scholarly journals Assessment of changes in genetic transcriptome in nasal epithelial cells exposed to ozone-aged black carbon and pollen allergen by high-throughput transcriptomics

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Yuhui Ouyang ◽  
Ying Li ◽  
Zhaojun Xu ◽  
Yusan An ◽  
Luo Zhang
Keyword(s):  
Epithelial Cells ◽  
Cell Viability ◽  
Black Carbon ◽  
Rna Sequencing ◽  
High Throughput ◽  
Pollen Allergen ◽  
Mast Cell Activation ◽  
Sequencing Analysis ◽  
Nasal Epithelial Cells ◽  
Go Terms

Abstract Background Air pollution may be associated with increased airway responsiveness to allergens in allergic rhinitis (AR). Ozone-aged environmental black carbon (O3BC) is an important constituent of atmospheric particulate matter (PM), for which the mechanisms underlying its effects have not been fully elucidated in AR. The objective of the present study was to determine the O3BC and pollen-induced alterations in the transcriptome in human nasal epithelial cells (hNECs) in vitro. Methods hNECs from nasal epithelial mucosal samples of healthy individuals undergoing nasal surgery (turbinoplasty or septoplasty) were established as air–liquid interface (ALI) cultures and exposed to O3BC, pollen, or a combination of O3BC+ pollen. Changes in cell viability were analyzed by fluorescence and changes in the transcriptome by high-throughput RNA sequencing (RNA-seq). Several differentially expressed genes were verified by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Enrichment analysis, based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) database, was performed to determine major biological functions and pathways involved. Results Exposure to ≥ 50 μg/ml O3BC or 25 μg/ml O3BC+ 200 μg /ml pollen significantly decreased cell viability of the hNECs compared to control (p < 0.05) or 25 μg/ml O3BC alone (p < 0.05); whereas exposure to pollen alone did not alter cell viability at any concentration investigated. High-throughput RNA sequencing analysis indicated that there was significant difference in gene expression between pollen or O3BC alone and O3BC+ pollen exposed cells. Exposure to 200 μg/ml O3BC was associated with hypoxia stress response GO terms, whereas exposure to 25 μg/ml O3BC+ 200 μg/ml pollen was associated with inflammatory response GO terms; including regulation of neutrophil migration and chemotaxis, macrophage differentiation and chemotaxis, mast cell activation, and phagocytosis. KEGG pathway analysis indicated the top 10 upstream regulators to be IL1B, CSF1, CCL2, TLR2, LPL, IGF8, SPP1, CXCL8, FCER1G and IL1RN; of which expressions of inflammation-related genes IL1B, CSF1 and FCER1G were significantly increased. Conclusion O3BC and pollen allergen combined exposure may induce innate immune and allergic inflammation in hNECs, and therefore potentially exacerbate the symptoms of AR in affected individuals.

Assessment of Changes in Genetic Transcriptome in Nasal Epithelial Cells Exposed to Black Carbon and Pollen Allergen by High-throughput Transcriptomics

2020 ◽  
Author(s):  
Yuhui Ouyang ◽  
Ying Li ◽  
Zhaojun Xu ◽  
Yusan An ◽  
Luo Zhang
Keyword(s):  
Epithelial Cells ◽  
Black Carbon ◽  
High Throughput ◽  
Quantitative Polymerase Chain Reaction ◽  
Neutrophil Migration ◽  
Pollen Allergen ◽  
Mast Cell Activation ◽  
Nasal Epithelial Cells ◽  
Human Nasal Epithelial Cells ◽  
Go Terms

