DNA Science Blog

A Little Girl With Giant Axons, a Deranged Cytoskeleton, and Someday Gene Therapy

By Ricki Lewis, PhD
Posted: May 16, 2013

Rating: +2 (from 4 votes)

Hannah, age 7. (Dr. Wendy Josephs)

“When you hear hoof beats, think horses, not zebras.” So goes the mantra of first-year medical students. If a common disease is a horse and a rare disease a zebra, then giant axonal neuropathy (GAN), with only 50 or so recognized cases worldwide, is surely a unicorn.

Five years ago this week, 9-year-old Hannah Sames of Rexford, New York, who lives near me, received a diagnosis of GAN, a disease much like amyotrophic lateral sclerosis. And this month, thanks in part to the herculean fundraising efforts of Hannah’s Hope Fund (HHF), the cover and lead article of the Journal of Clinical Investigation reveal most of the story behind the devastating inherited disease, with repercussions that will reach far beyond the tiny GAN community.

If all goes well at the next Recombinant DNA Advisory Committee meeting at the NIH, a phase 1 clinical trial may be underway before year’s end to evaluate gene therapy for GAN. “A fire started burning deep in my core exactly 5 years ago when Hannah was diagnosed. We will not rest until we have a successful treatment for our kids. They are rare, but they are no longer neglected,” says Lori Sames, Hannah’s mom and executive director of HHF.

CHARMING HANNAH
On March 5, 2004, when Lori and her husband Matt first glimpsed their newborn daughter’s kinky reddish fuzz, they were both delighted and puzzled. Madison, five, and Reagan, two, have stick-straight hair, as do Lori and Matt. When the birthing goop dried, Hannah’s cap of tight curls sprang to life.

For many months, the little girl seemed okay. She smiled, sat, crawled and hauled herself upright on schedule. But her footsteps were halting, hesitant. Hannah slowly grew clumsy, the strength ebbing from her legs. Lori made the usual rounds of specialists assuring her all was well, but already, filaments of protein were distending the long axons of the motor neurons running down Hannah’s legs, blocking messages to her muscles.

Lori Sames, Executive Director, Hannah’s Hope Fund

By Hannah’s third birthday, Lori and Matt suspected something was seriously wrong. Both of Hannah’s arches now bowed, and she tottered. More doctors gave false reassurances, hardly hiding their diagnosis of Lori as a helicopter mom. Then Lori’s sister showed cell phone video of Hannah walking to a physical therapist friend, who thought Hannah’s gait was like that of a child with muscular dystrophy. Six months of neurological tests followed, all results normal.

That’s what happens with a disease so rare that few physicians have seen it, or even heard of it. They can’t recognize a unicorn, don’t know what to test for. But finally an astute pediatric neurologist gave Matt and Lori an answer, and it didn’t come from an exome sequence or a sophisticated scan. “He took out a huge textbook and showed us a photo of a skinny little boy with kinky hair, a high forehead, and braces that went just below the knee – he looked exactly like Hannah. And he had GAN,” Lori recalls. Three days of tests at a children’s hospital in New York City confirmed the diagnosis.

Meeting with a genetic counselor was devastating. Lori recites what they learned: “Matt and I are each carriers of GAN, and we passed the disease to Hannah. Each of our two other daughters has a two in three chance of being a carrier. GAN is a rare ‘orphan genetic disorder’ for which there is no cure, no treatment, no clinical trial and no ongoing research.”

“So you are telling us this is a death sentence?” Lori recalls asking the genetic counselor.

“Yes.”

The disease would progress slowly, the counselor said. Hannah’s legs would continue to weaken. By first grade she’d likely need a walker in addition to her ankle supports, and soon after, a wheelchair. She might lose her sight and hearing, and eventually be bedridden.

Matt and Lori walked around like zombies for a few days. And then they founded Hannah’s Hope Fund. Their basement became a war room where they used their business backgrounds to assemble the first ever research conference for GAN. As Lori taught herself molecular biology, she became convinced that gene therapy was a logical approach, but at the same time recognized the value of learning anything about GAN. They were lucky to find Jude Samulski, director of the Gene Therapy Center at the University of North Carolina at Chapel Hill, and he recommended a young investigator, Steven Gray, to lead the team. It’ll be the first gene therapy delivered to the spinal cord. A clinical trial is incredibly expensive, and HHF’s fundraising efforts are amazing – they’ve earned $1 million in just the past 8 months. They’re just one of many not-for-profits in the rare disease community who have taken the helm of funding research.

Reproduced with permission from the American Society for Clinical Investigation; J. Clin. Invest. 2013; 123(5)

INTO THE INTERMEDIATE FILAMENTS
In parallel to the gene therapy efforts, HHF supports research into the nature of the cellular glitch behind GAN, in the labs of Robert Goldman and Puneet Opal at Northwestern University, Jean-Pierre Julien at Université Laval in Quebec, Pascale Bomont at the INSERM neurological institute in Montpelier, France, and others. The group reports on a remarkable set of experiments in May’s JCI that probe the out-of-control parts of the cell’s inner skeleton, the intermediate filaments (IFs).

GAN is the perfect disease to investigate IFs because it’s caused by a single gene and has a large, measurable effect. Other conditions may affect IFs secondarily, or reflect input from several genes or environmental exposures.

At fault in GAN is a protein called gigaxonin that normally interacts with the IFs. Most kids with GAN have abnormal forms of the protein; Hannah is highly unusual in that she lacks it entirely.

A cell’s inner scaffolding has three types of girders: microtubules made of the protein tubulin, microfilaments made of actin, and the intermediate filaments made of several other types of proteins. The recipes for IFs vary with cell type: keratins in hair, neurofilaments in neurons, and vimentin in fibroblasts, the connective tissue cells that make up much of our bodies. But all IFs share a basic dumbbell shape, with a head, a tail, and a long helix in the middle. The dumbbells align and aggregate into filaments.

(Dept. of Energy)

BLOCKING CELLULAR TRASH REMOVAL
Being a nerd, when I hear “T and A” I think “tubulin and actin.” And when I hear “UPS” I don’t think of brown delivery trucks spewing package-clutching people – I think of the ubiquitin-proteasome system. The UPS is how cells round up their garbage and get rid of it.

Ubiquitin is a molecule that tags other molecules bound for destruction, like marking rotten produce at a supermarket or the tire of a parked car exceeding the time limit. Other proteins help escort the debris to proteasomes, which resemble spools that tear apart what’s dumped into them, spewing out pieces that are then further degraded.

Gigaxonin – what Hannah’s cells lack – is technically an “E3 ubiquitin ligase adaptor,” based on its DNA sequence. In Hannah’s motor neurons, hair follicles, and probably other places, the utter absence of gigaxonin means the IFs aren’t broken down and recycled. They remain extended and build up, slowly, which is why Hannah was okay for the first two years. I don’t mean this in a bad way, but Hannah is, genetically speaking, like a knockout mouse because she has two deletions of a major part of her gigaxonin genes.

Green IFs enmesh orange mitochondria in these mouse fibroblasts. (Linda Parysek + Trudy Aebig)

Dr. Goldman and his group looked at fibroblasts from knockout mice and from three patients (called “GAN cells”; not including Hannah’s), tracking the interaction between vimentin and gigaxonin. Their discoveries confirm and extend what’s known about the disease:
• GAN affects IFs, leaving microtubules and microfilaments alone.

• GAN cells don’t overproduce intermediate filaments – the mRNA level for vimentin is normal. Rather, the filaments aren’t broken down on schedule, like garbage collectors going on strike.

• GAN cells are strikingly abnormal. Like a creeping wad of chewed gum, the glommed filaments pervade the cytoplasm, cling to the nucleus in clumps, and capture mitochondria, rendering these energy-extracting organelles swollen and misshapen. The cell’s organelles drown, swept up and suspended in the gunk of a deranged cytoskeleton.

Gigaxonin grabs onto vimentin by the helix part of the barbell. But the researchers were surprised to find that ubiquitin doesn’t enter the picture – gigaxonin must route the IFs to the proteasomes by some alternate pathway. However it happens, the researchers hypothesize, gigaxonin normally dismantles the long IFs into pieces that enzymes further chew up – like splintering a pile of logs into twigs.

GAN’s correctible! At least in a dish. Giving gigaxonin to GAN cells lowered IF levels within 72 hours, which is what gene therapy would ideally do. But kids aren’t collections of cells. If gene therapy goes off target, what could happen? If it works too well, will cells without IFs survive?

ON BEYOND ZEBRA
The research results may suggest new (or perhaps old) drug targets for GAN. Meanwhile, the slow crawl towards clinical trials continues.

(Dr. Wendy Josephs)

In a disturbing twist, Hannah will not be among the first to receive the experimental gene therapy, because she doesn’t make gigaxonin. So if genes placed in her spinal cord enable her motor neurons to make gigaxonin, her body will see a protein it’s never encountered before — a red flag to the immune system. And so before Hannah can join the clinical trial that has not yet begun, she must have treatments to accustom her immune system to gigaxonin. That means suppressing T cells or a stem cell transplant from one of her sisters.

This week at the American Society of Gene and Cell Therapy annual meeting in Salt Lake City, researchers are brainstorming ways to modulate the immune system to accept a protein introduced with gene therapy, with Hannah the case study. “How can they safely treat her? What is the best way to suppress her immunity? And how will they determine when it’s safe to wean her?” Lori asks. She’s there, of course.

Casey Davies Ketcham lost her battle with GAN in March.

The GAN extended family that Lori and Matt Sames brought together five years ago lost their first member March 26, beautiful and inspiring 21-year-old Casey Davies Ketcham. Blogged Lori at the time, “Today, I feel very angry, sad, agitated … Angry we were all given GAN… Angry this has taken so long to bring to a Phase 1 trial… Rest in peace Casey. With God’s continued grace we will conquer GAN. We will feel your strength and peace when our kids receive gene delivery. You wanted to be the first, and you will be there in your vibrant spirit.”

Casey’s legacy is also that what researchers learn about GAN will likely help many others. “IF aggregates form in several types of neurological disorders in addition to GAN—such as ALS and Parkinson’s disease,” says Dr. Goldman. Add to that variants of spinal muscular atrophy and Charcot-Marie-Tooth disease, Alexander disease, Lewy body dementia, and Alzheimer’s disease. ”Our results suggest new pathways for disease intervention. Finding a chemical component that can clear the aggregations and restore the normal distribution of intermediate filaments could one day lead to a therapeutic agent for many neurological disorders,” says lead author Saleemulla Mahammad, a postdoctoral researcher at Northwestern.

I hope the days when rare diseases were considered “orphans,” and ignored, are finally gone, as more and more families form not-for-profit organizations that push research far beyond what was once possible. What we learn about the unicorns and zebras can often help the horses too.

(Hannah’s story is told in chapters 10 and 11 of my book The Forever Fix: Gene Therapy And The Boy Who Saved It.)

Rating: +2 (from 4 votes)

Category: Uncategorized | Tagged American Society of Gene and Cell Therapy, cytoskeleton, GAN, gene therapy, giant axonal neuropathy, Hannah's Hope Fund, intermediate filaments | 6 Comments

Celebrating Gleevec – and Basic Research

By Ricki Lewis, PhD
Posted: May 9, 2013

Rating: +3 (from 3 votes)

Chronic myeloid leukemia cells (NCI).

