Comparing Adam Lanza’s DNA to Forensic DNA Databases: A Modest Proposal

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Is there a genetic signature for criminality? It’s an old and controversial question. (NHGRI)

In 1729, Jonathan Swift of Gulliver’s Travels fame published a satirical essay called “A Modest Proposal.” He suggested that a cure for poverty was for poor people to sell their children to rich people as food.

I’m borrowing Swift’s title to bring up another outrageous idea: analyzing forensic DNA databases for a genetic signature of criminality.

ADAM LANZA’S DNA
Days after the Newtown shootings of December 14, 2012, headlines trumpeted the state medical examiner’s request of University of Connecticut geneticists to examine mass murderer Adam Lanza’s DNA. What exactly that might entail wasn’t announced, but celebrity docs, geneticists, and bloggers weighed in, nearly all agreeing that (1) violent tendencies are due to complex interactions of many genetic and environmental factors and (2) probing Lanza’s DNA and finding anything even suggestive of causing his crime could lead to stigmatization of individuals who share suspect genome regions with him.

Behind the denials of a genetic explanation for criminality lies a history of just such associations.

Past candidates for criminal DNA, listed in many articles last week, include the extra Y chromosome of the 1960s and the monoamine oxidase (MOAO) mutation behind a Dutch family of rapists and arsonists, described in 1993. Shortly after, researchers identified a different gene variant that tracked with violence and suicide in Finnish families.

In January 2012, criminologists published a study that applied a “delinquency scale” to assess whether such behaviors as painting graffiti, lying to parents, running away, and stealing, were more likely to affect identical twins than fraternal twins, suggesting a genetic component. The headlines that their article in Criminology spawned, with the help of news release hype, were predictable: “Life of crime is in the genes, study claims.”

If an investigation of petty crimes inspires such strong headlines, the fear of unleashing genetic discrimination from analyzing Lanza’s DNA seems justified. Yet it appeared odd to me that several articles deemed any response to the sequencing of the killer’s DNA unlikely, because it would be a sample size of one.

We do, in fact, have sources of criminals’ DNA. And they’re extensive.

FORENSIC DNA DATABASES
A blog from the Council for Responsible Genetics, for example, claims that “Focusing on the results of the study [on Lanza] could also prove problematic since there is (sic) basically no data to compare it to,” then quotes a University of Massachusetts Medical School professor saying “we don’t have enough of a sample size.”

But forensic DNA databases in many countries have been storing the DNA of convicted criminals since the mid-1990s, many killers among them.

The UK led the way in DNA profiling (I wrote the cover story on it for Discover in June 1988), and their National DNA Database now has samples from more than 6 million individuals.

In the US, the Combined DNA Index System (CODIS) has more than 10 million samples. Thailand just signed on to use CODIS on voluntary samples from 100,000 inmates, and 39 other nations already use the system.

The lines of a DNA profile represent the numbers of short repeated sequences at 13 sites in the genome. (NHGRI)

CODIS generates a DNA profile for an individual based on 13 sites in the genome that vary in the number of repeats that they harbor. One such “short tandem repeat” (STR), for example, includes the DNA sequence “GATA” present in 5-16 copies on each of a person’s two chromosome 7’s. For that marker alone, 78 combinations are possible. Multiplying the frequencies of the different variant (allele) possibilities in a particular population for all 13 markers generates enough diversity to distinguish individuals.

Within the STR DNA profiles of these millions of convicted individuals may emerge a genetic pattern that’s more common among mass killers like Lanza. Maybe significantly so. And if researchers have access to DNA samples and not just CODIS profiles, they could, theoretically, compare any part of the genome. If there is such a thing as measurable inherited criminality, then as the numbers build in the databases, associations between DNA patterns and certain behaviors may strengthen, perhaps even suggesting a mechanism that can be used in drug discovery or repurposing. (I readily admit to not knowing the legalities of using forensic data for new purposes; I’m hoping an attorney will weigh in. I’m just the gene girl.)

A very large control group would also be necessary to weed out potential false positives, like showing that a disease-causing mutation is found only among patients.

DNA forensic data could and should be de-identified, because the crimes are important, not the names. According to the FBI CODIS fact sheet, “If all personally identifiable information is removed, DNA profile information may be accessed by criminal justice agencies for a population statistics database, for identification research and protocol development purposes, or for quality control purposes.“ And informed consent isn’t required of convicts.

Would use of a genetic signature for criminality plunge us into the world of Minority Report, the 2002 Tom Cruise film in which police in a dystopian society arrest people before they’ve committed crimes? I would hope not. But I can imagine a scenario in which a psychiatrist uses such a genetic test for a patient whose background suggests violent tendencies. The patient wouldn’t suffer Tom Cruise’s fate of premature punishment, but perhaps wouldn’t be allowed to purchase a gun.

TARGETING MINORITIES?
A powerful argument against the use of forensic DNA databases in crime research is that minorities such as African-Americans are overrepresented in prisons, and findings could be used in a discriminatory manner. This was the reasoning behing the yanking of NIH funding from a conference on “genetic factors in crime” in 1992 at the University of Maryland, with charges of it being a “modern-day version of eugenics” (which is actually timeless).

But times, and technologies, have changed. The 1992 objection to even investigating genetic factors in crime predates the DNA Identification Act of 1994 that led to forensic DNA testing by 1998 – now done in all 50 states. And consider the most notorious recent killing sprees. The perpetrator of the worst attack, at Virginia Tech in 2007, was an Asian, Seung-Hui Cho. The Columbine killers Eric Harris and Dylan Klebold were white, as is James Holmes of the midnight movie massacre in Aurora, CO in 2012. And the blurry, terrifying lone image of Adam Lanza is stark white.

I’m playing Devil’s advocate here. I agree with other geneticists that looking for clues to the Newtown tragedy in DNA could do more harm than good. I also agree that environmental influences on behavior and personality are as important if not more so than inherited factors. But at the same time, I can’t help thinking of those forensic DNA databases and the clues to violent behavior that they may hold, anonymously searchable by crime. And we now have the technology to derive much more information than we did when the technology was limited to selected repeats — we can sequence genomes. That’s a lot of information.

WHY NOT?
Uses of forensic DNA technology are already eclectic enough to embrace investigation of a criminal tendency profile.

STR typing has been used to identify disaster victims, to reunite Holocaust victims with their families, and to identify kidnapped children. And DNA profiling of footballs from Super Bowl games protects a vulnerable public against sports memorabilia fraud.

So despite lingering apprehension from the history of eugenics in the US in the early twentieth century, the threat of stigmatization, and growing acceptance of genetic determinism as genetic testing and genomes/exome sequencing become more widespread, I’m going to make that modest proposal.

I think that the DNA forensic databases may be important sources of information on the role, if any, of genetics in predisposition to violent behavior.

We have the data. Why not take a look? It’ll keep bioethicists busy for years to come – and might prevent a crime.

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The Curious Genetics of Werewolves

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The “wolf boy” brothers have Ambras syndrome, a single-gene condition that may have inspired the werewolf legend. (Gary Moore photo)

Growing up in the 1960s, I collected monster cards: The 60-foot-man and the 50-foot woman, duplicate bodies gestating in giant seed pods, unseen Martians that sucked children into sand pits and returned them devoid of emotion, with telltale marks on the back of the neck. One card featured a very young Michael Landon in “I Was a Teenage Werewolf.”

Forgive my lapse in political correctness, but I recalled those cards when I saw the word “hypertrichosis” in a recent paper in PLOS Genetics, because, unfortunately, the condition is also known historically as “werewolf syndrome.”

In the paper, geneticist Angela Christiano, PhD, and colleagues at Columbia University analyzed the genomes of a father and son with Ambras syndrome, a form of hypertrichosis – and found something intriguing about the causative mutation that has repercussions for genetic testing in general.

A WEREWOLF PRIMER
Before a genetic explanation for overactive hair follicles existed, werewolfism, aka lycanthropy, was thought to arise in eclectic ways: rubbing a magic salve into the skin, sleeping outdoors under a summer full moon, drinking from the pawprint of a wolf, or a devil’s curse. Werewolves were once considered to be giant extinct lemurs from Madagascar.

Armenian folklore describes a werewolf as a female criminal being punished by coming out at night and eating her children, and then her relatives’ children, in order of relatedness.

In 1963 a physician in London, where Warren Zevon tells us werewolves are prevalent, ascribed lycanthropy to the very rare blood disease congenital erythropoietic porphyria. With its attendant hairiness, reddish teeth, pink urine, and aversion to bright light, porphyria would later explain vampires too, although that idea has been discredited.

Some physicians suggested that hypertrichosis causes lycanthropy, but others argued that the genetic condition was too rare to account for the many werewolves loose on the streets of Europe.

ONLY 50 CASES KNOWN
Sources say that Ambras syndrome affects fewer than one in a billion people, and that only 50 cases have been described since the Middle Ages.

The name Ambras comes from Petrus Gonzales, who at age 12 in 1556 was brought as a slave from Tenerife in the Canary Islands to the court in France. He had a strikingly hairy face, married young, and had 4 children, 3 of whom were born hairy. His daughter Tognina and son Arrigo passed on the trait. Royalty, who called Petrus the “man of the woods,” thought he represented a race of hairy people from the Canary Islands. The celebrated family sat for many portraits, and one, displayed at a castle near Innsbruck called Ambras, led to their notoriety as the “family of Ambras,” and eventually their condition as “Ambras syndrome”. (An image of a little girl from the family graces the cover of Armand Marie Leroi’s fabulous book Mutants).

