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Yang Y, Huang J, Wang Q, Li J, Yu L, Xie X. Clinicopathologic and prognostic implications of HOXA gene and its associated long-noncoding RNAs expression in non-small cell carcinoma: A meta-analysis. Medicine (Baltimore) 2024; 103:e38087. [PMID: 39121297 PMCID: PMC11315518 DOI: 10.1097/md.0000000000038087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 04/11/2024] [Indexed: 08/11/2024] Open
Abstract
BACKGROUND We conducted an investigation into the correlation between HOXA and associated long-noncoding RNAs, along with their clinicopathologic and prognostic features in non-small cell lung cancer (NSCLC). METHODS A comprehensive search across multiple electronic databases, including PubMed and the Web of Science, was conducted to identify relevant studies. The association between HOXA, clinicopathologic parameters, and prognosis was assessed using relative risk (RR) and hazard ratio (HR) with a 95% confidence interval (CI). Data compilation was performed using STATA 12.0 software. RESULTS A total of 11 trials involving 2058 patients with NSCLC were included in our study. Significant correlations were observed between HOXA-AS2 and TNM stage (III-IV) (RR=2.173, 95% CI: 1.386-5.437, P< 0.05) and HOTTIP and age (≥60-year-old) (RR=2.628, 95% CI: 1.185-5.829, P< 0.05) and non-smoking (RR=0.387, 95% CI: 0.156-0.959, P< 0.05). The combined results indicated a significant association between HOXA5 and increased overall survival (HR = 0.69, 95% CI = 0.57-0.84, P < .001). Additionally, HOXA-AS2, HOXA11 and HOTTIP were identified as potential independent predictors for poorer OS (HOXA-AS2: HR =3.48, 95% CI = 1.95 to 6.21, P < 0.05; HOXA11: HR=1.39, 95%CI = 1.08 to 1.79, P < 0.05; HOTTIP: HR=2.44, 95%CI = 1.10 to 5.42, P < 0.05). The prognostic significance of HOXA1, HOXA3 and HOXA4 was uncertain (HOXA1: HR=1.40, 95% CI =0.28 to 7.06, P > 0.05; HOXA3: HR=1.20, 95% CI = 0.96 to 1.50, P > 0.05; HOXA4: HR=0.97, 95% CI = 0.77 to 1.23, P > 0.05). CONCLUSIONS The HOXA gene family has some potential to emerge as a novel prognostic factor for NSCLC and is correlated with some clinicopathological parameters such as the TNM stage, age and smoking. However, further meticulously designed prospective studies are warranted to substantiate these findings.
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Affiliation(s)
- Yanhui Yang
- Department of Thoracic Surgery, The First People’s Hospital of Neijiang, Neijiang Affiliated Hospital of Chongqing Medical University, Neijiang, Sichuan, P.R. China
| | - JinYang Huang
- Department of Cardiothoracic Surgery, Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, P.R. China
| | - Qi Wang
- Department of Cardiothoracic Surgery, Clinical Medical College of Chengdu Medical College, Chengdu, Sichuan, P.R. China
| | - Ji Li
- Department of Thoracic Surgery, The First People’s Hospital of Neijiang, Neijiang Affiliated Hospital of Chongqing Medical University, Neijiang, Sichuan, P.R. China
| | - Lei Yu
- Department of Thoracic Surgery, The First People’s Hospital of Neijiang, Neijiang Affiliated Hospital of Chongqing Medical University, Neijiang, Sichuan, P.R. China
| | - Xiaoyang Xie
- Department of Thoracic Surgery, The First People’s Hospital of Neijiang, Neijiang Affiliated Hospital of Chongqing Medical University, Neijiang, Sichuan, P.R. China
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Zhou Y, Wu Q, Guo Y. Deciphering the emerging landscape of HOX genes in cardiovascular biology, atherosclerosis and beyond (Review). Int J Mol Med 2024; 53:17. [PMID: 38131178 PMCID: PMC10781420 DOI: 10.3892/ijmm.2023.5341] [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: 08/05/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Atherosclerosis, a dominant driving force underlying multiple cardiovascular events, is an intertwined and chronic inflammatory disease characterized by lipid deposition in the arterial wall, which leads to diverse cardiovascular problems. Despite unprecedented advances in understanding the pathogenesis of atherosclerosis and the substantial decline in cardiovascular mortality, atherosclerotic cardiovascular disease remains a global public health issue. Understanding the molecular landscape of atherosclerosis is imperative in the field of molecular cardiology. Recently, compelling evidence has shown that an important family of homeobox (HOX) genes endows causality in orchestrating the interplay between various cardiovascular biological processes and atherosclerosis. Despite seemingly scratching the surface, such insight into the realization of biology promises to yield extraordinary breakthroughs in ameliorating atherosclerosis. Primarily recapitulated herein are the contributions of HOX in atherosclerosis, including diverse cardiovascular biology, knowledge gaps, remaining challenges and future directions. A snapshot of other cardiovascular biological processes was also provided, including cardiac/vascular development, cardiomyocyte pyroptosis/apoptosis, cardiac fibroblast proliferation and cardiac hypertrophy, which are responsible for cardiovascular disorders. Further in‑depth investigation of HOX promises to provide a potential yet challenging landscape, albeit largely undetermined to date, for partially pinpointing the molecular mechanisms of atherosclerosis. A plethora of new targeted therapies may ultimately emerge against atherosclerosis, which is rapidly underway. However, translational undertakings are crucially important but increasingly challenging and remain an ongoing and monumental conundrum in the field.
