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 Molecular Pathology Unit

| Introduction | Research | Diagnostic Services |

INTRODUCTION

The Molecular Pathology Unit, established in 1996, undertakes research in prioritized projects such as identification of new diagnostic and prognostic markers for Colorectal and Nasopharyngeal cancers. Other research involves screening of microalgae extracts to identify antiviral/anticancer compounds in collaboration with other universities.

The Centre will focus on the identification of potential tumour suppressor genes or oncogenes as potential therapeutic targets for drug development; genomic analysis of cancers; interactions between genetic variations and environmental factors in the development of cancer, and application of epidemiologic methods in prevention and control of cancers.

HISTORY

In the early 1990s, the Institute for Medical Research embarked on a large scale collaborative project with institutes in Japan, under the IMR-JICA Collaborative Project on Tropical Diseases. A major part of the collaborative project was technology transfer in which the staff of the institute were taught various molecular techniques by the JICA experts. An effort was then made to apply the techniques in various non-communicable diseases, through various research projects. To further strengthen the development of research in non-communicable diseases, particularly in cancer and genetic, the Division of Molecular Pathology (now called Molecular Pathology Unit) was set up in 1996.

In the mid 1990s, a project was carried to study BRCA1 mutations in breast cancer patients. The project was carried out in collaboration with the Breast Clinic of the Kuala Lumpur Hospital, under Dato’ Dr. Miss Suseela Nair and later under Dr. Hisham Abdullah (now Dato’ Dr. Hisham Abdullah, Deputy Director General of Health (Medical)). Our group published the first two papers 1,2 on BRCA1 mutations in the country and the first report of a novel mutation of this tumour suppressor gene not reported elsewhere. Since then, a number of other molecular genetic testing were carried out as research projects. Our group reported the seventh case in the world of RecQ4 gene mutation in a family with familial cancers, Rothmund Thomson syndrome 3. The report 4 was the first report of a novel homozygous mutation of this tumour suppressor gene affecting the splice site. The unit also reported mutation analysis of tumour suppressor genes - TSC1 5, TSC2 5, APC 6,7, CTNNB1 7 PTEN 8,p53 9 and Rb2 9, which were carried out as research projects. The unit also analyzed microsatellites 10,11 (short tandem repeats) for detection of deletions (loss of a dinucleotide repeat within the PAX6 gene in Wilms Tumor from a patient with WAGR syndrome) 12, homozygosity gene mapping 13, and to diagnose microsatellite instability (MSI) 7 in cases of colorectal carcinoma due to Hereditary Non-Polyposis Colorectal Carcinoma (HNPCC). Recently, the laboratory also analyzed microsatellites using the AmpFlSTR DNA Identifiler kit for DNA fingerprinting for research purposes.

Our group reported the first case of a novel unusual (complex) mutation (ie an insertion-deletion mutation) of the ornithine transcarbamylase gene in a large family in Malaysia 14. The functional consequences were predicted using homology modeling of the structure of the OTC protein 15. Recently, the unit undertook a collaborative study to identify mutation of the CYP21 gene which causes congenital adrenal hyperplasia 16. Among the techniques used are polymerase chain reaction, sequencing, Southern blots and Multiplex Ligation Probe Amplification. Fragment analysis of short tandem repeats are also carried out.

Since 2000, the unit began to provide a limited number of molecular genetic tests. The test offered includes methylation specific PCR for Angelman/Pradder Willi Syndrome 17, as well as PCR-based testing for MELAS, SMA and NARP/Leighs. The test for uniparental disomy of the Angelman/Pradder Willi Syndrome has recently been set up and is being verified. The unit also provides services for the primary culture of fibroblasts from skin biopsies.

Staff of the unit provided advice for planning for activities in cancer research and genetics as well as as a member of the Expert Committee on Polymerase Chain Reaction under the Health Technology Assessment Unit of the Ministry of Health of Malaysia. The unit was involved in 1. research training/laboratory attachment training of pediatricians undergoing subspecialization, 2. attachment training of other staff of the Ministry of Health and Universities and 3. training of university students undergoing industrial attachment. The unit was also involved in the Biotechnology Module of the Diploma in Applied Parasitology and Entomology and the Diploma in Medical Microbiology Programs.