Shwe-Maong was another noted person with Ambras syndrome, from Burma. Wrote an observer in 1826: “… the whole face, with the exception of the red portion of the lips, were covered with fine hair.” The hairs were 4 to 8 inches long, straight and silky.

Born in the hill country outside the capitol, people encouraged Shwe-Maon to whoop like a monkey and act dumb. Like Petrus, he became a royal favorite, given a wife at a young age. They had 4 children, including a girl whose entire body was covered in a pelt of long, silky grey hair. Her name was Maphoon. She married and had two hairy sons, one of whom passed on the trait.

Charles Darwin mentioned Maphoon in The Descent of Man and Selection in Relation to Sex (1859), but it was his readers who brought up that the striking hairiness was atavistic, a turning-on of an ancestral trait silenced through evolutionary time. But the quality of the hair isn’t like that of an orangutan or gorilla. It‘s silky, and covers places, especially on the face, where our ape cousins don’t have hair. People with Ambras syndrome aren’t throwbacks.

Some individuals with Ambras syndrome ended up in circus sideshows, such as Julia Pastrana, the “bearded lady” who toured Europe and North America in the 1850s. In 1884 PT Barnum exhibited 16-year-old Fedor Jepticheff as “Jo-Jo the dog-faced man,” who became the inspiration for Disney’s Beast and a Phish song. Jo-Jo played along, barking on cue for PT Barnum, although he was very intelligent and made quite a good living from his genetic misfortune.

Russian dermatologist Nikolai Mansurov took this photograph of a patient with Ambras syndrome, circa 1857. (National Library of Medicine)

Documentation of Ambras syndrome appears in the medical literature a generation after Jo-Jo, when Russian dermatologist Nikolai Mansurov (1834–92) took photographs and commissioned wood carvings to illustrate an article on “hairy people,” then called polytrichia.

Lycanthropy may also be a delusion. A report in the November 1975 issue of the Canadian Psychiatric Association Journal described 20-year-old Mr. H, who claimed that after ingesting strychnine in a forest in Europe while serving in the military, he suddenly grew fur on his face and hands and was overwhelmed with a craving to eat live rabbits.

The Russian patient appears in this wood carving too.

People with Ambras syndrome still occasionally make the news. In 2011 the Guinness Book of World Records listed Supatra (“Nat”) Sasuphan, a 12-year-old from Thailand, as the “world’s hairiest girl.” She considers this a step up from being called “wolf girl” and “monkey face.” Since her birth, long silky grayish hair has cascaded down her face, like a veil starting at her bushy eyebrows.

Earlier this year a mother and her 3 children taunted for their “werewolf syndrome” sought help in Nepal and YouTube
features several other families with Ambras syndrome.

BACK TO BIOLOGY
Ambras syndrome is a disruption of the crosstalk between the epidermis and the dermis as hair follicles form in the 3-month fetus at the eyebrows and spread down to the toes. Signals from the dermis send the messages to form follicles. As a follicle forms, it sends signals to prevent the area around it from also becoming a follicle, establishing equal spacing of our 5 million or so follicles. Most body parts ignore the messages to form follicles, and so we’re relatively hairless.

An area called the bulge about halfway down each follicle houses the stem cells that keep hair growing. Hairs cycle through phases. In anagen (growth phase) cells divide, for  2 to 6 years. In catagen, which lasts about 2 weeks, the follicle renews itself.  Telogen is a 1-4 month long rest. About 85% of our hairs are in anagen at any given time, 10-15% in telogen, and a few in the transitional stage of catagen.

Human hairs are of a different quality in the scalp, brows, lashes, and pubic area. And our hair is of three basic types. Lanugo is the fuzz that coats a fetus, and may cling to the newborn. Vellus is the fine and light hair on most of the body, seen on the arms and faces of children. Terminal hair, the third type, is on the scalp and forms the eyebrows and lashes.

In Ambras syndrome, vellus hair streams down the face and curls from the ears, flowing down the shoulders. Facial features are coarse, the nose long, and the face triangular. Teeth may be absent, fingers and nipples extra.

THE BIGGER PICTURE – WHEN IS A MUTATION A MUTATION?
Since the official naming of Ambras syndrome in 1993, several studies have implicated a site on the short arm of chromosome 8, where individuals had inverted or deleted genetic material.

The responsible gene, Trps1, is a zinc finger transcription factor that regulates a suite of genes involved in hair and bone development. One of the genes it regulates is Sox9, which in turn regulates stem and progenitor cells in the bulge region of the developing hair follicle.

In a 2004 paper, Dr. Christiano and colleagues described a “position effect” behind Ambras syndrome. That is, DNA elsewhere can alter the expression of Trps1, and that of the genes it controls.  Their 2012 paper unravels the genetic controls behind the position effect.

Whole genome SNP arrays on a father and son with Ambras syndrome revealed a 1½-million-base-long duplicated stretch of DNA between Sox9 on chromosome 17 and the chromosome tip, like a repeated paragraph near the end of a book. And so the position effect is on one of the genes that Trps1 regulates.

The idea of a position effect isn’t new – I remember it from my Drosophila days in the 70s; fly eyes had patches of different colors because a gene had been moved to a different chromosomal address. Position effects could cause problems with the interpretation of sequenced genomes.

The key word is sequence, because the classic Ambras cases with inverted chromosome 8s and the variegated fly eyes indicate that a gene’s neighborhood affects what it does. Copy numbers also affect gene expression – like the big duplication in the Ambras father and son who have normal Trps1 genes. Genome sequencing technology is beginning to include copy number variant analysis, but detecting rearrangement breakpoints – such as inversions and translocations — is still a challenge, and in fact recently complicated the sequencing of fetal genomes.

The Ambras position effect reminds me of another recent paper that found the opposite: “Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing.”

As part of the 1000 Genomes Consortium, researchers checked the genomes of 179 people against mutation databases. And it turns out that even healthy folk have lots of mutations. Apparently redundancies built into our genomes can protect us.

Here’s the deal:

a. You can have a mutation (a disease-causing genotype), yet not be sick.

b. You can be sick, yet not have the associated disease-causing genotype.

c. You can be sick and have a causative mutation.

d. All of the above, for many different genes

So just as people are starting to get their genomes sequenced as prices tumble, uncertainty, albeit based on long-known concepts of genetics,  blooms. And unfortunately people taking direct-to-consumer genetic tests, or even some health care professionals who are asked to interpret test results, may not be all that familiar with the fact that DNA science doesn’t always yield clear answers.

Will a consumer using testing websites learn enough about the subtleties of genetics to realize that a test result is not a crystal ball? Will the increasing delivery of genetic counseling services via videos or the phone suffice to convey the inherent uncertainty?

Like any pioneers, the first few thousand people to have their genomes sequenced will get a lot of this gray-area information. But the only way we’re going to learn what all of our gene variants mean is to decipher all possible gene interactions, and all possible perturbations, including sequences, copy number variants, and rearrangements. And that will require many more genome sequences.

If genetic analysis is not clear cut for a phenotype and inheritance pattern as obvious as those of Ambras syndrome, how will we understand the many common conditions that reflect the inputs of many genes, interacting in ways we may not yet even understand?

As in all things scientific, and despite the evolution of genetics into a medical science, the more we learn, the more we realize we do not yet know.

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Gene Therapy for Canavan Disease: Max’s Story

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Max Randell had his first gene therapy for Canavan disease shortly before his first birthday. His mother Ilyce holds him. (Photo: Mike Randell)

I’m thrilled about the encouraging gene therapy results just published in Science Translational Medicine from Paola Leone, PhD and Jude Samulski, PhD, colleagues. “Long-term follow-up after gene therapy for Canavan Disease” updates a project that has its origins in the mid 1990s. Canavan disease is a brain disorder present from birth.

I’ve been following some of the kids who’ve had the gene therapy. One patient in particular – Max Randell – has been in my  human genetics textbook since age three, his progress updated with each edition.

Max has had two gene therapies. For the first, when he was 11 months old, liposomes carried the healing genes into his brain. For the second gene therapy, as part of the clinical trial reported this week, viruses delivered the genes, through catheters snaked into six tiny burr holes in his skull.

Max celebrated his 15th birthday on October 13, 2012. His best friend is his brother Alex, a future neuroscientist.

Without gene therapy, Max might not have lived past age 8 – but I recently attended his 15th birthday party fundraiser, where I sat next to Dr. Leone. She’s an associate professor of cell biology at the University of Medicine and Dentistry of New Jersey, and is widely recognized as an international leader in Canavan disease translational research. But to the Canavan families who adore her, she’s Auntie Paola.

I saw her in action at Max’s birthday party. The diminutive neuroscientist knelt beside a little girl in a wheelchair, took her hand, and began to nay and whinny, shaking her silky hair against the girl’s cheek. The child’s face exploded with joy at the researcher who had remembered her favorite animal. Dr. Leone moved around the table to another child, and became a chicken.