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Affiliation(s)
- Yu Zhou
- Medical College, Guizhou University, Guiyang, Guizhou 550025, P.R. China
- Department of Cardiology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Qiang Wu
- Department of Cardiology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Yingchu Guo
- Department of Clinical Laboratory, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
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Xiao F, Zhang H, Ding H, An C, Gu C. Change in expressional level and clinicopathological significance of miR-193b-3p in non-small cell lung cancer. Medicine (Baltimore) 2023; 102:e35918. [PMID: 37960820 PMCID: PMC10637511 DOI: 10.1097/md.0000000000035918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023] Open
Abstract
To investigate and analyze changes in the expression level and clinicopathological significance of miR-193b-3p in non-small cell lung cancer (NSCLC). In the present study, Gene Expression Omnibus (GEO), Targetscan, starBase, and Metastases databases were retrieved for bioinformatics analysis. qRT-PCR was conducted to determine the expression level of miR-193b-3p in the serum or tissues of NSCLC patients. The correlation between the expression level of serum miR-193b-3p and the clinical characteristics of NSCLC patients was analyzed, and receiver operating characteristic (ROC) curves were analyzed to assess the diagnostic significance of serum expression of miR-193b-3p in NSCLC. The GEO2R tool was used to analyze the GSE102286 dataset in the GEO database, indicating that miR-193b-3p is one of the overexpressed miRNAs in NSCLC. Databases, such as TargetScan and starBase, were used to predict miR-193b-3p target genes. Finally, 153 target genes were retrieved, and gene ontology (GO) and KEGG analyses were conducted based on the Metascape database, which indicated that all 153 target genes participated in multiple biological processes and signaling pathways closely correlated with the genesis and progression of NSCLC. miR-193b-3p is highly expressed in the serum and cancer tissues of patients with NSCLC. The high miR-193b-3p expression group had a lower degree of cancer differentiation, a higher proportion of late TNM stage, and a greater incidence of lymph node metastasis. ROC curve analysis reported that the area under the curve was 0.89 (95% CI: 0.85-0.92). High miR-193b-3p expression levels were detected in NSCLC patients and were closely correlated with the degree of malignancy in NSCLC. miR-193b-3p expression levels have a diagnostic effect on NSCLC.
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Affiliation(s)
- Feng Xiao
- Department of Pathology, Affiliated Nantong Hospital 3 of Nantong University (Nantong Third People’s Hospital), Nantong, Jiangsu, China
| | - Haiyan Zhang
- Department of Pathology, Affiliated Nantong Hospital 3 of Nantong University (Nantong Third People’s Hospital), Nantong, Jiangsu, China
| | - Haiping Ding
- Department of Pathology, Affiliated Nantong Hospital 3 of Nantong University (Nantong Third People’s Hospital), Nantong, Jiangsu, China
| | - Chaolun An
- Cardiothoracic Surgery, Affiliated Nantong Hospital 3 of Nantong University (Nantong Third People’s Hospital), Nantong, Jiangsu, China
| | - Chunyan Gu
- Department of Pathology, Affiliated Nantong Hospital 3 of Nantong University (Nantong Third People’s Hospital), Nantong, Jiangsu, China
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Yi C, Wei W, Wan M, Chen Y, Zhang B, Wu W. Expression Patterns of HOX Gene Family Defines Tumor Microenvironment and Immunotherapy in Hepatocellular Carcinoma. Appl Biochem Biotechnol 2023; 195:5072-5093. [PMID: 36976502 DOI: 10.1007/s12010-023-04443-8] [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] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
Hepatocellular carcinoma (HCC) pathophysiology is prevalently related with HOX genes. However, the study on associations of extensive HOX genes with tumor microenvironment and drug sensitivity of HCC remains scarce. The data sets of HCC were downloaded from TCGA, ICGC, and GEO by bioinformatics method and analyzed. Based on a computational frame, HCC samples were divided into a high and a low HOXscore group, and significantly shorter survival time in the high HOXscore was observed relative to low HOXscore group using survival analysis. Gene set enrichment analysis (GSEA) revealed that the high HOXscore group was more likely to be enriched in cancer-specific pathways. Furthermore, the high HOXscore group was involved in the infiltration of inhibitory immune cells. In response to anti-cancer drugs, the high HOXscore group was more sensitive to mitomycin and cisplatin. Importantly, the HOXscore was associated with the therapeutic efficacy of PD-L1 blockade, suggesting that the development of potential drugs targeting these HOX genes to aid the clinical benefits of immunotherapy is needed. In addition, RT-qPCR and immunohistochemistry showed 10 HOX genes mRNA expression was higher in HCC compared to the normal tissues. This study provides a comprehensive analysis of HOX genes family in HCC and revealed the potential function of these HOX genes family in tumor microenvironment (TME) and identified their therapeutic liability in targeted therapy and immunotherapy. Eventually, this work highlights the cross-talk and potential clinical utility of HOX genes family in HCC therapy.
