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He J, Hu J, Liu H. A three-gene random forest model for diagnosing idiopathic pulmonary fibrosis based on circadian rhythm-related genes in lung tissue. Expert Rev Respir Med 2023; 17:1307-1320. [PMID: 38285622 DOI: 10.1080/17476348.2024.2311262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/24/2024] [Indexed: 01/31/2024]
Abstract
BACKGROUND The disorder of circadian rhythm could be a key factor mediating fibrotic lung disease Therefore, our study aims to determine the diagnostic value of circadian rhythm-related genes (CRRGs) in IPF. METHODS We retrieved the data on CRRGs from previous studies and the GSE150910 dataset. The participants from the GSE150910 dataset were divided into training and internal validation sets. Next, we used several various bioinformatics methods and machine learning algorithms to screen genes. Next, we identified SEMA5A, COL7A1, and TUBB3, which were included in the random forest (RF) diagnostic model. Finally, external validation was conducted on data retrieved from the GSE184316 datasets. RESULTS The results revealed that the RF diagnostic model could diagnose patients with IPF in the internal validation set with the area under the ROC curve (AUC) value of 0.905 and in the external validation with the AUC value of 0.767. Furthermore, real-time quantitative PCR and western blotting results revealed a significant decrease in SEMA5A (p < 0.05) expression level and an increase in COL7A1 and TUBB3 expression levels in TGF-β1-treated normal human lung fibroblasts. CONCLUSION We constructed an RF diagnostic model based on SEMA5A, COL7A1, and TUBB3 expression in lung tissue for diagnosing patients with IPF.
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Affiliation(s)
- Jie He
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Jun Hu
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Otolaryngology - Head and Neck Surgery, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
| | - Hairong Liu
- Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, China
- Department of Geriatric Medicine, The First Affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan, China
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Danek PJ, Daniel WA. The Novel Atypical Antipsychotic Lurasidone Affects Cytochrome P450 Expression in the Liver and Peripheral Blood Lymphocytes. Int J Mol Sci 2023; 24:16796. [PMID: 38069119 PMCID: PMC10706667 DOI: 10.3390/ijms242316796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Lurasidone is a novel atypical antipsychotic drug acting on dopaminergic, serotonergic and noradrenergic receptors; it is applied for the long-term treatment of schizophrenia and depression in patients with bipolar disorders. We aimed at performing a comparative study on the influence of chronic treatment with lurasidone on the expression of cytochrome P450 enzymes in the liver and in peripheral blood lymphocytes, and to evaluate the relationship between changes in the expression of CYP enzymes in the two experimental models. The obtained results show a fairly similar expression pattern of the main CYP enzymes in the rat livers and lymphocytes, and they indicate that in the liver, lurasidone exerts an inhibitory effect on the activity, protein and mRNA levels of CYP2B1/2 (not CYP2B2 mRNA), CYP2C11 and CYP2E1, while in the case of CYP3A1 and CYP3A2, it causes enzyme induction. At the same time, lurasidone decreases the expression of CYP2B, CYP2C11 (CYP2C11 protein only) and CYP2E1 but increases that of CYP3A2 (not CYP3A1) in lymphocyte cells. In conclusion, chronic treatment with lurasidone simultaneously and in the same way influences the expression and activity of CYP2B, CYP2C11, CYP2E1 and CYP3A2 in the liver and peripheral blood lymphocytes of rats. Thus, the lymphocyte cytochrome P450 profile may be utilized as an indicator of the hepatic cytochrome P450 profile in further clinical studies with lurasidone, and lymphocytes may serve as easily available surrogates for examining the impact of new drugs and chronic in vivo treatments on CYP enzyme expression, as well as to estimate drug-drug interactions and toxicity risk.