Max’s little brother Alex, a fifth grader, told me that night that he plans to become a neuroscientist, just like Dr. Leone, so he can help Max and others. “How I feel about Max is beyond words. He is my hero.”

BODY IMPAIRED, MIND INTACT

Fewer than 1,000 people in the US are known to have Canavan disease. Due to deficiency of an enzyme (aspartoacylase, or ASPA), the cells that make myelin, the white insulation on brain neurons, can’t process certain precursors. As a result, N-acetyl aspartic acid (NAA) builds up in the brain, which turns the white matter into a spongy mass of fluid-filled bubbles. Gene therapy provides the ASPA gene that enables brain neurons to secrete the enzyme, allowing production of some myelin.

Babies with Canavan disease are limp and listless from day one, given not even the few months or years of nervous system normalcy of a child with Tay-Sachs disease or adrenoleukodystrophy. Most never speak, walk, or even turn over. Yet their facial expressions and responses indicate an uncanny awareness. A child laughs when his dad makes a fart-like noise; a little girl moves her fingers as if they are on a keyboard when a friend plays piano. They’re smart kids.

Like other genetic diseases, Canavan was once considered uniformly lethal in childhood because doctors didn’t recognize patients with milder cases. But patients can live into adulthood. Some have milder mutations; others with devastating mutations can outlive the odds thanks to excellent supportive care.

A COLORFUL HISTORY
The small Canavan disease community has experienced more than its share of drama.
• The initial case description, in 1931, came from Myrtelle Canavan, a Harvard physician never granted full faculty status because of her two X chromosomes.
• The disease came to the Jewish community in the US from the Vilna ghetto in Lithuania in 1943. After the Nazis massacred 60,000 people, 250 or so survivors escaped to the forest,  and of the handful of refugees who made it here, two were carriers of Canavan disease.
• The first two children to receive gene therapy – both now in their late teens – did so in New Zealand in 1996, where the initial principle investigator (Matt During, MD) has citizenship. He was accused in the pages of Science of trying to skirt FDA regulations.
• In the classic case “Greenberg et al. v. Miami Children’s Hospital Researcher Institute,” filed in 2000, the discoverer of the Canavan gene patented it, and as a result parents who’d donated their children’s brains to help his research faced fees for diagnostic tests for their other children. (The case was settled, which is why “gene patent” is today synonymous with “BRCA” and not Canavan.)
• In 1998, 14 children, including Max, received gene therapy at Yale University. Some of the kids did well, recovering vision and becoming more mobile, but they all needed a second gene therapy. In 1999, after Dr. Leone had begun collaborating with Dr. Samulski, who directs the University of North Carolina’s Gene Therapy Center, to develop a viral vector to replace the less efficient liposomes, 18-year-old Jesse Gelsinger died following gene therapy for a different disease, using adenovirus. As gene therapy trials stalled, the Canavan kids backslid.

RESULTS!

Paola Leone, PhD, aka Auntie Paola

The clinical trial using adeno-associated virus subtype 2 (AAV2) began in 2001 at the Cell & Gene Therapy Center, University of Medicine & Dentistry of New Jersey, and treated 13 patients by 2005. “As the trial continued, the FDA let us go to younger and younger patients. We were successful in being able to treat a 3-month-old infant who was diagnosed in utero. That child is alive today and is the youngest person who has ever been treated with gene therapy,” Dr. Samulski said. The study compared the children who received the gene therapy for Canavan disease to 15 untreated patients. Max had his second gene therapy there.

Now, several years later, it’s clear that the viruses are safe. And the gene therapy appears to be working. For most of the children, brain levels of NAA have decreased, brain atrophy slowed, mobility and head control improved, and alertness increased. The younger the child when treated, the greater the slowing of the disease – something seen in gene therapies for other conditions too. For optimal effect, gene therapy will have to be tied in to newborn screening to find patients as young as possible.

Gene therapy for Canavan disease using AAV2 was delivered through 6 burr holes. Experiments in mice indicate that intravenous delivery with a different vector may be possible. (Credit: Paola Leone)

The research team is very careful to counter possible hype in the news release announcing the paper: “Today, all of the patients are alive and their quality of life has improved.” Gene therapy for the disease “can be” safe and effective, and “may offer the best opportunity” to reduce symptoms and stabilize neurological function. And efficacy is also a matter of perspective. As the parents of the very first child to receive the gene therapy point out in a video Dr. Leone has made, others may see no change, but they know gene therapy has helped their daughter. I remember speaking with them on Lindsay’s 16th birthday, when she was able to eat cake without a feeding tube.

I’d like to add a different sort of improvement I was privileged to be a part of, a response that is perhaps too emotional to capture on a brain scan or mobility rating scale. It happened when Max’s mom Ilyce read him the part of my gene therapy book describing a scene at his 13th birthday party fundraiser. I’d watched Max watching the other kids running around, and wondered what he was thinking. (The excerpt is on my website. Four of the book’s 20 chapters are on Canavan disease.)

Here’s part of Ilyce’s email:

“Hi Ricki,

I have to tell you how moved I was with your description of Maxie, and how meeting him helped change your view of some of these brain diseases. We have always felt that Max’s life and battle would help give hope to people. That is one of the reasons we started our foundation. When I read the part where you spoke about the fundraiser, I started crying so hard that Mike came to see what was wrong with me. Then after I tried to regain my composure I read it aloud to Mike, Max and Alex.

I sat on the couch where Max was laying down. I was sitting by his upper body, it was hard to read again and I was still crying, but Max managed to reach out his little hand and grab my arm. He does this pretty often when he wants to touch me, or get my attention. But this was different, he was comforting me. This time he looked me directly in the eyes, with a really serious look, I swear he was letting me know that he’s okay with his life, that he is happy. He was agreeing with your assessment of that night. I hope that people can see the happiness and love that children like Maxie bring to the world.” Ilyce

Reading that, I suddenly no longer cared that the New York Times had ignored my book. Max’s response was the best review any author could hope for – not to mention a validation of gene therapy.

For further information and to donate, see Canavan Research Illinois, Jacob’s Cure, and the Canavan Research Foundation. All three support Dr. Leone’s research, or donate directly to her research program.

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When An Arm is Really a Leg

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The hands of a person with Liebenberg syndrome resemble feet; the arms resemble legs. (Credit: Dr. Malte Spielmann)

Flipping the X-ray showed Stefan Mundlos, MD, that his hunch was right – the patient’s arms were peculiar and stiff because the elbows were actually knees.

The recent report from Dr. Mundlos’ group at the Max Planck Institute for Molecular Genetics, complete with a genetic explanation for the condition, flew under the radar of  the press-release-driven science news aggregators. But I noticed it because I worked on this sort of thing in grad school – flies with legs growing out of their heads.

LITTLE-KNOWN LIEBENBERG SYNDROME
An ungoogleable researcher named F. Liebenberg described in 1973 a family with the condition that would take his name: “A pedigree with unusual anomalies of the elbows, wrists and hands in 5 generations.” In the white South African family, four males and six females had stiff elbows and wrists, and short fingers held in a way that made them look strangely out of place. The pedigree revealed classic autosomal dominant inheritance – each child of a weird-limbed person had a 50:50 shot at being so too.

A second family appeared in the pages of the Journal of Medical Genetics in 2000. Those researchers noted that when a patient stood in the “anatomical position” – palms forward – he or she couldn’t bend the arms at the elbow, and the restricted movement had been present since birth.

In X-rays of patients, the elbow joints looked too big. Those of a 6-month-old were the size of elbows of a 3½-year-old, with stubby fingers. Similarly, a 2½-year -old’s elbow was the size of an 8-year-old’s. And like an episode of Law and Order in which a suspect showing up in the first 15 minutes can’t possibly be the perp, those researchers implicated a gene on chromosome 17. That wasn’t it.

Then in 2010 a report appeared on identical twin girls with the curious stiff elbows and long arms of Liebenberg syndrome, in Plastic and Reconstructive Surgery. These researchers noted that the lengths and shapes of the fingers and toes were the same.

IF IT LOOKS LIKE A DUCK …
Noting that the muscles and tendons of the elbows, as well as the bones, weren’t quite right, Dr. Mundlos and colleagues, experts in the distinctions between vertebrate forelimbs and hindlimbs, realized that the stiff elbows were acting like knees.

The human elbow joint is a hinge in one plane and rotates the forearm in another. The knee is a bit tighter. It extends the lower leg but the kneecap stabilizes the lateral rotation, which is why I constantly injure it in zumba class.

The Max Planck researchers analyzed three unrelated families with Liebenberg syndrome. “The phenotype wasn’t easy to interpret at first glance. It looked like a malformation of the elbow joint and an abnormality of the wrist bones. But wrist bone abnormalities aren’t unusual, in particular fusion of bones,” Dr. Mundlos explained.

But the Liebenberg elbows had a peculiar enlargement, and that was a major clue.

The areas in the white dots are patella — knee — that are parts of the elbow joint. (Credit: Malte Spielmann)

“Normally the elbow joint consists of the humerus, which sits in a socket of an elongation of the elbow, the olecranon, with the radius forming a smaller part of this complex joint. In the patients the olecranon was missing and the joint had a flat appearance, unlike the normal hinge joint of the elbow,” Dr. Mundlos said.

