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Aouabdi S, Nedjadi T, Alsiary R, Mouffouk F, Ansari HR. Transcriptomics Demonstrates Significant Biological Effect of Growing Stem Cells on RGD-Cotton Scaffold. Tissue Eng Part A 2024. [PMID: 38666698 DOI: 10.1089/ten.tea.2023.0333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024] Open
Abstract
Stem cell therapy provides a viable alternative treatment for degenerated or damaged tissue. Stem cells have been used either alone or in conjunction with an artificial scaffold. The latter provides a structural advantage by enabling the cells to thrive in three-dimensional (3D) settings, closely resembling the natural in vivo environments. Previously, we disclosed the development of a 3D scaffold made from cotton, which was conjugated with arginyl-glycyl-aspartic acid (RGD), to facilitate the growth and proliferation of mesenchymal stem cells (MSCs). This scaffold allowed the MSCs to adhere and proliferate without compromising their viability or their stem cell markers. A comprehensive analysis investigation of the molecular changes occurring in MSCs adhering to the cotton fibers will contribute to the advancement of therapy. The objective of this study is to analyze the molecular processes occurring in the growth of MSCs on a cotton-RGD conjugated-based scaffold by examining their gene expression profiles. To achieve this, we conducted an experiment where MSCs were seeded with and without the scaffold for a duration of 48 h. Subsequently, cells were collected for RNA extraction, cDNA synthesis, and whole-transcriptomic analysis performed on both populations. Our analysis revealed several upregulated and downregulated differently expressed genes in the MSCs adhering to the scaffold compared with the control cells. Through gene ontology analysis, we were able to identify enriched biological processes, molecular functions, pathways, and protein-protein interactions in these differentially expressed genes. Our data suggest that the scaffold may have the potential to enhance osteogenesis in the MSCs. Furthermore, our results indicate that the scaffold does not induce oxidative stress, inflammation, or aging in the MSCs. These findings provide valuable insights for the application of MSCs in tissue engineering and regenerative medicine.
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Affiliation(s)
- Sihem Aouabdi
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Taoufik Nedjadi
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Rawiah Alsiary
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Fouzi Mouffouk
- Department of Chemistry, Kuwait University, Kuwait, Kuwait
| | - Hifzur Rahman Ansari
- King Abdullah International Medical Research Center, Jeddah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
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2
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Mohamed TIA, Ezugwu AE, Fonou-Dombeu JV, Mohammed M, Greeff J, Elbashir MK. A novel feature selection algorithm for identifying hub genes in lung cancer. Sci Rep 2023; 13:21671. [PMID: 38066059 PMCID: PMC10709567 DOI: 10.1038/s41598-023-48953-1] [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: 07/06/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Lung cancer, a life-threatening disease primarily affecting lung tissue, remains a significant contributor to mortality in both developed and developing nations. Accurate biomarker identification is imperative for effective cancer diagnosis and therapeutic strategies. This study introduces the Voting-Based Enhanced Binary Ebola Optimization Search Algorithm (VBEOSA), an innovative ensemble-based approach combining binary optimization and the Ebola optimization search algorithm. VBEOSA harnesses the collective power of the state-of-the-art classification models through soft voting. Moreover, our research applies VBEOSA to an extensive lung cancer gene expression dataset obtained from TCGA, following essential preprocessing steps including outlier detection and removal, data normalization, and filtration. VBEOSA aids in feature selection, leading to the discovery of key hub genes closely associated with lung cancer, validated through comprehensive protein-protein interaction analysis. Notably, our investigation reveals ten significant hub genes-ADRB2, ACTB, ARRB2, GNGT2, ADRB1, ACTG1, ACACA, ATP5A1, ADCY9, and ADRA1B-each demonstrating substantial involvement in the domain of lung cancer. Furthermore, our pathway analysis sheds light on the prominence of strategic pathways such as salivary secretion and the calcium signaling pathway, providing invaluable insights into the intricate molecular mechanisms underpinning lung cancer. We also utilize the weighted gene co-expression network analysis (WGCNA) method to identify gene modules exhibiting strong correlations with clinical attributes associated with lung cancer. Our findings underscore the efficacy of VBEOSA in feature selection and offer profound insights into the multifaceted molecular landscape of lung cancer. Finally, we are confident that this research has the potential to improve diagnostic capabilities and further enrich our understanding of the disease, thus setting the stage for future advancements in the clinical management of lung cancer. The VBEOSA source codes is publicly available at https://github.com/TEHNAN/VBEOSA-A-Novel-Feature-Selection-Algorithm-for-Identifying-hub-Genes-in-Lung-Cancer .
