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Dual-Specificity Tyrosine Phosphorylation-Regulated Kinase 3 Expression and Its Correlation with Prognosis and Growth of Serous Ovarian Cancer: Correlation of DYRK3 with Ovarian Cancer Survival Int. J. Genom. (IF 2.9) Pub Date : 2024-3-18 Jia Sun, Yingzi Zhang, Aijie Li, Hao Yu
Background. Epithelial ovarian cancer, primarily serous ovarian cancer (SOC), stands as a predominant cause of cancer-related mortality among women globally, emphasizing the urgent need for comprehensive research into its molecular underpinnings. Within this context, the dual-specificity tyrosine phosphorylation-regulated kinase 3 (DYRK3) has emerged as a potential key player with implications for
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Pangenome Analysis of Helicobacter pylori Isolates from Selected Areas of Africa Indicated Diverse Antibiotic Resistance and Virulence Genes Int. J. Genom. (IF 2.9) Pub Date : 2024-3-4 Biigba Yakubu, Edwin Moses Appiah, Andrews Frimpong Adu
The challenge facing Helicobacter pylori (H. pylori) infection management in some parts of Africa is the evolution of drug-resistant species, the lack of gold standard in diagnostic methods, and the ineffectiveness of current vaccines against the bacteria. It is being established that even though clinical consequences linked to the bacteria vary geographically, there is rather a generic approach to
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A Novel Splicing Mutation Leading to Wiskott-Aldrich Syndrome from a Family Int. J. Genom. (IF 2.9) Pub Date : 2024-2-19 Lingyu Wang, Jie Zhang, Linna Lu, Juan Ren, Yaofang Zhang, Lidong Zhao, Wukang Shen, Xucheng Hu, Shuai Fang, Xiaomei Lu, Gang Wang, Linhua Yang
Wiskott-Aldrich syndrome (WAS) is a rare X-linked recessive genetic disease characterized by clinical symptoms such as eczema, thrombocytopenia with small platelets, immune deficiency, prone to autoimmune diseases, and malignant tumors. This disease is caused by mutations of the WAS gene encoding WASprotein (WASP). The locus and type of mutations of the WAS gene and the expression quantity of WASP
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Overexpression of FERM Domain Containing Kindlin 2 (FERMT2) in Fibroblasts Correlates with EMT and Immunosuppression in Gastric Cancer Int. J. Genom. (IF 2.9) Pub Date : 2024-2-6 Sheng-yan Yin, Yuan-jie Liu, Jie-pin Li, Jian Liu
The mesenchymal feature, dominated by epithelial mesenchymal transition (EMT) and stromal cell activation, is one of the main reasons for the aggressive nature of tumors, yet it remains poorly understood. In gastric cancer (GC), the fermitin family homolog-2 (FERMT2) is involved in macrophage signaling, promoting migration and invasion. However, the function of FERMT2 in fibroblasts remains unclear
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Identification of ZIC2 as a Potential Biomarker Linked with the Clinical Progression and Immune Infiltration of Oral Cancer: A Multicenter Study Int. J. Genom. (IF 2.9) Pub Date : 2024-1-24 Li Gao, Shi-Bai Yan, Fang-Cheng Jiang, Zhi-Guang Huang, Dong-Ming Li, Yu-Lu Tang, Jia-Yuan Luo, Gang Chen, Dan-Ming Wei
Aim. To investigate the specific expression profile, clinicopathological significance and mechanism of Zic family member 2 (ZIC2) in oral cancer were unclear. Patients and Methods. We explored the expression pattern and clinicopathological significance of ZIC2 in oral cancer through performing in-house tissue microarray and integrated analysis global RNA-seq and microarrays containing large samples
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Physiological Characteristic Changes and Transcriptome Analysis of Maize (Zea mays L.) Roots under Drought Stress Int. J. Genom. (IF 2.9) Pub Date : 2024-1-17 Chenglin Zou, Hua Tan, Kaijian Huang, Ruining Zhai, Meng Yang, Aihua Huang, Xinxing Wei, Runxiu Mo, Faqian Xiong
Water deficit is a key limiting factor for limiting yield in maize (Zea mays L.). It is crucial to elucidate the molecular regulatory networks of stress tolerance for genetic enhancement of drought tolerance. The mechanism of drought tolerance of maize was explored by comparing physiological and transcriptomic data under normal conditions and drought treatment at polyethylene glycol- (PEG-) induced
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A Mid-Density Single-Nucleotide Polymorphism Panel for Molecular Applications in Cowpea (Vigna unguiculata (L.) Walp) Int. J. Genom. (IF 2.9) Pub Date : 2024-1-9 Patrick Obia Ongom, Christian Fatokun, Abou Togola, Ana Luisa Garcia-Oliveira, Eng Hwa Ng, Andrzej Kilian, Stefano Lonardi, Timothy J. Close, Ousmane Boukar
Molecular markers are increasingly being deployed to accelerate genetic gain in crop plants. The objective of this study was to assess the potential of a mid-density genotyping panel for molecular applications in cowpea breeding. A core set of 2,602 targeted diversity array technology (DArTag) single-nucleotide polymorphisms (SNPs) was designed from an existing 51,128 Cowpea iSelect Consortium Array
