scholarly journals Computational Analysis of Missense Variants in the Human Transmembrane Protease Serine 2 (TMPRSS2) and SARS-CoV-2

2021 ◽  
Vol 2021 ◽  
pp. 1-17
Author(s):  
Asmae Saih ◽  
Meryem Bouqdayr ◽  
Hanâ Baba ◽  
Salsabil Hamdi ◽  
Samya Moussamih ◽  
...  
Keyword(s):  
Cancer Progression ◽  
Viral Entry ◽  
Posttranslational Modifications ◽  
Computational Analysis ◽  
3D Structure ◽  
Target Cells ◽  
Prostate Cancer Progression ◽  
Missense Variants ◽  
Stability Structure ◽  
And Function

The human transmembrane protease serine 2 (TMPRSS2) protein plays an important role in prostate cancer progression. It also facilitates viral entry into target cells by proteolytically cleaving and activating the S protein of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the current study, we used different available tools like SIFT, PolyPhen2.0, PROVEAN, SNAP2, PMut, MutPred2, I-Mutant Suite, MUpro, iStable, ConSurf, ModPred, SwissModel, PROCHECK, Verify3D, and TM-align to identify the most deleterious variants and to explore possible effects on the TMPRSS2 stability, structure, and function. The six missense variants tested were evaluated to have deleterious effects on the protein by SIFT, PolyPhen2.0, PROVEAN, SNAP2, and PMut. Additionally, V160M, G181R, R240C, P335L, G432A, and D435Y variants showed a decrease in stability by at least 2 servers; G181R, G432A, and D435Y are highly conserved and identified posttranslational modifications sites (PTMs) for proteolytic cleavage and ADP-ribosylation using ConSurf and ModPred servers. The 3D structure of TMPRSS2 native and mutants was generated using 7 meq as a template from the SwissModeller group, refined by ModRefiner, and validated using the Ramachandran plot. Hence, this paper can be advantageous to understand the association between these missense variants rs12329760, rs781089181, rs762108701, rs1185182900, rs570454392, and rs867186402 and susceptibility to SARS-CoV-2.

scholarly journals Alterations in chromosome spatial compartmentalization classify prostate cancer progression

2021 ◽  
Author(s):  
Rebeca San Martin ◽  
Priyojit Das ◽  
Renata Dos Reis Marques ◽  
Yang Xu ◽  
Rachel Patton McCord
Keyword(s):  
Prostate Cancer ◽  
Cancer Progression ◽  
3D Structure ◽  
Gene Clusters ◽  
Metastatic Potential ◽  
Chromosome 21 ◽  
Prostate Cancer Progression ◽  
Normal Epithelium ◽  
Chromosome Conformation ◽  
Cancer Aggressiveness

Prostate cancer aggressiveness and metastatic potential are influenced by gene expression, genomic aberrations, and cellular morphology. These processes are in turn dependent in part on the 3D structure of chromosomes, packaged inside the nucleus. Using chromosome conformation capture (Hi-C), we conducted a systematic genome architecture comparison on a cohort of cell lines that model prostate cancer progression, ranging from normal epithelium to bone metastasis. Here, we describe how chromatin compartmentalization identity (A- open vs. B-closed) changes with progression: specifically, we find that 48 gene clusters switch from the B to the A compartment, including androgen receptor, WNT5A, and CDK14. These switches could prelude transcription activation and are accompanied by changes in the structure, size, and boundaries of the topologically associating domains (TADs). Further, compartmentalization changes in chromosome 21 are exacerbated with progression and may explain, in part, the genesis of the TMPRSS2-ERG translocation: one of the main drivers of prostate cancer.  These results suggest that discrete, 3D genome structure changes play a deleterious role in prostate cancer progression. 

scholarly journals Circular RNA circANKS1B as the Sponge of miR-152-3p Promotes Prostate Cancer Progression by up-Regulating TGF-α Expression

