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Article ; Online: Investigating neural differentiation of mouse P19 embryonic stem cells in a time-dependent manner by bioinformatic, microscopic and transcriptional analyses

Moazeny, Marzieh / Dehbashi, Moein / Hojati, Zohreh / Esmaeili, Fariba

Mol Biol Rep. 2023 Mar., v. 50, no. 3 p.2183-2194

2023

Abstract: BACKGROUND: As an available cell line, mouse pluripotent P19 has been widely employed for neuronal differentiation studies. In this research, by applying the in vitro differentiation of this cell line into neuron-like cells through retinoic acid (RA) ... ...

Abstract	BACKGROUND: As an available cell line, mouse pluripotent P19 has been widely employed for neuronal differentiation studies. In this research, by applying the in vitro differentiation of this cell line into neuron-like cells through retinoic acid (RA) treatment, the roles of some genes including DNMT3B, ICAM1, IRX3, JAK2, LHX1, SOX9, TBX3 and THY1 in neural differentiation was investigated. METHODS AND RESULTS: Bioinformatics, microscopic, and transcriptional studies were conducted in a time-dependent manner after RA-induced neural differentiation. According to bioinformatics studies, we determined the engagement of the metabolic and developmental super-pathways and pathways in neural cell differentiation, particularly focusing on the considered genes. According to our qRT-PCR analyses, JAK2, SOX9, TBX3, LHX1 and IRX3 genes were found to be significantly overexpressed in a time-dependent manner (p < 0.05). In addition, the significant downregulation of THY1, DNMT3B and ICAM1 genes was observed during the experiment (p < 0.05). The optical microscopic investigation showed that the specialized extensions of the neuron-like cells were revealed on day 8 after RA treatment. CONCLUSION: Accordingly, the neural differentiation of P19 cell line and the role of the considered genes during the differentiation were proved. However, our results warrant further in vivo studies.
Keywords	bioinformatics ; cell differentiation ; cell lines ; intercellular adhesion molecule-1 ; mice ; neurons ; retinoic acid ; transcription (genetics)
Language	English
Dates of publication	2023-03
Size	p. 2183-2194.
Publishing place	Springer Netherlands
Document type	Article ; Online
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-022-08166-7
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Article ; Online: Investigating neural differentiation of mouse P19 embryonic stem cells in a time-dependent manner by bioinformatic, microscopic and transcriptional analyses.

Moazeny, Marzieh / Dehbashi, Moein / Hojati, Zohreh / Esmaeili, Fariba

Molecular biology reports

2022 Volume 50, Issue 3, Page(s) 2183–2194

Abstract: Background: As an available cell line, mouse pluripotent P19 has been widely employed for neuronal differentiation studies. In this research, by applying the in vitro differentiation of this cell line into neuron-like cells through retinoic acid (RA) ... ...

Abstract	Background: As an available cell line, mouse pluripotent P19 has been widely employed for neuronal differentiation studies. In this research, by applying the in vitro differentiation of this cell line into neuron-like cells through retinoic acid (RA) treatment, the roles of some genes including DNMT3B, ICAM1, IRX3, JAK2, LHX1, SOX9, TBX3 and THY1 in neural differentiation was investigated. Methods and results: Bioinformatics, microscopic, and transcriptional studies were conducted in a time-dependent manner after RA-induced neural differentiation. According to bioinformatics studies, we determined the engagement of the metabolic and developmental super-pathways and pathways in neural cell differentiation, particularly focusing on the considered genes. According to our qRT-PCR analyses, JAK2, SOX9, TBX3, LHX1 and IRX3 genes were found to be significantly overexpressed in a time-dependent manner (p < 0.05). In addition, the significant downregulation of THY1, DNMT3B and ICAM1 genes was observed during the experiment (p < 0.05). The optical microscopic investigation showed that the specialized extensions of the neuron-like cells were revealed on day 8 after RA treatment. Conclusion: Accordingly, the neural differentiation of P19 cell line and the role of the considered genes during the differentiation were proved. However, our results warrant further in vivo studies.
MeSH term(s)	Animals ; Mice ; Cell Differentiation ; Tretinoin/pharmacology ; Neurons/metabolism ; Cell Line ; Embryonic Stem Cells/metabolism
Chemical Substances	Tretinoin (5688UTC01R)
Language	English
Publishing date	2022-12-24
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-022-08166-7
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Article: Identification of Circulating

Heydari, Maryam / Hojati, Zohreh / Dehbashi, Moein

Cell journal

2021 Volume 23, Issue 2, Page(s) 211–217

Abstract: Objective: Alzheimer's disease (AD) is a type of dementia. Currently, there are not any existing and reliable methods for the prognosis or diagnosis of AD. Hence, finding a diagnostic/prognostic biomarker for AD helps physicians to prescribe the ... ...

