Can Cancer Cells Solve the Puzzle of Junk DNA?

April 12, 2013, 7:47 p.m. ET

Can Cancer Cells Solve the Puzzle of Junk DNA?

By MATT RIDLEY

The usually placid world of molecular biology has been riven with two fierce disputes recently. Although apparently separate, the two conflagrations are converging.

The first row concerns the phrase “junk DNA.” Coined in 1972 by the geneticist Susumu Ohno, it is an attempt to explain why vast stretches of animal genomes, far more in some species than in others, seem to serve no purpose. Genes of all kinds and their control sequences make up maybe 9% of the human genome at the very most. The rest may be nonfunctional “junk,” mainly there because it is good at getting itself duplicated. Yet the phrase has always caused a surprising amount of offense. Reports of the discrediting of junk-DNA theory have been frequent.

Why does it matter? Partly because scientists want to know if they are right to focus on part of the genome, ignoring the rest, but mainly because the issue tests an evolutionary theory about how DNA sequences can proliferate even if they do not benefit the body.Late last year, a huge team of scientists running a consortium called Encode published an analysis of the human genome that they said showed some kind of activity in 80% of the genome. They later conceded that perhaps 20% is actually functional, yet insisted the phrase “junk DNA” could now be “totally expunged from the lexicon.”

According to Dan Graur of the University of Houston and his colleagues, even this is a wild overestimate—not least because it uses a “causal role” definition of function that is all wrong, as if you were to describe among the heart’s functions adding 10.5 ounces to the weight of the body, along with pumping blood. After a few exchanges, the Encode team leader Ewan Birney conceded that in hindsight, the team overstated its conclusions. But he added that whatever the interpretation, the Encode data are sound.

Are they? Here’s where the junk-DNA row meets the other conflagration in molecular biology. All the Encode data were derived from cancer-cell lines. To describe human cancer cells as having the human genome looks increasingly unwise. Most cancer cells have extra chromosomes, fragmented and rearranged DNA and unusual patterns of gene activity.

As if to illustrate the point, last month a consortium of scientists based in Heidelberg, Germany, analyzed and sequenced the genome of one type of HeLa cell, an immortal laboratory cell line widely used since 1952. They described a genome that looks like a bomb has gone off in it. There are three copies of most chromosomes, yet only one copy of many genes. Hefty chunks have been reshuffled to other chromosomes, and some chromosomes have suffered from “chromothripsis,” which one of the scientists describes as being “blown apart and stuck back together in a random order.” A person with this genome could never be born.

Yet—and here’s the source of the controversy—the HeLa cell line was derived from the tumor that killed a poor, black tobacco farmer named Henrietta Lacks in Baltimore in 1951. As Rebecca Skloot has documented in a remarkable best seller (“The Immortal Life of Henrietta Lacks”), the medical community never got her consent and treated her family with tactless disrespect for years—until Ms. Skloot’s book began to make a difference.

Not enough of a difference, apparently. The German team did not seek the consent of the Lacks family before publishing the HeLa sequence, claiming it revealed nothing specific about Ms. Lacks’s own genome. “Your claim is so wrong that I don’t know where to start,” replied one geneticist. The sequence has since been unpublished.

So here’s the paradox: A cancer genome like HeLa may not be sufficiently representative of human genomes to resolve the junk DNA question, but may still give away private information about the human being from whom it derived.