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Article ; Online: Human polyomavirus 9 as a potential threat in kidney transplant recipients; lessons from BKPyV.

Razizadeh, Mohammad Hossein / Tabibzadeh, Alireza

2023 Volume 80, Page(s) 101894

Abstract: As a therapeutic method, kidney transplantation significantly improved the life quality and prognosis of patients with the end-stage renal disease. Since a key element in stable kidney transplantation is continuous therapy with immunosuppressive agents, ... ...

Abstract	As a therapeutic method, kidney transplantation significantly improved the life quality and prognosis of patients with the end-stage renal disease. Since a key element in stable kidney transplantation is continuous therapy with immunosuppressive agents, an inhibited immune response makes patients vulnerable to opportunistic viral and bacterial infections. Polyomavirus (PyV), from the Polyomaviridae family, includes a well-known BK virus (BKPyV) and less publicized human polyomavirus 9 (HPyV9). Both these viruses may inflict significant damage to kidney transplants because of their high prevalence and pathogenesis. While a great body of knowledge was accumulated about the BKPyV-caused nephropathy, much less information is about the potential threat from the HPyV9-caused damage to kidney transplants. The current review provides a glimpse of general information about the PyV-associated nephropathy with a special focus on the role of the HPyV9 in pathogenesis of nephropathy in kidney transplants.
MeSH term(s)	Humans ; Kidney Transplantation/adverse effects ; Polyomavirus Infections/epidemiology ; Polyomaviridae ; Kidney Diseases ; BK Virus/physiology ; Transplant Recipients ; Tumor Virus Infections/epidemiology
Language	English
Publishing date	2023-07-04
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	1160846-8
ISSN	1878-5492 ; 0966-3274
ISSN (online)	1878-5492
ISSN	0966-3274
DOI	10.1016/j.trim.2023.101894
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Article ; Online: Investigation of Fibroblast Growth Factor Peptide Antagonist on Mouse Model Breast Tumor through ERK/MAPK and PI3K/AKT Signaling Pathways.

Ghadirian, Shahrzad / Tabibzadeh, Alireza / Rezvani, Hamid / Jafarzadeh, Mehrzad

Asian Pacific journal of cancer prevention : APJCP

2024 Volume 25, Issue 2, Page(s) 473–483

Abstract: Background: In the majority of cancers, metastasis of tumor cells is the main cause of treatment failure. This study intended to investigate the effectiveness of basic fibroblast growth factor (bFGF) peptide designed to inhibit tumor growth in 4T1 ... ...

Abstract	Background: In the majority of cancers, metastasis of tumor cells is the main cause of treatment failure. This study intended to investigate the effectiveness of basic fibroblast growth factor (bFGF) peptide designed to inhibit tumor growth in 4T1 metastatic breast cancer through the PI3K/AKT and ERK/MAPK signal transduction pathways. Methods: The tumor was induced through 4T1 tumor graft in BALB/c mice. The designed peptide was injected intraperitoneal at three selected doses after two weeks for 14 days. The PBS and doxorubicin were used as the negative and positive control groups, respectively. Tumor size was measured and after the treatment period, the mice underwent a surgery and tumors were used for the western blot examinations. Results: the peptide injection was effective in reducing or inhibiting tumor growth in mice model and in vitro. The western blot analysis results showed that the p-AKT and p-ERK levels in peptide treated tumors were reduced (p<0.05). Conclusion: The peptide injection was effective in mice model. Findings showed that in the two signal transduction pathways, the p-AKT and p-ERK levels were significantly different from the negative control group.
MeSH term(s)	Animals ; Mice ; Proto-Oncogene Proteins c-akt/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Fibroblast Growth Factors ; Signal Transduction ; Neoplasms ; Disease Models, Animal ; Cell Line, Tumor
Chemical Substances	Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; Fibroblast Growth Factors (62031-54-3)
Language	English
Publishing date	2024-02-01
Publishing country	Thailand
Document type	Journal Article
ZDB-ID	2218955-5
ISSN	2476-762X ; 1513-7368
ISSN (online)	2476-762X
ISSN	1513-7368
DOI	10.31557/APJCP.2024.25.2.473
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Article ; Online: Autophagy-related genes polymorphism in hepatitis B virus-associated hepatocellular carcinoma: A systematic review.

