Researching the
Genetic Attributes of Sarcomas
March / April 2004
Sarcoma is cancer of bone (bone, cartilage, lesions)/ soft
tissue (muscle, fat, and synovial fluid) and accounts for
just two percent of all cancers. Patients most often present
with either pain or a lump and treatment includes surgery,
radiation and/or chemotherapy. Approximately 95 percent of
patients receive limb-sparing treatment, which may involve
removing the tumor and replacing the bone with a metal prosthesis,
and the remaining five percent of patients undergo an amputation.
At Penn, there is a multidisciplinary approach to this disease
with treatment from a team of sarcoma experts including orthopaedic
surgeons, hematologists/ oncologists, radiation therapists,
pathologists, radiologists, surgical oncologists, general
surgeons, and rehabilitation specialists. As part of this
work, researchers are currently studying several different
tumor types including osteosarcoma and chondrosarcoma.
“We hope that by obtaining a genetic signature of these
tumors we will find more effective classifications of sarcomas.
If we look at the processes that make these tumors grow, we
can try to develop a drug that can inhibit some of these processes
and better direct chemotherapy,” says Richard
D. Lackman, MD, chairman of the department of Orthopaedic
Surgery at Penn. Of the approximate 8,000 new sarcoma cases
each year in the United States, Dr. Lackman, his partner,
Christian Ogilive, MD, orthopaedic surgeon at Penn and assistant
professor in the department of Orthopaedic Surgery, and their
colleagues evaluate and treat about 200 patients.
.
Array CGH
Barbara
L. Weber, MD, director of the Breast Cancer Program,
the Cancer Risk Evaluation Program, and the Cancer Genomics
Program
at the Abramson Family Cancer Research Institute at Penn
and professor in the department of Hematology/Oncology, has
implemented
an enhanced array comparative genome hybridization (array
CGH), a high throughput screening method that looks for changes
in these tumors at the subchromosomal level. “The idea
behind this is to be able to get a much more in-depth view
of what’s wrong with the genes in these tumors. This
may be very helpful in sorting out what new treatments might
be most effective in the sarcomas,” says Dr. Weber,
who has been applying this technology to a number of tissues,
but specifically the sarcomas.
With array CGH, the genome is covered evenly with probes
to measure genetic changes in the tumor, which gives very
accurate data. These arrays can also directly identify genetic
changes in about 500 genes that are known to be important
in cancer. “Instead of clusters of tightly grouped clones
to represent the genome and then gaps, we have filled in all
those gaps and evened out the spacing with more sensitivity,”
explains Dr. Weber. “This way we do not miss important
genetic changes in the tumor that might be important for treatment.”
“This technology allows us to analyze the genome of
a tumor with much more resolution and look for new subchromosomal
changes in the tumor. Furthermore, this may lead us to find
new oncogenes that cause a tumor to grow or new tumor suppressor
genes that normally prevent a tumor from growing,” says
Anne-Marie Martin, PhD, molecular biologist in the Pathology
Department at Pennsylvania Hospital. Dr. Martin also holds
an adjunct position at the University of Pennsylvania and
is an active member of Dr. Weber’s laboratory. She is
supervising the array CGH component of the sarcoma project
and conducts gene expression molecular profiling.
GeneChip Further Classifies Data
Once the subchromosomal changes are identified by array CGH,
researchers at Penn use GeneChip Microarray Technology
to
measure the expression of every known gene in the human genome
in one experiment.
The GeneChip consists of a small microscope glass slide encased
in plastic and is manufactured using processes similar to
those used for making computer microchips. Synthetic strands
of DNA sequences identical to the sequence of a normal gene
are applied to surface of each chip. The chip surface can
hold up to 33,000 different synthetic sequence strands representing
33,000 different genes. The GeneChip permits scientists to
perform screens of many tumor samples and determine which
are expressed differently in tumor cells as compared to normal
cells. Although the technology has become widespread in the
past few years, the University of Pennsylvania Health System
has an exceptionally large and unique resource of sarcoma
tissue which advances its genetic research program using these
genomic technologies.
Clustering the Data
Normally, scientists will perform either gene expression analysis
or examine regions of genetic change based on a CGH analysis,
but researchers in Dr. Weber’s lab have developed a
software program that allows them to visualize data from multiple
experiments and peform “cluster analyses,” which
groups the information based on patterns of genetic change
across tumors from different patients and various types of
sarcoma. “After we have performed the identical analysis
on each tumor individually, we can use the clustering tools
to find out which tumors are most similar to each other,”
explains Dr. Martin. “This combination strengthens the
overall analysis. By combining both platforms we are able
to obtain a much better understanding of which genes are most
important and focus our search much more specifically.”
“This is a much quicker way to understand the genetic
abnormalities that cause cancer, as opposed to non-genomic
approaches that require the evaluation of one gene at a time.
Once we can understand the genetic abnormalities in the sarcomas,
then we can target treatments specifically at those abnormalities,”
explains Dr. Weber. “These experiments have already
identified regions of great interest with novel genetic changes
that had not been described in sarcoma before.”
This genetic research is part of an overall effort to further
enhance sarcoma treatment. Dr. Lackman and his colleagues
continue to develop new methods of treating benign and malignant
musculoskeletal tumors. Recently they have published scientific
studies concerning the treatment of giant cell tumors of the
base of the spine with embolization and the use of low-dose
chemotherapy for desmoid tumors. Both of these techniques
are able to prevent the need for large, debilitating surgeries
in most of the patients involved. “The work we are doing
is very exciting, but as far as finding the answers for sarcoma
— we are just scratching the surface,” adds Dr.
Lackman.
|
