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Title of Thesis

Molecular Genetic Characterization of Breast cancer in Pakistani Population


Muhammad Faraz Arshad Malik

Institute/University/Department Details
Department Of Molecular Genetics / COMSATS Institute of Information Technology, Islamabad
Molecular Genetics
Number of Pages
Keywords (Extracted from title, table of contents and abstract of thesis)
Molecular, Genetic, Characterization, Breast, cancer, metastasis, suppressor, Germline, Pakistani, Population

Breast cancer has been identified as the most common malignancy among Pakistani women, accounting for 34.6% of all female cancers. Around 80-90% cases are sporadic in nature. Multiple factors, including genetic as well as epigenetic factors are responsible for the initiation of breast cancer. In the present study, we carried out genetic characterization of breast cancer in our local population. Diagnosed breast cancer patients having a mean age of 53yrs were included in this study. These patients were analyzed for mutations in BRCA1 and two metastasis suppressor genes (KAI1 and Kiss1). Germline mutations of three genes BRCA1, Kiss1 and KAI1 were investigated in already diagnosed sporadic breast cancer females. BRCA1, a tumour suppressor gene is found responsible for majority of breast cancer cases of familial history. However its involvement in sporadic breast cancer cases (especially of Pakistani population) is still an area that requires further research. BRCA1 proteins binding domain encoding regions were screened in this regard. Five silent mutations along with one novel splice site mutation were observed on BRCA1. However, most of the BRCA1 portions analyzed remained conserved at genomic levels. This study thus indirectly highlights the involvement of other signaling cascade molecules as well as transcriptional and translational regulatory mechanism responsible for breast cancer. Metastasis is among one of most lethal attribute of cancer. In this study, two metastasis suppressor genes (Kiss1 and KAI1) were screened for any germline mutations/polymorphism in these patients. So far no previous findings with respect to these genes have been reported. In our study no exon or introns deletions had been observed on these genes. Altered expression (down-regulation) of these genes has extensively been reported in the literature in relation to different types of cancers. However, expressional correlation of KAI1 with disease progression is established for the first time by this study. Significant decrease in KAI1 expression has been observed in localized and invasive cancer cells when compared to normal cells. Significant correlation of KAI1 with TNM staging (Tumour, node and metastasis) has also been established (p=0.045).
Patients showing higher expression of KAI1 showed better survival rate (after median follow up of 120 months) when compared to those showing less or almost negative expression (p=0.0136). Thus potential involvement of KAI1 molecule as a marker of prognostic significance is established. Interaction of KAI1, tetraspanin family member, with FAK, Shh, EGFR and integrins was done as preliminary screening to find its potential involvement in the metastatic cascade. A chain of in vitro assays were conducted to explore KAI1 cellular response. Two transgenes based effective knock outs (MDA-MB-231KAI1KO1, MDA-MB-231KAI1KO2) and one forced expression (MCF-7KAI1Exp1) were successfully generated through the aid of molecular tools. Expression levels of KAI1 in both MDA-MB-231 and MCF-7 were confirmed through RTPCR and western blot. No significant association of KAI1 on cancer cells growth had been observed. This shows that KAI1 does not influence cell proliferation. However, a direct relationship of KAI1 with intracellular attachment to basement membrane has been established in both knock out as well forcedly expressing breast cancer cell lines. Increased expression of KAI1 resulted in strong cells adhesion to basement membrane in MCF-7 KAI1Exp1 when compared to both wild type and controls (MCF-7Wt, MCF-7Ct) with p value of 0.021. Similarly weak adhesion of cancer cells has been observed in MDA-MB-231KAI1KO1 and MDA-MB-231 KAI1Ko2 when compared with MDAMB-231Wt and MDA-MB-231Ct) with p values of 0.002 and 0.0004 respectively. A significant increase in cancer cell invasion was observed in both ribozymes based KAI1 knock outs (MDA-MB-231KAI1KO1 and MDA-MB-231KAI1Ko2 in relation to control (MDA-MB-231Ct) with p values of 0.0063 and 0.007 respectively. Furthermore, MCF-7KAI1Exp1 cells showed reduced cell invasiveness in relation to MCF-7wt and MCF-7Ct (p=0.022). Cell motility was also analyzed in both absence and forcedly expressing KAI1 cell lines. MDA-MB-231 KAI1KO1 and MDA-MB-231 KAI1KO2 showed restricted cell migration (p=0.003 vs control) towards the wound. Increased cellular migrations in time lapse based video (up to 90min) recording of MCF-7 KAI1Exp1 was observed (p-0.024 vs control). This study has shown that both genetic and epigenetic factors are mainly responsible for systematic progression. Although the contributory role of gene mutations is low but expressional regulation of these genes is an area which can help in identifying the missing links. Establishing a marker of prognostic
significance as well as its potential role in metastatic cascade suppression can help in designing most promising gene therapy for breast tumour affected patients.