Yousefi, Parastoo / Tabibzadeh, Alireza / Jawaziri, Abdulhussain Kadhim / Mehrjoo, Mohsen / Akhavan, Mandana / Allahqoli, Leila / Salehiniya, Hamid

Immunity, inflammation and disease

2024 Volume 12, Issue 2, Page(s) e1182

Abstract: Background: Chronic hepatitis B (CHB) virus is the most common risk factor for developing liver malignancy. Autophagy is an essential element in human cell maintenance. Several studies have demonstrated that autophagy plays a vital role in liver cancer ... ...

Abstract	Background: Chronic hepatitis B (CHB) virus is the most common risk factor for developing liver malignancy. Autophagy is an essential element in human cell maintenance. Several studies have demonstrated that autophagy plays a vital role in liver cancer at different stages. In this systematic review, we intend to investigate the role of polymorphism and mutations of autophagy-related genes (ATGs) in the pathogenesis and carcinogenesis of the hepatitis B virus (HBV). Materials and methods: The search was conducted in online databases (Web of Science, PubMed, and Scopus) using Viruses, Infections, Polymorphism, Autophagy, and ATG. The study was conducted based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses criteria. Results: The primary search results led to 422 studies. By screening and eligibility evaluation, only four studies were relevant. The most important polymorphisms in hepatocellular carcinoma were rs2241880 in ATG16L1, rs77859116, rs510432, and rs548234 in ATG5. Furthermore, some polymorphisms are associated with an increased risk of HBV infection including, rs2241880 in ATG16L1 and rs6568431 in ATG5. Conclusion: The current study highlights the importance of rs2241880 in ATG16L1 and rs77859116, rs510432, and rs548234 in ATG5 for HBV-induced HCC. Additionally, some mutations in ATG16L1 and ATG5 were important in risk of HBV infection. The study highlights the gap of knowledge in the field of ATG polymorphisms in HBV infection and HBV-induced HCC.
MeSH term(s)	Humans ; Autophagy/genetics ; Carcinoma, Hepatocellular/genetics ; Genetic Predisposition to Disease ; Hepatitis B virus ; Liver Neoplasms/genetics
Language	English
Publishing date	2024-02-14
Publishing country	England
Document type	Journal Article ; Systematic Review
ZDB-ID	2740382-8
ISSN	2050-4527 ; 2050-4527
ISSN (online)	2050-4527
ISSN	2050-4527
DOI	10.1002/iid3.1182
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Article ; Online: A survey of ORF8 sequence and immunoinformatics features during alpha, delta, and wild type peaks of the SARS-CoV-2 pandemic in Iran.

Tabibzadeh, Alireza / Karbalaie Niya, Mohammad Hadi / Keyvani, Hossein / Karampoor, Sajad / Yousefi, Parastoo / Razizadeh, Mohammad Hossein / Mousavizadeh, Leila / Esghaei, Maryam

Malawi medical journal : the journal of Medical Association of Malawi

2024 Volume 35, Issue 2, Page(s) 101–105

Abstract: Background: The Coronavirus disease 2019 (COVID-19) pandemic influences all around the world. The SARS-CoV-2 ORF8 accessory gene represents multiple functions in virus-host interaction. The current study aimed to compare the ORF8 substitutions and ... ...

