1.Keloid nomogram prediction model based on weighted gene co-expression network analysis and machine learning.
Zhengyu LI ; Baohua TIAN ; Haixia LIANG
Journal of Biomedical Engineering 2023;40(4):725-735
Keloids are benign skin tumors resulting from the excessive proliferation of connective tissue in wound skin. Precise prediction of keloid risk in trauma patients and timely early diagnosis are of paramount importance for in-depth keloid management and control of its progression. This study analyzed four keloid datasets in the high-throughput gene expression omnibus (GEO) database, identified diagnostic markers for keloids, and established a nomogram prediction model. Initially, 37 core protein-encoding genes were selected through weighted gene co-expression network analysis (WGCNA), differential expression analysis, and the centrality algorithm of the protein-protein interaction network. Subsequently, two machine learning algorithms including the least absolute shrinkage and selection operator (LASSO) and the support vector machine-recursive feature elimination (SVM-RFE) were used to further screen out four diagnostic markers with the highest predictive power for keloids, which included hepatocyte growth factor (HGF), syndecan-4 (SDC4), ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2), and Rho family guanosine triphophatase 3 (RND3). Potential biological pathways involved were explored through gene set enrichment analysis (GSEA) of single-gene. Finally, univariate and multivariate logistic regression analyses of diagnostic markers were performed, and a nomogram prediction model was constructed. Internal and external validations revealed that the calibration curve of this model closely approximates the ideal curve, the decision curve is superior to other strategies, and the area under the receiver operating characteristic curve is higher than the control model (with optimal cutoff value of 0.588). This indicates that the model possesses high calibration, clinical benefit rate, and predictive power, and is promising to provide effective early means for clinical diagnosis.
Humans
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Keloid/genetics*
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Nomograms
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Algorithms
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Calibration
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Machine Learning
2.Whole-genome sequencing on one case of Han familial keloids.
Guodong TENG ; Minliang CHEN ; Chang LIU ; Liming LIANG
Chinese Journal of Plastic Surgery 2016;32(1):52-55
OBJECTIVETo screen SNP information of keloid pedigrees through whole genome sequencing.
METHODSWe Collected information and clinical data of the keloid pedigree and constructed charts of the pedigree. The DNA was extracted from peripheral venous blood samples of the pedigree to sequence the whole genome.
RESULTS27 SNP and 8 disease-associated genes were screened out.
CONCLUSIONSWhole genome sequencing technology can select new genetic mutations associated with keloid, and provide a new way for the research of keloid.
China ; ethnology ; Genome, Human ; Humans ; Keloid ; genetics ; Mutation ; Pedigree ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA
3.Hsp70 Knockdown by siRNA Decreased Collagen Production in Keloid Fibroblasts.
Jung U SHIN ; Won Jai LEE ; Thanh Nga TRAN ; Inhee JUNG ; Ju Hee LEE
Yonsei Medical Journal 2015;56(6):1619-1626
PURPOSE: There are currently no consistently effective treatments for the excessive collagen produced by keloid fibroblasts. Previously, we reported that heat shock protein 70 (Hsp70) is up-regulated in keloid fibroblasts and keloid tissue. We, therefore, investigated whether Hsp70 is related to excessive collagen production in keloid fibroblasts. MATERIALS AND METHODS: We inhibited Hsp70 in keloid fibroblasts by RNA interference and examined the resulting collagen expression. Thus, we selected small interfering RNAs (siRNAs) specific for human Hsp70, transfected them into keloid fibroblasts, and evaluated the resulting phenotypes and protein production using real-time polymerase chain reaction (PCR), Western blot, and a collagen assay. RESULTS: The siRNAs dramatically suppressed Hsp70 mRNA expression, resulting in a decrease in collagen production in the keloid fibroblasts compared with controls. The siRNAs did not influence the viability of the keloid fibroblasts. CONCLUSION: Hsp70 overexpression likely plays an important role in the excessive collagen production by keloid fibroblasts. RNA interference has therapeutic potential for the treatment of keloids.
