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Mansouri V, Arjmand B, Hamzeloo-Moghadam M, Rezaei Tavirani M, Razzaghi Z, Ahmadzadeh A, Rostami Nejad M, Mohamoud Robati R. Introducing Critical Genes in Response to Photodynamic Therapy: A Network Analysis. J Lasers Med Sci 2023; 14:e25. [PMID: 37744009 PMCID: PMC10517577 DOI: 10.34172/jlms.2023.25] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/17/2023] [Indexed: 09/26/2023]
Abstract
Introduction: Photodynamic therapy (PDT) is applied as an efficient method for preventing the progress of cancers. Light and a photosensitive compound which is known as photosensitizer (PS) are the main parts of PDT. In the present study, molecular events after using PDT in the presence of a super lethal dose of a PS were assessed via protein-protein interaction (PPI) analysis. Methods: Data were extracted from Gene Expression Omnibus (GEO). The gene expression profiles of the treated human Sk-Cha1 cells via PDT were compared with the control cells. Expressed change analysis and PPI network analysis were administrated via Cytoscape software v 3.7.2 to find the critical differentially expressed genes (DEGs). Regulatory relationships between the central DEGs were evaluated and the highlighted genes were identified. Results: The significant amounts of gene expression values were grouped and a few DEGs characterized by tremendously expressed values were identified. EGFR, CANX, HSPA5, MYC, JUN, ITGB1, APP, and CDH1 were highlighted as hub-bottleneck DEGs. EGFR, CDH1, and JUN appeared as a set of SEGs, which play a crucial role in response to PDT in the treated Sk-Cha1 cells. Conclusion: In conclusion, regulatory relationships between EGFR, CDH1, and JUN, which have an effect on the regulation of cellular survival, differentiation, and proliferation, were highlighted in the present investigation.
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Affiliation(s)
- Vahid Mansouri
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Iranian Cancer Control Center (MACSA), Tehran, Iran
| | - Maryam Hamzeloo-Moghadam
- Traditional Medicine and Materia Medica Research Center, School of Traditional Medicine Shahid, Beheshti University of Medical Sciences, Tehran, Iran 5 Laser Application in Medical Sciences Research C
| | - Mostafa Rezaei Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zahra Razzaghi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Alireza Ahmadzadeh
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Rostami Nejad
- Celiac Disease and Gluten Related Disorders Research Center, Research Institute for Gastroenterology and Liver Disease, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza Mohamoud Robati
- Skin Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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2
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Qazi S, Uckun FM. Upregulated Expression of ErbB1 in Diffuse Large B-Cell Lymphoma as a Predictor of Poor Overall Survival Outcome. J Pers Med 2023; 13:jpm13050770. [PMID: 37240940 DOI: 10.3390/jpm13050770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
We examined the transcript-level expression of ErbB family protein tyrosine kinases, including ERBB1, in primary malignant lymphoma cells from 498 adult patients with diffuse large B-cell lymphoma (DLBCL). ERBB1 expression in DLBCL cells was significantly higher than in normal B-lineage lymphoid cells. An upregulated expression of ERBB1 mRNA in DLBCL cells was correlated with an amplified expression of mRNAs for transcription factors that recognized ERBB1 gene promoter sites. Notably, amplified ERBB1 expression in DLBCL and its subtypes were associated with significantly worse overall survival (OS). Our results encourage the further evaluation of the prognostic significance of high-level ERBB1 mRNA expression and the clinical potential of ERBB1-targeting therapeutics as personalized medicines in high-risk DLBCL.
