Nor Aina Emran

Gene expression patterns distinguish breast carcinomas from normal breast tissues: The Malaysian context

Genomic and transcriptomic alterations that affect cellular processes, such as cell proliferation, differentiation, apoptosis and invasion, commonly occur in breast oncogenesis. Epidemiological evidence has proven that the risk of breast cancer predisposition varies among different ethnicities. This study aims to identify the transcriptome changes that commonly occur during the transition of normal breast epithelium to carcinoma in three local ethnic groups (Malays, Chinese and Indians). The gene expression patterns of 43 breast carcinomas with 43 patient-matched normal breast tissues were investigated using Affymetrix U133A GeneChip (containing 22,283 probe sets targeting approximately 18,400 different transcripts) and analyzed with GeneSpring GX10. Our findings revealed a total of 33 significantly differentially expressed genes, which showed>2-fold change at a 99.9% confidence interval level (p<0.001). The significantly differentially expressed genes included CD24, CD36, CD9, TACSTD1, TACSTD2, HBB, LEP, LPL, AKR1C1, AKR1C2 and AKR1C3. Our results indicate that the vast majority of gene expression changes, from normal breast epithelial to carcinoma, found in our three major ethnic populations are similar to those in the Caucasian population. Further study of the differentially expressed genes identified in our present study is needed to search for potential breast tumor biomarkers. This will eventually help to improve the therapeutic and treatment strategies for breast cancer patients in the future.

Dietary changes among breast cancer patients in Malaysia.

Background: Breast cancer patients often show an interest in making dietary changes after diagnosis of breast cancer to improve their health condition and prevent cancer recurrence. Objective: The objective of the study was to determine changes in dietary intake 2 years after diagnosis among breast cancer patients. Methods: One hundred sixteen subjects were asked to complete a semiquantitative food frequency questionnaire, diet recalls, and dietary changes questionnaire to assess dietary intake before and after diagnosis. The information on sociodemographic background, cancer treatment history, and anthropometric indices was also collected. Results: Seventy-two subjects considered diet as a contributing factor to breast cancer, and 67 subjects changed their dietary habits after breast cancer diagnosis. The reasons for changes in diet were physician and dietitian advice and desire to cure cancer. The sources of information were derived from their physician, mass media, and family members. Total energy, protein, total fat, fatty acids, and vitamin E intake were significantly decreased after diagnosis. Meanwhile, the intake of &bgr;-carotene and vitamin C increased significantly after diagnosis. The changes included reduction in red meat, seafood, noodles, and poultry intake. An increased consumption of fruits, vegetables, fish, low-fat milk, and soy products was observed. The subjects tended to lower high-fat foods intake and started to eat more fruits and vegetables. Conclusion: Breast cancer patients had changed to a healthier diet after breast cancer diagnosis, although the changes made were small. Implications for Practice: This will be helpful to dietitians in providing a better understanding of good eating habits that will maintain patients’ health after breast cancer diagnosis.

Complementary and alternative medicine (CAM) use and delays in presentation and diagnosis of breast cancer patients in public hospitals in Malaysia.

Complementary and alternative medicine (CAM) is widely used among the breast cancer patients in Malaysia. Delays in presentation, diagnosis and treatment have been shown to impact the disease prognosis. There is considerable use of CAM amongst breast cancer patients. CAM use has been cited as a cause of delay in diagnosis and treatments in qualitative studies, however there had not been any confirmatory study that confirms its impact on delays. The purpose of this study was to evaluate whether the use of CAM among newly diagnosed breast cancer patients was associated with delays in presentation, diagnosis or treatment of breast cancer. This multi-centre cross-sectional study evaluating the time points of the individual breast cancer patients’ journey from first visit, resolution of diagnosis and treatments was conducted in six public hospitals in Malaysia. All newly diagnosed breast cancer patients from 1st January to 31st December 2012 were recruited. Data were collected through medical records review and patient interview by using a structured questionnaire. Complementary and alternative medicine (CAM) was defined as the use of any methods and products not included in conventional allopathic medicine before commencement of treatments. Presentation delay was defined as time taken from symptom discovery to first presentation of more than 3 months. The time points were categorised to diagnosis delay was defined as time taken from first presentation to diagnosis of more than 1 month and treatment delay was defined as time taken from diagnosis to initial treatment of more than 1 month. Multiple logistic regression was used for analysis. A total number of 340 patients participated in this study. The prevalence of CAM use was 46.5% (n = 158). Malay ethnicity (OR 3.32; 95% CI: 1.85, 5.97) and not interpreting symptom as cancerous (OR 1.79; 95% CI: 1.10, 2.92) were significantly associated with CAM use. The use of CAM was associated with delays in presentation (OR 1.65; 95% CI: 1.05, 2.59), diagnosis (OR 2.42; 95% CI: 1.56, 3.77) and treatment of breast cancer (OR 1.74; 95% CI: 1.11, 2.72) on univariate analyses. However, after adjusting with other covariates, CAM use was associated with delays in presentation (OR 1.71; 95% CI: 1.05, 2.78) and diagnosis (OR 2.58; 95% CI: 1.59, 4.17) but not for treatment of breast cancer (OR 1.58; 95% CI: 0.98, 2.55). The prevalence of CAM use among the breast cancer patients was high. Women of Malay ethnicity and not interpreting symptom as cancerous were significantly associated with CAM use. The use of CAM is significantly associated with delay in presentation and resolution of diagnosis. This study suggests further evaluation of access to breast cancer care is needed as poor access may cause the use of CAM. However, since public hospitals in Malaysia are heavily subsidized and readily available to the population, CAM use may impact delays in presentation and diagnosis.