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Transcription Analysis of the THBS2 Gene through Regulation by Potential Noncoding Diagnostic Biomarkers and Oncogenes of Gastric Cancer in the ECM-Receptor Interaction Signaling Pathway: Integrated System Biology and Experimental Investigation Int. J. Genom. (IF 2.9) Pub Date : 2023-12-22 Ali Barani, Kamyar Beikverdi, Benyamin Mashhadi, Naeimeh Parsapour, Mohammad Rezaei, Pegah Javid, Mansoureh Azadeh
Background. Gastric cancer (GC) is the second most frequent cause of cancer-related death worldwide and the fourth most common malignancy. Despite significant improvements in patient survival over the past few decades, the prognosis for patients with GC remains dismal because of the high recurrence rate. In this comprehensive system biology and experimental investigation, we aimed to find new novel
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Transmembrane and Ubiquitin-Like Domain-Containing 1 Promotes Glioma Growth and Indicates Unfavorable Prognosis Int. J. Genom. (IF 2.9) Pub Date : 2023-12-19 Yinggang Liu, Changcheng Cai, Ke Wu, Libo Hu
Background. Ubiquitin-related proteins have garnered increasing attention for their roles in tumorigenesis. Transmembrane and ubiquitin-like domain-containing 1 (TMUB1) is a recently discovered protein in the ubiquitin-like domain family, yet its involvement in glioma remains poorly understood. This study is aimed at investigating the functional significance and clinical relevance of TMUB1 in glioma
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Validation of a Proteomic-Based Prognostic Model for Breast Cancer and Immunological Analysis Int. J. Genom. (IF 2.9) Pub Date : 2023-12-16 Yunlin Yu, Linhuan Dong, Changjun Dong, Xianlin Zhang
Breast cancer (BC) has emerged as an extremely destructive malignancy, causing significant harm to female patients and society at large. Proteomic research holds great promise for early diagnosis and treatment of diseases, and the integration of proteomics with genomics can offer valuable assistance in the early diagnosis, treatment, and improved prognosis of BC patients. In this study, we downloaded
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The Oncogenic Role of KLF7 in Colon Adenocarcinoma and Therapeutic Perspectives Int. J. Genom. (IF 2.9) Pub Date : 2023-12-12 Zhenjia Li, Qi Liu
Colon adenocarcinoma, a highly prevalent and aggressive form of colorectal cancer, necessitates a comprehensive understanding of its molecular mechanisms to identify potential therapeutic targets. The Krüppel-like factor 7 (KLF7), a transcription factor, has been associated with various malignancies, yet its specific role in colon adenocarcinoma remains largely unexplored. Here, we aimed to determine
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CTSK and PLAU as Prognostic Biomarker and Related to Immune Infiltration in Pancreatic Cancer: Evidence from Bioinformatics Analysis and qPCR Int. J. Genom. (IF 2.9) Pub Date : 2023-11-29 Yuntao Ding, Zhangzuo Li, Huizhi Wang, Qi Wang, Han Jiang, Zhengyue Yu, Min Xu
Pancreatic adenocarcinoma (PAAD) is a malignancy with the highest mortality rate worldwide. There is a pressing need for novel biomarkers that can facilitate early detection and serve as targets for therapeutic interventions beyond the commonly utilized CA199 marker. This study utilized microarray datasets (GSE15471, GSE62165, and GSE28735) from the Gene Expression Omnibus (GEO) to identify differentially
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OSM May Serve as a Biomarker of Poor Prognosis in Clear Cell Renal Cell Carcinoma and Promote Tumor Cell Invasion and Migration Int. J. Genom. (IF 2.9) Pub Date : 2023-11-21 Shuzhang Wei, Yin Chen, Xiaokai Shi, Li Zuo, Lifeng Zhang
Background. Currently, the role of oncostatin M (OSM) in clear cell renal cell carcinoma (ccRCC) has not been investigated. This study will explore the impact of OSM on ccRCC expression, prognosis, and cell function. Materials and Methods. In this study, we used The Cancer Genome Atlas (TCGA) database to evaluate OSM expression characteristics, pathogenic factor distribution, and prognostic aspects
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KYNU as a Biomarker of Tumor-Associated Macrophages and Correlates with Immunosuppressive Microenvironment and Poor Prognosis in Gastric Cancer Int. J. Genom. (IF 2.9) Pub Date : 2023-11-2 Kaiyu Shen, Binyu Chen, Liu Yang, Wencang Gao
Background. Kynureninase (KYNU) is a potential prognostic marker for various tumor types. However, no reports on the biological effects and prognostic value of KYNU in gastric cancer (GC) exist. Methods. GC-associated single-cell RNA sequencing and bulk RNA sequencing (bulk-seq) data were obtained from the Gene Expression Omnibus and The Cancer Genome Atlas databases, respectively. The differential
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Correlation between LSM1 Expression and Clinical Outcomes in Glioblastoma and Functional Mechanisms Int. J. Genom. (IF 2.9) Pub Date : 2023-11-2 Changcheng Cai, Xingyu Chen, Jimin He, Chengwei Xiang, Yinggang Liu, Ke Wu, Ke Luo
Background. Glioblastoma (GBM) is an aggressive form of brain tumor characterized by limited treatment options and a bleak prognosis. Although the role of Like-Sm 1 (LSM1), a component of the mRNA splicing machinery, has been studied in various cancers, its significance in GBM remains unclear. The purpose of this research was to investigate the expression of LSM1 and its role in driving GBM progression
