Genomics Used by NIH Team to Distinguish Squamous Cell Carcinomas


Molecular characteristics that link the genomic profiles of squamous cell carcinomas from 5 areas of the body have been uncovered by a team of researchers supported by the NIH.

Molecular characteristics that link the genomic profiles of squamous cell carcinomas (SCCs) from 5 areas of the body have been uncovered by a team of researchers supported by the National Institutes of Health (NIH).

By helping researchers develop tailored strategies for specific cancer subtypes, the findings will help set SCCs apart from other cancers, and the research could potentially lead to more effective diagnosis, and more timely treatment for patients.

Results from the work was published in the journal Cell Reports in an article titled, “Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas.” The researchers, Carter Van Waes, M.D., Ph.D., and his colleague Zhong Chen, M.D., Ph.D., from the Head and Neck Surgery Branch of NIH’s National Institute on Deafness and Other Communication Disorders (NIDCD) used a large dataset of SCCs from the head and neck, lung, esophagus, cervix, and bladder, that certain features were present in tumors associated with both smoking and human papillomavirus (HPV) infection, while others were exclusive to only one of the two.1

“We need better ways to treat head and neck cancers so we can preserve patients’ voices and improve their quality of life,” said Van Waes, NIDCD clinical director and chief of the NIDCD Head and Neck Surgery Branch in a press release. “These findings provide us with important insights into these cancers and some squamous cell cancers in other areas of the body that will help us target pathways for prevention and treatment.”2

In the study, multiple platforms of genomic data were combined from 1,400 SCC samples into integrated analyses, creating visual clusters of tumors based on their genomic characteristics.

“We uncovered a significant mutually exclusive relationship between gains in 3q or 11q22 affecting the majority of SCCs,” it was stated in the study. “This finding supports these as possible alternative drivers for a recently described mechanism by which 3q genes ACTLA6 and ΔNp63 were found to repress squamous differentiation and promote activation of Hippo growth pathway transcriptional factor YAP1. This inverse relationship in 11q22 and 3q CN gain is independently supported by a reciprocal pattern of YAP1 and p63 protein immunostaining observed previously in HNSC tissue arrays.”

It was found by the researchers that SCCs in the 5 studied areas have comparable genomic features that set them apart from other cancer types. The most common shared alterations include gains or losses of the sections of certain chromosomes where DNA is packaged, making it likely that these regions harbor 3q, 5q, and other genes critical to the development of SCCs.

It was concluded that SCCs show chromosome or methylation alterations affecting multiple related genes, and regulate squamous stemness, differentiation, growth, survival, and inflammation. The changes affect the expression of many more genes than previously understood, enabling new possibilities for future exploration.

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1. Al-Ramahi I, Srinivas Panapakkam Giridharan S, Chen YC, Patnaik S, et al. Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas. Cell Reports. 2018; 2018.03.063. doi: 10.1016

2. NIH researchers use genomics to set squamous cell carcinomas apart from other cancers [news release]. Bethesda, MD: NIH; April 2018. Accessed April 6, 2018.

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