Surveying the Genomic Landscape of Modern Mammals

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A rhesus macaque and a Tasmanian devil.

A rhesus macaque and a Tasmanian devil.

A study published today in Cell  compares regulatory DNA sequences among 20 species of modern mammals, showcasing how mammalian genomes have found new uses for ancient genes.

The evolution of mammals has been ongoing for about 180 million years, with a burst of numbers and diversity about 66 million years ago. Then, an asteroid impact led to mass extinctions, and the small, scurrying, hairy ones found vacated real estate.

(NHGRI)

(NHGRI)

Fossils help in studying past life, but even more useful is to compare DNA sequences among modern species. The more of a gene or genome sequence a pair of species shares, the more recently they shared an ancestor. That is a more likely explanation for similarity at the DNA level, I think, than that two species ended up with nearly identical sequences by chance. And if researchers know the mutation rate for a specific gene, then they can assign approximate time frames to species’ divergence.

DISSECTING REGULATORY SEQUENCES
Diego Villar, from the University of Cambridge Cancer Research UK, Paul Flicek, head of Vertebrate Genomics at the European Molecular Biology Lab EMBL-EBI, and their colleagues identified promoter and enhancer regions in DNA from liver cells from the selected 20 species of placental mammals.

Promoters are short sequences at the starts of genes that control their transcription into RNA, from which protein is translated. Enhancers are short DNA sequences, typically located a bit away from the genes that they control, that bring different genes together as the chromosome unwinds and loops about itself. So both promoters and enhancers control gene expression, one from near, one from afar.

Tree shrew (wikispecies)

Tree shrew (wikispecies)

The list of participating mammals in the study is diverse, but heavy on primates, rodents, and sea dwellers: human, macaque, vervet and marmoset (primates); mouse, rat, naked mole rat and guinea pig (rodents); dolphin and two whales (cetaceans); and rabbit, tree shrew, pig, ferret, dog, cow, cat, opossum, and Tasmanian devil.

The researchers discovered that promoters tend to have evolved recently – which means over the past 40 million years. In contrast, most enhancers are derived from sequences that have been around for more than 100 million years, but have been co-opted to take on new functions. So species and their genomes can retain what’s worked in the past via natural selection, but can also tap into ancient sequences for new uses.

I’d use the word “repurpose” to describe enhancers’ links to past DNA, but “purpose” is a banned word in evolutionary biology, because it implies intent, which implies a creator. The researchers use the slightly less teleological “redeployment of ancestral DNA.” This approach is different from the gene duplication route to microevolutionary change I learned in graduate school. In that model a gene doubles, perhaps by a slip during DNA replication at a short repeated sequence, and then one copy, through mutation, acquires a novel function that persists if it does no harm.

An evolutionary success

An evolutionary success

It’s reassuring that a genome has more than one way to change, because that’s what evolution is: change. It is not directional, not leading towards someone’s concept of perfection, and we are certainly no more highly evolved, whatever that means, than a bacterium or cockroach. They’ve been around a lot longer than we have.

In 1982, Stephen Jay Gould and Elizabeth Vrba coined the term  exaptation to distinguish novel use of old information from natural selection, which instead results in an adaptation (a trait that makes it more likely to leave fertile offspring.) Exaptation is a little like what my daughter Heather says whenever I want to buy new furniture. “Use something already in the house.

My husband Larry demonstrating his exaptation of kitchen tools to capture rodents. He is a retired chemist with nearly 100 patents.

My husband Larry has exapted kitchen tools to capture rodents. He is a retired chemist with nearly 100 patents.

ALTERNATE VIEWS OF EVOLUTION
Some popular explanations of biological diversity do not take advantage of the endless information to be mined from DNA sequences. Consider the appearance of everything living within the span of a week, plunked down on the lovely Earth by a supernatural force.

According to Genesis, on day 5, God said, “Let the water teem with living creatures, and let birds fly above the earth across the vault of the sky.” Day 5 would seemingly cover the dolphin and pair of whales featured in the Cell paper, but the biblical description is classification by habitat, so includes fish and birds too.

bibleLet the land produce living creatures according to their kinds: the livestock, the creatures that move along the ground, and the wild animals, each according to its kind,” sayeth God on day 6. Towards the end of that great day, we humans came along to lord over everyone else, a situation evidenced by the terms “livestock” and “wild,” a somewhat more subjective taxonomy than comparing DNA sequences and mutation rates. Presumably this day would include the other species in the Cell paper not yet specifically mentioned.

Another skewed view of evolution is the common line-up of creatures, with humans coming after chimps as the most “advanced” species. Cartoonists sometimes put stooped-over office workers in the final slot, or someone hunched over a cell phone. These alignments are offshoots of the “Great Chain of Being,” a religious ordering of everything in the universe.

HaeckelBut evolution tends to be branching, not linear. We share an ancestor with chimps, from around 6 to 7 million years ago, but we didn’t morph directly from them. Even when a lineage appears to be linear, likely offshoots died out along the way, perhaps leaving a bit of themselves lurking in modern genomes, like the Neanderthals.

So now I’ve angered the anti-GMO folk in last week’s post, and the intelligent design crowd in this week’s post. Perhaps I should take next week off.

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From GMOs to GROs: Will Life Find a Way?

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openerA pair of papers in this week’s Nature introduces GROs — “genomically recoded organisms” — whose altered genetic code makes them require a synthetic amino acid to survive. Although this new type of biocontainment indeed keeps microorganisms from spreading to where they aren’t wanted, at least in a lab, I don’t think the approach is likely to convert many anti-GMO folks to biotech fans, based on my experience.

ROTTEN TOMATOES
Several years ago, I spoke about genetically modified organisms (GMOs) to a group of citizen environmentalists, my goal to explain the precise procedures behind the vague term “genetic engineering.” Alas, the audience rapidly nodded off as I distinguished a transgenic organism from a knockout. They didn’t believe my tale of the first GMO released to the environment, “ice-minus” bacteria, that were sprayed onto strawberry plants by Advanced Genetic Sciences in 1987 to block ice nucleation. Activists destroyed a treated strawberry patch, unaware that the GM bacteria actually lacked a gene, rather than harboring a foreign one.

Unlike these unadulterated tomatoes, the  FlavrSavr failed not because it was genetically modified to have a long shelf life, but because it tasted bad.

Unlike these unadulterated tomatoes, the FlavrSavr failed not because it was genetically modified to have a long shelf life, but because it tasted bad.

The audience woke up, and became enraged, when I stated that traditional breeding is less precise than genetic manipulation. They yelled over my insistence that the same DNA triplets encode the same amino acids in all species. So unpleasant was the anti-science sentiment that I vowed never to speak about GMOs again.

My experience revealed that people fear GMOs – particularly plants – for a biological reason and an ethical reason:

#1: GMOs are perceived as not as safe to eat as unaltered vegetables and fruits.

#2 Any genetic manipulation beyond crossing and breeding is just wrong, an assault on nature.

Back then there was less concern about GMOs forcing reliance on certain herbicides and pesticides, and of “escape” to fields beyond where they’re intended to grow, two objections with which I agree.

TRIPLE-HEADED PURPLE MONSTERS
When I was in graduate school for genetics in the mid 1970s, the dawn of modern agricultural biotechnology, my mentor Thom Kaufman dubbed the unfounded fear of anything involving DNA the “triple-headed purple monster” mindset. It persists.

Even decades since we began regularly eating GMO crops, fear of their danger lingers. A January 17 article in the Washington Post proclaims “Over 80 Percent of Americans Support Mandatory Labels on Foods Containing DNA,” possibly the most idiotic headline of all time. Ever had a burger or banana that doesn’t contain DNA? All organisms do. And all use the same genetic code.

Golden rice is genetically modified to produce beta-carotene, upping vitamin A levels.

Golden rice is genetically modified to produce beta-carotene, upping vitamin A level.

I can’t fathom why people vehemently object to GM corn and soybeans, but not to vaccines and pharmaceuticals consisting of recombinant DNA translated into protein in non-human cells. Does anyone find offensive the candidate Ebola vaccines and drugs that include genes from different viruses grown in tobacco cells? “You Won’t Believe How They’re Growing the Ebola Vaccine” shouted another recent headline, above an article that repeatedly refers to “a bacteria” (that’s plural), and confuses bacteria with viruses. I wrote about producing recombinant DNA-derived proteins in tobacco plants in “Building a Better Tomato” in High Technology magazine, circa 1984.

The fact that 80% of those polled are demanding labels announcing the presence of DNA in their food confirms that the palpable fear and anger I felt years ago still simmers. And if that’s so, then the new studies about altering the genetic code may ignite a firestorm, despite the initial news emphasis on the fact that GROs have a genetic “safety lock.”

INTRODUCING GENETICALLY RECODED ORGANISMS
The Nature papers are a bit hard to follow, and require familiarity with the genetic code. It is the 64 possible mRNA triplets (codons) that are combinations of the four types of RNA bases (uracil, cytosine, adenine, and guanine), which are complementary to 64 types of DNA triplets. Of the 64 RNA codons, 61 encode any of 20 types of biological amino acids, and 3 mean “stop”: UAA, UAG, and UGA. A protein being synthesized along an mRNA molecule is complete when it encounters a stop codon. UAA, UAG, and UGA spell “stop” in all organisms, as well as in viruses. (Disclaimer: I have a UGA stop codon tee shirt.)

George Church of Personal Genome Project fame, who is the Robert Winthrop Professor of Genetics at Harvard Medical School, and colleagues report in the January 21 Nature that they replaced UAG “stop” codons in E. coli with UAA codons altered to bind and insert a “nonstandard amino acid” (NSAA) into a growing protein. An NSAA is not among the 20 that the natural genetic code specifies. The result is a GRO: a genomically recoded organism. It can’t survive without the NSAA.