When 23-year-old Glamour magazine editor Erin Zammett Ruddy went for a routine physical in November 2001, she expected reassurance that her healthy lifestyle had been keeping her well. After all, she felt great.

What Erin received, a few days later, was a shock. Instead of having 4,000 to 10,000 white blood cells per milliliter of blood, she had more than 10 times that number – many of the cells cancerous. Erin had chronic myeloid leukemia (CML). Two years before her diagnosis, CML was a death sentence. But the drug Gleevec saved her and many others. It offers perhaps the best example of translational medicine.

A LIFE TURNED UPSIDE DOWN BY CANCER
“I had just returned from a nice, long lunch to find a message from my doctor. Could I call back? Something had come up in my blood work,” Erin told me in 2007, when I met her at her office in midtown Manhattan.

I’d read Erin’s blog and invited her to tell her story in my human genetics textbook, which she did, with a photo of her grimacing during one of her many bone marrow samplings. And what a success story it’s been!

Next week Erin celebrates the start of her 11th year with the cancer essentially gone, thanks to Gleevec. Also next week the story of the drug, The Philadelphia Chromosome by fellow PLOS blogger Jessica Wapner, will be published. At the same time panoramic yet detailed, the new book chronicles the researchers and molecules behind Gleevec, beautifully complementing Erin’s 2005 book “My So-Called (Normal) Life.”

When Erin was diagnosed, Glamour had just published a story about the new drug, which the FDA had approved in May 2001. Erin contacted the physician heading the 3-center clinical trial, Brian Druker, MD, director of the Knight Cancer Institute at the Oregon Health & Science University and Howard Hughes Medical Institute Investigator. She flew to Portland for tests, and soon began taking one pill of Gleevec every day. After a short bout of stomach cramps and a little eye puffiness, she, like nearly everyone to receive the drug, responded.

Over a few weeks, Erin’s cancer ebbed away — and stayed away, even with brief hiatuses for two pregnancies. She announced her third last week.

Before Erin’s story, my textbook had covered the discoveries that led up to Gleevec, because they are a classic in genetics. I’d thought the story would make a terrific book, but couldn’t see how I could tell such a complicated and technical tale. Now Jessica Wapner has done exactly that, in her masterpiece “The Philadelphia Chromosome.”

BRAIDING THE RESEARCH THREADS

Peter Nowell and David Hungerford discovered the Philadelphia chromosome (Penn Medicine)

Gleevec arose from an unexpected assembly of pieces that no one initially realized went to the same puzzle. First came the discovery of an unusual “minute” (small) chromosome in 1960, in two men with CML whose cells wound up in the lab of pathologist Peter Nowell at the University of Pennsylvania, where PhD student in cytogenetics David Hungerford, from the nearby Fox Chase Cancer Center, worked. Nowell and Hungerford’s telltale “Philadelphia chromosome” – Ph1 — showed up in other CML patients too. Dr. Nowell tells the story in the Journal of Clinical Investigation.

It wasn’t until 1972 that Janet Rowley at the University of Chicago, using new, higher resolution chromosome stains and famously spreading out her images on her kitchen table, discovered that the Philadelphia chromosome is a translocation – one chromosome 9 and one chromosome 22 swap parts (chromosomes are numbered by size, 1 the largest).

By 1984, with generic chromosome staining having evolved into the DNA-sequence-specific “FISH,” (fluorescence in situ hybridization) researchers zeroed in on the two genes juxtaposed in the translocation: the Abelson oncogene (abl) from #9, and the breakpoint cluster region (bcr) from #22.

The two genes, cut and rejoined, generate two unusual chromosomes. The larger, #9 with a bit of #22, has no known effect; the other, tiny #22 with a smidgeon of #9, called the bcr-abl fusion gene, drives certain white blood cells to divide like crazy, becoming leukemia.

The cancer isn’t inherited; it just happens, for cancer is a genetic alteration of somatic cells. “The only difference between normal cells and CML cells was that in the former, bcr and abl were separate and that in the latter, bcr and abl were fused. And that fusion turned the once harmless abl into an oncogene,” Wapner writes.

The BCR-ABL oncoprotein that the bcr-abl fusion gene encodes was already very familiar to drug developers – it’s a tyrosine kinase, a member of a family of enzymes that oversee signal transduction pathways. But pharma had been focusing on cancers more common than CML.

If the pharmaceutical industry learned anything from this saga, it was that curing the rare can lead to curing the common. And the BCR-ABL oncoprotein was the key to halting Erin’s cancer, CML. The drug-to-be was first called CGP-57148B while at Ciba-Geigy and largely ignored, then STI-571 when Ciba-Geigy and Sandoz merged to beget Novartis. After clinical trials and lightning-speed FDA approval – 10 weeks — STI-571 became Gleevec in the US, soon Glivec elsewhere.

Gleevec

HOW GLEEVEC WORKS
The drug fits into a pocket of the BCR-ABL oncoprotein, displacing the energy molecule ATP. This prevents the jettisoning of a lone phosphate that starts the bucket-brigade-like passing that sends signals inside the cell. A tyrosine kinase is an enzyme that adds a phosphate to a tyrosine amino acid on a particular protein. When ATP binds the abnormal oncoprotein, continuous cell division results. Slapping on Gleevec is a little like shutting up a blabbermouth.

(NCI)

Preclinical experiments took years – in rodents, beagles, rabbits, monkeys, and most tellingly, the bone marrow cells of CML patients, where the drug worked. In people the intravenous infusion that the company pushed was ineffective, but the pills that some of the researchers and Dr. Druker favored did work – as a far less invasive daily orange pill. And that wasn’t the only unusual thing – compared to standard chemo, Gleevec has no side effects, other than transient eye puffiness, cramps, and bone pain as the cancer cells die off.

Gleevec is the first drug to combat cancer at its source, rather than targeting cancer cells by their excess antigens, the way that the breast cancer drug Herceptin works. And the clinical trial results for Gleevec were astonishing. I remember reading the abstract in the April 5, 2001 New England Journal of Medicine many times, in utter disbelief. Of 54 patients, 53 responded to the drug.

As Gleevec did its job, three measures of success were clear. Numbers plummeted: leukemic cells, Philadelphia chromosomes, and copies of the messenger RNA representing the fusion gene. The speed of FDA’s evaluation and approval of the submitted data set a record that still holds. “The Philadelphia chromosome” opens with one patient’s experience as this happened, and the book includes the names and contributions of the many individuals who made Gleevec a reality.

Wapner flawlessly weaves the three threads of Gleevec’s beginnings into a tightly knit fabric: how viruses subvert normal cell division genes into killer oncogenes, the development of kinase inhibitors, and the Philadelphia chromosome tale. The success was most stunning in the sickest patients. She writes:

“The responses began within a week after starting STI-571. Among several dying patients, white blood cell counts dropped, making room for restorative red blood cells to proliferate and heal the body. The color returned to their faces. They gained strength. They got up and out of their wheelchairs and walked out of the hospital.”

Wapner also captures Dr. Druker’s realization that what he’d predicted had actually happened, as the first patients brought back from the brink of death tearfully thanked him. “I realized they were so far ahead of me. They already accepted that this drug had worked and had changed their lives,” Dr. Druker said.

NOBELS NEXT?
Gleevec was 41 years in the making, from 1960, when two young medical researchers in Philadelphia noted an unusual tiny chromosome that their leukemia patients shared, to FDA approval in 2001. Writes Wapner, with hindsight, “The story of how the Philadelphia chromosome led to CML was like a hundred painters applying brushes to a canvas at some time or another over twenty-five years, driven only by curiosity and, sometimes, a vague hope that their work might eventually be relevant to human cancer. There’d been no final picture in mind and no awareness that they were even painting something together. And yet there it was. A scientific masterpiece.”

On May 17, Peter Nowell, Janet Rowley, and Brian Druker will share the
Albany Medical Center Prize in Medicine and Biomedical Research for their work on Gleevec. “Their collective achievements opened new fields of cancer research and have improved the lives of many,” said Joseph R. Testa, Ph.D., co-director of the Cancer Biology Program at the Fox Chase Cancer Center. Dr. Hungerford died in 1993, at age 66, of lung cancer.

The Gleevec story didn’t end with Erin’s rare cancer, CML. Gleevec is currently approved in the U.S. to treat 10 cancers, and has been tweaked so that patients whose cells become resistant can continue to benefit. And Druker has developed other drugs for when resistance persists, always staying one step ahead of the cancer.

More than fifteen kinase inhibitors have been FDA-approved, treating different cancers, with 500 more in clinical trials at half that many companies. Gleevec led the way.

“This type of targeted therapy is the future of cancer drug therapy and the future is here,” said Druker on learning of the Albany prize. “With the technology we have available today, what took 40 years — the discovery of the Philadelphia chromosome to the approval of Gleevec — can happen in a matter of months. It’s an exciting time to work in this field.”

THE PHILADELPHIA CANCER STORY: THE SEQUEL
A small molecule like Gleevec is only one new way to combat cancer. A completely different type of cancer treatment based on an engineered immune system molecule is unfolding, again in Philadelphia, right now. Novartis, sponsor of Gleevec, has given $20 million to build a facility for “chimeric antigen receptor,” or CAR, technology, on the Penn campus. CAR technology is in clinical trials to treat several cancers and HIV infection.

A chimeric antigen receptor is part T cell receptor, part antibody segment, its mosaic gene delivered aboard lentivirus (disabled HIV) to T cells. The CAR leads the T cells to the cancer cells distinguished by their many copies of the corresponding antigen. Zelig Eshhar, at the Weizmann Institute of Science, originated the general idea of retooling T cell receptors in the 1980s .

CAR technology was pioneered on patients with acute lymphoblastic leukemia (ALL), which affects 70,000 people in the U.S.. The New York Times chronicled the recovery of 6-year-old Emma Whitehead. Bruce Levine, one of the inventors of CAR technology with Carl June and others, told me all about Emma and the other patients now in complete remission, at a recent gene therapy conference – which I’ll cover in a future blog.

Let’s celebrate the translation of knowledge of the basic life sciences — cell biology, biochemistry, genetics, and immunology — into saving lives.

Rating: +3 (from 3 votes)

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Confessions of a D Orbital

By Ricki Lewis, PhD
Posted: May 2, 2013

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Organic chemistry has changed! Not the science, but the way it’s taught.

SUNY Stony Brook, Fall semester, 1973. 500+ wannabe doctors pack into the lecture hall, squinting as a small figure up front slaps down overheads, scribbling CHNOPS atoms and various dots and dashes, changing the acetate sheets faster than any human brain can register them. Each night after a lecture, like fatty acids emanating from the glycerol backbone of a triglyceride, we’d align in the library to copy the incomprehensible overheads at 3 Xerox machines.

Stony Brook University, Fall Semester, 2012. The professor, wearing a remote microphone and holding an iPad, walks about the cavernous lecture hall, as the students, in groups, work problems, helped by a troop of last year’s students. The entire event is available online for those who can’t make it to class.

Recently I received an e-mail from the new chairperson of chemistry at Stony Brook, Nicole Sampson, describing organic chemistry as “a bad memory for those pursuing the dream of entering a health profession.” I read on. “Fortunately, this situation has changed at Stony Brook. Professor Frank Fowler has been applying advances in the cognitive sciences, in combination with new technologies, to teach students how to take a complex set of data and use it to solve problems.”

