Researchers identify new genetic cause of severe immune disorder

Severe congenital neutropenia leaves young patients to contract infection after infection, leading to life-threatening situations. A team of Leuven scientists has identified a novel genetic mutation, pointing to a new causative mechanism for this severe immune disorder.

The story starts with patient Jane Doe, now 19 years old, but diagnosed with severe congenital neutropenia when she was just 2 years old. By that time, she had already suffered an ear abscess, recurring ear infections, bronchitis, sinusitis, tonsillitis and several gum infections.

After yet another infection, this time of her intestine, a detailed investigation revealed a striking shortage of neutrophils, white blood cells that are recruited as first-responders to the site of injury or infection within our body. Having an abnormally low concentration of neutrophils in the blood is referred to as neutropenia. When it is severe and present from birth (congenital), that is where the diagnosis of severe congenital neutropenia comes in.

“Severe congenital neutropenia is very scary, because these kids develop serious infections that can be lethal for infants,” explains Erika Van Nieuwenhove. “As if that’s not enough, they are also at increased risk for other conditions such as leukemia.”

Van Nieuwenhove is both an MD and PhD, who combines clinical work in the university hospital with Carine Wouters, with research at VIB and KU Leuven under the guidance of Adrian Liston and Stephanie Humblet-Baron.

Together with John Barber and several other colleagues, she set out to understand why Jane Doe developed SCN in the first place. Van Nieuwenhove: “For up to 50% of severe congenital neutropenia patients, we have no clue what causes the disease. It was the same for our patient, whose parents are both healthy.”

A new mutation in a familiar gene

After Jane Doe tested negative for mutations in all the genes with known ties to neutropenia, the researchers performed whole exome sequencing, probing every gene in the DNA, to trace back the genetic defect underlying the disorder.

“We identified a new mutation in a gene called SEC61A1, which encodes one of three subunits of the Sec61 complex. This molecular complex plays a crucial role in both protein transport and in maintaining the calcium balance of the cell,” explains Humblet-Baron. “Our experiments revealed that the genetic defect led to both a lower expression and a reduced efficacy of the SEC61A1 protein, and that these quantitative and qualitative defects in turn disturb neutrophil differentiation and maturation.”

Interestingly, SEC61A1 has recently been picked up in other studies that were not focused on neutropenia. Different mutations in the same gene were reported in two families with a rare kidney disease and in two additional families with an antibody deficiency.

“The fact that there are different mutations in the same gene indicates there may be overlapping mechanisms among the different disorders. With the low number of currently known patients, it is still too early to predict which mutations can lead to which symptoms,” explains Liston.

“What’s clear from our findings is that SEC61A1 mutations can also cause severe congenital neutropenia. Considering this gene’s link with other disorders, the clinical implications of our work reach far beyond the patient with whom it all started here in Leuven.”

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Read the original paper: Defective SEC61α1 underlies a novel cause of autosomal dominant severe congenital neutropenia. Van Nieuwenhove et al. JACI 2020

When will we have a Coronavirus vaccine?

Vaccines are very unusual medicines. Most medications are developed for the purpose of treating sick people. Vaccines, on the other hand, are developed for the purpose of treating healthy people, ideally for an infection that most people won't get exposed to. This means that vaccine development is in one way much harder than any other drug. This is because every medication needs to do more good than harm to the person receiving it. A drug designed to treat a disease has an easy cost-benefit ratio to achieve: if that disease is serious and the drug is effective in at least some people, then even relatively frequent adverse effects may be tolerated. In the case of vaccines, however, because you are treating healthy people the cost-benefit ratio means you can almost never have any substantial adverse effects and the vaccine has to work in almost every person. Add on to this the fact that vaccines are designed to give ideally life-long protection. A drug for a disease might be acceptable if it worked if taken once a day. A vaccine should give at least 10 years of protection, although there are a few exceptions. Plus vaccines are most effective when everyone gets them, meaning you need to be able to mass produce them for almost nothing and they should be stable even without cold storage, etc. In short, vaccines are exceptionally difficult to make because they have to be nearly perfect before they get approved.

