Abstract P501: Comprehensive Analysis Of Alternative Polyadenylation In Human Left Ventricle Failure By Using The Novel Algorithm: Polya-miner

2021 ◽  
Vol 129 (Suppl_1) ◽  
Author(s):  
Rahul Neupane ◽  
Hari Krishna Yalamanchili ◽  
Rajasekaran Mahalingam ◽  
Scott D Collum ◽  
Keith Youker ◽  
...  
Keyword(s):  
Left Ventricle ◽  
Alternative Polyadenylation ◽  
Significant Shift ◽  
Gene Expressions ◽  
Additional Layer ◽  
Functional Consequences ◽  
Cleavage And Polyadenylation ◽  
Length Regulation ◽  
Specificity Factor ◽  
Human Left Ventricle

Background: Alternative polyadenylation (APA) is an emerging post-transcriptional mechanism for gene regulation that generates distinct isoforms of mRNA with different 3′ untranslated regions (3’UTR) lengths. APA plays an important role in different biological processes and dysregulation of APA leads to many human diseases. However, the functional consequences of APA events in the left ventricle (LV) failure in humans remain unexplored. Objective: To identify whether the 3′UTR length is modulated by APA in the LV failure in humans compared to healthy LV. Methods and Results: We used Poly(A)-ClickSeq RNA sequencing and PolyA-miner algorithm to measure the global patterns of APA in healthy and failing human LV specimens. We determined shortening versus lengthening of 3′UTRs based on the PolyA index, a metric unit that determines the length of 3′UTR. Based on these scores, we identified 129 genes with a significant shift of cleavage site usage in failing LV compared to healthy LV specimens. By examining polyadenylation events in these hearts, we identified disease-specific APA signatures in many genes. In addition, differential APA events in LV failure regulate many pathways important for the progression of LV failure. Finally, the regulator proteins of APA including cleavage and polyadenylation specificity factor (CPSF) 6 and 7, cleavage factor Im (CFIm) 25 and 59 have been regulated in LV failure compared to healthy LV specimens. Conclusions: Our results provide genome-wide, polyadenylation maps of the human heart and show that APA of mRNA is dynamic in the progression of LV failure in humans. Demonstrating that APA mediated 3’UTR length regulation provides the additional layer of gene expressions in LV failure.

Abstract 17448: Comprehensive Characterization of Alternative Polyadenylation in Human Right Ventricle Failure

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Rajarajan Amirthalingam Thandavarayan ◽  
Scott D Collum ◽  
Keith Youker ◽  
Rajaseakaran Mahalingam ◽  
Leng Han ◽  
...  
Keyword(s):  
Right Ventricle ◽  
Rna Processing ◽  
Alternative Polyadenylation ◽  
Specific Gene ◽  
Gene Expressions ◽  
Human Right ◽  
Additional Layer ◽  
Cleavage And Polyadenylation ◽  
Specificity Factor ◽  
The Right

Background: Alternative cleavage and polyadenylation (APA) an emerging post-transcriptional mechanism for gene regulation that generates distinct isoforms of mRNA with different 3’UTR lengths. APA plays an important role in different biological processes and dysregulation of APA leading to many human diseases. However, the functional consequences of APA events in the right ventricle (RV) failure in humans remain unexplored. Objective: To identify whether the 3′UTR length is modulated by APA in the RV failure in humans compared to healthy RV. Methods and Results: We used Poly A tail RNA sequencing and a novel algorithm called DaPars to measure the global patterns of APA in healthy and failing human RV specimens. We revealed 3'UTR shortening and lengthening of many genes in failing RV compared to healthy RV specimens. The lengthened 3’UTR genes were enriched for functional groups such as RNA processing and splicing. Whereas the shortened 3’UTR genes were enriched for nucleic acid metabolic process and chromatin organization. In addition, differential APA events in RV failure regulates many pathways important for the progression of the RV failure. Finally, the regulator proteins of APA including cleavage and polyadenylation specificity factor (CPSF) 6 and 7, cleavage factor Im (CFIm) 25 and 59 have been regulated in RV failure compared to healthy RV specimens. Conclusions: Our results highlight important roles of APA in the progression of RV failure in humans, including RNA processing, splicing, and specific gene expression. Demonstrating that APA mediated 3’UTR length regulation provides the additional layer of gene expressions in RV failure.