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Affiliation(s)
| | - Władysława A. Daniel
- Department of Pharmacokinetics and Drug Metabolism, Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland;
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Hasan F, Katiyar T, Maurya SS, Yadav V, Yadav S, Pandey R, Mehrotra D, Hadi R, Singh S, Bhatt ML, Parmar D. Similarities in mRNA expression of peripheral blood drug metabolizing enzymes and cancer marker genes with biopsy samples of head and neck cancer patients. Biomarkers 2019; 24:574-583. [PMID: 31002268 DOI: 10.1080/1354750x.2019.1609090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Purpose: To develop peripheral blood mRNA expression profiles of drug metabolizing enzymes (DMEs) as a surrogate to monitor tobacco induced head and neck squamous cell carcinoma (HNSCC), attempts were made to investigate (i) similarities in alterations with the cancer marker genes in biopsy samples and (ii) if alterations similar to that seen in biopsy samples are reflected in peripheral blood. Methods: Total RNA from eight soft gingival tissues and eight biopsy samples of HNSCC patients and total DNA and RNA from blood of healthy controls (n = 150) and HNSCC patients (n = 150) was processed for expression and genotyping studies. Blood from patients receiving chemo-radiotherapy was processed for follow-up study. Results: qRT-PCR revealed significant increase in mRNA expression of DMEs in biopsy and blood samples of HNSCC patients when compared to controls. Similar alterations were observed in cancer marker genes in these samples. Patients with variant genotypes of DMEs showed greater magnitude of alterations in mRNA expression when compared to wild type controls. Responders of chemo-radiotherapy showed significant decline in induction of mRNA expression of DMEs and cancer marker genes Conclusions: The data suggest that peripheral blood expression profiles could be used to monitor tobacco-induced HNSCC as well as the treatment response.
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Affiliation(s)
- Feza Hasan
- a Developmental Toxicology Laboratory, System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR) , Lucknow , India.,b School of Dental Sciences, Department of Biochemistry, Babu Banarsi Das University , Lucknow , India
| | - Tridiv Katiyar
- a Developmental Toxicology Laboratory, System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR) , Lucknow , India.,b School of Dental Sciences, Department of Biochemistry, Babu Banarsi Das University , Lucknow , India
| | - Shailendra S Maurya
- a Developmental Toxicology Laboratory, System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR) , Lucknow , India
| | - Vinay Yadav
- a Developmental Toxicology Laboratory, System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR) , Lucknow , India
| | - Sanjay Yadav
- a Developmental Toxicology Laboratory, System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR) , Lucknow , India
| | - Rahul Pandey
- c Department of Radiotherapy & Department of Oral and Maxillofacial Surgery, King George's Medical University , Lucknow , India
| | - Divya Mehrotra
- c Department of Radiotherapy & Department of Oral and Maxillofacial Surgery, King George's Medical University , Lucknow , India
| | - Rahat Hadi
- d Department of Radiation Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences , Lucknow , India
| | - Sudhir Singh
- c Department of Radiotherapy & Department of Oral and Maxillofacial Surgery, King George's Medical University , Lucknow , India
| | - Madan L Bhatt
- c Department of Radiotherapy & Department of Oral and Maxillofacial Surgery, King George's Medical University , Lucknow , India
| | - Devendra Parmar
- a Developmental Toxicology Laboratory, System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR) , Lucknow , India
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Hasan F, Yadav V, Katiyar T, Yadav S, Pandey R, Mehrotra D, Hadi R, Singh S, Bhatt MLB, Parmar D. Validation of gene expression profiles of candidate genes using low density array in peripheral blood of tobacco consuming head and neck cancer patients and auto/taxi drivers with preneoplastic lesions. Genomics 2019; 112:513-519. [PMID: 30951801 DOI: 10.1016/j.ygeno.2019.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/11/2019] [Accepted: 04/01/2019] [Indexed: 12/17/2022]
Abstract
TaqMan Low-Density Array (TLDA) based Real-Time PCR (RT-PCR) of selected genes showed increased expression of polycyclic aromatic hydrocarbons (PAHs) metabolizing cytochrome P450s (CYPs), glutathione S-transferases (GSTs) and associated transcription factors in biopsy and peripheral blood samples isolated from head and neck squamous cell carcinoma (HNSCC) patients when compared to the controls. The genes involved in DNA repair, signal transduction pathway, EMT pathway, apoptosis, and cell adhesion/motility were found to be altered in both peripheral blood and biopsy samples of HNSCC patients. Transcription profiles in blood isolated from auto/taxi drivers, with pre-neoplastic lesions and history of tobacco use, also showed similar alterations. The present TLDA data thus demonstrates that low-density array of selected genes in peripheral blood has the potential to be used as a surrogate for providing insight into cancer progression pathways and possibly as an early biomarker for monitoring tobacco induced HNSCC.