Adolescent
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Adult
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Blotting, Western
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Collagen/*drug effects/metabolism
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Female
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Fibroblasts/metabolism
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Gene Expression Regulation
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HSP70 Heat-Shock Proteins/genetics/metabolism/*pharmacology
;
Humans
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Keloid/*drug therapy/genetics/metabolism
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Male
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RNA, Messenger/*genetics
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RNA, Small Interfering/*genetics
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Real-Time Polymerase Chain Reaction
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Transfection
;
Up-Regulation
4.In vitro study of TGF-β1-induced epithelial-mesenchymal transition of keloid epithelial cells.
Li YAN ; Rui CAO ; Bo PAN ; Lianzhao WANG ; Xiaoyan LYU ; Xuejian SUN ; Ran XIAO
Chinese Journal of Plastic Surgery 2015;31(2):128-133
OBJECTIVETo construct and characterize the TGF-β1, induced epithelial-mesenchymal transition (EMT) model of keloid epithelial cells in vitro, and to investigate the expression of epithelial stem cells related surface markers in keloid epithelial cells during EMT induction.
METHODSThe epithelial cells from 3 keloid samples of ears were cultured in vitro and induced by transforming growth factor betal (TGF-β1, 1 ng/ml) for 5 days, which was the experimental group, the same cells untreated were considered as the negative control group. The expressions of EMT-associated markers and regulative genes were detected using immunofluorescence staining, real-time PCR and western blot analysis. Then the surface markers of epithelial stem cells were detected using real-time PCR. Statistical significance was determined using Independent-Samples t Test, a p value less than 0. 05 was considered statistically significant.
RESULTSThe mRNA expression of transcription factor snail2 and mesenchymal-specific marker vimentin increased significantly in TGF-β1, induced keloid epithelial cells (P < 0. 05), in which snail2 increasing from 0. 91 ± 0. 23 to 1. 69 ± 0. 10, and vimentin from 5. 86 ± 2. 07 to 24. 29 ± 5. 39. Whereas the mRNA expression of epithelial-specific marker E-cadherin decreased from 1. 06 ± 0. 19 to 0. 65 ± 0. 09. The mRNA expression of CD29 and Lgr6, two surface markers of epithelial stem cells, significantly increased after induction of the TGF-β1, (P < 0. 05), from 0. 55 ± 0. 14 and 1. 61 ± 0. 31 to 1. 19 ± 0. 12 and 3. 84 t 0. 62 respectively. In induced cells, the immunofluorescence results showed staining of E- cadherin became faint, but the number of positive staining cells of vimentin increased. Western blot confirmed the protein expression of E-cadherin weakened, and the vimentin and p-Smad3 enhanced (P < 0. 05).
CONCLUSIONSTGF-β1, initiated EMT in keloid epithelial cells by inducing the up-regulation of snail2, and TGF-β1,/Smad3 signaling pathway was involved in EMT. EMT could change the phenotype of epithelial stem cells in keloid.
Biomarkers ; metabolism ; Cadherins ; genetics ; metabolism ; Epithelial Cells ; drug effects ; physiology ; Epithelial-Mesenchymal Transition ; drug effects ; physiology ; Humans ; In Vitro Techniques ; Keloid ; pathology ; RNA, Messenger ; metabolism ; Signal Transduction ; Smad3 Protein ; genetics ; metabolism ; Snail Family Transcription Factors ; Transcription Factors ; genetics ; metabolism ; Transforming Growth Factor beta1 ; metabolism ; pharmacology ; Up-Regulation ; Vimentin ; genetics ; metabolism
5.Analysis on polymorphism at -509 C/T site of TGF-β1 gene in patients with keloids.
Chinese Journal of Burns 2014;30(6):482-486
OBJECTIVETo analyze the polymorphism at -509C/T site of TGF-β1 gene in patients with keloids, and to explore its relationship with the occurrence of keloid and its influence on the plasma level of TGF-β1.