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Affiliation(s)
- Sanjive Qazi
- Immuno-Oncology Program, Ares Pharmaceuticals, St. Paul, MN 55110, USA
| | - Fatih M Uckun
- Immuno-Oncology Program, Ares Pharmaceuticals, St. Paul, MN 55110, USA
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3
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Maadurshni GB, Nagarajan M, Priyadharshini S, Singaravelu U, Manivannan J. System-wide health risk prediction for 4-methyl-2,4-bis(4-hydroxyphenyl)pent-1-ene(MBP), a major active metabolite of environmental pollutant and food contaminant - Bisphenol A. Toxicology 2023; 485:153414. [PMID: 36587891 DOI: 10.1016/j.tox.2022.153414] [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: 11/27/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022]
Abstract
Human exposure to plastic contaminated foods and environmental micro/nano plastic derived chemicals necessitates system-wide health risk assessment. Hence, current study intend to explore the mode of action (MoA) based adverse outcome pathways of 4-methyl-2,4-bis(4-hydroxyphenyl)pent-1-ene (MBP), the major active metabolite of bisphenol A (BPA). The computational study employed broad range of target prediction, systems biology tools and molecular docking protocols. Further, validation of MBP targets was done using protein-ligand fluorescence quenching assay, endothelial cell culture and chicken embryo vascular angiogenesis models. Interestingly, the current results illustrate that various physiological signaling pathways (MAPK and VEGF related angiogenesis signaling) and disease progression pathways (hypertension, cancer and endocrine disorders) were enriched as potential targets of MBP. Further, docking studies highlights the possible binding mechanism of MBP with important targets including endothelial nitric oxide synthase (eNOS) and serum albumin (BSA). In addition, the validation studies on MBP-BSA interaction (fluorescence quenching), eNOS derived nitric oxide (NOx) generation in endothelial cells and chicken embryo angiogenesis support the system-wide impacts of MBP with highlights on cardiovascular pathogenesis. Thus, the current observation provides novel insights into the system wide impacts of MBP for the futuristic health risk assessment of plastic derived chemicals.
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Affiliation(s)
| | - Manigandan Nagarajan
- Environmental Health and Toxicology Laboratory, Department of Environmental Sciences, School of Life Sciences, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Saravanan Priyadharshini
- Integrated Biocomputing Lab, Department of Bioinformatics, School of Life Sciences, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Usha Singaravelu
- Integrated Biocomputing Lab, Department of Bioinformatics, School of Life Sciences, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - Jeganathan Manivannan
- Environmental Health and Toxicology Laboratory, Department of Environmental Sciences, School of Life Sciences, Bharathiar University, Coimbatore, Tamil Nadu, India.
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Uckun FM, Qazi S. ERBB1/EGFR and JAK3 Tyrosine Kinases as Potential Therapeutic Targets in High-Risk Multiple Myeloma. ONCO 2022; 2:282-304. [PMID: 36311273 PMCID: PMC9610889 DOI: 10.3390/onco2040016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Our main objective was to identify abundantly expressed tyrosine kinases in multiple myeloma (MM) as potential therapeutic targets. We first compared the transcriptomes of malignant plasma cells from newly diagnosed MM patients who were risk-categorized based on the patient-specific EMC-92/SKY-92 gene expression signature values vs. normal plasma cells from healthy volunteers using archived datasets from the HOVON65/GMMG-HD4 randomized Phase 3 study evaluating the clinical efficacy of bortezomib induction/maintenance versus classic cytotoxic drugs and thalidomide maintenance. In particular, ERBB1/EGFR was significantly overexpressed in MM cells in comparison to normal control plasma cells, and it was differentially overexpressed in MM cells from high-risk patients. Amplified expression of EGFR/ERBB1 mRNA in MM cells was positively correlated with increased expression levels of mRNAs for several DNA binding proteins and transcription factors with known upregulating activity on EGFR/ERBB1 gene expression. MM patients with the highest ERBB1/EGFR expression level had significantly shorter PFS and OS times than patients with the lowest ERBB1/EGFR expression level. High expression levels of EGFR/ERBB1 were associated with significantly increased hazard ratios for unfavorable PFS and OS outcomes in both univariate and multivariate Cox proportional hazards models. The impact of high EGFR/ERBB1 expression on the PFS and OS outcomes remained significant even after accounting for the prognostic effects of other covariates. These results regarding the prognostic effect of EGFR/ERBB1 expression were validated using the MMRF-CoMMpass RNAseq dataset generated in patients treated with more recently applied drug combinations included in contemporary induction regimens. Our findings provide new insights regarding the molecular mechanism and potential clinical significance of upregulated EGFR/ERBB1 expression in MM.
