1.Screening of differentially expressed genes in gastric cancer based on GEO database and function and pathway enrichment analysis
Yihao LIANG ; Yingjun LAI ; Yanwen YUAN ; Wei YUAN ; Xibo ZHANG ; Bashan ZHANG ; Zhifeng LU
Journal of Southern Medical University 2024;44(3):605-616
Objective To explore the core genes related to the diagnosis and prognosis of gastric cancer(GC)based on Gene Expression Omnibus(GEO)database and screen the molecular targets involved in the occurrence and development of GC.Methods GC microarray data GSE118916,GSE54129 and GSE79973 were downloaded from GEO database,and the differentially expressed genes(DEGs)were screened.Enrichment analysis of the signaling pathways and molecular functions were preformed and protein-protein interaction networks(PPI)were constructed to identify the hub genes,whose expression levels and diagnostic and prognostic values were verifies based on gastric adenocarcinoma data from TCGA.The expression levels of these core genes were also detected in different GC cell lines using qRT-PCR.Results Seventy-seven DEGs were identified,which encodes proteins located mainly in the extracellular matrix and basement membrane with activities of oxidoreductase and extracellular matrix receptor and ligand,involving the biological processes of digestion and hormone metabolism and the signaling pathways in retinol metabolism and gastric acid secretion.Nine hub genes were obtained,among which SPARC,TIMP1,THBS2,COL6A3 and THY1 were significantly up-regulated and TFF1,GKN1,TFF2 and PGC were significantly down-regulated in GC.The abnormal expressions of SPARC,TIMP1,THBS2,COL6A3,TFF2 and THY1 were significantly correlated with the survival time of GC patients.ROC curve analysis showed that aberrant expression of TIMP1,SPARC,THY1 and THBS2 had high diagnostic value for GC.High expressions of SPARC,TIMP1,THBS2 and COL6A3 were detected in GC tissues.In the GC cell lines,qRT-PCR revealed different expression patterns of these hub genes,but their expressions were largely consistent with those found in bioinformatics analyses.Conclusion SPARC,TIMP1,THBS2 and other DEGs are probably involved in GC occurrence and progression and may serve as potential candidate molecular markers for early diagnosis and prognostic evaluation of GC.
2.Screening of differentially expressed genes in gastric cancer based on GEO database and function and pathway enrichment analysis
Yihao LIANG ; Yingjun LAI ; Yanwen YUAN ; Wei YUAN ; Xibo ZHANG ; Bashan ZHANG ; Zhifeng LU
Journal of Southern Medical University 2024;44(3):605-616
Objective To explore the core genes related to the diagnosis and prognosis of gastric cancer(GC)based on Gene Expression Omnibus(GEO)database and screen the molecular targets involved in the occurrence and development of GC.Methods GC microarray data GSE118916,GSE54129 and GSE79973 were downloaded from GEO database,and the differentially expressed genes(DEGs)were screened.Enrichment analysis of the signaling pathways and molecular functions were preformed and protein-protein interaction networks(PPI)were constructed to identify the hub genes,whose expression levels and diagnostic and prognostic values were verifies based on gastric adenocarcinoma data from TCGA.The expression levels of these core genes were also detected in different GC cell lines using qRT-PCR.Results Seventy-seven DEGs were identified,which encodes proteins located mainly in the extracellular matrix and basement membrane with activities of oxidoreductase and extracellular matrix receptor and ligand,involving the biological processes of digestion and hormone metabolism and the signaling pathways in retinol metabolism and gastric acid secretion.Nine hub genes were obtained,among which SPARC,TIMP1,THBS2,COL6A3 and THY1 were significantly up-regulated and TFF1,GKN1,TFF2 and PGC were significantly down-regulated in GC.The abnormal expressions of SPARC,TIMP1,THBS2,COL6A3,TFF2 and THY1 were significantly correlated with the survival time of GC patients.ROC curve analysis showed that aberrant expression of TIMP1,SPARC,THY1 and THBS2 had high diagnostic value for GC.High expressions of SPARC,TIMP1,THBS2 and COL6A3 were detected in GC tissues.In the GC cell lines,qRT-PCR revealed different expression patterns of these hub genes,but their expressions were largely consistent with those found in bioinformatics analyses.Conclusion SPARC,TIMP1,THBS2 and other DEGs are probably involved in GC occurrence and progression and may serve as potential candidate molecular markers for early diagnosis and prognostic evaluation of GC.