“We now have the first example of genome-scale engineering rather than gene editing or genome copying. This is the most radically altered genome to date in terms of genome function. We have not only a new code, but also a new amino acid, and the organism is totally dependent on it,” said Dr. Church in a news release.

The genetic code. (NHGRI)

The genetic code. (NHGRI)

By swapping in the altered UAAs at many places in the bacterial genome, plus required tRNAs and “computationally redesigned” enzymes, protein synthesis incorporates the unnatural amino acids. As a result, DNA can’t move from cell to cell aboard viruses and other mobile DNA elements (horizontal gene transfer) or be replicated and passed to the next generation (vertical gene transfer), unless the NSAA is present.

Dr. Church calls the feat “irreversible, inescapable dependency.” All of this work is in very early stages and uses the standard E. coli and its T viruses, the stuff of classic molecular biology experiments from the 1960s and 1970s, and the microorganism in which many biological drugs are “pharmed.” It is a long way from being applied to fields of rhubarb.

GROs made their debut in a 2013 paper in Science from Dr. Church’s group, and were a candidate for the magazine’s “breakthrough of the year” in 2014. The 2013 paper describes the ability of GROs to resist viral infection, because they can’t be make viral proteins, as infected cells normally would. Viral infection can be disastrous for producing biopharmaceuticals or bioremediation agents.

In the second article on GROs in this week’s Nature, Farren J. Isaacs, an assistant professor of molecular, cell and developmental biology at Yale University, who did postdoctoral research in the Church lab, and colleagues describe retooling the UAG stop codons where they naturally occur in E. coli, but also introduce them into several essential genes. Their bacteria require two unnatural amino acids.

Dr. Isaacs and the Yale team also published an article with a headline I did like, “Multilayered genetic safeguards limit growth of microorganisms to defined environments,” in Nucleic Acids Research online January 7. They colorfully describe their multi-pronged approach as including “engineered riboregulators that tightly control expression of essential genes, and an engineered addiction module based on nucleases that cleaves the host genome.”

A NEW ROUTE TO BIOCONTAINMENT
In microbiological terms, a GRO is a “synthetic auxotroph.” Like bacteria before it genetically modified to resist an antibiotic or require a nutrient in order to survive, thereby providing a means of selection, the new breed of GROs depends on the NSAAs in the environment to make proteins, to stay alive and reproduce. A GRO can’t escape to where it isn’t wanted if it can’t get its NSAA.

In contrast to insecticide- or herbicide-resistant GMOs forcing reliance on a big company’s products, GROs work when something unnatural is not available in the environment. So they’d grow where the NSAA is, but not where it isn’t — if the technology ever extends beyond closed laboratory situations.

1024px-Jurassic_Park_4WD_and_dinosaur_at_Islands_of_AdventureWherever GROs end up, the researchers hope the altered genetic code will enable them to circumvent nature’s ways of surviving. New detoxifying mutations won’t help, for there is no toxin. Nor can natural selection or even horizontal gene transfer remove the altered codons. And GROs can’t suck up useful nutrients from neighbors – they need those NSAAs. But as mathematician Ian Malcolm pointed out in Jurassic Park, where genetically altered dinosaurs ran amok, “nature finds a way.”

256px-X-Files_Dana_Scully_CosplayBiocontainment based on altering the genetic code is an idea that was unimaginable back when such measures were first hammered out at the Asilomar conference on recombinant DNA held in 1975. In the 1990s, Dr. Dana (“I’m a scientist!”) Scully from the TV show The X-Files waxed melodramatic about a 5-base genetic code introduced by space aliens. It happens.

While GROs extend the NIH Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules, the new papers are more proof-of-concept than practical, for now. None of the trillion E. coli that the Church lab grew over two weeks bolted. That’s “10,000 times better than the NIH recommendation for escape rate for genetically modified organisms,” Dr. Church said.

1000px-Mad_scientist.svgTHE MEDIA RESPONSE TO GROs

I eagerly awaited the media response to the reports on GROs, anticipating an uproar if the news aggregators went beyond the cautious news release to borrow phrases from the papers such as “whole organisms capable of sampling new evolutionary landscapes” and “reliance on synthetic metabolites.” Altering the genetic code is HUGE, a much more profound change than boosting beta carotene levels in rice or creating tomatoes with longer shelf lives, traits that result from single-gene changes.

The media coverage, so far, has been far less than I anticipated, with the usual suspects – the New York Times, Science Daily – doing a terrific job. But it wasn’t the stuff of CNN or the NBC evening news, and stories such as underinflated footballs, a cop singing along with Taylor Swift, and the arrest on corruption charges of the speaker of the New York State assembly, naturally got more coverage.

What would the anti-GMO organizations, places I don’t ordinarily visit since my traumatic lecture experience, say?

Greenpeace was concerned mainly with polar bears and whales. But GMO Awareness was apparently unaware that researchers had rewritten the genetic code and applied it to bacteria in a technology that could, someday, be used to reign in errant altered crops. The “breaking news” on their website is from October, and the featured story on their Facebook page concerns all-natural burgers, which I suspect in fact harbor some DNA.

It’s possible that the environmental groups do not yet comprehend the significance of what synthetic biology can do, or understand how it works. But maybe I’m wrong about that. Give it a few weeks.

Many questions remain, especially if GROs transition from initial roles in bioremediation and specialty chemicals and pharmaceuticals to food production. Will the NSAAs harm health if eaten or spread in the environment? Will the approach work for plants, which are so much more complex than E. coli?

As for me, I was recently asked again to speak about GMOs, in an adult education course next fall. I initially said no. But these two papers are so exciting that I’ve changed my mind.

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New Miracle Drugs: What Would You Pay?

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Levi Collazo, before and after Kalydeco treatment for cystic fibrosis.

Levi Collazo, before and after taking Kalydeco for CF.

Levi Collazo, a biology major at Southwestern Oklahoma State University, has cystic fibrosis (CF).

“In the first photo, I was making fun of my own weight. I’ve always used humor as a defense mechanism. I weighed 110 pounds. I’m 5’10″. After taking Kalydeco for 2 years, I’m up to 148 pounds,” he wrote on the Facebook page Kalydeco Miracles.

The success of Kalydeco for some people with CF – “K” to its fans – is astonishing. The drug corrects misfolding of the CFTR protein that certain mutations cause.

THE STORY OF ‘K’
When the daily pill, developed by Vertex Pharmaceuticals, came on the market in 2012, only the 2,000 or so patients who have a specific mutation could use it. The drug cost $294,000 a year. Since then, further clinical trials have swelled the patient pool to about 3,100. The FDA approved the drug for a tenth mutation December 29, 2014.

Families still fight insurance companies for coverage, but the Cystic Fibrosis Foundation has funded development of Kalydeco and recently sold royalty rights, and is using the $3.3 billion to help patients and fund further research. With 75,000 people in North America, Europe and Australia having CF and trials on extension to other mutations continuing, the market may increase, and perhaps the price decrease.

Madi Vanstone, age 12, learned in June that the Ontario Drug Benefit formulary would cover the cost of her K and of everyone else’s in the province with a treatable mutation. Before that, insurance had been paying half of the $348,000 annual cost and Vertex 30%, leaving $60,000 for the family to cover. Without daily K, Madi would have needed a lung transplant in a few years and might not have survived her teens. Now, she has a future.

What would you pay to treat a debilitating and deadly disease?

Over the past few months, we’ve seen incredible price tags for groundbreaking new medical treatments.

Glybera is the first gene therapy approved in the western world. It treats lipoprotein lipase deficiency.

Glybera is the first gene therapy approved in the western world. It treats lipoprotein lipase deficiency.

GLYBERA, THE FIRST GENE THERAPY
Like Kalydeco, Glybera debuted in 2012. Amsterdam-based company UniQure with partner Chiesi make Glybera, the only approved gene therapy in the western world.

Glybera treats painful and lethal lipoprotein lipase deficiency (LPLD). The price in Germany, announced in late November, set a new record for a medicine to treat a rare disease: $1.4 million for the one-time series of 42 intramuscular injections that should banish the disease.

In LPLD triglycerides build up in the pancreas, liver, skin, and spleen. About 1,000 Europeans have LPLD, and it affects one in a million in the US – about 323 people. Prevalence is greater in Quebec due to a founder effect: French and Scottish settlers introduced two mutations three centuries ago. In the province 1 in about 6,000 people has the disease.

John Kastelein, Colin Ross, and Michael Hayden recall Glybera’s long developmental trajectory, which began in Hayden’s lab at the University of British Columbia, in a compelling article in Human Gene Therapy. In September 1986 they met a 19-year-old with sky-high triglycerides, painful pancreatitis, and skin lesions, and identified his LPLD mutation. A severely fat-restricted diet hadn’t helped.

A natural cat model and mice led to development of gene therapy for LPLD.

A natural cat model and mice led to development of gene therapy for LPLD.

Experiments using mice and cats followed, and eventually clinical trials tested several versions of a gene therapy delivered in adeno-associated virus. In severely affected patients, abdominal pain diminished, lipid levels fell, and they could eat more, including foods they couldn’t tolerate before. One patient even had a baby.

What would you pay to treat a painful and deadly disease?

Glybera costs so much because it is first-of-its-kind, was decades in development, and encountered an unusually thick regulatory morass. And the market is very small, so the monumental development costs must be divided by a small number of patients.

But Glybera is the test case for much wider application of the technology, which UniQure is exploring for several other indications. One is hemophilia B, the clotting disorder mentioned in the Talmud and seen in Queen Victoria and some of her descendants.

rbcs and clotHEMOPHILIA AND BLINDNESS GENE THERAPY WILL BE CHEAPER
Doing the math for hemophilia B, it’s easy to see how gene therapy will earn out its development cost. This is the less common form of the clotting disorder, affecting 4,000 people in the US.

