1
|
Ogbodo AK, Mustafov D, Arora M, Lambrou GI, Braoudaki M, Siddiqui SS. Analysis of SIGLEC12 expression, immunomodulation and prognostic value in renal cancer using multiomic databases. Heliyon 2024; 10:e24286. [PMID: 38268823 PMCID: PMC10803920 DOI: 10.1016/j.heliyon.2024.e24286] [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: 06/04/2023] [Revised: 11/30/2023] [Accepted: 01/05/2024] [Indexed: 01/26/2024] Open
Abstract
Siglecs belong to a family of immune regulatory receptors predominantly found on hematopoietic cells. They interact with Sia, resulting in the activation or inhibition of the immune response. Previous reports have suggested that the SIGLEC12 gene, which encodes the Siglec-XII protein, is expressed in the epithelial tissues and upregulated in carcinomas. However, studies deciphering the role of Siglec-XII in renal cancer (RC) are still unavailable, and here we provide insights on this question. We conducted expression analysis using the Human Protein Atlas and UALCAN databases. The impact of SIGLEC12 on RC prognosis was determined using the KM plotter, and an assessment of immune infiltration with SIGLEC12 was performed using the TIMER database. GSEA was conducted to identify the pathways affected by SIGLEC12. Finally, using GeneMania, we identified Siglec-XII interacting proteins. Our findings indicated that macrophages express SIGLEC12 in the kidney. Furthermore, we hypothesize that Siglec-XII expression might be involved in the increase of primary RC, but this effect may not be dependent on the age of the patient. In the tumour microenvironment, oncogenic pathways appeared to be upregulated by SIGLEC12. Similarly, our analysis suggested that SIGLEC12-related kidney renal papillary cell carcinomas may be more suitable for targeted immunotherapy, such as CTLA-4 and PD-1/PD-L1 inhibitors. These preliminary results suggested that high expression of SIGLEC12 is associated with poor prognosis for RC. Future studies to assess its clinical utility are necessitated.
Collapse
Affiliation(s)
- Amobichukwu K. Ogbodo
- School of Life and Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield AL10 9AB, United Kingdom
- #Current Address: Nuffield Department of Population Health, University of Oxford, Richard Doll Building, Old Road Campus, Oxford OX3 7LF, United Kingdom
| | - Denis Mustafov
- School of Life and Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield AL10 9AB, United Kingdom
- College of Health, Medicine, and Life Science, Brunel University London UB8 3PH, United Kingdom
| | - Mohit Arora
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi 110029, India
| | - George I. Lambrou
- Choremeio Research Laboratory, First Department of Paediatrics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece, Thivon & Levadeias 8, 11527, Goudi, Athens, Greece
- University Research Institute of Maternal and Child Health & Precision Medicine, National and Kapodistrian University of Athens, Thivon & Levadeias 8, 11527 Athens, Greece
| | - Maria Braoudaki
- School of Life and Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield AL10 9AB, United Kingdom
| | - Shoib S. Siddiqui
- School of Life and Medical Sciences, University of Hertfordshire, College Lane Campus, Hatfield AL10 9AB, United Kingdom
| |
Collapse
|
2
|
Ahmed FF, Das AD, Sumi MJ, Islam MZ, Rahman MS, Rashid MH, Alyami SA, Alotaibi N, Azad AKM, Moni MA. Identification of genetic biomarkers, drug targets and agents for respiratory diseases utilising integrated bioinformatics approaches. Sci Rep 2023; 13:19072. [PMID: 37925496 PMCID: PMC10625598 DOI: 10.1038/s41598-023-46455-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 11/01/2023] [Indexed: 11/06/2023] Open
Abstract
Respiratory diseases (RD) are significant public health burdens and malignant diseases worldwide. However, the RD-related biological information and interconnection still need to be better understood. Thus, this study aims to detect common differential genes and potential hub genes (HubGs), emphasizing their actions, signaling pathways, regulatory biomarkers for diagnosing RD and candidate drugs for treating RD. In this paper we used integrated bioinformatics approaches (such as, gene ontology (GO) and KEGG pathway enrichment analysis, molecular docking, molecular dynamic simulation and network-based molecular interaction analysis). We discovered 73 common DEGs (CDEGs) and ten HubGs (ATAD2B, PPP1CB, FOXO1, AKT3, BCR, PDE4D, ITGB1, PCBP2, CD44 and SMARCA2). Several significant functions and signaling pathways were strongly related to RD. We recognized six transcription factor (TF) proteins (FOXC1, GATA2, FOXL1, YY1, POU2F2 and HINFP) and five microRNAs (hsa-mir-218-5p, hsa-mir-335-5p, hsa-mir-16-5p, hsa-mir-106b-5p and hsa-mir-15b-5p) as the important transcription and post-transcription regulators of RD. Ten HubGs and six major TF proteins were considered drug-specific receptors. Their binding energy analysis study was carried out with the 63 drug agents detected from network analysis. Finally, the five complexes (the PDE4D-benzo[a]pyrene, SMARCA2-benzo[a]pyrene, HINFP-benzo[a]pyrene, CD44-ketotifen and ATAD2B-ponatinib) were selected for RD based on their strong binding affinity scores and stable performance as the most probable repurposable protein-drug complexes. We believe our findings will give readers, wet-lab scientists, and pharmaceuticals a thorough grasp of the biology behind RD.