3.Study on Myocardial Lymphangiogenesis Disorder in Dilated Cardiomyopathy Mice Induced by Doxorubicin and the Protective Mechanism of Kuoxin Decoction
Yidan DONG ; Mengjiao MA ; Longping PENG ; Maolin ZHOU ; Qianqian LIANG ; Qiong WU ; Yanwen WANG ; Youhua WANG
World Science and Technology-Modernization of Traditional Chinese Medicine 2023;25(10):3293-3303
Objective To observe the dynamic changes of cardiac lymphangiogenesis in Doxorubicin(DOX)-induced dilated cardiomyopathy(DCM)model mice,and to study the the protective mechanism of Kuoxin Decoction.Methods The DCM mouse model was established by intraperitoneal injection of DOX,and the dynamic observation was performed every week.On this basis,60 C57BL/6 mice were randomly divided into 6 groups(n=10):control group,Model group,L-KXD,M-KXD and H-KXD groups and Captopril group.After successful modeling,the KXD and the positive control drug Captopril were administered continuously for 28 days.Echocardiography was used to detect cardiac function in mice,HE staining and Masson staining were used to observe pathological and morphological changes of the heart,Whole-mount immunofluorescent staining was used to detect the expression of LYVE-1 and Podoplanin in epicardial lymphatic vessels,Western blot was used to detect the expression of VEGFR-3 protein,and qPCR was used to detect the expression of VEGFR-3 mRNA.Results DCM mice induced by DOX showed significant cardiac function decline from the third week(DOX:15 mg·kg-1,P<0.05),and significant ventricular remodeling at the fifth week(DOX:15 mg·kg-1,P<0.01);The lymphatic vessel area of the mouse heart decreased significantly from the fourth week(DOX:20 mg·kg-1,P<0.0001),and the expression of VEGFR-3 decreased significantly from the third week(DOX:15 mg·kg-1,P<0.01).Conclusion KXD can improve ventricular remodeling and cardiac function in DOX-induced DCM mice,promote cardiac lymphangiogenesis,and upregulate the expression of VEGFR-3 at protein and mRNA levels,with a better effect than captopril.DOX-induced cardiac lymphangiogenesis in DCM mice leads to severe myocardial fibrosis and weakened cardiac function,which gradually worsens with the accumulation of modeling time and dose.KXD can promote cardiac lymphangiogenesis and improve cardiac function in DOX-induced DCM mice.The mechanism may be related to the up-regulation of VEGFR-3 expression.
4.Establishment and evaluation of pre-metastatic niche mouse model labelled with luciferase in lewis lung cancer cells.
Haixia MING ; Ming SHEN ; Yanwen CHEN ; Yang LI ; Lingling YANG ; Qiankun LIANG ; Zhaohua LIU
Chinese Journal of Cellular and Molecular Immunology 2023;39(12):1083-1088
Objective This study aimed to establish a pre-metastatic niche mouse model utilizing luciferase-labeled Lewis (Luc-Lewis) lung cancer cells and to assess the efficacy of this model employing both qualitative and quantitative methods. Methods C57BL/6 mice were categorized into two groups: a normal control group and a model group, each containing 15 individual mice. The pre-metastatic niche model was established via tail vein injection of Luc-Lewis lung cancer cells. Body mass were measured daily for all groups. Tumor fluorescence signals within the mice were detected using a high-throughput enzyme marker instrument. Lung tissue specimens were harvested to evaluate metastatic progression. HE staining was used to assess histopathological changes. Real-time quantitative PCR and Western blot analysis were used to detect the mRNA and protein expression of lysyl oxidase (LOX), matrix metalloproteinase 9 (MMP9), versican (VCAN), and fibronectin (FN), which are the specific markers for the formation of the microenvironment of lung tissues before metastasis. Results Significant declines in body mass and observable lethargy were noted in the model group when compared to the control group. Distinct fluorescence signals were observed in the lung tissue of the model group, demonstrating a positive correlation with the duration of model establishment. By day 14, elevated mRNA and protein expression levels of LOX, MMP9, VCAN, and FN were significantly evident. In addition, histopathological evaluations revealed augmented interstitial thickness, alveolar atrophy and significant inflammatory cell infiltration within the lung tissues of the model group. By the 21st day, metastatic lesions manifested in the lung tissues of the model group, suggesting an approximate pre-metastatic niche maturation timeline of 14 days. Conclusion A pre-metastatic niche mouse model for Lewis lung cancer is successfully established.