On the other hand, vaccines are easier to make than most other drugs. For most drugs, we first need to understand the molecular basis of disease in incredible detail, down to the atomic precision of the key proteins. Only then can we start to design small molecules that disrupt pathology, with a long and painful process of screening and improving that leaves most drug candidates dead before they hit a trial. Even once we get into patients, we are still highly likely to find that the drugs do more harm than good, or are only effective in a handful of patients. Vaccines, on the other hand, are not really drugs at all. You can best think of a vaccine as a trigger to instruct the body on how to make its own natural drugs, antibodies. The more we know about a virus the better we can design the vaccine trigger, but a lot of the best vaccines just come from randomly blasted bits of dead virus. There are exceptions, where the viruses biology works against us. HIV and herpes viruses are really difficult to make vaccines against, because they hide out inside our body. Fortunately, COVID-19 looks like a fairly standard virus in this respect, and is unlikely to be unusually problematic. There are already promising small-scale trials indicating that antibodies against COVID-19 would work. These were done by taking antibodies from a recovered patient and injecting it into the sick patient, but the principle is the same. There is still some concern that COVID-19 may be more complicated, based on some results indicating that recovered people can get reinfected, but at the moment this is most likely due to false negative screening rather than a true re-infection. It does need to be considered though - we just don't know enough about the biology to be sure.

With vaccines being both harder and easier to make than other drugs, how long will it be before we get a vaccine? Here I don't have any inside commercial knowledge, but it seems very likely that we will have a vaccine developed, tested and approved in 2020. The key here is that the cost-benefit ratio is completely different for a COVID-19 vaccine than it is for a normal vaccine. As I said, normal vaccines have to be almost perfect before they are approved, with any serious side-effects resulting in the vaccine being shelved. During a global pandemic, however, the risk of adverse effects needs to be balanced against the advantage of moving fast. Let's say we got a vaccine that only worked in 50% of people and caused minor adverse effects (sore arm for a week) in 10% of people. Right now, who wouldn't line up to get vaccinated? 

So expect a poor vaccine in 2020, assuming that immunologists are given sufficient funding to develop it. It will skip a lot of the normal safety and efficacy steps, and it will likely not protect everyone and possibly cause side-effects. That said, it would still be a useful tool for controlling a pandemic. Then towards the end of 2021 I would expect to see the roll-out of better vaccines, with higher levels of efficacy and fewer adverse effects. At some point in the future, every child will likely be given a vaccine for COVID-19 as part of their routine vaccination schedule, but that is much more likely to be a third- or forth-generation vaccine, with the optimal properties that we expect.

Lab tech position

Job opportunity: we need a junior lab technician at the University of Leuven to be trained for PBMC isolation and flow cytometry analysis, to place a key role in clinical trials. We are after someone who is willing to listen and takes their work seriously. If you already know flow cytometry, great, if not, we will train you. Apply here, and take on a job that matters. 

Congratulations Dr Erika Van Nieuwenhove!

A huge round of congratulations for Dr Erika Van Nieuwenhove, who successfully defended her PhD. Erika set for gold standard for PhD defences, with an outstanding presentation and masterful question time. Erika's thesis was on inborn errors of immunity, with her PhD covering multiple new genetic mechanisms for PIDs, including mutations in ADA2 and Ikaros, plus a machine learning-driven approach to the diagnosis of JIA. The work is not yet finished either - stayed tuned for more Van Nieuwenhove papers on new genetic causes of neutropenia! A future leader in pediatric immunology and rheumatology!