So I e-mailed professor Fowler, who’d taught my husband’s organic lab. Larry, as a chem major, had small classes where professors actually talked to students. I was among the great horde of pre-meds.

“Sure, I’d love to talk to anyone who’ll listen. The old days were not the good days,” Fowler answered to my first e-mail.

CULLED FROM THE HERD
If it weren’t for organic chemistry, I’d be an MD.

I knew by the first chemistry test freshman year 1972 that my childhood dream of becoming a doctor was over. By the end of my third semester of chemistry – the first of organic – I’d earned my third “D,” and was henceforth known as the D orbital. (By a statistical fluke, I got a C for the fourth semester. It happens.) I did, however, earn A’s in the lab, so I was not a complete moron.

I hadn’t yet taken biochemistry, so didn’t think anything that flew past in organic was of any relevance to medicine. At the risk of inducing an anxiety attack, I just unearthed Morrison and Boyd, the classic textbook (who knew I’d grow up to write those things myself?), to see if I’d have a flashback. And I did.

I looked up Friedel-Crafts alkylation, a phrase hovering in my distant memory, and soon discovered that this is the addition of a carbon-containing group to a benzene ring. According to the textbook, “In Friedel-Crafts alkylation, the electrophile is typically a carbonium ion. It, too, is formed in an acid-base equilibrium, this time in the Lewis sense,” followed by several reactions.

“What has this to do with setting a bone, removing a spleen, delivering a baby, or treating cancer?” I bellowed to my husband.

“The human body is a giant chemistry set that’s making and breaking covalent bonds,” he answered, obviously brainwashed. So I asked the same of the good Dr. Fowler.

“If anything, a molecular knowledge is more important for physicians and people going into health care now than it ever was. My dermatologist said, ‘I never use organic!’ But skin cancer is a perfect example of photochemistry of the skin,” Fowler said.

A NEW ORGANIC
“So what’s changed?” I asked Fowler on the phone.

“We understand better how students learn, and it’s not when you talk at them. They learn by doing.”

The 1100 students in his two classes use the “inverted classroom” paradigm that is sweeping education and is working well in teaching genetics – students learn the material on their own time (hence delaying the extinction of textbook authors like me), then work in groups to solve problems during class.

“Work in groups? In organic?” I blurted, astonished.

“A group without a lot of smart people can get the right answer more frequently than just a smart person. This is very important in solving problems in the future,” Fowler said, insisting that today’s students are different. They eagerly work together, free of the anger and competitive streak that pervaded my own class, when everyone did anything to get the highest grades possible, lest they fail at the lofty goal of getting into med school. I even saw one student, whose name I still remember, spit into someone’s flask in lab, to better his own grade.

But I don’t think even a group of Einsteins could have helped me, because I just couldn’t see molecules in three dimensions. It’s inborn. Today, I can’t follow a dance instructor who faces the class – my brain can’t flip the perspective.

I thought that being able to rotate molecules on a laptop would have helped me, seeing the active site come into view as its substrate approaches, like this molecule of the drug Gleevec nestling into its target kinase (subject of next week’s blog). But Dr. Fowler still relies on handheld, tinker-toy like molecular models. “Life is 3D. You won’t understand problems in medicine if you don’t understand that a lot of molecules look alike because of their shape.”

He timidly brings up the gender factor. Do boy toys, like tools and model kits, better prepare kids to see molecular interactions in three dimensions, compared to Barbies? I think it’s a case-by-case thing. I grew up with model kits and war toys, and all I ever did with dolls was rip their heads off.

I might have benefited from Powerpoint presentations, though, which bridge the overheads of my time with modern animations too fluid to follow. “With Powerpoint you only see stuff come in and disappear. You can take a single topic, maybe 8 slides worth, and no student can tell when I go from one to the next. I can tell a much smoother story,“ Dr. Fowler says. He also uses “clickers” so that students can provide real-time feedback on whether or not a concept is penetrating.

A NEW WAY TO RECRUIT MED STUDENTS

The day after I spoke with Dr. Fowler, a Perspective by David Muller, from Mt. Sinai ‘s Icahn School of Medicine, appeared in the New England Journal of Medicine, describing a new way to prepare students for medical school that absolves them from much of the misery of organic chemistry.

The pre-med mantra of science courses, Muller wrote, was “used to cull the herd of talented aspiring physicians.” Sociologist Donald A. Barr from Stanford University and colleagues from there and UC Berkeley also point out in “Chemistry courses as the turning point for premedical students“ that students from under-represented minority groups have a particularly difficult time staying on the path to a career in medicine, a problem largely attributed to chemistry courses.

Since 1987, Mount Sinai has encouraged humanities majors to apply to the medical school. Those accepted can learn “clinically relevant” parts of organic chemistry and physics in an 8-week summer session, and no Medical College Admissions Test, the MCAT. The Humanities and Medicine Program (HuMed) did so well in preparing future doctors that it’s evolved into FlexMed, which encourages students of all majors to pursue medicine at Mt. Sinai.

Half of each new medical school class at Mt. Sinai will consist of these more broadly-trained individuals. The school will recruit students as sophomores and “assure” them of acceptance by summer, junior year. As undergrads they’ll take two semesters each of biology, chemistry, any science lab, and one semester of physics, statistics, ethics, and health policy (or global health or public health). Proficiency in Spanish or Mandarin is strongly encouraged.

A person can now become a physician yet avoid the year of organic chemistry with lab. Ditto the MCAT. (My favorite sentence about reliance on MCAT scores: they “effectively exclude bright, creative, motivated students who aren’t strong test takers.” Me.) But I imagine selection will be challenging. “We will use many of the same metrics we use in our other selection models: evidence of excellence in research, community service, clinical exposure, athletics or the arts, clinical experiences, evidence of leadership ability, etc. We will also look to grades and SAT or ACT scores for some general sense of academic competence, but they won’t be the deciding factor,” Dr. Muller wrote in an e-mail.

If I weren’t out to pasture since being culled from the herd, I’d sign up.

THE “HEALTH HALO” OF ORGANIC FOODS
Organically-grown, soon shortened to simply organic, foods became popular shortly after my traumatic encounter with organic chemistry. At first I wondered how a food could NOT be organic, NOT contain carbon. But of course the designation refers to freedom from pesticides, as if manure doesn’t contain carbon.

According to the dictionary, “organic” means “derived from living matter” or
“compounds containing carbon.” But the meaning has morphed into “natural,” “good,” or “better than that chemical-drenched crap.” The word that still gives me palpitations and makes me think of ketones and aldehydes has come to be nearly synonymous with “healthy,” and people will readily pay three times what the regular stuff costs, for that illusion of superiority.

Researchers at Cornell University’s Food and Brand Lab recently described a “health halo effect” that refers to consumers’ perception of superior taste, appearance, fewer calories, and overall value to any food bearing the flag “organic.” They asked 115 folks in an Ithaca, NY mall to compare organic versus regular versions of yogurt, cookies, and potato chips. The pairs were, of course, identical, the perceptions not. Anything labeled organic was deemed healthier, tastier, and even less caloric. Perhaps the investigators should have compared, say, carrots instead of prepared foods.

I survived my three D’s in organic chemistry. Occasionally I still have a nightmare of being in that lecture hall, trying and failing to fathom anything, re-living the desperation of knowing my score on an exam would equal the number of answers I got right by chance. My husband has helped by taking the same approach as allergy treatments, desensitizing me with a tee-shirt bearing the citric acid cycle. In the end, I found the clear logic of the relationship among three types of molecules much more comforting than the mysterious named reactions of organic chemistry: DNA, RNA, and protein.

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DNA Day and World Malaria Day: The Sickle Cell/Malaria Link Revisited

By Ricki Lewis, PhD
Posted: April 25, 2013

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Today is both DNA Day and World Malaria Day. As I was pondering how to connect the topics, e-mail arrived from my “son,” a medical student in Liberia. He had malaria, again, and this time it had gone to his brain.

I “met” Emmanuel in 2007, when he e-mailed me after finding my contact info at the end of my human genetics textbook, which he was using in his senior year of high school. He is my personal link between DNA Day and World Malaria Day. But the dual commemoration also reminds me of the classic study that revealed, for the first time, how hidden genes can protect us – that carriers of sickle cell disease do not get severe malaria.

The goal of the DNA Science blog is “genetics in context,” and what better time to do that than today, by linking genetics to infectious disease. (Also see A GPS View of the Human Genome from two weeks ago.)

OUR AFRICAN SON
Emmanuel’s charm and intelligence came through easily in his e-mails and Facebook posts, and soon, my husband and daughters began to correspond with him too. He called us Mom and Dad, calling himself “Your Son.” This made me uneasy at first – I didn’t want to insult his mother – but Eman assured us that this is the way in Africa. When my husband had a hernia operation unnoticed by the rest of the world because Michael Jackson and Farrah Fawcett died that day, Eman somehow found a phone and called, worried.

It’s very expensive to mail anything to Liberia, and most stuff that makes it is stolen. Eman sent us traditional clothing through a friend traveling here. I sent Obama tee-shirts, which miraculously arrived, and Eman proudly gave them to his siblings. President Obama is much loved in this country founded by American slaves.

Eman wrote often that he wanted to fight the infectious diseases that plague his nation, as he did in this letter to a geneticist colleague of mine seeking sponsorship:

“I am Emmanuel, age 21. After my studies in biology, I wish to become a medical doctor. In a country of 3.5m people and a little over 200 medical doctors (mostly foreign) there remains a great distance between health workers and healthy people. Most doctors live and work in urban areas, leaving those in rural areas vulnerable to diseases and little or no health care. Every day in Liberia, people die of curable diseases and that is very devastating. I have decided to pursue studies in Medicine to help change this situation. I hope that one day I will be of help to Liberia and the world. I want to become a doctor of the people, mostly based in the rural area where people rarely get access to health care.”

We encouraged and supported Eman, and he was almost through his second year of med school in mid-March, when he sent this e-mail:

Dear Mom and Dad,

I was admitted at a local hospital yesterday after I fell off. According to the nurse, onlookers took me to the hospital. I do not know what happened. I will get to know once the Doctor gets to see me tomorrow.”

I asked what he fell off of, and this turned out to be one of several linguistic misunderstandings we’ve had. “I mean I fainted. Loss of consciousness and postural tone,” he answered, already sounding like a doctor.

Two days passed, and then we got an e-mail from Eman’s brother that he’d been readmitted, with stage 3+ malaria. I didn’t know what that meant.

“3+ means it is severe. That could even lead to madness. His blood is very low maybe due to the typhoid. We hope he gets better for school soonest,” wrote Eman’s brother. Parasite-stuffed red blood cells were obstructing small blood vessels in his brain, causing his unconsciousness. If he didn’t die, I read, he’d probably be okay. Since then, our African son has been on a roller-coaster ride of chills and fever, trying to get back to school.

Plasmodium_vivax_macrogametocyte_5942_lores_blank

A Plasmodium sex cell (CDC).

I try to imagine what’s happening in his body. The life cycle for malaria is complicated. An Anopheles mosquito delivers protozoa (Plasmodium species) with its bite, and the parasites settle in the liver. Then they head to the red blood cells, where they persist in asexual forms (while fever and chills ensue). Some of them burst out, forming sex cells that are sucked up by another mosquito, which then injects the infectious cargo into another person.

Despite the decrease in annual malaria deaths by a third over the past two decades, the disease remains the #1 cause of morbidity and mortality in Liberia, where live expectancy is 59. In Africa, a child dies of malaria every 60 seconds.