It was when Dr. Mundlos examined a patient’s X-ray from a different perspective that the truth popped out. “I realized that the entire limb had the appearance of a leg. Normally you would look at the upper limb X-ray with the hand up whereas the lower limb is looked at foot down. If you turn the X-ray around, it looks just like a leg,” he recalled.

To anyone familiar with developmental biology, a body part in the wrong place evokes one word: HOMEOTIC. (Warning: spellcheck and autofill convert this to homoerotic.)

HOMEOTIC MUTATIONS: A DETOUR IN DEVELOPMENT (AND IN MY CAREER)
A homeotic mutation mixes up body parts, so that a fly grows a leg on its head or antennae on its mouth. Assignment of body parts begins in the early embryo, when cells look alike but are already fated to become what they will become, thanks to gradients of “morphogen” proteins that program a particular region to elaborate particular structures. Mix up the messages, and a leg becomes an antenna, or an elbow a knee.

Just months after I got my PhD in Thom Kaufman’s lab at Indiana University circa 1980, where I savagely murdered millions of fruit flies, post-doc Matt Scott and fellow grad student Amy Weiner discovered how homeotics happen. They identified the homeobox. This 180-base-sequence encodes a protein domain that binds other proteins that turn on sets of other genes – crafting an embryo, section by section. Researchers at the University of Basel found the homeobox at about the same time. (For a fly’s eye view of life with homeosis see The Making of a Mutant, A Fruit Fly Love Story, which I will re-post here for Valentine’s Day.)

Once developmental biologists knew what to look for, homeoboxes turned up in all manner of genomes, affecting the positions of petals, legs, and larval segments. Humans have four clusters of homeotic genes, plus controls.

Homeotic genes line up on their chromosomes in the precise order in which they’re deployed in development, like chapters in an instruction manual to build a body. And they’re ancient. A fruit fly given a mutant homeotic gene from a chicken sports an antennal leg, one species reading the DNA sequence of a very distant other. The homeotic mutants from the Kaufman lab even starred in an episode of The X-Files, about which I recall little except that it featured a Cher impersonator.

In an Antennapedia fly, the antennae develop as legs. (Credit: Rudi Turner)

I left bench science because I’d thought homeotic mutations were a quirk of only fruit flies, mice, and mosquitoes. But after the homeobox discovery, researchers quickly found them in people. In lymphomas, white blood cells detour onto the wrong lineage, and in DiGeorge syndrome, the abnormal ears, nose, mouth, and throat echo the abnormalities in Antennapedia, the legs-on-the-head fly in the photo. Extra and fused fingers and various bony alterations also stem from homeotic mutations.

But nothing could quite match, in a human anomaly, the dramatically mutant fruit flies — until I saw photos of children’s faces with lower jaws turned into upper jaws, in the May 2012 issue of the American Journal of Human Genetics). (See Scientific American blogs for that story.)

The partial arm-to-leg transformation in people, once you know what it is, is even more astonishing.

FINDING THE ARM-TO-LEG MUTATION, USING TOOLS OLD AND NEW

The homeotic hypothesis explained a lot about Liebenberg syndrome.

This wrist is more like an ankle. (Credit: Malte Spielmann)

“The transformation affects the bones, tendons and muscles of the elbows, wrists and hands. The olecranon of the elbow is completely missing in the patients and the bones of the wrist form a large structure similar to the bones of the ankle. In the 3D CT scans of the elbow you can see a structure similar to the patella of the knee that is fused to the head of the humerus. The bones of the hands are too long and look similar to bones of the feet,” explained Malte Spielmann, MD, lead author of the paper.

Although the researchers ultimately used techniques we are accustomed to these days – genome sequencing, and comparative genomic hybridization (CGH) to detect deletions and copy number variants – their search began as many genetic searches have since the 1950s: with abnormal chromosomes.

Two of the three Liebenberg syndrome families have deletions (missing DNA), and the third has a translocation (two chromosomes exchanging parts). The families share a glitch in the same general region of chromosome 5, providing a toehold in the genome.

Genome sequencing didn’t turn up any likely suspects in the translocation family, but CGH found a 134 kilobase deletion in their genomes. Apparently 134,000 DNA bases were lost when the translocation initially happened, like lopping off letters when cutting-and-pasting text.

The missing DNA in all three families corresponded to the same “gene desert,” a genome region festooned with so-called “dark matter” that doesn’t encode protein. But one candidate DNA sequence did emerge from the regulatory wasteland: a gene called PITX1.

The gene doesn’t encode protein but controls other genes that do. And not only is the gene “highly conserved” – in many species and therefore pretty important – but it controls limb development in mouse embryos.

The researchers had found their gene.

In the Liebenberg families, missing genetic material places an enhancer gene near PITX1, altering its expression in a way that mixes up developmental signals. And so the forming arm gets mixed up, and fashions part of a leg — at first glance barely noticeable, as in this doll. Fortunately the condition appears more an annoying oddity than a disease, and because the gangly arms don’t seem to disrupt everyday life too much, you won’t find Liebenberg syndrome in the rare disease databases like CheckOrphanNORD, or the global genes project.

LARGER LESSONS
I like the arm-to-leg story so much that I hardly know where to begin.

#1 I feel better at having spent four years trying to figure out how flies grew legs on their heads, yet worse for having left the field.

#2 I marvel anew at the elegant evolutionary tale that the homeotic mutations tell. When mutation derails development so similarly in such different species as a plant and a person, descent from a common ancestor is the most logical explanation.

#3 Looking at an image from an unusual perspective revealed what no one else had seen. With all the fuss over genome sequencing and nano-everything, we shouldn’t lose sight of the power of larger-scale observation in science.

#4 The homeotic mutations steer development to an alternate pathway. They symbolize, for me, my veering from the path to becoming a scientist shortly after getting my doctorate.

The late paleontologist and science writer Stephen Jay Gould helped me. In his essay “Hopeful Monsters” published in the October 1980 issue of Natural History magazine, reprinted in his 1983 book “Hen’s Teeth and Horse’s Toes,” he wrote about the work in the Kaufman lab, mentioning us lowly graduate students – Barbara Wakimoto, Tulle Hazelrigg, and me.

Thrilled, I wrote to him. And he wrote back, five hand-scrawled pages, encouraging me to follow my instincts to become a writer at a time when many were telling me not to stray from science.

Two decades later, I was to thank him again, unfortunately in an obituary. And now, a decade later, I do so yet again. Thank you, Steve, for telling an unsure graduate student that it’s okay to follow an unusual path.

And congrats to Drs. Mundlos and Spielmann and their co-workers for their insightful discovery.

 

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XYY Men

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This karyotype includes one X and one Y chromosome –  normal. A man with XYY “syndrome” has an extra Y, but the only effect this may have is to be tall. (Figure credit: Darryl Leja, NHGRI)

by Jack El-Hai

This week’s New England Journal of Medicine has four articles about the new precision in reproductive genetic testing. (See www.medscape.com/viewarticle/775687) Yet as genetic information increases, so too does the risk of genetic determinism – defining ourselves by our genes. But this is hardly a new idea. This week’s guest blog recalls a classic example of genetic judgment – the case of the man with an extra Y chromosome.

Jack El-Hai is the author of The Lobotomist: A Maverick Medical Genius and His Tragic Quest to Rid the World of Mental Illness and the forthcoming book The Nazi and the Psychiatrist. He often writes on the history of medicine and science.

A battered paperback entitled The XYY Man, by Kenneth Royce, leans in a corner of my bookshelf. It’s a spy novel that chronicles the adventures of “Spider” Scott, an ex-felon who wants to become law-abiding, but finds that he is genetically predisposed to criminality because he has an extra chromosome. Unlike most men whose XY sex karyotype imparts their maleness, Scott has been endowed with an XYY karyotype by his novelist creator.

This condition is not fanciful. XYY syndrome first appeared in the medical literature in 1962, eight years before Royce published his book. A team of researchers from Roswell Park Medical Institute in Buffalo, N.Y., described the first XYY person on record, a 44-year-old man who had undergone genetic testing because one of his children had Down syndrome. Though never before reported, this extra-chromosome condition produced during early cell division has turned out to be not tremendously rare, affecting about 1 in 1,000 boys. In most men who have it, the 47th chromosome causes no problems whatsoever, and more than 95 percent of XYY guys don’t realize they are specially endowed.

For decades, however, geneticists argued over the reputed social hazards of XYY syndrome. Did the extra chromosome make its bearers “supermales,” men who behaved as if they were amped up on too much testosterone? Some believed that XYY men, like “Spider” Scott, were inherently violent and prone to committing criminal acts. The dispute captured the public’s imagination, spawning several sequels to Royce’s novel along with numerous movies and TV shows (such as Law and Order) featuring dangerous and socially conflicted XYY characters.

During the late 1960s, geneticists, sociologists, and others began looking at prison populations to see if XYY men were disproportionately represented. (Note: Patricia Jacobs was lead author on the most famous paper about XYY, “Aggressive behavior, mental sub-normality and the XYY male,” and for this reason XYY is also called Jacobs syndrome.) Many people asserted that not only did XYY men commonly have violent criminal tendencies — the biochemist Mary Telfer characterized them as “perhaps too highly sexually motivated” — but that such males could be diagnosed by physical and mental traits, which included tall stature, long limbs, facial acne, mild mental retardation, and aggressive behavior.

