De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress

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.

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Faculty Opinions recommendation of Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.733883362.793555704 ◽

2019 ◽

Author(s):

Miles Wilkinson

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Cell Fate ◽

Sequencing Analysis ◽

Single Cell Rna Sequencing ◽

Human Spermatogenesis

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RNA-sequencing Analysis of Differentially Expressed Genes in Wild-type andBnERF-transgenic Arabidopsis Under Submergence Treatment

CHINESE BULLETIN OF BOTANY ◽

10.3724/sp.j.1259.2015.00321 ◽

2015 ◽

Vol 50 (3) ◽

pp. 321

Author(s):

Lü Yanyan ◽

Fu Sanxiong ◽

Chen Song ◽

Zhang Wei ◽

Qi Cunkou

Keyword(s):

Rna Sequencing ◽

Differentially Expressed Genes ◽

Transgenic Arabidopsis ◽

Differentially Expressed ◽

Sequencing Analysis ◽

Wild Type

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Single Cell RNA Sequencing Analysis of Human Kidney Reveals the Presence of ACE2 Receptor: A Potential Pathway of COVID-19 Infection

SSRN Electronic Journal ◽

10.2139/ssrn.3544810 ◽

2020 ◽

Cited By ~ 2

Author(s):

Qiyu He ◽

Tsz Ngai Mok ◽

Liang Yun ◽

Chengbo He ◽

Jieruo Li ◽

...

Keyword(s):

Single Cell ◽

Rna Sequencing ◽

Human Kidney ◽

Sequencing Analysis ◽

Single Cell Rna Sequencing

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Whole-exome sequencing with targeted analysis and epilepsy after acute symptomatic neonatal seizures

Pediatric Research ◽

10.1038/s41390-021-01509-3 ◽

2021 ◽

Author(s):

Adam L. Numis ◽

Gilberto da Gente ◽

Elliott H. Sherr ◽

Hannah C. Glass

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

De Novo ◽

List Type ◽

Sequencing Analysis ◽

Neonatal Seizures ◽

Pathogenic Variants ◽

Targeted Analysis ◽

Whole Exome ◽

Epilepsy Gene

Abstract Background The contribution of pathogenic gene variants with development of epilepsy after acute symptomatic neonatal seizures is not known. Methods Case–control study of 20 trios in children with a history of acute symptomatic neonatal seizures: 10 with and 10 without post-neonatal epilepsy. We performed whole-exome sequencing (WES) and identified pathogenic de novo, transmitted, and non-transmitted variants from established and candidate epilepsy association genes and correlated prevalence of these variants with epilepsy outcomes. We performed a sensitivity analysis with genes associated with coronary artery disease (CAD). We analyzed variants throughout the exome to evaluate for differential enrichment of functional properties using exploratory KEGG searches. Results Querying 200 established and candidate epilepsy genes, pathogenic variants were identified in 5 children with post-neonatal epilepsy yet in only 1 child without subsequent epilepsy. There was no difference in the number of trios with non-transmitted pathogenic variants in epilepsy or CAD genes. An exploratory KEGG analysis demonstrated a relative enrichment in cell death pathways in children without subsequent epilepsy. Conclusions In this pilot study, children with epilepsy after acute symptomatic neonatal seizures had a higher prevalence of coding variants with a targeted epilepsy gene sequencing analysis compared to those patients without subsequent epilepsy. Impact We performed whole-exome sequencing (WES) in 20 trios, including 10 children with epilepsy and 10 without epilepsy, both after acute symptomatic neonatal seizures. Children with post-neonatal epilepsy had a higher burden of pathogenic variants in epilepsy-associated genes compared to those without post-neonatal epilepsy. Future studies evaluating this association may lead to a better understanding of the risk of epilepsy after acute symptomatic neonatal seizures and elucidate molecular pathways that are dysregulated after brain injury and implicated in epileptogenesis.

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The molecular taxonomy of primate amygdala via single-nucleus RNA-sequencing analysis

Science Bulletin ◽

10.1016/j.scib.2021.01.017 ◽

2021 ◽

Author(s):

Lei Zhang ◽

Yanyong Cheng ◽

Shihao Wu ◽

Yufeng Lu ◽

Zhenyu Xue ◽

...

Keyword(s):

Rna Sequencing ◽

Molecular Taxonomy ◽

Sequencing Analysis ◽

Single Nucleus

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CTIM-06. DENDRITIC CELL VACCINE STUDY FOR RECURRENT, HIGH-GRADE GLIOMA: TISSUE-BASED RNA SEQUENCING AND SERUM CYTOKINE LEVELS AS POTENTIAL BIOMARKERS

Neuro-Oncology ◽

10.1093/neuonc/noaa215.140 ◽

2020 ◽

Vol 22 (Supplement_2) ◽

pp. ii33-ii34

Author(s):

Macarena De La Fuente ◽

Tulay Koru-Sengul ◽

Deborah Heros ◽

Feng Miao ◽

Alain Fernandez Marrero ◽

...