Traditional treatment is the missing protein, clotting factor IX (FIX). It came first from blood donations, then using recombinant DNA techniques after HIV in the blood supply infected 90% of people with hemophilia in the 1980s.

Giving FIX protein to treat hemophilia B is expensive, painful, frequent, and not entirely effective. It costs $100,000 a year if used only to treat “bleeds,” and up to $250,000 if given 2 or 3 times a week to prevent bleeding. That’s about $20 million over a lifetime.

But giving the FIX gene — the instructions for cells to make the protein — could last forever and costs about $30,000. The lower price may be because the gene is small and simpler to insert into the viruses that carry out gene therapy than others, and a tiny jump in FIX level makes a huge difference in clotting time and how a patient feels. The promise of hemophilia B gene therapy is why several teams are racing to get it to the clinic. (Spark Therapeutics recently partnered with Pfizer to develop the gene therapy). I predict it will be among the first gene therapy approvals here.

My #1 prediction for first-to-be-approved gene therapy in the US is for Leber congenital amaurosis type 2 (LCA2), chronicled in my book The Forever Fix (shameless book plug in honor of pub date anniversary, today.) The treatment for this form of hereditary blindness won’t cost much, for several reasons: delivery into the eye is well-established, the inventors have forsaken earning anything, and kits are ready to ship to ophthalmologists.

Another intriguing new drug is Cerdelga™, to treat type 1 Gaucher disease. The FDA approved it in 2014.

Bone loses cells in Gaucher disease.

Bone loses cells in Gaucher disease.

GAUCHER DISEASE – FROM INFUSION TO PILL
Gaucher disease type 1 causes an enlarged liver and spleen, anemia, poor clotting, collapsed hips, arthritis, impaired lung function, bone pain and fractures. Cells become packed with lipids, and symptoms may begin at any time. It’s autosomal recessive, but carriers may develop a Parkinson-like condition later in life.

An earlier treatment for Gaucher, Ceredase, came on the market in 1991. Developed at Genzyme Corporation, Ceredase was an infusion and the first enzyme replacement therapy. In 1994. Cerezyme replaced it, made using recombinant DNA technology and altered to target fat-engorged Gaucher cells. Globally 5,000 people take Cerezyme, including 1,500 in the US.

Cerezyme works, but delivery isn’t easy. Dose and schedule of IV administration must suit each patient.

”For people receiving Cerezyme for a long time, that adds up to a lot of infusions and having to be poked every few weeks limits one’s schedule,” Gerald Cox, MD, PhD, Vice President of Clinical Development for Rare Diseases at Genzyme told me. A pharmacist must provide the drug and a nurse administer it, at home or at a clinic. “When we asked patients what more they would like from a treatment, they all wanted a pill,” Dr. Cox said.

(Genzyme)

(Genzyme)

So Genzyme researchers sought another way to intervene in the biochemistry – alleviate the buildup of substrate that occurs when an enzyme is blocked, as it is in Gaucher. FDA approved the substrate reducer Cerdelga – a capsule! – last year. Clinical trials were complicated, requiring patient volunteers to give up Cerezyme to test its new cousin.

The price per patient? $310,250 a year, a little more than its predecessor. Dr. Cox explains why.

“Orphan diseases follow a little different set of ground rules. There’s a lot of investment. But we have to go through all the regulatory hurdles that all the other companies do for common diseases, and when they want to recoup that investment there are 10 million people who are going to use the drug. You can keep the cost low because so many people are going to use it. But for an orphan disease with 5,000 worldwide, if you invest and divide by the number of patients, it winds up being a high price.” Relaxing regulations and shift of drug development towards academia might help for the ultrarare diseases, he adds, or foundations or governments stepping in, like for Kalydeco.

What would you pay to treat a painful and highly disruptive disease?

DOING THE MATH FOR USE IN THE US

Kalydeco for CF: 3,100 patients, ~$300,000/year each. For a 10-year-old who lives Logodollar2until 60, that’s about $15 million.
Glybera for LPLD: 323 patients, ~$1.4 million/lifetime
Cerdelga for Gaucher: 1,400 patients, ~$310,000/year each.

We’ve all heard the big pharma mantra, “R&D for a drug takes 10 to 15 years and more than $1 billion.” Add the costs of buying companies (like Sanofi bought Genzyme), and of discontinued clinical trials. Yet the treatments are justified when there isn’t anything else or existing approaches don’t work well or for everyone.

Now let’s look at hepatitis C.

Hepatitis C virus

Hepatitis C virus

THE HEP C CONUNDRUM
Hepatitis C is hardly a rare disease. About 2% to 3% of the global population has it – that’s  130 to 170 million people, including 3.2 million in the US. It’s more prevalent than HIV infection, and many people are unaware that they have it and can spread it. You’d think that’s enough people to keep costs down.

For more than two decades, treatment for hepatitis C infection has been the cytokine interferon and the antiviral ribavirin, which only some patients can take and which can make people pretty miserable. Availability of new drugs, based on the success of HIV antivirals, was good news indeed.

Last April, the World Health Organization called for assessing all infected people for two new drugs, because more treated people can block transmission.

An editorial in the New England Journal of Medicine was unusually optimistic: “Collectively, these regimens promise to transform hepatitis C from a condition requiring complex, unsatisfactory therapies and specialist care to one that can be effectively treated and easily managed by a general physician with few contraindications and side effects.”

But consider the price.

My friend Fred took the 3-month course of interferon/ribavirin/Solvadi. “My insurer paid. I paid only $20 for the whole course. That’s the good news. The bad news is that I relapsed after 90 days and am now on a newer combination drug, Harvoni. It’s reported to cost even more ($1,124) per tablet and I’ll need to take it for 6 months.” Solvadi is about $1,000 a pill.

Fred hopes he doesn’t get any surprise bills. “Keep your fingers crossed for me, this time I’m going to win!”’ Success rates for the new drugs are in the mid 90% range.

800px-HepC_replicationThe drug combinations are confusing. Harvoni is Solvadi plus a viral inhibitor called ledipasvir. Both combinations are from Gilead Sciences.

Olysio, at $733 a day, is from Janssen Pharmaceuticals and is taken with Solvadi, interferon, and ribavirin.

Viekira Pak, developed by AbbVie and approved last month, for about $925 a pill, combines three new antivirals and one old one. Like the hugely successful HIV drugs, these newcomers target various steps in the choreography of viral entry into human cells and replication.

Why do the hepatitis C drugs cost so much? A New York Times article lists a few justifications: R&D expenses, superiority to older treatments, future savings from preventing complications. True, the drugs seem to cure, compared to the HIV drugs that lighten viral load (unless hepatitis C virus peeks out in a few years). And Gilead paid $11 billion to the company that originated Sovaldi. But I don’t get it.

Prices in Pakistan, Egypt, China and India will reportedly be much lower. And by one estimate, cost to manufacture is actually about $150 to $250 per patient. A medical economist posited that it will take treating about 150,000 patients to recoup development costs.

What would you pay to stop a deadly disease? And how long would you wait?

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Adult Polyglucosan Body Disease (APBD): A Diagnostic Challenge

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Globs of a carbohydrate called polyglucosan accumulate in astrocytes in APBD. (photo credit: Jensflorian)

Globs of a carbohydrate called polyglucosan accumulate in astrocytes in APBD. (photo credit: Jensflorian)

When Susan Coddon, a member of the board of directors of the Adult Polyglucosan Body Disease Research Foundation (APBDRF) e-mailed me a few weeks ago, I was intrigued. “Polyglucosan” didn’t ring any bells. Her husband learned he had the underrecognized condition in 2007, following a misdiagnosis of multiple sclerosis years earlier.

The APBDRF website describes a typical case: “In my early 50’s, I first experienced numbness in my hands, cramps, stiffness and heaviness in my legs. Also muscle twitching, soreness, foot drag and stumbling. Initially, I was incorrectly diagnosed with hereditary peripheral neuropathy. It took 13 years for a proper diagnosis.”

A recent article in the Jewish Daily Forward relates Hollywood photographer Robert Zuckerman’s multi-year diagnostic odyssey. That’s not unusual.

“Almost every patient we speak to goes on a 2 to 10 year search, in some cases even families of neurologists. We’re trying to get the word out, because APBD is very hard to distinguish from many other diseases,” Jeff Levenson, DMD, senior advisor to the APBDRF, told me.

Polyglucosan accumulates in astrocytes, a type of neuroglia. (Database Center for Life Science)

Polyglucosan accumulates in astrocytes, a type of neuroglia. (Database Center for Life Science)

APBD is inherited as an autosomal recessive trait, although many carriers have late-onset symptoms, making them “manifesting heterozygotes.” A genetic diagnosis may emerge from sequencing the exome, the protein-encoding part of the genome. Because APBD is actually an “atypical presentation” of a more familiar condition, tests for common neurological disorders are negative.

The particular problem of diagnosing APBD, however, may have more to do with its name than its DNA.

A COLLECTION OF COMMON SYMPTOMS

APBD begins, typically after age 35, with a numb foot that drags during walking. The hands too may exhibit this peripheral neuropathy, and the numbness may progress towards the body’s center. Fatigue sets in, and then urinary frequency and incontinence begin. There may be mild cognitive impairment.

Alarm bells may sound. Is it ALS? MS? Prostate cancer? Parkinson’s disease?

APBD is a leukodystrophy, a disorder of the white matter of the brain. This brain is from a toddler with an undiagnosed leukodystrophy. (Dr. Laughlin Dawes)

APBD is a leukodystrophy, a disorder of white matter. This brain is from a toddler with an undiagnosed leukodystrophy. (Dr. Laughlin Dawes)

Evaluation begins: blood tests, electromyograms, spinal taps, brain MRIs, which might show the telltale lack of white matter myelin of a leukodystrophy. But which one? Initial genetic tests come back normal, not surprising because the symptoms do not exactly match those of the more prevalent or better-studied inherited leukodystrophies.

