Good Days and Bad in 2011

January 10, 2012 | First Base | It must be so much fun being a physicist right now. Scientists have discovered two monster black holes—the largest on record—with masses several billion times that of the Sun. And in the Goldilocks Zone of a nearby galaxy, a planet known as Kepler 22b orbits with a balmy atmosphere of 72° F, a prime candidate for life off earth. 

At the other end of the matter scale, scientists have caught their first glimpse of the Higgs boson, the so-called “God particle.” And we are still waiting with baited breath for confirmation that neutrinos can travel faster than the speed of light, as hinted a few months ago. 

In reflecting on the past year in life sciences and IT, however, such notable feats are somewhat harder to find. A list of the top ten science stories of 2011 in the Guardian, compiled by veteran science correspondent Robin McKie, includes three of the physical sciences standouts above, but only a couple of items in contemporary biology.  

One was the rather sad exit of biotechnology pioneer Geron from the human embryonic stem cell field it helped to create. The other, more cheerily, was the imaging study of a female brain experiencing orgasm, but while imaging is an important technology we cover with enthusiasm, that is, I fear, just slightly beyond our scope.  

In 2011, Bio•IT World hosted Stephen Wolfram and a record attendance at the Bio-IT World Expo, and convened its first Cloud Computing conference, reflecting the rapidly growing capacity to spin up supercomputing tasks as well as the expanding acceptance of the potential of infrastructure-as-a-service. We also enjoyed covering the potential of new technologies in the form of “wellness chips” (see, “Turning Blood into Gold,” Bio•IT World, July 2011) and “SNP-doctors,” (see, “Powering Preventative Medicine,” Bio•IT World, September 2011) as well as the creation of the New York Genome Center (see, “Genome Center for Gotham,Bio•IT World, November 2011). Some of our New Year’s well wishes go to its founders in strengthening what must be at times a tempestuous alliance of Big Apple egos. 

Cancer Connections 

A story that did not receive as much media attention as it should was the approval by the Food and Drug Administration in August 2011 of a pair of targeted cancer drugs and their companion diagnostics. One was Pfizer’s Xalkori, which treats a small percentage of patients with advanced non-small-cell lung cancer (NSCLC) harboring mutations in a gene called ALK. (A diagnostic test from Abbott Molecular reveals the mutation.) The other was the melanoma drug Zelboraf (Plexxikon), which is accompanied by a BRAF mutation test.  

While on the topic of cancer, two papers published this year by the team of Rick Wilson, Elaine Mardis, Timothy Ley and colleagues at Washington University in St Louis, illustrated the potential of individual genome sequencing in revealing molecular aberrations in cancer patients, even if the ensuing targeted treatments don’t always prevail or arrive in time. 

Ironically, two of the most famous cancer patients to pass away in 2011—Steve Jobs and Christopher Hitchens—both underwent genome sequencing. According to Walter Isaacson’s best-selling biography, Jobs had his genome sequenced by researchers from Stanford, Johns Hopkins, Harvard and the Broad Institute. Hitchens, following a recommendation from a person the Daily Mail headline called an “evangelical Christian doctor”—perhaps better known as NIH director Francis Collins—was sequenced by the St Louis group in early 2011 as he battled stage IV (metastasized) esophageal cancer. 

Hitchens himself revealed that as a result of the sequencing, he was now taking Gleevec, the Novartis drug for leukemia, begging the question: what did the doctors find in his DNA? While for obvious reasons, Washington University could not comment on Hitchens’ prognosis, at a conference last October, Mardis presented an intriguing case study of a patient with a long history of tobacco and alcohol abuse, referred to simply as “ESC1” (esophageal cancer patient #1). 

ESC1’s tumor, it turned out, carried mutations in a gene called DDR2. A quick PubMed search reveals a couple of interesting facts: first, DDR2 mutations have been associated with several metastatic cancers. Second, the protein encoded by this gene is a potent target of Gleevec and related tyrosine kinase inhibitors. So one can see the rationale for switching this patient to Gleevec. ESC1 responded well at first, but Mardis stressed that her colleagues were not managing the patient’s care and did not have up-to-date information. 

Hitchens, who said cancer was like a “malignant alien” in his body, died from pneumonia in December at the M.D. Anderson Cancer Center in Houston, writing columns and meeting deadlines to the end. His death hit me harder than Jobs’, I suppose because we had a few things in common: scotch-loving British journalists and authors, both graduates of Oxford University. Of course, there the comparison ends. 

In one of his last interviews, Hitchens told the BBC: “Whatever day came that the newspapers came out and I wasn’t there to read them, I’ve always thought that would be a bad day—at least for me.”  

And us, Christopher. Cheers. • 

This article also appeared in the January 2012 issue of Bio-IT World magazine.