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The Potential Mechanism of Curcumin in Treating Oral Squamous Cell Carcinoma Based on Integrated Bioinformatic Analysis Int. J. Genom. (IF 2.9) Pub Date : 2023-10-14 Wu Siyuan, Lv Xiaozhi, Wu Jialin, Haigang Wei, Shiwei Liu, Chen Zou, Jing Song, Li Xia, Ai Yilong
Aims. This study explores the effects of curcumin as a therapeutic agent against oral squamous cell carcinoma (OSCC). Methods. We acquired the targets of curcumin from three digital databases, including the Comparative Toxicogenomics Database, Search Tool for Interactions of Chemicals, and SwissTargetPrediction. Then, we identified the differentially expressed genes (DEGs) and the weighted gene coexpression
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Identification of a Novel Variant of PDGFC Associated with Nonsyndromic Cleft Lip and Palate in a Chinese Family Int. J. Genom. (IF 2.9) Pub Date : 2023-9-21 Xin Yu, Simin Yang, Wenqian Xia, Xiaorong Zhou, Meiqin Gao, Hui Shi, Yan Zhou
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) accounts for 70% of the total number of patients with cleft lip with or without cleft palate (CL/P) and is the most common type of congenital deformity of the craniomaxillofacial region. In this study, whole exome sequencing (WES) and Sanger sequencing were performed on affected members of a Han Chinese family, and a missense variant in the
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tRNA-Uridine Aminocarboxypropyltransferase DTW Domain Containing 2 Suppresses Colon Adenocarcinoma Progression Int. J. Genom. (IF 2.9) Pub Date : 2023-9-16 Yun Qian, Yu-Jiang Li, Yi-Wei Fu, Cui-Xia Liu, Juan Wang, Bin Yang
Background. DTW Domain Containing 2 (DTWD2) is a newly identified transfer RNA-uridine aminocarboxypropyltransferase. Dysregulated expression of DTWD1 has been reported in several malignancies, nevertheless, the role of DTWD2 in cancers remains completely unknown. Here, we aimed to initially investigate the expression and role of DTWD2 in colon adenocarcinoma. Methods. We first evaluated the transcription
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An Analysis of the Gene Expression Associated with Lymph Node Metastasis in Colorectal Cancer Int. J. Genom. (IF 2.9) Pub Date : 2023-9-7 Hongjie Yang, Jiafei Liu, Peishi Jiang, Peng Li, Yuanda Zhou, Zhichun Zhang, Qingsheng Zeng, Min Wang, Luciena Xiao Xiao, Xipeng Zhang, Yi Sun, Siwei Zhu
Objective. This study aimed to explore the genes regulating lymph node metastasis in colorectal cancer (CRC) and to clarify their relationship with tumor immune cell infiltration and patient prognoses. Methods. The data sets of CRC patients were collected through the Cancer Gene Atlas database; the differentially expressed genes (DEGs) associated with CRC lymph node metastasis were screened; a protein–protein
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Identification of Potential Abnormal Methylation-Modified Genes in Coronary Artery Ectasia Int. J. Genom. (IF 2.9) Pub Date : 2023-8-26 Xiuchun Yang, Yijun Zong, Zhentian Zhang, Yan Zhao, Xueying Gao, Jie Zhang, Qian Hou, Renyi Li, Bing Xiao
Background. Coronary artery ectasia (CAE) is an easily recognized abnormality of coronary artery anatomy and morphology. However, its pathogenesis remains unclear. Objectives. This study aimed to identify abnormal methylation-modified genes in patients with CAE, which could provide a research basis for CAE. Methods. Peripheral venous blood samples from patients with CAE were collected for RNA sequencing
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Stratifin Promotes Hepatocellular Carcinoma Progression by Modulating the Wnt/β-Catenin Pathway Int. J. Genom. (IF 2.9) Pub Date : 2023-8-8 Shan-Ping Ye, Hong-Xin Yu, Wei-Jie Lu, Jun-Fu Wang, Tai-Yuan Li, Jun Shi, Xiao-Ye Cheng
Abnormal stratifin (SFN) expression is closely related to the progression of several human cancers, but the potential roles of SFN in hepatocellular carcinoma (HCC) remain largely unknown. In this study, we found that SFN was upregulated in HCC cell lines and tissues and was positively associated with tumor size, poor differentiation, Tumor Node Metastasis (TNM) stage, and vascular invasion. In addition
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circ_0008285 Regulates Glioma Progression via the miR-384/HMGB1 Axis Int. J. Genom. (IF 2.9) Pub Date : 2023-8-3 Manli Yan, Caihong Hu, Qi Hu, Heran Ma, Changjiang Lei, Yamei Liu
Background. Recent studies indicate that circular RNAs (circRNAs) have been implicated in the initiation or progression of a wide spectrum of diseases. In the current study, we explored the potential engagement of circ_0008285 in glioma and investigated the downstream regulators. Methods. The detection of circ_0008285 level in glioma specimens and cell lines was conducted by quantitative real-time
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Genomic Regions and Candidate Genes Associated with Milk Production Traits in Holstein and Its Crossbred Cattle: A Review Int. J. Genom. (IF 2.9) Pub Date : 2023-7-27 R. Bekele, M. Taye, G. Abebe, S. Meseret