Dokter Algoritme

Algoritmen kunnen inzichten bereiken waar een mens moeilijk toe komt. Computeralgoritmen kunnen almaar beter moeilijke diagnosen stellen, soms zelfs beter dan artsen. Immunologe Erika Van Nieuwenhove van de Leuvense tak aan het Vlaams Instituut voor Biotechnologie (VIB) en haar collega’s melden in Annals of the Rheumatic Diseases dat ze een zelflerend algoritme hebben ontwikkeld dat met bijna 90 procent zekerheid artritis bij kinderen kan vaststellen, louter op basis van een bloedtest.

Het gaat om de vaakst voorkomende vorm van reuma bij kinderen, maar omdat de ernst en de evolutie van de symptomen sterk kunnen variëren, is een diagnose stellen niet altijd gemakkelijk. Het algoritme evalueert alleen de samenstelling van het immuunsysteem van de patiënten. Het zal nuttig zijn om te bepalen welke behandeling aangewezen is.

Knack - 24 Apr. 2019 - Page 86

Using machine learning to diagnose disease

Profiling the immune system in paediatric arthritis patients offers hope for improved diagnosis and treatment

A team of scientists from VIB and KU Leuven has developed a machine learning algorithm that identifies children with juvenile arthritis with almost 90% accuracy from a simple blood test. The new findings, published this week in Annals of the Rheumatic Diseases, pave the way for the use of machine learning to improve diagnosis and to predict which juvenile arthritis patients may respond best to different treatment options. The work was led by Professor Adrian Liston, a group leader at the Babraham Institute in Cambridge, UK and at VIB and KU Leuven in Leuven, Belgium.

Juvenile idiopathic arthritis is the most common rheumatic disease in children, but it presents in many different severities and forms. This diversity makes clinical assessment and patient classification difficult.

A team of researchers at Belgian research organisations VIB, KU Leuven and UZ Leuven undertook a detailed biological characterisation of the immune system of hundreds of children with and without juvenile arthritis to help the diagnosis or treatment decisions for this disease.

“Essentially, we took blood samples from more than 100 children, two thirds of whom had childhood arthritis,” explains Erika Van Nieuwenhove (VIB-KU Leuven), and first author of the study. “We analysed their immune system at a greater level of detail than was ever done before for this disease, and simply using this data we then used machine learning to see if we could tell which children had arthritis.”

The results were quite remarkable: the algorithm was about 90% accurate at identifying the children with the disease. “Using only information on the immune system, and no clinical data at all, we could design a machine learning algorithm that was about 90% accurate at spotting which kids had arthritis,” says Professor Adrian Liston (Babraham Institute, Cambridge, UK and VIB-KU Leuven). “This result is a proof-of-principle demonstration that immune phenotyping combined with machine learning holds huge potential to diagnose disease. Similar approaches could be applied to improve patient selection for treatments and clinical trials.”

The researchers are hopeful about the impact of this research in improving patient outcomes. “The tool needs further validation but otherwise there are no scientific barriers to this approach being quickly translated to the clinic,” comments Professor Carine Wouters (UZ Leuven), who was the clinical lead for this study. “Down the line, we could use this kind of detailed classification information—and machine learning analysis—to identify which patients will respond best to specific treatment options.”

Identical twins light the way for new genetic cause of arthritis

Identical twin girls who presented with severe arthritis helped scientists to identify the first gene mutation that can single-handedly cause a juvenile form of this inflammatory joint disease. By investigating the DNA of individual blood cells of both children and then modelling the genetic defect in a mouse model, the research team led by Adrian Liston (VIB-KU Leuven) was able to unravel the disease mechanism. The findings will help to develop an appropriate treatment as well.

Juvenile idiopathic arthritis is the most common form of all childhood rheumatic diseases. It is defined as arthritis that starts at a young age and persists throughout adulthood, but which does not have a defined cause. Patients present with a highly variable clinical picture, and scientists have long suspected that different combinations of specific genetic susceptibilities and environmental triggers drive the disease.