In 2006, the unit further intensified its focus on carrying out cutting-edge research in cancer with a special focus on nasopharyngeal carcinoma. The unit is carrying out studies in cell signaling which form the basis of targeted therapy. (see Background of Current Research Activities at the Molecular Pathology Unit, CaRC and NPC Research Program)

References

  1. Khoo AS , Balraj P, Volpi L, Nair S. A new BRCA1 germline mutation (E879X) in a Malaysian breast cancer patient of Chinese descent. Human Mutation 2000. 15: 485.
  2. Balraj P, Khoo AS, Volpi L, Tan JAMA, Nair S, Abdullah A. Mutation analysis of the BRCA1 gene in Malaysian breast cancer patients. Singapore Medical Journal 2002. 43: 194 - 197.
  3. Miozzo M, Castorina P, Riva P, Dalpra L, Fuhrman Conti MA, Volpi L, Hoe TS, Khoo A, Wiegant J, Rosenberg C, Larizza L. Chromosomal Instability in fibroblasts and mesenchymal tumors from 2 sibs with Rothmund-Thomson Syndrome. International Journal of Cancer . 1998. 77: 504-510.
  4. Balraj P, Concannon P, Beghini A, Rahmal J., Hoe T.S, Khoo AS, Volpi L. An unusual intronic mutation in RECQ4 gene leading to Rothmund-Thomson syndrome. Mutation Research 2002. 508:99-105 .
  5. Balraj P, Choy YS, Bock SW, Siti R, Harziah G. (2001). Mutational analysis of the TSC genes for patients with tuberous sclerosis. Proceedings of the 13 th National Biotechnology Seminar, 10-13 November 2001. p374
  6. Tan LP, Ng BK, Balraj P, Poh BH, Lim PKC, Peh SC. APC gene mutations. Human Gene Mutations, Human Genetics 2005. 118:539-549.
  7. Tan LP, Ng BK, Balraj P, Lim PKC, Peh SC. No difference in the occurrence of MMR defects and APC and CTNNB1 genes mutation in a multi-racial colorectal carcinoma patient cohort. Pathology. 2007. 39:228-234.
  8. Balraj P, Siti R. PTEN mutation studies in Malaysian colorectal cancer patients. Asia Pacific Journal of Molecular Biology and Biotechnology 2007. 15(1):23-25
  9. Hoe SL, Sam CK. Mutational analysis of p53 and RB2/p130 genes in Malaysian nasopharyngeal carcinoma samples: a preliminary report. Malaysian J Pathol. 2006. 28(1):35-9.
  10. Khoo ASB, Volpi L, Balraj P, Larizza P, Hoe TS, Lim ABK, Jamal R, Gan EC, Mak JW. 1997. Application of microsatellites for the identification of molecular markers of diseases. Proceedings of the Ninth National Biotechnology Seminar., 1997. pp. 259 - 61.
  11. Khoo A, Ng AB, Nair S, Mak JW. A Non-radioactive Detection System for PCR Microsatellite Length Polymorphism. Sixth National Biotechnology Seminar, Penang, 16-18 November 1994
  12. Khoo ASB, Balraj P, Volpi L, Gregory AR, Ten SK, Zakaria Z, Choy YS, Eni J, Khurziah R. Loss of heterozygosity of a dinucleotide repeat within the PAX-6 gene in Wilms tumour from a patient with WAGR syndrome. Third Asia-Pacific Conf. Med. Genet., 1997
  13. Khoo ASB, Volpi L, Balraj P, Larizza L, Riva P, Miozzo M, Castorina P, Hoe TS, Lim ABK, Jamal R, Gan EC, Mak JW. In search of the gene for Rothmund-Thomson Syndrome - A preliminary report. 4th. International Congress of Tropical Paediatrics, Kuala Lumpur, 7 - 11 July 1996
  14. Khoo AS, Balraj P, Rachedi A, Chin CN, Volpi L. A novel complex mutation of the OTC (ornithine transcarbamylase) gene in a Malaysian pedigree.Hum Mutat 1999 Nov;14(5):448
  15. Khoo ASB, Balraj P, Rachedi, A.,Volpi L., Chin CN. Clinical Correlation of A novel mutant Orinithine Transcarbamylase (OTCase) homology Model. 10th National Biotechnology Seminar ,27&28 October 1998.
  16. Lim PG, Balraj P, Huraizah S, Mohd Rodi I, Choy YS, Wu LL, Khoo A. Genotype versus phenotype in salt wasting congenital adrenal hyperplasia due to 21-hydroxylase deficiency in Malaysian population. 7th. Ministry of Health - Academy of Medicine Scientific Meeting, Penang 2007. Journal of Health Management, September 2007 (Supplement), p. 93
  17. Bock SY, Choy YS, Tan SK, Pauline G. Balraj, Munirah A, Huraizah S, Alan Khoo SB. Methylation-specific Polymerase Chain Reaction for Diagnosis of Prader-Willi Syndrome and Angelman Syndrome. 17th. National Scientific Conference of the Malaysian Institute of Medical Laboratory Sciences. Kuala Lumpur, 2006.
  18. Heng HS, WT Keng WT, Vigneswari G, Norsiah M Desa, Munirah A. Maternallly inherited Leigh Syndrome associated with mitochondrial DNA T8993G point mutation: First confirmed case in Malaysia.. Medical Genetics Conference, 16-19 Nov 2007, Bukit Tinggi Pahang.
  19. Chu TL, Choy YS, Munirah A, Alan Khoo SB. Establishment of Primary Fibroblast Cell Culture. 17th. National Scientific Conference of the Malaysian Institute of Medical Laboratory Sciences. Kuala Lumpur, 2006.