METHODSOne hundred and sixty-nine patients with keloids and hospitalized from June 2011 to April 2014 were included as keloid group, and 119 healthy blood donors were enrolled as healthy control group. Venous blood of study subjects was collected. The -509C/T genotype of TGF-β1 gene was determined with PCR-restriction fragment length polymorphism technique combined with DNA sequence analysis, and the frequency of allele C or T was calculated. The theoretical frequency of the 3 genotypes CC, CT, and TT was calculated according to the theory of Hardy-Weinberg equilibrium to determine whether the gene frequency of the study subject was group representative or not. The distribution of -509C/T genotype of TGF-β1 gene among patients in keloid group was analyzed by grouping in gender, age, with or without family history of keloid, and the number of keloid respectively. Plasma level of TGF-β1 of all study subjects was determined with ELISA, and the plasma level TGF-β1 of patients with various -509C/T genotypes of TGF-β1 gene in keloid group was analyzed. The relative risk of allele frequency of patients in keloid group was analyzed by Logistic regression analysis, and the other data were processed with chi-square test and t test.
RESULTSAmong the -509C/T genotypes of TGF-β1 gene between subjects in the two groups, the distribution of genotypes CC, CT, and TT was quite similar, and they were respectively 38 cases (22.5%), 79 cases (46.7%), and 52 cases (30.8%) in keloid group and 39 persons (32.8%), 52 persons (43.7%), and 28 persons (23.5%) in healthy control group (χ² = 4.225, P>0.05). The distribution frequency of alleles C and T in the two groups were obviously different, and they were respectively 45.9% and 54.1% in keloid group and 54.6% and 45.4% in healthy control group (χ² = 4.291, P<0.05). The theoretical frequency values of the three kinds of genotypes of CC, CT, and TT were respectively 35 cases (21.0%), 84 cases (49.7%), and 50 cases (29.3%) in keloid group, and 35 persons (29.8%), 59 persons (49.6%), and 25 persons (20.6%) in healthy control group. There were no statistically significant differences between the actual genotype frequency and the theoretical values (with χ² values respectively 0.581 and 1.672, P values above 0.05), showing that the research group reached Hardy-Weinberg equilibrium. Relative risk analysis of allele frequency showed that the risk of suffering from keloid of patients carrying allele C was 1.421 times of that of patients without carrying allele C (odds ratio = 1.421, with 95% confidence interval 1.109-1.983, P < 0.05). The distribution of -509C/T genotypes of TGF-β1 gene among patients in keloid group was similar by grouping in gender, age, and number of keloid (with χ² values 0.895-5.008, P values above 0.05). Between patients with or without family history of keloid, the differences of distribution frequencies of genotypes CC and CT were significantly different, which were respectively 61.8% (21/34) and 37.8% (51/135) in patients with family history of keloid and 14.7% (5/34) and 34.1% (46/135) in patients without a family history of keloid, with χ² values respectively 6.391 and 4.835, P values below 0.05; the distribution frequency of genotype TT was close (χ² = 0.292, P > 0.05). The plasma level of TGF-β1 of patients in keloid group was (42 ± 9) µg/L, which was significantly higher than that of people in healthy control group \[(34 ± 8) µg/L, t = 4.408, P < 0.05\]. In keloid group, the plasma level of TGF-β1 in patients with genotype CC and that of patients with genotype CT was quite similar, which were respectively (43 ± 9) and (40 ± 9) µg/L (t = 0.680, P > 0.05), and they were significantly higher than that of patients with genotype TT \[(34 ± 8) µg/L, with t values respectively 2.676 and 2.137, P values below 0.05\].
CONCLUSIONSTGF-β1 gene -509C/T polymorphism was shown to be present in patients with keloids who were admitted to our hospital. It was shown to influence the plasma level of TGF-β1 in patients. The individuals who carry TGF-β1 allele C may increase the risk of developing keloid by promoting the expression of TGF-β1.
Alleles ; Gene Frequency ; Genotype ; Humans ; Keloid ; genetics ; Polymorphism, Genetic ; Transforming Growth Factor beta1 ; blood ; genetics
6.Effect of lentivirus-mediated hIL-24 gene on proliferation, migration and invasion of keloid fibroblasts.
Wu ZHIYUAN ; Shi YUCANG ; Liang JIE ; Xu XIAXING ; Wu ZHIXIAN ; Li RAN
Chinese Journal of Plastic Surgery 2014;30(5):359-364
OBJECTIVETo investigate the effect of hIL-24 gene on proliferation, migration and invasion activity of human keloid fibroblasts (KFs).
