scholarly journals Detailed Analyses of the Expression Patterns of Potential Severe Acute Respiratory Syndrome Coronavirus 2 Receptors in the Human Heart Using Single-Nucleus RNA Sequencing

2021 ◽  
Vol 8 ◽  
Author(s):  
Jie Ren ◽  
Yuze Zhang ◽  
Shishi Liu ◽  
Xiangjie Li ◽  
Xiaogang Sun
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Human Heart ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Cardiac Injury ◽  
Cell Types ◽  
Cardiovascular Complications ◽  
High Sequence Similarity ◽  
Ventricular Cells ◽  
Single Nucleus

Cardiac injury is a common complication of coronavirus disease 2019 (COVID-19), but the exact mechanisms have not been completely elucidated. The virus receptors on subsets of cells are key determinants of susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Due to its high sequence similarity to SARS-CoV, SARS-CoV-2 also utilizes ACE2 as the cell entry receptor. A growing number of studies have indicated that other receptors apart from ACE2 are involved in SARS-CoV-2 infection. This study aimed to elucidate the expression characteristics of SARS-CoV-2 cellular receptors in the heart. We first investigated ACE2 expression in a comprehensive transcriptional landscape of the human heart comprising single-nucleus RNA-seq (snRNA-seq) data for >280,000 cells. Then, the expression distributions of novel SARS-CoV-2 receptors were analyzed at the single-cell level to clarify the cardiovascular complications in COVID-19. We observed a higher percentage of ACE2-positive cells in pericytes (8.3%), fibroblasts (5.1%), and adipocytes (4.4%) in the human heart, compared to other cell types. The frequency of ACE2-positive cells in each cell type from the ventricles was significantly higher than that in the atria, suggesting that the ventricular cells are more susceptible to SARS-CoV-2 infection. The distribution patterns of other receptors (BSG, HSPA5, KREMEN1, NRP1, ANPEP, AXL) were significantly different from those of ACE2, demonstrating higher expression levels in ventricular cardiomyocytes. Moreover, our results suggest that fibroblasts and adipocytes, aside from pericytes, may be vulnerable targets for SARS-CoV-2 infection in the human heart. Our study presents potential targets for future clinical studies and interventions for cardiac injury in patients with COVID-19.

scholarly journals The expression of delta opioid receptor mRNA in adult male zebra finches (Taenopygia guttata)

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256599
Author(s):  
Pooja Parishar ◽  
Neha Sehgal ◽  
Soumya Iyengar
Keyword(s):  
Opioid Receptors ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Auditory Pathway ◽  
Zebra Finches ◽  
Endogenous Opioid System ◽  
Endogenous Opioid ◽  
High Sequence Similarity ◽  
Brain Functions ◽  
Song Control

The endogenous opioid system is evolutionarily conserved across reptiles, birds and mammals and is known to modulate varied brain functions such as learning, memory, cognition and reward. To date, most of the behavioral and anatomical studies in songbirds have mainly focused on μ-opioid receptors (ORs). Expression patterns of δ-ORs in zebra finches, a well-studied species of songbird have not yet been reported, possibly due to the high sequence similarity amongst different opioid receptors. In the present study, a specific riboprobe against the δ-OR mRNA was used to perform fluorescence in situ hybridization (FISH) on sections from the male zebra finch brain. We found that δ-OR mRNA was expressed in different parts of the pallium, basal ganglia, cerebellum and the hippocampus. Amongst the song control and auditory nuclei, HVC (abbreviation used as a formal name) and NIf (nucleus interfacialis nidopallii) strongly express δ-OR mRNA and stand out from the surrounding nidopallium. Whereas the expression of δ-OR mRNA is moderate in LMAN (lateral magnocellular nucleus of the anterior nidopallium), it is low in the MSt (medial striatum), Area X, DLM (dorsolateral nucleus of the medial thalamus), RA (robust nucleus of the arcopallium) of the song control circuit and Field L, Ov (nucleus ovoidalis) and MLd (nucleus mesencephalicus lateralis, pars dorsalis) of the auditory pathway. Our results suggest that δ-ORs may be involved in modulating singing, song learning as well as spatial learning in zebra finches.