Collapse
Affiliation(s)
- Fee Faysal Ahmed
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
| | - Arnob Dip Das
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Mst Joynab Sumi
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Zohurul Islam
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- High Performance Computing (HPC) Laboratory, Department of Mathematics, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Shahedur Rahman
- Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
- Bioinformatics and Microbial Biotechnology Laboratory, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Md Harun Rashid
- Department of Mathematics, Faculty of Science, Jashore University of Science and Technology, Jashore, 7408, Bangladesh
| | - Salem A Alyami
- Department of Mathematics and Statistics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 13318, Riyadh, Saudi Arabia
| | - Naif Alotaibi
- Department of Mathematics and Statistics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 13318, Riyadh, Saudi Arabia
| | - A K M Azad
- Department of Mathematics and Statistics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), 13318, Riyadh, Saudi Arabia
| | - Mohammad Ali Moni
- Artificial Intelligence and Data Science, School of Health and Rehabilitation Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| |
Collapse
|
3
|
Omit SBS, Akhter S, Rana HK, Rana ARMMH, Podder NK, Rakib MI, Nobi A. Identification of Comorbidities, Genomic Associations, and Molecular Mechanisms for COVID-19 Using Bioinformatics Approaches. BIOMED RESEARCH INTERNATIONAL 2023; 2023:6996307. [PMID: 36685671 PMCID: PMC9848821 DOI: 10.1155/2023/6996307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/09/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023]
Abstract
Several studies have been done to identify comorbidities of COVID-19. In this work, we developed an analytical bioinformatics framework to reveal COVID-19 comorbidities, their genomic associations, and molecular mechanisms accomplishing transcriptomic analyses of the RNA-seq datasets provided by the Gene Expression Omnibus (GEO) database, where normal and infected tissues were evaluated. Using the framework, we identified 27 COVID-19 correlated diseases out of 7,092 collected diseases. Analyzing clinical and epidemiological research, we noticed that our identified 27 diseases are associated with COVID-19, where hypertension, diabetes, obesity, and lung cancer are observed several times in COVID-19 patients. Therefore, we selected the above four diseases and performed assorted analyses to demonstrate the association between COVID-19 and hypertension, diabetes, obesity, and lung cancer as comorbidities. We investigated genomic associations with the cross-comparative analysis and Jaccard's similarity index, identifying shared differentially expressed genes (DEGs) and linking DEGs of COVID-19 and the comorbidities, in which we identified hypertension as the most associated illness. We also revealed molecular mechanisms by identifying statistically significant ten pathways and ten ontologies. Moreover, to understand cellular physiology, we did protein-protein interaction (PPI) analyses among the comorbidities and COVID-19. We also used the degree centrality method and identified ten biomarker hub proteins (IL1B, CXCL8, FN1, MMP9, CXCL10, IL1A, IRF7, VWF, CXCL9, and ISG15) that associate COVID-19 with the comorbidities. Finally, we validated our findings by searching the published literature. Thus, our analytical approach elicited interconnections between COVID-19 and the aforementioned comorbidities in terms of remarkable DEGs, pathways, ontologies, PPI, and biomarker hub proteins.
