Monday, 20 January 2014 00:00

Unmasking Cancer Stem Cells and Sequencing on Mars—Fuchs and Venter Give ASCB 2013 Keynotes

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fuchs and venterJ. Craig Venter (left) and Elaine Fuchs (right) shared the
keynote platform with talks that showed just how much
cell biology has changed in 12 years.
Photo credit: ASCB
Consider it a triumphant return appearance. Their roles and most of all their science had changed in the dozen years since Elaine Fuchs, then president of the ASCB, introduced her keynote speaker at the 2001 ASCB Annual Meeting, Craig Venter. That had been during Venter's first big moment in the world media spotlight as head of Celera, his private "shotgun" gene sequencing company that had just completed the first draft of the human genome in an uneasy alliance with the public consortium led by the National Institutes of Health. Already a leading investigator of stem cells, a term that was just coming into the public consciousness in 2001, Fuchs was about to move to the Rockefeller University in New York City. In New Orleans last month for the 2013 ASCB Annual Meeting, Fuchs and Venter shared the keynote platform with talks that showed just how much cell biology has changed in 12 years. (Videos of both keynotes are here.)

Fuchs spoke on the origins of the term stem cell, tracing it back to the German biologist Ernst Haeckel in 1877 and its popularization by the American biologist E.B. Wilson in 1896 as a synonym for what we would now call a germ cell in developmental biology. The modern meaning of stem cell as the pluripotent source for all subsequent differentiated cells in a lineage took decades to evolve, and it wasn't until 1961 that James Till and Ernest McCulloch clearly demonstrated the existence of hematopoietic stem cells in bone marrow. The successful culturing of adult stem cells took until the mid-1970s, by which time Fuchs was already at the forefront as a postdoc in the Massachusetts Institute of Technology laboratory of Howard Green. The Green lab discovered how epithelial stem cells required an exquisitely tuned niche to protect their "stemness." The stem cell niche controls the stem cell's decision to remain quiescent, to make tissue, or to stop making tissue. Fuchs said that understanding in detail how that decision is regulated has been her single research objective from her earliest days in the Green lab through to the present.

Stem cells and the tissues they generate turn over at different rates in response to different events, Fuchs explained. The epithelial cells that line the intestines have a life span of three to five days from their differentiation in the crypts of Lieberkühn to being sloughed off. In contrast, the stem cells that generate sweat gland tissue are quiescent for decades, responding only to deep wounding. Her favorite system, though, is the hair follicle, where the stem cells move through "cyclical bouts" of growth and rest. "Unfortunately the resting stages get longer and longer as we age," she added. But the follicle's nuanced response to external and internal signals makes it an ideal model system to understand what drives stem cells from quiescence to activation and back. Using the hair follicle as a model system, the Fuchs lab has thrown light on a variety of basic biology questions from signaling pathways to epigenetic labeling and most recently on what Fuchs described as "so-called cancer stem cells."

The mechanisms that control a hair follicle stem cell's decision to make tissue or remain quiescent are closely related to those that drive cancer stem cells. "In fact, when we began to study the basic mechanism by which stem cells sit in quiescence or begin to make tissue, when we over-activated that system, we got mice that were tumor prone and when we under-activated that system we got mice that were tumor resistant," Fuchs said. "That began to tell us that cancer, effectively cancer stem cells, have hijacked the basic mechanisms that stem cells utilize in order to activate and make tissue."

Squamous cell carcinomas arise in the same epidermal population as normal hair follicle stem cells, Fuchs explained. By fractionating tissue samples of squamous cell tumors and analyzing gene expression patterns, her lab came up with a few common features—squamous tumors have their own "stem" niches and express high levels of self-renewal genes characteristic of stem cells—but hundreds of differences between cancer stem cells and their normal counterparts. The differences include "everybody's favorite list of cancer genes," said Fuchs. "This is not what normal stem cells look like."

To home in on those critical differences, the Fuchs lab has painstakingly developed a novel genomic screen. It targets the single cell layer of epidermal progenitors that develops in the mouse embryo right after gastrulation. Using lentiviral transfection and short hairpin RNA interference, the Fuchs lab is working through the entire mouse genome. "This has opened up the pathway for us to understand more about cancer stem cells and the [niche] tumor initiating cells and their behavior."