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Affiliation(s)
- Tehnan I A Mohamed
- School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, KwaZulu-Natal, King Edward Avenue, Pietermaritzburg Campus, Pietermaritzburg, 3201, South Africa
- Department of Computer Science, Faculty of Mathematical and Computer Sciences, University of Gezira, Wad Madani, 11123, Sudan
| | - Absalom E Ezugwu
- Unit for Data Science and Computing, North-West University, Potchefstroom, South Africa.
| | - Jean Vincent Fonou-Dombeu
- School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, KwaZulu-Natal, King Edward Avenue, Pietermaritzburg Campus, Pietermaritzburg, 3201, South Africa
| | - Mohanad Mohammed
- School of Mathematics, Statistics, and Computer Science, University of KwaZulu-Natal, KwaZulu-Natal, King Edward Avenue, Pietermaritzburg Campus, Pietermaritzburg, 3201, South Africa
| | - Japie Greeff
- School of Computer Science and Information Systems, Faculty of Natural and Agricultural Sciences, North-West University, Vanderbijlpark, South Africa
| | - Murtada K Elbashir
- Department of Information Systems, College of Computer and Information Sciences, Jouf University, 72388, Sakaka, Saudi Arabia
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Khan MS, Hanif W, Alsakhen N, Jabbar B, Shamkh IM, Alsaiari AA, Almehmadi M, Alghamdi S, Shakoori A, Al Farraj DA, Almutairi SM, Hussein Issa Mohammed Y, Abouzied AS, Rehman AU, Huwaimel B. Isoform switching leads to downregulation of cytokine producing genes in estrogen receptor positive breast cancer. Front Genet 2023; 14:1230998. [PMID: 37900178 PMCID: PMC10611502 DOI: 10.3389/fgene.2023.1230998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023] Open
Abstract
Objective: Estrogen receptor breast cancer (BC) is characterized by the expression of estrogen receptors. It is the most common cancer among women, with an incidence rate of 2.26 million cases worldwide. The aim of this study was to identify differentially expressed genes and isoform switching between estrogen receptor positive and triple negative BC samples. Methods: The data were collected from ArrayExpress, followed by preprocessing and subsequent mapping from HISAT2. Read quantification was performed by StringTie, and then R package ballgown was used to perform differential expression analysis. Functional enrichment analysis was conducted using Enrichr, and then immune genes were shortlisted based on the ScType marker database. Isoform switch analysis was also performed using the IsoformSwitchAnalyzeR package. Results: A total of 9,771 differentially expressed genes were identified, of which 86 were upregulated and 117 were downregulated. Six genes were identified as mainly associated with estrogen receptor positive BC, while a novel set of ten genes were found which have not previously been reported in estrogen receptor positive BC. Furthermore, alternative splicing and subsequent isoform usage in the immune system related genes were determined. Conclusion: This study identified the differential usage of isoforms in the immune system related genes in cancer cells that suggest immunosuppression due to the dysregulation of CXCR chemokine receptor binding, iron ion binding, and cytokine activity.