Collapse
Affiliation(s)
- Shudeb Babu Sen Omit
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Salma Akhter
- Department of Environmental Science and Disaster Management, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh, Dhaka 1207, Bangladesh
| | - A. R. M. Mahamudul Hasan Rana
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Nitun Kumar Podder
- Department of Computer Science and Engineering, Khulna University of Engineering & Technology, Khulna 9203, Bangladesh
| | - Mahmudul Islam Rakib
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Ashadun Nobi
- Department of Computer Science and Telecommunication Engineering, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| |
Collapse
|
4
|
Signatures of Co-Deregulated Genes and Their Transcriptional Regulators in Lung Cancer. Int J Mol Sci 2022; 23:ijms231810933. [PMID: 36142846 PMCID: PMC9504879 DOI: 10.3390/ijms231810933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/13/2022] [Indexed: 11/24/2022] Open
Abstract
Despite the significant progress made towards comprehending the deregulated signatures in lung cancer, these vary from study to study. We reanalyzed 25 studies from the Gene Expression Omnibus (GEO) to detect and annotate co-deregulated signatures in lung cancer and in single-gene or single-drug perturbation experiments. We aimed to decipher the networks that these co-deregulated genes (co-DEGs) form along with their upstream regulators. Differential expression and upstream regulators were computed using Characteristic Direction and Systems Biology tools, including GEO2Enrichr and X2K. Co-deregulated gene expression profiles were further validated across different molecular and immune subtypes in lung adenocarcinoma (TCGA-LUAD) and lung adenocarcinoma (TCGA-LUSC) datasets, as well as using immunohistochemistry data from the Human Protein Atlas, before being subjected to subsequent GO and KEGG enrichment analysis. The functional alterations of the co-upregulated genes in lung cancer were mostly related to immune response regulating the cell surface signaling pathway, in contrast to the co-downregulated genes, which were related to S-nitrosylation. Networks of hub proteins across the co-DEGs consisted of overlapping TFs (SOX2, MYC, KAT2A) and kinases (MAPK14, CSNK2A1 and CDKs). Furthermore, using Connectivity Map we highlighted putative repurposing drugs, including valproic acid, betonicine and astemizole. Similarly, we analyzed the co-DEG signatures in single-gene and single-drug perturbation experiments in lung cancer cell lines. In summary, we identified critical co-DEGs in lung cancer providing an innovative framework for their potential use in developing personalized therapeutic strategies.
Collapse
|
5
|
Liu W, Zhang Y, Huang F, Ma Q, Li C, Liu S, Liang Y, Shi L, Yao Y. The Polymorphism and Expression of EGFL7 and miR-126 Are Associated With NSCLC Susceptibility. Front Oncol 2022; 12:772405. [PMID: 35494025 PMCID: PMC9046731 DOI: 10.3389/fonc.2022.772405] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/21/2022] [Indexed: 01/02/2023] Open
Abstract
Previous investigations have reported that microRNA-126 (miR-126) and its host gene, epidermal growth factor-like domain-containing protein 7 (EGFL7) are involved in lung cancer progression, suggesting EGFL7 and miR-126 play a joint role in lung cancer development. In this study, we analyzed the methylation-associated regulation of EGFL7 and miR-126 in non-small cell lung cancer (NSCLC) and further investigated the association between EGFL7/miR-126 polymorphisms and NSCLC susceptibility in the Han Chinese population. Based on our data, relative to those in adjacent normal tissue, both EGFL7 expression and miR-126 expression were decreased significantly in lung cancer tissue (P = 3x10-4 and P < 1x10-4), and the expression of EGFL7 mRNA and miR-126 was significantly correlated in both NSCLC tissue n = 46, r = 0.43, P = 0.003 and adjacent normal tissue n = 46, r = 0.37, P = 0.011. Differential methylation analysis indicated that methylation levels of multiple CG loci in EGFL7 were significantly higher in the lung cancer samples than in the normal samples (P < 0.01). Moreover, EGFL7 mRNA and miR-126 were significantly upregulated after treatment with the DNA demethylating agent 5-aza-2′-deoxycytidine (5-Aza-CdR) in lung cancer cell lines. In addition, the A allele of rs2297538 was significantly associated with a decreased NSCLC risk (OR = 0.68, 95% CI: 0.52~0.88), and the expression of EGFL7 and miR-126 was significantly lower in rs2297538 homozygous G/G tumor tissue than in A/G+A/A tumor tissue (P = 0.01 and P = 0.002). Our findings suggest that the expression of EGFL7 and miR-126 in NSCLC can be concomitantly downregulated through methylation and the EGFL7/miR-126 polymorphism rs2297538 is correlated with NSCLC risk. Together, these results provide new insights into the pathogenesis of NSCLC.
