Chimp change

Noah Woods

Humans are clearly different from chimpanzees. The question is, why? According to researchers at the School of Medicine, it may boil down in part to what we don’t have, rather than what we do. The scientists found that the loss of snippets of regulatory DNA could be the reason, for example, humans lack the penile spines found in many other mammals, and why specific regions of our brains are larger than those of our closest relatives.

Understanding these and other differences may help us learn what it means to be human. But it took the recent advent of whole-genome sequencing of several species and an open-minded, combined computational and experimental approach to reveal the particular two-steps-forward, one-step-back evolutionary dance that set us apart from other primates millions of years ago.

“Rather than looking for species-specific differences in specific genes or genomic regions that exist in humans, we asked, ‘Are there functional, highly conserved genetic elements in the chimpanzee genome that are completely missing in humans?’” says Gill Bejerano, PhD, assistant professor of developmental biology and of computer science. “We found several hundred locations that, as far as we could see, are absent in our species alone.”

Losing small pieces of regulatory DNA rather than the genes they control means that the related changes are likely to be subtle: Although the location or the timing of the expression of the gene within the body may change, the gene product itself remains functional. The distinction causes viable differences among individuals that can eventually lead to the development of new traits and species.

Bejerano and David Kingsley, PhD, professor of developmental biology, are co-senior authors of the research, published March 10 in Nature.

The researchers compared the genomes of several species to identify 510 regions that are highly conserved among chimpanzees and other mammals but are missing in humans. They then used a software program developed in Bejerano’s laboratory, called the Genomic Regions of Enrichment of Annotations Tool, to see whether these regions preferentially occurred near certain types of genes. (GREAT is publicly available at http://great.stanford.edu.)

The researchers found that one of the missing regions normally drives the expression of the androgen receptor in sensory whiskers and genitalia. Androgen is a sex hormone responsible for growth of sensory hairs, or vibrissae, and surface spines found on the penises of many mammals. The loss of these structures in humans decreases tactile sensitivity and increases the duration of intercourse in humans relative to other species.

Another region was adjacent to a gene that suppresses neural growth in a particular part of the brain. Loss of expression of this inhibitory gene could thus contribute to an expansion of neural production in humans and a larger brain.

The resulting changes may have paved the way for monogamous pair-bonding and the complex social structure necessary to raise our species’ relatively helpless infants, the scientists speculate. — Krista Conger

 

The work was supported by Stanford’s Bio-X Program; a Ruth L. Kirschstein National Research Service Award; a National Defense Science and Engineering graduate fellowship; a national science scholarship of the Agency of Science, Technology and Research; the National Institutes of Health; the Edward Mallinckrodt, Jr. Foundation; and the Howard Hughes Medical Institute.

Bladder matters

The bladder is a supple, muscular organ with a well-defined task: Store urine and release it at an appropriate time. Unlike its workhorse neighbor, the intestine, it doesn’t need a lot of fussy cell division to get the job done. But when the bladder becomes infected, it launches a massive, scorched-earth attack, sloughing off the innermost layer of cells to keep invading bacteria from latching onto and burrowing into its inner lining.

Now scientists at the School of Medicine have identified the key molecular pathways that form a control circuit involved in kick-starting cell division in the bladder to repair the damage.

“We suspect that this pathway of regeneration might be important in cancer development and metastasis in the bladder and other organs, like the prostate,” says developmental biology professor Philip Beachy, PhD, who is the senior author of the research, published online March 9 in Nature.

About 10 percent of women each year experience bacterial infections of the bladder that can range in severity from irritating to painfully debilitating. The body’s natural defense of shedding at least a portion of the inner lining in which the bacteria hide out works pretty well, but it’s not perfect; over one-quarter of women will experience a recurrence within one year, sometimes even when antibiotics are used to treat the infection.

The bladder’s inner lining is made up of a tightly connected layer of umbrella cells that protect the underlying cells from toxins and waste in the urine. Under them are intermediate and basal epithelial cells (together these umbrella, intermediate and basal cells make up the urothelium), then a non-epithelial layer of cells called the stroma. The stroma is separated from the urothelium by a thin structure called the basement membrane.

