Science self-corrects: cancer gene does not pass reproducibility test

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Feb 14, 2018, 11:50 ET

COLD SPRING HARBOR, N.Y., Feb. 14, 2018 /PRNewswire/ -- A decade ago, several labs discovered that a gene called MELK is overexpressed, or turned on to a high degree, in many cancer cell types. This prompted multiple ongoing clinical trials to test whether drugs that inhibit MELK can treat cancer in patients. Now, Cold Spring Harbor Laboratory (CSHL) researchers, led by CSHL Fellow Jason Sheltzer, report that MELK is not actually involved in cancer.

The growth of human colon cancer cells (raised in culture) is unaffected by presence or absence of MELK. Top row: untreated cells; bottom row: cells treated with a MELK inhibitor. Left two columns, control cells; right two columns, cells in which MELK gene has been knocked out. CSHL researchers conclude that MELK is not involved in cancer proliferation.

Furthermore, Sheltzer and his colleagues suggest the discrepancy with previous findings results from inherent flaws in the scientific techniques used to link MELK to cancer.

"Our study is a good illustration of the self-correcting nature of science," Sheltzer says.

Sheltzer and Stony Brook University students Chris Giuliano and Ann Lin have been performing genomic analyses on tumors surgically removed from cancer patients. Their goal has been to identify genes whose activity levels are correlated with low patient survival rates. The researchers then planned to use a gene-editing technology called CRISPR to eliminate the genes from different cancer cell lines one at a time to see if they could kill the cells.

This is where MELK comes in. "Like other labs, we found that MELK tended to be very highly expressed in patients who did not survive very long," Sheltzer says.

Because so many previous studies using multiple other methods had shown that MELK was essential for cancer cells, Sheltzer believed his team could use the gene as a positive control in their CRISPR experiments. "We thought we would eliminate MELK and show that it killed cancer cells. Then we could know that our CRISPR techniques were working," Sheltzer says. "But, to our great surprise, the cancer cells didn't die. They just didn't care."

The researchers then performed several experiments to ensure the CRISPR technique was working. "We eventually had to conclude that our technique was fine," Sheltzer says. "Rather, it was the previous findings about MELK's role in cancer that were incorrect."

Sheltzer thinks some of the techniques have been prone to error due to what scientists call "off-target effects." One such technique, called RNA interference, harnesses a cellular mechanism controlling gene expression to switch off specific genes. "You think you're knocking down one gene, but in reality those techniques are not very specific, so you're also hitting a number of other different genes," Sheltzer says.

"We think this might be a common problem," Sheltzer adds. "There may be other genes like MELK out there, and we want to use CRISPR to identify the best possible targets for drug development."

Funding
National Institutes of Health

About Cold Spring Harbor Laboratory

Founded in 1890, Cold Spring Harbor Laboratory has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. Home to eight Nobel Prize winners, the private, not-for-profit Laboratory employs 1,100 people including 600 scientists, students and technicians. For more information, visit www.cshl.edu.

SOURCE Cold Spring Harbor Laboratory