Knowing the genome sequences of all the players in malaria – the vector, the parasite, and the host – are important in better understanding the disease. But when I think about malaria today, on this dual DNA/Malaria day, I cringe at some uses of DNA testing.

Here in the U.S., people are getting their exomes sequenced to know what conditions they might develop decades hence, while a world away, people still die in days from the types of infectious diseases that Eman has battled. Two years ago he had cholera, malaria, and amoebic dysentery all at once. Meanwhile, Americans send their spit to genetic testing companies that reveal such vital information as eye color, whether cilantro tastes like soap, or whether they sneeze in bright sunlight.

THE CLASSIC SICKLE CELL/MALARIA PAPER
The worlds of DNA and malaria collided back in 1953, the year that Watson and Crick published their famous paper on DNA’s structure.

Anthony Allison, a British doctor with a degree in biochemistry and genetics from Oxford, grew up at the epicenter of human evolution, in the Great Rift Valley in Kenya. As a young man he met Louis Leakey, at the Olduvai Gorge in Tanzania. Steeped in the central idea underlying evolution — that diversity drives it — Allison set out to investigate how the one inherited trait that could be easily followed back then varied among tribes: blood types. In 1949, right before he left on the research trip that would lead to his string of papers in 1954, a colleague wondered aloud about the high incidence of sickle cell disease. Inherited conditions that kill early in life tend to be extremely rare — only carriers and new mutations sustain it.

Intrigued, Allison surveyed the incidence of sickle cell disease among members of 35 tribes in East Africa. And it was staggeringly high – up to 40% — but only in areas where malaria was endemic.

The mutation rate for the beta globin gene would have to be extraordinarily high to keep it so common. Was there another explanation? Could carriers have a health advantage that enables them to survive to reproduce, passing on the mutation?

256px-Malaria_versus_sickle-cell_trait_distributions

Anthony Allison observed that the malaria and sickle cell geographic distributions in Africa are superimposable.

When Dr. Allison looked at maps of the distribution of both diseases, the connection jumped out at him. Where malaria was most prevalent, so too was sickle cell disease. When he counted the numbers of malaria parasites in the red blood cells of carriers versus non-carriers, like Eman, the puzzle pieces assembled.

Dr. Allison concluded that “persons with the sickle-cell trait have a considerable natural resistance to infection with Plasmodium falciparum,” in Transactions of the Royal Society of Tropical Medicine and Hygiene.

A name for this dual disease phenomenon already existed, coined by Dr. Allison’s mentor at Oxford, E. B. Ford: balanced polymorphism. A heterozygote (carrier, with two different alleles of a gene) has a survival advantage over either homozygote (2 identical alleles). People with 2 copies of the mutant hemoglobin allele (hemoglobin S) die young of sickle cell disease, but those with 2 copies of the healthy allele (hemoglobin A), if bitten by a disease-carrying mosquito, contract and likely succumb to malaria.

The idea was striking, but not entirely novel. In 1948, J.B.S. Haldane had noted a relationship between another disease of beta globin, beta thalassemia, and malaria – but he didn’t connect the dots, as Dr. Allison did.

Anopheles mosquito (James D. Gathany)

Once the malaria-sickle cell connection emerged, looking back at history explained malaria’s stronghold in Africa — and raises fears today about the effects of global warming in creating mosquito habitats.

Around 1000 B.C.E., Malayo-Polynesian sailors from southeast Asia traveled in canoes to East Africa, introducing wonderful new crops – coconuts, yams, bananas, and taros. Clearing the jungle to cultivate these newcomers provided breeding grounds for mosquitoes.

A cycle set in. Settlements with many sickle cell carriers – people who escaped both diseases – were able to clear more land to grow food. The mosquitoes, and their stowaways, flourished. This rapid changing of allele frequencies is the most profound illustration of evolution that I know.

But we still don’t know exactly how sickle cell carriers are protected against malaria. Asexual parasites soak up oxygen from the hemoglobin inside red blood cells, shriveling some of a carrier’s red blood cells into their characteristic crescent shapes. The cells are shunted to the spleen, slated for destruction along with their parasite stowaways. If carriers do get malaria, it’s mild. But other mechanisms may be at play too.

I don’t know if Dr. Allison is still around, but if he is, I hope a reader will send him this blog. He told Economist writer Laura Spinney in 2009, “Every generation likes to rediscover me.” We should celebrate his contribution today. It’s every bit as important as the DNA discovery.

OTHER DISEASE PAIRS
Sickle cell disease and malaria remain the “textbook example” of balanced polymorphism, but others are equally intriguing:

• Cystic fibrosis protects against certain diarrheal diseases because intestinal lining cells of carriers have fewer intact chloride channels, keeping bacteria or their toxins out.

• Phenylketonuria (PKU) persists because pregnant women who are carriers don’t lose their fetuses to ochratoxin, a poison made by fungi on rotting vegetables. People ate tainted vegetables during times of famine, which is why the world’s highest prevalence of PKU is in Ireland.

• Prions are infectious proteins that lie behind mad cow disease and related conditions. People who are heterozygotes for the prion protein gene make prion protein that can’t twist into the infectious form. In the mid-1990s, the several people in the UK who developed the human form of mad cow disease were all homozygotes, with two identical copies of the gene. Again, carrier status protects.

Another example of carrier advantage is just an hypothesis, and I don’t know who originated it. Several of the dozen-and-a-half “Jewish genetic diseases” affect the brain – terrible conditions such as Tay-Sachs, Canavan, Alzheimer, Niemann-Pick, and Batten diseases. Their prevalence reflects the serial shrinking of the Jewish gene pool in the wake of purges such as pogroms and the holocaust, so that distant cousins inadvertently marry distant cousins, unknowingly joining mutant genes in small children who suffer from these brain diseases. But maybe balanced polymorphism is favoring their carrier relatives. What might be their advantage?

Intelligence.

Might quick-witted ghetto occupants or prisoners been more likely to escape, keeping the mutations in the gene pool? If a good sense of humor is a surrogate for intelligence, then a second line of evidence might be the overrepresentation of Jewish people among comedians. Call it the Seinfeld effect.

(NHGRI)

DISCOVERING THE HUMAN PROTECTOME
How many other protective carrier states are hiding in our genomes? We have the computational tools to find them, but it’s difficult to detect omissions. Researchers must identify which diseases the carriers of the same single-gene conditions never get. That’s negative evidence, but it’s how we can unveil our “protectome.” We’ve been following these diseases for decades. The data await mining.

And it all started with the work of Anthony Allison, on malaria and sickle cell disease – the joining of genetic and infectious disease that we mark today.

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DNA Day and 20 Years of Writing a Human Genetics Textbook

By Ricki Lewis, PhD
Posted: April 18, 2013

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This month we celebrate the DNA anniversaries: unveiling of DNA’s structure in 1953, and the human genome sequence in 2003.

From now until DNA Day, April 25, bloggers will be worshipping the human genome. Nature.com will offer podcasts (PastCasts) and last week, Eric Green, director of the National Human Genome Research Institute, spoke to reporters, summarizing the “quantitative advances since the human genome project.”

It’s also the 20th anniversary of my textbook, Human Genetics: Concepts and Applications. Writing the 10 editions has given me a panoramic view of the birth of genomics perhaps different from those of researchers, physicians, and journalists. Here are a few observations on the evolution of genetics to genomics, as I begin the next edition.

A LONG AND WINDING ROAD
My textbook almost didn’t happen. Back in 1980, when I pitched it to the acquisitions editors descending on the zoology department at Miami University, no one cared.

“Human genetics? How about intro bio? Not enough sales in genetics.”

In 1992, the year my intro text was finally published, I found myself next to my favorite editor at a dinner. Human genetics had recently edged onto the editorial radar, thanks to media attention to the fledgling human genome project. I scribbled a table of contents on a dinner napkin, which served as a makeshift contract, and soon the project was a go. But the publisher still thought of genetics as an obscure outpost of academia, so the editors left me pretty much on my own.

I’m a storyteller, and so from the beginning, the textbook featured true tales from families with genetic diseases: A mom whose 5-year-old died from missing part of chromosome 5; a young man with XXY syndrome; and a 16-year-old wondering why visitors at an exhibit on spina bifida at a local science museum voted that people with this condition, which he has, should never have been born. Including the voices of real people added so much humanity to the textbook – the competitors tended to feature white male scientists – that one critic accused me of “writing like a woman.”

10 years since sequencing the first human genomes (NHGRI)

When I wrote the first edition, I couldn’t have imagined that the exome – a term not yet invented – would one day be sequenced from DNA in a spit sample, and sent, for $99, to an also-not-yet-invented web-based company. And according to the NHGRI, sequencing a human genome, which initially took 6-8 years and about a billion dollars, now can be done in a day or two for $3,000-$5,000.

GENETICS HEADLINES 20 YEARS AGO
What else was happening, and hadn’t yet happened, in human genetics when I wrote the first edition, circa 1992?

• The Huntington’s disease mutation had just, finally, been discovered, after a decade-long “chromosome walk” from a marker out on the tip of chromosome 4.

• Gene therapy basked in the afterglow of the first clinical trial, to treat an immune deficiency; 18-year-old Jesse Gelsinger hadn’t yet died from gene therapy for a urea cycle disorder, which derailed the field. The first FDA approval for gene therapy in the US may come this year, marking another “3” year in the history of genetics.

• The Human Genome Project, public consortium version, was getting underway, but the Celera Genomics team didn’t exist, as such.

• The first genome of a free-living organism had yet to be sequenced – that would happen two years later.

• The film GATTACA was four years away from dramatizing a society crippled by misuse of genetic information.

A look at Nature Genetics from September 1993 reveals the state of genetics.

The lead editorial probed the now infamous paper by Dean Hamer from the National Cancer Institute introducing what would become known as the gay gene on the X chromosome, ushering in the era of genetic determinism. Other articles mapped genes for infertility, migraine, and an assortment of rarities. A study about a baby with “leprechaunism” caught my eye – it’s been deemed offensive since then and is now called Donohue syndrome. That will probably soon become something about an insulin receptor gene mutation, following the trend to get away from eponyms.

Over the editions, the number of genes fell by an order of magnitude, from 200,000 to about 20,300 today. Other things increased. Today we recognize more types of RNA, species of Australopithecus, cancer-causing genes, sequenced genomes (humans and others), and genome regions that don’t encode protein.

PAST EXCEPTIONS ARE TODAY’S NEW RULES
As genetics has become genomics, the focus has shifted from the traditional study of diseases and mutants towards normal function and inherited variation.

Some chapters grew so large with all that added normalcy that they split, like giant amoebae redistributing their biomass into two individuals. “Multifactorial Traits” spun off “Behavior,” and “DNA Action” (the trek from DNA to RNA to protein) begat “Gene Expression.”

I’ve long wondered what to do with Gregor Mendel. Pea plant experiments may seem archaic, but I apply the laws they revealed whenever I counsel a couple about their chances of having a child with a single-gene disease. Yet responses to my Scientific American blog on what the heck to do with Mendel argued for minimizing him.

The problem isn’t the stretch from peas to humans – it’s more that the either-or simplicity of Mendel’s laws isn’t very helpful in the clinic, where individual genes do not operate as autonomously as a pea plant with wrinkled or smooth seeds.

