Chromosome Microarray Analysis Differentiated Between Benign and Cancerous Fatty Tissue Tumors

Dr. Shuanzeng (Sam) Wei, investigator on the study and associate professor in the Department of Pathology and medical director of the Clinical Genomics Laboratory at Fox Chase.
Dr. Shuanzeng (Sam) Wei, investigator on the study and associate professor in the Department of Pathology and medical director of the Clinical Genomics Laboratory at Fox Chase.

PHILADELPHIA (June 18, 2021)–Researchers at Fox Chase Cancer Center are using a powerful single nucleotide polymorphism-based chromosome microarray (CMA) to differentiate between benign and cancerous lipomatous tumors.

The majority of lipomatous tumors are benign fatty tumors, said Shuanzeng (Sam) Wei, MD, PhD, associate professor in the Department of Pathology and medical director of the Clinical Genomics Laboratory at Fox Chase. However, some of these tumors will be diagnosed as cancers of the fatty tissue, called liposarcoma.

“To make this distinction, we have a very good marker, MDM2,” Wei said. “Typically we only have two copies of MDM2, but if amplification is found—multiple copies of the gene—using fluorescence in situ hybridization, also known as FISH, a liposarcoma diagnosis can be made.”

However, Fox Chase is one of the only cancer centers in the region certified for the use of a more powerful genomic tool—CMA. Unlike FISH, which can only detect a limited number of genomic changes, CMA can detect genome-wide alterations, Wei said. “CMA allows us know all of the chromosomal changes, including gains, amplifications, and losses.”

Wei conducted the recently published study with Fox Chase researchers Jianming Pei, MD; Jacqueline N. Talarchek; Douglas B. Flieder, MD; Arthur S. Patchefsky, MD; and Harry S. Cooper, MD. In order to prove whether CMA could accurately detect MDM2 amplification in daily practice, Wei and colleagues used CMA to analyze specimens taken from 16 liposarcomas and 19 benign lipomatous tumors.

All of the liposarcomas had variable chromosomal abnormalities and all had MDM2 amplification. Ten of the liposarcomas also had CDK4 amplification; all cases without CDK4 amplification were from the thigh. In addition to MDM2 amplification, all 16 of the liposarcoma samples had amplification of YEATS4, CPM, and FRS2.

“This finding is important because right now there is a targeted therapy for CDK4 amplification being tested in clinical trials,” Wei said.

The liposarcoma samples were tested using FISH, and those results were completely consistent with the CMA results. Use of CMA technology provided the researchers more information about the benign tumors, Wei said. For example, seven of the 19 benign lipomatous tumors had variable chromosomal changes, including two spindle cell lipomas that had loss of chromosome segment 13q14.

Wei and colleagues have also used the CMA technology for more accurate subtyping of renal cell carcinomas.

“CMA gives us a better overall picture,” Wei said. “The CMA platform continues to give us more opportunities for accurate diagnosis and more personalized medicine, and Fox Chase is one of the pioneers in implementing the CMA assay for patient care.”

The paper, “Clinical Application of Chromosome Microarray Analysis in the Diagnosis of Lipomatous Tumors,” was published in Applied Immunohistochemistry & Molecular Morphology.

Fox Chase Cancer Center (Fox Chase), which includes the Institute for Cancer Research and the American Oncologic Hospital and is a part of Temple Health, is one of the leading comprehensive cancer centers in the United States. Founded in 1904 in Philadelphia as one of the nation’s first cancer hospitals, Fox Chase was also among the first institutions to be designated a National Cancer Institute Comprehensive Cancer Center in 1974. Fox Chase is also one of just 10 members of the Alliance of Dedicated Cancer Centers. Fox Chase researchers have won the highest awards in their fields, including two Nobel Prizes. Fox Chase physicians are also routinely recognized in national rankings, and the Center’s nursing program has received the Magnet recognition for excellence five consecutive times. Today, Fox Chase conducts a broad array of nationally competitive basic, translational, and clinical research, with special programs in cancer prevention, detection, survivorship, and community outreach. It is the policy of Fox Chase Cancer Center that there shall be no exclusion from, or participation in, and no one denied the benefits of, the delivery of quality medical care on the basis of race, ethnicity, religion, sexual orientation, gender, gender identity/expression, disability, age, ancestry, color, national origin, physical ability, level of education, or source of payment.

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