Numerical simulation of pulsatile blood flow in the human left ventricle

2007 ◽  
Vol 55 (S 1) ◽  
Author(s):  
W Schiller ◽  
K Spiegel ◽  
T Schmid ◽  
H Rudorf ◽  
S Flacke ◽  
...  
Keyword(s):  
Numerical Simulation ◽  
Blood Flow ◽  
Left Ventricle ◽  
Pulsatile Blood Flow ◽  
Human Left Ventricle

scholarly journals The Detection and Bioinformatic Analysis of Alternative 3′ UTR Isoforms as Potential Cancer Biomarkers

2021 ◽  
Vol 22 (10) ◽  
pp. 5322
Author(s):  
Nitika Kandhari ◽  
Calvin A. Kraupner-Taylor ◽  
Paul F. Harrison ◽  
David R. Powell ◽  
Traude H. Beilharz
Keyword(s):  
Gene Expression ◽  
Cell Transformation ◽  
Alternative Polyadenylation ◽  
Cancer Biomarkers ◽  
Bioinformatic Analysis ◽  
Alternative Transcript ◽  
Clinical Parameters ◽  
Transcript Cleavage ◽  
Cleavage And Polyadenylation ◽  
Potential Cancer

Alternative transcript cleavage and polyadenylation is linked to cancer cell transformation, proliferation and outcome. This has led researchers to develop methods to detect and bioinformatically analyse alternative polyadenylation as potential cancer biomarkers. If incorporated into standard prognostic measures such as gene expression and clinical parameters, these could advance cancer prognostic testing and possibly guide therapy. In this review, we focus on the existing methodologies, both experimental and computational, that have been applied to support the use of alternative polyadenylation as cancer biomarkers.

scholarly journals Alternative polyadenylation: methods, mechanism, function, and role in cancer

2021 ◽  
Vol 40 (1) ◽  
Author(s):  
Yi Zhang ◽  
Lian Liu ◽  
Qiongzi Qiu ◽  
Qing Zhou ◽  
Jinwang Ding ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Single Gene ◽  
Alternative Polyadenylation ◽  
Length Change ◽  
Suppressor Gene ◽  
Gene Expressions ◽  
Related Factors ◽  
Mrna Maturation

AbstractOccurring in over 60% of human genes, alternative polyadenylation (APA) results in numerous transcripts with differing 3’ends, thus greatly expanding the diversity of mRNAs and of proteins derived from a single gene. As a key molecular mechanism, APA is involved in various gene regulation steps including mRNA maturation, mRNA stability, cellular RNA decay, and protein diversification. APA is frequently dysregulated in cancers leading to changes in oncogenes and tumor suppressor gene expressions. Recent studies have revealed various APA regulatory mechanisms that promote the development and progression of a number of human diseases, including cancer. Here, we provide an overview of four types of APA and their impacts on gene regulation. We focus particularly on the interaction of APA with microRNAs, RNA binding proteins and other related factors, the core pre-mRNA 3’end processing complex, and 3’UTR length change. We also describe next-generation sequencing methods and computational tools for use in poly(A) signal detection and APA repositories and databases. Finally, we summarize the current understanding of APA in cancer and provide our vision for future APA related research.

scholarly journals Unique Features of Plant Cleavage and Polyadenylation Specificity Factor Revealed by Proteomic Studies

2009 ◽  
Vol 151 (3) ◽  
pp. 1546-1556 ◽  
Author(s):  
Hongwei Zhao ◽  
Denghui Xing ◽  
Qingshun Quinn Li
Keyword(s):  
Cleavage And Polyadenylation ◽  
Specificity Factor

scholarly journals Simultaneous Endocardial Mapping in the Human Left Ventricle Using a Noncontact Catheter

Circulation ◽  
1998 ◽  
Vol 98 (9) ◽  
pp. 887-898 ◽  
Author(s):  
Richard J. Schilling ◽  
Nicholas S. Peters ◽  
D. Wyn Davies
Keyword(s):  
Left Ventricle ◽  
Endocardial Mapping ◽  
Human Left Ventricle

Human left ventricle transcriptome signatures and signalling pathways in patients with high and low intramyocardial lipid

2021 ◽  
Vol 331 ◽  
pp. e41
Author(s):  
J.P. Hobkirk ◽  
A. Burska ◽  
Y. Haqzad ◽  
A. Gemmink ◽  
S. Carroll ◽  
...  
Keyword(s):  
Left Ventricle ◽  
Signalling Pathways ◽  
Human Left Ventricle

MAAPER: model-based analysis of alternative polyadenylation using 3' end-linked reads

2021 ◽  
Author(s):  
Wei Vivian Li ◽  
Dinghai Zheng ◽  
Ruijia Wang ◽  
Bin Tian
Keyword(s):  
Single Cell ◽  
Robust Statistics ◽  
Single Cell Analysis ◽  
Alternative Polyadenylation ◽  
Computational Method ◽  
Model Based ◽  
Eukaryotic Genes ◽  
Counting Strategy ◽  
Cleavage And Polyadenylation ◽  
Model Based Analysis