Venter was happy once again to follow Fuchs to the podium. "I learned tonight that I'm not bald," Venter declared. "I just have quiescent stem cells." And with that, Venter plunged into a dizzying account of his post-Celera career. Now the head of his own J. Craig Venter Institute (JCVI), Venter has steadily pursued his goal of creating a pure "digital biology," a new kind of synthetic biology where the nucleotide bases of DNA can be read out rapidly as binary software, re-engineered, and then recreated anywhere as a functional organism or even as a new species.

As proof of principle, Venter described how the JCVI synthesized the entire genome of a bacterium, Mycoplasma mycoides, by assembling sections as DNA "cassettes," transplanting them into yeast, and then inserting the entire synthesized genome (with a synthesized centriole) into a distantly related bacterium that the genome took over, molecule for molecule. In 2010, this labor-intensive effort yielded what Venter described at the first human-made species.

Venter told the Annual Meeting audience that his institute's advances in rapid sequencing revealed many of our earlier views of genomics to be simplistic. The first human genome sequenced was a haploid conglomerate of four individuals (including Venter), and the common wisdom at the time was that we, humans, would all have a mostly common sequence with only a few variants. This is not accurate, said Venter. As the sequencing price has fallen and the number of individual sequenced genomes piles up, it's become clear that every one of us has in our own genomes a significant number of non-synonymous substitutions. The first diploid genome to be sequenced in 2007 was Venter's own, and it showed significant variation within a single human. We are all "compound heterozygotes," Venter declared. By sequencing individual sperm, Venter's lab found an average of one crossover sequence per cell and the same holds true for eggs. Increasingly, said Venter, the question has become, what is a normal human phenotype?

Nor are we alone in our genomes and our bodies, according to Venter. Shotgun sequencing of the human gut biome shows that while we all have roughly 100 trillion human cells, we are also joined by 200 trillion bacteria. If we all have 20,000 or so human genes, we also live with 10 million microbial genes. Our resident microfauna affect us, Venter said, pointing to new studies linking the composition of the microbiome to diseases such as obesity and diabetes. Beyond the biome, said Venter, is the human metabolome, which is the mix of all chemicals circulating in your blood. Human cells can produce about 2,400 different chemical compounds, but studies have shown that about 500 compounds are circulating at any one time. The bacterial residents of our microbiome churn out a key portion of the metabolome. Analysis of these compounds has shown that about 60% are of human origin, 30% can be traced to the plants and animals in our diet, but 10%, or 50 chemicals, are of bacterial origin.

Beyond the crowded human genome, Venter took the audience into outer space with an explanation of his Digital Biological Converter (DBC), a bio-robot that would be able to sequence species in far away places and email the digitized results for transformation by a kind of DNA printer. Venter's lab has been testing a DBC prototype system in a suitably remote location, the Mojave Desert, where researchers have been sampling lichen growing under quartz rocks and sending the digitized sequences back to San Diego for re-creation. Venter's ultimate test would put a DBC robot on Mars with a deep soil probe to recover Martian life forms from the permafrost or deep water deposits, sequence them, and transmit the digitized genome within minutes to Earth, where high-level biosafety labs could print out the alien life forms.

Sequencing on Mars or using the epidermal surface of a mouse embryo as a genetic Petri dish—none of this was on the agenda in 2001 when Venter and Fuchs last spoke to ASCB. In her talk, Fuchs pointed out that it was nearly a century from Ernest Haeckel's introduction of the term "stem cell" to Howard Green's first successful culture of adult stem cells, but it took only seven years from that to Gail Martin's culturing of embryonic stem cells in mice. The "explosion" of stem cell culturing methodologies in the 1990s accelerated the pace, and the first reprogramming of human skin cells to induced pluripotent stem (iPS) cells by Shinya Yamanaka in 2007 has picked up the pace yet again. But Fuchs reassured her audience of young scientists, "There is still a lot of exciting science left to do."

Young or established, scientists shouldn't be too cautious, Fuchs advised. "Often you can think of 20 different reasons why an experiment won't work but sometimes, it's a good idea to have a beer with your buddies and ask, 'Why not? Maybe it will work.'"

John Fleischman