In my textbook, the seeming exceptions to Mendel’s laws grew from a tacked on mention in edition #1, to an entire chapter (““Exceptions and Extensions to Mendel’s Laws”) in edition #2, to a renaming by edition #8, circa 2008, to “Beyond Mendel’s Laws,” recognizing that the exceptions had become the rules.

The oddities no longer considered odd are the forces that alter how we experience single-gene traits and illnesses, such as the environment (epigenetics) and other genes. These factors explain why some people with disease-causing mutation combinations don’t get the disease (“incomplete penetrance”) and why some mutations cause differing degrees of illness in different individuals (“variable expressivity”). Complicating diagnosis is “genetic heterogeneity,” when mutations in more than one gene cause a disease or trait, and “phenocopy,” when an environmentally-caused condition resembles an inherited one.

ALLELIC DISEASES – WE STILL DON’T UNDERSTAND SINGLE GENES
Edition #10 (2011) introduced yet another complexity lurking in simple Mendelian genetics — allelic diseases. That’s when different mutations in the same gene cause different diseases, depending upon the gene part and body part affected.

I started thinking about allelic diseases before they had a name. Once the cystic fibrosis (CF) gene was discovered in 1989 and researchers identified hundreds of mutations, clinical variations could be detected. Most people have the classic lung and pancreas symptoms, but some people only have frequent sinus infections or bronchitis, and men may have only infertility. These manifestations are all considered to be CF. Yet different mutations in the beta globin gene had been known for decades, and the diseases that they cause considered to be separate clinical entities, such as sickle cell disease, methemoglobinemia, and beta thalassemia. Why weren’t the distinctive guises of CF considered separate illnesses, too?

By the time I was writing the 10th edition, allelic diseases had started to accumulate, and they grew more and more intriguing. One mutation in a gene greatly elevates risk for Alzheimer disease, yet another variant of the same gene causes severe acne. The gene that causes Menkes disease, with its trademark ultra-kinky hair, lies behind peripheral neuropathy too. Marfan syndrome can also be stiff skin syndrome. The inborn error Gaucher disease (glucocerebrosidase deficiency) shares a gene with Parkinson’s disease.

The list of allelic diseases is growing. Finding the underlying commonalities among these peculiar pairs of illnesses may reveal shared mechanisms and potential drug targets. But the subtler lesson is that while the news is full of sequencing genomes, we haven’t yet figured out all the relationships among the variants of well-studied genes.

(NHGRI)

GENETIC TESTING
Perhaps the most astonishing evolution has been in genetic testing; it starts every edition of my textbook.

Edition #1 opened with the story of how a mother’s astute observation that her children’s pee smelled weird led to development of the diet to prevent symptoms of phenylketonuria (PKU). It’s still one of the best single-gene stories because it has a happy ending.

Editions #2 and 3, from 1997, looked ahead a few years to fetal testing that was just becoming widely used. Edition #4, from 2001, introduced college students Mackenzie and Laurel, named for soap opera characters. In each subsequent edition, they took a changing menu of genetic tests, laying the groundwork for the genetic testing that exploded from the clinic to spit-in-a-tube direct-to-consumer testing in 2008.

I invented Laurel and Mackenzie, although the tests they took in the first pages of each edition existed. Gradually descriptions of the first real sequenced human genomes began to appear, but I put them in the final chapter, on genomics. Edition #9 featured the first three genomes, from Craig Venter, James Watson, and “YH,” a Chinese man. Said Dr. Venter at the 2008 annual meeting of the American Society of Human Genetics of his and Dr. Watson’s genome results: “You probably wouldn’t suspect this based on our appearance — we are both bald, white scientists.”

The current edition ends with the genome of Stephen Quake , a pioneer of high-throughput DNA sequencing and one of the first to talk about his genome. In the 3 years since I wrote that, articles and books discussing someone’s genome seem to appear on a weekly basis.

What will I do for edition #11? By the time it’s published, genome sequencing will certainly be available for under $1,000, and will be well on its way to becoming part of standard health care. It’s hard to believe that in just 20 years, coverage of human genome sequencing in my book grew from a brief boxed reading, to part of a chapter on gene mapping, to its own chapter.

But now, as I embark on edition #11, I might shrink or drop the “human genome” chapter altogether, for it has now become a lens through which we must view every other aspect of the science we once called genetics.

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A GPS View of the Human Genome

By Ricki Lewis, PhD
Posted: April 11, 2013

Rating: +6 (from 6 votes)

A connectome for the gene TLR3. The circles represent genes most closely related in function to TLR3. (Casanova lab; PNAS early edition)

Taking cues from global positioning satellites, Yuval Itan, PhD, a postdoctoral researcher at Rockefeller University and his colleagues have created the “human gene connectome” (HGC), unveiled in
Proceedings of the National Academy of Sciences.

A MAP BASED ON FUNCTION
Researchers have been deducing gene lineages for decades, based on DNA sequence similarities that presumably reflect descent from shared ancestors. Dr. Itan’s approach is different: he’s looking for shared physiology, or “biological proximity.” That’s when a set of genes is related functionally to one core gene that’s already implicated in a particular disease.

Like evolution, the strategy uses existing information in a novel way. Dr. Itan works in the lab of Jean-Laurent Casanova, MD, PhD, at the St. Giles Laboratory of Human Genetics of Infectious Diseases. The group’s goal is to identify “monogenic holes” in the immune defense that make otherwise well children highly susceptible to specific devastating, life-threatening infectious diseases. With colleagues from Necker Hospital for Sick Children, the Pasteur Institute, and Ben-Gurion University, the researchers teamed the Dijkstra algorithm – developed in the 1950s and used in GPS technology – with other public databases: String (5 million protein-protein interactions), FunCoup (model organisms protein connections), and HumanNet (18,000 human gene interactions).

Researchers have used HumanNet to evaluate genome-wide association study (GWAS) data to analyze polygenic diseases, in which many genes contribute to small and unequal degrees to an illness. In contrast, Dr. Itan focused on single-gene (Mendelian) diseases, and considered only gene pairs related by shared function shown empirically, not simply shared sequences. He used these observable connections to assign distances between genes.

The human gene connectome is like reaching a site in a city from different starting points.

“It was exactly like driving from New York to Texas. GPS software does this using the same type of information that I have, the algorithm finds shortest way to get there. So why not use the same approach to navigate better between genes?” Dr. Itan asked. Facebook’s ability to connect people through shared contacts also influenced his metaphorical thinking of finding genes that are all functionally related to one core gene, and not to each other.

So the researchers tested the idea.

GENE DISCOVERY
Case #1: The Toll-like receptor 3 (TLR3) gene, discovered in the Casanova lab years earlier, causes the life-threatening brain inflammation herpes simplex virus 1 encephalitis (HSE) in children. TLR3 controls innate immunity, impairing a specific interferon.

The human gene connectome produced results both expected and not. “We took 2 patients who had HSE and had very recently been discovered to have a disease-causing gene called TBK1,” Dr. Itan told me. “So we thought if we take gene variations and run them by their distance to TLR3, would TBK1 show up? In both patients, it showed up first, purely based on this computational prediction.” The TLR3-specific connectome revealed two novel TLR3 pathway genes prior to their experimental validation — EFGR and SRC.

In a second test case, a mutation in a collagen gene that causes a form of Ehlers-Danlos syndrome pulled out 26 other genes associated with the Ehlers-Danlos syndrome and its genetic pathway.

Finding new genes behind what was thought to be a single-gene disease can identify new pathways for pharmaceutical interrogation, and perhaps suggest repurposing of existing drugs. And as in most genomic matters, power and possibilities will grow as other researchers contribute data, and the connections expand.

Dr. Itan sees the human gene connectome as not just a research tool, but as a way to cut through the needle-in-a-haystack situation that clinical sequencing in today’s early guise can impose. If a patient’s symptoms don’t match anything in a physician’s experience, the HGC can save time. “Until now you’d have to go through the literature and look at hundreds of genes. It could take months.” Dr. Itan can’t patent the human gene connectome, because, at the risk of a double negative, it isn’t non-obvious, and it’s based on publicly available information.

A practical application of the human gene connectome was in my blog from a few weeks ago, although I didn’t know of it yet — diagnosing novel forms of a single-gene disease.

Genetic heterogeneity is when mutation in more than one gene can cause a phenotype (disease or trait). The blog mentioned parents of a child with osteogenesis imperfecta (“brittle bone disease”) accused of abuse because they carry unknown mutations and therefore are negative on a standard genetic test. Hemophilia is another example, with different forms of the blood clotting disorder resulting from mutations that disable different enzymes.

BRCA1 (http://www.ebi.ac.uk/)

Not recognizing that mutations in different genes can have the same clinical consequences can lead to false assurances from genetic testing. This is the case for the BRCA1 breast cancer gene. A person can be tested through a health care provider using the Myriad Genetics test, or for the most common mutations through the direct-to-consumer company 23andMe, and if no mutations show up, think all is well. But BRCA1 interacts with several other genes, all part of the pathways that repair DNA. Mutations in those genes can cause breast cancer too.

I’ve gotten a lot of flak for blogging that I don’t want to know my genome sequence. My primary reason is that the information isn’t reliable until we know all gene-gene interactions. Now, thanks to the human gene connectome, we’re on the way to working out all the ways that genes can cause disease. I might have to get my sequence done after all.

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Genetic Modifiers: Healthy Mutants Fuel Drug Discovery

By Ricki Lewis, PhD
Posted: April 4, 2013

Rating: +2 (from 2 votes)

Healthy people with disease-causing mutations may help in drug discovery. (NHGRI)

I’m uneasy counseling a patient for mutations in the BRCA1 or BRCA2 cancer susceptibility genes. Typically, she’ll have a “first degree relative” – usually a mother or sister – with a related cancer, or might even have a test result in hand. This happened a week ago.

FUZZY GENETIC INFORMATION

My patient comes from a long line of female relatives who’d died young from breast or ovarian cancer. She’s already been tested and knows she has a BRCA1 mutation. Will she get the family’s cancer? Knowing would enable her to decide whether and when to undergo surgery to remove her breasts, ovaries, and uterus.

I quoted risk figures — 65% for breast cancer and 39% for ovarian cancer by age 70 — from a meta analysis that didn’t consider the strength of family history. The initial families Mary Claire King and colleagues analyzed to discover the BRCA genes back in the early 1990s had many cases, leading to high risk estimates that were lowered as data accrued.

My patient’s risk is high, no matter what the studies say, due to the young ages of her affected close relatives. If she had Ashkenazi Jewish ancestors, her risk would be even higher, as much as 87%. The environment can play a role in reproductive cancers too, such as exposure to environmental estrogens.

Patients like yes or no answers; in genetics, risks are often all we have. But we can use uncertainty to better understand disease, and that can lead to new treatments. Identifying “healthy mutants” is one way to do that.

INCOMPLETE PENETRANCE LEADS TO A NEW DRUG – TAFAMIDIS
The enigma of inheriting a disease-causing genotype, but not having the disease, is called incomplete penetrance. It’s genetic luck. Incomplete penetrance lies behind fuzzy risk estimates. The only disease I know of that approaches complete penetrance is Huntington’s disease – those who get the mutation eventually get the disease.

When I was in grad school in the 1970s, we attributed incomplete penetrance to a “modifier effect” – a second mutation in the responsible gene or in a different gene that counters the disease. Evoking modifiers then was just hand-waving, for we lacked today’s tools to interrogate exomes (protein-encoding DNA) and genomes.