Most eukaryotic genes harbor multiple cleavage and polyadenylation sites (PASs), leading to expression of alternative polyadenylation (APA) isoforms. APA regulation has been implicated in a diverse array of physiological and pathological conditions. While RNA sequencing tools that generate reads containing the PAS, named onSite reads, have been instrumental in identifying PASs, they have not been widely used. By contrast, a growing number of methods generate reads that are close to the PAS, named nearSite reads, including the 3' end counting strategy commonly used in single cell analysis. How these nearSite reads can be used for APA analysis, however, is poorly studied. Here, we present a computational method, named model-based analysis of alternative polyadenylation using 3' end-linked reads (MAAPER), to examine APA using nearSite reads. MAAPER uses a probabilistic model to predict PASs for nearSite reads with high accuracy and sensitivity, and examines different types of APA events, including those in 3'UTRs and introns, with robust statistics. We show MAAPER's accuracy with data from both bulk and single cell RNA samples and its applicability in unpaired or paired experimental designs. Our result also highlights the importance of using well annotated PASs for nearSite read analysis.

Abstract 131: C-kit+ Cells Generated From Failed Heart Do Not Improve Failed Heart Function

2013 ◽  
Vol 113 (suppl_1) ◽  
Author(s):  
Liudmila Zakharova ◽  
Hikmet Nural ◽  
James R Nimlos ◽  
Snjezana Popovic ◽  
Lorraine Feehery ◽  
...  
Keyword(s):  
Heart Failure ◽  
Left Ventricle ◽  
Diastolic Pressure ◽  
Heart Function ◽  
Smooth Muscle Actin ◽  
Functional Improvement ◽  
Gene Expressions ◽  
Coronary Vein ◽  
Mesenchymal Transition

A pilot clinical study using autologous c-Kit+ cells showed improvement in cardiac functions in congestive heart failure (CHF), however, it is unclear if c-Kit+ cells isolated from CHF hearts are equally as potent as cells from controls. To test the potency of CHF c-Kit+ cells, myocardial infarction (MI) was created by permanent ligation of the left anterior descending coronary artery. Six weeks after MI, animals with left ventricle end-diastolic pressure (LVEDP) ≥20 mmHg and scar size ≥30% of left ventricle (LV) were designated as CHF rats. We found that CHF atrial explants generated less c-Kit+ cells compared to shams (15.7% vs. 11% sham vs. CHF). CHF c-Kit+ cells exhibited elevated levels of epicardial to mesenchymal transition markers, including Snail (2.5 fold) and Pai1 (3 fold), while the expression level of epithelial marker, E-cadherin was 3 fold lower in CHF c-Kit+ cells. Moreover, CHF c-Kit+ cells exhibited reduced gene expressions of pluripotency markers; 2.1 fold decrease in Nanog and 4.5 fold decrease in Sox 2 compared to sham cells. To evaluate the potency of the c-Kit+ cells, 1 x 10 6 cells isolated from CHFs or shams were delivered to 3 weeks post-MI CHF hearts. Cells were pre-labeled with GFP to enable their tracing in vivo and delivered to the infarcted myocardium via left coronary vein by a retrograde coronary sinus cell infusion (RCI). RCI delivery resulted in a cell distribution of LV (30%), right atrium (30%) and right ventricle (20%), while only 10% of cells were found in a left atrium. Three weeks after cells delivery, rats transplanted with sham c-Kit+ cells showed improved LVEDP (29.4 ± 6 vs. 11.7 ± 3.5 mmHg, CHF vs. CHF+ sham c-Kit+ cells) and a rise in peak rate of pressure (dPdt max) (3988 ± 520 vs. 5333 ± 597 mmHg/s). In contrast, no functional improvement was detected in rats transplanted with CHF c-Kit+ cells. Histological analysis demonstrated that transplanted c-Kit+/GFP+ cells were mostly incorporated into blood vessels and co-localized with endothelial marker vWf, and α-smooth muscle actin. Our results showed that left coronary vein is an efficient route for c-Kit+ cell delivery and that c-Kit+ cells isolated from CHF rats are less potent when transplanted in chronic heart failure rat model compared to those isolated from control.

The effect of upright tilt on the volume of the failing human left ventricle

1975 ◽  
Vol 90 (6) ◽  
pp. 735-743 ◽  
Author(s):  
Miltiadis A. Stefadouros ◽  
Manfouz El Shahawy ◽  
Frieda Stefadouros ◽  
A.Calhoun Witham
Keyword(s):  
Left Ventricle ◽  
Human Left Ventricle ◽  
Upright Tilt
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