scholarly journals NADPH-dependent extracellular superoxide production is vital to photophysiology in the marine diatom Thalassiosira oceanica

2019 ◽  
Vol 116 (33) ◽  
pp. 16448-16453 ◽  
Author(s):  
Julia M. Diaz ◽  
Sydney Plummer ◽  
Colleen M. Hansel ◽  
Peter F. Andeer ◽  
Mak A. Saito ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Cell Types ◽  
Redox Balance ◽  
Superoxide Production ◽  
Marine Phytoplankton ◽  
Marine Diatom ◽  
High Sequence Similarity ◽  
Whole Cells ◽  
Wide Range ◽  
Diphenylene Iodonium

Reactive oxygen species (ROS) like superoxide drive rapid transformations of carbon and metals in aquatic systems and play dynamic roles in biological health, signaling, and defense across a diversity of cell types. In phytoplankton, however, the ecophysiological role(s) of extracellular superoxide production has remained elusive. Here, the mechanism and function of extracellular superoxide production by the marine diatom Thalassiosira oceanica are described. Extracellular superoxide production in T. oceanica exudates was coupled to the oxidation of NADPH. A putative NADPH-oxidizing flavoenzyme with predicted transmembrane domains and high sequence similarity to glutathione reductase (GR) was implicated in this process. GR was also linked to extracellular superoxide production by whole cells via quenching by the flavoenzyme inhibitor diphenylene iodonium (DPI) and oxidized glutathione, the preferred electron acceptor of GR. Extracellular superoxide production followed a typical photosynthesis-irradiance curve and increased by 30% above the saturation irradiance of photosynthesis, while DPI significantly impaired the efficiency of photosystem II under a wide range of light levels. Together, these results suggest that extracellular superoxide production is a byproduct of a transplasma membrane electron transport system that serves to balance the cellular redox state through the recycling of photosynthetic NADPH. This photoprotective function may be widespread, consistent with the presence of putative homologs to T. oceanica GR in other representative marine phytoplankton and ocean metagenomes. Given predicted climate-driven shifts in global surface ocean light regimes and phytoplankton community-level photoacclimation, these results provide implications for future ocean redox balance, ecological functioning, and coupled biogeochemical transformations of carbon and metals.

scholarly journals A Method for Cryopreservation and Single Nucleus RNA-sequencing of Normal Adult Human Interventricular Septum Heart Tissue Reveals Cellular Diversity and Function

2020 ◽  
Author(s):  
Amy Larson ◽  
Michael T. Chin
Keyword(s):  
Single Cell ◽  
Human Heart ◽  
Expression Patterns ◽  
Interventricular Septum ◽  
Cell Types ◽  
Heart Tissue ◽  
Gene Expression Patterns ◽  
High Quality ◽  
Normal Human ◽  
Human Heart Tissue

Abstract Background: Single cell sequencing of human heart tissue is technically challenging and methods to cryopreserve heart tissue for obtaining single cell information have not been standardized. Studies published to date have used varying methods to preserve and process human heart tissue, and have generated interesting datasets, but development of a biobanking standard has not yet been achieved. Heart transcription patterns are known to be regionally diverse, and there are few single cell datasets for normal human heart tissue. Methods: Using pig tissue, we developed a rigorous and reproducible method for tissue mincing and cryopreservation that allowed recovery of high quality single nuclei RNA. We subsequently tested this protocol on normal human heart tissue obtained from organ donors and were able to recover high quality nuclei for generation of single nuclei RNA-seq datasets, using a commercially available platform from 10x Genomics. We analyzed these datasets using standard software packages such as CellRanger and Seurat. Results: Human heart tissue preserved with our method consistently yielded nuclear RNA with RNA Integrity Numbers of greater than 8.5. We demonstrate the utility of this method for single nuclei RNA-sequencing of the normal human interventricular septum and delineating its cellular diversity. The human IVS showed unexpected diversity with detection of 23 distinct cell clusters that were subsequently categorized into different cell types. Cardiomyocytes and fibroblasts were the most commonly identified cell types and could be further subdivided into 5 different cardiomyocyte subtypes and 6 different fibroblast subtypes that differed by gene expression patterns. Ingenuity Pathway analysis of these gene expression patterns suggested functional diversity in these cell subtypes. Conclusions: Here we report a simple technical method for cryopreservation and subsequent nuclear isolation of human interventricular septum tissue that can be done with common laboratory equipment. We show how this method can be used to generate single nuclei transcriptomic datasets that rival those already published by larger groups in terms of cell diversity and complexity and suggest that this simple method can provide guidance for biobanking of human myocardial tissue for complex genomic analysis.