In 1970 geneticist H. Bentley Glass advocated the relaxation of abortion laws to allow women to end pregnancies if the fetus was XYY. Speculation even ran that Richard Speck, the infamous murderer of eight student nurses in Chicago in 1966, owed his propensity to violence to an extra Y chromosome. That proved untrue. In one notorious case of the mid-1970s, a British court wrongfully convicted Stefan Kiszko of the murder of an 11-year-old girl largely because of his XYY karyotype, and it took more than 15 years for him to win release from prison. For further historical takes on the misunderstood extra chromosome see Y Envy.

In recent years, geneticists have learned more about the actual effects of the XYY condition. XYY boys may be delayed in maturation, are taller on average and more physically active, and sometimes display learning and behavioral problems. Their intelligence, testosterone levels, aggressiveness, sexual development, and fertility typically fall within the normal range. They grow into men who are unrecognizable to the general public.

In the mid-1970s, a Danish study showed that XYY men were not more likely to commit violent crimes, although they did have more convictions for other crimes. A long-running follow-up study published this year confirmed those findings and attributed the higher conviction rate for such crimes as sexual abuse, arson, and burglary to “unfavorable living conditions” — poverty, joblessness, and other disadvantages resulting from a lack of childhood support that many XYY men experience. (See Ricki’s take on a 2012 twin study on XYY.)

Slowly, as the suppositions of the 1960s give way to current research, the public is changing its thinking on XYY syndrome. Few people today believe that an extra Y chromosome condemns its owner to a life of violent crime. Genetic counselors explain the condition to families and teach ways to nurture XYY boys. Men like the fictional “Spider” Scott can exercise their free will without fear that a sex chromosome has turned them bad.

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Cialis Comes Full Circle — Help for Muscular Dystrophy

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One symptom of Becker muscular dystrophy is fatigue and injury of exercising muscles, such as in gripping a weight.

Becker muscular dystrophy is a muscle wasting disease that is rarer and less severe than the more familiar Duchenne muscular dystrophy. Both conditions are basically untreatable. But according to a study published today in Science Translational Medicine, Cialis may alleviate the associated muscle fatigue and damage.

Yes, Cialis. The erectile dysfunction drug.

To anyone who’s followed the Viagra story, use of its cousin Cialis to treat muscle disease is not so much repurposing as it is a logical extension, based on regulating blood flow.

Viagra, developed in 1989, began its ascent three years later, when participants in a clinical trial to treat angina, which is chest pain due to blocked blood flow, reported strikingly improved erections. Taking a pill to treat what was about to evolve from “impotence” to “erectile dysfunction” trumped penile implants and injections, or older approaches of ingesting camel hump fat, jackal bile, or various herbs. Pfizer introduced Viagra to the world in 1998.

BOOSTING BLOOD FLOW – IN PENISES, LUNGS, AND FOREARMS
The biochemistry is actually fairly complicated. Here’s a short version (skip to next section if you like.)

In order for blood to fill out a vessel, nitric oxide, a simple gas, relaxes the smooth muscle in the vessel wall by binding cGMP (cyclic guanosine 3’5’-monophosphate). Drugs like Viagra and Cialis inhibit the enzyme (phosphodiesterase 5) that breaks down cGMP. So with more available cGMP, the vessel widens, providing more oxygen to the surrounding muscle.

Different phosphodiesterases work in different body parts. Blocking the enzyme in a penis sustains an erection; in the lungs, it counters high blood pressure. And now a team led by Ronald Victor, MD, at Cedars-Sinai Medical Center, has successfully tested Cialis on men with Becker muscular dystrophy. Their work adds an important new piece to the picture of the biochemistry behind control of blood flow.

Maintaining supplies of NO requires another enzyme, appropriately-named nitric oxide synthase (NOS). It must nestle into the smooth muscle cell’s outer membrane (sarcolemma) to produce the needed NO, and another protein, dystrophin, does this. Dystrophin is what is missing, abnormal, or misplaced in Duchenne and Becker muscular dystrophies. Without its escort, what little NOS remains ends up in the cytosol, the liquidy insides of the smooth muscle cell, rather than in the sarcolemma, where it must be tethered to function.

Cialis keeps cGMP around longer, giving what little NO is produced more of a chance to work. And it does.

THE NEW STUDY
Cialis improved muscle function in mdx mice, which have the same dystrophin mutations as people. “From the mouse paper we thought the drug could be a blockbuster in humans” for muscular dystrophy, Dr. Victor told me.

The new study was straightforward. First, the researchers compared blood flow to the forearm at rest in 10 BMD patients and 7 healthy controls – it was the same.

Next the men performed a handgrip exercise while the lower halves of their bodies were in a chamber that had negative pressure, a common test to simulate cardiovascular stress. Normally the body maintains blood pressure by countering the ballooning of blood vessels in the legs with constriction elsewhere, but it tempers the constriction so that other body parts still get blood. The healthy men did this. But in the men with BMD, the blood vessels in the exercised forearm stayed narrowed, impairing blood flow. This is why the disease causes muscle damage and fatigue with exercise.

In a second experiment, each man with BMD took one Cialis (aka tadalafil) or placebo pill, had blood flow to the exercised forearm assessed, waited 2 weeks, then took the opposite pill.

“The tadalafil effect was both marked and immediate, occurring with a single dose,” the researchers write, in 8 of the 10 men, with no effect of placebo. The other two men had unusual mutations that might indicate their disease was too mild to show a response. Dr. Victor hopes that an ongoing multicenter prospective trial will support the findings of success.

He’s understandably ecstatic; he’s worked on this problem for two decades. “So little research has been done on Becker because it’s so rare. I hope we’ll provide the evidence to make this another indication for the drug. We finally have some hope for a therapeutic benefit for people with muscular dystrophy, and it’s really exciting.”

Dr. Victor is, however, concerned that patients with muscle disorders will seek the drugs before the larger trial can validate the findings. Yet at the same time, he and his co-workers envision additional new markets, pointing to the work of Ronald Cohn, MD, at Johns Hopkins University. His team’s work suggests that the drugs may be useful in boosting blood flow in neuropathies such as amyotrophic lateral sclerosis and spinal muscular atrophy, in the low-muscle-tone hypotonias, and in a host of myopathies (metabolic, mitochondrial, congenital, inflammatory, steroid-induced and critical illness associated).

Ground squirrels maintain muscle tone while hibernating — their physiology may hold clues to muscle-wasting diseases. (Photo: Dr. Wendy Josephs)

The research may actually veer back to non-human animals, thanks to Dr. Cohn’s discovery that hibernating ground squirrels maintain blood flow to muscles in a way that other mammals can’t. “Squirrels can still target NOS. There must be some important secrets there,” Dr. Victor said.

NOT A PERFORMANCE-ENHANCER
Since many people have muscle conditions and many men take Cialis or Viagra, I wondered whether anyone had inadvertently discovered that their ED pills relieved their tired muscles. A guest blog, “Viagra for muscular dystrophy and publicity for accidental insight” indeed tells such a tale.

In 2005, a 57-year-old man with limb-girdle muscular dystrophy asked his doctor, Jeoffry B. Gordon, MD, MPH of San Diego, for Viagra for the usual reason. The patient reported back that in addition to an improved sex life, his muscles felt stronger. He happily did standing push-ups and chair and balance exercises to test his new abilities, which waxed and waned with the taking of the blue pills.

I tried to find Dr. Gordon but got caught up in the morass of doc websites that never actually provide any info. His blog laments the medical journals, media outlets, organizations, and even Pfizer itself, that ignored his report of a beneficial effect of Viagra on muscle strength, seven years ago.

The lack of interest in Dr. Gordon’s anecdotal blog, low on the totem pole of medical publishing, bodes well for my concern that when the news breaks (if it does, one can never tell) about Cialis and Becker muscular dystrophy, men (and maybe some women) will go the Lance Armstrong route and try to use the pills to boost athletic performance.

But it probably won’t work.

“The drug doesn’t enhance performance, it doesn’t make people supernormal. These drugs seem to work under stressful conditions, such as exercise of diseased muscles,” Dr. Victor cautions. This is one reason why he was so careful about doing a double-blinded, placebo-controlled experiment.

THE BIGGER PICTURE
I think repurposed drugs are the greatest thing since Spanx. I recently blogged here about the repurposing of a shelved childhood brain tumor drug finding new use to treat the ultra-rare rapid-aging disease progeria, and perhaps run-of-the-mill atherosclerosis. I love that ED drugs may help people with muscle diseases.

My interest in repurposing drugs is a bit of a turnaround, because for the past few years I’ve been immersed in writing my book, “The Forever Fix: Gene Therapy and the Boy Who Saved It” (shameless holiday-time book plug, paperback due out 1/8). Gene therapy is about as opposite repurposing drugs as one can get.

Hannah Sames has giant axonal neuropathy, a very rare disease that is similar to ALS. Here she is with her mom, Lori. (photo: Dr. Wendy Josephs)

The book’s title comes from Lori Sames, whose little girl Hannah has giant axonal neuropathy. And even though Hannah’s Hope Fund is trying desperately to raise funds for a phase 1 clinical trial of gene therapy, reports on the first approved gene therapy – in Europe, for Glybera, on November 2 – are sobering.