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Affiliation(s)
| | - Waqar Hanif
- Department of Bioinformatics, Department of Sciences, School of Interdisciplinary Engineering & Science (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Nada Alsakhen
- Department of Chemistry, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Basit Jabbar
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Israa M. Shamkh
- Chemo and Bioinformatics Lab, Bio Search Research Institution, Giza, Egypt
| | - Ahad Amer Alsaiari
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Mazen Almehmadi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Afnan Shakoori
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Dunia A. Al Farraj
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saeedah Musaed Almutairi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Amr S. Abouzied
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, Saudi Arabia
- Department of Pharmaceutical Chemistry, National Organization for Drug Control and Research (NOD CAR), Giza, Egypt
| | - Aziz-Ur Rehman
- Keystone Pharmacogenomics LLC, Bensalem, PA, United States
| | - Bader Huwaimel
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Hail, Hail, Saudi Arabia
- Medical and Diagnostic Research Center, University of Hail, Hail, Saudi Arabia
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4
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Bölük A, Yavuz M, Takanlou MS, Avcı ÇB, Demircan T. In vitro anti-carcinogenic effect of andarine as a selective androgen receptor modulator on MIA-PaCa-2 cells by decreased proliferation and cell-cycle arrest at G0/G1 phase. Biochem Biophys Res Commun 2023; 671:132-139. [PMID: 37302286 DOI: 10.1016/j.bbrc.2023.06.016] [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: 05/24/2023] [Revised: 05/25/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023]
Abstract
Pancreatic cancer (PC) continues to be devastating due to its highly malignant nature and poor prognosis. The limited benefits of the chemotherapeutic drugs and increasing resistance pose a critical challenge to overcome and warrant investigations for new therapeutic agents. Several preclinical and clinical studies have suggested a possible role of the androgen receptor (AR) signaling pathway in PC development and progression. Nevertheless, the studies are limited and inconclusive in explaining the molecular link between AR signaling and PC. Selective androgen receptor modulators (SARMs) are small molecule drugs with high affinity for the androgen receptor. SARMs elicit selective anabolic activities while abrogating undesired androgenic side effects. There is no study focusing on the utility of SARMs as inhibitors of PC. Here, we report the first study evaluating the possible anti-carcinogenic influences of andarine, a member of the SARMs, on PC. The data we presented here has illustrated that andarine repressed PC cell growth and proliferation via cell cycle arrest at G0/G1 phase. Gene expression analysis revealed that it downregulates CDKN1A expression level accordingly. Furthermore, we established that the anti-carcinogenic activity of andarine is not mediated by the PI3K/AKT/mTOR signaling pathway, a crucial regulator of cell survival. Our findings suggest that andarine might be considered as a prospective drug for PC.
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Affiliation(s)
- Aydın Bölük
- School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Mervenur Yavuz
- Institute of Natural Sciences, Department of Molecular Biology and Genetics, Muğla Sıtkı Koçman University, Muğla, Turkey
| | - Maryam Sabour Takanlou
- Institute of Health Sciences, Department of Medical Biology, Ege University, İzmir, Turkey
| | - Çığır Biray Avcı
- Medical Biology Department, School of Medicine, Ege University, İzmir, Turkey
| | - Turan Demircan
- Medical Biology Department, School of Medicine, Muğla Sıtkı Koçman University, Muğla, Turkey.