Collapse
Affiliation(s)
- Weipeng Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Yunyun Zhang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Fengdan Huang
- Graduate School of Yunnan University, Yunnan University, Kunming, China
| | - Qianli Ma
- Department of Thoracic Surgery, The 3rd Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Chuanyin Li
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Shuyuan Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Yan Liang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Li Shi
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
- *Correspondence: Li Shi, ; Yufeng Yao, ;
| | - Yufeng Yao
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
- *Correspondence: Li Shi, ; Yufeng Yao, ;
| |
Collapse
|
6
|
Li Z, Fei H, Lei S, Hao F, Yang L, Li W, Zhang L, Fei R. Identification of HMMR as a prognostic biomarker for patients with lung adenocarcinoma via integrated bioinformatics analysis. PeerJ 2022; 9:e12624. [PMID: 35036134 PMCID: PMC8710063 DOI: 10.7717/peerj.12624] [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: 05/17/2021] [Accepted: 11/19/2021] [Indexed: 12/11/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the most prevalent tumor in lung carcinoma cases and threatens human life seriously worldwide. Here we attempt to identify a prognostic biomarker and potential therapeutic target for LUAD patients. Methods Differentially expressed genes (DEGs) shared by GSE18842, GSE75037, GSE101929 and GSE19188 profiles were determined and used for protein-protein interaction analysis, enrichment analysis and clinical correlation analysis to search for the core gene, whose expression was further validated in multiple databases and LUAD cells (A549 and PC-9) by quantitative real-time PCR (qRT-PCR) and western blot analyses. Its prognostic value was estimated using the Kaplan-Meier method, meta-analysis and Cox regression analysis based on the Cancer Genome Atlas (TCGA) dataset and co-expression analysis was conducted using the Oncomine database. Gene Set Enrichment Analysis (GSEA) was performed to illuminate the potential functions of the core gene. Results A total of 115 shared DEGs were found, of which 24 DEGs were identified as candidate hub genes with potential functions associated with cell cycle and FOXM1 transcription factor network. Among these candidates, HMMR was identified as the core gene, which was highly expressed in LUAD as verified by multiple datasets and cell samples. Besides, high HMMR expression was found to independently predict poor survival in patients with LUAD. Co-expression analysis showed that HMMR was closely related to FOXM1 and was mainly involved in cell cycle as suggested by GSEA. Conclusion HMMR might be served as an independent prognostic biomarker for LUAD patients, which needs further validation in subsequent studies.
Collapse
Affiliation(s)
- Zhaodong Li
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Hongtian Fei
- Department of Pharmacology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Siyu Lei
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Fengtong Hao
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Lijie Yang
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Wanze Li
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China
| | - Laney Zhang
- The College of Arts and Sciences, Cornell University, New York, USA
| | - Rui Fei
- Department of Cell Biology, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, China.,Key Laboratory of Lymphatic Surgery Jilin Province, Jilin University, Changchun, Jilin, China
| |
Collapse
|
7
|
Transcription factors linked to the molecular signatures in the development of hepatocellular carcinoma on a cirrhotic background. Med Oncol 2021; 38:121. [PMID: 34468893 DOI: 10.1007/s12032-021-01567-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/19/2021] [Indexed: 02/06/2023]
Abstract
Mechanisms underlying the regulation of gene expression in cancer have been surveyed for decades to find novel prognostic factors and new targets for molecular targeted therapies in cancer. Because most cases of liver cancer are associated with liver cirrhosis, we aimed to analyze the gene expression signatures and the gene regulatory mechanism in hepatocellular carcinoma (HCC) on a cirrhotic background using high-throughput data analysis. In the present study, three valid array-based datasets containing HCC and liver cirrhosis samples were obtained to identify common differentially expressed genes (DEGs). Moreover, a comprehensive data analysis was conducted based on RNA-Seq data and using Kaplan-Meier curve analysis to find molecular signatures that reduce patients' survival rate. Furthermore, we proposed a gene regulatory network (GRN) to explore the possible regulatory mechanism of these molecular signatures by transcription factors in HCC progression from cirrhosis. Besides, we analyzed protein-protein interactions, gene ontology (GO), and pathway enrichment to elucidate the cellular and molecular function of the GRN elements in HCC. In this way, we found a list of 231 molecular signatures in HCC derived from cirrhosis. We also found the importance of TCF4, RUNX1, HINFP, KDM2B, MAF, JUN, NR5A2, NFYA, and AR as key differentially expressed transcription factors (DETFs) in the progression of HCC from cirrhosis. In conclusion, the identified molecular signatures and their transcription factors propose candidate prognostic markers and possible molecular targets in the progression of HCC.