Genome-wide association studies (GWAS) are a powerful tool for identifying genomic regions and causative genes associated with economically important traits in dairy cattle, particularly complex traits, such as milk production. This is possible due to advances in next-generation sequencing technology. This review summarized information on identified candidate genes and genomic regions associated with
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Comprehensive Analysis to Identify LINC00511–hsa-miR-625-5p–SEMA6A Pathway Fuels Progression of Skin Cutaneous Melanoma Int. J. Genom. (IF 2.9) Pub Date : 2023-7-3 Guanghua Chen, Jia Yan, Zhou Fu
Objective. Skin cutaneous melanoma (SKCM) is a highly lethal malignancy that poses a significant threat to human health. Recent research has shown that competing endogenous RNA (ceRNA) regulatory networks play a critical role in the development and progression of various types of cancer, including SKCM. The objective of this study is to investigate the ceRNA regulatory network associated with the transmembrane
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Hsa_circ_0003220 Drives Chemoresistance of Human NSCLC Cells by Modulating miR-489-3p/IGF1 Int. J. Genom. (IF 2.9) Pub Date : 2023-6-16 Shaofeng Xia, Chenliang Wang
Circular RNAs (circRNAs) have been shown to have critical roles in developing cancer and treatment resistance in an increasing body of research. The aim was to look into the functions and processes of hsa_circ_0003220 in the non-small cell lung cancer (NSCLC) chemoresistance. The NSCLC cell lines H460 and A549 were employed in present work. hsa_circ_0003220, miR-489-3p, and insulin-like growth factors
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The Comprehensive Analysis Illustrates the Role of CDCA5 in Breast Cancer: An Effective Diagnosis and Prognosis Biomarker Int. J. Genom. (IF 2.9) Pub Date : 2023-5-30 Yang Gao, Shuting Liu, Junyuan Yang, Min Su, Jingjing Xu, Hua Wang, Jingwei Zhang
Background. Several studies have been conducted to investigate the role of cell division cycle-associated 5 (CDCA5) in cancer. Its role in breast cancer, however, remains unknown. Methods. The Gene Expression Omnibus and Cancer Genome Atlas Program databases provided the open-access information needed for the research. The CCK8 and colony formation assays were used to measure cell proliferation. The
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Investigation of Underlying Biological Association and Targets between Rejection of Renal Transplant and Renal Cancer Int. J. Genom. (IF 2.9) Pub Date : 2023-5-23 Yinwei Chen, Zhanpeng Liu, Qian Yu, Xu Sun, Shuai Wang, Qingyi Zhu, Jian Yang, Rongjiang Jiang
Background. Post-renal transplant patients have a high likelihood of developing renal cancer. However, the underlying biological mechanisms behind the development of renal cancer in post-kidney transplant patients remain to be elucidated. Therefore, this study aimed to investigate the underlying biological mechanism behind the development of renal cell carcinoma in post-renal transplant patients. Methods
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Changes in Gene Expression of Whiteflies, Bemisia tabaci MED Feeding on Tomato Plants Infected by One of the Criniviruses, Tomato Chlorosis Virus through Transcriptome Analysis Int. J. Genom. (IF 2.9) Pub Date : 2023-5-22 Jing Zhao, Xiaoan Sun, Huijie Dai, Xianping Zhang, Dezhen Zhang, Xiaoping Zhu
Tomato chlorosis virus (ToCV), transmitted by the whitefly, Bemisia tabaci (Gennadius; Hemiptera: Aleyrodidae) has been continuously emerging on tomato plants and causing a significant economic loss throughout China. In the current study, RNA-Seq analysis was used to explore the gene expression profiles of B. tabaci Mediterranean (MED) that fed on both ToCV-infected and -uninfected tomato plants for
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Combination of BFHY with Cisplatin Relieved Chemotherapy Toxicity and Altered Gut Microbiota in Mice Int. J. Genom. (IF 2.9) Pub Date : 2023-5-19 Yuan Feng, Ying Jiang, Ying Zhou, Zhan-hua Li, Qi-qian Yang, Jin-feng Mo, Yu-yan Wen, Li-ping Shen
Aim. We sought to profile gut microbiota’s role in combination of Bu Fei Hua Yu (BFHY) with cisplatin treatment. Methods. Non-small cell lung cancer (NSCLC) mice model were constructed followed by treatment with cisplatin alone or combined with BFHY. Mice weight and tumor volume were measured during the experiment. And mice cecum were detected by hematoxylin and eosin, cecum contents were collected
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An In silico Approach towards Finding the Cancer-Causing Mutations in Human MET Gene Int. J. Genom. (IF 2.9) Pub Date : 2023-5-9 Fayeza Sadia Laskar, Md. Nazmul Islam Bappy, Md. Sowrov Hossain, Zenifer Alam, Dilruba Afrin, Sudeb Saha, Kazi Md. Ali Zinnah
Mesenchymal–epithelial transition (MET) factor is a proto-oncogene encoding tyrosine kinase receptor with hepatocyte growth factor (HGF) or scatter factor (SF). It is found on the human chromosome number 7 and regulates the diverse cellular mechanisms of the human body. The impact of mutations occurring in the MET gene is demonstrated by their detrimental effects on normal cellular functions. These
