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Article ; Online: Identification of microRNA-mRNA Regulatory Networks with Therapeutic Values in Alzheimer's Disease by Bioinformatics Analysis.

Kavoosi, Sakine / Shahraki, Ali / Sheervalilou, Roghayeh

2024 Volume 98, Issue 2, Page(s) 671–689

Abstract: Background: Alzheimer's disease (AD) is the most prevalent neurological disorder worldwide, affecting approximately 24 million individuals. Despite more than a century of research on AD, its pathophysiology is still not fully understood.: Objective: ... ...

Abstract	Background: Alzheimer's disease (AD) is the most prevalent neurological disorder worldwide, affecting approximately 24 million individuals. Despite more than a century of research on AD, its pathophysiology is still not fully understood. Objective: Recently, genetic studies of AD have focused on analyzing the general expression profile by employing high-throughput genomic techniques such as microarrays. Current research has leveraged bioinformatics advancements in genetic science to build upon previous efforts. Methods: Data from the GSE118553 dataset used in this investigation, and the analyses carried out using programs such as Limma and BioBase. Differentially expressed genes (DEGs) and differentially expressed microRNAs (DEmiRs) associated with AD identified in the studied areas of the brain. Target genes of the DEmiRs identified using the MultiMiR package. Gene ontology (GO) completed using the Enrichr website, and the protein-protein interaction (PPI) network for these genes drawn using STRING and Cytoscape software. Results: The findings introduced DEGs including CTNNB1, PAK2, MAP2K1, PNPLA6, IGF1R, FOXL2, DKK3, LAMA4, PABPN1, and GDPD5, and DEmiRs linked to AD (miR-106A, miR-1826, miR-1253, miR-10B, miR-18B, miR-101-2, miR-761, miR-199A1, miR-379 and miR-668), (miR-720, miR-218-2, miR-25, miR-602, miR-1226, miR-548K, miR-H1, miR-410, miR-548F2, miR-181A2), (miR-1470, miR-651, miR-544, miR-1826, miR-195, miR-610, miR-599, miR-323, miR-587 and miR-340), and (miR-1282, miR-1914, miR-642, miR-1323, miR-373, miR-323, miR-1322, miR-612, miR-606 and miR-758) in cerebellum, frontal cortex, temporal cortex, and entorhinal cortex, respectively. Conclusions: The majority of the genes and miRNAs identified by our findings may be employed as biomarkers for prediction, diagnosis, or therapy response monitoring.
MeSH term(s)	Humans ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Gene Regulatory Networks/genetics ; Alzheimer Disease/genetics ; Alzheimer Disease/therapy ; RNA, Messenger/genetics ; Gene Expression Profiling/methods ; Computational Biology/methods ; Poly(A)-Binding Protein I/genetics
Chemical Substances	MicroRNAs ; RNA, Messenger ; PABPN1 protein, human ; Poly(A)-Binding Protein I ; MIRN1322 microRNA, human ; MIRN1323 microRNA, human ; MIRN1826 microRNA, human ; MIRN218 microRNA, human ; MIRN340 microRNA, human ; MIRN410 microRNA, human ; MIRN587 microRNA, human ; MIRN599 microRNA, human ; MIRN602 microRNA, human ; MIRN610 microRNA, human ; MIRN758 microRNA, human ; microRNA761 microRNA, human
Language	English
Publishing date	2024-03-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1440127-7
ISSN	1875-8908 ; 1387-2877
ISSN (online)	1875-8908
ISSN	1387-2877
DOI	10.3233/JAD-230966
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Article ; Online: The Traces of Dysregulated lncRNAs-Associated ceRNA Axes in Retinoblastoma: A Systematic Scope Review.

Shahraki, Kourosh / Najafi, Amin / Ilkhani Pak, Vida / Shahraki, Kianoush / Ghasemi Boroumand, Paria / Sheervalilou, Roghayeh

Current eye research

2024 , Page(s) 1–14

Abstract: Purpose: Long non-coding RNAs are an essential component of competing endogenous RNA regulatory axes and play their role by sponging microRNAs and interfering with the regulation of gene expression. Because of the broadness of competing endogenous RNA ... ...