Mice
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Animals
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Lung Neoplasms/pathology*
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Matrix Metalloproteinase 9
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Mice, Inbred C57BL
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Carcinoma, Lewis Lung
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Disease Models, Animal
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RNA, Messenger
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Tumor Microenvironment
5.The chemical reprogramming of unipotent adult germ cells towards authentic pluripotency and de novo establishment of imprinting.
Yuhan CHEN ; Jiansen LU ; Yanwen XU ; Yaping HUANG ; Dazhuang WANG ; Peiling LIANG ; Shaofang REN ; Xuesong HU ; Yewen QIN ; Wei KE ; Ralf JAUCH ; Andrew Paul HUTCHINS ; Mei WANG ; Fuchou TANG ; Xiao-Yang ZHAO
Protein & Cell 2023;14(7):477-496
Although somatic cells can be reprogrammed to pluripotent stem cells (PSCs) with pure chemicals, authentic pluripotency of chemically induced pluripotent stem cells (CiPSCs) has never been achieved through tetraploid complementation assay. Spontaneous reprogramming of spermatogonial stem cells (SSCs) was another non-transgenic way to obtain PSCs, but this process lacks mechanistic explanation. Here, we reconstructed the trajectory of mouse SSC reprogramming and developed a five-chemical combination, boosting the reprogramming efficiency by nearly 80- to 100-folds. More importantly, chemical induced germline-derived PSCs (5C-gPSCs), but not gPSCs and chemical induced pluripotent stem cells, had authentic pluripotency, as determined by tetraploid complementation. Mechanistically, SSCs traversed through an inverted pathway of in vivo germ cell development, exhibiting the expression signatures and DNA methylation dynamics from spermatogonia to primordial germ cells and further to epiblasts. Besides, SSC-specific imprinting control regions switched from biallelic methylated states to monoallelic methylated states by imprinting demethylation and then re-methylation on one of the two alleles in 5C-gPSCs, which was apparently distinct with the imprinting reprogramming in vivo as DNA methylation simultaneously occurred on both alleles. Our work sheds light on the unique regulatory network underpinning SSC reprogramming, providing insights to understand generic mechanisms for cell-fate decision and epigenetic-related disorders in regenerative medicine.
Male
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Mice
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Animals
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Cellular Reprogramming/genetics*
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Tetraploidy
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Pluripotent Stem Cells/metabolism*
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Induced Pluripotent Stem Cells/metabolism*
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DNA Methylation
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Spermatogonia/metabolism*
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Germ Cells/metabolism*
6.Effects of GYP mRNA alternative splicing on cell surface localization of MNS blood group glycoprotein GPA and GPB
Yanlian LIANG ; Yanwen LIANG ; Jiansuo LIN ; Hongxing WANG ; Shuai CHEN ; Yunping XU
Chinese Journal of Blood Transfusion 2022;35(9):887-891
【Objective】 To analyze the polymorphisms of GYPA and GYPB mRNA spliceosomes associated with MNS blood group, and to explore the mechanism of subcellular localization of GPA and GPB protein isomerism encoded by various spliceosomes as well as the expression of MNS blood group antigen. 【Methods】 Ten blood samples of voluntary blood donors were randomly selected. The total mRNA of peripheral blood was extracted and reversed into cDNA. Nested PCR was used to amplify reading open frame of GYPA and GYPB gene, and sequencing was performed by Sanger. The base sequence obtained was compared with GYPA(NCBI: NM_002099) and GYPB(NCBI: Nm_002100.5). After the wild type and various splicing isomer of the open reading frame of GYPA and GYPB had been obtained, they were fused with the encoding gene of green fluorescent protein (GFP) by fusion PCR technology, then cloned and transfected into HEK293 cells for over expression. The subcellular localization of GPA-GFP and GPB-GFP fused fluorescent proteins was monitored by focusing laser scanning microscope. 【Results】 Exon-1 and Exon-2 were missing in GYPA mRNA of the 2 samples, and 2~26 amino acids were missing in the predicted GPA isomer, and the full length sequence of GYPB mRNA was complete. GYPA mRNA was intact in 6 samples, exon-2 was missing in GYPB mRNA, 13~45 amino acids were missing in the predicted GPB protein isomer, and other exon sequences were intact. One sample had intact GYPA mRNA, and 364~385 bases in exon-5 of GYPB mRNA were replaced by AG, indicating truncation of amino acid signal peptide. The GYP mRNA sequences of other samples were complete. The fluorescence signal of GP-GFP fusion protein showed that all GPA and GPB glycoprotein isomers, cloned according to various RNA splicing, could demonstrate the orientation distribution on the cell membrane surface, while some alternative splicing leaded to different degrees of protein dispersion in the cell, and affected the distribution speed and proportion of protein on the cell surface, which might be one of the reasons for the strength variation of MNS antigen. 【Conclusion】 The GYP mRNA spliceosome is obviously polymorphic, but the partial deletion of GYP mRNA fragment does not affect the localization and distribution of the protein isomers encoded by GYP mRNA on the cell surface, which can ensure the expression of MNS antigen characteristics.