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Transcript Characteristics on the Susceptibility Difference of Bovine Respiratory Disease Int. J. Genom. (IF 2.9) Pub Date : 2023-5-4 Hang Cao, Chao Fang, Qiong Wang, Ling-Ling Liu, Wu-Jun Liu
Bovine respiratory disease (BRD) is one of the major health issues in the cattle industry, resulting in significant financial crises globally. There is currently no good treatment, and cattle are made resistant to pneumonia through disease-resistant breeding. The serial blood samples from six Xinjiang brown (XJB) calves were collected for the RNA sequencing (RNA-seq). The obtained six samples were
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Identification of Biomarkers Associated with Heart Failure Caused by Idiopathic Dilated Cardiomyopathy Using WGCNA and Machine Learning Algorithms Int. J. Genom. (IF 2.9) Pub Date : 2023-4-25 Mengyi Sun, Linping Li
Background. The genetic factors and pathogenesis of idiopathic dilated cardiomyopathy-induced heart failure (IDCM-HF) have not been understood thoroughly; there is a lack of specific diagnostic markers and treatment methods for the disease. Hence, we aimed to identify the mechanisms of action at the molecular level and potential molecular markers for this disease. Methods. Gene expression profiles
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Inhibition of lncRNA NFIA-AS1 Alleviates Abnormal Proliferation and Inflammation of Vascular Smooth Muscle Cells in Atherosclerosis by Regulating miR-125a-3p/AKT1 Axis Int. J. Genom. (IF 2.9) Pub Date : 2023-4-4 Yi Zhu, Xiaofeng Tian, Yan Wang, Chengxiang Wang, Naiquan Yang, Lianghong Ying, Hongyan Niu
Vascular smooth muscle cells (VSMCs) are critical elements of the vascular wall and play a crucial role in the genesis and development of atherosclerosis (AS). Increasingly, studies have indicated that long noncoding RNAs (lncRNAs) regulate VSMC proliferation, apoptosis, and other biological processes. Nevertheless, the role of lncRNA NFIA-AS1 (hereinafter referred to as NFIA-AS1) in VSMCs and AS remains
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Regulatory Networks of lncRNAs, miRNAs, and mRNAs in Response to Heat Stress in Wheat (Triticum Aestivum L.): An Integrated Analysis Int. J. Genom. (IF 2.9) Pub Date : 2023-3-30 Dwijesh Chandra Mishra, Sayanti Guha Majumdar, Anuj Kumar, Jyotika Bhati, K. K. Chaturvedi, Ranjeet Ranjan Kumar, Suneha Goswami, Anil Rai, Neeraj Budhlakoti
Climate change has become a major source of concern, particularly in agriculture, because it has a significant impact on the production of economically important crops such as wheat, rice, and maize. In the present study, an attempt has been made to identify differentially expressed heat stress-responsive long non-coding RNAs (lncRNAs) in the wheat genome using publicly available wheat transcriptome
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Eight Aging-Related Genes Prognostic Signature for Cervical Cancer Int. J. Genom. (IF 2.9) Pub Date : 2023-2-25 Meilin Yin, Yanhua Weng
This study searched for aging-related genes (ARGs) to predict the prognosis of patients with cervical cancer (CC). All data were obtained from Molecular Signatures Database, Cancer Genome Atlas, Gene Expression Integration, and Genotype Organization Expression. The R software was used to screen out the differentially expressed ARGs (DE-ARGs) between CC and normal tissues. A protein–protein interaction
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Identification of a Necroptosis-Related Prognostic Signature and Associated Regulatory Axis in Lung Adenocarcinoma Int. J. Genom. (IF 2.9) Pub Date : 2023-2-22 Libo Sun, Wenwen Li, Zhenhuan Zhao, Yanhua Zuo, Zhiwu Han
Background. Lung cancer is considered to be the second most aggressive and rapidly fatal cancer after breast cancer. Necroptosis, a novel discovered pattern of cell death, is mediated by Receptor-interacting serine/threonine-protein kinase 1 (RIPK1), Receptor-interacting serine/threonine-protein kinase 3 (RIPK3), and Mixed Lineage Kinase Domain Like Pseudokinase (MLKL). Methods. For the purpose of
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A Five-LLPS Gene Risk Score Prognostic Signature Predicts Survival in Hepatocellular Carcinoma Int. J. Genom. (IF 2.9) Pub Date : 2023-2-22 Wenwen Lai, Defu Li, Qiong Ge, Yehong Yan, Shiwen Luo, Quqin Lu
Background. Primary liver cancer, dominated by hepatocellular carcinoma (HCC), is one of the most common cancer types and the third leading cause of cancer death in 2020. Previous studies have shown that liquid–liquid phase separation (LLPS) plays an important role in the occurrence and development of cancer including HCC, but its influence on the patient prognosis is still unknown. It is necessary
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An Investigation of the Prognostic Role of Genes Related to Lipid Metabolism in Head and Neck Squamous Cell Carcinoma Int. J. Genom. (IF 2.9) Pub Date : 2023-2-10 Ling Qian, Chenyu Zhou, Keyi Wang, Liuyang Li, Wenhui Xia, Yuan Fan