A single gene mutation

In a new study by researchers at VIB, KU Leuven and UZ Leuven, the cause of juvenile arthritis in a young pair of identical twins was traced back to a single genetic mutation.

"Single-cell sequencing let us track what was going wrong in every cell type in the twin’s blood, creating a link from genetic mutation to disease onset,” explains Dr. Stephanie Humblet-Baron, one of the researchers involved in the study. “It was the combination of next generation genetics and immunology approaches that allowed us to find out why these patients were developing arthritis at such a young age.”

Of mice and men

Parallel studies in mice confirmed that the gene defect found in the patients’ blood cells indeed led to an enhanced susceptibility to arthritis. Prof. Susan Schlenner, first author of the study, stresses the relevance of this approach: "New genetic editing approaches bring mouse research much closer to the patient. We can now rapidly produce new mouse models that reproduce human mutations in mice, allowing us to model the disease of individual patients."

According to immunology prof. Adrian Liston such insights prove invaluable in biomedical research: “Understanding the cause of the disease unlocks the key to treating the patient.”

From cause to cure

Liston’s team collaborated closely with prof. Carine Wouters, who coordinated the clinical aspect of the research: "The identification of a single gene that can cause juvenile idiopathic arthritis is an important milestone. A parallel mouse model with the same genetic mutation is a great tool to dissect the disease mechanism in more detail and to develop more effective targeted therapies for this condition.”

And the little patients? They are relieved to know that scientists found the cause of their symptoms: "We are delighted to know that an explanation has been found for our illness and more so because we are sure it will help other children."

Thankfully, the children’s arthritis is under good control at the moment. Thanks to the new scientific findings, their doctors will be in a much better position to treat any future flare-ups.

NFIL3 mutations alter immune homeostasis and sensitise for arthritis pathology 

Schlenner et al. 2018 Annals of the Reumatic Diseases

Stephanie Humblet-Baron tackles one immune disease after the other

In two recent studies, the same team of scientists has uncovered the mechanisms underlying two distinct immunological disorders affecting both children and adults. Stephanie Humblet-Baron(VIB-KU Leuven) was the researcher at the helm of both projects.

A pediatrician by training, Stephanie Humblet-Baron is building a career unravelling immunological disorders that affect children. She divides her time between the clinic and the lab, where she is a senior team leader in the lab of Adrian Liston (VIB-KU Leuven).

From disease to biology and back again

Ever since the start of her medical training, Humblet-Baron developed a special interest in unraveling the biological mechanisms that cause immunological problems. Many immune diseases are poorly understood, and this lack of knowledge also limits treatment options and choices.

“People sometimes refer to these diseases as rare,” says Humblet-Baron, “but we all carry risk factors for many immunological diseases. Even if a given mutation is rare, the accumulated variation in immunological responses affect a broad set of outcomes, for example how someone responds to cancer treatment or drugs for cardiovascular conditions. That is why understanding the mechanisms underlying immune-dysregulation is so important.”

In her most recent work, Humblet-Baron, together with her colleagues in the lab of Adrian Liston (VIB-KU Leuven), focused on the mechanisms causing myeloproliferative disease and hemophagocytic lymphohistiocytosis, two diseases that are fatal unless given aggressive treatment.

Myeloproliferative disorder: a partner in crime for dendritic cells

Dendritic cells are specialized antigen-presenting cells that play a crucial role in coordinating innate and adaptive immune responses. In both patients and mice, depletion of dendritic cells leads to myeloproliferative disorder, but how or why—no one really knew.

“To understand what was going wrong, we created a mouse model where dendritic cells were present in normal numbers, but were functionally impaired,” explains Humblet-Baron. “We found that without the antigen-presenting capacity of dendritic cells, the mice developed myeloproliferative disorder.”

The team uncovered that it was not the number of dendritic cells, but their partnership with CD4 T cells of the immune system that was crucial for disease development. When CD4 T cells were absent as well, the mice showed no symptoms of myeloproliferative disease.

