Alan was one of the first people in Australia to receive a diagnosis from whole genome sequencing that has changed his treatment – and, in Alan’s case, transformed his health.
Once gravely ill with an immune condition that was destroying his own cells, Alan is now an energetic boy who delights in Lego adventures and light-sabre duels. His medical saga is not yet over, but the improvement in his condition has been immense.
Alan’s remarkable story is one of close collaboration between his clinicians at Sydney Children’s Hospital, Randwick and researchers at Garvan. It’s also a story of world-leading technology that is capable of rapid, high-quality genome sequencing and analysis, and of a dedicated search for answers by his parents and his clinical team.
Alan's young life tells the story of one family's tireless quest for answers to a life-threating genetic disorder. But their story also signifies a hopeful new chapter for others with immune disease — thanks to new technology that reads our very code of life.
Alan is a bright, affectionate seven-year-old boy with expressive brown eyes. He enacts lively Lego adventures with his mother Berna, who studies accounting, and delights in energetic light sabre battles with father Tansel, an IT professional.
Alan, however, has fought his own very real battle for survival since age three.
When immune systems go rogue
The first signs of trouble came while the family was based in Turkey. When Alan's parents questioned doctors about small red dots on his skin, tests revealed dangerously low platelet levels. 'In that situation,' says Tansel, 'if you have any bleeding, it's virtually impossible to stop.' Alan was rushed to hospital to treat this condition, thrombocytopenia.
Alan responded well enough to return home. But six months later his white blood cell count plummeted dramatically. Since these immune cells, called neutrophils, form the body's first line of defence against infections, this neutropenia left Alan very susceptible to infections.
Next, and worst, Alan's immune system began to destroy his red blood cells. This condition, haemolytic anaemia, is immediately life threatening. 'We had to do whatever we can to stop it,' says Tansel, 'and there's no way to do it unless you go to hospital, and he's under very serious care.'
Alan's immune system was aiming its arsenal of weaponry at normal parts of his body, instead of fighting infections. But why?
The diagnostic odyssey
After the family returned to Australia in 2013, Alan came under care of doctors at Sydney Children's Hospital, Randwick; haematologist Dr Susan Russell, then paediatric immunologists Dr Brynn Wainstein and Dr Paul Gray.
His physicians searched intensively for the cause of Alan's perplexing disease. Suspecting it was genetic, they tested for known immune deficiency genes. But pinpointing the 'smoking gun' was extremely difficult, especially since many genes are unavailable for testing in Australia or globally.
Rare genes, collective challenges
Alan's autoimmune disease is extremely rare. But his experience mirrors millions of others' worldwide with monogenic disorders (also called Mendelian disorders). Caused by modification to a single gene found in all cells of the body, they lead to thousands of diseases, depending on the gene affected. Yet the underlying genetic cause is known in only about half these diseases.
For these families, the first medical hurdle of diagnosis can be huge. 'We call it the diagnostic odyssey,' says Dr Tony Roscioli, of the Garvan Institute's Kinghorn Centre for Clinical Genomics. Of the 6 thousand babies born annually in Australia with a genetic condition, 80% of the conditions are undiagnosed.
The toll of uncertainty
'The frustration in cases like this,' says Dr Wainstein, of Sydney Children's Hospital, Randwick, 'is you don't really know, unless you have an underlying diagnosis, what to expect. You don't know where this is going to go, you don't know what the best therapies are.' This explains why rare diseases, collectively, make up the majority of hospital paediatric health budgets and admissions.
Diagnostic limbo also takes a toll on families. 'We talk about the concept of uncertainty a lot with our patients,' says Sydney Children's Hospital, Randwick genetic counsellor Rebecca Macintosh, who counsels Alan's family.
'Not knowing is really hard,' agrees Tansel, 'my way of dealing with this was to read as much as I could.' Tansel scoured thousands of medical abstracts for answers to Alan's perplexing disease.
Most of Alan's health problems stem from his aggressive immune response against his own cells. Not only his red and white blood cells, but also his lungs and gut.
A life in the balance
In spring 2015, Alan's autoimmune disease flared up again. By October, Alan had lost a lot of weight and lay extremely ill in the Intensive Care Unit of Sydney Children’s Hospital, Randwick.
'We were very worried,' says Dr Wainstein. Alan had severe diarrhoea and exceedingly low platelet counts. 'Obviously you can imagine,' says Dr Gray, 'if you bleed from your gut with lots of diarrhoea, that's life-threatening.' Dr Gray informed Dr Roscioli the diagnostic quest was now extremely urgent.
Piecing together a genetic puzzle
'On that day I dropped everything,' says Dr Roscioli. Working through the sequencing data, he scrutinised genes known to cause immunodeficiency. Within a couple of hours, he pinpointed the smoking gun: a gene called LRBA.
Alan's genome, the results showed, contained two exceedingly rare pathogenic (disease-causing) variants of the LRBA gene. Both Alan's copies interrupted its function.
