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Article: Chimeric antigen receptor-T cells immunotherapy for targeting breast cancer.

Rahimmanesh, Ilnaz / Khanahmad, Hossein

2021 Volume 16, Issue 5, Page(s) 447–454

Abstract: Redirected chimeric antigen receptor (CAR) T-cells can recognize and eradicate cancer cells in a major histocompatibility complex independent manner. Genetic engineering of T cells through CAR expression has yielded great results in the treatment of ... ...

Abstract	Redirected chimeric antigen receptor (CAR) T-cells can recognize and eradicate cancer cells in a major histocompatibility complex independent manner. Genetic engineering of T cells through CAR expression has yielded great results in the treatment of hematological malignancies compared with solid tumors. There has been a constant effort to enhance the effectiveness of these living drugs, due to their limited success in targeting solid tumors. Poor T cell trafficking, tumor-specific antigen selection, and the immunosuppressive tumor microenvironment are considered as the main barriers in targeting solid tumors by CAR T-cells. Here, we reviewed the current state of CAR T-cell therapy in breast cancer, as the second cancer-related death in women worldwide, as well as some strategies adopted to keep the main limitations of CAR T-cells under control. Also, we summarized various approaches that have been developed to enhance the therapeutic outcomes of this treatment in solid tumors targeting.
Language	English
Publishing date	2021-08-19
Publishing country	Iran
Document type	Journal Article ; Review
ZDB-ID	2400156-9
ISSN	1735-9414 ; 1735-5362
ISSN (online)	1735-9414
ISSN	1735-5362
DOI	10.4103/1735-5362.323911
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Prospective Prediction of Treatment Response in High-Grade Glioma Patients using Pre-Treatment Tumor ADC Value and miR-222 and miR-205 Expression Levels in Plasma.

Heidari, Maryam / Amouheidari, Alireza / Hemati, Simin / Khanahmad, Hossein / Rahimmanesh, Ilnaz / Jafari, Peyman / Shokrani, Parvaneh

Journal of biomedical physics & engineering

2024 Volume 14, Issue 2, Page(s) 111–118

Abstract: Background: Treatment response in High-grade Glioma (HGG) patients changes based on their genetic and biological characteristics. MiRNAs, as important regulators of drug and radiation resistance, and the Apparent Diffusion Coefficients (ADC) value of ... ...

Abstract	Background: Treatment response in High-grade Glioma (HGG) patients changes based on their genetic and biological characteristics. MiRNAs, as important regulators of drug and radiation resistance, and the Apparent Diffusion Coefficients (ADC) value of tumor can be used as a prognostic predictor for glioma. Objective: This study aimed to identify some of the pre-treatment individual patient features for predicting the treatment response in HGG patients. Material and methods: In this prospective study, 18 HGG patients, who were candidated for chemo-radiation treatment, participated after informed consent of the patients. The investigated features were the expression level of miR-222 and miR-205 in plasma, the ADC value of tumor, Body Mass Index (BMI), and age. Treatment response was assessed, and Least Absolute Shrinkage and Selection Operator (LASSO) regression was used to obtain a model to predict the treatment response. Mann-Whitney U test was also applied to select the variables with a significant relationship with patients' treatment response. Results: The LASSO coefficients for miR-205, miR-222, tumor's mean ADC value, BMI, and age were 3.611, -1.683, 2.468, -0.184, and -0.024, respectively. Mann-Whitney U test results showed miR-205 and tumor's mean ADC significantly related to treatment response ( Conclusion: The miR-205 expression level of the patient in plasma and tumor's mean ADC value has the potential for prognostic predictors in HGG.
Language	English
Publishing date	2024-04-01
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2673599-4
ISSN	2251-7200
ISSN	2251-7200
DOI	10.31661/jbpe.v0i0.2108-1376
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Article: Conceptual Framework for SARS-CoV-2-Related Lymphopenia.