Abstract	Background: The Coronavirus disease 2019 (COVID-19) pandemic influences all around the world. The SARS-CoV-2 ORF8 accessory gene represents multiple functions in virus-host interaction. The current study aimed to compare the ORF8 substitutions and epitope features of these substitutions in the various SARS-CoV-2 outbreaks including delta, alpha, and wild type variants in Iran from 2020 to 2022. In addition, we evaluate B cell, HLA I and II epitopes, by in-silico approach to ORF8 binding site prediction. Methods: The samples were collected from patients diagnosed with SARS-CoV-2 infection via a real-time PCR assay. Then, a conventional PCR was carried out for ORF8 mutations analysis and further Sanger sequencing. Possible important alterations in epitope features of the ORF8 were evaluated by epitope mapping. B cell, HLA class I and II epitopes, evaluated by online databases ABCpred, NetMHCpan-4.1, and NetMHCIIpan-3.2, respectively. Results: The current study results could not represent novel variations in seven full-length ORF8 sequences or major ORF8 deletions in 80 evaluated samples. In addition, we could not find any ORF8 A382 during each outbreak of variants. Epitope mapping represents differences between the Alpha and other variants, especially in B cell potential epitopes and HLA I. Conclusion: The immunoinformatic evaluation of ORF8 suggested epitopes represent major differences for the Alpha variant in comparison with other variants. In addition, having mild pathogenesis of the Omicron variant does not seem to be associated with ORF8 alteration by phylogenetic evaluation. Future in-vitro studies for a clear conclusion about the epitope features of ORF8 are required.
MeSH term(s)	Humans ; COVID-19 ; Epitopes ; Immunoinformatics ; Iran ; Pandemics ; Phylogeny ; SARS-CoV-2/genetics ; Viral Proteins/genetics
Chemical Substances	Epitopes ; ORF8 protein, SARS-CoV-2 ; Viral Proteins
Language	English
Publishing date	2024-01-23
Publishing country	Malawi
Document type	Journal Article
ISSN	1995-7270 ; 1995-7262
ISSN (online)	1995-7270
ISSN	1995-7262
DOI	10.4314/mmj.v35i2.5
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Article ; Online: The potential importance of autophagy genes expression profile dysregulation and ATG polymorphisms in COVID-19 pathogenesis.

Yousefi, Parastoo / Tabibzadeh, Alireza / Keyvani, Hossein / Esghaei, Maryam / Karampoor, Sajad / Razizadeh, Mohammad Hossein / Mousavizadeh, Leila

APMIS : acta pathologica, microbiologica, et immunologica Scandinavica

2023 Volume 131, Issue 4, Page(s) 161–169

Abstract: Autophagy is one of the important mechanisms in cell maintenance, which is considered associated with different pathological conditions such as viral infections. In this current study, the expression level and polymorphisms in some of the most important ... ...

Abstract	Autophagy is one of the important mechanisms in cell maintenance, which is considered associated with different pathological conditions such as viral infections. In this current study, the expression level and polymorphisms in some of the most important genes in the autophagy flux in COVID-19 patients were evaluated. This cross-sectional study was conducted among 50 confirmed COVID-19 patients and 20 healthy controls. The COVID-19 patients were divided into a severe group and a mild group according to their clinical features. The expression levels of ATG5, ATG16L1, LC3, and BECN1 were evaluated by the 2
MeSH term(s)	Humans ; Female ; Male ; Genetic Predisposition to Disease ; Cross-Sectional Studies ; Polymorphism, Single Nucleotide ; Autophagy-Related Proteins/genetics ; COVID-19/genetics ; Autophagy/genetics
Chemical Substances	Autophagy-Related Proteins
Language	English
Publishing date	2023-02-01
Publishing country	Denmark
Document type	Journal Article
ZDB-ID	93340-5
ISSN	1600-0463 ; 0903-4641
ISSN (online)	1600-0463
ISSN	0903-4641
DOI	10.1111/apm.13286
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Article ; Online: Coagulopathy and thromboembolic events a pathogenic mechanism of COVID-19 associated with mortality: An updated review.

Yousefi, Parastoo / Soltani, Saber / Siri, Goli / Rezayat, Sara Akhavan / Gholami, Ali / Zafarani, Alireza / Razizadeh, Mohamad Hossein / Alborzi, Ehsan / Mokhtary-Irani, Golnaz / Abedi, Behnam / Karampoor, Sajad / Tabibzadeh, Alireza / Farahani, Abbas

Journal of clinical laboratory analysis

2023 Volume 37, Issue 11-12, Page(s) e24941

Abstract: During 2019, the SARS-CoV-2 emerged from China, and during months, COVID-19 spread in many countries around the world. The expanding data about pathogenesis of this virus could elucidate the exact mechanism by which COVID-19 caused death in humans. One ... ...