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5
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Li D, Liang H, Qin P, Wang J. A self-training subspace clustering algorithm based on adaptive confidence for gene expression data. Front Genet 2023; 14:1132370. [PMID: 37025450 PMCID: PMC10070828 DOI: 10.3389/fgene.2023.1132370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023] Open
Abstract
Gene clustering is one of the important techniques to identify co-expressed gene groups from gene expression data, which provides a powerful tool for investigating functional relationships of genes in biological process. Self-training is a kind of important semi-supervised learning method and has exhibited good performance on gene clustering problem. However, the self-training process inevitably suffers from mislabeling, the accumulation of which will lead to the degradation of semi-supervised learning performance of gene expression data. To solve the problem, this paper proposes a self-training subspace clustering algorithm based on adaptive confidence for gene expression data (SSCAC), which combines the low-rank representation of gene expression data and adaptive adjustment of label confidence to better guide the partition of unlabeled data. The superiority of the proposed SSCAC algorithm is mainly reflected in the following aspects. 1) In order to improve the discriminative property of gene expression data, the low-rank representation with distance penalty is used to mine the potential subspace structure of data. 2) Considering the problem of mislabeling in self-training, a semi-supervised clustering objective function with label confidence is proposed, and a self-training subspace clustering framework is constructed on this basis. 3) In order to mitigate the negative impact of mislabeled data, an adaptive adjustment strategy based on gravitational search algorithm is proposed for label confidence. Compared with a variety of state-of-the-art unsupervised and semi-supervised learning algorithms, the SSCAC algorithm has demonstrated its superiority through extensive experiments on two benchmark gene expression datasets.
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Affiliation(s)
- Dan Li
- Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Hongnan Liang
- Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, Liaoning, China
| | - Pan Qin
- Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, Liaoning, China
- *Correspondence: Pan Qin, ; Jia Wang,
| | - Jia Wang
- Department of Breast Surgery, The Second Hospital of Dalian Medical University, Dalian, Liaoning, China
- *Correspondence: Pan Qin, ; Jia Wang,
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6
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Integrative, In Silico and Comparative Analysis of Breast Cancer Secretome Highlights Invasive-Ductal-Carcinoma-Grade Progression Biomarkers. Cancers (Basel) 2022; 14:cancers14163854. [PMID: 36010848 PMCID: PMC9406168 DOI: 10.3390/cancers14163854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 11/16/2022] Open
Abstract
Globally, BC is the most frequently diagnosed cancer in women. The aim of this study was to identify novel secreted biomarkers that may indicate progression to high-grade BC malignancies and therefore predict metastatic potential. A total of 33 studies of breast cancer and 78 of other malignancies were screened via a systematic review for eligibility, yielding 26 datasets, 8 breast cancer secretome datasets, and 18 of other cancers that were included in the comparative secretome analysis. Sequential bioinformatic analysis using online resources enabled the identification of enriched GO_terms, overlapping clusters, and pathway reconstruction. This study identified putative predictors of IDC grade progression and their association with breast cancer patient mortality outcomes, namely, HSPG2, ACTG1, and LAMA5 as biomarkers of in silico pathway prediction, offering a putative approach by which the abovementioned proteins may mediate their effects, enabling disease progression. This study also identified ITGB1, FBN1, and THBS1 as putative pan-cancer detection biomarkers. The present study highlights novel, putative secretome biomarkers that may provide insight into the tumor biology and could inform clinical decision making in the context of IDC management in a non-invasive manner.
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7
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Nisar M, Paracha RZ, Adil S, Qureshi SN, Janjua HA. An Extensive Review on Preclinical and Clinical Trials of Oncolytic Viruses Therapy for Pancreatic Cancer. Front Oncol 2022; 12:875188. [PMID: 35686109 PMCID: PMC9171400 DOI: 10.3389/fonc.2022.875188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
Chemotherapy resistance and peculiar tumor microenvironment, which diminish or mitigate the effects of therapies, make pancreatic cancer one of the deadliest malignancies to manage and treat. Advanced immunotherapies are under consideration intending to ameliorate the overall patient survival rate in pancreatic cancer. Oncolytic viruses therapy is a new type of immunotherapy in which a virus after infecting and lysis the cancer cell induces/activates patients’ immune response by releasing tumor antigen in the blood. The current review covers the pathways and molecular ablation that take place in pancreatic cancer cells. It also unfolds the extensive preclinical and clinical trial studies of oncolytic viruses performed and/or undergoing to design an efficacious therapy against pancreatic cancer.