Although genetics/genomics journals and posters at conferences feature people with inherited disease, it’s their healthy relatives who may be most helpful to research. Healthy mutants led to development of the drug Tafamidis, which the European Medicines Agency approved in late 2011 to treat a form of amyloidosis.

The green is amyloid, aggregating outside cells in TRR amyloidosis. (Peggy Wallace)

The green is amyloid, aggregating outside cells in TTR amyloidosis. (Peggy Wallace)

The 30 types of amyloidoses drown organs in proteins. The types of proteins vary, like soups with different ingredients but the same texture. In one form of Alzheimer disease the offending gunk is amyloid beta; in a form of Parkinson’s disease, it’s alpha synuclein.

Tafamidis treats transthyretin (TTR) amyloidosis, which affects peripheral nerves (causing familial amyloid polyneuropathy) and the heart. Made in the liver, TTR proteins normally form quartets that haul around retinol and, in more ancient species, thyroid hormone. We transport the hormone on other proteins, but our TTR’s retain the binding sites – a vestige of evolution.

In the disease, the TTR quartets fall apart and reform into gummy fibrils, the organ-stifling amyloid. Jeffery Kelly, PhD, who heads a lab at the Scripps Research Institute, was searching for a small molecule drug to nestle into the defunct thyroid hormone binding sites. This would, he hypothesized, stabilize the TTR quartets so they couldn’t break down and glom into the sticky fibrils of amyloid.

Then Teresa Coelho, MD, director of Unidade Clinica de Paramiloidose in Portugal, published a report on a family who had the well-studied mutation known to cause TTR amyloidosis – V30M (translation: valine at the 30th amino acid becomes methionine) – but who weren’t very sick. Intrigued, she discovered a family member with the mutation, but not the disease. What protected him?

It was a second mutation, in the other copy of the TTR gene on chromosome 18, at a different site in the DNA sequence. The protective mutation was T119M – a methionine at the 119th amino acid instead of threonine. The family’s genetic quirk dovetailed with the Kelly lab’s work, confirming that they were targeting the right part of the protein. They screened more than 1,000 small molecules, as FoldRx Pharmaceuticals, until they found what Pfizer now markets in Europe as Vyndaqel. Approval in the US awaits further data analysis. CureFFI.org is a blog that beautifully tells the whole story.

A breast cancer cell (NHGRI).

BACK TO BRCA

The star of the TTR amyloidosis story is a modifier within a gene. Last week, two articles in PLOS Genetics reported modifiers of the BRCA genes that lie outside them. The researchers, from the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), analyzed clinical data from dozens of centers, providing the power to detect subtle genetic effects.

In the BRCA2 paper, the researchers scoured the genome for differences (single nucleotide polymorphisms, or SNPs) among 4,330 women with BRCA2 mutations who have cancer, compared to 3,881 women who have the mutation but not the cancer. Thirteen modifiers were known; this study revealed a 14th. It lowers risk of cancer, but only among women with BRCA2 mutations.

The BRCA1 paper reports two modifiers associated with increased breast cancer risk and two with elevated ovarian cancer risk. Although one of these risk SNPs applies only to women with BRCA1 mutations, the others might be predictive in women who don’t have mutations, suggesting wider utility. That may be the case for TRR amyloidosis too, in which the protective mutation seems to boost health and longevity in the general population.

Incorporating the effects of modifier genes can refine the risks for particular patients, telling them whether they’re at the high or low end of the wide range. For the BRCA1 study, modifiers result in a risk of 28%-50% for the 5% of patients at lowest risk and of 81-100% for the 5% at the higher end. That type of information could make a difference to my patient and many others.

INSPIRATION FROM PARENTS

Parents and researchers join forces to tackle genetic disease.

I started thinking about the value of healthy mutants at the recent first research meeting of the Cure Retinal Blindness Foundation. Kristin and Mike Smedley, who have two boys with Leber congenital amaurosis, started the organization. (I blogged about them on Rare Disease Day.)

We met in a conference room at Shriner’s Pediatrics Hospital at Temple University School of Medicine on a Saturday, March 23. The large room was set up with an inner ring of researchers and an outer ring of parents forming the executive board. I was honored to sit with the researchers, although my function was to listen, type, and translate for the organization’s website.

Mickey Selzer, MD, PhD, professor of neurology at Temple, eloquently opened the meeting:

“Families of affected children yearn for a cure. Scientists are trained to revere the basic science, what we learn from disease. But scientists hunger to see their work translated into practical things that help people. We hope both the families trying to raise money and the scientists trained in ivory towers have a common goal of seeing a blueprint to developing a treatment in animals and translating it into a clinical trial.”

The researchers took turns presenting their work. Patsy Nishina, PhD, of the Jackson Laboratory, related an amazing finding about the mouse version of the “crumbs” (CRB1) mutation that causes the visual loss in the Smedley’s two boys. (Evolution, again.) When mice were bred to have the mutation, but in a different genetic background from which it arose, their visual impairment vanished – a modifier gene was at work.

The families knew instantly what that meant – maybe sighted siblings of their blind children also had the double dose of the CRB1 mutation, but were protected by another variant, in the same or a different gene. The unaffected siblings’ protective mutations hadn’t been discovered because their vision was okay – why would anyone look? Exome sequencing of healthy mutants in such families – now possible for under $750 in a research setting — could reveal modifier gene candidates.

The next step is to look for healthy mutants whose families do not have inherited diseases. But how can clinicians identify these folks, to refer them to studies, if the people aren’t sick? Like errors of omission, healthy mutants are hard to find.

That’s where searching for known disease-causing genes in the exomes of healthy people will be invaluable. If the numbers grow large enough, modifiers might emerge, and the nature of their protective proteins used to develop drugs, as happened for TTR amyloidosis. Researchers can annotate and archive sequence information without names, because identity isn’t important – information is. Sequencing genomes would be even better than exomes, because they’d include control sequences. Direct-to-consumer DNA testing companies such as 23andMe already have samples stored from many healthy people — perhaps this is part of their goal is to collect information on a million people by year’s end.

It’s ironic. I spent my grad school years scrutinizing flies with legs growing out of their heads to dissect and infer the controls of normal development. And human genetics has historically focused on mutants: the sick, the unusual, the abnormal. But the secrets to vanquishing many of our ills in this new age of genomics may lie among the healthy.

Rating: +2 (from 2 votes)

Category: Uncategorized | Tagged 23andMe, Alzheimer's disease, BRCA, genetic counseling, genetic modifiers, Huntington's disease, Parkinson's disease, Tafamidis, TTR amyloidosis | Leave a comment

Mayonnaise Taxonomy

By Ricki Lewis, PhD
Posted: March 28, 2013

Rating: +1 (from 1 vote)

I had a serious genetics topic all set to go today, but then something more timely and compelling arose. I began to wonder about what, exactly, mayonnaise is, and more importantly, how do the types of mayonnaise differ?

My musings started with Passover, and the importance of eggs at this time of year. At the Passover seder, we dip a hard-boiled egg in salt water, to commemorate the tears of the oppressed Jews in long-ago Egypt. Trying to make this step more palatable, my daughter Sarah suggested we instead make deviled eggs.

A great idea, but we soon encountered a problem. Should we use Hellman’s Light, my favorite, or Vegenaise, hers? Sarah’s a vegetarian; I’m a low-carber. And so began my experimentation. (Caveat: I omitted Miracle Whip because it is slimy “dressing”, not mayo. It has mostly the same ingredients as real mayo, more spices, and evil high-fructose corn syrup and cornstarch.)

Initially, I’d sent my husband out to get Hellman’s Light, but he inexplicably brought back Hellman’s Low Fat concoction. I returned it without even reading the label, because “low fat” is synonymous (usually) with “high carb” and such products can even have more calories. Compare ice cream cartons to see this. So that’s not part of my comparison.

After exchanging the offensive low-fat Hellman’s for Light, I stopped at the health food store for Sarah’s entrant. Vegenaise is not dairy, not gluten, not genetically modified organism-tainted, and also not cheap. It’s twice the price of the others. We used it to make the eggs, and no one was the wiser.

Today, post-seder, I visited the condiment aisle at Target, where I lined up the species of mayonnaise and recorded their attributes.

First, the ingredients. A tablespoon of Hellman’s “real” mayonnaise is an emulsion consisting of, in descending order, soybean oil, water, eggs, vinegar, and spices. That’s about 90 calories, 100% of which are from fats, courtesy of the soybeans. So that’s the baseline.

The variations on the mayo theme I evaluated were Hellman’s olive oil, Hellman’s canola, and Hellman’s Light, plus the Vegenaise (the links are to their respective genome projects). All have about 85% fat. Vegenaise has the highest calorie count — 90 — and Light wins at 35, with runner-up canola offering 40 calories per dollop.

The oils are telling. Fortunately all the participating organisms have had their genomes sequenced and available (except canola aka rapeseed, its sequence apparently owned by a company) and their lipids helpfully evaluated by the Cleveland Clinic. And the chicken, donor of the eggs, has been sequenced too. So we may someday be able to come up with a genetically modified organism that secretes mayo when shaken.

The more-caloric-and-costly Vegenaise comes out on top in the oil stakes, forsaking the ubiquitous soybean for grapeseed oil.

The more healthful grapeseed oil is 17% monounsaturated (meaning one carbon-carbon double bond), 73% polyunsaturated (more than one double bond), and 10% saturated (all the hydrogens the carbon skeleton can hold, the bad stuff). Soybeans’ stats are 25%, 60%, and 15%. I think the excess saturated fat in soybeans cancels out its win for monounsaturated.

Vegenaise’s one gram of saturated fat is twice that of Hellman’s Light, even though Vegenaise’s major claim is its freedom from eggs, which admittedly lurk amid the creamy swirls of Hellman’s Light. The label on this “healthy mayo alternative” claims to raise HDL, the “good cholesterol,” although HDL is no longer considered a valid predictor of myocardial infarction. Still, the jar is festooned with an image of a heart, with the words “Follow Your Heart.” It might help those individuals in whose families HDL is a valid biomarker.

I discovered some things. Hellman’s Light has more water than fat, and probably a lot of air. Alas, it harbors potato starch, poison to a low-carber. And Vegenaise, despite its claim of zero carbs, has brown rice syrup and mustard flour.

So which product wins? The portion size is too small to probably matter much, but unless you prefer the Vegenaise for political or social reasons, I’ll stick to my Hellman’s Light. Lower in calories and a better oil profile.

Back to serious genetics next week …

Rating: +1 (from 1 vote)

Category: Uncategorized | Leave a comment

Second Gene Causes Retinoblastoma

By Ricki Lewis, PhD
Posted: March 21, 2013

Rating: +2 (from 2 votes)

This beautiful little boy has heritable retinoblastoma. The white spots in his eyes are from light reflecting off of tumors.

In a list of famous genes, RB1 would probably be #1. It’s the tumor suppressor gene whose “loss of function” is behind the childhood eye cancer retinoblastoma, and that Alfred Knudson investigated to deduce the 2-hit mechanism of cancer.

In 1971, the idea that a gene’s normal function could be to prevent cancer was revolutionary. Now a new study finds that an amplified oncogene can cause the eye cancer too — with just one hit.