Abstract	Objective: Alzheimer's disease (AD) is a type of dementia. Currently, there are not any existing and reliable methods for the prognosis or diagnosis of AD. Hence, finding a diagnostic/prognostic biomarker for AD helps physicians to prescribe the treatments and methods preventing disease progression. Circulating microRNAs (miRNAs) are the most promising biomarkers due to their non-invasive and easily accessible for diagnosis and prognosis of AD. The aim of current study is to evaluate expression levels of two unwell-known circulating miRNAs including Materials and methods: In this case and control study, to get the gene targets related to these two miRNAs, TargetScan, miRTargetLink Human and mirDIP web servers were applied. In addition, gene networks and gene ontology enrichment analysis were performed by STRING 10.5, KEGG and ShinyGO v0.41. Experimentally, expression levels of these two miRNAs in the serum of 21 patients with AD and 23 healthy individuals were compared using the quantitative reverse transcription polymerase chain reaction (qRT-PCR) method. Results: The pathophysiological pathways associated with these two miRNAs were nucleotide metabolism and cellular response to stress pathway. Furthermore, the upregulated expression levels of Conclusion: Non-significant results were obtained from the expression levels of AD patients and two significant pathways were obtained by networks and gene enrichment analysis.
Language	English
Publishing date	2021-05-26
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2647430-X
ISSN	2228-5814 ; 2228-5806
ISSN (online)	2228-5814
ISSN	2228-5806
DOI	10.22074/cellj.2021.7047
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Article ; Online: MiR-373 Suppresses Cell Proliferation And Apoptosis Via Regulation Of SIRT1/PGC-1α/NRF2 Axis In Pancreatic Cancer

Maryam Heydari / Zohreh Hojati / Moein Dehbashi

Cell Journal, Vol 23, Iss 2, Pp 211-

2021 Volume 217

Abstract: Objective: Alzheimer’s disease (AD) is a type of dementia. Currently, there are not any existing and reliable methods for the prognosis or diagnosis of AD. Hence, finding a diagnostic/prognostic biomarker for AD helps physicians to prescribe the ... ...

Abstract	Objective: Alzheimer’s disease (AD) is a type of dementia. Currently, there are not any existing and reliable methods for the prognosis or diagnosis of AD. Hence, finding a diagnostic/prognostic biomarker for AD helps physicians to prescribe the treatments and methods preventing disease progression. Circulating microRNAs (miRNAs) are the most promising biomarkers due to their non-invasive and easily accessible for diagnosis and prognosis of AD. The aim of current study is to evaluate expression levels of two unwell-known circulating miRNAs including hsa-miR-324-3p and hsa-miR-331-3p in serums of AD patients and to understand their roles in AD physiopathogenesis by in silico analysis. Materials and Methods: In this case and control study, to get the gene targets related to these two miRNAs, TargetScan, miRTargetLink Human and mirDIP web servers were applied. In addition, gene networks and gene ontology enrichment analysis were performed by STRING 10.5, KEGG and ShinyGO v0.41. Experimentally, expression levels of these two miRNAs in the serum of 21 patients with AD and 23 healthy individuals were compared using the quantitative reverse transcription polymerase chain reaction (qRT-PCR) method. Results: The pathophysiological pathways associated with these two miRNAs were nucleotide metabolism and cellular response to stress pathway. Furthermore, the upregulated expression levels of hsa-miR-324-3p and hsa-miR-331-3p in comparison with the healthy control serums were not statistically significant (P>0.05). Conclusion: Non-significant results were obtained from the expression levels of AD patients and two significant pathways were obtained by networks and gene enrichment analysis.
Keywords	alzheimer’s disease ; micrornas ; quantitative reverse transcription polymerase chain reaction ; serum ; Medicine ; R ; Science ; Q
Subject code	610
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Royan Institute (ACECR), Tehran
Document type	Article ; Online
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Article ; Online: The Highlighted Roles of Metabolic and Cellular Response to Stress Pathways Engaged in Circulating hsa-miR-494-3p and hsa-miR-661 in Alzheimer's Disease.