Abstract Background: Evidence suggests that air pollution may be associated with an increase in airway responsiveness to allergens, an increase in bioavailability of airborne allergens and possibly exacerbation of allergic rhinitis (AR). Environmental black carbon (BC) is an important constituent of atmospheric particulate matter (PM), for which the mechanisms underlying its effects have not been fully elucidated in AR. The objective of the present study was to determine the BC and pollen-induced alterations in the transcriptome in human nasal epithelial cells (hNECs) in vitro.Methods: hNECs were prepared from nasal epithelial mucosal samples of healthy individuals undergoing nasal surgery (turbinoplasty or septoplasty). The hNECs were established as air-liquid interface (ALI) cultures and exposed to BC alone or in combination with pollen allergen. The changes in the transcriptome were analyzed by high-throughput RNA sequencing (RNA-Seq). Some of the differentially expressed genes were verified by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Enrichment analysis based on Gene Ontology (GO) and KEGG database for each Gene was performed to determine their major biological functions and pathways.Results: Exposure to ≥50 μg/ml BC or 25μg/ml BC + 200g /ml pollen significantly decreased cell viability in the hNECs compared to control (p<0.05) or 25μg/ml BC alone (p<0.05). Expression of 114 genes (including 80 up-regulated and 34 down-regulated) and 293 genes (including 233 up-regulated and 60 down-regulated genes) was significantly altered following exposure to 200 μg/ml BC and 25 μg/ml BC =200 μg/ml pollen respectively. For 200 μg/ml BC, up-regulated GO terms were mainly associated with hypoxia stress response, whereas for 25 μg/ml BC + 200 μg/ml pollen treatment the top enriched GO terms were associated with inflammatory response including regulation of neutrophil migration and chemotaxis, macrophage differentiation and chemotaxis, mast cell activation, and phagocytosis. KEGG pathway analysis indicated the top 10 upstream regulators to be IL1B, CSF1, CCL2, TLR2, LPL, IGF8, SPP1, CXCL8, FCER1G and IL1RN. The expressions of inflammation related gene IL1B, CSF1 and FCER1G were elevated as measured by RT-qPCR assay.Conclusion: BC and pollen allergen may induce innate immune and allergic inflammation in hNECs, and therefore potentially exacerbate the symptoms of AR in affected individuals.

scholarly journals EPA and DHA Inhibit Myogenesis and Downregulate the Expression of Muscle-related Genes in C2C12 Myoblasts

Genes ◽  
2019 ◽  
Vol 10 (1) ◽  
pp. 64 ◽  
Author(s):  
Jing Zhang ◽  
Xin Xu ◽  
Yan Liu ◽  
Lin Zhang ◽  
Jack Odle ◽  
...  
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Cell Proliferation ◽  
Cell Viability ◽  
Rna Sequencing ◽  
Cell Counting ◽  
Sequencing Analysis ◽  
C2c12 Myoblasts ◽  
Epa And Dha ◽  
Proliferation And Differentiation

This study was conducted to elucidate the biological effects of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) on cell proliferation, differentiation and gene expression in C2C12 myoblasts. C2C12 were treated with various concentrations of EPA or DHA under proliferation and differentiation conditions. Cell viability was analyzed using cell counting kit-8 assays (CCK-8). The Edu assays were performed to analyze cell proliferation. To analyze cell differentiation, the expressions of myogenic marker genes were determined at the transcriptional and translational levels by qRT-PCR, immunoblotting and immunofluorescence. Global gene expression patterns were characterized using RNA-sequencing. Phosphorylation levels of ERK and Akt were examined by immunoblotting. Cell viability and proliferation was significantly inhibited after incubation with EPA (50 and 100 μM) or DHA (100 μM). Both EPA and DHA suppressed C2C12 myoblasts differentiation. RNA-sequencing analysis revealed that some muscle-related genes were significantly downregulated following EPA or DHA (50 μM) treatment, including insulin-like growth factor 2 (IGF-2), troponin T3 (Tnnt3), myoglobin (Mb), myosin light chain phosphorylatable fast skeletal muscle (Mylpf) and myosin heavy polypeptide 3 (Myh3). IGF-2 was crucial for the growth and differentiation of skeletal muscle and could activate the PI3K/Akt and the MAPK/ERK cascade. We found that EPA and DHA (50 μM) decreased the phosphorylation levels of ERK1/2 and Akt in C2C12 myoblasts. Thus, this study suggested that EPA and DHA exerted an inhibitory effect on myoblast proliferation and differentiation and downregulated muscle-related genes expression.

scholarly journals RNA-Seq analysis of Clerodendrum inerme (L.) roots in response to salt stress

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuping Xiong ◽  
Haifeng Yan ◽  
Hanzhi Liang ◽  
Yueya Zhang ◽  
Beiyi Guo ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Rna Sequencing ◽  
Plant Hormone ◽  
De Novo ◽  
Sequencing Analysis ◽  
Salt Tolerant ◽  
Mangrove Plant ◽  
Next Generation Sequencing Technology ◽  
Go Terms