Head and neck squamous cell carcinoma (HNSCC) has become a prevalent malignancy, and its incidence and mortality rate are increasing worldwide. Accumulating evidence has indicated that lipid metabolism-related genes (LMRGs) are involved in the occurrence and development of HNSCC. This study investigated the latent association of lipid metabolism with HNSCC and established a prognostic signature based
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A Review of the GSTM1 Null Genotype Modifies the Association between Air Pollutant Exposure and Health Problems Int. J. Genom. (IF 2.9) Pub Date : 2023-2-6 Dwi Aris Agung Nugrahaningsih, Hevi Wihadmadyatami, Sitarina Widyarini, Rahmi Ayu Wijayaningsih
Air pollution is one of the significant environmental risks known as the cause of premature deaths. It has deleterious effects on human health, including deteriorating respiratory, cardiovascular, nervous, and endocrine functions. Exposure to air pollution stimulates reactive oxygen species (ROS) production in the body, which can further cause oxidative stress. Antioxidant enzymes, such as glutathione
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LncRNA MIAT Upregulates NEGR1 by Competing for miR-150-5p as a Competitive Endogenous RNA in SCIRI Rats Int. J. Genom. (IF 2.9) Pub Date : 2022-12-28 Zheng Wang, Jianguang Liu, Qiuxiang Yang, Mengjie Ma
Objective. Spinal cord ischemia–reperfusion injury (SCIRI) can cause a pathological state of irreversible delayed death of neurons in the spinal cord tissue and a range of complications, such as spinal cord dysfunction and motor function impairment. This study aimed to determine whether the long-stranded non-coding ribonucleic acid (lncRNA), myocardial infarction-associated transcript (MIAT), could
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A Genomic Analysis of Bacillus megaterium HT517 Reveals the Genetic Basis of Its Abilities to Promote Growth and Control Disease in Greenhouse Tomato Int. J. Genom. (IF 2.9) Pub Date : 2022-12-27 Wei Yang, Yingnan Zhao, Yang Yang, Minshuo Zhang, Xiaoxi Mao, Yanjie Guo, Xiangyu Li, Bu Tao, Yongzhi Qi, Li Ma, Wenju Liu, Bowen Li, Hong J. Di
Bacillus megaterium is well known as a plant growth-promoting rhizobacterium, but the relevant molecular mechanisms remain unclear. This study aimed to elucidate the effects of B. megaterium HT517 on the growth and development of and the control of disease in greenhouse tomato and its mechanism of action. A pot experiment was conducted to determine the effect of B. megaterium on tomato growth, and
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Molecular Characterization and Clinical Characteristics of m5C-Based RNA Methylation in Spinal Cord Injury: Validated by qPCR Int. J. Genom. (IF 2.9) Pub Date : 2022-12-20 Liang Cao, Wen Jun Pi, Qiang Zhang, Qing Li
Aberrant patterns of 5-methylcytosine (m5C)-based ribonucleic acid (RNA) methylation have critical roles in various human diseases, but their importance in spinal cord injury (SCI) is largely unknown. We explore the expression patterns and potential roles of m5C-based regulators of RNA modification after SCI. We analyzed 16 m5C-based regulators of RNA modification in tissues with SCI and normal rats
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The Novel Action of miR-193b-3p/CDK1 Signaling in HCC Proliferation and Migration: A Study Based on Bioinformatic Analysis and Experimental Investigation Int. J. Genom. (IF 2.9) Pub Date : 2022-12-13 Xue Pang, Wei Wan, Xingxing Wu, Yu Shen
Hepatocellular carcinoma (HCC) is a common human malignancy with high mortality and dismal prognosis. A growing number of novel targets underlying HCC pathophysiology have been detected using microarray high throughput screening platforms. This study carried out bioinformatics analysis to explore underlying biomarkers in HCC and assessed the potential action of the miR-193b-3p/CDK1 signaling pathway
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IL1RN and PRRX1 as a Prognostic Biomarker Correlated with Immune Infiltrates in Colorectal Cancer: Evidence from Bioinformatic Analysis Int. J. Genom. (IF 2.9) Pub Date : 2022-11-29 Qi Wang, Xufeng Huang, Shujing Zhou, Yuntao Ding, Huizhi Wang, Weiye Jiang, Min Xu
The extensive morbidity of colorectal cancer (CRC) and the inferior prognosis of terminal CRC urgently call for reliable prognostic biomarkers. For this, we identified 704 differentially expressed genes (DEGs) by intersecting three datasets, GSE41328, GSE37364, and GSE15960 from Gene Expression Omnibus database, to maximize the accuracy of the results. Preliminary analysis of the DEGs was then performed
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A Novel Insight into Paraptosis-Related Classification and Signature in Lower-Grade Gliomas Int. J. Genom. (IF 2.9) Pub Date : 2022-11-14 Xi-Feng Qian, Jia-Hao Zhang, Yue-Xue Mai, Xin Yin, Yu-Bin Zheng, Zi-Yuan Yu, Guo-Dong Zhu, Xu-Guang Guo
Lower-grade gliomas (LGG) are the most common intracranial malignancies that readily evolve to high-grade gliomas and increase drug resistance. Paraptosis is defined as a nonapoptotic form of programmed cell death, which is gradually focused on patients with gliomas to develop treatment options. However, the specific role of paraptosis in LGG and its correlation is still vague. In this study, we first