TWO ROUTES TO A TUMOR
Like the earth being flat, proteins being the genetic material, and genes being contiguous, the idea that mutations in RB1 are the sole cause of retinoblastoma has vanished. A multinational team of researchers, led by Brenda Gallie of Impact Genetics and the Toronto Western Hospital Research Institute, discovered that in a very small proportion of children with retinoblastoma, an oncogene, MYCN, is the cause. Their report is in Lancet Oncology. (Dr. Gallie, who supplied the photos here, heads an international effort to bring care for RB to the 92% of the thousands of children who have the disease who live in developing countries.)

Untreated retinoblastoma, circa 1806.

Retinoblastoma has a long history. A 2000 B.C. Mayan stone carving shows a child with a bulging eye. A Dutch anatomist provided the earliest clinical description, a growth “the size of two fists.” In 1886 researchers noted that the cancer can be inherited, and in those families, secondary tumors can arise, usually in bone. Once flash photography was invented, parents would notice the disease as white spots in the pupil, from light reflecting off a tumor.

About 1 in 20,000 infants has RB. In 40% of cases, both eyes develop tumors. This means that the child inherited a predisposition mutation in all cells, and the cancer develops when a second mutation “hits” a retinal cell. Of the 60% of cases where only one eye is affected, most (85%) result from 2 hits in the same retinal cell, without the inherited (aka germline or constitutional) mutation.

The road to finding the new gene began when the investigators in Toronto noticed that 7 children who had a tumor in just one eye didn’t have the expected RB1 mutation. Instead, one of the genes that typically comes into play later in the disease is present in extra copies – the oncogene MYCN. It’s known to cause neuroblastoma, another cancer that begins so early that babies are born with it. Just one amplified MYCN, like a genetic stutter, is sufficient to trigger the eye cancer. In genetics lingo, it’s a dominant, “gain-of-function” mutation.

Rosette structures are seen in classic RB tumors, but not in the newly discovered kind.

Researchers from New Zealand, France, Germany, and the Netherlands added cases, for a total of 1068, that included more children with the newly-recognized form of the disease, dubbed MYCN RB. The MYCN tumor itself, for those who like to look at such things, appears different. The rosette-like structures and coalesced nuclei seen in classic RB are absent, and the cells look like those of neuroblastoma. “It’s a subtle enough distinction that pathologists who received an eye removed under suspicion of RB would be excused if they say it looks like RB,” Timothy Corson PhD, assistant professor of ophthalmology, biochemistry and molecular biology at the Indiana University School of Medicine, told me.

The tumors of MYCN RB are large, invasive, and so aggressive that they usually appear before a child is six months old. In fact, 18% of one-eye retinoblastomas in kids this young are of the new type.

CLINICAL IMPLICATIONS
The finding of a new form of retinoblastoma has implications both specific and general.

Knowledge improves the lives of patients and their families. “If an infant with a single tumor is diagnosed with MYCN RB, then it’s not heritable. These kids don’t have the risk to pass it on to offspring, nor do they face a greater risk for subsequent cancers,” Corson said. That’s because the new form of RB arises anew in one gene in a retinal cell, not in sperm or eggs.

Follow-up is easier. “The exams through childhood are not simply going to an ophthalmologist and he or she looks in the eye. An infant must be put under general anesthesia to be still enough to carefully evaluate the eyes for tumors,” Corson says.

Treatment changes too. The first eye of a child with a family history of the disease is usually treated with chemo, rather than being removed, because the second eye is likely to develop tumors too. Preserving the eye saves sight. But in MYCN RB, “since the disease is particularly aggressive, and the other eye will not become involved, surgical removal of the diseased eye is the correct therapeutic course,” says Joan O’Brien, MD, chair of ophthalmology at the University of Pennsylvania School of Medicine.

A retinoblastoma tumor grows on the retina.

In addition to RB1 being a famous gene, the new finding enhances what is already a medical success story. “In ophthalmology we don’t often deal in life and death issues. Retinoblastoma is uniformly fatal if not treated. It’s wonderful that most of these young kids are cured nowadays,”shares Shalom Kieval, MD, associate clinical professor of ophthalmology, Albany Medical College, president of RetinaCare Consultants, Albany, New York, and chief of ophthalmology at Albany Memorial Hospital. One of his patients, whom he first met as a premature infant, brings her three kids to see him now. The mother and two of her kids have been successfully treated for RB. “The retinoblastoma story is another unsung but intensely gratifying accomplishment of modern medical science,” he adds.

THE BIGGER PICTURE

“Genetic heterogeneity” is when more than one genotype (gene variant combo) is responsible for the same phenotype (disease or trait). Hearing loss, for example, has more than 100 different genetic causes. And Leber congenital amaurosis, the main story in my gene therapy book , comes in at least 18 guises, LCA itself a subtype of retinitis pigmentosa.

A broken bone in a patient with OI type V. (Shakata GaNai)

Genetic heterogeneity has explained false accusations of child abuse. In osteogenesis imperfect (OI), aka “brittle bone disease,” bones break, often before birth. Like retinoblastoma, OI has left marks on history. An Egyptian mummy from 1000 B.C. had it, as did 9th century Viking “Ivan the Boneless,” who was reportedly comported into battle aboard a shield and whose remains were exhumed and burnt by King William I, forever obscuring the true diagnosis.

Until 1979, mutation in a single collagen gene was thought to cause OI. But cases arose of parents bringing babies with shattered bones to hospitals, and charges of child abuse filed. If social workers or other medical people knew about OI, the parents would be tested – but sometimes the tests were negative, even though the distraught parents insisted they hadn’t harmed their child.

Discovery of the second IO gene absolved some parents, but false accusations still happened. Then a third OI gene was found. I just checked Online Mendelian Inheritance in Man – the bible of geneticists – and found 14 types, but it’s confusing. Different types reflect mutations in the same gene, yet the same type can embrace different genes. The 14 types arise from 7 chromosomal addresses.

Whatever the terminology, the origins of discovering some of the recessive types are fascinating, often involving consanguinity (genetics speak for inbreeding).

OI type II was traced to the Mozobites, a polygamous sect in southern Algeria that had brother-sister/husband-wife pairs. Type VII came from a First Nations community in northern Quebec, where two generations of three interrelated families had many babies born with broken bones. Type IX families are from Pakistan, Senegal, and the Irish Traveller’s ethnic group and type XI derives from 5 consanguineous families from northern Turkey. Inbred families often illuminate rare single-gene diseases because parents share mutations inherited from their shared ancestors. The mutations are extremely rare in the outbred population in the area.

Annotation of the human genome is revealing more instances of genetic heterogeneity, explaining people who have clear symptoms of a known genetic disease yet test negative – like in retinoblastoma and osteogenesis imperfecta.

I hope the genetic testing industry, both clinical and direct-to-consumer, can keep up, and that patients/customers aren’t falsely reassured by low risks that don’t tell the whole story – because we may not know all of it, as was the case for retinoblastoma.

So while we’re busy sequencing all those exomes and genomes, keep in mind that we don’t know all there is to know. Single genes can still surprise us.

(For a more technical version of this information see Medscape.)

Rating: +2 (from 2 votes)

Category: Uncategorized | Tagged direct-to-consumer genetic testing, exome sequencing, Foundation for Retinal Research, genetic heterogeneity, Leber congenital amaurosis, ophthalmology, osteogenesis imperfecta, retinitis pigmentosa, retinoblastoma, tumor suppressor | 1 Comment

Do Cats With FIV Foretell HIV’s Future?

By Ricki Lewis, PhD
Posted: March 14, 2013

Rating: +4 (from 4 votes)

Romeo, my third immunodeficient cat, looks like Sylvester.

Since my January 24 blog “My Cat Has AIDS,” about my two feline immunodeficiency virus (FIV)-positive cats, we’ve acquired a third, the handsome Romeo. He, too, came to us from Orange Street Cats, on Valentine’s Day.

Romeo was found in an inner city park where people who can barely afford to feed their families nevertheless care for the burgeoning population of stray cats. “His origins are unknown, but I’d been feeding him along with other backyard cats where I live, a short distance from the vet,” said Ethel, the kind woman who saved him. “When Romeo injured his front leg, I trapped him and took him to the vet. The leg wasn’t broken, but they determined he is FIV positive, with no symptoms, so I couldn’t keep him,” because she already had an adult, indoor cat.

Ethel probably could have kept Romeo, for FIV doesn’t pass easily among indoor adult cats. “A lot of people take a positive FIV result for a death sentence, and it sets off waves of panic,” said my cats’ vet, “Dr. Bart” Forlano. Some infected cats never get sick. Others go through phases similar to a person with AIDS, with initial symptoms and then a long period of stasis, like my #1 FIV cat Juice, star of my January blog. Only a few FIV-infected cats get very sick.

Juice assists in writing an NSF grant.

Romeo, the sweetest, friendliest cat, apparently not a bit traumatized by his life on the streets, was fine on Valentine’s Day. But yesterday I noticed sores like those that plagued Juice in the weeks after he became infected. Romeo is meeting Dr. Bart as soon as I post this.

In this blog, part 2 of my FIV tale, I’ll cover the here and now – why vets don’t usually offer FIV vaccination – and the bigger, evolutionary picture that might impact the relationship between humans and HIV.

THE FIV VACCINE
Vets might never mention an FIV vaccine, while routinely vaccinating against the different disease, feline leukemia, for several reasons.

#1 Logic. Cats most likely to be infected with FIV are outdoor males. “FIV is a disease of young cats with outdoor exposure. That’s the segment of the cat population that should be vaccinated,” explained Arne Zislin, a veterinarian and Technology Manager, Pet Marketing for Boehringer Ingelheim, which produces the vaccine. It’s considered a “core vaccine“ for this group of felines. A captured cat, or pet that goes outdoors, would have an initial vaccine, then yearly boosters, and get a microchip (more on that below), he added. But the homeless outdoor cats are the hardest to catch, says my friend the vet from Texas. “They fight and inoculate each other with bites and scratches. Sexual transmission is an uncommon exposure route.”

#2 An indoor cat wouldn’t need the vaccine. “The chances of a household cat being infected with FIV is virtually nil, and even the chances of a neutered cat allowed outdoors from time-to-time becoming infected is also extremely low. Many FIV-infected pet cats live comfortable lives among non-FIV infected pet cats with a very low risk of passing the infection,” Niels Pedersen, DVM, PhD, director of the Center for Companion Animal Health at the University of California, Davis and co-inventor of the vaccine, told me.

#3 Practicality: Neither Dr. Bart nor my vet friend sees enough FIV-positive cats to justify vaccination. “I go through all my feline leukemia virus vaccine, but have thrown away trays of FIV because it has expired…you do that a few times and it makes you re-evaluate the need,” said TexVet.

#4 Insufficient protection: Like flu vaccine, FIV vaccine only protects against some viral strains. What worked in California in 2002 when the vaccine came on the market might not work in New York, and doesn’t cover my Texas friend’s cat population. Three doses of the vaccine, according to some studies, provide a 0-80% protection rate – too much of a swing for many vets.

#5 Mistaken euthanasia at shelters. An FIV-vaccinated cat makes antibodies against the virus for the rest of its life – as does an infected cat, even one without symptoms. “If you vaccinate a cat it will confound the typical test in a veterinary hospital to determine if a cat has FIV,” said Dr. Zislin. Shelters have euthanized pets testing positive from vaccination.