Collapse
|
8
|
Ramachandran S, Verma AK, Dev K, Goyal Y, Bhatt D, Alsahli MA, Rahmani AH, Almatroudi A, Almatroodi SA, Alrumaihi F, Khan NA. Role of Cytokines and Chemokines in NSCLC Immune Navigation and Proliferation. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:5563746. [PMID: 34336101 PMCID: PMC8313354 DOI: 10.1155/2021/5563746] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/23/2021] [Accepted: 06/28/2021] [Indexed: 12/14/2022]
Abstract
With over a million deaths every year around the world, lung cancer is found to be the most recurrent cancer among all types. Nonsmall cell lung carcinoma (NSCLC) amounts to about 85% of the entire cases. The other 15% owes it to small cell lung carcinoma (SCLC). Despite decades of research, the prognosis for NSCLC patients is poorly understood with treatment options limited. First, this article emphasises on the part that tumour microenvironment (TME) and its constituents play in lung cancer progression. This review also highlights the inflammatory (pro- or anti-) roles of different cytokines (ILs, TGF-β, and TNF-α) and chemokine (CC, CXC, C, and CX3C) families in the lung TME, provoking tumour growth and subsequent metastasis. The write-up also pinpoints recent developments in the field of chemokine biology. Additionally, it covers the role of extracellular vesicles (EVs), as alternate carriers of cytokines and chemokines. This allows the cytokines/chemokines to modulate the EVs for their secretion, trafficking, and aid in cancer proliferation. In the end, this review also stresses on the role of these factors as prognostic biomarkers for lung immunotherapy, apart from focusing on inflammatory actions of these chemoattractants.
Collapse
Affiliation(s)
- Sowmya Ramachandran
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Main Campus, Penang, Malaysia
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Amit K Verma
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Kapil Dev
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Yamini Goyal
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Deepti Bhatt
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Mohammed A Alsahli
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraidah, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraidah, Saudi Arabia
| | - Ahmad Almatroudi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraidah, Saudi Arabia
| | - Saleh A Almatroodi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraidah, Saudi Arabia
| | - Faris Alrumaihi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraidah, Saudi Arabia
| | - Naushad Ahmad Khan
- Department of Biochemistry, Faculty of Medical Sciences, Alatoo International University, Bishkek, Kyrgyzstan
- Department of Trauma and Surgery, Hamad Medical Corporation, Doha, Qatar
| |
Collapse
|
9
|
Li G, Yang J, Zhao G, Shen Z, Yang K, Tian L, Zhou Q, Chen Y, Huang Y. Dysregulation of ferroptosis may involve in the development of non-small-cell lung cancer in Xuanwei area. J Cell Mol Med 2021; 25:2872-2884. [PMID: 33528895 PMCID: PMC7957160 DOI: 10.1111/jcmm.16318] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 02/05/2023] Open
Abstract
The Xuanwei area of Yunnan Province, China, is one of the regions suffering from the highest occurrence and mortality rate of lung cancer in the world. Local residents tend to use bituminous coal as domestic fuel, which causes serious indoor air pollution and is established as the main carcinogen. After the local government carried out furnace and stove reform work, lung cancer rate including incidence and mortality among residents remains high. We herein wonder if there are specific mechanisms at protein level for the development of non-small-cell lung cancer (NSCLC) in this area. We investigated the changes of protein profiling in tumour of the patients from Xuanwei area. Tandem mass tag (TMT) was employed to screen the differential proteins between carcinoma and para-carcinoma tissues. We identified a total of 422 differentially expressed proteins, among which 162 proteins were significantly up-regulated and 260 were downregulated compared to para-carcinoma tissues. Many of the differentially expressed proteins were related to extracellular matrix (ECM)-receptor interaction, focal adhesion, PI3K/AKT pathway and ferroptosis. Further experiments on the two differential proteins, thioredoxin 2 (TXN2) and haptoglobin (HP), showed that the change of their expressions could make the lung cancer cell lines more resistant to erastin or RSL-induced ferroptosis in vitro, and promote the growth of tumour in nude mice. In conclusion, this study revealed that aberrant regulation of ferroptosis may involve in the development of lung cancer in Xuanwei area.