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Expression and Prognostic Significance of PDIA3 in Cervical Cancer Int. J. Genom. (IF 2.9) Pub Date : 2022-11-11 Jing Zhang, Hui Li, Huling Li, Dandan Lin, Xiaoyan Wang, Kai Wang
To investigate the expression of protein disulfide isomerase A3 (PDIA3/ERP57) in cervical cancer and its clinical prognostic significance as well as its function and possible action mechanism in the progression of cervical cancer. Based on TIMER2.0 database, the human protein map (Human Protein Atlas) was used to determine the expression level of PDIA3 protein for the analysis of PDIA3 expression in
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Detection of Complement C1q B Chain Overexpression and Its Latent Molecular Mechanisms in Cervical Cancer Tissues Using Multiple Methods Int. J. Genom. (IF 2.9) Pub Date : 2022-10-20 Si-Tong Lin, Zi-Qian Liang, Xiao-Yu Chen, Xin-Qing Ye, Yu-Yan Pang, Jia-Yuan Luo, Jun-Hong Chen, Yi-Wu Dang, Gang Chen
Aim. The aim of this study is to demonstrate the expression and clinicopathological significance of complement C1q B chain (C1QB) in cervical cancer. Methods. In total, 120 cervical cancer tissues, as well as 20 samples each of high-grade squamous intraepithelial lesions (HSILs), low-grade squamous intraepithelial lesions (LSILs), and benign cervical tissue, were collected to evaluate the expression
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Comparison of In Silico Tools for Splice-Altering Variant Prediction Using Established Spliceogenic Variants: An End-User’s Point of View Int. J. Genom. (IF 2.9) Pub Date : 2022-10-13 Woori Jang, Joonhong Park, Hyojin Chae, Myungshin Kim
Assessing the impact of variants of unknown significance on splicing has become a critical issue and a bottleneck, especially with the widespread implementation of whole-genome or exome sequencing. Although multiple in silico tools are available, the interpretation and application of these tools are difficult and practical guidelines are still lacking. A streamlined decision-making process can facilitate
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ALDH1A3–Linc00284 Axis Mediates the Invasion of Colorectal Cancer by Targeting TGFβ Signaling via Sponging miR-361-5p Int. J. Genom. (IF 2.9) Pub Date : 2022-10-13 Chunlin Ke, Minmin Shen, Peirong Wang, Zhihua Chen, Suyong Lin, Feng Dong
ALDH1A3 and Linc00284 involve in colorectal cancer (CRC) development; however, the regulatory mechanism is still unclear. In this study, we collected clinicopathological characteristics and tissue samples from 73 CRC patients to analyze the expression of ALDH1A3, Linc00284, TGFβ signaling and miR-361-5p using qPCR, Western blotting, and ELISA. Multiple CRC cell lines were evaluated in this study, and
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Identification of Differentially Expressed microRNAs Associated with Ischemic Stroke by Integrated Bioinformatics Approaches Int. J. Genom. (IF 2.9) Pub Date : 2022-10-10 Shengqiang Jiang, Jie Wu, Yan Geng, Yuting Zhang, Yupeng Wang, Jinrong Wu, Chunqu Lu, Guoxuan Luo, Jie Zan, Yong Zhang
Ischemic stroke (IS) is one of the leading causes of disability and mortality worldwide. This study aims to find the crucial exosomal miRNAs associated with IS by using bioinformatics methods, reveal potential biomarkers for IS, and investigate the association between the identified biomarker and immune cell pattern in the peripheral blood of IS patients. In this study, 3 up-regulated miRNAs (hsa-miR-15b-5p
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Expression Profiles of Differentially Expressed Circular RNAs and circRNA–miRNA–mRNA Regulatory Networks in SH-SY5Y Cells Infected with Coxsackievirus B5 Int. J. Genom. (IF 2.9) Pub Date : 2022-10-10 Jing Li, Heng Yang, Huaran Shi, Jihong Zhang, Wei Chen
Coxsackievirus B5 (CVB5) is the causative agent of hand, foot, and mouth disease (HFMD) that can cause neurological complications and fatalities. Circular RNA (circRNA) has been shown to play an important role in regulating pathogenic processes. However, the functions of circRNA in response to CVB5 infection remain unclear. In our research, RNA-seq was employed to analyze the expression profiles of
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LncRNA BANCR Promotes Endometrial Stromal Cell Proliferation and Invasion in Endometriosis via the miR-15a-5p/TRIM59 Axis Int. J. Genom. (IF 2.9) Pub Date : 2022-10-10 Lixue Liu, Ru Bai, Debang Li, Bai Dai, Ya Tuo
Long non-coding RNA (LncRNA) emerges as a regulator in various diseases, including endometriosis (EM). This study aims to uncover the role of long non-coding RNA BRAF-activated non-protein coding RNA (lncRNA BANCR)-mediated competing endogenous RNA mechanism in endometrial stromal cell (ESC) proliferation and invasion in EM by regulating miR-15a-5p/TRIM59. ESCs were isolated from eutopic and ectopic
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In Silico Study of Mercury Resistance Genes Extracted from Pseudomonas spp. Involved in Bioremediation: Understanding the Promoter Regions and Regulatory Elements Int. J. Genom. (IF 2.9) Pub Date : 2022-08-12 Duguma Dibbisa, Gobena Wagari