2020 ◽  
Author(s):  
Liangjun Tao ◽  
Xinyuan Pan ◽  
Jiawei Wang ◽  
Li Zhang ◽  
Lingsong Tao ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cancer Progression ◽  
Circular Rna ◽  
Luciferase Reporter ◽  
Migration And Invasion ◽  
Prostate Cancer Progression ◽  
Luciferase Reporter Gene ◽  
Gene Assay ◽  
And Function ◽  
The Impact

Abstract Background: Growing studies indicate that circRNAs play critical roles in human diseases, and show great potential as biomarkers and therapeutic targets. This study aims to investigate the expression and function of circANKS1B in prostate cancer (PC).Methods: The expression of circANKS1B and miRNA-152-3p were determined by real-time qRT-PCR. The cell migration and invasion were measured by transwell assay. The interaction between circANKS1B and miR-152-3p was confirmed by dual-luciferase reporter gene assay. Rescue experiments were conducted to demonstrate whether circANKS1B regulated the migration and invasion of PC cells by the circANKS1B-miR-152-3p-TGF-α pathway.Results: The expression of circANKS1B was dramatically up-regulated both in PC cells and tissues. Moreover, high circANKS1B expression was associated with a poor prognosis of PC patients. Dual-luciferase reporter assay indicated that circABKS1B directly bound to miRNA-152-3p. Furthermore, circANKS1B negatively regulated miR-152-3p expression. Knockdown of circANKS1B remarkably suppressed PC cells invasion and TGF-α expression, while the effects of circANKS1B silencing were reversed by miR-152-3p deficiency. In addition, the impact of miR-152-3p silencing on PC cell invasion was also abrogated by TGF-α deficiency. In all, circANKS1B as the sponge of miR-152-3p promotes prostate cancer progression by up-regulating TGF-α expression.Conclusion: Our findings reveal that circANKS1B could be a potential prognostic biomarker and therapeutic target of PC.

scholarly journals Expression, Localization, and Function of the Nucleolar Protein BOP1 in Prostate Cancer Progression

2021 ◽  
Vol 191 (1) ◽  
pp. 168-179
Author(s):  
Jordan E. Vellky ◽  
Emily A. Ricke ◽  
Wei Huang ◽  
William A. Ricke
Keyword(s):  
Prostate Cancer ◽  
Cancer Progression ◽  
Nucleolar Protein ◽  
Prostate Cancer Progression ◽  
And Function

scholarly journals Identification and Computational Analysis of 3D-Structure Of MOCS1

2021 ◽  
Author(s):  
Maham Hamid ◽  
uzma habib ◽  
Javeria Batool ◽  
Arshemah Qaisar ◽  
Rehan Zafar Paracha
Keyword(s):  
Binding Sites ◽  
Biosynthetic Pathway ◽  
Computational Analysis ◽  
Tertiary Structure ◽  
3D Structure ◽  
Structure And Function ◽  
Molybdenum Cofactor ◽  
Recognition Method ◽  
And Function ◽  
Ramachandran Plots

Abstract Cyclic pyranopterin monophosphate (cPMP) is one of the most stable intermediates in Molybdenum cofactor (MoCo) biosynthetic pathway. In humans, synthesis of cPMP from Guanosine triphosphate (GTP) requires functional genes i.e. Molybdenum Cofactor Synthesis-1 (MOCS1) genes that contains for two catalytic proteins MOCS1A and MOCS1B. Importance of MOCS1A and MOCS1B for biosynthesis of MoCo reveals from the fact that its deficiency leads to MoCo type A deficiency. As there is no structure available for MOCS1 genes in the literature, tertiary structure of MOCS1 genes were investigated in this research via threading or folds recognition method by i-TASSER and validation was done using ERRAT, Verify3D and Ramachandran plots. Binding sites were predicted and validated. Docking of MOCS1A with GTP and MOCS1B with 3, 8 dihydroguanosine was done using Autodock via PyRx. Apart from this, highly confident mutations were also predicted using SIFT and polyphen2 that can alter the structure and function of MOCS1 gene.