METHODShIL-24 gene was cloned into lentivirus vector, then the lentivirus particles expressing hlL-24 were infected into KF cells. Real-time PCR and Western blot were performed to examine the expression of hIL-24 in lentivirus infected cells. The growth ability was detected by MTT assay. The cell cycle was analyzed by flow cytometry, The invasion and migration were detected by matrigel invasion assay and wound healing assay.
RESULTSComparing to controls group and KF-NC group, the expression levels of hIL-24 mRNA and protein were both significantly up-regulated after 4 days of hIL-24 lentivims infection. Comparing with the KF-NC group, MTT assay showed that the A490 of KF-hlL-24 group was down-regulated after lentivims infection ( P < 0. 05 ). Comparing with the KF-NC group, Cell cycle test revealed hlL-24 gene could block KF cells in G1 [(75. 40 ±2. 10)% ] , the proportion of KF cells was decreased in S phase [(4. 96 ± 1. 60)% ] and G2 phase [(0.01 ± 0.01)% ]. After KF cells were infected(P <0.01). Transfection of hlL-24 lentivirus inhibited the migration and invasion activity of KF cells.
CONCLUSIONLentivirus-mediated hlL-24 gene efficiently inhibits proliferation, cell cycle progression, migration and invasion activity of KF cells.
Cell Cycle ; Cell Line, Tumor ; Cell Movement ; genetics ; Cell Proliferation ; genetics ; Down-Regulation ; Fibroblasts ; physiology ; virology ; Genetic Vectors ; Humans ; Interleukins ; genetics ; physiology ; Keloid ; genetics ; pathology ; Lentivirus ; RNA, Messenger ; metabolism ; Transfection ; methods
7.The preliminary study of structure variation related to keloid based on the whole-gene resequencing technique.
Chang LIU ; Guodong TENG ; Minliang CHEN ; Kui MA ; Tongtong YAN
Chinese Journal of Plastic Surgery 2014;30(4):279-282
OBJECTIVETo investigate the genome structure variation (SV) related with keloid using the whole-gene resequencing technology.
METHODSWe studied a keloid pedigree containing 4 generation of 27 people. 5 people (4 cases of keloid patients, and 1 case of normal) were selected to extract the genomic DNA. Then the whole-gene resequencing technique was used to check the variations.
RESULTSThrough database comparison and variation annotation analysis, we obtained 2 SVs associated with keloid formation. We used DAVID software to do the gene ontology and pathway analysis. We found a 168 bp inversion in gene tetraspanin 8 (TSPAN8) in all keloid patients, which contained the forth exon of TSPAN8.
CONCLUSIONSThere was no report about SVs related to keloid. In this study, we found 2 SVs associated with keloid, especially TSPAN8. The tumor cells express the TSPAN8 can up-regulate the vascular endothelial growth factor and its receptors, promote the adjacent fibroblasts secrete matrix metalloproteinases and uridylyl phosphate adenosine. So we hypothesis that the inversion of the forth exon in TSPAN8 may lead to the signal transduction disorder in the keloid patients. This study was a preliminary research. It needs a further study containing large sample to confirm.
Base Sequence ; Female ; Humans ; Keloid ; genetics ; Male ; Molecular Sequence Data ; Pedigree ; Sequence Analysis ; methods ; Tetraspanins ; genetics
8.Preliminary study on CASK/Id1 pathway in fibroblasts of human keloid.
Liang XIAO ; Zhibo SUN ; Yong KE ; Zhihong YU ; Guangzhao HE ; Yuhan REN
Chinese Journal of Plastic Surgery 2014;30(2):105-111
OBJECTIVETo verify the existence and significance of calcium/calmodulin dependent serine protein kinase/inhibitors of differentiation 1 (CASK/Id1) pathway in fibroblasts of human keloid.
METHODSImmunofluorescence laser was used to confirm CASK and Id1 protein expression and localization in fibroblasts of the keloid and normal skin. RT-PCR and Western-blot were adopted to analysis the CASK and Id1 expression and differences between keloid and normal skin fibroblasts. The natural combination of CASK and Id1 protein of keloid fibroblasts was tested by immunoprecipitation.
