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Last Updated: October 22, 2012

TCGA Research Network Reports the First Comprehensive Characterization of Squamous Cell Lung Cancer

Emma J. Spaulding

In the Sept. 27, 2012 edition of the journal Nature, The Cancer Genome Atlas (TCGA) Research Network published the first comprehensive characterization of squamous cell lung carcinoma, the second most common type of lung cancer. In addition to TCGA’s expansive analysis, a selection of these samples underwent whole genome sequencing. From this first look at the entire genomic sequence of lung squamous cells, TCGA researchers have developed a greater understanding of genes known to be associated with cancer, and also made novel findings that may contribute to promising therapeutics.

First Whole Genome Sequence for Lung Squamous Cell Carcinoma

The researchers performed whole genome sequencing on 19 tissue pairs, the donor’s tumor sample and normal tissue. Whole genome sequencing is the most comprehensive type of sequencing because in addition to the gene sequence, it shows researchers the regions between genes, an area about which scientists are still learning. On average, each piece of DNA was covered by at least 50 times. This amount of coverage is a sign of how greatly sequencing technology has improved. The first attempts at sequencing the human genome came nowhere near this level of sensitivity.

The TCGA Research Network scientists found an average of 165 rearrangements in each tumor, more than other whole genome sequencing studies have found in other tumor types. Whole genome sequencing was a key resource in finding many of these changes. To confirm these changes, the researchers examined the RNA sequence, another data type that TCGA generates and shares with the community. If there were a mutation in the coding part of the DNA, then it would be expressed in the RNA, allowing researchers to affirm these changes. RNA sequencing can be a good option to verify changes found through other platforms. By combining these types of data, researchers were able to identify tumor suppressor genes that were inactivated by rearrangements between chromosomes or on the same chromosome. The majority of these fusions were validated. This finding wouldn’t have been possible without integration of genomic data and whole genome sequence.

Changes in CDKN2A: An Underestimated Frequency

This study provided further elucidation of the CDKN2A locus. CDKN2A, a cyclin dependent kinase inhibitor, is a well-known tumor suppressor gene in lung squamous cell carcinoma. It encodes two proteins: ARF, which works with the tumor suppressor p53, and INK4A, which inhibits a protein involved in cell cycle progression. In 72 percent of TCGA’s lung squamous cell carcinoma cases, CDKN2A was inactivated, leaving cells unguarded against cancer growth. CDKN2A was inactivated through several means: epigenetic silencing by methlylation, an inactivating mutation, skipping an important exon or deletion of the gene on both chromosomes. By analyzing mRNA expression data, researchers found that CDKN2A expression data grouped into four patterns: absence of ARF and INK4A because both copies of CDKN2A were deleted, high expression of ARF and INK4A, high expression of ARF and absence of INK4A or a transcript that splices the two together, making a new but ineffective protein. This more detailed picture of CDKN2A may help researchers develop better methods to detect and remedy inactivation of this important gene.

In the 28 percent of tumors that did not show changes in CDKN2A, many had mutations in RB1, another tumor suppressor. These findings suggest that changes in either CDKN2A or RB1 are common in lung squamous cell carcinoma and, until now, their prevalence has been underestimated.

Criteria for Therapeutic Potential Targets

In contrast to treatment of lung adenocarcinoma, treatment of lung squamous cell carcinoma has been difficult. The changes in the genes EGFR and KRAS that make lung adenocarcinoma treatable through precision medicine are not present in lung squamous cell carcinoma. However, the TCGA Research Network’s comprehensive analysis has identified potentially targetable genes or pathways in most of the lung squamous cell carcinoma samples. These possible targets were based on several criteria. First, there must be an available FDA-approved targeted therapeutic agent, or one in clinical trials. Second, the change must be confirmed in whole genome sequence and RNA sequence. Third, the change must affect the protein expressed by the gene, as predicted by an algorithm. On this basis, the TCGA Research Network found that 64 percent of its cases exhibited a potentially targetable change. Many of these changes were in groups of tyrosine kinases, an enzyme established as a potential target in previous clinical or preclinical studies.

Switching On the Immune System to Fight Cancer

One of the hallmarks of cancer is that it can avoid detection by the body’s immune system, so activating the immune system against the tumor would provide a promising novel drug opportunity. Once cells mutate into cancer cells, they have changed so much that the body should no longer recognize them, and should treat them like something foreign. However, the cancer cells that grow and become tumors develop ways to protect themselves from the immune system. The tumors hide by sending signals to stop or downregulate the natural immune response against the cancer. Some of the changes that protect the cancer cells have been discovered in TCGA’s lung squamous cell carcinoma cases. These are mutations in the HLA-A gene. The HLA-A gene normally tells the immune system to attack the cancer cells, but the cancer has mutated so that this signal is turned off. This way the cancer is able to grow unfettered. However, new drugs which expose the cancer to the immune system for attack as it would anything foreign, have been reported as successful. With these drugs, the immune system could be harnessed to attack all of the cancer cells, making immune-regulatory therapy possible.

The TCGA Research Network has made all of these data available at the TCGA Data Portal and CGHub as a community resource. Hopefully, by taking advantage of these high-quality, standardized and robust data, scientists can progress towards developing new diagnostic and therapeutic opportunities.


The Cancer Genome Atlas Research Network. (27 Sept 2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature. 489(7417): 519-525. Read the full article