Contents & References of Investigating the expression of some miRNAs in retinoblastoma cancer derived cell lines overexpressing TGIF2LX due to exposure to SD-208 drug
List:
Chapter 1: Introduction and statement of the problem. 1
1.1 Retinoblastoma 2
1.1.1 Epidemiology. 2
1.1.2 Pathogenesis. 3
1.1.3 Clinical and diagnostic features. 5
1.2 Family history. 5
1.3 Diagnosis. 5
1.4- Assessment before treatment. 6
1.5 Treatment. 6
1.6- Molecular mechanism of cancer. 9
1.6.1 TGF? signaling pathway 9
1.6.1.1 TGF? ligand family. 11
1.6.1.2 Receptor type 1 and 2 (TGF?RI, II) 11
1.6.1.3 Phosphorylation of SMAD. 12
1.6.2 Regulation of TGF? signaling. 12
1.6.3 Involvement of TGF? signaling in cancer. 13
1.6.4 Homeobox genes 14
1.6.4.1 The structure of homeobox genes. 14
1.7 The role of Homeobox genes in causing cancer. 17
1.8 miRNA 18
1.8.1 biogenesis of miRNAs and how to inhibit translation. 19
1.9 miRNA and cancer. 20
1.10- miRNA is a tool to identify and diagnose cancer. 21
1.11 miRNA and cancer treatment. 22
1.12 Statement of the problem and importance of the research. 23
1.13 Research objectives. 24
1.13.1 The main goal. 24
1.13.2 Special objectives 24
1.13.3 Practical objective. 25
Chapter 2: review of texts. 26
2.1 Reviewing the texts related to the subject. 27
Chapter 3: Materials and methods 32
3.1 Chemicals and enzymes 33
3.1.1 Bacterial plasmid. 35
3.1.1.1 Properties of plasmid. 36
3.1.1.2 Host characteristics. 37
3.2 Methods 37
3.2.1 Bacteria culture. 37
3.2.1.1 Materials and tools needed for bacterial cultivation. 37
3.2.1.2 How to prepare liquid LB culture medium. 38
3.2.1.3 Stock glycerol. 38
3.2.2 The method of miniprepa extraction of plasmid DNA from bacteria. 39
3.2.2.1 Quantitative and qualitative examination of plasmid DNA. 41
3.2.3 Enzymatic digestion of extracted plasmids 45
3.2.4 Cell culture. 46
3.2.4.1 Cultivation environment. 46
3.2.4.2 FBS fetal bovine serum. 47
3.2.4.3 Preparing the environment for creating cells 47
3.2.4.4 Characteristics of the cells used in this thesis. 48
3.2.5 Determination of the lethality curve of G418 antibiotic. 48
3.2.6 Adaptation of cells 48
3.2.7 Transfection of Y79 cells with recombinant plasmid vector pEGFP-TGIF2LX. 49
3.2.8 Selection of positive cells. 50
3.2.9 Examining the expression of TGIF2LX gene in transfected cells at the mRNA level by Realtime RT-PCR 51
3.2.9.1 Protection of RNA. 52
3.2.9.2 RNA extraction. 55
3.2.9.3 Treatment of RNA sample with deoxyribonuclease I enzyme 59
3.2.9.4 Synthesis of complementary DNA (cDNA) 60
3.2.9.5 PCR (Polymerase chain reaction). 64
3.2.9.6 Realtime PCR reaction. 68
3.2.9.7 Analysis of data from Realtime RT-PCR reaction. 77
3.2.10 Checking the expression of eGFP-TGIF2LX at the protein level by Western blot 78
3.2.10.1 SDS-PAGE vertical electrophoresis. 78
3.2.10.2 SDS-PAGE staining. 84
3.2.10.3 Western blotting. 86
3.2.11 Checking the rate of cell proliferation by tetrazolium salt analysis. 90
3.2.11.1 Investigating the effect of increased expression of TGIF2LX in Y79 cells compared to the control. 90
3.2.11.2 Investigating the interaction effect of SD-208 and increased expression of TGIF2LX in Y79 cells compared to the control. 91
3.2.11.3 Cell counting protocol. 92
3.2.12 The study of the effect of SD-208 drug on the expression of TGIF2LX, miRNA Let7g,18a,34a,22,20 in transfected Y79 cells compared to control samples by Real time RT-PCR. 92
Chapter 4: Results and findings 96
4.1 Mini prep and plasmid DNA digestion to confirm the recombinant vector. 97
4.2- Examining the expression of TGIF2LX at the mRNA level. 98
4.2.1 Result of qualitative and quantitative analysis of RNA. 98
4.2.2 Quality review of cDNA. 99
4.3 Studying the expression of TGIF2LX in transfected cells 101
4.3.1 Studying the expression of TGIF2LX in transfected cells1 Study of TGIF2LX expression in transfected Y79 cells compared to control samples by microscopy 101 4.3.2 Confirmation of clear expression of GFP-TGIF2LX gene by Realtime RT-PCR. 102
4.3.3 Studying the expression of TGIF2LX gene in cells transfected with a vector containing GFP-TGIF2LX at the protein level by Western Blot 104
4.3.4 Studying the expression of the effect of SD-208 drug on the expression of TGIF2LX in transfected Y79 cells compared to control samples 105
4.4 Investigating the effect of increased expression of TGIF2LX on Y79 cells. 105
4.4.1- Microculture Tetrazolium Test (MTT) test results 105
4.4.2 Investigating the interaction effect of SD-208 and increased expression of TGIF2LX on Y79 cells compared to the control. 106
4.5- Examining the expression of miRNA Let7g,18a,34a.22,20a in transfected and control cells. 108
4.6 Studying the expression of the effect of SD-208 drug on the expression of miRNA Let7g,18a,34a.22,20 in transfected Y79 cells compared to control samples. 109
4.7 Ct in Realtime PCR reaction. 110
Chapter 5: discussion, conclusion and suggestions 113
5.1 Discussion 114
5.2 The effect of increased expression of TGIF2lX on cellular viability in Y79 cell line. 116
5.3 Effect of SD-208 drug on Cellular Viability in Y79 cell line overexpressing TGIF2LX and control 117
5.4 Effect of SD-208 on the expression of TGIF2LX in transfected Y79 cell line compared to control. 118
5.5 The interaction effect of SD-208 and TGIF2LX on the expression of studied miRNAs. 118
5.5.1 Interaction between SD-208 and TGIF2LX on miRNAlet7g expression in Y79 cell line. 118
5.5.2 Interaction between SD-208 and TGIF2LX on miRNA18a expression in Y79 cell line. 119
5.5.3 The interaction effect of SD-208 and TGIF2LX on miRNA34a expression in Y79 cell line. 119
5.5.4 Interaction between SD-208 and TGIF2LX on miRNA22 expression in cell line. 119
5.5.5 Interaction of SD-208 and TGIF2LX on miRNA20a expression in Y79 cell line. 120
5.6 Conclusion. 120
7.5 Suggestions. 121
Resources and references. 122
Appendices 131
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