Glybera is a gene therapy to treat lipoprotein lipase deficiency, which causes pancreatitis. The cost is staggering: about $2 million per patient. Even if it is a “forever fix,” who can afford it?

So I think a bioinformatics approach makes more sense. Wed the information pouring out of human genome sequencing to the stockpiles of drugs, those on the market and those warehoused awaiting homes. Using what we’ve already got makes more sense in treating patients now – particularly those with rare diseases who lie under the radar of new drug discovery.

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JIM: More Compelling Than GATTACA

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“Jim” is a terrific glimpse of a frightening future from Jeremy Morris-Burke, a self-taught filmmaker.

For 15 years, the film GATTACA has been synonymous with “genetic dystopian future,” and has become a mainstay of genetics classrooms. But I’ve found a better film. It’s called, simply, Jim.

I never could quite connect with GATTACA, the dark tale of an assumed genetic identity in a society where the quality of one’s genome dictates everything. Perhaps it was because 1997 was the pre-genome era, when the idea of ordering a DNA test over the Internet was still science fiction. But ironically GATTACA’s “not-too-distant” future, in which a genetically inferior “invalid” impersonates a “valid” to achieve a dream, sets up a too-obvious conflict, with the details and resolution contrived. I know this from years of reading fiction and watching soap operas.

Although Jim, released in late 2010, shares with GATTACA the premise of widespread genetic enhancement, it’s much more subtle and nuanced. The film struck me with its stunning possibility, and the intentional gaps in the glimpse of future history still have me thinking a week later.

My daughter and I discovered Jim on Netflix. We’d just suffered through an endless two hours waiting for the world to end in Melancholia, when Sarah found it.

Clones! Genetic enhancement! Apocalypse! This movie was made for you!”

She clicked Play but then frowned. “But now I have to listen to you scream at all the scientific errors!”

The movie started, and we both went back to our laptops, half listening, glancing up occasionally.

A little while later, Sarah looked at me, puzzled. “Why aren’t you yelling? There should’ve been mistakes by now.”

But I had already put my laptop aside, stunned.

“There aren’t any.”

“Not even a genetic code error?” My daughter knows me well.

“Nope.”

And for the next two hours, we were both completely sucked in.

Jim seeks reproductive help from biotech firm Lorigen.

WORLD 1: NOW
“Jim” juxtaposes the worlds of now and the future. The film opens with a being from a ruined future saying he’d been born many years after his parents died. And then we’re thrown back to the contemporary, familiar world of Jim (played by Dan Illian) and Susan (Vanessa Morris-Burke) Kotofsky, a thirty-something, financially-strapped couple contemplating parenthood, and presumably the future being’s parents.

Susan discovers a lump in her breast. After she dies from an experimental cancer treatment, Jim faces mounting medical bills, unemployment and the indignity of looking for work, and escalating isolation and despair. Fortunately (or not) Susan had her eggs frozen, and Jim sees a glimmer of hope in using them to have a child – with his sperm and the help of biotech company Lorigen.

I sat forward, alert for technical errors in the slick biotech sequences, but heard nary a one. I cheered when the white-coated, female biotech exec repeatedly said “genetic sequence” and not the perpetually misused “individual genetic codes.” (Hello, Jurassic Park.)

(The genetic code is, historically, the correspondence between DNA/RNA triplet and amino acid, deciphered in the 1960s, earning a Nobel. Today it’s used like “computer code,” which leads to semantic errors because the code, the correspondence, is universal – if it weren’t so, we wouldn’t have much of biotechnology. I admit I am a pain in the ass about this. But it comes from writing textbooks.)

Lorigen, which screens, filters, and modifies clients’ genes, offers Jim 3 options for genetically enhancing his child-to-be, from “self-starter” to “sure-thing” to ”executive privilege.” All carry the “legacy guarantee” that promises a 236-year lifespan, with an 88% chance that 230 of those years will be productive and healthy, with a quick and painless end. Jim can also purchase the “genetic sequencing enhancement” that offers perfect symmetry, resistance to bacteria and viruses, enhanced height, and a self-regulating metabolism.

In a distant future, Niskaa, descended from Jim and Susan, looks worriedly at a computer projection of a neural net cube. Does it explain why the clones have gone downhill over time?

WORLD 2: JIM AND SUSAN’S DESCENDANTS
On a future post-human, super-industrialized Earth, Niskaa (Michael Strelow), whom we met at the start, leads a race of worker clones that have clearly seen better days.

In this dead and devastated world, only a few naturally-born humans remain, the vast majority having long since left in an exodus to Mars. Over time, the clones have gone downhill, the consequence, I suspect, of accumulating nasty somatic mutations.

But one maintenance clone has mutated in a positive way. The androgynous # 3774 (Abigail Savage), like Data the loveable android from Star Trek: Next Generation, struggles with feelings and thoughts.

“I wish I was like the other clones. The world I saw in my dreams was so different. How did things get this way?” He/she too is a descendant of Jim and Susan’s augmented genetic material, and somehow sees Jim in dreams.

The film leaves key unanswered questions, from the practical – Under what circumstances did Jim and Susan’s child come into existence? How did Niskaa and the clones populate the Earth? – to the philosophical – What does it mean to be human?

Jeremy Morris-Burke, filmmaker and unofficial geneticist

FROM THE FILMMAKER
As the movie ended, I jotted down the name of its creator – self-taught filmmaker Jeremy Morris-Burke, whose wife Vanessa plays doomed Earth mother Susan. His Director’s Statement describes how he wrote, directed, shot and edited the film, an effort “about as DIY as it gets.” He has an MFA from NYU. Intrigued by his command of the science, I found him on LinkedIn, and picked his brain.

RL: How did you get the idea for “Jim”?

JMB: I was originally interested in a story for the stage about a typical Midwest guy getting pummeled by the pressures of life and society. I kept imagining him having a breakdown in his kitchen. One day a girl, Susan, shows up in his life and they go on this Bonnie and Clyde crazy spree in retaliation for their bad luck. They want to have a baby, but the law is closing in on them and they decide they’ll have to use some kind of genetic company so they can have the kid even if they’re arrested and kept apart.

The story evolved and became more subtle. An over-simplified explanation of genetics wouldn’t work, because people were beginning to understand so much more about genes as information. That seemed richer than any fiction I could dream up.

I started reading about the potential benefits and drawbacks of genetic modification and became fascinated by the ethical conundrums lurking around every corner. So I tried to rough out a story that included as many of those themes as I could, without getting too weighed down by technical details. I wanted to keep the focus on this man desperately trying to make something of his life before it all slips away, and on the idea of genes as legacy. That seemed a realistic way to make the bad decisions Jim makes seem plausible and sympathetic, while allowing me to bring in all the ideas about gene therapies and even cloning in a way that seemed not just possible, but imminent.

RL: You’re an artist, not a scientist, yet the film gets every detail right. How did you accomplish this?

JMB: The accuracy was borne of trying to make a story where you didn’t get pulled out of the characters’ world by obviously bad science. Also, I have such enormous respect for the people who are breaking new genetic ground and such a fascination with the idea that we can drive our own evolution, for better or worse, that it was very important to me to get it right. I really wanted to learn as much as I could about the advances being made because they’ll impact me as much as anyone.

Most of my research came from books. Francis Fukuyama’s “Our-Posthuman-Future” and the President’s Council on Bioethics were very informative and thought-provoking sources early on. And I especially liked that the council was approaching the issue as a humanist one, rather than religious or economic.

RL: How can people view the film?

JMB: Right now the best place to see the film is online via Amazon, YouTube, and Netflix. I hope to have DVDs by the end of the year.

RL: See it!

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Mice with Human Liverlets Test New Drugs

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Mice with human livers are better models for spotting drug-drug interactions than are mice with only their own livers.

“Scientists at Stanford have produced mice with human brains, pigs with human blood flowing through their veins, and a human born to mice parents and mice with human heads.”

So wrote a student summarizing the “Genetically Modified Organisms” chapter of my human genetics textbook a few years ago. Two of the four comments are true, sort of.

I’ve got a new example for her, also from Stanford: Using Chimeric Mice with Humanized Livers to Predict Human Drug Metabolism and a Drug-Drug Interaction, published in the Journal of Pharmacology and Experimental Therapeutics.

It’s a terrific advance, the making of mice just human enough to provide a new way to test drug toxicities before clinical trials get underway. The researchers tested a drug against hepatitis C. The work is important because mice and humans, despite our genomic similarities, do not metabolize many drugs in the same ways. And that can be costly, even tragic.

Ironically, I‘d read about the chimeric mice right after blogging here about a 1893 paper on the source of chimerism in human mothers, and was all set with the news – and then superstorm Sandy delayed publication of the paper. So now I’m back to the new mice.

MICE ARE NICE, BUT IMPERFECT, MODELS
When a drug fails, it’s often a metabolite – the chemical compound that forms as the drug breaks down – that’s at fault. If a mouse doesn’t make the same metabolites as a human, a drug candidate can test as safe in the rodent, yet poison a person.