EVOLVING VIRUSES
Because many FIV-positive cats live normal, relatively healthy lifespans, I began to wonder whether most or even all cats are infected, and the ones we know about have enough of a viral load to test positive – and very few cats are tested. “The ability of most naturally-infected cats to keep virus levels so low as not to be detectable and for many years explains why there is not much maternal transmission of the virus in nature and why cats can live such a long proportion of their lives in good health in face of chronic infection,” said Dr. Pedersen. The situation is a little like the baby who made news a few weeks ago for being “functionally cured” of HIV – the virus is there, but at levels too low to register, and, so far, apparently unable to replicate.

The evidence suggests a taming of FIV, a détente between the cat and viral genomes playing out over time. “In Australia, 30% of cats test positive, and are able to live with the viral infection without severe medical problems. That wouldn’t happen if it hadn’t been in the population a long time,” said Dr. Zislin. The good health of the lions of the Serengeti National Park suggest this is the case — all are infected, with any of three variants of FIV, and none are sick. The genetic diversity of the virus and dampened response to it suggests that it’s been around a long time, enough to accumulate mutations.

HIV (NHGRI)

Might this comfortable co-existence between cats and their lentivirus, FIV, come to pass for humanity and its lentivirus, HIV? If so, can we hasten the accommodation? The simian immunodeficiency virus (SIV) story adds evidence that maybe we can.

We can approximate when a virus inserted itself into a host genome by identifying pairs of modern species that carry the virus, and deducing how far back in time they shared an ancestor. (Evolution proceeds in a branching manner from shared ancestors.) Geneticists compare sequences of a gene common to the species – the more DNA base sequence similarities, the more recently the species diverged from an ancestor. Add mutation rates for specific genes, and you have a molecular clock going back thousands or millions of years.

Orangutans carry SIV but do not lose their immunity.

Forty or so species of monkeys and apes harbor SIV, but don’t get sick from it, because SIV is an ancient viral presence. Michael Emerman, PhD, a virologist at the Fred Hutchinson Cancer Research Center in Seattle and graduate student Alex Compton recently traced the origin of SIV infection to 5-6 million years ago by sequencing a host immunity gene called APOBEC3G that has mutated in parallel to a viral gene over time. The results are in the January 2013 PLOS Pathogens.

Lemurs carry SIV too, dating the infection back 12 million years — at least. (Brooke Crowley, University of Cincinnati)

But SIV may be even older than 6 million years. Some of its sequences are tucked into the genomes of ring-tailed lemurs, which are prosimians. Because lemurs branched from the ancestors of primates 12 million years ago, the virus goes back at least that far.

With SIV silently circulating amongst monkeys, apes, and even prosimians, at some point, likely several points, it moved into humans, maybe when they ate their evolutionary cousins. Various researchers have extrapolated the most recent transfer to 1884-1924, the start of HIV/AIDS in humans. I remember the date being repeatedly pushed back, starting in the early 1980s when the CDC began tracking what was then called gay-related immune deficiency (GRID). At first AIDS was thought to be brand new, arising somehow in “patient zero,” a gay flight attendant with many sexual partners. Researchers pushed the origin back a few years at a time, to 1960, then the 1930s.

Chimps likely passed SIV to humans as “bush meat.” (Tetsuro Matsuzuwa, Kyoto University)

The lentivirus that is SIV/HIV might have hopped around Africa for eons, flitting over from SIV in chimpanzee meat to isolated human populations, cloaked against the backdrop of endemic infectious diseases that kill much faster, especially among the immunocompromised. Left were survivors who may have been lucky, or may have been SIV-resistant, like people today who have two mutations in the CCR5 gene; HIV can’t bind to their cells. If HIV killed off susceptible individuals in isolated settlements, the infection might only have become noticeable once cities formed and pockets of people with immunodeficiency emerged.

Alfred Roca and his team at the College of Agricultural, Consumer and Environmental Sciences at the University of Illinois are investigating such a possible HIV origin event in people called the Biaka, who live near where SIV may have first appeared in chimp populations. Graduate student Kai Zhao, funded by the Bill and Melinda Gates Foundation, compared single nucleotide polymorphism patterns in Biaka samples and found selection signatures – genome regions that persist because they offer some advantage. Such signatures among the Biaka led to four genes known from other work to confer resistance to HIV infection or progression to AIDS.

(ASIDE: Dr. Roca is an expert in elephants and mammoths and is co-author of one of my favorite papers, The Near Eastern Origin of Cat Domestication. That study compared 979 cats to their wildcat cousins, all subspecies of Felis silvestris, also revealing the origin of Sylvester the cat. Domestic cats split from the wildcats at the dawn of agriculture, about 9,000 years ago, in the Fertile Crescent.)

Evolution is ongoing, always, and so the strain of SIV that came to us from chimps, SIVcpz, is still re-inventing itself. Sandrine Souquière and colleagues at the Center for International Medical Research of Franceville in Gabon reported in late 2012 in PLOS ONE a new strain in wild-born captive chimps from Gabon and Congo. The animals appear healthy, but have much lower CD4+ T cell counts than uninfected animals. There’s also evidence that people may have passed HIV back to chimps.

The SIV/HIV story seems to be recapitulating that of the hardy cat virus. This isn’t a new idea – Robert Olmsted and co-workers wrote in 1992 in the Journal of Virology that “…the transmission of FIV between feline species is infrequent and parallels in time the emergence of HIV from simian ancestors.”

Strains of FIV are less like each other, genetically speaking, than are SIV and HIV. Therefore, perhaps what is happening in today’s domestic cat population foretells what will happen in our own. SIV no longer sickens most wild primates because they’ve had 12 million years to adapt. Cat species around for a long time, like lions, are less likely to get sick from FIV than their more modern relatives, such as our domesticated friends. And then there’s us, who Olmsted et al call “merely the latest unfortunate species to have become infected via another mammalian species.”

Artie is our middle FIV child, adopted between Juice and Romeo.

Maybe people shouldn’t shun FIV-infected cats, which is how we came to adopt Juice, Artie, and Romeo. For within them may lie clues to hastening evolution in a way that will silence HIV forever.

Rating: +4 (from 4 votes)

Category: Uncategorized | Tagged cats, evolution, feline immunodeficiency virus, FIV, HIV, SIV | 1 Comment

About DNA Science Blog

Geneticist Ricki Lewis blogs from the cutting edge of genomics, including genetic testing, stem cells, gene therapy and more.

Ricki Lewis is a science writer with a PhD in genetics. The author of several textbooks and thousands of articles in scientific, medical, and consumer publications, Ricki's first narrative nonfiction book, "The Forever Fix: Gene Therapy and the Boy Who Saved It," was published by St. Martin's Press in March 2012. In addition to writing, Ricki provides genetic counseling for parents-to-be at CareNet Medical Group in Schenectady, NY and teaches "Genethics" an online course for master's degree students at the Alden March Bioethics Institute of Albany Medical Center.
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- A Little Girl With Giant Axons, a Deranged Cytoskeleton, and Someday Gene Therapy May 16, 2013
  “When you hear hoof beats, think horses, not zebras.” So goes the mantra of first-year medical students. If a common disease is a horse and a rare disease a zebra, then giant axonal neuropathy (GAN), with only 50 or so recognized cases worldwide, is surely a unicorn.… Read the rest […]
  Ricki Lewis, PhD
- Celebrating Gleevec – and Basic Research May 9, 2013
  When 23-year-old Glamour magazine editor Erin Zammett Ruddy went for a routine physical in November 2001, she expected reassurance that her healthy lifestyle had been keeping her well. After all, she felt great. What Erin received, a few days later, was a shock.… Read the rest […]
  Ricki Lewis, PhD
- Confessions of a D Orbital May 2, 2013
  Organic chemistry has changed! Not the science, but the way it’s taught. SUNY Stony Brook, Fall semester, 1973. 500+ wannabe doctors pack into the lecture hall, squinting as a small figure up front slaps down overheads, scribbling CHNOPS atoms and various dots and dashes, changing the acetate sheets faster than any human brain can register them.… Read the re […]
  Ricki Lewis, PhD
- DNA Day and World Malaria Day: The Sickle Cell/Malaria Link Revisited April 25, 2013
  Today is both DNA Day and World Malaria Day. As I was pondering how to connect the topics, e-mail arrived from my “son,” a medical student in Liberia. He had malaria, again, and this time it had gone to his brain.… Read the rest […]
  Ricki Lewis, PhD
- DNA Day and 20 Years of Writing a Human Genetics Textbook April 18, 2013
  This month we celebrate the DNA anniversaries: unveiling of DNA’s structure in 1953, and the human genome sequence in 2003. From now until DNA Day, April 25, bloggers will be worshipping the human genome. Nature.com will offer podcasts (PastCasts) and last week, Eric Green, director of the National Human Genome Research Institute, spoke to reporters, summari […]
  Ricki Lewis, PhD
- A GPS View of the Human Genome April 11, 2013
  Taking cues from global positioning satellites, Yuval Itan, PhD, a postdoctoral researcher at Rockefeller University and his colleagues have created the “human gene connectome” (HGC), unveiled in Proceedings of the National Academy of Sciences. A MAP BASED ON FUNCTION Researchers have been deducing gene lineages for decades, based on DNA sequence similaritie […]
  Ricki Lewis, PhD
- Genetic Modifiers: Healthy Mutants Fuel Drug Discovery April 4, 2013
  I’m uneasy counseling a patient for mutations in the BRCA1 or BRCA2 cancer susceptibility genes. Typically, she’ll have a “first degree relative” – usually a mother or sister – with a related cancer, or might even have a test result in hand.… Read the rest […]
  Ricki Lewis, PhD
- Mayonnaise Taxonomy March 28, 2013
  I had a serious genetics topic all set to go today, but then something more timely and compelling arose. I began to wonder about what, exactly, mayonnaise is, and more importantly, how do the types of mayonnaise differ? My musings started with Passover, and the importance of eggs at this time of year.… Read the rest […]
  Ricki Lewis, PhD
- Second Gene Causes Retinoblastoma March 21, 2013
  In a list of famous genes, RB1 would probably be #1. It’s the tumor suppressor gene whose “loss of function” is behind the childhood eye cancer retinoblastoma, and that Alfred Knudson investigated to deduce the 2-hit mechanism of cancer. In 1971, the idea that a gene’s normal function could be to prevent cancer was revolutionary.… Read the rest […]
  Ricki Lewis, PhD
- Do Cats With FIV Foretell HIV’s Future? March 14, 2013
  Since my January 24 blog “My Cat Has AIDS,” about my two feline immunodeficiency virus (FIV)-positive cats, we’ve acquired a third, the handsome Romeo. He, too, came to us from Orange Street Cats, on Valentine’s Day. Romeo was found in an inner city park where people who can barely afford to feed their families nevertheless care for the burgeoning populatio […]
  Ricki Lewis, PhD

DNA Science Blog

A Little Girl With Giant Axons, a Deranged Cytoskeleton, and Someday Gene Therapy

Celebrating Gleevec – and Basic Research

Confessions of a D Orbital

DNA Day and World Malaria Day: The Sickle Cell/Malaria Link Revisited

DNA Day and 20 Years of Writing a Human Genetics Textbook

A GPS View of the Human Genome

Genetic Modifiers: Healthy Mutants Fuel Drug Discovery

Mayonnaise Taxonomy

Second Gene Causes Retinoblastoma

Do Cats With FIV Foretell HIV’s Future?

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