Collapse
Affiliation(s)
- Guangjian Li
- Department of Thoracic Surgery I, The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Hospital, Kunming, China
| | - Jiapeng Yang
- Department of Thoracic Surgery I, The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Hospital, Kunming, China
| | - Guangqiang Zhao
- Department of Thoracic Surgery I, The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Hospital, Kunming, China
| | - Zhenghai Shen
- Department of Thoracic Surgery I, The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Hospital, Kunming, China
| | - Kaiyun Yang
- Department of Thoracic Surgery I, The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Hospital, Kunming, China
| | - Linwei Tian
- Shenzhen Institute of Hong Kong University, Shenzhen, China
| | - Qinghua Zhou
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Chen
- Department of Thoracic Surgery I, The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Hospital, Kunming, China
| | - Yunchao Huang
- Department of Thoracic Surgery I, The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Hospital, Kunming, China
| |
Collapse
|
10
|
Hao M, Wang H, Zhang C, Li C, Wang X. Minichromosome maintenance protein 5 is an important pathogenic factor of oral squamous cell carcinoma. Oncol Lett 2020; 20:109. [PMID: 32831928 PMCID: PMC7439113 DOI: 10.3892/ol.2020.11970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 07/08/2020] [Indexed: 01/29/2023] Open
Abstract
Oral squamous cell carcinoma is one of the most common causes of malignancy-associated death. Early diagnosis of oral squamous cell carcinoma (OSCC) is important in patient treatment and prognostic evaluation. Due to the lack of significant therapeutic benefit, the 5-year survival rate has not improved. Therefore, effective novel markers are needed to improve diagnosis. To determine novel promising diagnostic biomarkers for OSCC, 416 upregulated and 416 downregulated differentially expressed genes were screened from OSCC tissues using an RNA microarray. The results suggested that minichromosome maintenance protein (MCM5) mRNA was significantly overexpressed in OSCC tissues compared with that in adjacent normal tissues. Moreover, silencing of MCM5 expression an OSCC cell line (SCC-15) significantly impaired proliferation and colony formation. Furthermore, negative regulation of the mRNA and protein expression of MCM5 and demonstrated that MCM5 served as a cancer-promoting gene modulating OSCC cell proliferation through induced G2/M phase arrest. In this process, the mRNA expression of cyclin E and cyclin-dependent kinase 2 was downregulated, while p21 expression was upregulated. These results suggested that MCM5 may be an important pathogenic factor of OSCC. High expression levels of MCM5 may serve as a marker for the early diagnosis of OSCC.