scholarly journals Minimal functional domains of paralogues hnRNP L and hnRNP LL exhibit mechanistic differences in exonic splicing repression

2013 ◽  
Vol 453 (2) ◽  
pp. 271-279 ◽  
Author(s):  
Ganesh Shankarling ◽  
Kristen W. Lynch
Keyword(s):  
Sequence Similarity ◽  
Expression Patterns ◽  
Rna Recognition ◽  
High Sequence Similarity ◽  
Rna Recognition Motifs ◽  
Hnrnp Proteins ◽  
Functional Consequences ◽  
Recognition Motifs ◽  
Nuclear Ribonucleoprotein ◽  
Specific Control

Understanding functional distinctions between related splicing regulatory proteins is critical to deciphering tissue-specific control of alternative splicing. The hnRNP (heterogeneous nuclear ribonucleoprotein) L and hnRNP LL (hnRNP L-like) proteins are paralogues that have overlapping, but distinct, expression patterns and functional consequences. These two proteins share high sequence similarity in their RRMs (RNA-recognition motifs), but diverge in regions outside of the RRMs. In the present study, we use an MS2-tethering assay to delineate the minimal domains of hnRNP L and hnRNP LL which are required for repressing exon inclusion. We demonstrate that for both proteins, regions outside the RRMs, the N-terminal region, and a linker sequence between RRMs 2 and 3, are necessary for exon repression, but are only sufficient for repression in the case of hnRNP LL. In addition, both proteins require at least one RRM for maximal repression. Notably, we demonstrate that the region encompassing RRMs 1 and 2 of hnRNP LL imparts a second silencing activity not observed for hnRNP L. This additional functional component of hnRNP LL is consistent with the fact that the full-length hnRNP LL has a greater silencing activity than hnRNP L. Thus the results of the present study provide important insight into the functional and mechanistic variations that can exist between two highly related hnRNP proteins.

scholarly journals Duplicated Proteasome Subunit Genes in Drosophila melanogaster Encoding Testes-Specific Isoforms

Genetics ◽  
1996 ◽  
Vol 144 (1) ◽  
pp. 147-157 ◽  
Author(s):  
Xiaoqing Yuan ◽  
Mary Miller ◽  
John M Belote
Keyword(s):  
Drosophila Melanogaster ◽  
Genomic Library ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Primary Spermatocyte ◽  
Amino Acid Identity ◽  
High Sequence Similarity ◽  
New Genes ◽  
Cell Type Specific ◽  
Elongation Phase

