Research article

Frequent loss of heterozygosity and altered expression of the candidate tumor suppressor gene 'FAT' in human astrocytic tumors

Kunzang Chosdol¹ , Anjan Misra^1,4 , Sachin Puri^1,5 , Tapasya Srivastava¹ , Parthaprasad Chattopadhyay¹ , Chitra Sarkar² , Ashok K Mahapatra^3,6 and Subrata Sinha¹

¹Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India

²Pathology, All India Institute of Medical Sciences, New Delhi, India

³Neurosurgery, All India Institute of Medical Sciences, New Delhi, India

⁴Barrow Neurological Institute, St. Joseph's Hospital & Medical Center, Phoenix, AZ, USA

⁵Laboratory of Molecular & Tumor Immunology, Earle A Chiles Research Institute, Providence Portland Medical Center, 4805 NE Glisan Street Portland, OR, USA

⁶Sanjay Gandhi Postgraduate Institute of Medical Sciences (SGPGI), Raebareli Road Lucknow, India

author email corresponding author email

BMC Cancer 2009, 9:5doi:10.1186/1471-2407-9-5

Published:	7 January 2009

Abstract

Background

We had earlier used the comparison of RAPD (Random Amplification of Polymorphic DNA) DNA fingerprinting profiles of tumor and corresponding normal DNA to identify genetic alterations in primary human glial tumors. This has the advantage that DNA fingerprinting identifies the genetic alterations in a manner not biased for locus.

Methods

In this study we used RAPD-PCR to identify novel genomic alterations in the astrocytic tumors of WHO grade II (Low Grade Diffuse Astrocytoma) and WHO Grade IV (Glioblastoma Multiforme). Loss of heterozygosity (LOH) of the altered region was studied by microsatellite and Single Nucleotide Polymorphism (SNP) markers. Expression study of the gene identified at the altered locus was done by semi-quantitative reverse-transcriptase-PCR (RT-PCR).

Results

Bands consistently altered in the RAPD profile of tumor DNA in a significant proportion of tumors were identified. One such 500 bp band, that was absent in the RAPD profile of 33% (4/12) of the grade II astrocytic tumors, was selected for further study. Its sequence corresponded with a region of FAT, a putative tumor suppressor gene initially identified in Drosophila. Fifty percent of a set of 40 tumors, both grade II and IV, were shown to have Loss of Heterozygosity (LOH) at this locus by microsatellite (intragenic) and by SNP markers. Semi-quantitative RT-PCR showed low FAT mRNA levels in a major subset of tumors.

Conclusion

These results point to a role of the FAT in astrocytic tumorigenesis and demonstrate the use of RAPD analysis in identifying specific alterations in astrocytic tumors.