If a health care provider strongly suspects an atypical case of a common condition, treatment may begin. Neurontin, prednisone, anti-seizure meds. Or perhaps more than one illness is at play – benign prostatic hyperplasia might explain the urination changes, a neuropathy the distal limb numbness.

Physical or occupational therapists can help a patient with activities of daily living while the docs try to figure out why the patient isn’t fitting into any categories. And why would an internist or even a neurologist trying to diagnose a tired and shuffling 50-something with urgency issues suspect a glycogen storage disease known for fatally disrupting the heart, nerves, and muscles of babies?

For that’s what APBD is: glycogen storage disease type IV. The unfamiliar “polyglucosan” intrigued me, so I got out my old textbooks to investigate the term, which sounds more like a sushi ingredient than a polysaccharide.

Glycogen

Glycogen

A CONFUSING NAME

Polyglucosan is a form of glycogen, which is a chain of glucose molecules. Glucose is the 6-carbon sugar whose chemical bonds provide the energy that cells use to manufacture ATP, the biological energy currency.

Glycogen normally branches at every 12 to 18 glucose units, and an enzyme – glycogen branching enzyme 1 (GBE1) – makes this happen. APBD arises from specific mutations in the gene that encodes GBE1 that allow some residual enzyme activity. Long unbroken chains of glycogen grow and glom and gum up the astrocytes that keep neurons functioning. Meanwhile, at the whole-body level, fatigue sets in as glucose becomes tied up. Mutations that lead to no enzyme activity are fatal in early childhood.

The “body’ in the disease’s name refers to the clumps of abnormal glycogen, not the person. Detecting polyglucosan requires special staining of a biopsy from a leg vein, finding deficiency of the enzyme in muscle samples or skin fibroblasts, and identifying mutations in the GBE1 gene in saliva.

Neither Lehninger’s Principles of Biochemistry, Morrison and Boyd’s Organic Chemistry, nor Bloom and Fawcett’s Histology, all circa 1975, mentioned polyglucosan or even glucosan. Googling “polyglucosan” led repeatedly back to APBD. Then I found “glucosan” at drugs.com, which referred to standard medical dictionaries that say “see glucan.”

Phaseolus_lunatus_flower_(5563988396)The dictionaries define “glucan” as any glucose polymer. But that would include starch and cellulose, which aren’t found in animals, as well as glycogen, which is.

The medical literature is confusing too. A 1980 paper in the journal Brain, from Salvatore DiMauro’s group at Columbia University, offers a murky definition: “A general term – polyglucosan body – is introduced to refer to these structures in all the circumstances in which they may occur,” which includes rare inherited conditions such as Lafora’s disease, movement disorders, glycogen storage disease type IV, diabetes, and normal aging. The abstract of a 2011 paper from the group in Human Molecular Genetics defines polyglucosan as “a poorly branched form of glycogen,” which seems rather vague. Finally, the title of a 2013 Annals of Neurology report helps: “Abnormal glycogen in astrocytes is sufficient to cause adult polyglucosan body disease.

Given the terminology and the high prevalence of the individual symptoms, it isn’t surprising that APBD has a history of misdiagnoses, including Fabry diseaseALS, liver disease, and atypical Parkinsonism.

header-logoPerhaps the rhyming of three of the four letters of APBD, plus the fact that the term “polyglucosan” is broader and much less commonly used than “glycogen,” contributes to protracted diagnostic journeys. The condition may be fairly common, but often misidentified. In one study, among 380 Ashkenazi Jews the carrier rate was 1 in 34.5 – about the same as Tay-Sachs and other “Jewish genetic diseases.” But of course DNA doesn’t know the religious affiliation of the person in which it resides. Anyone can have APBD.

JScreen.org doesn’t yet list APBD but will do so soon, and it’s among the 14 glycogen storage disorder tests that Prevention Genetics offers. I wonder how common it is in other populations, and how often it is indeed shoehorned into other diagnostic codes, and patients receiving inappropriate treatments.

EMBRACING EXOME SEQUENCING

The APBD story offers a powerful example of the evolution of classifying disease by phenotype to the precision of classifying by genotype.

The polyglucosan disorders may remain an umbrella term, but within the grouping, APBD is distinct. For example, it’s different from a condition described in a 2013 Annals of Neurology report on a polyglucosan build-up that weakens muscles and affects the heart, but due to mutation in a different gene, RBCK1. (It encodes a ubiquitin ligase, part of the cell’s garbage disposal system.)

Panels of gene tests related by function are perhaps the dying embers of the “round-up-the-usual-suspects” approach to diagnose inherited disease. In contrast, exome sequencing can illuminate mutations in genes that clinicians might not have considered – like APBD being a glycogen storage disease.

Once exome sequencing becomes routine – say 5 years from now – a health care professional evaluating an adult with distal limb weakness, profound fatigue, and urinary urgency can pop a blood sample into a device that will quickly detect, or rule out, APBD – and other inherited conditions that it masquerades as. Meanwhile, APBD researchers are trying to get the word out about this illness that is still so easily confused with others.

I think all the ice buckets were used up on ALS, so I’m hoping that people with numb feet, fatigue, and urinary issues will mention the possibility of APBD to their health care providers.

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Why I Dislike “Best of” Lists and Eman Update from Liberia

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icebergI’m not a big fan of end-of-the-year lists, such as the “top-10-scientific-achievements of the year” and the “top-10-genetics-stories-for-2014.” Science shouldn’t be a popularity contest. I wouldn’t suggest such a list for DNA Science, because:

1. I can’t possibly know about all research from 2014.

2. Others have created those lists.

3. I know how news is generated.

THE TIP OF THE ICEBERG
Those of us who read news releases daily – as science journalists do – didn’t need the recent study published in the British Medical Journal to confirm that these missives often hype research to ridiculous degrees. But it isn’t just exaggeration, headlines that suggest a study in mice is actually in humans, and use of vague terms such as “genetic engineering” that bother me about news releases.

My beef: news releases are a tiny sampling of what’s really happening in science.

256px-Bullhorn_font_awesome.svgResearchers with recognizable names, who publish in journals with high impact factors, and come from prestigious institutions with media machines and relentless PR firms, will be in the news releases that dictate what the public hears and reads. With aggregators rewriting news releases, with blogs linking to blogs linking to blogs, and the unending echoes of twitter and Facebook, we’re continually bombarded with variations of the same information. I’m guilty too.

Add to that chatter the fact that news releases precede online publication that precedes actual publication, it’s little wonder that by the time well-meaning friends send me news articles, it’s as Yogi Berra once said, “déjà vu all over again.” Thanks to writing this blog, now I’m getting pre-news releases!

And get this — there’s now a list of the top 10 science news releases!

Disclaimer: after having successfully avoided ever being on anyone’s “best of” compilation (blog, article, book, whatever), I today find myself quoted on a list of the stupidest startups, which of course links to a blog post.

Rather than writing about what the PR folk want me and everyone else to cover, I’m more interested in the experience of a lone parent who tells me about a child who has an unrecognized disease, or a study far down in the table of contents of an obscure journal, or a poster at a meeting from a post-doc or graduate student.

So DNA Science‘s subject list for 2014 doesn’t parallel the “top 10” lists. And it’s not that the entries on those lists aren’t great. For example, I haven’t gotten around to covering CRISPR (a method of genome editing) just yet – I’m simply overwhelmed with all there is to learn.

Because there’s no plan behind what I write about here, and it is year’s end, I checked. My math skills unfortunately do not extend beyond Facebook likes and Google Analytics.

DNA science covers more zebras than horses.

DNA science covers more zebras than horses.

RARE DISEASES AND WEIRD TECHNOLOGIES
If DNA Science has a focus, it’s rare diseases. Posts combine history, personal accounts, and recent research to tell about inherited immune deficiencies and  blindness, alkaptonuria, Wilson diseaseSan Filippo syndrome, and classic inborn errors of metabolism. DNA Science got an initially inexplicable 13,000 Facebook likes for a post on the rapid-aging disorder progeria, because by chance I hit “publish” just as an embargo broke. It happens.

Several posts went beyond the exome/genome sequencing that gets so much attention:

pink-150x150freezing employees eggs
using stem cells from fingernails
choosing whom to date based on DNA
transplanting turds
tissue engineering vaginas
manipulating mitochondria
probing polar bodies to select embryos

I did 3 or 4 posts each for stem cells, DNA sequencing (exome and genome), gene therapy, and genetic testing. Some posts made connections: when  inherited disease protects against infectious disease and the link between genetic testing and eugenics.

No Ice Buckets or Pink Ribbons for Rare Genetic Diseases said what many were thinking: the ice bucket challenge, although raising funds and awareness, was idiotic. DNA Science posts about ALS research from August 6 and April 3 got far fewer Facebook likes than the one in which I threw cold water on the topic. The intense focus on one disease was agonizing for some rare disease families, but some organizations capitalized on the fleeting attention.

1000 genomeFILM AND TV REVIEWS RULE
According to Google Analytics, far and away the top three posts were:

#1 Dan Brown’s Inferno: Good Plot, Bad Science

#2 How Ebola Kills

#3 Syfy’s Helix: Tired Plot, Bad Science, Fun

I cannot stress enough how badly Dan Brown’s novel Inferno (soon to be a film) and the TV series Helix butchered genetics. The Inferno post got 25,814 unique visitors, and Helix 13,785. Yet my post about the astonishingly accurate Call The Midwife episode about cystic fibrosis got only 2,395 (see the special on TV tonight). That’s famous novelist vs SyFy channel vs PBS. Maybe science is a popularity contest.

Sonn and grandson (4)EMAN IS WELL!
The #2 post, How Ebola Kills, was my #1, with other posts about my “son” from Liberia, Emmanuel Gokpolu.