7.Status and obstacle factors of exercise in elderly maintenancehemodialysis patients
Chen LIANG ; Aixian LI ; Yanwen QIU ; Jinfeng SHI ; Xia QIN
Chinese Journal of Modern Nursing 2022;28(35):4857-4862
Objective:To explore the status and obstacle factors of exercise in elderly maintenance hemodialysis (MHD) patients, so as to provide a clinical evidence for exercise guidance and targeted intervention in elderly maintenance hemodialysispatients.Methods:A mixed method of consistent parallel design was adopted. A total of 180 elderly MHD patients in two ClassⅢ hospitals of Kunshan in December 2021 were enrolled using convenience sampling method and investigated by questionnaire. The statas of exercise and exercise self-efficacy were researched. Objective sampling method was used to interview 17 elderly MHD patients with semi-structured interviews. The obstacle factors of exercise were investigated.Results:A total of 180 valid questionnaires were collected in the quantitative study. The highest metabolicequivalent of leisure time physical activity was 1 188 MET-min/w, the lowest was 0 MET-min/w, and the median was 396 MET-min/w. Pearson correlation analysis showed that there was a positive correlation between exercise self-efficacy and physical activity in elderly MHD patients ( P<0.05). Qualitative study extracted 3 themes and 9 subthemes, including lack of exercise knowledge, low self-efficacy, family and social environment resource limitation. Conclusions:Elderly MHD patients lack ideal exercise state. In clinical practice, medical staff should popularize exercise knowledge, improve patients' exercise self-efficacy, carry out family support education, increase social support, and select suitable exercise methods and develop individualized exercise programs according to patients' disease characteristics, so as to improve their exercise status.
8.CT findings of primary pulmonary diffuse large B-cell lymphoma
Yanwen LIU ; Qin LIU ; Ruihong LIANG ; Huai CHEN ; Qingsi ZENG
Chinese Journal of Radiology 2020;54(8):769-773
Objective:To investigate characteristic CT manifestations of primary pulmonary diffuse large B-cell lymphoma (DLBCL).Methods:CT images of 14 patients [10 males and 4 females, age (54±2) years old, range 32 to 91] with pathologically-proved pulmonary DLBCL lymphoma were retrospectively analyzed.Plain CT and contrast enhanced CT imaging were performed in all 14 patients. Image characteristics including lesion size, locations and distribution, morphology and margin, density and enhancement degrees, bronchia and lesion surroundings, other thoracic extra-pulmonary manifestations, as well as distant metastasis were analyzed and recorded. The maximal diameter of mass and/or nodules, pre and post-contrast CT values were measured. Among all 14 cases, 8 cases were initially diagnosed as lung carcinoma, 5 cases as infection, one case as lymphoma.Results:Among all 14 primary lung DLBCL cases, there were 10 case with multiple lesions and 4 with single lesion. Masses and/or nodules were found in 12 cases, with the maximum diameter of the lesions as 0.8-8.2 cm, the median value as 5.3 (2.9, 7.8) cm. Two cases showed simple consolidation. The margins of the lesions were clear and smooth in 12 cases, and fuzzy in 2 cases. The density of the lesions on pre-contrast CT was relatively uniform, with mean CT value (35.1±1.0) HU. After contrast, 10 cases displayed mild to moderate homogeneous enhancement, 4 cases showed heterogenous enhancement. The mean CT value of post-contrast images was (61.8±1.5) HU. In arterial phase, the mean CT value was (50.9±1.3) HU. Angiographic sign was found in 9 cases in arterial phase. Of the 14 cases, bronchus was clear and smooth in 5 cases. In 4 cases, bronchus was found slight compressed or stenosis; and 5 cases showed intra-lesion bronchi invasion or occlusion. Interstitial tissue around the lesion was found slightly thickened in 8 cases. The pleura showed unevenly thickened and invaded in 8 cases. Mediastinal or hilar lymphadenopathy and fusion were found in 10 cases, with 3 cases involving mediastinal large blood vessels, and 7 cases displaying infiltrative growth pattern. There were 4 cases with pleural effusion. CT follow-up after treatment in 8 cases showed no distant metastasis (7 cases showed good prognosis, with lesions disappearing after radiotherapy, chemotherapy or surgical resection; 1 case showed progressed with lesion increased after chemotherapy). Six patients abandoned the treatment and discharged from the hospital.Conclusions:Primary DLBCL is a high invasive and malignant entity with certain CT characteristics. The confirmed diagnosis of pulmonary DLBCL depends on pathological results.