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Affiliation(s)
- Feza Hasan
- Developmental Toxicology Laboratory, System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, U.P., India; Babu Banarsi Das University, Faizabad Road, Lucknow 226028, U.P., India
| | - Vinay Yadav
- Developmental Toxicology Laboratory, System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, U.P., India
| | - Tridiv Katiyar
- Developmental Toxicology Laboratory, System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, U.P., India; Babu Banarsi Das University, Faizabad Road, Lucknow 226028, U.P., India
| | - Sanjay Yadav
- Developmental Toxicology Laboratory, System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, U.P., India
| | - Rahul Pandey
- Department of Radiotherapy, Department of Oral and Maxillofacial Surgery, King George's Medical University, Lucknow 226003, U.P., India
| | - Divya Mehrotra
- Department of Radiotherapy, Department of Oral and Maxillofacial Surgery, King George's Medical University, Lucknow 226003, U.P., India
| | - Rahat Hadi
- Department of Radiation Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Gomti Nagar, Lucknow 226010, U.P., India
| | - Sudhir Singh
- Department of Radiotherapy, Department of Oral and Maxillofacial Surgery, King George's Medical University, Lucknow 226003, U.P., India
| | - Madan L B Bhatt
- Department of Radiotherapy, Department of Oral and Maxillofacial Surgery, King George's Medical University, Lucknow 226003, U.P., India
| | - Devendra Parmar
- Developmental Toxicology Laboratory, System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, U.P., India.
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Zhang Y, Zhang W, Wang H, Yang B. miR-21 Contributes to Human Amniotic Membrane-Derived Mesenchymal Stem Cell Growth and Human Amniotic Membrane-Derived Mesenchymal Stem Cell-Induced Immunoregulation. Genet Test Mol Biomarkers 2018; 22:665-673. [PMID: 30481073 DOI: 10.1089/gtmb.2018.0116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Yan Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
| | - Wenjin Zhang
- Department of Neurosurgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, PR China
| | - Huancheng Wang
- Department of Blood Transfusion, The First People's Hospital of Nanyang, Nanyang, PR China
| | - Bo Yang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, PR China
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Katiyar T, Maurya SS, Hasan F, Singh AP, Khan AJ, Hadi R, Singh S, Bhatt MLB, Parmar D. Association of cytochrome P450 1B1 haplotypes with head and neck cancer risk. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:443-450. [PMID: 28556360 DOI: 10.1002/em.22098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 04/14/2017] [Accepted: 04/14/2017] [Indexed: 06/07/2023]
Abstract
Genetic polymorphisms have been reported in several cytochrome P450 (CYP) genes, including CYP1B1 which metabolically activates procarcinogens present in tobacco to carcinogenic intermediates. This study used a case-control approach in North Indian population to determine associations between genetic variants in CYP1B1 and risk of Head and Neck Squamous Cell Carcinoma (HNSCC). We examined the genotype and haplotype frequencies at various single-nucleotide polymorphisms (SNPs), including SNPs previously reported in the promoter region and intron 1 of CYP1B1 in Caucasians. Using cycle sequencing, 9 SNPs were identified in the promoter region, intron 1, and exons 2 and 3. Haplotype analysis revealed that 5 SNPs (those in the promoter region, intron, and Arg48Gly and Ala119Ser in exon 2) were in strong linkage disequilibrium (LD). Cases with the T-A-T-G-T haplotype were significantly associated with increased risk of HNSCC. Interestingly, qRT-PCR studies revealed a significant increase in mRNA expression of CYP1B1 in peripheral blood isolated from cases with the T-A-T-G-T haplotype compared with cases with the C-G-C-C-G haplotype, and in cases compared to controls for both main haplotypes. The data thus provide evidence that CYP1B1 haplotypes could be more effective in predicting HNSCC risk. Environ. Mol. Mutagen. 58:443-450, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Tridiv Katiyar