I introduced Eman in the April 25, 2013 post on World Malaria Day. In contrast to the families with rare genetic diseases, Eman has struggled repeatedly with cholera, malaria, and other highly prevalent infectious diseases. That initial post got few hits. He appeared again, mostly in his own words, on October 23 this year in Eman’s e-mails from Liberia and Eman Reports From Ebola Ground Zero on November 6.

In July, when Eman’s emails became increasingly frantic with the initial burst of Ebola cases, I pitched his story to NPR, the New York Times, even my local newspaper. I was proposing to use his words, not mine, but my timing was off.

Editors here wouldn’t care about Ebola until a man came to the U.S. from Liberia and fell ill. I wouldn’t have guessed last July that Ebola Fighters would be Time magazine’s Person of the Year, but I’m glad the world outside Africa has finally woken up to the reality of our interconnected planet and the spread of infectious disease.

Eman and his family have survived, although his cerebral malaria came back mid-November. With medical school still on hold, Eman has become very involved with public health and the organization Determined Youth for Progress. He wrote on November 8, “our recent campaigns have targeted forgotten communities and elderly people. I believe an elderly person can easily influence his/her children and then their grandchildren. That’s easy in Africa. We had a tough time accessing some of these communities, but the commitment of our team won the day.

11/9: “I had the opportunity to address our President’s son, Mr. Robert A. Sirleaf, about Ebola on thanksgiving day in our community. It was great!! I also got a call from Action Contre La Famine(ACF) to serve as a Volunteer Health Promoter. I’m looking up to this new task. It might take me out of Monrovia to somewhere rural. Health authorities are on the alert for new cases in parts of rural Liberia. It’s no time to relax. We must build upon the gains we have made and strategize better to completely kick out Ebola.”

12/1: “We were able to renovate/construct sick wells in various communities, easing access to safe water for those communities. Our Ebola campaigns are going excellent and so far, no one has contracted the disease where we operate.

We have also decided to have a program for children on Christmas day. There are lots of things to be achieved if this program becomes a possibility. School is not opening just yet, so we have designed programs for the kids keeping in mind the presence of Ebola in our country.”

12/17: “I am in Bomi county, volunteering with ACF, about 2 hours drive from Monrovia. Despite the short distance, it is mostly remote. It was an epicenter at the height of the Ebola crisis, and it is still a hotspot for Ebola due to the fact that it is very close to Sierra Leone. We have been distributing preventive Ebola kits and encouraging people to report themselves as soon as they feel sick. It has been challenging.”

I’m so proud of Emmanuel, and grateful that he has survived the Ebola crisis.

plos_logoThis is my 112th post since DNA Science began on September 27, 2012. Thank you PLOS for the freedom to find my own examples of how genetics and genomics are increasingly affecting our lives. And thank you readers. Happy New Year!

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How to Use the Genetic Code for Passwords

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Codons_aminoacids_tableNeed a password for a new device or service? Try the genetic code.

Messenger RNA triplets and the amino acids they specify provide nearly endless password possibilities. And it’s timely — the People’s Choice for Science magazine’s Breakthrough of the Year is “Giving Life a Bigger Genetic Alphabet.”

I began using the code for passwords years ago, when an IT-savvy friend setting up my clunky desktop computer told me a password should be:

• Alphanumeric
• More than 7 numbers or letters
• Obvious to me, but not to anyone else

The genetic code may seem like random gibberish to normal people, but can have meaning to biologists.

Francis Crick

Francis Crick

CRACKING THE CODE IN THE 1960s
The genetic code is the correspondence between the 20 types of amino acids and the 61 types of messenger RNA triplets (codons, representing DNA) that specify them. The same codons spell the same amino acids to all organisms. The RNAs of humans, hydras, hippos, hydrangeas, Haemophilus influenzae, and even viruses follow the same rules. This “universality” is why human proteins are manufactured in bacterial cells, bacterial insecticides are produced in corn, and an Ebola vaccine is made in tobacco cells.

Francis Crick proposed genetic code words (codons) as part of his “adaptor hypothesis,” which Marshall Nirenberg and Heinrich Matthaei at the NIH demonstrated with brilliant experiments in 1960 and 1961. They challenged bacterial cells to make tiny proteins using simple RNA molecules. When UUU… led to a string of phenylalanines, for example, they had the first piece to the puzzle. Fed more complex RNAs, the bacteria revealed more code words.

Marshall Nirenberg

Marshall Nirenberg

Wrote Dr. Nirenberg in his research notebook, “we would not have to get polynucleotide synthesis very far to break the coding problem … we could crack life’s code!” …“we would not have to get polynucleotide synthesis very far to break the coding problem … we could crack life’s code!” And so they did.

Crick, George Gamow, and other luminaries of the DNA discovery era famously formed the “RNA tie club,” in which each discoverer of a codon assignment was honored with a tie festooned with a double helix. The club had two dozen members, representing the 20 amino acids and 4 RNA bases.

Here are a few ways that combinations of codons and the standard three-letter amino acid abbreviations can make great passwords. (And a link to a list of amino acid abbreviations for those who don’t remember Bio 101.)

Data from the genetic code experiments.

Data from the genetic code experiments.

SUGGESTIONS

HISTORICAL
UUUpheAAAlysCCCpro (the first 3 pieces to the puzzle)
UUUAUApheilu (the first co-polymer in the experiments)

RANDOM
CUGleuAAUasnGUAval

PUNCTUATION
UAAUAGUGASTOP
AUGmetSTART

FASHION
Pink_UggsUGGtryptophan

CHEMISTRY
Sulfur-containing: AUAmetUGUcys
Rings: CCUproline   UAUtyrosine
Simplest: GGUglycine   GCAalanine   AGCserine

SYNONYMOUS (amino acids corresponding to more than one codon)
CUUCUCCUACUGleu   GCUGCCGCAGCGala

DISEASE-ASSOCIATED
Ehlers-Danlos syndrome: Arg134Cys
Huntington disease CAGglnx36HD
p53 oncogene UGAACAGUAp53
(Researchers should not use mutations they are working with. Someone will guess it.)

The genetic code is redundant — CCA and CCG both encode proline, for example – but passwords are not. Substitute the end G for the end A and your Amazon account won’t work.

gc posterPlan password choices, or have a chart of the genetic code in plain sight, as I do in my office. I got the poster after I had to change my Apple ID under time pressure, and I inadvertently typed in CAA for histidine, only to discover that I had specified glutamine.

Please send in other password suggestions!

Happy holidays and thanks for reading DNA Science!

 

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Sequencing Kids’ Exomes: More Good News

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1000 genomeExome” hasn’t yet entered the normal lexicon, like genome has. Yesterday, for example, I wore my clinical exome T-shirt from Ambry Genetics to Zumba class, and a woman came up and peered at my chest.

“What the heck is that? What are all those letters? And what’s that little gap? A misprint?”

So I explained to the class what an exome is, and that no, my shirt had a small deletion, not a fabric defect.

Within 5 years, though, I think people will know what an exome is, because analyzing it will be as common as a CBC or blood lipid profile is today before visiting the doc. As costs decrease and gene discoveries increase, we’ve reached a tipping point, by definition when “a series of small changes or incidents becomes significant enough to cause a larger, more important change.”

Until “exome” becomes a household world, clever studies are illuminating pioneering applications of the technology.

THE EVOLUTION OF EXOME STUDIES
The exome, the part of the genome that encodes protein, harbors 85% of disease-causing gene variants (we’re not supposed to say “mutation” anymore, but that’s what I mean). Results from several large studies have been published over the past 3 years, but a paper in last week’s Science Translational Medicine from Stephen Kingsmore’s group at Children’s Mercy–Kansas City offers the most promising results yet.

dna“It heralds the dawning of the new age of clinical genetics. We’ve been waiting for this to come around for 10 to 15 years, and it’s finally here,” says Robert Marion, MD, chief of the division of genetics at The Children’s Hospital at Montefiore and a  developmental pediatrician at the Albert Einstein College of Medicine, about the paper (he’s not part of the team). I devoured his book “Genetic-Rounds: A Doctor’s Encounters in the Field that Revolutionized-Medicine.”

Last month, the Journal of the American Medical Association published findings of two ongoing prospective exome sequencing studies of individuals with symptoms suggesting an inherited condition. A group from UCLA diagnosed 213 of 814 (26%) cases that hadn’t been diagnosed clinically or with single-gene tests or panels. The 26% rose to 31% if parents had their exomes sequenced too. The second report, from Baylor College of Medicine, diagnosed 504 of 2000 (25.2%) patients. Both studies weren’t just children.

I wrote in Medscape about the Baylor team’s interim results presented at the American Society of Human Genetics annual meeting in November 2012. At the same time I pitched the story to a top science magazine, whose editors had no idea what I was talking about. Now lots of magazines run kid exome stories. (I’ve a long history of being too-soon with biotech stories.)

By late 2012 the Baylor team had analyzed 300 exomes, with a 25% diagnosis rate. Most interesting to me, as always, were the cases. They reported several that illustrate two scenarios in which exome sequencing shines: a 2-year-old had Marfan syndrome but not the usual long limbs (“atypical presentation”), and a 9-year-old boy actually had two genetic diseases (“co-morbidities”).

Both boys were treated, once physicians knew what to treat. That also happened with the Children’s Mercy–Kansas City study that achieved a “molecular diagnosis” for 45% of their 100 families. They set up their study to extract a ton of information.

The more recent higher percentage – 45% compared to 25% — might be because the Children’s Mercy group considered only neurodevelopmental disorders (which include developmental delay, autism, and intellectual disability). By comparing newborns in intensive care units to older children who are veterans of multi-year “diagnostic odysseys,” the study revealed the great value of early exome sequencing. And they showed that the technology is cheaper and faster than a gene-by-gene approach.