Collapse
Affiliation(s)
- Miao Hao
- Scientific Research Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Huiyu Wang
- Department of Stomatology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Chu Zhang
- Department of Stomatology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Chunyan Li
- Department of Stomatology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Xiaofeng Wang
- Department of Stomatology, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| |
Collapse
|
11
|
Time course analysis of large-scale gene expression in incised muscle using correspondence analysis. PLoS One 2020; 15:e0230737. [PMID: 32210454 PMCID: PMC7094855 DOI: 10.1371/journal.pone.0230737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/06/2020] [Indexed: 11/23/2022] Open
Abstract
Studying the time course of gene expression in injured skeletal muscle would help to estimate the timing of injuries. In this study, we investigated large-scale gene expression in incision-injured mouse skeletal muscle by DNA microarray using correspondence analysis (CA). Biceps femoris muscle samples were collected 6, 12, and 24 hours after injury, and RNA was extracted and prepared for microarray analysis. On a 2-dimensional plot by CA, the genes (row score coordinate) located farther from each time series (column score coordinate) had more upregulation at particular times. Each gene was situated in 6 subdivided triangular areas according to the magnitude of the relationship of the fold change (FC) value at each time point compared to the control. In each area, genes for which the ratios of two particular FC values were close to 1 were distributed along the two border lines. There was a tendency for genes whose FC values were almost equal to be distributed near the intersection of these 6 areas. Therefore, the gene marker candidates for estimation of the timing of injuries were detectable according to the location on the CA plot. Moreover, gene sets created by a specific gene and its surrounding genes were composed of genes that showed similar or identical fluctuation patterns to the specific gene. In various analyses on these sets, significant gene ontology term and pathway activity may reflect changes in specific genes. In conclusion, analyses of gene sets based on CA plots is effective for investigation of the time-dependent fluctuation in gene expression after injury.
Collapse
|
12
|
Wang W, Mu S, Zhao Q, Xue L, Wang S. Identification of differentially expressed microRNAs and the potential of microRNA-455-3p as a novel prognostic biomarker in glioma. Oncol Lett 2019; 18:6150-6156. [PMID: 31788089 PMCID: PMC6865136 DOI: 10.3892/ol.2019.10927] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 09/09/2019] [Indexed: 02/07/2023] Open
Abstract
Glioma is an aggressive central nervous system malignancy. MicroRNAs (miRNAs/miRs) have been reported to be involved in the tumorigenesis of numerous types of cancer, including glioma. The present study aimed to identify the differentially expressed miRNAs in glioma, and further explore the clinical value of miR-455-3p in patients with glioma. GEO2R was used for the identification of the differentially expressed miRNAs according to the miRNA expression profiles obtained from the Gene Expression Omnibus database. OncomiR was used to analyze the relationship of miRNAs with the survival outcomes of the patients with glioma. A total of 108 patients with glioma were recruited to examine the expression levels of miR-455-3p and further explore its clinical value. The bioinformatics analysis results suggested that a total of 64 and 48 differentially expressed miRNAs were identified in the GSE90603 and GSE103229 datasets, respectively. There were 12 miRNAs in the overlap of the two datasets, of which three were able to accurately predict overall cancer survival, namely hsa-miR-7-5p, hsa-miR-21-3p and hsa-miR-455-3p. In patients with glioma, miR-455-3p was determined to be significantly upregulated (P<0.001). Additionally, patients with high miR-455-3p expression had significantly lower 5-year overall survival than those with low miR-455-3p expression (log-rank test, P=0.001). Cox regression analysis further determined that miR-455-3p was an independent prognostic indicator for overall survival in patients with glioma (hazard ratio=2.136; 95% CI=1.177–3.877; P=0.013). In conclusion, the present study revealed a series of miRNAs with potential functional roles in the pathogenesis of glioma, and provides findings that indicate miR-455-3p as a promising biomarker for the prognosis of glioma.
Collapse
Affiliation(s)
- Wei Wang
- Department of Neurosurgery, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, P.R. China
| | - Shuwen Mu
- Department of Neurosurgery, Dongfang Affiliated Hospital of Xiamen University, Fuzhou, Fujian 350025, P.R. China
| | - Qingshuang Zhao
- Department of Neurosurgery, 900 Hospital of The Joint Logistics Team, Fuzhou, Fujian 350025, P.R. China
| | - Liang Xue
- Department of Neurosurgery, 900 Hospital of The Joint Logistics Team, Fuzhou, Fujian 350025, P.R. China
| | - Shousen Wang
- Department of Neurosurgery, Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian 350025, P.R. China.,Department of Neurosurgery, 900 Hospital of The Joint Logistics Team, Fuzhou, Fujian 350025, P.R. China
| |
Collapse
|
13
|
Endocan Expression Profile in Different Grades of Oral Squamous Cell Carcinoma. INTERNATIONAL JOURNAL OF CANCER MANAGEMENT 2019. [DOI: 10.5812/ijcm.82413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|