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Affiliation(s)
- Changhong Yi
- Department of Interventional Radiology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Wei Wei
- Department of Interventional, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Maolin Wan
- Department of Interventional, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Ya Chen
- Department of Interventional, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Bo Zhang
- Department of Interventional, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China
| | - Wenze Wu
- Department of Interventional, Jingzhou Hospital Affiliated to Yangtze University, Jingzhou, China.
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HOXA5: A crucial transcriptional factor in cancer and a potential therapeutic target. Biomed Pharmacother 2022; 155:113800. [DOI: 10.1016/j.biopha.2022.113800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/20/2022] Open
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Cui Y, Zhang C, Li Y, Ma S, Cao W, Guan F. HOXD1 functions as a novel tumor suppressor in kidney renal clear cell carcinoma. Cell Biol Int 2021; 45:1246-1259. [PMID: 33559901 DOI: 10.1002/cbin.11568] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 01/07/2021] [Accepted: 02/07/2021] [Indexed: 12/23/2022]
Abstract
Kidney renal clear cell carcinoma (KIRC) is a common malignant tumor in human genitourinary system. Previous studies have shown that the homeobox-D (HOXD) cluster genes, which belong to the homeobox (HOX) family, are involved in the progression of multiple types of cancer. However, the expression profile and prognostic values of the HOXD genes in KIRC remain largely unknown. Herein, we comprehensively analyzed the transcriptional levels and prognosis of HOXD genes in KIRC using four online The Cancer Genome Atlas analysis databases (GEPIA, UALCAN, starBase v3.0, and LinkedOmics). We found that several members of the HOXD gene family were abnormally expressed in KIRC and correlated with patient prognosis. The messenger RNA levels of HOXD1, HOXD8, and HOXD10 were significantly downregulated in KIRC tissues as compared with the normal tissues. Low expression of HOXD1 or HOXD8 predicted poor overall survival (OS) of KIRC patients, and downregulated HOXD1, HOXD3, or HOXD4 indicated unfavorable patient disease-free survival (DFS) in KIRC. Through integrated analysis, we found that HOXD1 was lowly expressed in KIRC and correlated with patient OS, DFS and advanced tumor stages. Moreover, gene set enrichment analysis showed that HOXD1 may be mainly implicated in cell cycle regulation, tumor growth factor-β (TGF-β) and Wnt signaling pathways in KIRC. Furthermore, both loss-of-function and gain-of-function experiments demonstrated that HOXD1 inhibited cell proliferation, cell cycle and the TGF-β signaling in KIRC. Taken together, our findings suggest that HOXD1 is a novel potential tumor suppressor in KIRC.
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Affiliation(s)
- Yuanbo Cui
- Department of Translational Medicine Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China.,School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Chunyan Zhang
- Department of Clinical Laboratory, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Ya Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Shanshan Ma
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Wei Cao
- Department of Translational Medicine Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Fangxia Guan
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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Mahmoud D, El-Sisi O, Sheta M, Ahmed S, Fathy M, Gomaa K, Ramzy T. Association of miR-196a2 and miR-149 single-nucleotide polymorphisms with atherosclerotic ischemic stroke susceptibility. THE EGYPTIAN JOURNAL OF NEUROLOGY, PSYCHIATRY AND NEUROSURGERY 2020. [DOI: 10.1186/s41983-020-00219-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Beside common risk factors for stroke such as diabetes and hypertension, single-nucleotide variants occurring within micro RNA genes have been identified as susceptibility loci for ischemic stroke risk.
Objectives
Investigate the possible association of two variants in pre miRNA sequences, rs11614913 within miR-196a2 C > T and rs2292832 within miR-149 T > C, with ischemic stroke.
Subjects and methods
One hundred ischemic stroke patients and 100 age and sex-matched controls having > 1 risk factor for atherosclerosis were enrolled in a case-control study. Degree of atherosclerosis was assessed using ultrasonography. Micro RNA variants were assessed by real-time PCR TaqMan probe assay.
