Minute Amounts of DNA Used to Map Genetic Alterations

NEW YORK--Comparative geno-mic hybridization (CGH), a new molecularcytogenetic technique for mapping chromosomal and subchromosomal imbalances,is breaking new ground in cancer genetics.

According to speakers at an international meeting on CGH held at MemorialSloan-Kettering Cancer Center, CGH is being used to detect chromosomalaberrations in glioblastomas and bladder, prostate, and breast tumors,and to locate chromosomal regions that contain genes that may contributeto cancer.

In addition, the burgeoning amount of information yielded by CGH isnow being correlated with the clinical behavior of tumors.

Even minute amounts of genomic DNA are sufficient to perform CGH testsso that genetic alterations can be detected in a few microdissected tumorcells or cells from precursor lesions.

In CGH analysis, samples of normal and tumor DNA are simultaneouslyhybridized to metaphase chromosomes from a normal individual. If more ofthe tumor DNA than the normal DNA hybridizes to a chromosomal region, itmeans that there have been amplications in the tumor DNA. If less hybridizes,there have been deletions in the tumor DNA.

Guido Sauter, MD, of the Institute of Pathology, University of Basel,predicted that molecular cytogenetic analysis will be a powerful tool inthe diagnosis and prognosis of bladder cancer, since bladder cancer cellsare so easily accessible in the patient's urine.

Dr. Sauter reported finding marked genetic differences between minimallyinvasive and noninvasive bladder carcinomas. The minimally invasive tumors(pT1) had more aberrations than the noninvasive carcinomas (pTa). Yet,there was no significant increase of aberrations in muscle-invasive tumors(pT2-4). The difference in aberrations between pTa and pT1 tumors, Dr.Sauter said, challenges the validity of grouping pTa and pT1 tumors togetheras superficial bladder cancer.

Patterns of Aberrations

Burt Feuerstein, MD, PhD, of the Brain Tumor Research Center, Universityof California, San Francisco, reported finding patterns of genetic aberrationsassociated with the progression of neuroblastomas.

The aberrations fell into one of two categories. In one, whole copiesof chromosomes were lost. In the other, the pieces of chromosomes werescrambled. Patients whose tumors had whole chromosome additions or deletionsdid better than those whose tumor cells were marked by subchromosomal scrambling.

"Understanding the patterns of genetic aberrations will be usefulin discovering mechanisms of malignant progression, establishing the diagnosis,and planning therapy," Dr. Feuerstein said.

Lymphomas

Raju S.K. Chaganti, PhD, chief of Memorial Sloan-Kettering's CytogeneticsService and chairman of the CGH conference, reported that he is using CGHto identify genetic changes associated with non-Hodgkin's lymphoma progression.

Peter Lichter, PhD, of the German Cancer Research Center, Heidelberg,has used CGH to provide a genetic basis for a new subtype of lymphoma knownas primary mediastinal (thymic) B-cell lymphoma,which has previously beendefined by morphological and immunological criteria.

"Those of you who have ever tried to understand lymphoma classificationknow there are a lot of uncertainties," Dr. Lichter said. His analysisrevealed that more that half of the tumor set classified as primary mediastinalhad a gain along chromosome 19, while other forms of lymphomas did not.

Drug Resistance

In yet another application, CGH is being used by researchers at theNational Center for Human Genome Research (NCHGR), the NCI, and Fox ChaseCancer Center to study the relationship between DNA gains or losses andsensitivity or resistance to chemotherapeutic compounds.

These investigators are analyzing a panel of human tumor cell linesdeveloped by the NCI as a primary drug screen, Dr. Stanislas Du Manoir,of the NCHGR told Oncology News International. Detecting such relationshipswill help to identify a chemotherapeutic agent's mechanism of action and/orthe chromosomal location of genes involved in the metabolism of the drug.