RESULTSCASK and Id1 protein expression were both found in fibroblast cells of keloid and normal skin under normal circumstances. Most of CASK and Id1 were distributed in the cytoplasm and nucleus of fibroblasts. The results of RT-PCR showed that the expression of CASK mRNA in the keloid group was 0.658 +/- 0.024, which was lower than that in the normal control group (1.076 +/- 0.008, t = 11.159, P < 0.05). The expression of Id1 mRNA was 0.497 +/- 0.014, which was higher than that in the normal control group (0.307 +/- 0.017, t = 15.148, P < 0.05). The results of Western-blot showed that the expression level for CASK protein in the keloid group was 0.057 +/- 0.006, which was lower than that in the normal control group (0.168 +/- 0.012, t = 13.524, P < 0.05); the expression of Id1 protein was 0.812 +/- 0.035, which was higher than that in the normal control group (0.368 +/- 0.031, t = 16.356, P < 0.05). The results of immunoprecipitation showed that Id1 could be detected in the CASK precipitate, while CASK also could be detected in the Id1 precipitate. There was a natural binding of CASK and Id1 in keloid fibroblasts.
CONCLUSIONCASK/Id1 signal pathway may be existed and involved in the proliferation of keloid fibroblasts, which is related with the occurrence of keloid.
Cell Proliferation ; genetics ; Cyclin-Dependent Kinase Inhibitor Proteins ; genetics ; metabolism ; Fibroblasts ; metabolism ; Humans ; Inhibitor of Differentiation Protein 1 ; genetics ; metabolism ; Keloid ; metabolism ; pathology ; RNA, Messenger ; metabolism ; Signal Transduction
9.Identification of differently expressed microRNAs in keloid and pilot study on biological function of miR-199a-5p.
Zhi-Yuan WU ; Ling LU ; Xiao-Rui GUO ; Pei-Hua ZHANG
Chinese Journal of Plastic Surgery 2013;29(4):279-284
OBJECTIVETo screen out related microRNAs in keloid tissue, and identify their effect on the proliferation of keloid fibroblasts.
METHODS8 cases of keloid tissue and 8 cases of normal skin tissue were collected as specimens. The differently expressed miRNA in keloid tissue from normal skin tissue were screened out with gene chip( Exiqon company), which was validated with quantitative real-time PCR. Then miRNA mimics was transfected into keloid fibroblasts line to stimulate high expression of mature miRNA in cells. The effect on the proliferation of fibroblasts in keloid was tested by Edu.
RESULTS(1) A total of 17 differently expressed microRNAs were found, including miR-199a-5p. (2) The expression of miR-199a-5p had been verified by qRT-PCR to be down-regulated in keloid, which was consistent with the result of array. (3) The positive rate of EdU in miR-199a-5p mimics transfected group and negative control group was (20.72 +/- 2.50)% and (27.68 +/- 4.92)%, respectively. The proliferative rate of keloid fibroblasts turned down in miR-199a-5p-transfected group (t = 2.183, P = 0.047). Besides that, the cell cycle changed after transfection. The percentage of S and G2/M phase in miR-199a-5p mimics transfected group was 33.93 +/- 1.30 and 10.87 +/- 0.80, respectively, while it was 31.39 +/- 0.79 and 9.27 +/- 0.46 in negative control group, and the difference was statistically significant.
CONCLUSIONS(1) The miRNA expression profile is different between keloid and normal skin; (2) The expression of miR-199a-5p is down-regulated in keloid and miR-199a-5p can affect the cell cycle and suppress proliferation of keloid fibroblasts. It indicateds that miR-199a-5p may be involved in regulating fibroblastic proliferation.
Cell Proliferation ; Cells, Cultured ; Down-Regulation ; Female ; Fibroblasts ; metabolism ; Gene Expression Profiling ; Humans ; Keloid ; genetics ; metabolism ; pathology ; Male ; MicroRNAs ; genetics ; metabolism
10.Expressions of the related genes in fibroblasts of human keloid and the effect of artesunate.
Liang XIAO ; Guang-zhao HE ; Ze-hao YU ; Xiao-qing TANG ; Yu-han REN
Chinese Journal of Burns 2013;29(2):185-190
OBJECTIVETo verify whether abnormal expression of calcium/calmodulin dependent serine protein kinase (CASK) and inhibitors of differentiation 1 (ID1) exist in Fb of keloid, and to observe the effect of artesunate on two genes.