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Affiliation(s)
- Fatih M. Uckun
- Immuno-Oncology Program, Ares Pharmaceuticals, St. Paul, MN 55110, USA
- Division of Hematology-Oncology, Department of Pediatrics and Developmental Therapeutics Program, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine (USC KSOM), Los Angeles, CA 90027, USA
| | - Sanjive Qazi
- Immuno-Oncology Program, Ares Pharmaceuticals, St. Paul, MN 55110, USA
- Division of Hematology-Oncology, Department of Pediatrics and Developmental Therapeutics Program, Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine (USC KSOM), Los Angeles, CA 90027, USA
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Ma Y, Zhu S, Yi M, Zhang W, Xue Y, Liu X, Deng H. Profiling Glutathionylome in CD38-Mediated Epithelial-Mesenchymal Transition. J Proteome Res 2022; 21:1240-1250. [PMID: 35420434 DOI: 10.1021/acs.jproteome.1c00893] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein S-glutathionylation is an important posttranslational modification that regulates various cellular processes. However, changes in glutathionylome in epithelial-mesenchymal transition (EMT), a crucial cellular process for embryonic development, wound healing, and carcinoma progression and metastasis, have not been fully characterized. Our previous study revealed that CD38 overexpression decreased cellular nicotinamide adenine dinucleotide (NAD+) levels and caused cells to undergo EMT. In the present study, we engineered a cell system in which the glutathione synthetase (GS) mutant was expressed that catalyzed the formation of a glutathione analogue from azido-alanine to profile changes of glutathionylome in CD38-overexpressing cells. We identified 1298 glutathionylated proteins and revealed that proteins with changed glutathionylation levels involved in EMT associated pathways including epithelial adherens junction, actin cytoskeleton, and integrin signaling. Moreover, the glutathionylation level of 15-hydroxyprostaglandin dehydrogenase (15-PGDH) was increased in CD38-overexpressing cells. We further demonstrated that glutathionylation of Cys63 residue in 15-PGDH led to decreased enzymatic activity that could promote EMT by increasing prostaglandin E2 (PGE2). Taken together, these results indicate that the clickable glutathione is an effective probe for glutathionylome profiling, and glutathionylation of 15-PGDH on Cys63 inhibits its enzymatic activity to promote EMT.
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Affiliation(s)
- Yingying Ma
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Songbiao Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Meiqi Yi
- BeiGene (Beijing) Co., Ltd., Beijing 100084, China
| | - Wenhao Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuanyuan Xue
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohui Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systematic Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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He Y, Zhang H, Zhang Y, Wang P, Zhu K, Ba Y. Comprehensive Characterization of Transforming Growth Factor Beta Receptor 1 in Stomach Adenocarcinoma Identifies a Prognostic Signature for Predicting Clinical Outcomes and Immune Infiltrates. Int J Gen Med 2022; 15:3375-3391. [PMID: 35368798 PMCID: PMC8965104 DOI: 10.2147/ijgm.s353879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/08/2022] [Indexed: 11/30/2022] Open
Abstract
Background Stomach adenocarcinoma (STAD) ranks as the third leading cause of cancer death worldwide. TGF‑β receptor 1 (TGFBR1), serving important roles in the TGF‑β family, the mechanisms whereby TGFBR1 governs tumor progression, immune cell infiltration in STAD remains unintelligible. Methods We used the TCGA, GEPIA, and HPA databases to explore TGFBR1 expression in STAD, the correlation between TGFBR1 expression and the clinical features. A receiver operating characteristic (ROC) curve and nomogram were constructed, and LASSO (the Least Absolute Shrinkage and Selection Operator)-selected features were used to build the TGFBR1 prognostic signature. GSEA is used to find the potential mechanism of TGFBR1 to promote the malignant process of STAD. We explored the influence of the TGFBR1 on the immune microenvironment of STAD through the TIMER2.0 and GEPIA database. Results In our study, TGFBR1 expression was significantly elevated in STAD and positively co-expression with pathologic stage, lymph node metastases (LNM) stage and histopathological grade. Nine factors with non-zero coefficients were