Abstract	Purpose: Long non-coding RNAs are an essential component of competing endogenous RNA regulatory axes and play their role by sponging microRNAs and interfering with the regulation of gene expression. Because of the broadness of competing endogenous RNA interaction networks, they may help investigate treatment targets in complicated disorders. Methods: This study performed a systematic scoping review to assess verified loops of competing endogenous RNAs in retinoblastoma, emphasizing the competing endogenous RNAs axis related to long non-coding RNAs. We used a six-stage approach framework and the PRISMA guidelines. A systematic search of seven databases was done to locate suitable papers published before February 2022. Two reviewers worked independently to screen articles and collect data. Results: Out of 363 records, fifty-one articles met the inclusion criteria, and sixty-three axes were identified in desired articles. The majority of the research reported several long non-coding RNAs that were experimentally verified to act as competing endogenous RNAs in retinoblastoma: XIST/NEAT1/MALAT1/SNHG16/KCNQ1OT1, respectively. At the same time, around half of the studies investigated unique long non-coding RNAs. Conclusions: Understanding the many features of this regulatory system may aid in elucidating the unknown etiology of Retinoblastoma and providing novel molecular targets for therapeutic and clinical applications.
Language	English
Publishing date	2024-02-01
Publishing country	England
Document type	Journal Article
ZDB-ID	82079-9
ISSN	1460-2202 ; 0271-3683
ISSN (online)	1460-2202
ISSN	0271-3683
DOI	10.1080/02713683.2024.2306859
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Article ; Online: Promotor methylation in ocular surface squamous neoplasia development: epigenetics implications in molecular diagnosis.

Shahraki, Kourosh / Shahraki, Kianoush / Ghasemi Boroumand, Paria / Sheervalilou, Roghayeh

Expert review of molecular diagnostics

2023 Volume 23, Issue 9, Page(s) 753–769

Abstract: Introduction: Cancer is heavily influenced by epigenetic mechanisms that include DNA methylation, histone modifications, and non-coding RNA. A considerable proportion of human malignancies are believed to be associated with global DNA hypomethylation, ... ...

Abstract	Introduction: Cancer is heavily influenced by epigenetic mechanisms that include DNA methylation, histone modifications, and non-coding RNA. A considerable proportion of human malignancies are believed to be associated with global DNA hypomethylation, with localized hypermethylation at promoters of certain genes. Area covered: The present review aims to emphasize on recent investigations on the epigenetic landscape of ocular surface squamous neoplasia, that could be targeted/explored using novel approaches such as personalized medicine. Expert opinion: While the former is thought to contribute to genomic instability, promoter-specific hypermethylation might facilitate tumorigenesis by silencing tumor suppressor genes. Ocular surface squamous neoplasia, the most prevalent type of ocular surface malignancy, is suggested to be affected by epigenetic mechanisms, as well. Although the exact role of epigenetics in ocular surface squamous neoplasia has mostly been unexplored, recent findings have greatly contributed to our understanding regarding this pathology of the eye.
MeSH term(s)	Humans ; Epigenesis, Genetic ; DNA Methylation ; Eye Neoplasms/diagnosis ; Eye Neoplasms/genetics ; Eye Neoplasms/pathology ; Carcinogenesis ; Carcinoma, Squamous Cell/diagnosis ; Carcinoma, Squamous Cell/genetics
Language	English
Publishing date	2023-08-07
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2112530-2
ISSN	1744-8352 ; 1473-7159
ISSN (online)	1744-8352
ISSN	1473-7159
DOI	10.1080/14737159.2023.2240238
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Article ; Online: Identification of differentially expressed genes associated with the pathogenesis of gastric cancer by bioinformatics analysis.

Abdolahi, Fatemeh / Shahraki, Ali / Sheervalilou, Roghayeh / Mortazavi, Sedigheh Sadat

BMC medical genomics

2023 Volume 16, Issue 1, Page(s) 311

Abstract: Aim: Gastric cancer (GC) is one of the most diagnosed cancers worldwide. GC is a heterogeneous disease whose pathogenesis has not been entirely understood. Besides, the GC prognosis for patients remains poor. Hence, finding reliable biomarkers and ... ...