9.Expression of thymidylate synthase in breast cancer and its correlation with fluorouracil sensibility and patients' prognosis
Kai LU ; Yanwen LIU ; Dong LIU ; Hongling YE ; Liang XU ; Su LIU
Chinese Journal of Endocrine Surgery 2018;12(5):377-380
Objective To investigate the expression of thymidylate synthase (TS) in breast cancer and its relationship with fluorouracil sensibility and patients' prognosis.Methods TS expression in 80 cases of breast cancer was measured by RT-QPCR.The chemotherapy (CAF) was given.Relationship between TS and fluorouracil sensibility was studied,as well as the relation between TS expression and prognosis of breast cancer.Result Positive expression of TS gene was detected by Q-PCR 1n 27.5% of the breast cancer specimens.The expression of TS had no relation with age,lymphatic metastasis,histological grade or clinical stage,while it was obviously correlated with HER2 (P<0.01).The expression of TS had negative correlation with the antitumor effect of fluorouracil.The five-year survival rate of TS positive patients was lower than that of TS negative patients (P<0.01).Conclusions Breast cancer patients with low expression of TS may benefit from fluorouracil.TS can be used as a molecule marker for predicting efficacy of breast cancer chemotherapy.
10.Correction of β-thalassemia mutant by base editor in human embryos.
Puping LIANG ; Chenhui DING ; Hongwei SUN ; Xiaowei XIE ; Yanwen XU ; Xiya ZHANG ; Ying SUN ; Yuanyan XIONG ; Wenbin MA ; Yongxiang LIU ; Yali WANG ; Jianpei FANG ; Dan LIU ; Zhou SONGYANG ; Canquan ZHOU ; Junjiu HUANG
Protein & Cell 2017;8(11):811-822
β-Thalassemia is a global health issue, caused by mutations in the HBB gene. Among these mutations, HBB -28 (A>G) mutations is one of the three most common mutations in China and Southeast Asia patients with β-thalassemia. Correcting this mutation in human embryos may prevent the disease being passed onto future generations and cure anemia. Here we report the first study using base editor (BE) system to correct disease mutant in human embryos. Firstly, we produced a 293T cell line with an exogenous HBB -28 (A>G) mutant fragment for gRNAs and targeting efficiency evaluation. Then we collected primary skin fibroblast cells from a β-thalassemia patient with HBB -28 (A>G) homozygous mutation. Data showed that base editor could precisely correct HBB -28 (A>G) mutation in the patient's primary cells. To model homozygous mutation disease embryos, we constructed nuclear transfer embryos by fusing the lymphocyte or skin fibroblast cells with enucleated in vitro matured (IVM) oocytes. Notably, the gene correction efficiency was over 23.0% in these embryos by base editor. Although these embryos were still mosaic, the percentage of repaired blastomeres was over 20.0%. In addition, we found that base editor variants, with narrowed deamination window, could promote G-to-A conversion at HBB -28 site precisely in human embryos. Collectively, this study demonstrated the feasibility of curing genetic disease in human somatic cells and embryos by base editor system.
APOBEC-1 Deaminase
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genetics
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metabolism
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Base Sequence
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Blastomeres
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cytology
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metabolism
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CRISPR-Cas Systems
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Embryo, Mammalian
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metabolism
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pathology
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Female
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Fibroblasts
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metabolism
;
pathology
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Gene Editing
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methods
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Gene Expression
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HEK293 Cells
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Heterozygote
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Homozygote
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Humans
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Point Mutation
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Primary Cell Culture
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Promoter Regions, Genetic
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Sequence Analysis, DNA
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beta-Globins
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genetics
;
metabolism
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beta-Thalassemia
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genetics
;
metabolism
;
pathology
;
therapy

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