identified by LASSO-selected features. Survival analysis revealed that patients with high TGFBR1 had shorter OS, FP, and PPS. Multivariate Cox analysis revealed that TGFBR1 was an independent prognostic factor for OS in STAD. The ROC analysis suggested that high diagnostic value with the AUC of TGFBR1 was 0.739. GSEA revealed that high TGFBR1 expression was correlated with pathway in cancer, MAPK signaling pathway, NOTCH signaling pathway, and VEGF-C production. ssGSEA showed that TGFBR1 is correlated with NK cells, Tem and Th17 cells. Furthermore, elevated TGFBR1 expression was found to be significantly correlated with several immune checkpoint and immune markers associated with immune cell subsets. Conclusion In summary, TGFBR1 could be a prognostic biomarker and an important regulator of immune cell infiltration in STAD. The present study revealed the probable underlying molecular mechanisms of TGFBR1 in STAD and provided a potential target for improving the prognosis.
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Affiliation(s)
- Yi He
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, People’s Republic of China
| | - Haiyang Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, People’s Republic of China
| | - Yan Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, People’s Republic of China
- Department of Gastroenterology, Tianjin Haihe Hospital, Tianjin, 300350, People’s Republic of China
| | - Peiyun Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, People’s Republic of China
| | - Kegan Zhu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, People’s Republic of China
| | - Yi Ba
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin’s Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, People’s Republic of China
- Correspondence: Yi Ba, Email
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Li G, Song Z, Wu C, Li X, Zhao L, Tong B, Guo Z, Sun M, Zhao J, Zhang H, Jia L, Li S, Wang L. Downregulation of NEDD4L by EGFR signaling promotes the development of lung adenocarcinoma. J Transl Med 2022; 20:47. [PMID: 35090513 PMCID: PMC8800232 DOI: 10.1186/s12967-022-03247-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/11/2022] [Indexed: 12/24/2022] Open
Abstract
Cumulative evidence indicates that the abnormal regulation of the NEDD4 family of E3-ubiquitin ligases participates in the tumorigenesis and development of cancer. However, their role in lung adenocarcinoma (LUAD) remains unclear. This study comprehensively analyzed the NEDD4 family in LUAD data sets from public databases and found only NEDD4L was associated with the overall survival of LUAD patients. Gene set enrichment analysis (GSEA) indicated that NEDD4L might be involved in the regulation of mTORC1 pathway. Both cytological and clinical assays showed that NEDD4L inhibited the activity of the mTOR signaling pathway. In vivo and in vitro experiments showed that NEDD4L could significantly inhibit the proliferation of LUAD cells. In addition, this study also found that the expression of NEDD4L was regulated by EGFR signaling. These findings firstly revealed that NEDD4L mediates an interplay between EGFR and mTOR pathways in LUAD, and suggest that NEDD4L held great potential as a novel biomarker and therapeutic target for LUAD.
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Affiliation(s)
- Guoyin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China.,State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, China.,Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Zewen Song
- Department of Oncology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Changjing Wu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - XiaoYan Li
- Department of Blood Transfusion, Shanxi Province People's Hospital, Taiyuan, China
| | - Liping Zhao
- Department of Pathology, Shanxi Province People's Hospital, Taiyuan, China
| | - Binghua Tong
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Zhenni Guo
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Meiqing Sun
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Jin Zhao
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Huina Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Lintao Jia
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, China
| | - Shengqing Li
- Department of Pulmonary and Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Lei Wang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, China. .,Clinical Medical College, Yangzhou University, Yangzhou, China.
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