Low Prevalence of CHEK2 Gene Mutations in Multiethnic Cohorts of Breast Cancer Patients in Malaysia

CHEK2 is a protein kinase that is involved in cell-cycle checkpoint control after DNA damage. Germline mutations in CHEK2 gene have been associated with increase in breast cancer risk. The aim of this study is to identify the CHEK2 gene germline mutations among high-risk breast cancer patients and its contribution to the multiethnic population in Malaysia. We screened the entire coding region of CHEK2 gene on 59 high-risk breast cancer patients who tested negative for BRCA1/2 germline mutations from UKM Medical Centre (UKMMC), Hospital Kuala Lumpur (HKL) and Hospital Putrajaya (HPJ). Sequence variants identified were screened further in case-control cohorts consisting of 878 unselected invasive breast cancer patients (180 Malays, 526 Chinese and 172 Indian) and 270 healthy individuals (90 Malays, 90 Chinese and 90 Indian). By screening the entire coding region of the CHEK2 gene, two missense mutations, c.480A>G (p.I160M) and c.538C>T (p.R180C) were identified in two unrelated patients (3.4%). Further screening of these missense mutations on the case-control cohorts unveiled the variant p.I160M in 2/172 (1.1%) Indian cases and 1/90 (1.1%) Indian control, variant p.R180C in 2/526 (0.38%) Chinese cases and 0/90 Chinese control, and in 2/180 (1.1%) of Malay cases and 1/90 (1.1%) of Malay control. The results of this study suggest that CHEK2 mutations are rare among high-risk breast cancer patients and may play a minor contributing role in breast carcinogenesis among Malaysian population.

Exploring breast carcinogenesis through integrative genomics and epigenomics analyses

There have been many DNA methylation studies on breast cancer which showed various methylation patterns involving tumour suppressor genes and oncogenes but only a few of those studies link the methylation data with gene expression. More data are required especially from the Asian region and to analyse how the epigenome data correlate with the transcriptome. DNA methylation profiling was carried out on 76 fresh frozen primary breast tumour tissues and 25 adjacent non-cancerous breast tissues using the Illumina Infinium(®) HumanMethylation27 BeadChip. Validation of methylation results was performed on 7 genes using either MS-MLPA or MS-qPCR. Gene expression profiling was done on 15 breast tumours and 5 adjacent non-cancerous breast tissues using the Affymetrix GeneChip(®) Human Gene 1.0 ST array. The overlapping genes between DNA methylation and gene expression datasets were further mapped to the KEGG database to identify the molecular pathways that linked these genes together. Supervised hierarchical cluster analysis revealed 1,389 hypermethylated CpG sites and 22 hypomethylated CpG sites in cancer compared to the normal samples. Gene expression microarray analysis using a fold-change of at least 1.5 and a false discovery rate (FDR) at p>0.05 identified 404 upregulated and 463 downregulated genes in cancer samples. Integration of both datasets identified 51 genes with hypermethylation with low expression (negative association) and 13 genes with hypermethylation with high expression (positive association). Most of the overlapping genes belong to the focal adhesion and extracellular matrix-receptor interaction that play important roles in breast carcinogenesis. The present study displayed the value of using multiple datasets in the same set of tissues and how the integrative analysis can create a list of well-focused genes as well as to show the correlation between epigenetic changes and gene expression. These gene signatures can help us understand the epigenetic regulation of gene expression and could be potential targets for therapeutic intervention in the future.

Identification of Estrogen-Related Genes in Breast Cancer: The Malaysian Context~!2009-12-04~!2010-01-10~!2010-05-07~!

Estrogen receptor (ER) status is an important indicator used to predict hormone responsiveness and survival rate of breast cancer patients. Breast cancer patients with estrogen receptor positive (ER+) tumors are more likely to benefit from endocrine therapies and have better prognosis than those with estrogen receptor negative (ER-) tumors. Approximately 30% of the patients with ER+ phenotype do not benefit from anti-estrogen therapies. This circumstance suggests that additional biomarkers are needed to predict and improve the treatment strategies in breast cancer patients. We analyzed 28 ER+ and 18 ER- tumors to evaluate their gene expression patterns. We identified 180 differentially expressed genes in ER+ compared to the ER- group at 99% confidence interval level. Out of the 180 genes, 79 and 94 genes were determined respectively as positive and negative significant genes in Significance Analysis of Microarray (SAM). Eleven out of the 79 significant positive genes were more than two (>2) fold change. The differentially expressed genes identified in the ER+ group included CADM4, CD151, GATA3, Wnt2, PGR, TFF1 and TFF3. We randomly selected two genes, namely CD151 and LPIN1 for verification by Taqman qRT-PCR. Our qRT-PCR result is reproducible and comparable with the microarray data. Our preliminary findings revealed potential estrogen-responsive genes such as CADM4, CD151 and GATA3, which might play a crucial role in ER+ breast cancer development and progression in the Malaysian population. More extensive studies are however needed to investigate the role of these genes in the carcinogenesis of estrogen related breast cancers.