Keyword(s):

Dendritic Cells ◽

Rna Sequencing ◽

Tumor Antigens ◽

High Grade Glioma ◽

Treatment Discontinuation ◽

Sequencing Analysis ◽

High Grade ◽

Who Grade ◽

Cytokine Levels ◽

Grade 3

Abstract BACKGROUND Glioblastoma is the most common primary malignant brain tumor. Despite multimodality treatment approach, median progression-free survival (PFS) is only 8 months, median overall-survival (OS) 14 months and 5-year survival rate of under 10%. Dendritic cells (DCs) are the professional antigen presenting cells of the immune system. The rationale for sensitizing dendritic cells to a pool of non-selected tumor antigens is based on the marked heterogeneity present within glioblastoma tumor cells. METHODS Phase 1/feasibility study of DC vaccine for recurrent high-grade glioma was conducted. Pooled, non-selected tumor antigens collected via tumor cell lysate were used for DC sensitization. RNA sequencing analysis was performed on all tumor samples. Cytokine levels in serum were detected using a Luminex cytokine panel. RESULTS A total of 20 patients were enrolled onto this study (median age 58yrs, range: 39–74, 65% male). Pathology showed WHO grade IV glioblastoma in 14 (70%) and grade III anaplastic astrocytoma in 6 (30%) patients. IDH wild type in 19 (95%) patients. Treatment emergent adverse events (all grades, regardless of attribution) occurred in more than 15% of the patients (20% fatigue, 15% dizziness, 15% headache, none leading to treatment discontinuation). There were five grade 3–4 and none grade 5 events. One grade 4 event (seizure) probable related to investigational treatment leading to treatment discontinuation. Four grade 3 events (dysphasia, possible related; intracranial hemorrhage unrelated; muscle weakness, unlikely related and hematoma, unrelated). Median PFS was 3.8 months. Median OS was 11 months. RNA sequencing in tumor samples and correlation with cytokine levels in serum is currently been analyzed. CONCLUSION Tumor lysate pulsed DC vaccination demonstrates acceptable safety and tolerability in high-grade glioma patients. Evaluations of integrating molecular profiling RNA sequencing information and cytokine levels to identify potential subset of patients with significant clinical benefit will be provided.

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Reconstruction of the miR-506-Quaking axis in Idiopathic Pulmonary Fibrosis using integrative multi-source bioinformatics

Scientific Reports ◽

10.1038/s41598-021-89531-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Stevan D. Stojanović ◽

Maximilian Fuchs ◽

Chunguang Liang ◽

Kevin Schmidt ◽

Ke Xiao ◽

...

Keyword(s):

Data Mining ◽

Idiopathic Pulmonary Fibrosis ◽

Pulmonary Fibrosis ◽

Rna Sequencing ◽

In Silico ◽

Rna Binding ◽

Human Lung ◽

Model Systems ◽

Lung Fibroblasts ◽

Sequencing Analysis

AbstractThe family of RNA-binding proteins (RBP) functions as a crucial regulator of multiple biological processes and diseases. However, RBP function in the clinical setting of idiopathic pulmonary fibrosis (IPF) is still unknown. We developed a practical in silico screening approach for the characterization of RBPs using multi-sources data information and comparative molecular network bioinformatics followed by wet-lab validation studies. Data mining of bulk RNA-Sequencing data of tissues of patients with IPF identified Quaking (QKI) as a significant downregulated RBP. Cell-type specific expression was confirmed by single-cell RNA-Sequencing analysis of IPF patient data. We systematically analyzed the molecular interaction network around QKI and its functional interplay with microRNAs (miRs) in human lung fibroblasts and discovered a novel regulatory miR-506-QKI axis contributing to the pathogenesis of IPF. The in silico results were validated by in-house experiments applying model systems of miR and lung biology. This study supports an understanding of the intrinsic molecular mechanisms of IPF regulated by the miR-506-QKI axis. Initially applied to human lung disease, the herein presented integrative in silico data mining approach can be adapted to other disease entities, underlining its practical relevance in RBP research.

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Single C-to-T substitution using engineered APOBEC3G-nCas9 base editors with minimum genome- and transcriptome-wide off-target effects

Science Advances ◽

10.1126/sciadv.aba1773 ◽

2020 ◽

Vol 6 (29) ◽

pp. eaba1773 ◽

Cited By ~ 2

Author(s):

Sangsin Lee ◽

Ning Ding ◽

Yidi Sun ◽

Tanglong Yuan ◽

Jing Li ◽

...

Keyword(s):

Rna Sequencing ◽

High Precision ◽

Disease Modeling ◽

Human Cells ◽

Sequencing Analysis ◽

Injection Method ◽

Cell Embryo ◽

Human Apobec3g ◽

Target Effects

Cytosine base editors (CBEs) enable efficient cytidine-to-thymidine (C-to-T) substitutions at targeted loci without double-stranded breaks. However, current CBEs edit all Cs within their activity windows, generating undesired bystander mutations. In the most challenging circumstance, when a bystander C is adjacent to the targeted C, existing base editors fail to discriminate them and edit both Cs. To improve the precision of CBE, we identified and engineered the human APOBEC3G (A3G) deaminase; when fused to the Cas9 nickase, the resulting A3G-BEs exhibit selective editing of the second C in the 5′-CC-3′ motif in human cells. Our A3G-BEs could install a single disease-associated C-to-T substitution with high precision. The percentage of perfectly modified alleles is more than 6000-fold for disease correction and more than 600-fold for disease modeling compared with BE4max. On the basis of the two-cell embryo injection method and RNA sequencing analysis, our A3G-BEs showed minimum genome- and transcriptome-wide off-target effects, achieving high targeting fidelity.

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