METHODSFifteen samples of keloid and 12 samples of normal skin tissue (discarded) excised from patients admitted to our hospital were collected. Tissue particle adherent method was used in the primary culture of Fb, and cells from the third to the eighth passage were used for test. Expressions of CASK and ID1 in Fb harvested from both sources were observed with immunofluorescence staining. Fb of keloid were stimulated with artesunate in various concentration for different time, and the median inhibitory concentration (IC50) was determined with the MTT colorimetric assay, which served as the intervention concentration of artesunate. Fb of normal skin were set as normal control group (NC, treated with medium solution). Fb of keloid were divided into scar control group (SC, treated with medium solution) and scar administration group (SA, treated with artesunate in IC50). The cycle and apoptosis of Fb were detected with flow cytometric assay, and the nucleic acid and protein expressions of CASK and ID1 of Fb in each group were determined with RT-PCR and Western blotting. Data were processed with one-way analysis of variance and LSD-t test.
RESULTSExpressions of CASK and ID1 were detected in two kinds of Fb. The concentration of 75 mg/L was selected as the intervention concentration of artesunate. (1) There were statistically significant differences among the three groups in the percentages of cells in G0/G1 phase and G2/M phase (with F values respectively 118.064 and 163.840, P values all below 0.01). The percentage of cells in G0/G1 phase of group SA was (91.4 ± 1.4)%, which was significantly higher than that of group SC and group NC [respectively (80.7 ± 0.3)% and (82.4 ± 0.6)%, with t values respectively 12.740 and 9.872, P values all below 0.05]. The percentage of cells in G2/M phase of group SA was (6.9 ± 0.3)%, which was significantly lower than that of group SC and group NC [respectively (13.7 ± 0.3)% and (12.7 ± 0.8)%, with t values respectively 43.702 and 12.276, P values all below 0.05]. (2) There were statistically significant differences among the three groups in the early and late apoptotic rates (with F values respectively 61.879 and 4710.862, P values all below 0.01). The early and late apoptotic rates of group SA were respectively (7.1 ± 1.0)% and (14.9 ± 0.3)%, which were significantly higher than those of group SC and group NC [with early apoptotic rate respectively (2.6 ± 0.4)% and (2.7 ± 0.3)%, t values respectively 7.974 and 7.767, P values all below 0.05; with late apoptotic rate respectively (2.3 ± 0.3)% and (2.5 ± 0.4)%, t values respectively 72.882 and 69.792, P values all below 0.05]. (3) The mRNA expression of CASK in group SC was 0.658 ± 0.024, and it was lower than that of group NC (1.076 ± 0.008, t = 28.997, P < 0.01) and group SA (0.855 ± 0.008, t = 13.549, P < 0.01). The protein expression of CASK in group SC was 0.067 ± 0.007, and it was lower than that of group NC (0.179 ± 0.015, t = 12.042, P < 0.01) and group SA (0.132 ± 0.010, t = 9.498, P < 0.01). (4) The mRNA expression of ID1 in group SC was 0.416 ± 0.006, which was higher than that of group NC (0.317 ± 0.020, t = 8.299, P < 0.01) and group SA (0.217 ± 0.009, t = 32.417, P < 0.01). The protein expression of ID1 in group SC was 0.789 ± 0.034, and it was higher than that of group NC (0.366 ± 0.029, t = 16.341, P < 0.01) and group SA (0.114 ± 0.006, t = 33.978, P < 0.01).
CONCLUSIONSIt is speculated that CASK and ID1 participate in the proliferation of Fb in keloid. The mechanism of artesunate in inhibiting the proliferation of Fb in keloid may be related to the up-regulation of CASK and down-regulation of ID1.
Adolescent ; Adult ; Apoptosis ; drug effects ; Artemisinins ; pharmacology ; Cell Proliferation ; drug effects ; Cells, Cultured ; Female ; Fibroblasts ; metabolism ; Gene Expression Regulation ; Guanylate Kinases ; genetics ; metabolism ; Humans ; Inhibitor of Differentiation Protein 1 ; genetics ; metabolism ; Keloid ; metabolism ; pathology ; Male ; Middle Aged ; Young Adult

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