Rahimmanesh, Ilnaz / Kouhpayeh, Shirin / Azizi, Yadollah / Khanahmad, Hossein

Advanced biomedical research

2022 Volume 11, Page(s) 16

Abstract: The emerging of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak is associated with high morbidity and mortality rates globally. One of the most prominent characteristics of coronavirus disease-19 (COVID-19) is lymphopenia, which is ... ...

Abstract	The emerging of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak is associated with high morbidity and mortality rates globally. One of the most prominent characteristics of coronavirus disease-19 (COVID-19) is lymphopenia, which is in contrast to other viral infections. This controversy might be explained by the evaluation of impaired innate and adaptive immune responses, during the SARS-CoV-2 infection. During the innate immune response, poly-ADP-ribose polymerase hyperactivated due to virus entry and extensive DNA damage sequentially, leading to nicotinamide adenine dinucleotide (NAD)+ depletion, adenosine triphosphate depletion, and finally cell death. In contrast to the immune response against viral infections, cytotoxic T lymphocytes decline sharply in SARS-CoV-2 infection which might be due to infiltration and trapping in the lower respiratory tract. In addition, there are more factors proposed to involve in lymphopenia in COVID-19 infection such as the role of CD38, which functions as NADase and intensifies NAD depletion, which in turn affects NAD+-dependent Sirtuin proteins, as the regulators of cell death and viability. Lung tissue sequestration following cytokine storm supposed to be another reason for lymphopenia in COVID-19 patients. Protein 7a, as one of the virus-encoded proteins, induces apoptosis in various organ-derived cell lines. These mechanisms proposed to induce lymphopenia, although there are still more studies needed to clarify the underlying mechanisms for lymphopenia in COVID-19 patients.
Language	English
Publishing date	2022-02-28
Publishing country	India
Document type	Journal Article ; Review
ZDB-ID	2672524-1
ISSN	2277-9175
ISSN	2277-9175
DOI	10.4103/abr.abr_303_20
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Article: Identification of Significant Genes and Pathways Associated with Tenascin-C in Cancer Progression by Bioinformatics Analysis.

Rahimmanesh, Ilnaz / Fatehi, Razieh / Khanahmad, Hossein

Advanced biomedical research

2022 Volume 11, Page(s) 17

Abstract: Background: Tenascin-C (TNC) is a large glycoprotein of the extracellular matrix which associated with poor clinical outcomes in several malignancies. TNC over-expression is repeatedly observed in several cancer tissues and promotes several processes in ...

Abstract	Background: Tenascin-C (TNC) is a large glycoprotein of the extracellular matrix which associated with poor clinical outcomes in several malignancies. TNC over-expression is repeatedly observed in several cancer tissues and promotes several processes in tumor progression. Until quite recently, more needs to be known about the potential mechanisms of TNC as a key player in cancer progression and metastasis. Materials and methods: In the present study, we performed a bioinformatics analysis of breast and colorectal cancer expression microarray data to survey TNC role and function with holistic view. Gene expression profiles were analyzed to identify differentially expressed genes (DEGs) between normal samples and cancer biopsy samples. The protein-protein interaction (PPI) networks of the DEGs with CluePedia plugin of Cytoscape software were constructed. Furthermore, after PPI network construction, gene-regulatory networks analysis was performed to predict long noncoding RNAs and microRNAs associated with TNC and cluster analysis was performed. Using the Clue gene ontology (GO) plugin of Cytoscape software, the GO and pathway enrichment analysis were performed. Results: PPI and DEGs-miRNA-lncRNA regulatory networks showed TNC is a significant node in a huge network, and one of the main gene with high centrality parameters. Furthermore, from the regulatory level perspective, TNC could be significantly impressed by miR-335-5p. GO analysis results showed that TNC was significantly enriched in cancer-related biological processes. Conclusions: It is important to identify the TNC underlying molecular mechanisms in cancer progression, which may be clinically useful for tumor-targeting strategies. Bioinformatics analysis provides an insight into the significant roles that TNC plays in cancer progression scenarios.
Language	English
Publishing date	2022-02-28
Publishing country	India
Document type	Journal Article
ZDB-ID	2672524-1
ISSN	2277-9175
ISSN	2277-9175
DOI	10.4103/abr.abr_201_20
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Article ; Online: Conceptual framework for SARS-CoV-2–related lymphopenia