Microbial genes and their product were diverse and beneficial for heavy metal bioremediation from the contaminated sites. Screening of genes and gene products plays a significant role in the detoxification of pollutants. Understanding of the promoter region and its regulatory elements is a vital implication of microbial genes. To the best of our knowledge, there is no in silico study reported so far
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Comprehensive Expression Profiling and Molecular Basis of CDC28 Protein Kinase Regulatory Subunit 2 in Cervical Cancer Int. J. Genom. (IF 2.9) Pub Date : 2022-07-28 Li Qin, Xiaoqiong Luo, Xiao Qin, Hongbao Huang, Lianling Zhang, Shengcai Chen, Xiaoqin Wu, Bingsheng Huang, Jian Pan, Jingxi Wei
More and more evidence suggests the oncogenic function of overexpressed CDC28 protein kinase regulatory subunit 2 (CKS2) in various human cancers. However, CKS2 has rarely been studied in cervical cancer. Herein, taking advantage of massive genetics data from multicenter RNA-seq and microarrays, we were the first group to perform tissue microarrays for CKS2 in cervical cancer. We were also the first
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Weighted Gene Correlation Network Analysis (WGCNA) of Arabidopsis Somatic Embryogenesis (SE) and Identification of Key Gene Modules to Uncover SE-Associated Hub Genes Int. J. Genom. (IF 2.9) Pub Date : 2022-07-04 Kithmee K. de Silva, Jim M. Dunwell, Anushka M. Wickramasuriya
Somatic embryogenesis (SE), which occurs naturally in many plant species, serves as a model to elucidate cellular and molecular mechanisms of embryo patterning in plants. Decoding the regulatory landscape of SE is essential for its further application. Hence, the present study was aimed at employing Weighted Gene Correlation Network Analysis (WGCNA) to construct a gene coexpression network (GCN) for
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HMOX1 Attenuates the Sensitivity of Hepatocellular Carcinoma Cells to Sorafenib via Modulating the Expression of ABC Transporters Int. J. Genom. (IF 2.9) Pub Date : 2022-06-27 Xian Zhu, Yinfang Zhang, Yafei Wu, Wenjing Diao, Guilong Deng, Qin Li, Chuanxing Wu
Hepatocellular carcinoma (HCC) represents a common malignancy, and mechanisms of acquired sorafenib resistance during the treatment of HCC patients remain elusive. The present study performed integrated bioinformatics analysis and explored the potential action of heme oxygenase 1 (HMOX1) in sorafenib-resistant HCC cells. Differentially expressed genes (DEGs) of the sorafenib-resistant group as compared
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A Cell Component-Related Prognostic Signature for Head and Neck Squamous Cell Carcinoma Based on the Tumor Microenvironment Int. J. Genom. (IF 2.9) Pub Date : 2022-06-25 Siyu Li, Yajun Gu, Junguo Wang, Dengbin Ma, Xiaoyun Qian, Xia Gao
Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous disease with a high mortality rate. The tumor microenvironment (TME) is composed of numerous noncancerous cells that contribute to tumorigenesis and prediction of therapeutic effects. In this study, we aimed to develop a cell component-related prognostic model based on TME. We screened cell component enrichments from samples in The Cancer
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Role of Epigenetics in Modulating Phenotypic Plasticity against Abiotic Stresses in Plants Int. J. Genom. (IF 2.9) Pub Date : 2022-06-14 Fayaz Ahmad Dar, Naveed Ul Mushtaq, Seerat Saleem, Reiaz Ul Rehman, Tanvir Ul Hassan Dar, Khalid Rehman Hakeem
Plants being sessile are always exposed to various environmental stresses, and to overcome these stresses, modifications at the epigenetic level can prove vital for their long-term survival. Epigenomics refers to the large-scale study of epigenetic marks on the genome, which include covalent modifications of histone tails (acetylation, methylation, phosphorylation, ubiquitination, and the small RNA
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Significance of a Tumor Mutation Burden Gene Signature with Prognosis and Immune Feature of Gastric Cancer Patients Int. J. Genom. (IF 2.9) Pub Date : 2022-06-08 Li Xiang, Chuan Lan
Gastric cancer (GC) is a common digestive tumor which ranks the fourth most common malignancy worldwide. Immunotherapy is a promising treatment for GC, especially for advanced gastric cancer (AGC). However, in clinical practice, not all patients are sensitive to immunotherapy. Recent studies showed that tumor mutation burden (TMB) is closely correlated with the response of immunotherapy. The current
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Identification of Novel circRNA-Based ceRNA Network Involved in the Pathogenesis of Gastric Cancer Int. J. Genom. (IF 2.9) Pub Date : 2022-05-31 Dengfa Peng, Li Feng, Huqing Li
Objective. Evidence increasingly shows that circular RNAs (circRNAs) are closely associated with tumorigenesis and cancer progression. However, the roles of circRNAs and the underlying mechanism behind these circRNAs in gastric cancer (GC) remain to be elucidated. This study is aimed at conferring a better understanding of GC pathogenesis with a specific focus on circRNA-based ceRNA action. Methods