This has important implications for patients, where specific mutations also manifest both dendritic cell deficiency and myeloproliferative disorder. “Based on the original model disease model, the proposed line of treatment would be dendritic cell replacement, currently only possible through bone-marrow transplantation,” says prof. Adrian Liston. “But these new results indicate that attenuating the activatory signal from CD4 T cells could also reduce the development of myeloproliferative disorder.”

Hemophagocytic lymphohistiocytosis: New light on a deadly disease

Hemophagocytic lymphohistiocytosis, HLH for short, is a severe disease less than 2 out of 3 patients survive. It can be triggered by a variety of factors, including genetic defects, viral infections, anti-tumor responses or unchecked autoimmunity. Excessive production of interferon γ was assumed to be the key pathological step, but based on patient evidence and a pre-clinical mouse model of the disease, the Leuven research team has now found that there is much more to it.

Humblet-Baron: “We found that the production of interferon γ was only responsible for part of the features of the disease. Excessive consumption of the immune signaling molecule interleukin 2 by hyperactivated CD8 T cells, the suppressor cells of our immune system, had a much greater impact on the inflammation.”

This means that at least two different disease pathways are at play—knowledge that indicates that we could save the lives of more patients if we also targeted both pathways during treatment.

“This study not only provides a new paradigm for understanding HLH, with major implications for its treatment, but also gives us a broad insight into how hyperactivated CD8 T cells cause damage,” adds prof. Adrian Liston.

“We can learn so much from an in-depth analysis of the immune cells present in a simple sample of blood from patients,” concludes Humblet-Baron, who hopes to uncover the mechanisms underlying many more of these immunological problems. “Coupled with the power of biochemical and animal research, these insights are really changing how we diagnose and treat patients in the clinic.”

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Humblet-Baron, et al 2018 Blood. "Murine myeloproliferative disorder as a consequence of impaired collaboration between dendritic cells and CD4 T cells"

Humblet-Baron et al. 2018 Journal of Allergy and Clinical Immunology. "IFN-γ and CD25 drive distinct pathological features during CD8 T cell hyperactivation in hemophagocytic lymphohistiocytosis"

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Unlocking The Secrets Of A Rare Immune Disease

by Adrian Liston and Josselyn Garcia-Perez 

Primary immunodeficiencies (PID) are a heterogeneous group of disorders that disturb the host’s immunity, creating susceptibility to infections. PIDs are genetically diverse, with mutations in many different genes capable of causing immunodeficiency. The clinical symptoms of PIDs include, but are not limited to, susceptibility to infections, inflammation, and autoimmunity, although each gene mutated, and indeed each individual mutation, can lead to different manifestations.

Central to understanding PIDs is to understand which immune cell type is rendered defective by the mutation the patient carries. The type of infections the patient develops is often a key indicator of the underlying immunodeficiency; for example, pulmonary infections and bacterial septicemia are associated with B cell defect, whereas fungal susceptibility is associated with defects in certain types of T cells. Candidate pathways can be investigated using genetics and immune screening, and successful identification of the underlying causes allows a treatment program to be tailored to the patient.

Read the full story on Science Trends

Translational Immunology lab in the news

Our research was featured tonight on VRT News:

Speaking roles by Carine Wouters, Erika Van Nieuwenhove and Adrian Liston. Cameos from Stephanie Humblet-Baron, John Barber and Pier-Andree Penttila

 

 

Original research: Van Nieuwenhove et al. 2018 Journal of Allergy and Clinical Immunology. "A kindred with mutant IKAROS and autoimmunity"

If you would like to support our clinical research, and allow us to take on more cases like these, you can make a tax-deductable donation the Ped IMID fund, by transferring to IBAN-number BE45 7340 1941 7789, BIC-code: KREDBEBB with the label "voor EBD-FOPIIA-O2010".