“Humanizing” a mouse might make it possible to not only text toxicity of a drug, but also monitor drug-drug interactions, which happen frequently because so many of us take more than one medication. Sometimes drug-drug interactions – DDIs – don’t emerge until a drug is approved and enough people take it, while also taking something else.

Over the past few years, several groups have created mice that have bits of humanity, and used them first to test familiar chemicals, not necessarily drug candidates. But sometimes remaining mouse liver cells obscure the effects of the tested compounds.

I like to trace the trajectories of the “breakthroughs,” and in the mouse-tox story, two papers from early summer 2011 stand out (apologies if I’ve left anything out).

First, Alexander Ploss, PhD, a virologist at Rockefeller University and colleagues, created immunodeficient mice transgenic for two human immune system genes (CD81 and occludin) that enable hepatitis C to infect the rodents, which the viruses don’t naturally do. The mice in the just-published study needed to actually get hepatitis C in order to test the drug.

In a second paper, “Humanized mice with ectopic artificial liver tissues,” Sangeeta Bhatia, MD, PhD, a biomedical engineer at MIT and colleagues fashioned “human ectopic artificial livers” URL (HEALs). These implants consist of half a million human hepatocytes, mouse fibroblasts, and human liver endothelial cells to send the appropriate hormonal signals. It’s all packaged into a 20-millimeter long plastic scaffold, with pores that keep out immune system cells. The mice function for several weeks as if they harbor a human liver.

EVALUATING A REPURPOSED DRUG FOR HEPATITIS C
In the new work, a team from Stanford and Genentech, with collaborators in Turkey, Australia, New Zealand and Japan, transplanted human hepatocytes into the livers of 8-week-old immunodeficient mice, but added an old biotech trick from the 1980s: making the mouse liver cells display a molecule from herpes simplex type 1 viruses.

Exposing the animals – called humanized TK-NOG mice — to a drug that only kills virally-infected cells destroys their livers. “This enables transplanted human liver cells to develop into a ‘human organ’ with a characteristic 3-dimensional architecture and gene expression pattern, which could be stably maintained for a 6-month period,” explains Gary Peltz, MD, PhD, professor of anesthesiology, pain and perioperative medicine at Stanford and senior author.

The test case was clemizole, an antihistamine used widely in the 1950s and 1960s that also blocks hepatitis C replication. “The drug tends to accumulate in the liver, which is not ideal for a general-purpose antihistamine but could be very attractive for a virus like HCV that only infects the liver,” says Jeffrey Glenn, MD, PhD, associate professor of gastroenterology and hepatology, microbiology and immunology at Stanford and hepatitis expert on the team.

Clemizole is even more powerful in the presence of a second drug, the protease inhibitor ritonavir, which slows breakdown of the first, a common type of drug-drug interaction. In addition, a breakdown product of clemizole called M1 makes the drug stick around longer, and adds to the antiviral activity, but mice make only trace and transient amounts of it. The effect is missed in mice that have their own livers.

A slice of liver from a chimeric mouse shows islands of human tissue, indicated by the dashed line. (Courtesy Dr. Gary Peltz)

The researchers infected 8 humanized mice and 8 controls, then gave them both drugs. The more human the livers – from 13-70 percent — the more M1 appeared. And the ritonavir made the clemizole hang around longer. “Although this is only one example, it indicates that it is likely that the use of chimeric mice could improve the quality of pre-clinical drug assessment,” the researchers conclude in their paper.

The new mice provide an alternative to abandoning a promising drug in preclinical testing, or letting an unsafe one proceed to clinical trials or enabling a drug-drug interaction to appear only after the numbers build with marketing.

And I can add a new example to my textbook: mice with human livers.

 

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Direct-to-Consumer Genetic Testing: A New View

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San Francisco — On a Thursday night in October 2007, I sat with hundreds of geneticists at the American Society of Human Genetics annual meeting in San Diego, so stunned that we ignored the free dessert. At a table in front of the crowd were several very nicely-dressed physicians and genetic counselors representing a trio of companies gearing up to offer, in the coming year, direct-to-consumer (DTC) genetic testing.

Yes, ordinary people would be able to send samples of themselves – spit, it would turn out – to companies that would charge fees to return results right to them, circumventing health care professionals. The companies had names much catchier than those of the biotech companies of the past two decades: 23andmeNavigenics Inc., (absorbed into Life Technologies Corp last summer), and deCODE Genetics, part of Icelandic biobank fame.

We were collectively shocked, and in retrospect, I’m not sure why. But the chatter in the hallways and elevators afterwards, according to my unscientific survey and memory, was decidedly negative.

What a difference half a decade makes.

I’m at this year’s annual meeting of the American Society of Human Genetics, where another panel of DTC genetic testing company reps are fielding questions. But this time, the audience is asking about expanding DTC services to more diverse communities.

What’s changed? The DTC companies have proven their value.

After the first DTC testing companies began offering their services in April 2008, the media took notice. It was a great story. For me, the lowpoint of the derision was the New Yorker’s Talk of the Town piece extolling the hilarity of “spit parties.”

The popularity of the testing grew. A cottage industry of sorts arose as bioethicists and social scientists soon began to survey customers and dissect their characteristics, motivations, and use of the information.

For example, median age of the DTC genetic test consumer is the 40s. My interpretation: once people have settled down a bit, moved out of their parent’s homes, gotten jobs, maybe have kids in school but not yet college, they naturally start to think about how they will kick the bucket. And here were companies offering to look into a genetic crystal ball, without even the need to bleed.

Geneticists, much more familiar with human decrepitude, had more serious concerns about testing put directly in the hands of potential patients. But doubts have been fading. “Concerns over genetic testing are often disproportionate to the reality,” Tanya Moreno, PhD, Director of Research and Development at Pathway Genomics, said on the panel today.

Here are a few of those initial fears, and the realities that have come to pass:

FEAR: Customers’ private genetic information would be compromised.

REALITY: People are blogging, tweeting, emailing, and facebooking their intimate genetic information with abandon.

Sandra S-J Lee, PhD, Senior Research Scholar from the Stanford Center for Biomedical Ethics, spoke about a survey of 80 23andMe customers that probed social networking and personal genomics. They did phone interviews, surveys, and focus groups. Nearly half of them had announced their results on Facebook, and more than 2/3 had gone online to find another person with a shared condition – and that was from 2009, when fewer of us were permanently attached to our devices.

FEAR: DTC customers will focus on stupid stuff, like earwax consistency and bitter taste.

REALITY: 23andme assembled 3,426 cases and 29,624 controls to track down two new genes that contribute to Parkinson’s disease, much faster than would have been possible in academic medicine. That’s hardly frivolous. It’s crowdsourcing science, and although a self-selected sample, it works.

FEAR: Customers won’t know enough or be afraid to share important information with relatives who may be affected by a discovery.

REALITY: Customers learning they have a mutation in the BRCA1 or BRCA2 cancer risk genes indeed told their relatives. “One of the most surprising things was the extent to which people shared the information with both male and female family members. And there was a lack of extreme anxiety,” shared Joanna Mountain, PhD, Senior Director of Research at 23andMe.

FEAR: Customers would have to pay outrageous fees.

REALITY: The opposite has happened. My student L.W. took the 23andme test for the 3 most common BRCA1 and BRCA2 mutations shortly after her mother was diagnosed with breast cancer. 23andMe’s test told L.W. she hadn’t inherited her mother’s mutation – and also that she’s of Ashkenazi Jewish ancestry, something that her parents had hidden. And she spent about $100 – not the $3400 that Myriad Genetics charges to sequence the genes. L.W. and her mom contributed their DNA to the Parkinson’s disease project.

FEAR: Physicians don’t know enough to interpret many new genetic tests.

REALITY: That’s still somewhat true, for some physicians who rarely encounter genetic conditions or need to explain them. David Kaufman, PhD, Director of Research and Statistics at the Genetics and Public Policy Center at Johns Hopkins University, reported on a survey of 1,046 customers of 23andMe, Navigenics, and deCODE, conducted from January through May 2010. The top three reasons to take the tests were curiosity (94%), to learn about future diseases (91%), and to learn about ancestry (90%). Choosing DTC genetic testing following doctor recommendation was at the bottom of the list (7%).

Communication is a big part of providing care for a patient with an elevated risk of developing a genetic disease. Disconnects happen. “In one case a physician rated himself as doing an excellent job of explaining results. But the family was completely blown away. They didn’t understand anything,” said Cinnamon Bloss, PhD, Director of Social Sciences at the Scripps Translational Science Institute in La Jolla.

Perhaps the public expects too much because they confuse physicians and scientists, especially because some professionals are indeed both. The equating of “doctor” with “scientist” possibly dates to physician Dana Scully on the X-Files constantly calling herself a scientist.

“As a group doctors lack requisite knowledge in genomic medicine. Educational efforts are underway to bridge this gap,” Dr. Bloss said, perhaps referring to the first Master of Science in Genomic Medicine offered at the Miller School of Medicine at the University of Miami.

FEAR: The information from DTC genetic testing won’t be “actionable.”

REALITY: Dr. Kaufman’s survey of satisfied DTC customers found that 34% adopted a more healthful diet, 16% changed a drug or supplement, and 14% exercise more. Plus, 43% sought additional information on at least one tested condition, 28% discussed findings with a health care professional, and 9% followed up with additional lab tests.