Alan's healthy parents were silent carriers: each had one normal and one non-functional LRBA gene. Inherited singly in this way, the rare pathogenic variants could pass through generations without causing disease. Unfortunately Alan had inherited both non-functional genes, one from each parent. Doubled up, they caused his severe immunodeficiency.
Next, Dr Roscioli quickly confirmed the pattern of disease seen with LRBA deficiency matched Alan's immune problems. He also learned LRBA was on Alan's physicians' list of suspect genes. Remarkably, Tansel's own research had also led him to raise LRBA with the doctors. Yet LRBA deficiency is exceedingly rare. 'I don't expect to see another person in my life with this disease,' says Dr Roscioli.
'Once we had that diagnosis, we then at least understood what was going on,' says Dr Wainstein, 'and could finally put all the pieces of the puzzle together.'
Alan's missing brake
The LRBA gene codes for the LRBA protein. This protein is found inside some of the body’s immune cells, particularly T regulatory cells. The LRBA protein's job is to protect another molecule, CTLA-4, so it can build up on the outside of the cell. When LRBA is missing inside cells, they also lack CTLA-4 on the cell exterior.
These CTLA-4 molecules act as an important brake on the immune system. If this brake is missing, the immune system goes 'rogue', attacking normal body tissues, causing autoimmune disease.
Unfortunately, today very few genomic diagnoses for rare disease lead to direct therapies. These thousands of single-gene disorders, each with small numbers of patients, rarely enter drug companies' radar. However, as we shall see, genomics is helping bridge this therapy gap.
The power of genetic diagnosis
Yet even if no direct therapy is at hand, genomic diagnoses have wide benefits.
For families, certainty is one. 'They are looking for some closure,' says Ms Macintosh. Learning if and how a disease is inherited helps families plan their future (some gene variants are de novo, or new, not inherited). 'We call this restoring reproductive confidence,' says Dr Roscioli.
Genomic results can also rule out further diagnostic testing, along with its discomfort, risk and cost. And even without a direct therapy, genetic diagnoses still help physicians better manage patients. They can refocus therapies and discontinue costly but unhelpful drugs, saving the health system millions.
New gene insights, new therapies
Yet genomic discovery is also spearheading new therapies. Genomics yields valuable insights into how genes function and, when they malfunction, the biological pathways causing disease. These insights suggest ways to re-purpose existing drugs, including new ways to treat rare disease.
Matching rare cases across the world
This fast-paced world of genomic discovery delivered for Alan at a crucial time.
Dr Roscioli's findings marshalled the full clinical and research firepower behind the immunogenomics study. Prof Goodnow quickly investigated known findings on LRBA. Eight years earlier, he discovered, a child with a similar autoimmune disease was cared for at Cincinnati Children's Hospital in Ohio, USA.
Desperate for a treatment, the Cincinnati team had tried a new drug, Abatacept. Originally developed for organ transplant patients, Abatacept also helped with rheumatoid arthritis and psoriasis — both autoimmune conditions.
Abatacept, for reasons the Cincinnati team did not yet understand, rapidly corrected most of their patient's life-threatening symptoms. Over the next few years, they used Abatacept in 2 similar cases, again with strikingly positive results.
Then in 2012, UK researchers linked this spectrum of severe autoimmune problems to defects in a specific gene: LRBA.
The Cincinnati team subsequently learned that all 3 of their patients had this genetic LRBA deficiency. Joining forces with a team from the US National Institutes of Health they studied 6 more patients with LRBA deficiency, some also treated with Abatacept.
And they discovered why it works. Abatacept mimics the function of CTLA4. Remember, CTLA4 is the crucial immune system brake lacking in LRBA-deficient patients. Abatacept compensates for this lack of CTLA4, restoring this vital brake. It prevents the immune system from directing its arsenal at normal body cells.
For Alan, a brake in a bottle
Published in July 2015, just 3 months before Alan's diagnosis, the US teams' discovery gave Prof Goodnow vital insight into biochemical workings of Alan's disorder — and a possible therapy.
With Alan gravely ill in ICU, his medical team urgently sought and received approval from Sydney Children's Hospital, Randwick Review Board to use Abatacept. 'All of this was done in record time,' says Tansel, 'I know Dr Wainstein and Dr Gray and their team skipped their sleep to get these approvals.'
Alan began taking Abatacept in mid-October, funded through the Hospital. Cautiously optimistic, Alan's family and clinicians, together with a growing interdisciplinary team, watched, waited and hoped.
Alan recovered rapidly in the weeks after starting Abatacept. He was soon out of intensive care and into the children’s ward.
When Ms Macintosh and Dr Roscioli visited, they were surprised to find a boy, so recently gravely ill, completely transformed. Alan was smiling and dancing around the room with his lightsaber. 'I had never seen him like that before,’ says Ms Macintosh, 'he was a completely different child.'