Abstract Background Clerodendrum inerme (L.) Gaertn, a halophyte, usually grows on coastal beaches as an important mangrove plant. The salt-tolerant mechanisms and related genes of this species that respond to short-term salinity stress are unknown for us. The de novo transcriptome of C. inerme roots was analyzed using next-generation sequencing technology to identify genes involved in salt tolerance and to better understand the response mechanisms of C. inerme to salt stress. Results Illumina RNA-sequencing was performed on root samples treated with 400 mM NaCl for 0 h, 6 h, 24 h, and 72 h to investigate changes in C. inerme in response to salt stress. The de novo assembly identified 98,968 unigenes. Among these unigenes, 46,085 unigenes were annotated in the NCBI non-redundant protein sequences (NR) database, 34,756 sequences in the Swiss-Prot database and 43,113 unigenes in the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) database. 52 Gene Ontology (GO) terms and 31 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were matched to those unigenes. Most differentially expressed genes (DEGs) related to the GO terms “single-organism process”, “membrane” and “catalytic activity” were significantly enriched while numerous DEGs related to the plant hormone signal transduction pathway were also significantly enriched. The detection of relative expression levels of 9 candidate DEGs by qRT-PCR were basically consistent with fold changes in RNA sequencing analysis, demonstrating that transcriptome data can accurately reflect the response of C. inerme roots to salt stress. Conclusions This work revealed that the response of C. inerme roots to saline condition included significant alteration in response of the genes related to plant hormone signaling. Besides, our findings provide numerous salt-tolerant genes for further research to improve the salt tolerance of functional plants and will enhance research on salt-tolerant mechanisms of halophytes.

scholarly journals Olfactomedin 4 mediation of prostate stem/progenitor-like cell proliferation and differentiation via MYC

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hongzhen Li ◽  
Vijender Chaitankar ◽  
Jianqiong Zhu ◽  
Kyung Chin ◽  
Wenli Liu ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Epithelial Cells ◽  
Signaling Pathway ◽  
Rna Sequencing ◽  
Progenitor Cell ◽  
Sequencing Analysis ◽  
Normal Prostate ◽  
Prostate Epithelial Cells ◽  
Cell Proliferation And Differentiation ◽  
Proliferation And Differentiation

AbstractOlfactomedin 4 (OLFM4) is expressed in normal prostate epithelial cells and immortalized normal human prostate epithelial cells (RWPE1), but the identity of OLFM4-expressing cells within these populations and OLFM4’s physiological functions in these cells have not been elucidated. Using single-cell RNA sequencing analysis, we found here that OLFM4 was expressed in multiple stem/progenitor-like cell populations in both the normal prostate epithelium and RWPE1 cells and was frequently co-expressed with KRT13 and LY6D in RWPE1 cells. Functionally, OLFM4-knockout RWPE1 cells exhibited enhanced proliferation of the stem/progenitor-like cell population, shifts stem/progenitor-like cell division to favor symmetric division and differentiated into higher levels PSA expression cells in organoid assays compared with OLFM4-wild RWPE1 cells. Bulk-cell RNA sequencing analysis pinpointed that cMYC expression were enhanced in the OLFM4-knockout RWPE1 cells compared with OLFM4-wild cells. Molecular and signaling pathway studies revealed an increase in the WNT/APC/MYC signaling pathway gene signature, as well as that of MYC target genes that regulate multiple biological processes, in OLFM4-knockout RWPE1 cells. These findings indicated that OLFM4 is co-expressed with multiple stem/progenitor cell marker genes in prostate epithelial cells and acts as a novel mediator in prostate stem/progenitor cell proliferation and differentiation.

Ciliary Function, Cell Viability, and in Vitro Effect of Ribavirin on Nasal Epithelial Cells in Acute Rhinorrhea

CHEST Journal ◽  
1992 ◽  
Vol 102 (1) ◽  
pp. 284-287 ◽  
Author(s):  
Myrna B. Dolovich ◽  
P. Eng ◽  
James B. Mahony ◽  
Carole Chambers ◽  
Michael T. Newhouse ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Cell Viability ◽  
Nasal Epithelial Cells ◽  
Ciliary Function ◽  
Vitro Effect ◽  
Function Cell

scholarly journals RNA Sequencing of H3N2 Influenza Virus-Infected Human Nasal Epithelial Cells from Multiple Subjects Reveals Molecular Pathways Associated with Tissue Injury and Complications

Cells ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 986 ◽  
Author(s):  
Kai Sen Tan ◽  
Anand Kumar Andiappan ◽  
Bernett Lee ◽  
Yan Yan ◽  
Jing Liu ◽  
...  
Keyword(s):  
Influenza Virus ◽  
Epithelial Cells ◽  
Rna Sequencing ◽  
Viral Infections ◽  
Tissue Injury ◽  
Influenza Infection ◽  
Nasal Epithelium ◽  
Nasal Epithelial Cells ◽  
Human Nasal Epithelial Cells