“The bladder is a great system in which to look at this because it’s composed of a fairly simple, ordered tissue,” says Beachy. “Most of the time, the cells in this tissue undergo little or no cell division, but injury with chemicals or bacterial infection causes rapid proliferation.”

In fact, Beachy found that it normally takes about 10 months to replace about half of the cells in the inner lining in the bladders of female laboratory mice. In contrast, in the presence of harmful bacteria, the cells of the bladder begin dividing dramatically, and most turn over within 24 hours.

To conduct the experiments, the researchers used a type of bacteria that causes bladder infections in humans. They introduced the bacteria into the bladders of female mice and watched to see how the cells responded. They found that, after infection, the basal cells in the urothelium and the stromal cells on the other side of the basement membrane “talk” to one another using a protein involved in the hedgehog signaling pathway, called sonic hedgehog, and at least one other signaling pathway, called Wnt.

The process occurred in what’s known as a positive feedback loop: Sonic hedgehog stimulated the stromal cells to produce Wnt, and the Wnt stimulated the epithelial cells and the stromal cells to begin proliferating and make more sonic hedgehog. This loop serves to amplify the signal and encourages the cells of the urothelium to begin dividing quickly.

“Understanding the physiology and the regulation of these regenerative processes might give us a better handle on how to treat bladder cancers and urinary tract infections,” says Beachy. — Krista Conger

 

The research was supported by the Department of Defense, the National Institutes of Health and the Howard Hughes Medical Institute.

Rejection detection

Noah Woods

Heart transplant recipients and their physicians are likely more concerned with the function of the donated organ than with the donor’s DNA sequences that tag along in the new, healthy tissue. However, researchers at the School of Medicine have shown that an increase in the amount of the donor’s DNA in the recipient’s blood is one of the earliest detectable signs of organ rejection.

The finding implies that a simple blood draw could replace the regular surgical biopsies that are currently used to track the health of the donor heart. Closely tracking the dynamics of this concurrent “genome transplant” might also allow doctors to avoid the high doses of medication required to combat more advanced cases of rejection.

“Heart transplant recipients undergo at least 12 tissue biopsies during the first year after their transplant and two or three each year for about four additional years,” says Hannah Valantine, MD, professor of cardiovascular medicine. “The idea that we might now be able to diagnose rejection earlier and noninvasively is very, very exciting.”

“This approach, which we call genome transplant dynamics, solves a long-standing problem in cardiac transplantation,” says bioengineering professor Stephen Quake, PhD, who developed the sequencing technology used in the study. “It’s so difficult to find and implant a donor heart, and then doctors have to remove pieces of it every few months to test for rejection.”

Quake and Valantine are co-senior authors of the research, which was published online March 28 in the Proceedings of the National Academy of Sciences.

The study involved combining two methods of detecting organ rejection — a blood test Valantine pioneered in 2010 to determine whether the body has launched an attack on the donated organ, and a new technique developed by Quake (called microfluidic digital PCR) to measure levels of donor DNA released when cells in the transplanted heart are damaged, as occurs early in the rejection process.

Past efforts to pick out DNA from a transplanted organ have hinged on one easily identifiable difference — the presence of the male Y chromosome in the blood of female transplant recipients. The team’s first step was to confirm that Quake’s technique could identify the presence of the Y chromosome in stored blood samples from women who had received, and then rejected, a heart from a male donor.

However, because the pairing of female recipients and male donors accounts for less than one-quarter of organ transplants, the team wanted to determine if the approach could be used on a broader range of patients. As a test, they mixed reference DNA from two unrelated people in proportions varying from 0 to 7.5 percent, designating one as the donor and one as a recipient. The sequencing approach accurately identified the minute proportions of “donor” DNA in each sample. Following this proof of principle, the researchers applied the technique to three women who had received hearts from male donors, two of whom experienced episodes of rejection and one who did not, as well as four men who received hearts from male donors, who had all experienced rejection.