Cifrão_symbol.svgCOSTS CONVERGE
When it comes to genetic testing, more is indeed better. Finally.

It’s been clear that exome and even genome sequencing would eventually cost less than single-gene tests ever since Myriad Genetics began charging $3,200+ for sequencing just the two BRCA genes. The new study homes in on the converging costs.

The investigation began at Children’s Mercy 3 years ago when the Center for Pediatric Genomic Medicine formed. “This is a retrospective look at the first 100 families enrolled in the genome center repository for diagnosis of neurodevelopmental disabilities,” Sarah Soden, MD, a developmental pediatrician and first author of the paper, told me. The 119 kids of those first 100 families had symptoms that didn’t exactly match those of any of the 2,400 or so known single-gene nervous system conditions.

Given my non-existent math skills I appreciate the cut-off at 100 families. Fifteen of the families had children hospitalized in the neonatal or pediatric ICU, and the rest were veterans of the average 7-year trek to diagnosis. The acutely-ill 15% had their genomes sequenced too, because exome sequencing can miss genes buried in GC-rich genome regions, which confound DNA replication enzymes like a stutter disrupts speech. Illumina provided instruments that can sequence genomes in under 50 hours, although analyzing the data takes a few days.

(NHGRI)

(NHGRI)

Considering the kids by the direness of their clinical situation proved telling. Genome sequencing diagnosed 11 of 15 (73%) of the families with kids in the ICU, while exome sequencing diagnosed 34 of 85 (40%) of the families with older children. The older kids were less likely to be diagnosed because their years of testing had ruled out many illnesses.

And that previous testing was expensive: on average $19,100 per nonacute family. The researchers estimate that sequencing would be cost-effective at up to $7,640 per family. Plus, there’s no metric for diagnosis of a child that takes days rather than years.

Of the 119 children, 18 had many symptoms because they had two genetic diseases. Five young patients had been receiving the wrong treatment, which was stopped, and 12 were treated correctly following accurate molecular diagnosis. So exome/genome sequencing isn’t only informational, it’s practical.

TWO INTERESTING CASES
My favorite parts of exome and genome sequencing papers are the cases, as well as those I learn about when seeking comments for articles in Medscape. That happened when I talked recently with Dr. Marion, who says exome sequencing is already routine in clinical genetics.

“Our group had been following a family for 6 years, and they’d had every test that could be imagined. High-resolution chromosome testing, FISH, single gene mutation analysis for specific disorders — everything normal. The child had growth retardation, developmental delay, and multiple congenital anomalies,” he told me.

The parents, first cousins, knew that if the condition was inherited, they were carriers and every child would face a 1 in 4 risk. Dr. Marion sent a blood sample from the 6-year-old to have his exome sequenced just when the couple had become pregnant again.

“We found a mutation in a gene we’d considered (H syndrome), but the child didn’t fit completely. We then tested the fetus and unfortunately it was affected,” Dr. Marion continues. The parents ended the pregnancy because they felt they couldn’t care for two children with the condition, and appreciated the information. Only 50 cases of H syndrome have been reported.

Sequencing the exomes of parent-child trios, like in the syndrome H family, is especially informative because if the parents don’t have mutations that could cause the condition, then their child probably has a new and dominant mutation. And that means it’s unlikely to repeat in a sibling.

Dr. Soden describes a child in the Children’s Mercy trial who also “didn’t fit.” He had autism, up to 30 seizures a day, and by age 3 had a tremor and difficulty walking. By 10 he was wheelchair bound. A series of photos in the paper show his initially beautiful face becoming slightly skewed as he grew, a common finding in inherited conditions.

“This patient had gone years without diagnosis and enrolled for whole exome sequencing, with his parents. That identified a mutation in the PIGA gene that has historically been associated with a blood disease, but had very recently been associated with neurologic disability in infants. All patients described had passed away before a year of age, and this kid was 10 at the time,” Dr. Soden says. Pyridoxine (vitamin B6) has helped children with similar syndromes, so maybe it will help him.

TURNING THE TABLES: EXOMES FIRST
The new study shows that exome sequencing can reverse the diagnostic trajectory, going from genotype to phenotype. Dr. Soden loves it. “What’s so exciting about genomic medicine is the practical side. Diagnosing the patient provides answers to families and physicians, and at the same time we can make discoveries.”

But Dr. Marion waxes wistful about handing over the excitement of the hunt to the precise new tool that is exome sequencing.

Dr. Marion with a young patient. (Children's Hospital at Montefiore)

Dr. Marion with a young patient. (Children’s Hospital at Montefiore)

“The bad part for me, being a cranky old clinical geneticist, is that it takes out of our hands the art of clinical genetics. In the old days we’d look at a child and analyze the information and come up with a differential diagnosis that might include 3 or 4 disorders. We’d go through the list, ruling out diagnoses. Now we recognize a kid has multiple congenital anomalies and send off samples for testing and get answers and try to fit the kid into the identified condition. But it’s definitely worth the benefit to families, siblings and patients.” Dr. Marion has solved many such mysteries in his career. In the photo he’s with a patient, now a teen, whose genetic disease (mucopolysaccharidosis type VI) he could name just by looking at her, followed up with genetic testing of course.

Although studies from Baylor, UCLA, Children’s Mercy, the NIH’s Undiagnosed Diseases Program, and others have certainly validated exome (and back-up genome) sequencing, it might be a few more years until the neighborhood nurse practitioner or urgent care physician pops a patient’s sample into a sequencer before venturing a diagnosis. “People trained more than 5 to 10 years ago have no idea how to use this information and will have to be retrained to do so,” says Dr. Marion. Medical schools are educating future physicians  in genomics.

Sarah Soden, MD (Children's Mercy-Kansas City)

Sarah Soden, MD (Children’s Mercy-Kansas City)

Dr. Soden expects to see exome sequencing enter subspecialty care first, and Children’s Mercy is helping with the education effort. “We have a genomic medicine master class where physicians spend a week with us and really learn what genome medicine is all about. Broad applications may be down the road, but in a center like ours we’re going to see it faster,“ she says. And Illumina holds regular workshops for health care providers to have their own genomes sequenced and interpreted, to learn the potential for diagnosing their patients.

Exome sequencing could be done on newborn heelstick blood samples.

Exome sequencing could be done on newborn heelstick blood samples.

Dr. Marion suggests another way that exome sequencing may nudge into the medical mainstream. “There’s going to be pressure on state labs to offer this in newborns. It will come from industry, because they will market directly to pregnant women: ‘Send blood from the newborn and we’ll predict the child’s health for the rest of his or her life.’ State labs will then say, ‘we have a 2-tiered system in which families that can pay get better screening’ and state health departments will say ‘we have to fix that.’ Babies will go home from the hospital and pediatricians will get readouts from the state lab of every polymorphism and mutation and predict what the person’s health will be like.”

It’ll be like cord blood storage.

But Kevin Davies, PhD, author of “The $1,000 Genome” and publisher of Chemical & Engineering News, tempers exome excitement.

“Even newborn genome screening becomes more and more plausible as the cost of sequencing continues to drop, we still await definitive evidence that this makes medical sense. I’m thrilled by the wondrous stories of diagnostic odysseys ending thanks to genome screening, but we need more than intermittent anecdotal reports to judge the clinical benefits. Trials are underway to address this key question. I also think the genetics community has a massive task ahead to communicate the benefits of genome screening to a general public that is still nervous, skeptical and even afraid of losing their genomic privacy.”

Thoughts?

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James Watson On “Genetic Losers”

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640px-James_D_Watson_Genome_ImageI’m thrilled that Christie’s decided to auction off James Watson’s Nobel prize on a Thursday, DNA Science posting day! I’ve got some great quotes to add to the chatter.

Dr. Watson shared the Nobel prize with Francis Crick in 1962 for deducing and describing the three-dimensional structure of DNA, assembling clues from the experimental findings of many others. He went on to launch the human genome project at the National Institutes of Health, and is today Chancellor Emeritus of the Cold Spring Harbor Laboratory.

But Dr. Watson is also known for outrageous comments that insult anyone with dark skin, a fondness for the same sex, mental illness, a genetic disease, or two X chromosomes. Laura Helmuth excellently summarizes some of his comments at Slate.

(Dept. of Energy)

(Dept. of Energy)

I first heard Dr. Watson speak when I was in grad school, and too sleep-deprived to remember anything. Shortly after Francis Crick died in 2004, I decided to interview Dr. Watson while he was still around. So I spent 14 hours on Amtrak during a single day going from Schenectady, New York to Cold Spring Harbor Laboratory on Long Island, when I was writing for The Scientist. He was prompt, polite, and charming. And then I asked my first question.

“Dr. Watson, which do you think was more significant, deducing the structure of DNA, or sequencing the human genome?”

He sat back, smiled, and stroked his chin, seemingly deep in thought. It wasn’t a bad question to start. A pause, then …

“Ricki, do you consider yourself a girl or a woman?”

I never could get him to answer questions about science seriously, and I wonder now if that’s why I can’t find my piece at The Scientist website. I might have killed the story, which was to be a Q+A, before my editor had a chance to do so. And his comments were too misfired to make it into my human genetics textbook.

Maclyn McCarty, Francis Crick, and James Watson

Maclyn McCarty, Francis Crick, and James Watson

I heard Dr. Watson again at the opening session of the 12th International Congress of Human Genetics in Montreal in October, 2011. He was on a panel of “genome pioneers” who were among the first to be sequenced. Kevin Davies, author of “The $1,000 Genome  and presently publisher of Chemical & Engineering News, moderated.

Dr. Watson, who was the second to have his genome sequenced following Craig Venter, spoke first. I published a cleaned-up version soon after the conference, but yesterday found the offensive comments I’d left out earlier. They’re included in the Q and A below. Colleagues tell me they heard the “genetic losers” remarks at other conferences, but the statements don’t seem to be showing up in the news coverage, which as usual continually recycles the same info.

