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


CONCLUSIONS
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.
Chosdol
Kunzang
K
Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India. kunzangchosdol@yahoo.com
Misra
Anjan
A
Puri
Sachin
S
Srivastava
Tapasya
T
Chattopadhyay
Parthaprasad
P
Sarkar
Chitra
C
Mahapatra
Ashok K
AK
Sinha
Subrata
S
D001254:Astrocytoma / Q000235:genetics* / Q000473:pathology; D001665:Binding Sites; D015820:Cadherins / Q000235:genetics*; D016543:Central Nervous System Neoplasms / Q000235:genetics* / Q000473:pathology; D016172:DNA Fingerprinting / Q000379:methods; D017931:DNA Primers; D016147:Genes, Tumor Suppressor; D005909:Glioblastoma / Q000235:genetics / Q000473:pathology; D006801:Humans; D019656:Loss of Heterozygosity; D020641:Polymorphism, Single Nucleotide; D019105:Random Amplified Polymorphic DNA Technique / Q000379:methods; D020133:Reverse Transcriptase Polymerase Chain Reaction
D015820:Cadherins; D017931:DNA Primers; C502403:FAT1 protein, human