.3390/ijms22137214 ◽

2021 ◽

Vol 22 (13) ◽

pp. 7214

Author(s):

Samer Bazzi ◽

Emale El-Darzi ◽

Tina McDowell ◽

Helmout Modjtahedi ◽

Satvinder Mudan ◽

...

Keyword(s):

Enrichment Analysis ◽

Interferon Γ ◽

Gene Set Enrichment Analysis ◽

Specific Cell ◽

Sequencing Analysis ◽

Colony Stimulating Factor ◽

Macrophage Colony Stimulating Factor ◽

Macrophage Colony ◽

Mycobacterial Cell Wall ◽

Stimulating Factor

Macrophages (Mφs) are instrumental regulators of the immune response whereby they acquire diverse functional phenotypes following their exposure to microenvironmental cues that govern their differentiation from monocytes and their activation. The complexity and diversity of the mycobacterial cell wall have empowered mycobacteria with potent immunomodulatory capacities. A heat-killed (HK) whole-cell preparation of Mycobacterium obuense (M. obuense) has shown promise as an adjunctive immunotherapeutic agent for the treatment of cancer. Moreover, HK M. obuense has been shown to trigger the differentiation of human monocytes into a monocyte-derived macrophage (MDM) type named Mob-MDM. However, the transcriptomic profile and functional properties of Mob-MDMs remain undefined during an activation state. Here, we characterized cytokine/chemokine release patterns and transcriptomic profiles of lipopolysaccharide (LPS)/interferon γ (IFNγ)-activated human MDMs that were differentiated with HK M. obuense (Mob-MDM(LPS/IFNγ)), macrophage colony-stimulating factor M-MDM(LPS/IFNγ)), or granulocyte/macrophage colony-stimulating factor (GM-MDM(LPS/IFNγ)). Mob-MDM(LPS/IFNγ) demonstrated a unique cytokine/chemokine release pattern (interleukin (IL)-10low, IL-12/23p40low, IL-23p19/p40low, chemokine (C-x-C) motif ligand (CXCL)9low) that was distinct from those of M-MDM(LPS/IFNγ) and GM-MDM(LPS/IFNγ). Furthermore, M-MDM(LPS/IFNγ) maintained IL-10 production at significantly higher levels compared to GM-MDM(LPS/IFNγ) and Mob-MDM(LPS/IFNγ) despite being activated with M1-Mφ-activating stimuli. Comparative RNA sequencing analysis pointed to a distinct transcriptome profile for Mob-MDM(LPS/IFNγ) relative to both M-MDM(LPS/IFNγ) and GM-MDM(LPS/IFNγ) that comprised 417 transcripts. Functional gene-set enrichment analysis revealed significant overrepresentation of signaling pathways and biological processes that were uniquely related to Mob-MDM(LPS/IFNγ). Our findings lay a foundation for the potential integration of HK M. obuense in specific cell-based immunotherapeutic modalities such as adoptive transfer of Mφs (Mob-MDM(LPS/IFNγ)) for cancer treatment.

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Analysis of KIF2C, 4A, 10, 11, 14, 18B, 20A, and 23 in HCC and their clinical significance as new-born prognostic markers of HCC

10.21203/rs.3.rs-19479/v1 ◽

2020 ◽

Author(s):

Meng-jun Qiu ◽

Qiu-shuang Wang ◽

Xiao-xiao He ◽

Qiu-ting Li ◽

Xin Jiang ◽

...

Keyword(s):

Mrna Expression ◽

Prognostic Markers ◽

Malignant Tumors ◽

Prognostic Significance ◽

Enrichment Analysis ◽

Normal Control Group ◽

Gene Set Enrichment Analysis ◽

Control Group ◽

Gene Set Enrichment ◽

Different Levels

Abstract Background: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors. However, the molecular mechanism of its pathogenesis remains to be studied. This study aimed to identify potential KIF genes associated with HCC progression. Methods: We used bioinformatics to initially analyze the expression level and prognostic significance of KIF factors in HCC. Results: We found that compared with the normal control group, KIF2C, 4A, 10, 11, 14, 18B, 20A, and 23 mRNA expression levels increased significantly in HCC. 8 KIF factors had different levels of gene amplification, depth to delete, and missense mutation, and were closely related to the clinical-pathologic stage. Gene set enrichment analysis showed that high mRNA expression of 8 KIF factors in HCC patients were associated with cell cycle, mismatch repair, homologous recombination, and DNA replication. Conclusions: This study expands our understanding of KIF factors in HCC and can provide a theoretical basis for further basic and clinical research in HCC.

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