Ilnaz Rahimmanesh / Shirin Kouhpayeh / Yadollah Azizi / Hossein Khanahmad

Advanced Biomedical Research, Vol 11, Iss 1, Pp 16-

2022 Volume 16

Abstract	The emerging of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak is associated with high morbidity and mortality rates globally. One of the most prominent characteristics of coronavirus disease-19 (COVID-19) is lymphopenia, which is in contrast to other viral infections. This controversy might be explained by the evaluation of impaired innate and adaptive immune responses, during the SARS-CoV-2 infection. During the innate immune response, poly-ADP-ribose polymerase hyperactivated due to virus entry and extensive DNA damage sequentially, leading to nicotinamide adenine dinucleotide (NAD)+ depletion, adenosine triphosphate depletion, and finally cell death. In contrast to the immune response against viral infections, cytotoxic T lymphocytes decline sharply in SARS-CoV-2 infection which might be due to infiltration and trapping in the lower respiratory tract. In addition, there are more factors proposed to involve in lymphopenia in COVID-19 infection such as the role of CD38, which functions as NADase and intensifies NAD depletion, which in turn affects NAD+–dependent Sirtuin proteins, as the regulators of cell death and viability. Lung tissue sequestration following cytokine storm supposed to be another reason for lymphopenia in COVID-19 patients. Protein 7a, as one of the virus-encoded proteins, induces apoptosis in various organ-derived cell lines. These mechanisms proposed to induce lymphopenia, although there are still more studies needed to clarify the underlying mechanisms for lymphopenia in COVID-19 patients.
Keywords	adp-ribosyl cyclase 1 ; lymphopenia ; nad ; sars-cov-2 ; Medicine ; R ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of significant genes and pathways associated with tenascin-C in cancer progression by bioinformatics analysis

Ilnaz Rahimmanesh / Razieh Fatehi / Hossein Khanahmad

Advanced Biomedical Research, Vol 11, Iss 1, Pp 17-

2022 Volume 17

Abstract	Background: Tenascin-C (TNC) is a large glycoprotein of the extracellular matrix which associated with poor clinical outcomes in several malignancies. TNC over-expression is repeatedly observed in several cancer tissues and promotes several processes in tumor progression. Until quite recently, more needs to be known about the potential mechanisms of TNC as a key player in cancer progression and metastasis. Materials and Methods: In the present study, we performed a bioinformatics analysis of breast and colorectal cancer expression microarray data to survey TNC role and function with holistic view. Gene expression profiles were analyzed to identify differentially expressed genes (DEGs) between normal samples and cancer biopsy samples. The protein-protein interaction (PPI) networks of the DEGs with CluePedia plugin of Cytoscape software were constructed. Furthermore, after PPI network construction, gene-regulatory networks analysis was performed to predict long noncoding RNAs and microRNAs associated with TNC and cluster analysis was performed. Using the Clue gene ontology (GO) plugin of Cytoscape software, the GO and pathway enrichment analysis were performed. Results: PPI and DEGs-miRNA-lncRNA regulatory networks showed TNC is a significant node in a huge network, and one of the main gene with high centrality parameters. Furthermore, from the regulatory level perspective, TNC could be significantly impressed by miR-335-5p. GO analysis results showed that TNC was significantly enriched in cancer-related biological processes. Conclusions: It is important to identify the TNC underlying molecular mechanisms in cancer progression, which may be clinically useful for tumor-targeting strategies. Bioinformatics analysis provides an insight into the significant roles that TNC plays in cancer progression scenarios.
Keywords	gene regulatory network ; microarray analysis ; protein interaction maps ; tenascin-c ; Medicine ; R ; Biology (General) ; QH301-705.5
Subject code	570
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Wolters Kluwer Medknow Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Systems biology approaches toward autosomal dominant polycystic kidney disease (ADPKD).

