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Xue J, Yang W, Wang X, Wang P, Meng X, Yu T, Fan C. A transcriptome sequencing study on the effect of macro-pores in hydrogel scaffolds on global gene expression of laden human cartilage chondrocytes. Biomed Mater 2022; 17. [PMID: 35609582 DOI: 10.1088/1748-605x/ac7304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 05/24/2022] [Indexed: 11/12/2022]
Abstract
The macro-porous hydrogel scaffolds can not only enhance the proliferation of laden chondrocytes but also favor the deposition of hyaline cartilaginous extracellular matrix, however, the underlying molecular mechanism is still unclear. Herein, the global gene expression of human cartilage chondrocytes (HCCs) encapsulated in traditional hydrogel (Gel) constructs and micro-cavitary gel (MCG) constructs are investigated by using high-throughput RNA sequencing (RNA-seq). The differentially expressed genes (DEGs) between the HCCs cultured in Gel and MCG constructs have been identified via bioinformatics analysis. Significantly, the DEGs that promote cell proliferation (e.g. POSTN, MKI67, KIF20A) or neo-cartilage formation (e.g. COL2, ASPN, COMP, FMOD, FN1), are more highly expressed in MCG constructs than in Gel constructs, while the expressions of the DEGs associated with chondrocyte hypertrophy (e.g. EGR1, IBSP) are upregulated in Gel constructs. The expression of representative DEGs is verified at both mRNA and protein levels. Besides, cellular viability and morphology as well as the enriched signaling pathway of DEGs are studied in detail. These results of this work may provide data for functional tissue engineering of cartilage.
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Affiliation(s)
- Junqiang Xue
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266000, Shandong, People's Republic of China.,Department of Rehabilitation Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao 266000, Shandong, People's Republic of China
| | - Wei Yang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao 266021, Shandong, People's Republic of China.,School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, People's Republic of China
| | - Xinping Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao 266021, Shandong, People's Republic of China.,School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, People's Republic of China
| | - Peiyan Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao 266021, Shandong, People's Republic of China.,School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, People's Republic of China
| | - Xinyue Meng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao 266021, Shandong, People's Republic of China.,School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, People's Republic of China
| | - Tengbo Yu
- Department of Sports Medicine, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao 266000, Shandong, People's Republic of China
| | - Changjiang Fan
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, Qingdao Medical College, Qingdao University, Qingdao 266021, Shandong, People's Republic of China.,School of Basic Medicine, College of Medicine, Qingdao University, Qingdao 266071, Shandong, People's Republic of China
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Man J, Zhang X, Dong H, Li S, Yu X, Meng L, Gu X, Yan H, Cui J, Lai Y. Screening and identification of key biomarkers in lung squamous cell carcinoma by bioinformatics analysis. Oncol Lett 2019; 18:5185-5196. [PMID: 31612029 PMCID: PMC6781567 DOI: 10.3892/ol.2019.10873] [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: 04/26/2019] [Accepted: 08/22/2019] [Indexed: 12/21/2022] Open
Abstract
The high mortality rate of lung squamous cell carcinoma (LUSC) is in part due to the lack of early detection of its biomarkers. The identification of key molecules involved in LUSC is therefore required to improve clinical diagnosis and treatment outcomes. The present study used the microarray datasets GSE31552, GSE6044 and GSE12428 from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs). Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses were conducted to construct the protein-protein interaction network of DEGs and hub genes module using STRING and Cytoscape. The 67 DEGs identified consisted of 42 upregulated genes and 25 downregulated genes. The pathways predicted by KEGG and GO enrichment analyses of DEGs mainly included cell cycle, cell proliferation, glycolysis or gluconeogenesis, and tetrahydrofolate metabolic process. Further analysis of the University of California Santa Cruz and ONCOMINE databases identified 17 hub genes. Overall, the present study demonstrated hub genes that were closely associated with clinical tissue samples of LUSC, and identified TYMS, CCNB2 and RFC4 as potential novel biomarkers of LUSC. The findings of the present study contribute to an improved understanding of the molecular mechanisms of carcinogenesis and progression of LUSC, and assist with the identification of potential diagnostic and therapeutic targets of LUSC.