Abstract Using the previously cloned proteasome α-type subunit gene Pros28.1, we screened a Drosophila melanogaster genomic library using reduced stringency conditions to identify closely related genes. Two new genes, Pros28.1A (map position 92F) and Pros28.IB (map position 60D7), showing high sequence similarity to Pros28.1, were identified and characterized. Pros28.1A encodes a protein with 74% amino acid identity to PROS28.1, while the Pros28.1B gene product is 58% identical. The Pros28.1B gene has two introns, located in exactly analogous positions as the two introns in Pros28.1, while the Pros28.IA gene lacks introns. Northern blot analysis reveals that the two new genes are expressed only in males, during the pupal and adult stages. Tissue-specific patterns of expression were examined using transgenic flies carrying Zacz-fusion reporter genes. This analysis revealed that both genes are expressed in germline cells during spermatogenesis, although their expression patterns differed. Pros28.1A expression is first detected at the primary spermatocyte stage and persists into the spermatid elongation phase of spermiogenesis, while Pros28. IB expression is prominent only during spermatid elongation. These genes represent the most striking example of cell-type-specific proteasome gene expression reported to date in any system and support the notion that there is structural and functional heterogeneity among proteasomes in metazoans.

scholarly journals Isolation and Characterization of a Class III Peroxidase cDNA from Cucumber under Salt Stress

2014 ◽  
Vol 139 (5) ◽  
pp. 529-536
Author(s):  
Huai-Fu Fan ◽  
Wen Chen ◽  
Zhou Yu ◽  
Chang-Xia Du
Keyword(s):  
Salt Stress ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Class Iii ◽  
Salt Treatment ◽  
High Sequence Similarity ◽  
Coding Sequence ◽  
Cucumber Seedlings ◽  
Isolation And Characterization ◽  
Typical Sequence

Salt stress reduces the fresh weight, dry weight, and relative growth rate of cucumber (Cucumis sativus) seedlings and results in serious quality loss in cucumber production. Our previous study indicated that the netting-associated peroxidase (CsaNAPOD) protein in cucumber seedling roots was induced by salt stress. Here, we amplified the coding sequence of CsaNAPOD from a cDNA isolated from the roots of cucumber seedlings. Sequence analysis indicated that the coding sequence of CsaNAPOD is 1035 bp, encoding a deduced protein of 344 amino acids, with a predicated molecular weight of 37.2 kD and theoretical isoelectric point of 5.64. The deduced amino acid sequence of CsaNAPOD showed high sequence similarity to peroxidases (PODs) from other plant species. Moreover, CsaNAPOD possesses the typical sequence structures of class III PODs and indicated that CsaNAPOD belongs to this subfamily. CsaNAPOD was highly expressed in the roots and was weakly expressed in the stems and leaves of cucumber seedlings. Salt stress significantly increased the expression of CsaNAPOD in the leaves during the entire experimental period compared with the control, and the expression of CsaNAPOD in roots was reduced at 6 hours and induced at 48 and 72 hours by salt treatment. In stems, the expression of CsaNAPOD declined at 48 and 72 hours as a result of the salt treatment compared with the control. These results indicate that the expression of CsaNAPOD responded to salt stress in cucumber seedlings, and the expression patterns under salt stress in different tissues were not identical. Our research suggests that CsaNAPOD may have potential function during the plant response to salt stress.

scholarly journals Overcoming Barriers

2020 ◽  
Vol 40 (8) ◽  
pp. 1818-1829 ◽  
Author(s):  
Dakota Gustafson ◽  
Sneha Raju ◽  
Ruilin Wu ◽  
Crizza Ching ◽  
Shawn Veitch ◽  
...  
Keyword(s):  
Endothelial Dysfunction ◽  
Severe Acute Respiratory Syndrome ◽  
Respiratory Distress ◽  
Cardiac Injury ◽  
Systemic Circulation ◽  
Supplemental Oxygen ◽  
Cardiovascular Complications ◽  
Disease Course ◽  
Multiple Organs ◽  
Global Pandemic

