scholarly journals RNA-Seq Revealed a Circular RNA-microRNA-mRNA Regulatory Network in Hantaan Virus Infection

2020 ◽  
Vol 10 ◽  
Author(s):  
Shuang Lu ◽  
Ni Zhu ◽  
Weiwei Guo ◽  
Xin Wang ◽  
Kaiji Li ◽  
...  
Keyword(s):  
Virus Infection ◽  
Regulatory Network ◽  
Circular Rna ◽  
Hantaan Virus ◽  
Rna Seq

scholarly journals NKL Homeobox Gene VENTX Is Part of a Regulatory Network in Human Conventional Dendritic Cells

2021 ◽  
Vol 22 (11) ◽  
pp. 5902
Author(s):  
Stefan Nagel ◽  
Claudia Pommerenke ◽  
Corinna Meyer ◽  
Hans G. Drexler
Keyword(s):  
Dendritic Cells ◽  
Transcription Factors ◽  
Cell Lines ◽  
Expression Profiling ◽  
Regulatory Network ◽  
Homeobox Gene ◽  
Leukemia Cell Line ◽  
Specific Gene ◽  
Rna Seq ◽  
And Function

Recently, we documented a hematopoietic NKL-code mapping physiological expression patterns of NKL homeobox genes in human myelopoiesis including monocytes and their derived dendritic cells (DCs). Here, we enlarge this map to include normal NKL homeobox gene expressions in progenitor-derived DCs. Analysis of public gene expression profiling and RNA-seq datasets containing plasmacytoid and conventional dendritic cells (pDC and cDC) demonstrated HHEX activity in both entities while cDCs additionally expressed VENTX. The consequent aim of our study was to examine regulation and function of VENTX in DCs. We compared profiling data of VENTX-positive cDC and monocytes with VENTX-negative pDC and common myeloid progenitor entities and revealed several differentially expressed genes encoding transcription factors and pathway components, representing potential VENTX regulators. Screening of RNA-seq data for 100 leukemia/lymphoma cell lines identified prominent VENTX expression in an acute myelomonocytic leukemia cell line, MUTZ-3 containing inv(3)(q21q26) and t(12;22)(p13;q11) and representing a model for DC differentiation studies. Furthermore, extended gene analyses indicated that MUTZ-3 is associated with the subtype cDC2. In addition to analysis of public chromatin immune-precipitation data, subsequent knockdown experiments and modulations of signaling pathways in MUTZ-3 and control cell lines confirmed identified candidate transcription factors CEBPB, ETV6, EVI1, GATA2, IRF2, MN1, SPIB, and SPI1 and the CSF-, NOTCH-, and TNFa-pathways as VENTX regulators. Live-cell imaging analyses of MUTZ-3 cells treated for VENTX knockdown excluded impacts on apoptosis or induced alteration of differentiation-associated cell morphology. In contrast, target gene analysis performed by expression profiling of knockdown-treated MUTZ-3 cells revealed VENTX-mediated activation of several cDC-specific genes including CSFR1, EGR2, and MIR10A and inhibition of pDC-specific genes like RUNX2. Taken together, we added NKL homeobox gene activities for progenitor-derived DCs to the NKL-code, showing that VENTX is expressed in cDCs but not in pDCs and forms part of a cDC-specific gene regulatory network operating in DC differentiation and function.

Construction of an lncRNA–mRNA Co-Expression Regulatory Network Mediating Inflammation and Regeneration Following Acute Pancreatitis Injury

2021 ◽  
Author(s):  
Jing Wang ◽  
Tianjie Chen ◽  
Xiaohua Zhang ◽  
Shulei Zhao
Keyword(s):  
Acute Pancreatitis ◽  
Mrna Expression ◽  
Regulatory Network ◽  
Noncoding Rnas ◽  
Pancreatic Injury ◽  
Control Group ◽  
Rna Seq ◽  
Damage Repair ◽  
Injury And Repair ◽  
And Function