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S. No. Chapter Title of the Chapters Page Size (KB)


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1.1 Carcinogenesis
1.2 Etiology of cancer
1.3 Cascade of carcinogenesis
1.4 Breast cancer across the globe and Pakistani population
1.5 Introduction to mammary tissues and tumour types
1.6 Genetics of breast cancer
1.7 Risk factors associated with breast cancer
1.8 Rare affiliated breast cancer syndromes
1.9 Major genes involved in breast cancer
1.10 Role of BRCA1 in normal cell signaling and DNA repair
1.11 Metastasis in breast cancer
1.12 Are genes responsible for metastasis?
1.13 Role of metastasis suppressor genes in breast cancer
1.14 Expression of CD82 in normal cells
1.15 Expression of CD82 in cancer cells
1.16 Importance of germline mutations in cancer
1.17 Techniques used for germline mutation detection
1.18 Techniques involved in mutation detection
1.19 Plan of Study

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2.1 Materials
2.2 Patients identification and collection of samples
2.3 Isolation and quantification of human genome
2.4 Polymerase chain reaction (PCR)
2.5 Post-amplification agarose gel electrophoresis
2.6 Single strand conformation polymorphism
2.7 Sequencing protocol for the suspected samples
2.8 Expression analysis of metastasis suppressor gene
2.9 Post amplification gel electrophoresis
2.10 DNA staining and visualization
2.11 Real Time PCR (qPCR)
2.12 Breast cancer cell lines
2.13 Media and cancer cell lines Storage conditions
2.14 Detachment of adherent cells and cell counting
2.15 Storage of cell stocks in liquid nitrogen
2.16 In vitro analysis of KAI1 molecule on breast cancer cell lines
2.17 Selection and orientation analysis of positive colonies
2.18 Plasmid isolation and quantification
2.19 Sequencing of the insert for screening mutants
2.20 Transformation of mammalian cells using electroporation
2.21 Establishment of stable MDA-MB-231 and MCF-7 cell lines
2.22 Confirmation of transformation
2.23 In vitro characterization of KAI1 in breast cancer cell lines
2.24 Statistical analysis

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3.1 Samples outline in Pakistani population
3.2 Extracted and quantified DNA samples
3.3 Amplification check on agarose gel electrophoresis
3.4 Mutation detection using single strand conformational polymorphism (SSCP)
3.5 Sequencing of the suspected samples
3.6 Down-regulation of KAI1 molecule in breast cancer patients
3.7 Relation of KAI1 transcript with TNM Staging
3.8 Affect of KAI1 of patients survival
3.9 Expression of KAI1 in cancer cell lines
3.10 Successful generation and transformation of KAI1molecule
3.11 Successful generation and transformation of ribozymes
3.12 Isolation of bacterial plasmid
3.13 Generation of transformed breast cancer cell lines
3.14 Association of KAI1 with different molecules
3.15 Effect of KAI1 on cancer cells growth
3.16 Effect of KAI1 on cancer cell invasion
3.17 Effect of KAI1 on cancer cell adhesion
3.18 Effect of KAI1 molecule on cellular motility

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