Genetic Modifiers: Healthy Mutants Fuel Drug Discovery

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

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, PhDwho 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).

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.

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.

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