“In every case we could see an increase in donor DNA in the patient’s blood before the biopsy itself showed any sign of rejection,” says Valantine. —Krista Conger

 

The research was supported by the National Institutes of Health and the Howard Hughes Medical Institute. The researchers have filed a patent for use of the technique.

Stem cell PhD

Beginning in the fall of 2012, Stanford will offer what officials believe is the first PhD program devoted solely to stem cell science in the nation and, perhaps, the world. Prospective students can begin applying this fall.

School officials say the creation of a new doctoral program acknowledges the growing importance of stem cell research in biomedical science. They note that Stanford is among a small number of U.S. universities that have the necessary ingredients to create a program teaching the full range of stem cell science.

In particular, Stanford has received $192 million during the past five years — more than any other institution in the state — from the California Institute for Regenerative Medicine to advance stem cell research in the face of more-restrictive federal funding policies. The funds have enabled Stanford to build the Lorry I. Lokey Stem Cell Research Building, to develop educational outreach and tissue banking capabilities, and to recruit a number of renowned researchers and trainees from whom the new PhD students can learn both the science and ethics of human stem cell research.

While a few other schools have PhD programs involving stem cell biology, this is the first dedicated solely to stem cell biology and regenerative medicine, an emerging field that aims to repair or replace damaged tissues and organs. One of the program’s distingiushing features is that all students will undergo an immersive clinical rotation in which they will shadow attending surgeons, physicians, residents or fellows.

“Stem cell biology is a distinct discipline that requires unique skills and includes a scope of knowledge and a skill set that is not covered by other disciplines,” says Renee Reijo Pera, PhD, professor of obstetrics and gynecology and the new program’s director.

Theo Palmer, PhD, associate professor of neurosurgery and co-director of the doctoral program, says students helped spur its creation after voicing frustration that existing programs lacked the breadth of cross-disciplinary training needed for a successful career in regenerative medicine. “The new program not only engages subjects taught within the School of Medicine, it crosses the Stanford schools to capture fundamental principles in engineering, law, business and society,” Palmer says. — Christopher Vaughan

Embryo imbroglio

Noah Woods

It’s a waste. People who have completed in vitro fertilization procedures usually have leftover embryos, and they usually discard them. Meanwhile, scientists studying human development or stem cells would love to use those embryos for research.

These fertility clinic patients can choose to have them stored, disposed or donated for research, but the methods clinics use to ask their preferences vary. In general, clinics take a hands-off approach to avoid unethically influencing patients.

A new process developed by researchers at the School of Medicine and used by Stanford’s biobank allows these people to make this decision at home — without any interaction with clinic personnel or scientists who might benefit from the research — yet offers an easy route to more information about donation if they’re interested.

“There is concern that conflicts of interest and influence by researchers and clinicians may play a role in donor choice,” says bioethicist and senior author of a study of the method, Christopher Scott, who directs Stanford’s Program on Stem Cells in Society. “The Stanford biobank process allows people time to make the primary decision to donate on their own, when it’s right for them. It also allowed us to ask whether donors have preferences as to the type of research they will allow on their embryos.”

In the two-part procedure, described in the April 8 issue of Cell Stem Cell, the information about donation for research is included in the normal embryo-storage bill from the clinic. “At that point,” Scott says, “the recipients are free to throw the information away or put it on the coffee table to consider and talk about.” Only after the couple has made the initial decision to donate do they interact with Stanford biobank staff members.

People who indicated that they would like to donate were sent an informed-consent packet outlining the types of research that could be done with the embryos, such as creating embryonic stem cell lines or studying human development.

Once the potential donors had time to review the material, they took part in a phone interview with Stanford biobank staff members who were unconnected with either the original in vitro fertilization clinic or the researchers who might use the embryos. The staff members followed a script to confirm the donors’ preferences and make sure they understood their options.

The researchers found that donors were equally likely to give consent for their use in the creation of embryonic stem cell lines (30 percent of the eligible respondents) as for the study of human development (32 percent). Thirty-eight percent gave consent for their embryos to be used for either type of research. — Krista Conger

 

The research was funded by the California Institute for Regenerative Medicine and Stanford University.