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Background of Research Activities

The Molecular Pathology Unit of the Cancer Research Centre further increased its research work on cancers, with particular emphasis on nasopharyngeal carcinoma (NPC).

NPC is a cancer with unique geographical distribution. It is rare in the West but is highly prevalent in Asia and is a major cause of deaths due to cancer in Malaysia. Scientific knowledge about this cancer is still very limited in comparison with other major cancers.

Previous work in the unit identified a subfraction of a Malaysian algae extract which exhibited cytotoxic activity against NPC cells. Mutation studies were carried out on tumour suppressor genes in the cancer tissue. The current focus of research in the unit is on the molecular pathological basis of nasopharyngeal carcinoma (NPC). The work involves functional studies of various genes as well as transcriptional regulation and signal transduction, focusing on the mechanisms of cancer progression. Work is also carried out to develop model systems to study the cancer. The purpose is to verify potential targets for the development of targeted therapy and potential biomarkers for prognosis and prediction of response to the therapy. The Unit also coordinates a network of research groups and health facilities on nasopharyngeal carcinoma research. The unit was instrumental in setting up the Malaysian NPC Study Group, a network of hospitals, universities and organizations from across the country to study NPC. Several laboratory research projects are also being carried out on NPC. The NPC Research Coordinating Centre was set up at the unit to coordinate the work.

The areas of focus of the members of the group are as follows:

Institute for Medical Research (Molecular Pathology Unit): Molecular Pathogenetic mechanisms and Studies on Selected Biomarkers of Nasopharyngeal Carcinoma (NPC) (P.I. : Dr. Alan Khoo, Institute for Medical Research)

Clinical Research Centre, University of Malaya Medical Centre, Hospital Pulau Pinang, UNIMAS/Kuching Hospital, Universiti Sains Malaysia Kubang Kerian, Kuala Lumpur Hospital, Queen Elizabeth Hospital, Cancer Research Initiatives Foundation (CARIF), IMR- A multi institutional study on the Clinical Outcome of patients with nasopharyngeal carcinoma (NPC) (PI: Dr. Pua Kin Choo, Hospital Pulau Pinang)

Cancer Research Initiatives Foundation (CARIF) : Development of a NPC-specific peptide vaccine therapy as a neoadjuvant therapy for nasopharyngeal cancer (P.I. : Dr. Teo Soo Hwang)

University of Malaya ( Institute of Biological Sciences): Association study of selected candidate genes and NPC susceptibility (P.I.: Dr. Ng Ching Ching)

University of Malaya Medical Centre (Dept. of Molecular Medicine): Serum expression proteomics of patients with nasopharyngeal carcinoma. (P.I.: Prof. Dr. Onn Haji Hashim)

University Malaysia Sarawak (UNIMAS) (Faculty of Medicine and Health Sciences): The Involvement of Apoptosis in Chromosomal Rearrangement in Nasopharyngeal Carcinoma (P.I. : Dr. Sim Sai Ping @ Samirah Abdullah)

University Malaysia Sarawak (UNIMAS) (Faculty of Resource, Science and Technology): Nucleotide variation and gene expression studies of ribosomal protein genes in cases of nasopharyngeal carcinoma. (P.I. : Dr. Edmund Sim Ui Hang)

International Medical University: Nasopharyngeal Carcinoma: Roles of Epstein-Barr virus Latent Proteins in Invasion and Metastasis (P.I.: Dr. Tan Eng Lai)

A collaborative project is also being carried out with Monash University Sunway Campus on Kisspeptins and GnRH as potential therapy for cancer ( P.I. Dr. Alan Khoo, Institute for Medical Research, Co-principal investigator: Prof. Dr. Ishwar Parhar, Brain Research Institute, Monash University Sunway Campus)