Objective: Coronavirus disease 2019 (COVID-19) is a global pandemic involving >5 500 000 cases worldwide as of May 26, 2020. The culprit is the severe acute respiratory syndrome coronavirus-2, which invades cells by binding to ACE2 (angiotensin-converting enzyme 2). While the majority of patients mount an appropriate antiviral response and recover at home, others progress to respiratory distress requiring hospital admission for supplemental oxygen. In severe cases, deterioration to acute respiratory distress syndrome necessitating mechanical ventilation, development of severe thrombotic events, or cardiac injury and dysfunction occurs. In this review, we highlight what is known to date about COVID-19 and cardiovascular risk, focusing in on the putative role of the endothelium in disease susceptibility and pathogenesis. Approach and Results: Cytokine-driven vascular leak in the lung alveolar-endothelial interface facilitates acute lung injury in the setting of viral infection. Given that the virus affects multiple organs, including the heart, it likely gains access into systemic circulation by infecting or passing from the respiratory epithelium to the endothelium for viral dissemination. Indeed, cardiovascular complications of COVID-19 are highly prevalent and include acute cardiac injury, myocarditis, and a hypercoagulable state, all of which may be influenced by altered endothelial function. Notably, the disease course is worse in individuals with preexisting comorbidities that involve endothelial dysfunction and may be linked to elevated ACE2 expression, such as diabetes mellitus, hypertension, and cardiovascular disease. Conclusions: Rapidly emerging data on COVID-19, together with results from studies on severe acute respiratory syndrome coronavirus-1, are providing insight into how endothelial dysfunction may contribute to the pandemic that is paralyzing the globe. This may, in turn, inform the design of biomarkers predictive of disease course, as well as therapeutics targeting pathogenic endothelial responses.

scholarly journals CsLAZY1 mediates shoot gravitropism and branch angle in tea plants (Camellia sinensis)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaobo Xia ◽  
Xiaozeng Mi ◽  
Ling Jin ◽  
Rui Guo ◽  
Junyan Zhu ◽  
...  
Keyword(s):  
Plant Architecture ◽  
Sequence Similarity ◽  
Expression Patterns ◽  
Tea Plant ◽  
Plant Genome ◽  
Gravity Inversion ◽  
High Sequence Similarity ◽  
Branch Angle ◽  
Shoot Gravitropism ◽  
Tea Plants

Abstract Background Branch angle is a pivotal component of tea plant architecture. Tea plant architecture not only affects tea quality and yield but also influences the efficiency of automatic tea plant pruning. However, the molecular mechanism controlling the branch angle, which is an important aspect of plant architecture, is poorly understood in tea plants. Results In the present study, three CsLAZY genes were identified from tea plant genome data through sequence homology analysis. Phylogenetic tree displayed that the CsLAZY genes had high sequence similarity with LAZY genes from other plant species, especially those in woody plants. The expression patterns of the three CsLAZYs were surveyed in eight tissues. We further verified the expression levels of the key CsLAZY1 transcript in different tissues among eight tea cultivars and found that CsLAZY1 was highly expressed in stem. Subcellular localization analysis showed that the CsLAZY1 protein was localized in the plasma membrane. CsLAZY1 was transferred into Arabidopsis thaliana to investigate its potential role in regulating shoot development. Remarkably, the CsLAZY1 overexpressed plants responded more effectively than the wild-type plants to a gravity inversion treatment under light and dark conditions. The results indicate that CsLAZY1 plays an important role in regulating shoot gravitropism in tea plants. Conclusions The results provide important evidence for understanding the functions of CsLAZY1 in regulating shoot gravitropism and influencing the stem branch angle in tea plants. This report identifies CsLAZY1 as a promising gene resource for the improvement of tea plant architecture.

scholarly journals A method for cryopreservation and single nucleus RNA-sequencing of normal adult human interventricular septum heart tissue reveals cellular diversity and function

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Amy Larson ◽  
Michael T. Chin
Keyword(s):  
Single Cell ◽  
Human Heart ◽  
Expression Patterns ◽  
Interventricular Septum ◽  
Cell Types ◽  
Heart Tissue ◽  
Gene Expression Patterns ◽  
High Quality ◽  
Normal Human ◽  
Human Heart Tissue