Watson the guinea pig

Watson the guinea pig

(Disclosure: I had guinea pigs named Watson and Crick, and Watson was one of the smartest and longest-lived pets I ever had.)

PS: At the end of the panel discussion three years ago, I was the first to leap onstage to approach Dr. Watson, to ask him to review my soon-to-be-published gene therapy book. I was very dressed up (rare for me) and the only XX in the immediate vicinity. Hoards of young, XY groupies glared up at me from the audience as Dr. Watson turned on the charm and talked to me for nearly 5 minutes. I was clearly no longer a girl. But I sent him a galley of my book and he never responded.

So here are Kevin Davies’ questions, offending answers included amongst some very useful observations, as posed to Dr. Watson at the Congress of Human Genetics in Montreal in October, 2011. (Dr. Davies in CAPs, Dr. Watson in italics, me in non-italics.)

WHY DID YOU HAVE YOUR GENOME SEQUENCED?
“I thought, why not? I had no objection, with the exception of not wanting to know ApoE4. My grandmother had Alzheimer’s in her 90s, and the fact that I was in my 70s and didn’t have it didn’t reassure me I wouldn’t in my 90s.”

(ApoE4 and the surrounding DNA were deleted from Watson’s  published genome sequence. At the time people with two copies of a variant of this gene were thought to have a 15-fold increased risk of Alzheimer’s and people with one copy a 3-fold increased risk. However recent studies have found that the increase only applies to women and inheriting variants in other genes can counteract effects of ApoE4.)

WHAT DID YOU LEARN THAT WAS USEFUL?
“Finding that I am a slow metabolizer of antipsychotics and beta blockers. I have a slightly irregular heartbeat and the doctor put me on beta blockers. Two put me to sleep. Now I take them once a week, so knowing I’m a slow metabolizer was a real medical benefit. It also may have explained a mystery concerning my son. He almost died of neuroleptic malignant syndrome from an antipsychotic. I now know that if I go psychotic, I will tell people I can’t take those drugs.”

WAS ANY GENOME INFORMATION NOT HELPFUL?
“They told me I had something that should have killed me, a mutation in a DNA repair gene. And so I decided not to think about it. I didn’t go and look it up. Then they told me I was one base pair off the bad one. They told me I was a carrier for BRCA1 and so I thought I would have to phone my nieces because their mother had breast cancer. But before that 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.”

(Jonathan Bailey, NHGRI)

(Jonathan Bailey, NHGRI)

WHO SHOULD HAVE THEIR GENOMES SEQUENCED?
“I’d like to see children who have mental illness sequenced with their parents. My son has schizophrenia. The moment you have a son who is not normal, you wonder if you are the cause, or if you could have done something differently. Finding a mutation would make parents see that it was just genetic injustice, not anything they did. Knowing that won’t make their child healthy, but they won’t have the double whammy of thinking they did something wrong. I think an educated society doesn’t like genetics because it is so deterministic, and they would prefer it if you could have diets so you wouldn’t have a mentally ill child.

It is my belief that about 5% of children are born with rather bleak long-term futures. They really won’t be able to take care of themselves. They might become homeless later in life and I think making people aware of this goes back to Hermann Muller who worried about mutational load. We should think this way again.

Evolution means mutations and there are going to be losers who, 20,000 years ago, would not have lived very long. But now in our so-called compassionate society we should take care of them, but we do so very badly as they age. There are some born losers. It’s not that their parents were bad. But what’s the ethical responsibility to take care of the genetic losers? Having set up the ELSI (The Ethical, Legal and Social Implications) research program, I suspect that all the programs put together have yielded nothing of value. They’re talking about minor things. The major issue is, what do we do with people with mad genes? That’s never discussed.”

James Watson and Sydney Brenner at the Asilomar conference in 1975, where recombinant DNA research was born. (Natl Library of Medicine)

James Watson and Sydney Brenner at the Asilomar conference in 1975, where recombinant DNA research was born. (Natl Library of Medicine)

HAS YOUR SON INFLUENCED YOU TO HAVE YOUR GENOME SEQUENCED?
“My son would say yes, but he didn’t want to. He doesn’t want to discuss it. I would have a completely different view, that we might be able to help him and he should have no choice, but that is the sort of thing brought up at ELSI meetings. I find them counterproductive to help the people born with genetic disease.

I’m very conscious of genetic losers – other people want to deny their existence. Other people want to cure them.”

ARE YOU WORRIED ABOUT THE FLOOD OF DATA FROM SEQUENCING GENOMES?
“I’m more worried that we’ll get the flood of information and we won’t use it because of excessive concern about privacy. Right now I’d be pragmatic, be as free as possible with sequencing genomes, and then if disaster is the result, we’ll try to correct it. I’d hate for anyone to say ‘you can’t tell your child that he has a DNA change.’ I think parents, within limits, should have control over what their children know, and trying to regulate that would be just awful.

I’m very happy the $1000 genome exists. Genetics will help us to understand why people don’t fit in. Every time someone goes into a children’s hospital with a serious disease, it would be immoral NOT to sequence him.”

ATCG's Image with Group of PeopleIronically, this week Stephen Kingsmore’s group at Children’s Mercy-Kansas City report in Science Translational Medicine on 100 families for whom exome and genome sequencing led to diagnosis of children with hard-to-classify neurodevelopmental disorders, which include autism, intellectual disability, and developmental delay. I’ll cover this paradigm-shifting paper next week.

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Nailing a New Niche of Stem Cells

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Green highlights the stem cell niche of a mouse's nail. (Kobielak lab)

Green highlights the stem cell niche of a mouse’s nail. (Kobielak lab)

If my mother-in-law hadn’t just yanked off a toenail, I might not have noticed the news release from researchers at the University of Southern California’s Stem Cell Regenerative Medicine Initiative. Their elegant experiments in mice reveal the heretofore unknown collection of stem cells that enable the rodents, and presumably us, to regrow our nails.

Krzysztof Kobielak and colleagues (first authors are Yvonne Leung and Eve Kandyba) report their findings in the October 21 Proceedings of the National Academy of Sciences. It is unfortunately behind a paywall, so I will enlighten you.

Nails, skin and its glands, and hairs descend from the same layer of the embryo, the ectoderm. The nail is the last to reveal its stem cell secrets. Skin renews constantly, hair cycles every few months, and sweat glands don’t replace cells often if at all. A nail is the only ectodermal derivative able to completely regenerate if ripped totally out, as my mother-in-law just did.

It turns out that a nice niche of stem cells enables nails to regrow. This, to me, is the most fascinating part of stem cell science – discovering new aspects of anatomy and physiology, especially how parts initially form or regenerate.

A mouse's rear. (credit: Artie the Cat Lewis)

A mouse’s rear. (credit: Artie the Cat Lewis)

MOUSE MANICURES
The researchers created transgenic mice that had DNA sequences encoding:
• A keratin, expressed in the ectodermal derivatives
• Green fluorescent protein (GFP) from jellyfish, a standard way to track cells
• A protein that confers resistance to tetracycline antibiotics

The genetically modified mice had skin, nails, hair, and sweat glands that initially glowed greenly. But after a bit of development, and then a course of doxycycline, the color faded in all but the stem cells, which retained the GFP marker because unlike other types of nearby cells, being stem cells they didn’t readily divide. (The color became diluted as neighboring cells divided without further stimulation to express GFP.)

The stem cells form a distinctive ring in an area of a nail called the proximal fold, the bit of nail/skin boundary just underneath the tip. The investigators named the cells “nail proximal fold stem cells.” Production of keratin #15 distinguishes the stem cells, a little like hair colors. (Most types of mammals have about 50 keratin genes.)

Ick.

Ick.

To see how a nail regenerates following damage, the investigators induced “nail plucking injury,” presumably under non-torture conditions, and watched what happened. That meant a transcriptional profile, a look at the messenger RNAs made as the nail regrows, and compared profiles of healthy nails as well as in surrounding skin for both situations.

A lot goes on in nails. Hundreds of genes blink on and off, just to keep nails growing normally. As expected, transcriptional profiles change following injury. After subtractions eliminated housekeeping gene expression, two genes that regulate bone morphogenetic protein (BMP), called Bambi and Decorin, emerged as the controls of nail growth. Normally they dampen production of BMP, which favors growth of the skin around the nails. But whack off a nail and expression of these genes, and of the BMP that they control, increases.

So the stem cells can do two things: favor skin, or favor nail. And they can change what they do to suit environmental circumstance.

To test the findings further, the researchers bred mice that couldn’t make much BMP. And the animals had puny nails, especially at the tips, with overgrowth of surrounding skin.

The maimed mice regenerated their nails in just 2 weeks. I imagine things will move at a slower pace for my mother-in-law.

A_woman_with_nail_artOUTGROWTHS
As for most stem cell discoveries, knowing about nail proximal fold stem cells inspires the imagination.

• Understanding the signaling behind the shift from making-skin to making-nail may suggest new drug targets and candidates for assisting regeneration of human fingertips. Humans can regenerate fingers, but in a limited way compared to, say, the abilities of a starfish.

• Stem cells likely control shifts in repair at other bodily tissue interfaces. Perhaps we can tweak them, too, in therapeutic ways.

Jesse James was a famous bankrobber. DNA testing confirmed that the body in his grave was likely his.

Jesse James was a famous bankrobber. DNA testing confirmed that the body in his grave was likely his.

• Identifying the dead. Stem cells might protect DNA in a corpse, compared to a cell that normally divides often. Sampling stem cells from nails to confirm the identity of a corpse might be easier than obtaining other tissues. I’m thinking of the fuss over the DNA extracted from teeth and hair of outlaw Jesse James and the pelvic bone from 5300-year-old  Ötzi the Tyrolean Iceman.