FEAR: The companies will take advantage of their customers.

REALITY: “We’re thinking differently about the people who take part in research. We’re moving from calling them ‘human subjects’ to considering them to be collaborators and participants in research,” said Dr. Mountain.

23andMe regularly updates their participants on research findings pertinent to test results, pursues suggestions for new tests from the customers (such as sexual orientation), and publishes articles with participants in open access journals.

With consumers on board, scientists seeming to have accepted DTC testing, and doctors having to keep up with their patients who come in with test results, I think DTC genetic testing is here to stay – and poised to explode with exome and genome sequencing.

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Why I Don’t Want to Know My Genome Sequence

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Even after writing ten editions of a human genetics textbook, I don’t want to know my genome sequence. Yet.

Famous folk have been writing about their genome sequences for a few years now. But when I received two such reports at once last week – about genetics researcher Ron Crystal, MD, and a hypothetical (I think) story about President Obama, I knew it was time to take action.

Or, in my case, inaction.

After writing ten editions of a human genetics textbook and lots of articles, you’d think I’d be first in line to get my genome sequenced. But I prefer ignorance.

The quest to know ourselves by our DNA sequences began in the late 1980s, with the conception of the human genome project, and reached a milestone with the actual genome sequencing.

Revisiting the Genome Race

I still have my dog-eared copies of the journals unveiling the first draft of “the” human genome, from February 2001. The Science report hailed from the Celera Genomics/Craig Venter camp, with 5 individuals contributing to that composite genome, including CV himself, who has since gone on to creating life. The Nature report represented the International Human Genome Sequencing Consortium, which used genome pieces from several de-identified individuals.

On June 26, 2000, Francis Collins, MD, PhD and Craig Venter, PhD, flanked President Clinton in the White House rose garden to announce the great sequencing, because that was the only available date on the calendar. Both groups had made nice at the end of the race. Celera actually crossed the finish line first, as Dr. Venter told me that February off the record, lest the looming new edition of my textbook be obsolete. Today the race seems irrelevant.

The First Two: Craig Venter and James Watson

By 2007, individuals began to have their genomes sequenced, and speak and write about it. Dr. Venter was first, his genome presented in PLoS Biology. He pondered the implications at the American Society of Human Genetics annual meeting a year later.

Dr. Venter learned from his genome sequence that he has blue eyes and a tendency toward antisocial behavior, substance abuse, and novelty seeking. He found out he’s a fast caffeine metabolizer. “I can have two double lattes and wash it down with a Red Bull and not be affected by it,” he snarkily told the crowd. He also learned of elevated risk for Alzheimer disease and cardiovascular disease.

Next came James Watson, PhD, of double helix fame and first head of the human genome project. He discussed his genome at the 12th International Congress of Human Genetics in Montreal in October 2011, where Kevin Davies, PhD, author of “The $1,000 Genome” introduced him. Dr. Davies has subjected himself to all manner of genome probings too. Here’s the printable part of what Dr. Watson said:

Why did he do it? “Why not? I had no objection, with the exception of not wanting to know ApoE4. My grandmother had Alzheimer’s.” (Watson’s published genome sequence omits that risk gene, but people imputed it from the surrounding sequence.)

What did he learn that was useful?
“Finding that I am a slow metabolizer of antipsychotics and beta blockers.” His son nearly died from an antipsychotic. “So I now know that if I go psychotic, I can’t take those drugs.” And he learned why beta blockers for an irregular heartbeat knocked him out. He switched drugs.

What information wasn’t helpful?  “They told me I was a carrier for BRCA1. I thought I would have to phone my nieces because their mother had breast cancer. But I asked Mary-Claire King, who discovered the gene, and she said no, I had a harmless variant. So I’m glad I didn’t call my nieces because then they would have paid that disgraceful sum of money to Myriad Genetics.”

Dr. Watson ended with a situation he knows well. “I’d like to see children who have mental illness sequenced with their parents. Finding a mutation would make parents see that it was genetic injustice. Knowing that won’t make their child healthy, but they won’t have the double whammy of thinking they did something wrong.”

Dr. Venter wryly summed up the great personal value of he and Dr. Watson knowing their sequences. “You probably wouldn’t suspect this based on our appearances, but we are both bald, white scientists.”

Genome Sequencing in Sickness and in Health

Genome and exome sequencing are extremely valuable in diagnosing people whose symptoms don’t match known disorders. “Every time someone goes into a children’s hospital with a serious disease, it would be immoral NOT to sequence him,” Dr. Watson said. The first and most famous case is that of young Nicholas Volker and his intestinal condition; I’ve followed that of 4-year-old Gavin Stevens’s blindness gene. The cases of exome sequencing solving medical mysteries are mounting fast.

Steve Jobs and Christopher Hitchens had their cancer genomes sequenced, pancreatic and esophageal, respectively, and the information guided drug choices. Henry Louis Gates Jr. had his done to trace his ancestry. Glenn Close reportedly did it to better understand mental illness in her family, and I can’t guess why Ozzy Osbourne did it.

Ron Crystal, chairman of genetic medicine at Weill Cornell Medical College, had his genome sequenced to provide a control in a project to sequence the genomes of the people of Qatar. He discovered a mutation that explained his heavy bleeding following an injury from rappelling off a frozen waterfall a few years ago. He also discovered Viking roots, a recessive disease of children, and confirmed his baldness. But he voiced fears: his family learning things they didn’t want to know, even someone using his DNA sequence to frame him for a crime or to clone him.

Dr. Crystal isn’t the only one to cite potential repercussions of knowing one’s genome sequence. Said Seong-Jin Kim, the first Korean to have his genome sequenced, and that of his wife and two daughters. “Genetic disease in Korea is thought to disgrace families, and so it’s difficult to convince families with diseases to be sequenced.” A bad result could be regarded as a curse. But he was interested in using sequencing to better understand gastric cancer, which is the most common form in Asia. “Did it change attitudes? After we released our sequence, the number of sequencing companies increased.”

Why I Don’t Want to Know

I don’t want to know my genome sequence because of a fear that someone will clone me, but because the state of the science provides both too much and too little information.

On the TMI front, a genome sequence is a mega incidentaloma, an avalanche of information I don’t want. A panel discussion on the value of genome/exome sequencing at the international congress last year was telling.

Opinions ranged from moderator Han G. Brunner, of University Hospital St. Radboud in Nijmegen, the Netherlands, who asserted that “genome sequencing will yield an excess of information that is useless, uninterpretable, and possibly damaging to the patient” to Radoje Drmanac, co-founder and CSO of Complete Genomics, who claimed “We should have our genomes sequenced as early as possible. In my mind, this is not a question.” (Disclosure: Just before the panel discussion, I ate mozzarella sticks from Complete Genomics when I wandered into a cocktail party whilst hunting and gathering. I wonder if they got my DNA from the napkin.)

At the top of the list of diseases I don’t want to know about are those of the brain, Woody Allen’s second favorite organ. If I can’t prevent or delay them, why spend years worrying?

On the too little information front, we need to know more than a string of DNA letters or a list of gene variants. We need to know how our genes interact. It’s like reading a novel and considering each word in a vacuum, compared to understanding the unfolding story.

Learning our genetic story will require deciphering all possible gene interactions. Until then, I might learn about a disease-causing mutation, but not another that counters it, and then have to live with the knowledge. Computers and researchers will need to dissect and compare many thousands of sequenced human genomes to deduce the gene interactions.

All the needed analysis is costly. Bruce Korf, MD, PhD, director of the Heflin Center for Human Genetics at the University of Alabama at Birmingham has said, “We are close to having a $1,000 genome, but this may be accompanied by a $1 million interpretation.” And when Stephen Quake, a Stanford University engineer and co-inventor of a DNA sequencing device, laid his genetic self bare in the pages of The Lancet in 2010, interpretation required 32 physicians.

Like the others mentioned, Dr. Quake found the drug information the most valuable. He leads a very healthy lifestyle, but has gene variants that raise risk of cardiovascular disease. His genome revealed that a statin drug could save his life, the bloodthinner Plavix won’t work, nor would the diabetes drug metformin. But could carefully-chosen panels of single-gene pharmacogenetic tests provide the same information, based on the age-old tool of genetic counselors, asking good questions to build a useful family history?

Convince Me

Next week I’ll be at the American Society of Human Genetics annual meeting, attending workshops on exome/genome sequencing and hunting for more mozzarella sticks. And I’ll see if anyone can convince me to have my genome done.

Perhaps I’ll do it, eventually, as part of the Personal Genomes Project, for the greater good, but elect not to know the results. After all, I already know the obvious, like Craig Venter knows he’s bald and has blue eyes.

An osteoarthritis mutation manifested itself as an inability to play an F chord at age 33. A p53 mutation and then another that bloomed in response to years of orthodontia X-rays gave me thyroid cancer a few years after I gave up the guitar. And I don’t need a genetic test to know I didn’t inherit my father and grandfather’s psychotic depression.

Ron Crystal, even though he’s among the sequenced, has the right idea: don’t smoke, exercise, eat a healthy diet, and don’t worry about DNA sequences.

That’s good enough for me – at least for now.

 

 

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