Hojati, Zohreh / Omidi, Farzaneh / Dehbashi, Moein / Mohammad Soltani, Bahram

Iranian biomedical journal

2020 Volume 25, Issue 1, Page(s) 62–67

MeSH term(s)	Alzheimer Disease/blood ; Alzheimer Disease/genetics ; Area Under Curve ; Biomarkers/blood ; Case-Control Studies ; Computer Simulation ; Down-Regulation ; Gene Ontology ; Gene Regulatory Networks ; Humans ; MicroRNAs/blood ; MicroRNAs/genetics ; ROC Curve ; Signal Transduction/genetics ; Stress, Physiological/genetics
Chemical Substances	Biomarkers ; MIRN494 microRNA, human ; MIRN661 microRNA, human ; MicroRNAs
Language	English
Publishing date	2020-08-31
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2489282-8
ISSN	2008-823X ; 1028-852X
ISSN (online)	2008-823X
ISSN	1028-852X
DOI	10.29252/ibj.25.1.62
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Article ; Online: Association of xenobiotic-metabolizing genes polymorphisms with cervical cancer risk in the Tunisian population

Helaoui, Ahlem / Sfar, Sana / Boudhiba, Najet / Dehghanian, Fariba / Dehbashi, Moein / Bouchahda, Haifa / Hojati, Zohreh / Kenani, Abderraouf

Mol Biol Rep. 2023 Feb., v. 50, no. 2 p.949-959

2023

Abstract: BACKGROUND: Host genetic characteristics and environmental factors interactions may play a crucial role in cervical carcinogenesis. We investigated the impact of functional genetic variants of four xenobiotic-metabolizing genes (AhR, CYP1A1, GSTM1, and ... ...

Abstract	BACKGROUND: Host genetic characteristics and environmental factors interactions may play a crucial role in cervical carcinogenesis. We investigated the impact of functional genetic variants of four xenobiotic-metabolizing genes (AhR, CYP1A1, GSTM1, and GSTT1) on cervical cancer development in Tunisian women. METHODS: The AhR gene polymorphism was analyzed using the tetra-primer ARMS-PCR, whereas the CYP1A1 polymorphism genotypes were identified by PCR-RFLP. A multiplex ligation-dependent polymerase chain reaction approach was applied for the analysis of GSTM1 and GSTT1 polymorphisms. RESULTS: The homozygous A/A genotype of the AhR gene (rs2066853) and the heterozygous T/C genotype of the CYP1A1 SNP (CYP1A1-MspI) appeared to be associated with an increased risk of cervical tumorigenesis (ORᵃ = 2.81; ORᵃ = 5.52, respectively). Furthermore, a significantly increased risk of cervical cancer was associated with the GSTT1 null genotype (ORᵃ = 2.65). However, the null GSTM1 genotype showed any significant association with the risk of cervical cancer compared to the wild genotype (ORᵃ = 1.18; p = 0.784). Considering the combined effect, we noted a significantly higher association with cancer risk for individuals with at least two high-risk genotypes of CYP1A1/GSTT1 (ORᵃ = 4.2), individuals with at least two high-risk genotypes of CYP1A1/GSTT1/AhR (ORᵃ = 11.3) and individuals with at least two high-risk genotypes of CYP1A1/GSTM1/GSTT1/AhR exploitation low-risk genotype as a reference. CONCLUSION: This study indicated that the single-gene contribution and the combined effect of xenobiotic-metabolizing gene polymorphisms (AhR, CYP1A1-MspI, GSTM1, and GSTT1) may have a considerable association with increased cervical cancer risk.
Keywords	carcinogenesis ; genes ; genetic polymorphism ; heterozygosity ; homozygosity ; polymerase chain reaction ; risk ; uterine cervical neoplasms
Language	English
Dates of publication	2023-02
Size	p. 949-959.
Publishing place	Springer Netherlands
Document type	Article ; Online
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-022-07945-6
Database	NAL-Catalogue (AGRICOLA)

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Article: Designing and generating a single-chain fragment variable (scFv) antibody against IL2Rα (CD25): An

Navabi, Parnian / Ganjalikhany, Mohamad Reza / Jafari, Sepideh / Dehbashi, Moein / Ganjalikhani-Hakemi, Mazdak

Iranian journal of basic medical sciences

2021 Volume 24, Issue 3, Page(s) 360–368

Abstract: Objectives: IL-2Rα plays a critical role in maintaining immune function. However, expression and secretion of CD25 in various malignant disorders and autoimmune diseases are now well established. Thus, CD25 is considered an important target candidate ... ...