- System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, Uttar Pradesh, 226001, India
- Babu Banarsi Das University, BBD City, Lucknow, Uttar Pradesh, 226028, India
| | - Shailendra S Maurya
- System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, Uttar Pradesh, 226001, India
| | - Feza Hasan
- System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, Uttar Pradesh, 226001, India
- Babu Banarsi Das University, BBD City, Lucknow, Uttar Pradesh, 226028, India
| | - Arvind P Singh
- Department of Microbiology, Faculty of Life Sciences, Central University of Rajasthan, Kishangarh, Ajmer, Rajasthan, 305817, India
| | - Anwar J Khan
- Department of Gastroenterology, Sajay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226014, India
| | - Rahat Hadi
- Department of Radiation Oncology, Dr. Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh, 226010, India
| | - Sudhir Singh
- Department of Radiotherapy, King George's Medical University, Lucknow, Uttar Pradesh, 226003, India
| | - Madan L B Bhatt
- Department of Radiotherapy, King George's Medical University, Lucknow, Uttar Pradesh, 226003, India
| | - Devendra Parmar
- System Toxicology & Health Risk Assessment Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow, Uttar Pradesh, 226001, India
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Ande A, McArthur C, Kumar A, Kumar S. Tobacco smoking effect on HIV-1 pathogenesis: role of cytochrome P450 isozymes. Expert Opin Drug Metab Toxicol 2013; 9:1453-64. [PMID: 23822755 PMCID: PMC4007120 DOI: 10.1517/17425255.2013.816285] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
INTRODUCTION Tobacco smoking is highly prevalent among the HIV-1-infected population. In addition to diminished immune response, smoking has been shown to increase HIV-1 replication and decrease response to antiretroviral therapy, perhaps through drug-drug interaction. However, the mechanism by which tobacco/nicotine increases HIV-1 replication and mediates drug-drug interaction is poorly understood. AREAS COVERED In this review, the authors discuss the effects of smoking on HIV-1 pathogenesis. Since they propose a role for the cytochrome P450 (CYP) pathway in smoking-mediated HIV-1 pathogenesis, the authors briefly converse the role of CYP enzymes in tobacco-mediated oxidative stress and toxicity. Finally, the authors focus on the role of CYP enzymes, especially CYP2A6, in tobacco/nicotine metabolism and oxidative stress in HIV-1 model systems monocytes/macrophages, lymphocytes, astrocytes and neurons, which may be responsible for HIV-1 pathogenesis. EXPERT OPINION Recent findings suggest that CYP-mediated oxidative stress is a novel pathway that may be involved in smoking-mediated HIV-1 pathogenesis, including HIV-1 replication and drug-drug interaction. Thus, CYP and CYP-associated oxidative stress pathways may be potential targets to develop novel pharmaceuticals for HIV-1-infected smokers. Since HIV-1/TB co-infections are common, future study involving interactions between antiretroviral and antituberculosis drugs that involve CYP pathways would also help treat HIV-1/TB co-infected smokers effectively.
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Affiliation(s)
- Anusha Ande
- University of Missouri Kansas City, School of Pharmacy, Division of Pharmacology & Toxicology, Kansas City, MO 64108, USA
| | - Carole McArthur
- Professor, University of Missouri Kansas City, School of Dentistry, Department of Oral Biology, Kansas City, MO 64108, USA
| | - Anil Kumar
- Professor and Chair, University of Missouri Kansas City, School of Pharmacy, Division of Pharmacology & Toxicology, Kansas City, MO 64108, USA
| | - Santosh Kumar
- Assistant Professor, University of Missouri Kansas City, School of Pharmacy, Division of Pharmacology & Toxicology, 2464 Charlotte St. Kansas City, MO 64108, USA Tel: +1 816 235 5494 (Off); Fax: +1 816 235 1776;
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