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Affiliation(s)
- Maryum Nisar
- School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Rehan Zafar Paracha
- School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Sidra Adil
- School of Interdisciplinary Engineering & Sciences (SINES), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | | | - Hussnain Ahmed Janjua
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, Pakistan
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8
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Qin T, Xiao Y, Qian W, Wang X, Gong M, Wang Q, An R, Han L, Duan W, Ma Q, Wang Z. HGF/c-Met pathway facilitates the perineural invasion of pancreatic cancer by activating the mTOR/NGF axis. Cell Death Dis 2022; 13:387. [PMID: 35449152 PMCID: PMC9023560 DOI: 10.1038/s41419-022-04799-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/22/2022] [Accepted: 03/30/2022] [Indexed: 12/13/2022]
Abstract
Perineural invasion (PNI) is a pathologic feature of pancreatic cancer and is associated with poor outcomes, metastasis, and recurrence in pancreatic cancer patients. However, the molecular mechanism of PNI remains unclear. The present study aimed to investigate the mechanism that HGF/c-Met pathway facilitates the PNI of pancreatic cancer. In this study, we confirmed that c-Met expression was correlated with PNI in pancreatic cancer tissues. Activating the HGF/c-Met signaling pathway potentiated the expression of nerve growth factor (NGF) to recruit nerves and promote the PNI. Activating the HGF/c-Met signaling pathway also enhanced the migration and invasion ability of cancer cells to facilitate cancer cells invading nerves. Mechanistically, HGF/c-Met signaling pathway can active the mTOR/NGF axis to promote the PNI of pancreatic cancer. Additionally, we found that knocking down c-Met expression inhibited cancer cell migration along the nerve, reduced the damage of the sciatic nerve caused by cancer cells and protected the function of the sciatic nerve in vivo. Taken together, our findings suggest a supportive mechanism of the HGF/c-Met signaling pathway in promoting PNI by activating the mTOR/NGF axis in pancreatic cancer. Blocking the HGF/c-Met signaling pathway may be an effective target for the treatment of PNI.
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Affiliation(s)
- Tao Qin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ying Xiao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Weikun Qian
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xueni Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Mengyuan Gong
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Qiqi Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Rui An
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Liang Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Centre for Pancreatic Diseases of Xi'an Jiaotong University, Xi'an, China
| | - Wanxing Duan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
- Centre for Pancreatic Diseases of Xi'an Jiaotong University, Xi'an, China
| | - Qingyong Ma
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
- Centre for Pancreatic Diseases of Xi'an Jiaotong University, Xi'an, China.
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, China.
| | - Zheng Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
- Centre for Pancreatic Diseases of Xi'an Jiaotong University, Xi'an, China.
- Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Xi'an, China.
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Nisar M, Paracha RZ, Gul A, Arshad I, Ejaz S, Murad D, Khan S, Mustansar Z. Interaction Analysis of Adenovirus L5 Protein With Pancreatic Cancer Cell Surface Receptor to Analyze Its Affinity for Oncolytic Virus Therapy. Front Oncol 2022; 12:832277. [PMID: 35359382 PMCID: PMC8960272 DOI: 10.3389/fonc.2022.832277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
This study seeks to investigate the interaction profile of the L5 protein of oncolytic adenovirus with the overexpressed surface receptors of pancreatic cancer. This is an important area of research because pancreatic cancer is one of the most fatal malignancies with a very low patient survival rate. Multiple therapies to date to improve the survival rate are reported; however, they show a comparatively low success rate. Among them, oncolytic virus therapy is a type of immunotherapy that is currently under deliberation by researchers for multiple cancer types in various clinical trials. Talimogene laherparepvec (T-VEC) is the first oncolytic virus approved by the US Food and Drug Administration (FDA) for melanoma. The oncolytic virus not only kills cancer cells but also activates the anticancer immune response. Therefore, it is preferred over others to deal with aggressive pancreatic cancer. The