Rahimmanesh, Ilnaz / Fatehi, Razieh

Clinical and translational medicine

2020 Volume 9, Issue 1, Page(s) 1

Abstract: Background: Autosomal dominant polycystic kidney disease (ADPKD), a common of monogenetic disorder caused by the polycystic kidney disease-1 (PKD1) or PKD2 genes deficiency. In this study, we have re-analyzed a microarray dataset to generate a holistic ... ...

Abstract	Background: Autosomal dominant polycystic kidney disease (ADPKD), a common of monogenetic disorder caused by the polycystic kidney disease-1 (PKD1) or PKD2 genes deficiency. In this study, we have re-analyzed a microarray dataset to generate a holistic view of this disease. Methodology: GSE7869, an expression profiling dataset was downloaded from the Gene Expression Omnibus (GEO) database. After quality control assessment, using GEO2R tool of GEO, genes with adjusted p-value ≤ 0.05 were determined as differentially expressed (DE). The expression profiles from ADPKD samples in different sizes were compared. Using CluePedia plugin of Cytoscape software, the protein-protein interaction (PPI) networks were constructed and analyzed by Cytoscape NetworkAnalyzer tool and MCODE application. Pathway enrichment analysis of clustered genes by MCODE with the high centrality parameters in PPI networks was performed using Cytoscape ClueGO plugin. Moreover, by Enrichr database, microRNAs (miRNAs) and transcription factors (TFs) targeted DE genes were identified. Results: In this study to explore the molecular pathogenesis of kidney in ADPKD, mRNA expression profiles of cysts from patients in different sizes were re-analyzed. The comparisons were performed between normal with minimally cystic tissue (MCT) samples, MCTs with small cysts, and small cysts with large cysts. 512, 7024, and 655 DE genes were determined, respectively. The top central genes, e.g. END1, EGFR, and FOXO1 were identified with topology and clustering analysis. DE genes that were significantly enriched in PPI networks are critical genes and their roles in ADPKD remain to be assessed in future experimental studies beside miRNAs and TFs predicted. Furthermore, the functional analysis resulted in which most of them are expected to be associated with ADPKD pathogenesis, such as signal pathways that involved in cell growth, inflammation, and cell polarity. Conclusion: We have here explored systematic approaches for molecular mechanisms assay of ADPKD as a monogenic disease, which may also be used for other monogenetic diseases beside complex diseases to provide suitable therapeutic targets.
Language	English
Publishing date	2020-01-06
Publishing country	United States
Document type	Journal Article
ZDB-ID	2697013-2
ISSN	2001-1326
ISSN	2001-1326
DOI	10.1186/s40169-019-0254-5
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Article: Enhanced

Rahimmanesh, Ilnaz / Esmaili, Yasaman / Ghafouri, Elham / Hejazi, Seyed Hossein / Khanahmad, Hossein

Research in pharmaceutical sciences

2023 Volume 18, Issue 2, Page(s) 138–148

Abstract: Background and purpose: Despite the widespread utilization of cancer vaccines with specified antigens, the use of whole tumor cell lysates in tumor immunotherapy would be a very promising approach that can overcome several significant obstacles in ... ...