Abstract	During 2019, the SARS-CoV-2 emerged from China, and during months, COVID-19 spread in many countries around the world. The expanding data about pathogenesis of this virus could elucidate the exact mechanism by which COVID-19 caused death in humans. One of the pathogenic mechanisms of this disease is coagulation. Coagulation disorders that affect both venous and arterial systems occur in patients with COVID-19. The possible mechanism involved in the coagulation could be excessive inflammation induced by SARS-CoV-2. However, it is not yet clear well how SARS-CoV-2 promotes coagulopathy. However, some factors, such as pulmonary endothelial cell damage and some anticoagulant system disorders, are assumed to have an important role. In this study, we assessed conducted studies about COVID-19-induced coagulopathy to obtain clearer vision of the wide range of manifestations and possible pathogenesis mechanisms.
MeSH term(s)	Humans ; COVID-19/complications ; SARS-CoV-2 ; Blood Coagulation Disorders/etiology ; Thromboembolism/etiology ; Inflammation/complications ; Anticoagulants
Chemical Substances	Anticoagulants
Language	English
Publishing date	2023-07-11
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	645095-7
ISSN	1098-2825 ; 0887-8013
ISSN (online)	1098-2825
ISSN	0887-8013
DOI	10.1002/jcla.24941
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Article ; Online: Evaluation of the prevalence of bovine leukemia virus DNA in peripheral blood mononuclear cells of multiple sclerosis patients.

Jeda, Ali Salimi / Zarei, Anna / Ghabeshi, Soad / Tabibzadeh, Alireza / Lotfi, Mohsen / Etemadifar, Masoud / Niya, Mohammad Hadi Karbalaie / Ghorbanlou, Mehrdad / Esghaei, Maryam

IJID regions

2023 Volume 7, Page(s) 233–236

Abstract: Multiple sclerosis (MS) is an immune system-mediated neurodegenerative disease. Recent studies suggest that viral agents, especially the Epstein Barr virus (EBV), are etiological agents for MS. The roles of other viruses in MS have been investigated. ... ...

Abstract	Multiple sclerosis (MS) is an immune system-mediated neurodegenerative disease. Recent studies suggest that viral agents, especially the Epstein Barr virus (EBV), are etiological agents for MS. The roles of other viruses in MS have been investigated. Studies have shown an increase in the level of antibodies against bovine leukemia virus (BLV) in patients with MS. In this regard, our study aimed to examine the presence of BLV DNA in peripheral blood mononuclear cells (PBMCs) of MS patients in Iran. In this cross-sectional study, the presence of BLV in 109 Iranian MS patients and 60 healthy controls was evaluated. The isolated PBMCs were used for DNA extraction and PCR, using specific primers for two distinct genes. The mean age of the participants was 39 ± 9.5 years, and 27 (24.77%) of them were male. Clinical evaluation of these patients showed the most frequent MS type to be relapsing-remitting MS (RRMS) (71; 65.14%). BLV evaluation did not show any BLV DNA presence in the PBMCs of individuals in either the MS or healthy control groups. Therefore, our study showed no evidence of BLV infection in Iranian MS patients.
Language	English
Publishing date	2023-04-06
Publishing country	England
Document type	Journal Article
ISSN	2772-7076
ISSN (online)	2772-7076
DOI	10.1016/j.ijregi.2023.04.002
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Article ; Online: Forecasting influenza hemagglutinin mutations through the lens of anomaly detection.

Garjani, Ali / Chegini, Atoosa Malemir / Salehi, Mohammadreza / Tabibzadeh, Alireza / Yousefi, Parastoo / Razizadeh, Mohammad Hossein / Esghaei, Moein / Esghaei, Maryam / Rohban, Mohammad Hossein

Scientific reports

2023 Volume 13, Issue 1, Page(s) 14944

Abstract: The influenza virus hemagglutinin is an important part of the virus attachment to the host cells. The hemagglutinin proteins are one of the genetic regions of the virus with a high potential for mutations. Due to the importance of predicting mutations in ...