efficacy of therapy primarily depends on how effectively the oncolytic virus enters and infects the cancer cell. Cell surface receptors and their interactions with virus coat proteins are a crucial step for oncolytic virus entry and a pivotal determinant. The L5 proteins of the virus coat are the first to interact with host cell surface receptors. Therefore, the objective of this study is to analyze the interaction profile of the L5 protein of oncolytic adenovirus with overexpressed surface receptors of pancreatic cancer. The L5 proteins of three adenovirus serotypes HAdV2, HAdV5, and HAdV3 were utilized in this study. Overexpressed pancreatic cancer receptors include SLC2A1, MET, IL1RAP, NPR3, GABRP, SLC6A6, and TMPRSS4. The protein structures of viral and cancer cell protein were docked using the High Ambiguity Driven protein–protein DOCKing (HADDOCK) server. The binding affinity and interaction profile of viral proteins against all the receptors were analyzed. Results suggest that the HAdV3 L5 protein shows better interaction as compared to HAdV2 and HAdV5 by elucidating high binding affinity with 4 receptors (NPR3, GABRP, SLC6A6, and TMPRSS4). The current study proposed that HAdV5 or HAdV2 virus pseudotyped with the L5 protein of HAdV3 can be able to effectively infect pancreatic cancer cells. Moreover, the current study surmises that the affinity maturation of HAdV3 L5 can enhance virus attachment with all the receptors of cancer cells.
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Affiliation(s)
- Maryum Nisar
- Research Center for Modelling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Rehan Zafar Paracha
- Research Center for Modelling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan
- *Correspondence: Rehan Zafar Paracha,
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Iqra Arshad
- Research Center for Modelling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Saima Ejaz
- Research Center for Modelling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Didar Murad
- Research Center for Modelling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Shahzeb Khan
- Department of Pharmacy, University of Malakand, Chakdara, Pakistan
- Discipline of Pharmaceutical Sciences, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Zartasha Mustansar
- Research Center for Modelling and Simulation (RCMS), National University of Sciences and Technology (NUST), Islamabad, Pakistan
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10
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Zhang L, Li Y, Dong YC, Guan CY, Tian S, Lv XD, Li JH, Su X, Xia HF, Ma X. Transplantation of umbilical cord-derived mesenchymal stem cells promotes the recovery of thin endometrium in rats. Sci Rep 2022; 12:412. [PMID: 35013490 PMCID: PMC8748676 DOI: 10.1038/s41598-021-04454-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/20/2021] [Indexed: 12/25/2022] Open
Abstract
The endometrium plays a critical role in embryo implantation and pregnancy, and a thin uterus is recognized as a key factor in embryo implantation failure. Umbilical cord mesenchymal stem cells (UC-MSCs) have attracted interest for the repair of intrauterine adhesions. The current study investigated the repair of thin endometrium in rats using the UC-MSCs and the mechanisms involved. Rats were injected with 95% ethanol to establish a model of thin endometrium. The rats were randomly divided into normal, sham, model, and UC-MSCs groups. Endometrial morphological alterations were observed by hematoxylin-eosin staining and Masson staining, and functional restoration was assessed by testing embryo implantation. The interaction between UC-MSCs and rat endometrial stromal cells (ESCs) was evaluated using a transwell 3D model and immunocytochemistry. Microarray mRNA and miRNA platforms were used for miRNA-mRNA expression profiling. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses were performed to identify the biological processes, molecular functions, cellular components, and pathways of endometrial injury and UC-MSCs transplantation repair and real-time quantitative reverse transcription PCR (qRT-PCR) was performed to further identify the expression changes of key molecules in the pathways. Endometrium thickness, number of glands, and the embryo implantation numbers were improved, and the degree of fibrosis was significantly alleviated by UC-MSCs treatment in the rat model of thin endometrium. In vitro cell experiments showed that UC-MSCs migrated to injured ESCs and enhanced their proliferation. miRNA microarray chip results showed that expression of 45 miRNAs was downregulated in the injured endometrium and upregulated after UC-MSCs transplantation. Likewise, expression of 39 miRNAs was upregulated in the injured endometrium and downregulated after