Abstract	Aim: Gastric cancer (GC) is one of the most diagnosed cancers worldwide. GC is a heterogeneous disease whose pathogenesis has not been entirely understood. Besides, the GC prognosis for patients remains poor. Hence, finding reliable biomarkers and therapeutic targets for GC patients is urgently needed. Methods: GSE54129 and GSE26942 datasets were downloaded from Gene Expression Omnibus (GEO) database to detect differentially expressed genes (DEGs). Then, gene set enrichment analyses and protein-protein interactions were investigated. Afterward, ten hub genes were identified from the constructed network of DEGs. Then, the expression of hub genes in GC was validated. Performing survival analysis, the prognostic value of each hub gene in GC samples was investigated. Finally, the databases were used to predict microRNAs that could regulate the hub genes. Eventually, top miRNAs with more interactions with the list of hub genes were introduced. Results: In total, 203 overlapping DEGs were identified between both datasets. The main enriched KEGG pathway was "Protein digestion and absorption." The most significant identified GO terms included "primary alcohol metabolic process," "basal part of cell," and "extracellular matrix structural constituent conferring tensile strength." Identified hub modules were COL1A1, COL1A2, TIMP1, SPP1, COL5A2, THBS2, COL4A1, MUC6, CXCL8, and BGN. The overexpression of seven hub genes was associated with overall survival. Moreover, among the list of selected miRNAs, hsa-miR-27a-3, hsa-miR-941, hsa-miR-129-2-3p, and hsa-miR-1-3p, were introduced as top miRNAs targeting more than five hub genes. Conclusions: The present study identified ten genes associated with GC, which may help discover novel prognostic and diagnostic biomarkers as well as therapeutic targets for GC. Our results may advance the understanding of GC occurrence and progression.
MeSH term(s)	Humans ; Gene Expression Profiling/methods ; Stomach Neoplasms/genetics ; Stomach Neoplasms/pathology ; MicroRNAs/genetics ; Computational Biology/methods ; Biomarkers
Chemical Substances	Collagen Type I, alpha2 Subunit ; MicroRNAs ; Biomarkers ; Mirn129 microRNA, human
Language	English
Publishing date	2023-12-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2411865-5
ISSN	1755-8794 ; 1755-8794
ISSN (online)	1755-8794
ISSN	1755-8794
DOI	10.1186/s12920-023-01720-7
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Article ; Online: Identification of differentially expressed genes associated with the pathogenesis of gastric cancer by bioinformatics analysis

Fatemeh Abdolahi / Ali Shahraki / Roghayeh Sheervalilou / Sedigheh Sadat Mortazavi

BMC Medical Genomics, Vol 16, Iss 1, Pp 1-

2023 Volume 15

Abstract: Abstract Aim Gastric cancer (GC) is one of the most diagnosed cancers worldwide. GC is a heterogeneous disease whose pathogenesis has not been entirely understood. Besides, the GC prognosis for patients remains poor. Hence, finding reliable biomarkers ... ...

Abstract	Abstract Aim Gastric cancer (GC) is one of the most diagnosed cancers worldwide. GC is a heterogeneous disease whose pathogenesis has not been entirely understood. Besides, the GC prognosis for patients remains poor. Hence, finding reliable biomarkers and therapeutic targets for GC patients is urgently needed. Methods GSE54129 and GSE26942 datasets were downloaded from Gene Expression Omnibus (GEO) database to detect differentially expressed genes (DEGs). Then, gene set enrichment analyses and protein-protein interactions were investigated. Afterward, ten hub genes were identified from the constructed network of DEGs. Then, the expression of hub genes in GC was validated. Performing survival analysis, the prognostic value of each hub gene in GC samples was investigated. Finally, the databases were used to predict microRNAs that could regulate the hub genes. Eventually, top miRNAs with more interactions with the list of hub genes were introduced. Results In total, 203 overlapping DEGs were identified between both datasets. The main enriched KEGG pathway was “Protein digestion and absorption.” The most significant identified GO terms included “primary alcohol metabolic process,” “basal part of cell,” and “extracellular matrix structural constituent conferring tensile strength.” Identified hub modules were COL1A1, COL1A2, TIMP1, SPP1, COL5A2, THBS2, COL4A1, MUC6, CXCL8, and BGN. The overexpression of seven hub genes was associated with overall survival. Moreover, among the list of selected miRNAs, hsa-miR-27a-3, hsa-miR-941, hsa-miR-129-2-3p, and hsa-miR-1-3p, were introduced as top miRNAs targeting more than five hub genes. Conclusions The present study identified ten genes associated with GC, which may help discover novel prognostic and diagnostic biomarkers as well as therapeutic targets for GC. Our results may advance the understanding of GC occurrence and progression.
Keywords	Differentially expressed genes (DEGs) ; Gastric cancer (GC) ; Bioinformatics ; microRNA ; Biomarkers ; Internal medicine ; RC31-1245 ; Genetics ; QH426-470
Language	English
Publishing date	2023-12-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Recent advances in iron oxide nanoparticles for brain cancer theranostics: from

Sheervalilou, Roghayeh / Shirvaliloo, Milad / Sargazi, Saman / Ghaznavi, Habib

Expert opinion on drug delivery

2021 Volume 18, Issue 7, Page(s) 949–977

Abstract: ... ...