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Affiliation(s)
- Jun Man
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Xiaomei Zhang
- Department of Respiratory Medicine, Dongfang Hospital, Beijing University of Chinese Medicine, Beijing 100078, P.R. China
| | - Huan Dong
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Simin Li
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Xiaolin Yu
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Lihong Meng
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Xiaofeng Gu
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Hong Yan
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Jinwei Cui
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
| | - Yuxin Lai
- Department of Internal Medicine of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, P.R. China
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Guo B, Zheng Q. Using Naïve Bayes Algorithm to Estimate the Response to Drug in Lung Cancer Patients. Comb Chem High Throughput Screen 2019; 21:734-748. [PMID: 30686250 DOI: 10.2174/1386207322666190125151624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/11/2018] [Accepted: 11/02/2018] [Indexed: 11/22/2022]
Abstract
AIM AND OBJECTIVE Lung cancer is a highly heterogeneous cancer, due to the significant differences in molecular levels, resulting in different clinical manifestations of lung cancer patients there is a big difference. Including disease characterization, drug response, the risk of recurrence, survival, etc. Method Clinical patients with lung cancer do not have yet particularly effective treatment options, while patients with lung cancer resistance not only delayed the treatment cycle but also caused strong side effects. Therefore, if we can sum up the abnormalities of functional level from the molecular level, we can scientifically and effectively evaluate the patients' sensitivity to treatment and make the personalized treatment strategies to avoid the side effects caused by over-treatment and improve the prognosis. RESULT & CONCLUSION According to the different sensitivities of lung cancer patients to drug response, this study screened out genes that were significantly associated with drug resistance. The bayes model was used to assess patient resistance.
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Affiliation(s)
- Baoling Guo
- Department of Oncology, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan, China
| | - Qiuxiang Zheng
- Department of Oncology, Longyan First Hospital, Affiliated to Fujian Medical University, Longyan, China
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Zhang D, Liu E, Kang J, Yang X, Liu H. MiR-3613-3p affects cell proliferation and cell cycle in hepatocellular carcinoma. Oncotarget 2017; 8:93014-93028. [PMID: 29190974 PMCID: PMC5696240 DOI: 10.18632/oncotarget.21745] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/23/2017] [Indexed: 12/20/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common types of malignant tumors with poor sensitivity to chemotherapy drugs and poor prognosis among patients. In the present study, we downloaded the original data from the Gene Expression Omnibus and compared gene expression profiles of liver cancer cells in patients with HCC with those of colon epithelial cells of healthy controls to identify differentially expressed genes (DEGs). After filtering target microRNAs (miRNA) from core DEGs, we cultured HepG2 cells in vitro, knocked down the miRNA and core mRNAs, and analyzed the effects. We found 228 differentially expressed genes between liver cancer tissue and healthy control tissue. We also integrated the protein-proteininteraction network and module analysis to screen 13 core genes, consisting of 12 up-regulated genes and 1 down-regulated gene. Five core genes were regulated hsa-miR-3613-3p, therefor we hypothesized that hsa-miR-3613-3p was a critical miRNA. After the transfection procedure, we found that changes in hsa-miR-3613-3p were the most obvious. Therefore, we speculated that hsa-miR-3613-3p was a main target miRNA. In addition, we transfected with si (BIRC5, CDK1, NUF2, ZWINT and SPC24), to target genes that can be targeted by miR-3613-3p. Our data shows that BIRC5, NUF2, and SPC24 may be promising liver cancer biomarkers that may not only predict disease occurrence but also potential personalized treatment options.
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Affiliation(s)
- Donghui Zhang
- Department of Infectious Disease, Linyi People's Hospital, Linyi 276000, China
| | - Enqin Liu
- Department of Infectious Disease, Linyi People's Hospital, Linyi 276000, China
| | - Jian Kang
- Department of Colorectal Surgery, Tai’an City Central Hospital, Tai’an 271000, China
| | - Xin Yang
- Culverhouse College of Commerce and Business Administration, The University of Alabama, Tuscaloosa, AL 35401, USA
| | - Hong Liu
- Department of Infectious Disease, Linyi People's Hospital, Linyi 276000, China
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Boyarskikh UA, Kondrakhin YV, Yevshin IS, Sharipov RN, Komelkov AV, Musatkina EA, Tchevkina EM, Sukoyan MA, Kolpakov FA, Kashkin KN, Filipenko ML. Prediction of nonsmall cell lung cancer sensitivity to cisplastin and paclitaxel based on marker gene expression. Mol Biol 2011. [DOI: 10.1134/s0026893311030034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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