• Cosmetic possibilities. Might a coating of BMP-spiked color or hardener halt nail growth, preserving the perfect pedicure?

200px-Stem_cell_division_and_differentiation.svgDEFINING STEM CELLS
Finding an accessible stem cell niche, even in a structure as seemingly non-vital as a toenail, is important, because tweaking the fates of any stem cells’ daughter cells might provide therapeutic cells tailored to the individual. Imagine bolstering a failing heart with cells from one’s nails.

Media gripe: many articles still define stem cells as “turning into any cell typ,” No need for links, just google that phrase.

If stem cells turned into “any cell type,” they’d soon be depleted. Rather, when a stem cell divides, it produces another stem cell (“self renewal”) and also gives rise to daughter cells that may go on, perhaps dividing more, to specialize.

The biological significance of a stem cell is the ability to perpetuate its stemness. In the illustration above, only the cells ringed in purple are stem cells.

Sweetsgiving_Feast_SpreadAn analogy. If turkey, dried bread hunks, butter, celery, potatoes, green beans, mushroom soup and other Thanksgiving fare spontaneously assembled into casseroles and such, and people ate it all, there’d be nothing left for seconds or thirds unless the fridge magically filled with more of the basic ingredients. Like the gobbled up Thanksgiving feast, an organ that uses up its stem cells and must grow to stay alive is in trouble. And that’s why stem cell science is so exciting — it uses our body’s natural reserves.

OK, so I’m not great with analogies. Have a happy Thanksgiving, and thanks to all readers of DNA Science!

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When Mutation Counters Infection: From Sickle Cell to Ebola

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Brass_scales_with_flat_trays_balanced While pharmaceutical companies focus on drug discovery for Ebola virus disease, a powerful clue is coming from a rare “Jewish genetic disease” that destroys the brain. People with Niemann-Pick C1 disease can’t get Ebola, adding to the list of disease pairs that arise from a fascinating form of natural selection.

Balanced polymorphism, aka heterozygote advantage, is a terrific illustration of ongoing evolution. And it pits the human body against all sorts of invaders – prions, viruses, bacteria, protozoa, and fungi.

sickleThe textbook example of balanced polymorphism is the protection that being a carrier for sickle cell disease confers against malaria, published in 1954.

The blood of a person with full-blown sickle cell disease is too thick to accommodate the malaria parasite, and the red blood cells too bent to house them. A carrier has enough sickled cells to quell the parasite, but not enough to block circulation and cause the pain and anemia of the inherited disease. Alpha thalassemia, hemoglobin C and G6PD deficiency are other single-gene diseases that affect red blood cells in ways that lower risk of malaria.

The link between genetic disease and Ebola virus disease dates from 2011, when Thijn Brummelkamp, PhD and co-workers, at the Whitehead Institute for Biomedical Research, reported in Nature that cells of people with the rare single-gene Niemann-Pick C1 disease keep out Ebola.

Ebola virus particles (NHGRI)

Ebola virus particles (NHGRI)

The gene that is mutant in Niemann-Pick C1 disease encodes a transporter protein that normally binds cholesterol — and it’s also the receptor for Ebola virus. Carriers of the inherited disease, with half the normal number of transporters, might have some protection against the viral disease. (A recent article in the Wall Street Journal discusses the carrier situation, but doesn’t cite the standard sickle cell example – commenters did.)

The tango between us and our pathogens is more complex than examples within ourselves of conditions canceling each other out. The poor clotting of hemophilia shields against dangerous blood clotting; the extremely low serum cholesterol level of Smith-Lemli-Opitz syndrome, which causes intellectual disability and a host of strange birth defects, counters cardiovascular disease. These don’t involve a second party.

Examples of balanced polymorphism are like mystery stories, beginning with the clue of why a seemingly harmful recessive genetic disease hangs around. New mutation is one answer, but more common is the protection that the heterozygous state offers. Here are some of the stories.

CFTR ion channel, open and blocked

CFTR ion channel, open and blocked

CYSTIC FIBROSIS AND DIARRHEAL DISEASE
In cholera a bacterial toxin opens chloride channels in small intestine cells, and salt and water pour out in a torrent of diarrhea. The misfolded CFTR protein behind many cases of cystic fibrosis, which is a chloride channel, does the opposite, failing to reach the cell surface and trapping salt and water inside cells, drying secretions. A person with misfolded CFTR won’t get cholera, while a CF carrier, with enough working chloride channels to breathe okay, but not enough to welcome toxin-spewing pathogens, suffers neither disease.

The cholera epidemics that have swept through human history favored individuals who carry or have CF. But geography and history suggest that the story goes farther back, because CF arose in western Europe and cholera in Africa. Perhaps a different diarrheal infection, typhoid fever, triggered the initial favoring of mutant CF alleles that perhaps arose from mutation.

The bacterium behind typhoid fever, Salmonella typhi, enters small intestine cells through CFTR channels. In people with severe CF the channels are too mangled to reach the cell surface. Bacteria can’t enter. Cells of CF carriers only let in a few bacteria. Protection against infections that produce the runs may therefore have kept CF around.

The Guthrie test began the era of newborn screening -- half a century ago.

The Guthrie test began the era of newborn screening — half a century ago.

PKU AND A FUNGAL TOXIN
Testing for phenylketonuria – PKU – ushered in the era of newborn screening with the Guthrie test, invented in 1957 and one of my favorite genetics stories. It tests blood from a newborn’s heel so that dietary intervention can prevent the profound intellectual disability of the disease.

PKU is a classic “inborn error of metabolism.” A missing enzyme causes the amino acid phenylalanine to build up, devastating the nervous system. Carriers have excess phenylalanine — not enough to damage their brains, but enough to counter the effects of a fungal poison called ochratoxin A that causes spontaneous abortion.

In 1986, PKU guru L. I. Woolf published a brief letter in the American Journal of Human Genetics explaining how a fungus could maintain a rare inherited disease of humans. Ochratoxin A is a derivative of phenylalanine that binds to the enzyme that places phenylalanine into proteins as they form. With one of the 20 amino acid types blocked from joining proteins, the embryo quickly stops developing – unless the pregnant woman’s body makes excess phenylalanine, which counters the effects of the toxin. That happens in PKU carriers. Thanks to newborn screening PKU is caught early enough today to be treated, but ochratoxin causes a kidney disease in Eastern Europe called Balkan endemic nephropathy.

Ochratoxin on moldy grain altered genetic history

Ochratoxin A on moldy grain altered genetic history

It isn’t coincidence that PKU is most prevalent in Ireland and Scotland. In the dampness of those lands, the Aspergillis and Penicillium fungi that produce the toxin grow on grains, which people were forced to eat during times of famine. Because pregnant PKU carriers were more likely to have healthy children than non-carriers, who suffered miscarriage due to the fungal toxin, the PKU mutation increased in the population. That’s natural selection. Evolution. It happens.

Mad_cowPRIONS AND CANNIBALISM
Prions are proteins that can fold into infectious forms that cause transmissible spongiform encephalopathies. The most familiar are those that come from eating the proteins, such as mad cow disease. The classic example is kuru, which caused brain degeneration among the Foré people in Papua New Guinea in women and children eating the brains of honored dead relatives. The Australian government halted the practice in the mid-1950s.

But we also make our own prion protein – the gene that encodes it is on chromosome 20. Normal prion protein is abundant in the brain, and likely plays a role in synaptic plasticity in early development. This story is more complicated than those of Ebola, CF, and PKU, because the same protein comes from inside and outside the body, and it is the protein, in abnormal form, that is the pathogen. Prion protein is a shape-shifter, able to assume the infectious form right inside ourselves.

Back to New Guinea. Some of the female Foré brain eaters are still alive, and an investigation of the prion protein gene among 30 of them revealed that 23 are heterozygotes for the prion protein gene on chromosome 20, meaning that they have two slightly different versions of the gene. Population genetics statistics predicted only 15 of them should have been so.

The carriers have the amino acid valine at amino acid position 129 on one chromosome 20 and a methionine on the other. And this somehow prevents the infectious misfolding. Plus, everyone in the UK who developed mad cow disease had only methionine at position 129.

And so cannibalism may have fueled the overrepresentation of carriers of the infectious form of prion protein. Protected, the carriers slowly accumulated in the population.

Brass_scales_with_flat_trays_balancedWHY IT MATTERS
For many years, the central dogma reigned, the idea that DNA encodes RNA which encodes protein. Our genomes were thought to encode protein, and do nothing else, although people hypothesized vague “controls” amongst our regular genes.

Then introns (non-protein-encoding parts of genes) came along in 1977 and turned our simplistic view on its head. Most of us in genetics never thought the “rest” of the genome was “junk.” If I remember correctly, that was an unfortunate utterance from Francis Crick that the media ran with, and it stuck.

Today we know that the human genome comes complete with all manner of controls. Some are indeed embedded in the non-protein encoding sequences that make up most of the genome. Other controls are in short RNAs that fold themselves up in ways that glom onto and turn off certain genes, and in the numbers of short repeated sequences that pepper genomes. The human genome is a little like a fancy TV with a zillion remotes that somehow knows how to control itself without the user knowing how it all works.

Balanced polymorphism is yet another form of genetic information. It reveals a story, a subtext to our genes written by our own actions throughout history, and the scourges that felled some of our ancestors, enabling individuals carrying particular mutations to survive to reproduce, perpetuating those mutations.

Making sense of the intriguing pairings of genetic and infectious diseases can reveal ways to fight those infections. Let’s hope this approach works for Ebola virus disease.

(Parts of this post are based on passages in my textbook, Human Genetics: Concepts and Applications (Amazon doesn’t yet list the new, 11th, edition). For each edition I struggle to limit myself to 2 examples of balanced polymorphism. It is difficult to choose!)

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