scholarly journals Dissecting the roles of the androgen receptor in prostate cancer from molecular perspectives

Tumor Biology ◽  
2017 ◽  
Vol 39 (5) ◽  
pp. 101042831769225 ◽  
Author(s):  
Jieping Hu ◽  
Gongxian Wang ◽  
Ting Sun
Keyword(s):  
Prostate Cancer ◽  
Androgen Receptor ◽  
Cancer Progression ◽  
Protein Modification ◽  
Prostate Cancer Progression ◽  
Castration Resistant Prostate Cancer ◽  
Castration Resistant ◽  
Receptor Signal ◽  
Androgen Receptor Variants ◽  
And Function

Androgen receptor plays a pivotal role in prostate cancer progression, and androgen deprivation therapy to intercept androgen receptor signal pathway is an indispensable treatment for most advanced prostate cancer patients to delay cancer progression. However, the emerging of castration-resistant prostate cancer reminds us the alteration of androgen receptor, which includes androgen receptor mutation, the formation of androgen receptor variants, and androgen receptor distribution in cancer cells. In this review, we introduce the process of androgen receptor and also its variants’ formation, translocation, and function alteration by protein modification or interaction with other pathways. We dissect the roles of androgen receptor in prostate cancer from molecular perspective to provide clues for battling prostate cancer, especially castration-resistant prostate cancer.

Chromosome compartmentalization alterations in prostate cancer cell lines model disease progression

2021 ◽  
Vol 221 (2) ◽  
Author(s):  
Rebeca San Martin ◽  
Priyojit Das ◽  
Renata Dos Reis Marques ◽  
Yang Xu ◽  
Justin M. Roberts ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Cell Lines ◽  
Cancer Progression ◽  
Genome Structure ◽  
3D Structure ◽  
Gene Clusters ◽  
Chromosome 21 ◽  
Prostate Cancer Progression ◽  
Cancer Aggressiveness

Prostate cancer aggressiveness and metastatic potential are influenced by gene expression and genomic aberrations, features that can be influenced by the 3D structure of chromosomes inside the nucleus. Using chromosome conformation capture (Hi-C), we conducted a systematic genome architecture comparison on a cohort of cell lines that model prostate cancer progression, from normal epithelium to bone metastasis. We describe spatial compartment identity (A-open versus B-closed) changes with progression in these cell lines and their relation to gene expression changes in both cell lines and patient samples. In particular, 48 gene clusters switch from the B to the A compartment, including androgen receptor, WNT5A, and CDK14. These switches are accompanied by changes in the structure, size, and boundaries of topologically associating domains (TADs). Further, compartment changes in chromosome 21 are exacerbated with progression and may explain, in part, the genesis of the TMPRSS2-ERG translocation. These results suggest that discrete 3D genome structure changes play a deleterious role in prostate cancer progression. 

Repurposing Nimesulide, a Potent Inhibitor of the B0AT1 Subunit of the SARS-CoV-2 Receptor, as a Therapeutic Adjuvant of COVID-19

2020 ◽  
Vol 25 (10) ◽  
pp. 1171-1173 ◽  
Author(s):  
Mariafrancesca Scalise ◽  
Cesare Indiveri
Keyword(s):  
Viral Entry ◽  
3D Structure ◽  
World Health ◽  
Effective Vaccine ◽  
Target Cells ◽  
Physical Interaction ◽  
Disease Symptoms ◽  
Angiotensin Converting Enzyme 2 ◽  
Global Pandemic ◽  
Health Organization

