Profile of Shinya Yamanaka

More than a decade ago, Shinya Yamanaka gazed through a microscope at human embryos growing in a laboratory dish at a fertility clinic in Osaka, Japan. The pulsating blobs struck a primitive chord in the young researcher. “Watching the embryos, I felt that if there was a way to find cures for human diseases without destroying them, then that's what I should pursue,” recalls Yamanaka, a stem cell biologist at Japan's Kyoto University and a newly elected foreign associate of the National Academy of Sciences. That close encounter with a kernel of human life led to a scientific exploration with a societal undertow. Years later, Yamanaka discovered a genetic recipe that allows researchers to bypass the use of human embryos to create a range of cell types implicated in diseases. His magic ingredients? A quartet of gene switches that could help turn adult human cells into an embryo-like state, leading to disease models, drug tests, and, someday, even replacements for diseased human tissues. Today, Yamanaka's accomplishment is acclaimed as nearly unmatched in its impact on regenerative medicine.

Shinya Yamanaka.

Dopaminergic neurons derived from human iPS cells.

In Osaka, a bustling commercial hub and home to electronics giants like Panasonic and Sanyo, Yamanaka was born to parents who manufactured spare parts for sewing machines. When he was 10 his family moved east to Nara, where iconic temples bear witness to a Buddhist landscape. From an early age, Yamanaka's father motivated him to pursue a career in medicine instead of enlisting him in the family enterprise. Add to his father's influence a childhood spent recovering from sports injuries, and Yamanaka's choice of a career in orthopedic surgery seemed cast in stone. “I suffered from bone fractures more than 10 times from playing judo in school. I went to orthopedic clinics so often, it was natural for me to be interested in orthopedic surgery,” he says. In 1981 he joined Kobe University School of Medicine, working toward his chosen specialty, which he began practicing upon graduation. While at Kobe University, he completed a 3-month laboratory stint in forensic medicine, using mass spectrometry to investigate aspects of alcohol metabolism in people. The experience ignited his interest in laboratory science, one that he has kept up with a career-defining drive.

From Surgery to Stem Cells

During his residency, Yamanaka began to have doubts about his calling; he reckoned that surgery, no matter how lifesaving, cannot solve medicine's abiding mysteries. Nor was he cut out, he realized, for the sedulous craft of surgery. As a result, he signed up for doctoral studies in pharmacology at Osaka City University Graduate School of Medicine in 1989, upon the suggestion of senior physician Mamoru Okubo. At Osaka City University he designed, performed, and interpreted experiments, all while attending to patients. Under the tutelage of pharmacologists Kenjiro Yamamoto and Katsuyuki Miura, he examined the role of a lipid named platelet-activating factor in lowering blood pressure in dogs. The findings, published in a 1992 issue of Circulation Research, made plain the lipid's mechanism of action: platelet-activating factor, he found, triggers the synthesis of a hormone-like molecule called prostacyclin, which dilates blood vessels and lowers blood pressure (1).

In 1992, when transgenic technology was stretching the limits of possibility for molecular biologists, Yamanaka graduated with a PhD in pharmacology. In the wake of biochemist Mario Capecchi's Nobel Prize-winning discovery that among the tens of thousands of then-known mammalian genes, individual genes could be singled out for silencing to create so-called “knockout” mice, Yamanaka became interested in transgenic technology as a way to probe the function of genes in mammalian cells. Determined to work in the United States, where the technology originated, he sent off dozens of letters seeking a postdoctoral position in molecular genetics, hoping to beat the seemingly insurmountable odds facing a surgeon-researcher with scant experience in genetics.

It was the willingness of University of California, San Francisco (UCSF) geneticist Thomas Innerarity at the Gladstone Institute of Cardiovascular Disease that led to Yamanaka's break in molecular biology. At Gladstone, the duo engineered an enzyme into the liver cells of mice to lower the levels of apolipoprotein B, a biochemical precursor of bad cholesterol that can cause diseases like atherosclerosis. To the researchers’ puzzlement, the transgenic mice sprouted liver tumors, suggesting that overproducing the enzyme could trigger cancer. Yamanaka reported those findings in a 1995 PNAS paper, following up 2 years later with a partial explanation for the unexpected outcome (2, 3). The enzyme, it turned out, also altered the levels of another protein named Nat1, whose function remained a mystery. Probing deeper, Yamanaka set to work on a knockout mouse for Nat1, as he isolated, cultured, and engineered mouse embryonic stem cells. But he returned to Osaka before he could solve the mystery of Nat1. “I wanted to stay on in the United States forever, but my wife wanted a Japanese elementary school education for my daughters,” he recalls.