Abstract	Objectives: IL-2Rα plays a critical role in maintaining immune function. However, expression and secretion of CD25 in various malignant disorders and autoimmune diseases are now well established. Thus, CD25 is considered an important target candidate for antibody-based therapy. This study aimed to find the most suitable linker peptide to construct a functional anti-CD25 single-chain fragment variable (scFv) by bioinformatics studies and its production in a bacterial expression system. Materials and methods: Here, the 3D structures of the scFvs with different linkers were predicted and molecular dynamics simulation was performed to compare their structures and dynamics. Then, interactions between five models of scFv and human CD25 were calculated via molecular docking. According to MD and docking results, the anti-CD25 scFvs with (Gly4Ser)3 linker were constructed and cloned into pET-22b(+). Then, recombinant plasmids were transformed into Results: In silico Conclusion: Conclusively, our work provides a theoretical and experimental basis for production of an anti-CD25 scFv, which may be applied for various malignant disorders and autoimmune diseases.
Language	English
Publishing date	2021-04-08
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2500485-2
ISSN	2008-3874 ; 2008-3866
ISSN (online)	2008-3874
ISSN	2008-3866
DOI	10.22038/ijbms.2021.51709.11728
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Article ; Online: ‌RNA secondary structure and qRT-PCR analyses pertained to expressed anti-CD25 CAR in NK-92 cell line

Moein Dehbashi / Zohreh Hojati / Majid Motovali-bashi / Mazdak Ganjalikhani-Hakemi

Majallah-i Dānishgāh-i ̒Ulūm-i Pizishkī-i Qum, Vol 14, Iss 2, Pp 1-

2020 Volume 12

Abstract: Background and Objectives: Tumor-infiltrating regulatory T (TI-Treg) cells perform the significant function in cancer immune escape. In this study, the third generation CAR construct was designed against human CD25 antigen, the significant cell surface ... ...

Abstract	Background and Objectives: Tumor-infiltrating regulatory T (TI-Treg) cells perform the significant function in cancer immune escape. In this study, the third generation CAR construct was designed against human CD25 antigen, the significant cell surface biomarker of TI-Tregs. Methods: Initially, the construct of anti-CD25 CAR was designed. Using RNAfold web server, the RNA secondary structure was evaluated. Also, utilizing lentiviral vectors, NK-92 cell line was transduced. Afterward, the expression level of anti-CD25 CAR RNA was assessed by qRT-PCR in NK-92 cells transduced with CAR and mock transfer vectors and also untreated cells. Results: The RNA secondary structure was stable. Also, the expression level of anti-CD25 CAR RNA in transduced NK-92 cells by pCDH-513B-1-anti-CD25 CAR transfer vector was significantly higher than transduced NK-92 cells by mock transfer vector and untreated cells (p˂0.0001). Conclusion: The present study on anti-CD25 CAR RNA showed that this type of CAR transcripts were stable and expressed at high level. In fact, this type of CAR can be further studied in the future as a tool to remove the cancer immune escape in all types of solid and liquid cancers.
Keywords	bioinformatic ; qrt-pcr ; anti-cd25 car ; transduction ; cancer immune escape ; Medicine (General) ; R5-920
Subject code	616
Language	Persian
Publishing date	2020-05-01T00:00:00Z
Publisher	Qom University of Medical Sciences
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Association of xenobiotic-metabolizing genes polymorphisms with cervical cancer risk in the Tunisian population.

Helaoui, Ahlem / Sfar, Sana / Boudhiba, Najet / Dehghanian, Fariba / Dehbashi, Moein / Bouchahda, Haifa / Hojati, Zohreh / Kenani, Abderraouf

Molecular biology reports

2022 Volume 50, Issue 2, Page(s) 949–959

Abstract: Background: Host genetic characteristics and environmental factors interactions may play a crucial role in cervical carcinogenesis. We investigated the impact of functional genetic variants of four xenobiotic-metabolizing genes (AhR, CYP1A1, GSTM1, and ... ...

