She Had Her Own Mutation, Sequencing Led to a Treatment and Major Genetic Discovery – Then She Died of COVID

It isn’t often that an investigation of a single patient who has a devastating, unrecognized disease leads to finding an existing drug that works, but also reveals something entirely new about gene function. A study from Dusan Bogunovic, PhD, Director of the Center for Inborn Errors of Immunity at the Icahn School of Medicine at Mount Sinai and colleagues just published in the journal Immunity, tells such a tale.

The young woman was only 18 when the investigation began. Her death from COVID-19 tragically juxtaposes the challenges of treating an ultrarare genetic disease with those of a pandemic infectious disease.

“We were so so sad when she passed. She was doing so well for the first time in her life for full 2 years. She was very happy, and her family was very happy to see her that way,” said Dr. Bogunovic.

An Immune Response in Overdrive

Problems started right away.

The patient was born with an oozing rash that striped the left side of her body – which would turn out to be a clue. At a year of age she developed persistent diarrhea and vomiting, and tests showed massive inflammation along her digestive tract. At age three she ballooned with sudden water weight as protein seeped into her urine from damaged kidney tubules. But her overactive immune system rejected a transplant, anti-rejection drugs weakened her, and she went on dialysis.

Then asthma and food and environmental allergies kicked in. Her growth slowed.

Although her condition didn’t have a name, it was clearly autoinflammatory. The innate immune response, the part that controls the signals that release cytokines, was always in overdrive, inflaming her own tissues.

The researchers found the patient in an “undiagnosed disease program” at Mt. Sinai, one of several that the National Institutes of Health sponsors, where patients with unusual collections of signs and symptoms, many of them children who’ve been through grueling “diagnostic odysseys,” have their genomes searched for causative mutations. The programs help connect patients and researchers.

The young woman had a previously unknown mutation in a well-studied gene called JAK1. Matching a mutation in a single gene to a disease is valuable because it can identify a specific glitch in a protein, and that can suggest therapeutic strategies – including existing treatments. In this case, a drug already available to treat two other autoimmune conditions, rheumatoid arthritis and psoriatic arthritis, made sense: tofacitinib, known from drug ads as Xeljanz. It’s a daily pill, a “JAK inhibitor.”

The researchers nailed down the mechanism using a powerful and increasingly prevalent technique, “custom single-cell RNA sequencing.” Scrutinizing one cell at a time better reflects molecular happenings than analyzing all the RNAs that fall out of a mashed up tissue sample consisting of more than one cell type. It’s a signal-to-noise issue.

A Unique Mutation Weird in Different Ways

The four types of JAK genes – that stands for “Janus kinase” – encode enzymes (kinases) that turn on other genes. The JAK genes control production of cytokines, and the gene that was mutant in the young woman – JAK1 – controls more than 25 of them. Cytokines must be in precise, dynamic balance to prevent infections while not raging out of control and backfiring, which happens in the “cytokine storms” that kill during COVID.

The young woman’s mutation was unusual in several ways.

First, instead of abolishing a gene’s function, it not only ramps it up, but affects cytokine types that JAK enzymes usually don’t. In genetics we call this a “toxic gain-of-function.”

A second peculiarity is that the mutation was only in some of the young woman’s cells, making her a genetic mosaic. Perhaps the mutation had never been identified before because having it in every cell is unsurvivable. There’s precedent for a mosaic being a milder case. Jesse Gelsinger, the young man who died in a gene therapy trial in 1999, was a mosaic for a metabolic disorder; infants with the mutation in every cell die without treatment.

The woman’s phenotype – her symptoms – had actually suggested mosaicism: the striped appearance of her rash at birth, and the fact that limbs were uneven lengths. Further testing – of blood, cheek cells, and biopsies – confirmed that some cells had the mutation while others didn’t. The mutation was in about a quarter of her tested cells.

But there was more amiss than just being a mosaic.

The third distinction was that the cells that had the mutation also had a normal copy of the gene – but only the mutant one was active, used to make the kinase.

“Most genes use both their maternal and paternal copies, called alleles. Our findings show the JAK1 mutation in this patient used only one copy per cell. This challenges the textbook principles of genetics and may help explain irregularities that are frequently encountered across genetic diseases,” explained Dr. Bogunovic. I write those textbooks and can attest that the finding is indeed unexpected.

With hindsight, clues to the mosaicism were there, early. The striped rash emerged from cells expressing the mutation in the embryo sticking together as they divided. And the limbs of different lengths were as if the cells were listening to different growth factors. The patient was different, genetically speaking, in different parts of her body.

But the researchers didn’t suspect mosaicism at first, because mutations that only affect some of a patient’s cells tend not to show up in DNA sequencing protocols.

The mutation replaces one amino acid with another in a critical part of the encoded enzyme that controls the cytokines. The enzyme is so important that it can only show up in a mosaic, someone who doesn’t have it in all of her cells.

When the researchers plucked cells from different body parts and kept track of where the mutation was expressed, they realized that the mutational event must have happened before day 14. That’s when the embryo normally folds into three layers, a phenomenon that determines cell fates. The outer ectoderm becomes skin and nerves, the inner endoderm begets the digestive tract, and middle mesoderm gives rise to everything else. A mutation affecting members of all three layers must have happened early.

That is, where the mutation is expressed hints at when it acts: before the first dozen cell divisions in the embryo.

The mutation originated in the patient – her parents didn’t have it. But that’s not unusual for a change that severely affects health. And so the woman’s mutation was genetic, but not inherited.

Repurposing Xeljanz

The manifestations were weird, the mutation novel, but did a treatment already exist? Knowing the gene that bears the mutation made that a possibility. As a JAK inhibitor, Xeljanz seemed to fit the bill.

It worked.

“She rapidly improved within weeks. Her skin lesions cleared, her daily gastrointestinal symptoms resolved, and the clinical signs of inflammation went away, putting the patient in remission for two years until her unfortunate demise from coronavirus-related illness,” said Dr. Bogunovic.

What happened? Had the drug suppressed her immunity too much, especially since she also received oral corticosteroids and the immunosuppressant drug tacrolimus?

“Despite doing well, she was on dialysis as her kidneys were not functional, and she was on immunosuppression due to the transplant she had years ago. So she was at high risk, and unfortunately got infected with SARS-COV-2. It broke our hearts, but at least we were able to improve her quality of life substantially, if only for 2 years,” said Dr. Bogunovic.

I can’t name the young woman due to privacy laws, but I wish I could. What would become her sacrifice has opened up further research into drugs that impact the JAK cytokine signaling pathways, perhaps helping future patients and possibly providing insight into COVID pathogenesis. A few clinical trials are evaluating the drug in managing COVID-19.

How tragically ironic that the researchers unraveled such a mysterious and ultrarare disease and successfully treated their patient, only to lose her to the no-longer-so-novel coronavirus that is sweeping the planet.