Those initial efforts at Gladstone heralded coming discoveries in stem cell biology. Back at Osaka City University, where he was hired as an assistant professor with the support of pharmacologist Hiroshi Iwao, Yamanaka found that the protein Nat1 shepherded mouse embryonic stem cells in their developmental pathway. There, he studied how the cells differentiate into adult cells, as his interest in them deepened, he wrote in a Nature Medicine commentary, from “research tool to research subject” (4).

Yet the tepid response to his basic research subject at Osaka City University's medical school made him yearn for the vivifying ferment of American research settings. Fortunately, an associate professorship in 1999 at Nara Institute of Science and Technology, where he was charged with establishing a knockout mouse facility, satisfied his yearning. “The scientific environment at the institute in Nara was very important to my career,” Yamanaka says.

Anchored in History

Yamanaka's work in stem cell biology harks back to the 1998 isolation of human embryonic stem cells by University of Wisconsin stem cell biologist James Thomson. The technical feat followed that of British Nobelist Martin Evans, who, in the early 1980s, devised a way to grow entire mice from mouse embryonic stem cells. Hailed as a breakthrough, Thomson's discovery pointed to a wealth of potential medical applications for stem cells. Because stem cells in the embryo are a sort of developmental blank slate, they can be prodded to adopt specific fates—to turn into adult muscle, heart, liver, brain, and other cell types—with combinations of chemicals and conditions. Researchers can use adult cells derived from embryonic stem cells to learn what goes awry in certain diseases, to test candidate drugs for those diseases, and to potentially create a pipeline of replacement parts for diseased tissues. But ethical concerns surrounding embryonic stem cell research have mired the field in controversy; stem cells are typically extracted by destroying human embryos that fertility clinics often discard. At Nara, Yamanaka developed a workaround by upending a logic underlying regenerative medicine. He found a way to turn adult cells into an embryo-like state, establishing what could be a wellspring of cell types.

Yamanaka's workaround is rooted in the history of regenerative biology, marked by a 1962 milestone discovery by University of Cambridge biologist Sir John Gurdon, who created frogs in the laboratory by transplanting the nucleus of a tadpole's fully developed intestinal cell into the enucleated egg cell of an African clawed toad. More than three decades later, nuclear transplantation moved into the mainstream when British embryologist Ian Wilmut gave the world its first cloned sheep, Dolly. From Gurdon's frogs to Wilmut's sheep, researchers had long suspected the existence of mysterious factors in egg cells that reprogrammed the nucleus of an adult cell to an embryonic state. But the factors remained elusive until Yamanaka began to look for his workaround in the late 1990s.

Though Yamanaka is best known for his technique to bypass the use of embryos in stem cell research, the reason behind his rise to scientific prominence is his insight into the nature and transferability of those fate-changing factors in embryonic cells. With his team at the Nara Institute, he homed in on 24 gene switches that could turn adult mouse cells into a state called pluripotent, enabling them to further morph into many cell types. “It took us almost 5 years to identify those candidates,” Yamanaka recalls. Meanwhile, Thomson's isolation of human embryonic stem cells meant that Yamanaka could move the field's frontiers by replicating those findings in human cells; the embryonic stem cells would serve as a benchmark. “But the institute in Nara does not have a medical school or hospital, so getting human embryonic stem cells was difficult,” Yamanaka recalls. That is partly why he accepted a professorship at the Institute of Frontier Medical Sciences at Kyoto University, where at first he whittled down his list of 24 gene switches to no more than four, namely Oct3/4, Sox2, Klf4, and c-Myc—genes with near-magical ability to reset the developmental clock in mouse cells. That landmark 2006 discovery announced the advent of stem cell technology in the pages of Cell (5). A year later, Yamanaka and Thomson separately demonstrated the transformation of adult human skin cells—removed from the face or foreskin—into an embryonic state. Those findings are widely regarded as the bedrock of today's stem cell biology (6, 7).

Soon thereafter, reports from other researchers trickled in, demonstrating the conversion of adult human cells into a range of cell types—heart cells, brain cells, and pancreatic cells—affected in conditions like cardiovascular disease, Parkinson's disease, and diabetes. The cells helped researchers test the safety and efficacy of drugs against those diseases in Petri dishes, and even develop models for those diseases. Because cells derived from a patient's own cells can be transplanted into the patient for therapeutic purposes someday, Yamanaka's method can potentially sidestep adverse immune reactions triggered by transplanting cells derived from an embryo. For findings that solidified his position in the field of stem cell biology, Yamanaka shared the 2009 Lasker Basic Medical Research Award with Gurdon, an accomplishment whose singular nature is underscored by the years that separate the researchers’ careers. “Sir John Gurdon performed his experiment in nuclear reprogramming in 1962; that's when I was born. It is a tremendous honor to share the award with him,” Yamanaka explains.