Over the next half year, as Abatacept's effects built up, Alan's red blood cells and platelets rebounded into normal range. Haemolytic anaemia and thrombocytopenia, his most serious threats, are now under control. Alan is also less vulnerable to infection, able to cope without heading to emergency for antibiotics.
With the Cincinnati cases as their guide, Alan's doctors have reason to be optimistic his remission will last. For Alan's parents, the relief has been immense. 'The surprising thing, 'says Tansel, 'is that if we had this diagnosis 3 years ago, we had no cure.'
The quest for a complete therapy
Some of Alan's health conditions persist. His new immune brake is less effective for his gut problems. Severe diarrhoea sent Alan back to hospital in the months since starting Abatacept. Again, this mirrors the US patients' experience.
Enter Alan's mouse avatar
The Garvan Institute aims to help turn Alan's partial fix into a complete one. Armed with Dr Roscioli's insights into Alan's LRBA gene, Prof Robert Brink, a lab head of the Garvan's Immunology Division, moved quickly to have Alan's very own mouse avatar produced.
Like avatars in movies and online games, avatar mice are stand-ins for real people. They allow medical researchers to study responses to drug therapies, to prove their safety and effectiveness. Exciting breakthroughs have led to a 10-fold decrease in the time required to make these living models, Prof Brink says. Using technology called CRISPR/Cas9, his lab designs 'molecular scissors' to slice and modify genomes with remarkable ease and finesse.
Ready in February 2016, Alan's avatar mice mirror his genetic deficiency; their T regulatory cells lack the crucial CTLA-4 immune brake, tests show.
A striking difference
Unlike Alan, however, these avatar mice are perfectly healthy, despite this missing immune brake. These mice are reared in a biobubble, isolated from infections — much like the 'bubble boy' of movie fame.
Exposure to infections could be a critical factor. Could immune systems without LRBA stay on track if, like the mouse avatar, no infection pushes the immune system's accelerator pedal? The answers could reveal much for Alan and thousands of others with immune disorders.
At the start of June 2016, Alan returned home. He is eating on his own and is almost back to normal weight, thanks to new drug combinations that greatly reduce his diarrhoea symptoms.
Alan's therapy is holding his autoimmune problems at bay, but his family realises their medical saga is not yet over. Tansel, ever vigilant, still combs medical journals for new insights, his eyes firmly fixed on the rapidly advancing horizon of genomic medicine. 'You know how fast knowledge in this area goes,' he says 'so I'm hopeful.'
In its first year the immunogenomics project helped Alan find a diagnosis and a life changing treatment. Yet Prof Goodnow has even bigger aspirations.
From the clinic to lab and back
The immunogenomics project began with discussions between Prof Goodnow and immunology colleagues who saw the potential of whole genome sequencing to illuminate the complex causes of immune disease and open the door for new treatments.
The Garvan Institute offered an excellent environment to bring their plans to life with its world-class technology, researchers and connections to hospitals. With the support of the Bill and Patricia Ritchie Foundation, Prof Goodnow began funding sequencing for patients with rare immune disorders in 2015.
They set up a pathway from the clinic to the lab, and back again. Just like in Alan’s case, the pathway begins when doctors identify patients with unusual immune disorders that they think could have a genetic basis. These patients are referred to have their genomes sequenced in the hope that this will provide a long sought after diagnosis and vital information for the management of their disease. Further lab work, like the use of avatar mice, provides additional insights.
Prof Goodnow never expected to see such rapid success. 'What really is extraordinary,' says Goodnow, 'is that in a year those pieces of the puzzle have actually all come together.'
Connecting expertise across disciplines has been critical as immunogenomics moves from the whole immune system down to the genes and molecules.
Bridging disciplines has been critical as immunogenomics involves expertise at many levels, from the whole immune system down to genes and molecules. ‘We’ve got so many bright and talented people who really are at the top of their game in all these different specialties, and have just come together to make something very special happen,’ says Goodnow.
Beyond rare disease
Prof Goodnow believes that cases like Alan’s can have an impact beyond rare diseases, ‘what we’re going to learn from Alan is a whole new way of looking at adult onset autoimmune disease.’
The biological processes that make Alan’s condition life threatening are complex, yet the cause is easy to spot as he is missing one crucial gene. Many of the more common immune disorders, such as Type 1 Diabetes and Rheumatoid Arthritis, are much harder to explain.
By studying cases like Alan’s, researchers can better understand how the immune system works and why some treatments are effective. This knowledge can then be applied to the study and treatment of other disorders, potentially helping millions of people in Australia and around the world.
These insights might also help improve important new cancer therapies called checkpoint inhibitors. They turn off the immune brake, allowing the immune system to attack cancer cells. In effect they mimic Alan’s disease, so understanding more about how his treatment works could help reduce their serious side effects.
The future looks bright for the immunogenomics team, ‘At the end of the day everyone will feel that they have made a difference, not just for these cases but for the whole practice of medicine.’