The human nasal epithelium is the primary site of exposure to influenza virus, the initiator of host responses to influenza and the resultant pathologies. Influenza virus may cause serious respiratory infection resulting in major complications, as well as severe impairment of the airways. Here, we elucidated the global transcriptomic changes during H3N2 infection of human nasal epithelial cells from multiple individuals. Using RNA sequencing, we characterized the differentially-expressed genes and pathways associated with changes occurring at the nasal epithelium following infection. We used in vitro differentiated human nasal epithelial cell culture model derived from seven different donors who had no concurrent history of viral infections. Statistical analysis highlighted strong transcriptomic signatures significantly associated with 24 and 48 h after infection, but not at the earlier 8-h time point. In particular, we found that the influenza infection induced in the nasal epithelium early and altered responses in interferon gamma signaling, B-cell signaling, apoptosis, necrosis, smooth muscle proliferation, and metabolic alterations. These molecular events initiated at the infected nasal epithelium may potentially adversely impact the airway, and thus the genes we identified could serve as potential diagnostic biomarkers or therapeutic targets for influenza infection and associated disease management.

scholarly journals Single-cell RNA-sequencing analysis of estrogen- and endocrine-disrupting chemical-induced reorganization of mouse mammary gland

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Noriko Kanaya ◽  
Gregory Chang ◽  
Xiwei Wu ◽  
Kohei Saeki ◽  
Lauren Bernal ◽  
...  
Keyword(s):  
Mammary Gland ◽  
Epithelial Cells ◽  
Single Cell ◽  
Rna Sequencing ◽  
Mammary Tissue ◽  
M2 Macrophage ◽  
Sequencing Analysis ◽  
Endocrine Disrupting ◽  
Single Cell Rna Sequencing ◽  
Luminal Epithelial Cells

Abstract Menopause is a critical window of susceptibility for its sensitivity to endocrine disrupting chemicals due to the decline of endogenous estrogen. Using a surgical menopausal (ovariectomized) mouse model, we assessed how mammary tissue was affected by both 17β-estradiol (E2) and polybrominated diphenyl ethers (PBDEs). As flame retardants in household products, PBDEs are widely detected in human serum. During physiologically-relevant exposure to E2, PBDEs enhanced E2-mediated regrowth of mammary glands with terminal end bud-like structures. Analysis of mammary gland RNA revealed that PBDEs both augmented E2-facilitated gene expression and modulated immune regulation. Through single-cell RNA sequencing (scRNAseq) analysis, E2 was found to induce Pgr expression in both Esr1+ and Esr1− luminal epithelial cells and Ccl2 expression in Esr1+ fibroblasts. PBDEs promote the E2-AREG-EGFR-M2 macrophage pathway. Our findings support that E2 + PBDE increases the risk of developing breast cancer through the expansion of estrogen-responsive luminal epithelial cells and immune modulation.

scholarly journals CXCR4 Regulates Temporal Differentiation via PRC1 Complex in Organogenesis of Epithelial Glands

2021 ◽  
Vol 22 (2) ◽  
pp. 619
Author(s):  
Junchul Kim ◽  
Sang-Woo Lee ◽  
Kyungpyo Park
Keyword(s):  
Epithelial Cells ◽  
Rna Sequencing ◽  
Immune Cell ◽  
Ex Vivo ◽  
Embryonic Stem ◽  
Sequencing Analysis ◽  
Cxcr4 Signaling ◽  
Signaling Axis ◽  
Ex Vivo Culture ◽  
Epigenetic Modulation

CXC-chemokine receptor type 4 (CXCR4), a 7-transmembrane receptor family member, displays multifaceted roles, participating in immune cell migration, angiogenesis, and even adipocyte metabolism. However, the activity of such a ubiquitously expressed receptor in epithelial gland organogenesis has not yet been fully explored. To investigate the relationship between CXCL12/CXCR4 signaling and embryonic glandular organogenesis, we used an ex vivo culture system with live imaging and RNA sequencing to elucidate the transcriptome and protein-level signatures of AMD3100, a potent abrogating reagent of the CXCR4-CXCL12 axis, imprinted on the developing organs. Immunostaining results showed that CXCR4 was highly expressed in embryonic submandibular gland, lung, and pancreas, especially at the periphery of end buds containing numerous embryonic stem/progenitor cells. Despite no significant increase in apoptosis, AMD3100-treated epithelial organs showed a retarded growth with significantly slower branching and expansion. Further analyses with submandibular glands revealed that such responses resulted from the AMD3100-induced precocious differentiation of embryonic epithelial cells, losing mitotic activity. RNA sequencing analysis revealed that inhibition of CXCR4 significantly down-regulated polycomb repressive complex (PRC) components, known as regulators of DNA methylation. Treatment with PRC inhibitor recapitulated the AMD3100-induced precocious differentiation. Our results indicate that the epigenetic modulation by the PRC-CXCR12/CXCR4 signaling axis is crucial for the spatiotemporal regulation of proliferation and differentiation of embryonic epithelial cells during embryonic glandular organogenesis.

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