UC-MSCs transplantation. The miRNA-mRNA interactions showed the changes in the miRNA and mRNA network during the processes of endometrial injury and repair. GO and KEGG analyses showed that the process of endometrial injury was mainly attributed to the decomposition of the extracellular matrix (ECM), protein degradation and absorption, and accompanying inflammation. The process of UC-MSCs transplantation and repair were accompanied by the reconstruction of the ECM, regulation of chemokines and inflammation, and cell proliferation and apoptosis. The key molecules involved in ECM-receptor interaction pathways were further verified by qRT-PCR. Itga1 and Thbs expression decreased in the model group and increased by UC-MSCs transplantation, while Laminin and Collagen expression increased in both the model group and MSCs group, with greater expression observed in the latter. This study showed that UC-MSCs transplantation could promote recovery of thin endometrial morphology and function. Furthermore, it revealed the expression changes of miRNA and mRNA after endometrial injury and UC-MSCs transplantation repair processed, and signaling pathways that may be involved in endometrial injury and repair.
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Affiliation(s)
- Lu Zhang
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Ying Li
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Yi-Chao Dong
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Chun-Yi Guan
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Shi Tian
- Haidian Maternal and Child Health Hospital, Beijing, China
| | - Xiao-Dan Lv
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Jian-Hui Li
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Xing Su
- National Research Institute for Family Planning, Beijing, 100081, China
- Graduate School, Peking Union Medical College, Beijing, China
| | - Hong-Fei Xia
- National Research Institute for Family Planning, Beijing, 100081, China.
- Graduate School, Peking Union Medical College, Beijing, China.
| | - Xu Ma
- National Research Institute for Family Planning, Beijing, 100081, China.
- Graduate School, Peking Union Medical College, Beijing, China.
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Du B, Su F, Wang H, Liang H, Song X, Shao Z, Wei Y. Identification of potential core genes at single-cell level contributing to pathogenesis of pancreatic ductal adenocarcinoma through bioinformatics analysis. Cancer Biomark 2022; 34:1-12. [PMID: 35068444 DOI: 10.3233/cbm-210271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) prognosis has not improved over the last decades because of the lack of effective diagnostic and therapeutic methods in the early stage of the disease. METHODS Several gene expression profiles were downloaded from the Expression Omnibus (GEO) database. We calculated the differentially expressed mRNAs (DEGs) and miRNAs (DEmiRs). Then, we constructed a miRNA-mRNA regulatory network by using the miRWalk database. For the DEGs regulated by DEmiRs, we introduced GEPIA to confirm these DEGs' expression and effect on overall survival. We used other GEO datasets and mRNA-miRNA target databases to validate these DEGs and their relationship with DEmiRs. All these potential core DEGs regulated by DEmiRs were also analyzed at the single-cell level to confirm their cell type source. RESULTS CCNB2 and KCNN4, which were regulated by several micro RNAs, showed relatively high expression levels in PDAC patients and significant association with worse overall survival. Furthermore, we identified many DEGs at single-cell level and found that 10 oncogenes were significantly upregulated in type 2 ductal cell type, thereby further demonstrating that type 2 ductal cells might be major sources of malignant cells and are valuable therapeutic targets in PDAC. CONCLUSIONS Our data added some new insights into the molecular mechanism of PDAC and may be helpful for finding potential biomarkers for diagnosis. These discovery at single-cell level may also be useful for developing new therapeutic targets for PDAC patients.
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Affiliation(s)
- Bingqing Du
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fang Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hao Wang
- Department of Gastrointestinal Surgery, Lab of Surgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Huihong Liang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaodong Song
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zili Shao
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yisheng Wei
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Gastrointestinal Surgery, Lab of Surgery, the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
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