Abstract Long noncoding RNAs (lncRNAs) play important roles in the occurrence and development of many diseases and can be used as targets for diagnosis and treatment. However, the expression and function of lncRNAs in the injury and repair of acute pancreatitis (AP) are unclear. To decipher lncRNAs’ regulatory roles in AP, we reanalyzed an RNA-seq dataset of 24 pancreatic tissues, including those of normal control mice (BL), those 7 days after mild AP (D7), and those 14 days after mild AP (D14). The results showed significant differences in lncRNA and mRNA expression of D7/D14 groups compared with the control group. Co-expression analysis showed that differentially expressed (DE) lncRNAs were closely related to immunity- and inflammation-related pathways by trans-regulating mRNA expression. The lncRNA–mRNA network showed that the lncRNAs Dancer, Gmm20488, Terc, Snhg3, and Snhg20 were significantly correlated with AP pathogenesis. WGCNA and cis regulation analysis also showed that AP repair-associated lncRNAs were correlated with extracellular and inflammation-related genes, which affect the repair and regeneration of pancreatic injury after AP. In conclusion, the systemic dysregulation of lncRNAs is strongly involved in remodeling AP’s gene expression regulatory network, and the lncRNA–mRNA expression network could identify targets for AP treatment and damage repair.

scholarly journals A Case of Graves' Disease Combined with Hantaan Virus Infection

2009 ◽  
Vol 24 (1) ◽  
pp. 158 ◽  
Author(s):  
Heung Yong Jin ◽  
Seon Mee Kang ◽  
So Young Kim ◽  
Ji Hyun Park ◽  
Hong Sun Baek ◽  
...  
Keyword(s):  
Virus Infection ◽  
Hantaan Virus ◽  
Graves Disease

scholarly journals DEBKS: A Tool to Detect Differentially Expressed Circular RNA

2020 ◽  
Author(s):  
Zelin Liu ◽  
Huiru Ding ◽  
Jianqi She ◽  
Chunhua Chen ◽  
Weiguang Zhang ◽  
...  
Keyword(s):  
Open Source ◽  
Rna Sequencing ◽  
Open Source Software ◽  
Simulated Data ◽  
Circular Rna ◽  
Host Gene ◽  
Circular Rnas ◽  
Biological Processes ◽  
Rna Seq ◽  
Disease Pathogenesis

AbstractCircular RNAs (circRNAs) are involved in various biological processes and in disease pathogenesis. However, only a small number of functional circRNAs have been identified among hundreds of thousands of circRNA species, partly because most current methods are based on circular junction counts and overlook the fact that circRNA is formed from the host gene by back-splicing (BS). To distinguish between expression originating from BS and that from the host gene, we present DEBKS, a software program to streamline the discovery of differential BS between two rRNA-depleted RNA sequencing (RNA-seq) sample groups. By applying real and simulated data and employing RT-qPCR for validation, we demonstrate that DEBKS is efficient and accurate in detecting circRNAs with differential BS events between paired and unpaired sample groups. DEBKS is available at https://github.com/yangence/DEBKS as open-source software.

scholarly journals Expression Profiling and Functional Analysis of Circular RNAs in Inner Mongolian Cashmere Goat Hair Follicles

2021 ◽  
Vol 12 ◽  
Author(s):  
Fangzheng Shang ◽  
Yu Wang ◽  
Rong Ma ◽  
Zhengyang Di ◽  
Zhihong Wu ◽  
...  
Keyword(s):  
Hair Follicle ◽  
Signaling Pathway ◽  
Expression Profiling ◽  
Regulatory Network ◽  
Expression Profiles ◽  
Circular Rna ◽  
Hair Follicles ◽  
Luciferase Reporter ◽  
Circular Rnas ◽  
Cashmere Goats