Results
The TT genotype and T allele frequencies of miR-196a2 C > T were protective against ischemic stroke (OR 0.168, P 0.001; OR 0.482, P < 0.001 respectively). While among miR-149 T > C variants, CC genotype was associated with increased risk by threefold (OR 3.061, P 0.005) and C allele was associated with about 1.9 fold risk of stroke (OR 1.909, P 0.002). Haplotypes analysis revealed miR-196a2T/-149 T allele combination was significantly lower among stroke patients than the controls (P < 0.001) with a protective effect (OR 0.196, 95% CI 0.083-0.466).
Conclusion
A decrease in the incidence of ischemic stroke is associated with miR-196a2 TT genotype and T allele and increases in the likelihood risk of ischemic stroke are associated with CC genotype and C allele within miR-149, and the two miRNAs under study are closely associated with vascular damage responses.
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A cancer stem cell-like phenotype is associated with miR-10b expression in aggressive squamous cell carcinomas. Cell Commun Signal 2020; 18:61. [PMID: 32276641 PMCID: PMC7146875 DOI: 10.1186/s12964-020-00550-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
Background Cutaneous squamous cell carcinomas (cSCC) are the primary cause of premature deaths in patients suffering from the rare skin-fragility disorder recessive dystrophic epidermolysis bullosa (RDEB), which is in marked contrast to the rarely metastasizing nature of these carcinomas in the general population. This remarkable difference is attributed to the frequent development of chronic wounds caused by impaired skin integrity. However, the specific molecular and cellular changes to malignancy, and whether there are common players in different types of aggressive cSCCs, remain relatively undefined. Methods MiRNA expression profiling was performed across various cell types isolated from skin and cSCCs. Microarray results were confirmed by qPCR and by an optimized in situ hybridization protocol. Functional impact of overexpression or knock-out of a dysregulated miRNA was assessed in migration and 3D-spheroid assays. Sample-matched transcriptome data was generated to support the identification of disease relevant miRNA targets. Results Several miRNAs were identified as dysregulated in cSCCs compared to control skin. These included the metastasis-linked miR-10b, which was significantly upregulated in primary cell cultures and in archival biopsies. At the functional level, overexpression of miR-10b conferred the stem cell-characteristic of 3D-spheroid formation capacity to keratinocytes. Analysis of miR-10b downstream effects identified a novel putative target of miR-10b, the actin- and tubulin cytoskeleton-associated protein DIAPH2. Conclusion The discovery that miR-10b mediates an aspect of cancer stemness – that of enhanced tumor cell adhesion, known to facilitate metastatic colonization – provides an important avenue for future development of novel therapies targeting this metastasis-linked miRNA.
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Mishra NK, Southekal S, Guda C. Survival Analysis of Multi-Omics Data Identifies Potential Prognostic Markers of Pancreatic Ductal Adenocarcinoma. Front Genet 2019; 10:624. [PMID: 31379917 PMCID: PMC6659773 DOI: 10.3389/fgene.2019.00624] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 06/14/2019] [Indexed: 12/12/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common and among the deadliest of pancreatic cancers. Its 5-year survival is only ∼8%. Pancreatic cancers are a heterogeneous group of diseases, of which PDAC is particularly aggressive. Like many other cancers, PDAC also starts as a pre-invasive precursor lesion (known as pancreatic intraepithelial neoplasia, PanIN), which offers an opportunity for both early detection and early treatment. Even advanced PDAC can benefit from prognostic biomarkers. However, reliable biomarkers for early diagnosis or those for prognosis of therapy remain an unfulfilled goal for PDAC. In this study, we selected 153 PDAC patients from the TCGA database and used their clinical, DNA methylation, gene expression, and micro-RNA (miRNA) and long non-coding RNA (lncRNA) expression data for multi-omics analysis. Differential methylations at about 12,000 CpG sites were observed in PDAC tumor genomes, with about 61% of them hypermethylated, predominantly in the promoter regions and in CpG-islands. We correlated promoter methylation and gene expression for mRNAs and identified 17 genes that were previously recognized as PDAC biomarkers. Similarly, several genes (B3GNT3, DMBT1, DEPDC1B) and lncRNAs (PVT1, and GATA6-AS) are strongly correlated with survival, which have not been reported in PDAC before. Other genes such as EFR3B, whose biological roles are not well known in mammals are also found to strongly associated with survival. We further identified 406 promoter methylation target loci associated with patients survival, including known esophageal squamous cell carcinoma biomarkers, cg03234186 (ZNF154), and cg02587316, cg18630667, and cg05020604 (ZNF382). Overall, this is one of the first studies that identified survival associated genes using multi-omics data from PDAC patients.
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Affiliation(s)
- Nitish Kumar Mishra
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Siddesh Southekal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, United States
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