Riding an Obstacle Course

But the technique's shortfalls soon diminished its promise. One of the gene switches Yamanaka used to induce pluripotency can lead to cancer, which the switch promptly triggered in some animal experiments. Moreover, the retrovirus used to ferry the switches into adult human cells can slip into chromosomes and sabotage gene regulation, also leading to cancer. To further complicate matters, stem cells derived through the technique were not always identical to embryonic stem cells; subtle differences came to light when the cells were induced to adopt specific fates. Some researchers reported mutations that seemed to have arisen through reprogramming. Others found that induced pluripotent stem cells retained a memory of their adult cell of origin, resisting attempts to turn them into a different type of adult cell. Which is partly why, Yamanaka says, the need for research on human embryonic stem cells remains as pressing as ever—to provide researchers with a standard for comparison.

But the field suffered a setback in 2010 when a federal judge in Washington, DC blocked President Obama's efforts to expand human embryonic stem cell research beyond the small number of previously established cell lines on the grounds that federal money could not be used to destroy human embryos for research. As federally funded stem cell researchers in the United States grappled with a brief moratorium, scrambling to save their experiments, the decision—overturned on appeal a year later—raised the temperature of a long-simmering debate over stem cells. Yamanaka's stance toward the ethical conundrum surrounding stem cells is categorical: “My position has always been that if we can avoid using human embryos we should. At the moment, we are not 100% sure that human-induced pluripotent stem cells are equivalent to human embryonic stem cells. To confirm that, we have to use several human embryonic stem cell lines. Without any question, human embryonic stem cell research is crucial.”

Following that line of reasoning, Yamanaka continues to work on human embryonic stem cells in Kyoto, traveling every month to San Francisco, where he holds appointments at Gladstone and UCSF. Over the years, he has honed his technique to address some of its shortcomings. In 2007, he reported that the technique worked even when the cancer-causing Myc gene switch was left out of his reprogramming recipe (8). The following year, his team reported a technique to induce pluripotency in mouse cells without using a viral ferry; the switches were carried aboard DNA circles called plasmids that deliver their cargo without inserting themselves into the cells’ genomes, thus reducing the risk of cancer (9). And in 2011 he described a way to generate human pluripotent cells without using viruses (10).

Meanwhile, other researchers have put Yamanaka's technique to promising preclinical use. Harvard University stem cell biologist Douglas Melton successfully treated diabetic mice with insulin-secreting pancreatic beta cells—normally destroyed by diabetes—derived from another type of pancreatic cell. Molecular biologist Bruce Spiegelman at the Dana-Farber Cancer Institute turned harmful white fat cells, which can cause obesity, into calorie-burning brown fat cells.

Shadow over Promise

Though treatments based on Yamanaka's technique have yet to reach the clinic, a few may be around the corner. For example, a team at Stanford University led by dermatologist Alfred Lane is exploring the use of induced pluripotent stem cells to replace damaged skin cells in people afflicted with a rare genetic disorder called epidermolysis bullosa, which causes skin to slough off upon physical stress. The US Food and Drug Administration has greenlighted Massachusetts-based biotechnology firm Advanced Cell Technology's phase II trial of adult stem cell therapy for patients in the late stages of congestive heart failure without recourse to heart transplants. And researchers at Japan's renowned RIKEN Center for Developmental Biology in Kobe, Yamanaka says, have generated human retinal pigment epithelial cells from induced pluripotent stem cells. The RIKEN group, he adds, hopes to begin a clinical trial of a treatment for age-related macular degeneration, a leading cause of blindness among millions of people worldwide.

As research on induced pluripotent stem cells advances, the field faces fresh challenges. In May 2011, researchers at the University of California, San Diego reported that induced pluripotent stem cells derived from the skin cells of mice suffered immune rejection when implanted into genetically identical mice, suggesting that the manner in which pluripotency is induced might influence immune rejection in patients. Reports of incomplete or insufficient reprogramming often baffle stem cell researchers. But Yamanaka counters that the findings on immunogenicity are far from conclusive and that such problems may be surmounted in the near future, raising fresh hope for the technology's promise to help treat human diseases. “The main hurdle is safety associated with the use of induced pluripotent stem cells in people,” he adds.

Recognizing the technology's potential, despite the roadblocks facing the clinical application of stem cells, Japan's Inamori Foundation awarded the 2010 Kyoto Prize in Advanced Technology to Yamanaka. Dismissing widespread speculation of his odds of winning science's most coveted prize in the not-so-distant future, Yamanaka says, “The technology is still very young. Ten years from now, we hope to have created an effective treatment using patient-specific, iPS cell-derived cells. We also hope that the technology will lead to clinical trials for diseases like Parkinson's and macular degeneration.”