BackgroundInner Mongolian cashmere goats have hair of excellent quality and high economic value, and the skin hair follicle traits of cashmere goats have a direct and important effect on cashmere yield and quality. Circular RNA has been studied in a variety of tissues and cells.ResultIn this study, high-throughput sequencing was used to obtain the expression profiles of circular RNA (circRNA) in the hair follicles of Inner Mongolian cashmere goats at different embryonic stages (45, 55, 65, and 75 days). A total of 21,784 circRNAs were identified. At the same time, the differentially expressed circRNA in the six comparison groups formed in the four stages were: d75vsd45, 59 upregulated and 33 downregulated DE circRNAs; d75vsd55, 61 upregulated and 102 downregulated DE circRNAs; d75vsd65, 32 upregulated and 33 downregulated DE circRNAs; d65vsd55, 67 upregulated and 169 downregulated DE circRNAs; d65vsd45, 96 upregulated and 63 downregulated DE circRNAs; and d55vsd45, 76 upregulated and 42 downregulated DE circRNAs. Six DE circRNA were randomly selected to verify the reliability of the sequencing results by quantitative RT-PCR. Subsequently, the circRNA corresponding host genes were analyzed by the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. The results showed that the biological processes related to hair follicle growth and development enriched by GO mainly included hair follicle morphogenesis and cell development, and the signaling pathways related to hair follicle development included the Notch signaling pathway and NF-κB signaling pathway. We combined the DE circRNA of d75vsd45 with miRNA and mRNA databases (unpublished) to construct the regulatory network of circRNA–miRNA–mRNA, and formed a total of 102 pairs of circRNA–miRNA and 126 pairs of miRNA–mRNA interactions. The binding relationship of circRNA3236–chi-miR-27b-3p and circRNA3236–chi-miR-16b-3p was further verified by dual-luciferase reporter assays, and the results showed that circRNA3236 and chi-miR-27b-3p, and circRNA3236 and chi-miR-16b-3p have a targeted binding relationship.ConclusionTo summarize, we established the expression profiling of circRNA in the fetal skin hair follicles of cashmere goats, and found that the host gene of circRNA may be involved in the development of hair follicles of cashmere goats. The regulatory network of circRNA–miRNA–mRNA was constructed and preliminarily verified using DE circRNAs.

Acute Appendicitis Associated with Hantaan Virus Infection

2021 ◽  
Author(s):  
Sung-Chul Lim ◽  
Young Min Lee ◽  
Choon-Mee Kim ◽  
Na Ra Yun ◽  
Dong-Min Kim
Keyword(s):  
Virus Infection ◽  
Peripheral Nerve ◽  
Hemorrhagic Fever ◽  
Hantaan Virus ◽  
Nerve Bundle ◽  
Rt Pcr ◽  
Antibody Assay ◽  
Immunofluorescent Antibody ◽  
Virus Antigens ◽  
Indirect Immunofluorescent

Hantaviruses are Bunyaviridae viruses that cause hemorrhagic fever with renal syndrome (HFRS). Appendicitis caused by Hantaan virus has not been reported previously. An 81-year-old man who underwent laparoscopic appendectomy for suspected appendicitis based on abdominal pain, fever, hypotension, and computed tomography findings. Based on a suspicion of hemorrhagic fever with renal syndrome, the patient’s plasma was simultaneously analyzed using an indirect immunofluorescent antibody assay and nested reverse transcription–polymerase chain reaction (RT-PCR). The appendix tissue was also analyzed using nested RT-PCR and immunohistochemical (IHC) staining to identify the presence of Hantaan virus. Nested RT-PCR detected the presence of Hantaan virus, and indirect immunofluorescent antibody assay results revealed the presence of elevated antibody levels. Furthermore, IHC staining of the appendix tissue confirmed Hantaan virus antigens in the peripheral nerve bundle. Based on these findings, we confirmed the nerve tropism of the Hantaan virus. Hantaan virus in plasma and appendix tissue samples was confirmed using PCR and phylogenetic tree analysis. Moreover, we detected hypertrophy of the submucosa and periappendiceal adipose tissue nerve bundle along with Hantaan virus antigens in peripheral nerve bundles using IHC staining. Hence, we report that Hantaan virus infection may be accompanied by appendicitis.

scholarly journals Differential regulatory network-based quantification and prioritization of key genes underlying cancer drug resistance based on time-course RNA-seq data

2019 ◽  
Vol 15 (11) ◽  
pp. e1007435 ◽  
Author(s):  
Jiajun Zhang ◽  
Wenbo Zhu ◽  
Qianliang Wang ◽  
Jiayu Gu ◽  
L. Frank Huang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Regulatory Network ◽  
Time Course ◽  
Cancer Drug ◽  
Rna Seq ◽  
Cancer Drug Resistance ◽  
Key Genes
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