Abstract Background Single cell sequencing of human heart tissue is technically challenging and methods to cryopreserve heart tissue for obtaining single cell information have not been standardized. Studies published to date have used varying methods to preserve and process human heart tissue, and have generated interesting datasets, but development of a biobanking standard has not yet been achieved. Heart transcription patterns are known to be regionally diverse, and there are few single cell datasets for normal human heart tissue. Methods Using pig tissue, we developed a rigorous and reproducible method for tissue mincing and cryopreservation that allowed recovery of high quality single nuclei RNA. We subsequently tested this protocol on normal human heart tissue obtained from organ donors and were able to recover high quality nuclei for generation of single nuclei RNA-seq datasets, using a commercially available platform from 10× Genomics. We analyzed these datasets using standard software packages such as CellRanger and Seurat. Results Human heart tissue preserved with our method consistently yielded nuclear RNA with RNA Integrity Numbers of greater than 8.5. We demonstrate the utility of this method for single nuclei RNA-sequencing of the normal human interventricular septum and delineating its cellular diversity. The human IVS showed unexpected diversity with detection of 23 distinct cell clusters that were subsequently categorized into different cell types. Cardiomyocytes and fibroblasts were the most commonly identified cell types and could be further subdivided into 5 different cardiomyocyte subtypes and 6 different fibroblast subtypes that differed by gene expression patterns. Ingenuity Pathway analysis of these gene expression patterns suggested functional diversity in these cell subtypes. Conclusions Here we report a simple technical method for cryopreservation and subsequent nuclear isolation of human interventricular septum tissue that can be done with common laboratory equipment. We show how this method can be used to generate single nuclei transcriptomic datasets that rival those already published by larger groups in terms of cell diversity and complexity and suggest that this simple method can provide guidance for biobanking of human myocardial tissue for complex genomic analysis.

Abstract 16742: Single-Cell Transcriptional and Epigenomic Dissection of Human Heart in Health and Coronary Artery Disease Reveals Cell-type-Specific Driver Genes and Pathways

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Suvi Linna Kuosmanen ◽  
Eloi Schmauch ◽  
Kyriakitsa Galani ◽  
Carles Boix ◽  
Yongjin P Park ◽  
...  
Keyword(s):  
Coronary Artery Disease ◽  
Single Cell ◽  
Human Heart ◽  
Target Genes ◽  
Expression Patterns ◽  
Cell Types ◽  
Heart Cell ◽  
Cell Type ◽  
Cell Type Specific ◽  
Artery Disease

Genome-wide association studies have uncovered over 200 genetic loci underlying coronary artery disease (CAD), providing great hope for a deeper understanding of the causal mechanisms leading to this disease. However, in order to understand CAD at the molecular level, it is necessary to uncover cell-type-specific circuits and to use these circuits to dissect driver variants, genes, pathways, and cell types, in normal and diseased tissues. Here, we provide the most detailed single-cell dissection of human heart cell types, using cardiac biopsies collected during open-heart surgery from healthy, CAD, and CAD-related heart failure donors, and profiling both transcriptional (scRNA-seq) and epigenomic (scATAC-seq) changes. Using this approach, we identify 12 major heart cell types, including typical cardiovascular cells (cardiomyocytes, endothelial cells, fibroblasts), rarer cell types (B cells, neurons, Schwann cells), and previously-unrecognized layer-specific epithelial and endothelial cell types. We define markers for each cell type, providing the first extensive reference set for the living human heart. In addition, we define differential gene expression patterns in CAD relative to control samples, revealing substantial differences in cell-type-specific expression of disease-related genes, emphasizing, for example, the importance of the vascular endothelium in the pathogenesis of CAD. Strikingly, further clustering of the cell types based on specific subtypes revealed important differences in their expression patterns of disease-associated genes. These changes enrich in known CAD genetic loci, enabling us to recognize their likely target genes from scRNA-seq expression changes, candidate driver variants based on scATAC-seq localization and differential DNA accessibility, and candidate upstream regulators based on their enriched motif occurrences in scATAC loci. Overall, our results highlight the relevance and potential of single-cell transcriptional and epigenomic analyses to gain new biological insights into cardiovascular disease, and to recognize novel therapeutic target genes, pathways, and the cell types where they act.

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