Abstract	Introduction
MeSH term(s)	Brain Neoplasms/diagnostic imaging ; Brain Neoplasms/drug therapy ; Ferric Compounds ; Humans ; Magnetic Iron Oxide Nanoparticles ; Magnetic Resonance Imaging ; Magnetite Nanoparticles ; Nanoparticles ; Precision Medicine
Chemical Substances	Ferric Compounds ; Magnetite Nanoparticles
Language	English
Publishing date	2021-04-01
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2167286-6
ISSN	1744-7593 ; 1742-5247
ISSN (online)	1744-7593
ISSN	1742-5247
DOI	10.1080/17425247.2021.1888926
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Article ; Online: The recent development of carbon-based nanoparticles as a novel approach to skin tissue care and management - A review.

Hajishoreh, Negar Karimi / Jamalpoor, Zahra / Rasouli, Ramin / Asl, Amir Nezami / Sheervalilou, Roghayeh / Akbarzadeh, Abolfazl

Experimental cell research

2023 Volume 433, Issue 2, Page(s) 113821

Abstract: Since the skin is the first barrier of the body's defense against pathogens, delays in the healing process are affected by infections. Therefore, applying advanced substitute assistance improves the patient's quality of life. Carbon-based nanomaterials ... ...

Abstract	Since the skin is the first barrier of the body's defense against pathogens, delays in the healing process are affected by infections. Therefore, applying advanced substitute assistance improves the patient's quality of life. Carbon-based nanomaterials show better capabilities than conventional methods for managing skin wound infections. Due to their physicochemical properties such as small size, large surface area, great surface-to-volume ratio, and excellent ability to communicate with the cells and tissue, carbon-based nanoparticles have been considered in regenerative medicine. moreover, the carbon nano family offers attractive potential in wound healing via the improvement of angiogenesis and antibacterial compared to traditional approaches become one of the particular research interests in the field of skin tissue engineering. This review emphasizes the wound-healing process and the role of carbon-based nanoparticles in wound care management interaction with tissue engineering technology.
MeSH term(s)	Humans ; Quality of Life ; Skin ; Wound Healing ; Tissue Engineering/methods ; Nanoparticles/therapeutic use ; Nanoparticles/chemistry
Language	English
Publishing date	2023-10-17
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1493-x
ISSN	1090-2422 ; 0014-4827
ISSN (online)	1090-2422
ISSN	0014-4827
DOI	10.1016/j.yexcr.2023.113821
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Article ; Online: Non-coding RNA-mediated epigenetic alterations in Grave's ophthalmopathy: A scoping systematic review.

Shahraki, Kourosh / Pak, Vida Ilkhani / Najafi, Amin / Shahraki, Kianoush / Boroumand, Paria Ghasemi / Sheervalilou, Roghayeh

Non-coding RNA research

2023 Volume 8, Issue 3, Page(s) 426–450

Abstract: Background: It is becoming more and more apparent that Grave's Ophthalmopathy (GO) pathogenesis may be aided by epigenetic processes such as DNA methylation modifications, histone tail covalent modifications, and non-coding RNA (ncRNA)-based epigenetic ... ...