Abstract	Background and purpose: Despite the widespread utilization of cancer vaccines with specified antigens, the use of whole tumor cell lysates in tumor immunotherapy would be a very promising approach that can overcome several significant obstacles in vaccine production. Whole tumor cells provide a broad source of tumor-associated antigens and can activate cytotoxic T lymphocytes and CD4+ T helper cells concurrently. On the other hand, as an effective immunotherapy strategy, recent investigations have shown that the multi-targeting of tumor cells with polyclonal antibodies, which are also more effective than monoclonal antibodies at mediating effector functions for target elimination, might minimize the escape variants. Experimental approach: We prepared polyclonal antibodies by immunizing rabbits with the highly invasive 4T1 breast cancer cell line. Findings/results: In vitro Conclusion and implications: Serial intravenous injections of tumor cell immunized rabbit serum significantly inhibited tumor cell proliferation and induced apoptosis
Language	English
Publishing date	2023-01-19
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2400156-9
ISSN	1735-9414 ; 1735-5362
ISSN (online)	1735-9414
ISSN	1735-5362
DOI	10.4103/1735-5362.367793
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Article ; Online: Systems biology approaches toward autosomal dominant polycystic kidney disease (ADPKD)

Ilnaz Rahimmanesh / Razieh Fatehi

Clinical and Translational Medicine, Vol 9, Iss 1, Pp 1-

2020 Volume 8

Abstract: Abstract Background Autosomal dominant polycystic kidney disease (ADPKD), a common of monogenetic disorder caused by the polycystic kidney disease-1 (PKD1) or PKD2 genes deficiency. In this study, we have re-analyzed a microarray dataset to generate a ... ...

Abstract	Abstract Background Autosomal dominant polycystic kidney disease (ADPKD), a common of monogenetic disorder caused by the polycystic kidney disease-1 (PKD1) or PKD2 genes deficiency. In this study, we have re-analyzed a microarray dataset to generate a holistic view of this disease. Methodology GSE7869, an expression profiling dataset was downloaded from the Gene Expression Omnibus (GEO) database. After quality control assessment, using GEO2R tool of GEO, genes with adjusted p-value ≤ 0.05 were determined as differentially expressed (DE). The expression profiles from ADPKD samples in different sizes were compared. Using CluePedia plugin of Cytoscape software, the protein–protein interaction (PPI) networks were constructed and analyzed by Cytoscape NetworkAnalyzer tool and MCODE application. Pathway enrichment analysis of clustered genes by MCODE with the high centrality parameters in PPI networks was performed using Cytoscape ClueGO plugin. Moreover, by Enrichr database, microRNAs (miRNAs) and transcription factors (TFs) targeted DE genes were identified. Results In this study to explore the molecular pathogenesis of kidney in ADPKD, mRNA expression profiles of cysts from patients in different sizes were re-analyzed. The comparisons were performed between normal with minimally cystic tissue (MCT) samples, MCTs with small cysts, and small cysts with large cysts. 512, 7024, and 655 DE genes were determined, respectively. The top central genes, e.g. END1, EGFR, and FOXO1 were identified with topology and clustering analysis. DE genes that were significantly enriched in PPI networks are critical genes and their roles in ADPKD remain to be assessed in future experimental studies beside miRNAs and TFs predicted. Furthermore, the functional analysis resulted in which most of them are expected to be associated with ADPKD pathogenesis, such as signal pathways that involved in cell growth, inflammation, and cell polarity. Conclusion We have here explored systematic approaches for molecular mechanisms assay of ADPKD as a ...
Keywords	Autosomal dominant polycystic kidney disease ; Microarray ; Protein interaction network ; Signal pathway ; Medicine (General) ; R5-920
Subject code	570
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The possible role of glucose-6-phosphate dehydrogenase deficiency in COVID-19 global prevalence and distribution.

Khanahmad, Negar / Khanahmad, Hossein / Shariati, Laleh / Rahimmanesh, Ilnaz / Kouhpayeh, Shirin

Journal of research in medical sciences : the official journal of Isfahan University of Medical Sciences

2020 Volume 25, Page(s) 92

Language	English
Publishing date	2020-10-28
Publishing country	India
Document type	Journal Article
ZDB-ID	2513029-8
ISSN	1735-7136 ; 1735-1995
ISSN (online)	1735-7136
ISSN	1735-1995
DOI	10.4103/jrms.JRMS_322_20
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