Abstract	The influenza virus hemagglutinin is an important part of the virus attachment to the host cells. The hemagglutinin proteins are one of the genetic regions of the virus with a high potential for mutations. Due to the importance of predicting mutations in producing effective and low-cost vaccines, solutions that attempt to approach this problem have recently gained significant attention. A historical record of mutations has been used to train predictive models in such solutions. However, the imbalance between mutations and preserved proteins is a big challenge for the development of such models that need to be addressed. Here, we propose to tackle this challenge through anomaly detection (AD). AD is a well-established field in Machine Learning (ML) that tries to distinguish unseen anomalies from normal patterns using only normal training samples. By considering mutations as anomalous behavior, we could benefit existing rich solutions in this field that have emerged recently. Such methods also fit the problem setup of extreme imbalance between the number of unmutated vs. mutated training samples. Motivated by this formulation, our method tries to find a compact representation for unmutated samples while forcing anomalies to be separated from the normal ones. This helps the model to learn a shared unique representation between normal training samples as much as possible, which improves the discernibility and detectability of mutated samples from the unmutated ones at the test time. We conduct a large number of experiments on four publicly available datasets, consisting of three different hemagglutinin protein datasets, and one SARS-CoV-2 dataset, and show the effectiveness of our method through different standard criteria.
MeSH term(s)	Animals ; Humans ; Influenza, Human ; Hemagglutinins ; COVID-19 ; SARS-CoV-2 ; Influenza Vaccines ; Mutation ; Unionidae
Chemical Substances	Hemagglutinins ; Influenza Vaccines
Language	English
Publishing date	2023-09-11
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-42089-y
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Article ; Online: The role of cholesterol 25-hydroxylase in viral infections: Mechanisms and implications.

Yousefi, Parastoo / Gholami, Ali / Mehrjo, Mohsen / Razizadeh, Mohammad Hossein / Akhavan, Mandana / Karampoor, Sajad / Tabibzadeh, Alireza

Pathology, research and practice

2023 Volume 249, Page(s) 154783

Abstract: Viral infections pose significant threats to human health, causing various diseases with varying severity. The intricate interactions between viruses and host cells determine the outcome of infection, including viral replication, immune responses, and ... ...

Abstract	Viral infections pose significant threats to human health, causing various diseases with varying severity. The intricate interactions between viruses and host cells determine the outcome of infection, including viral replication, immune responses, and disease progression. Cholesterol 25-hydroxylase (CH25H) is an enzyme that catalyzes the conversion of cholesterol to 25-hydroxycholesterol (25HC), a potent antiviral molecule. In recent years, increasing evidence has highlighted the critical involvement of CH25H in modulating immune responses and influencing viral infections. Notably, the review discusses the implications of CH25H in viral pathogenesis and the development of therapeutic strategies. It examines the interplay between CH25H and viral immune evasion mechanisms, highlighting the potential of viral antagonism of CH25H to enhance viral replication and pathogenesis. Furthermore, it explores the therapeutic potential of targeting CH25H or modulating its downstream signaling pathways as a strategy to control viral infections and enhance antiviral immune responses. This comprehensive review demonstrates the crucial role of CH25H in viral infections, shedding light on its mechanisms of action in viral entry, replication, and immune modulation. Understanding the complex interplay between CH25H and viral infections may pave the way for novel therapeutic approaches and the development of antiviral strategies aimed at exploiting the antiviral properties of CH25H and enhancing host immune responses against viral pathogens. In the current review, we tried to provide an overview of the antiviral activity and importance of CH25H in viral pathogenesis.
MeSH term(s)	Humans ; Disease Progression ; Steroid Hydroxylases ; Virus Diseases
Chemical Substances	cholesterol 25-hydroxylase (EC 1.14.99.38) ; Steroid Hydroxylases (EC 1.14.-)
Language	English
Publishing date	2023-08-24
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	391889-0
ISSN	1618-0631 ; 0344-0338
ISSN (online)	1618-0631
ISSN	0344-0338
DOI	10.1016/j.prp.2023.154783
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Article ; Online: ORF8 ∆382 Mutation: A Possible Viral Prognostic Biomarker for the Severity of the COVID-19.

Tabibzadeh, Alireza / Esghaei, Maryam / Zamani, Farhad / Soltani, Saber / Yousefi, Parastoo / Karbalaie Niya, Mohammad Hadi

Iranian biomedical journal

2021 Volume 25, Issue 4, Page(s) 308–309

MeSH term(s)	Biomarkers/metabolism ; COVID-19/diagnosis ; COVID-19/genetics ; COVID-19/pathology ; Humans ; Mutation/genetics ; Prognosis ; Severity of Illness Index ; Viral Proteins/genetics
Chemical Substances	Biomarkers ; ORF8 protein, SARS-CoV-2 ; Viral Proteins
Language	English
Publishing date	2021-07-01
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2489282-8
ISSN	2008-823X ; 1028-852X
ISSN (online)	2008-823X
ISSN	1028-852X
DOI	10.52547/ibj.25.4.308
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