The global pandemic caused by the SARS-CoV-2 infection is a health emergency that needs to be addressed immediately. The international scientific community, following World Health Organization (WHO) indications, launched different trials for testing drugs putatively able to block the SARS-CoV-2 infection or treat the COVID-19 disease symptoms. In parallel, studies devoted to a better understanding of SARS-CoV-2 biology are in the course for designing an effective vaccine. One of the human membrane proteins known to be docked by the virus is angiotensin-converting enzyme 2 (ACE2), proposed to be responsible for viral entry in target cells. Recently, the 3D structure of ACE2 has been obtained, showing its physical interaction with B0AT1 (SLC6A19), a plasma membrane transporter involved in the trafficking of amino acids in cells. The receptor targeted by SARS-CoV-2 is a supercomplex formed by a dimer of ACE2-B0AT1, in which ACE2 binds the viral protein and B0AT1 stabilizes the heterodimer. As a serendipity occurrence, nimesulide was shown to abolish the transport function of B0AT1. Here we suggest including nimesulide in the list of drugs to be tested for the identification of co-adjuvants in the treatment of COVID-19.

scholarly journals Posttranslational Modifications of Smurfs: Emerging Regulation in Cancer

2021 ◽  
Vol 10 ◽  
Author(s):  
Longtao Yang ◽  
Wenwen Zhou ◽  
Hui Lin
Keyword(s):  
Cancer Progression ◽  
Protein Interactions ◽  
Posttranslational Modifications ◽  
Epithelial Mesenchymal Transition ◽  
Functional Expression ◽  
Biological Processes ◽  
Mesenchymal Transition ◽  
Control Tumor ◽  
And Function ◽  
Upstream Regulators

Smad ubiquitination regulatory factors (Smurfs) belong to the Nedd4 subfamily of HECT-type E3 ubiquitin ligases. Under normal situations, Smurfs are exactly managed by upstream regulators, and thereby strictly control tumor biological processes, including cell growth, differentiation, apoptosis, polarization, epithelial mesenchymal transition (EMT), and invasion. Disruption of Smurf activity has been implicated in cancer progression, and Smurf activity is controlled by a series of posttranslational modifications (PTMs), including phosphorylation, ubiquitination, neddylation, sumoylation, and methylation. The effect and function of Smurfs depend on PTMs and regulate biological processes. Specifically, these modifications regulate the functional expression of Smurfs by affecting protein degradation and protein interactions. In this review, we summarize the complexity and diversity of Smurf PTMs from biochemical and biological perspectives and highlight the understanding of their roles in cancer.

scholarly journals SARS-CoV-2 Infection Modulates ACE2 Function and Subsequent Inflammatory Responses in Swabs and Plasma of COVID-19 Patients

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1715
Author(s):  
Lucía Gutiérrez-Chamorro ◽  
Eva Riveira-Muñoz ◽  
Clara Barrios ◽  
Vanesa Palau ◽  
Maria Nevot ◽  
...  
Keyword(s):  
Inflammatory Response ◽  
Inflammatory Cytokines ◽  
Viral Entry ◽  
Inflammatory Responses ◽  
Target Cells ◽  
Upper Respiratory Tract ◽  
Angiotensin Converting Enzyme 2 ◽  
Early Biomarker ◽  
And Function ◽  
Ace2 Gene

Angiotensin converting enzyme 2 (ACE2) is a host ectopeptidase and the receptor for the SARS-CoV-2 virus, albeit virus-ACE2 interaction goes far beyond viral entry into target cells. Controversial data exists linking viral infection to changes in ACE2 expression and function, which might influence the subsequent induction of an inflammatory response. Here, we tested the significance of soluble ACE2 enzymatic activity longitudinally in nasopharyngeal swabs and plasma samples of SARS-COV-2 infected patients, along with the induction of inflammatory cytokines. Release of soluble functional ACE2 increases upon SARS-CoV-2 infection in swabs and plasma of infected patients, albeit rapidly decreasing during infection course in parallel with ACE2 gene expression. Similarly, SARS-CoV-2 infection also induced the expression of inflammatory cytokines. These changes positively correlated with the viral load. Overall, our results demonstrate the existence of mechanisms by which SARS-CoV-2 modulates ACE2 expression and function, intracellular viral sensing and subsequent inflammatory response, offering new insights into ACE2 dynamics in the human upper respiratory tract and pointing towards soluble ACE2 levels as a putative early biomarker of infection severity.

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