Abstract	Background: It is becoming more and more apparent that Grave's Ophthalmopathy (GO) pathogenesis may be aided by epigenetic processes such as DNA methylation modifications, histone tail covalent modifications, and non-coding RNA (ncRNA)-based epigenetic processes. In the present study, we aimed to focus more on the miRNAs rather than lncRNAs due to lack of investigations on these non-coding RNAs and their role in GO's pathogenesis. Methods: A six-stage methodology framework and the PRISMA recommendation were used to conduct this scoping review. A comprehensive search was conducted across seven databases to discover relevant papers published until February 2022. The data extraction separately, and quantitative and qualitative analyses were conducted. Results: A total of 20 articles were found to meet inclusion criteria. According to the results, ncRNA were involved in the regulation of inflammation (miR-146a, LPAL2/miR-1287-5p axis, LINC01820:13/hsa miR-27b-3p axis, and ENST00000499452/hsa-miR-27a-3p axis), regulation of T cell functions (miR-146a/miR-183/miR-96), regulation of glycosaminoglycan aggregation and fibrosis (miR-146a/miR-21), glucocorticoid sensitivity (miR-224-5p), lipid accumulation and adipogenesis (miR-27a/miR-27b/miR-130a), oxidative stress and angiogenesis (miR-199a), and orbital fibroblast proliferation (miR-21/miR-146a/miR-155). Eleven miRNAs (miR-146a/miR-224-5p/miR-Let7d-5p/miR-96-5p/miR-301a-3p/miR-21-5p) were also indicated to have the capacity to be used as biomarkers. Conclusions: Regardless of the fact that there is significant documentation of ncRNA-mediated epigenetic dysfunction in GO, additional study is needed to thoroughly comprehend the epigenetic connections concerned in disease pathogenesis, paving the way for novel diagnostic and prognostic tools for epigenetic therapies among the patients.
Language	English
Publishing date	2023-05-16
Publishing country	Netherlands
Document type	Journal Article
ISSN	2468-0540
ISSN (online)	2468-0540
DOI	10.1016/j.ncrna.2023.04.001
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Article ; Online: WITHDRAWN: In silico and Experimental Analysis of miR-125b-5 and miR-485-5p Expression in Serum of Patients with Breast Cancer

Bahmanpour, Zahra / Sheervalilou, Roghayeh / Khaniani, Mahmoud Shekari / Poursheikhani, Arash / Montazeri, Vahid / Tahmasebivand, Mahsa / Derakhshan, Sima Mansoori

MicroRNA (Shariqah, United Arab Emirates)

2022

Language	English
Publishing date	2022-05-23
Publishing country	United Arab Emirates
Document type	Journal Article
ISSN	2211-5374
ISSN (online)	2211-5374
DOI	10.2174/2211536611666220523100057
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Article ; Online: Diagnostic accuracy of clinically applied nanoparticle-based biosensors at detecting SARS-CoV-2 RNA and surface proteins in pharyngeal swabs compared to RT-PCR as a reference test.

Shirvaliloo, Milad / Sheervalilou, Roghayeh / Ahmadpour, Ehsan / Safiri, Saeid / Bannazadeh Baghi, Hossein

Expert review of molecular diagnostics

2022 Volume 22, Issue 9, Page(s) 881–894

Abstract: Introduction: Nanoparticle-based biosensors (NPBs) are point-of-care diagnostic platforms that can be used for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high accuracy.: Areas covered: EBSCOhost Web, Embase, ... ...

Abstract	Introduction: Nanoparticle-based biosensors (NPBs) are point-of-care diagnostic platforms that can be used for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with high accuracy. Areas covered: EBSCOhost Web, Embase, ProQuest, PubMed/MEDLINE, Scopus, Web of Science, and WHO Global Literature on Coronavirus Disease 2019 (COVID-19) were searched for relevant records published from 1 November 2019 to 30 April 2022. Records reporting original data on the accuracy of clinically applied nanoparticle-based biosensors at detecting SARS-CoV-2 RNA and surface proteins from pharyngeal swab specimens were considered. Findings were reported based on the PRISMA 2020 statement. The QUADAS-2 tool was used for assessment of quality and risk of bias among the included studies. Expert opinion: A total of 50 relevant records were identified, of which 13 were included. The included studies explored the diagnostic performance of 13 clinically applied distinct nanoparticle-based biosensors in a total of 789 pharyngeal swabs collected from 376 COVID-19 patients and 413 otherwise healthy individuals. The mean sensitivity, specificity, and accuracy were 97.07%, 94.43%, and 96.91%, respectively, in comparison to RT-qPCR as the reference test. Considering their ease-of-operation, portability, low-cost manufacturing, NPBs could be considered suitable candidate diagnostic platforms for substituting RT-qPCR.
MeSH term(s)	Humans ; SARS-CoV-2/genetics ; Reverse Transcriptase Polymerase Chain Reaction ; COVID-19/diagnosis ; RNA, Viral/genetics ; COVID-19 Testing ; Membrane Proteins/genetics ; Sensitivity and Specificity ; Biosensing Techniques ; Nanoparticles
Chemical Substances	RNA, Viral ; Membrane Proteins
Language	English
Publishing date	2022-10-19
Publishing country	England
Document type	Systematic Review
ZDB-ID	2112530-2
ISSN	1744-8352 ; 1473-7159
ISSN (online)	1744-8352
ISSN	1473-7159
DOI	10.1080/14737159.2022.2135434
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