Abstract	Background: Host genetic characteristics and environmental factors interactions may play a crucial role in cervical carcinogenesis. We investigated the impact of functional genetic variants of four xenobiotic-metabolizing genes (AhR, CYP1A1, GSTM1, and GSTT1) on cervical cancer development in Tunisian women. Methods: The AhR gene polymorphism was analyzed using the tetra-primer ARMS-PCR, whereas the CYP1A1 polymorphism genotypes were identified by PCR-RFLP. A multiplex ligation-dependent polymerase chain reaction approach was applied for the analysis of GSTM1 and GSTT1 polymorphisms. Results: The homozygous A/A genotype of the AhR gene (rs2066853) and the heterozygous T/C genotype of the CYP1A1 SNP (CYP1A1-MspI) appeared to be associated with an increased risk of cervical tumorigenesis (OR Conclusion: This study indicated that the single-gene contribution and the combined effect of xenobiotic-metabolizing gene polymorphisms (AhR, CYP1A1-MspI, GSTM1, and GSTT1) may have a considerable association with increased cervical cancer risk.
MeSH term(s)	Humans ; Female ; Cytochrome P-450 CYP1A1/genetics ; Uterine Cervical Neoplasms/genetics ; Xenobiotics ; Polymorphism, Genetic ; Glutathione Transferase/genetics ; Genotype ; Genetic Predisposition to Disease ; Risk Factors ; Case-Control Studies
Chemical Substances	Cytochrome P-450 CYP1A1 (EC 1.14.14.1) ; Xenobiotics ; Glutathione Transferase (EC 2.5.1.18)
Language	English
Publishing date	2022-11-14
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	186544-4
ISSN	1573-4978 ; 0301-4851
ISSN (online)	1573-4978
ISSN	0301-4851
DOI	10.1007/s11033-022-07945-6
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Designing and generating a single-chain fragment variable (scFv) antibody against IL2Rα (CD25)

Parnian Navabi / Mohamad Reza Ganjalikhany / Sepideh Jafari / Moein Dehbashi / Mazdak Ganjalikhani-Hakemi

Iranian Journal of Basic Medical Sciences, Vol 24, Iss 3, Pp 360-

An in silico and in vitro study

2021 Volume 368

Abstract: Objective(s): IL-2Rα plays a critical role in maintaining immune function. However, expression and secretion of CD25 in various malignant disorders and autoimmune diseases are now well established. Thus, CD25 is considered an important target candidate ... ...

Abstract	Objective(s): IL-2Rα plays a critical role in maintaining immune function. However, expression and secretion of CD25 in various malignant disorders and autoimmune diseases are now well established. Thus, CD25 is considered an important target candidate for antibody-based therapy. This study aimed to find the most suitable linker peptide to construct a functional anti-CD25 single-chain fragment variable (scFv) by bioinformatics studies and its production in a bacterial expression system. Materials and Methods: Here, the 3D structures of the scFvs with different linkers were predicted and molecular dynamics simulation was performed to compare their structures and dynamics. Then, interactions between five models of scFv and human CD25 were calculated via molecular docking. According to MD and docking results, the anti-CD25 scFvs with (Gly4Ser)3 linker were constructed and cloned into pET-22b(+). Then, recombinant plasmids were transformed into Escherichia coli Bl21 (DE3) for expression using IPTG and lactose as inducers. Anti-CD25 scFv was purified from the periplasm and detected by SDS-PAGE and Western blot. Afterward, functionality was evaluated using ELISA.Results: In silico analysis showed that the model containing (Gly4Ser)3 as a linker has more stability compared with other linkers. The results of SDS-PAGE, Western blot, and ELISA confirmed the accuracy of anti-CD25 scFv production and its ability to bind to the human CD25. Conclusion: Conclusively, our work provides a theoretical and experimental basis for production of an anti-CD25 scFv, which may be applied for various malignant disorders and autoimmune diseases.
Keywords	cd25 daclizumab il ; 2rα protein engineering single ; chain variable fragment (scfv) ; Medicine ; R
Subject code	572
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Mashhad University of Medical Sciences
Document type	Article ; Online
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