In this week’s New England Journal of Medicine, an international team of investigators based in Europe and Africa, report the results of a study to identify a gene expression signature for childhood tuberculosis (TB). They found that the majority of childhood TB cases can be distinguished from other childhood diseases by the signature of 51 genes activated or suppressed in the affected child’s blood. The findings offer new hope for improved diagnosis of childhood TB.
According to WHO 6% of the patients suffering from TB worldwide are children, with approximately 530,000 new cases diagnosed each year. However, the true global burden of childhood TB is unknown due to the difficulty in diagnosis of TB in children. Whereas TB in adults is usually readily diagnosed by detection of the TB bacterium in sputum or by characteristic symptoms and chest x-ray findings, children with TB have non-specific symptoms, common to many other childhood diseases, and the TB bacterium is generally not detectable in sputum. As a result of the difficulty in establishing the diagnosis, the disease is often diagnosed late, when the child has become critically unwell, and when the infection has spread from the lungs to the brain (causing TB meningitis) or to other organs. As a result of late diagnosis and spread of the infection throughput the body, more than 70,000 children die from TB each year and surviving children may suffer long term consequences as a result of brain damage from TB meningitis or bone destruction from TB of the spine. Conversely, because the diagnosis of TB in children is so difficult to establish with certainty, many children are treated with long courses of potentially toxic TB drugs based only on the suspicion that they might have TB, when actually they are suffering from other conditions. There is thus an urgent need for better methods to diagnose TB in children.
Current tests to identify TB in children are based on the Tuberculin skin test, or identifying the TB bacillus in sputum, both of which are very unreliable. Rather than searching for the bacteria, the researchers aimed to identify the pattern of human genes expressed in the blood in response to the TB infection, using sophisticated molecular methods to examine many thousands of genes that might be switched on or off during any infection.
The study was conducted by an international consortium of investigators, funded by an EU Action for Diseases of Poverty program grant, and included researchers from the UK (Imperial College London, London School of Hygiene & Tropical Medicine, Sussex University, Liverpool School of Tropical Medicine and Liverpool University), South Africa (University of Cape Town), Malawi (Malawi College of Medicine/Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre), Kenya (Wellcome Trust/ KEMRI Research Unit, Kilifi), and the Genome Institute of Singapore. The investigators studied over 2,800 children admitted to hospitals in South Africa, Malawi and Kenya with symptoms of TB, and identified those who had proven TB and those in whom TB was excluded as the cause of the child’s illness.
A sample of each child’s blood was then examined using RNA expression microarrays. This technique simultaneously examines all genes in the human genome (over 30,000 genes) and identifies genes which are either activated or suppressed in each child’s blood. The South Africa and Malawi patient samples were used to discover a “signature” of TB, and the samples from the Kenyan children were used to confirm that the same â€œTB signatureâ€ can be found in a completely separate group of children with TB.
After comparing the pattern of genes expressed in the blood of children with TB with the pattern in other diseases (and in children with latent TB infection), the investigators used novel statistical methods to identify the smallest number of genes that accurately distinguished TB from other diseases. They found that TB could be distinguished from other diseases with a signature of just 51 genes, and TB could be distinguished from healthy children who harbor TB but have no symptoms (latent TB infection) with a 42 gene signature. Using novel statistical approaches, they found that the information in the gene signature of TB can be combined to give a single “TB risk score” for each child, which accurately diagnosed over 80% of the children with TB in the Kenyan validation cohort.
Using current detection methods, TB tests are often time consuming, involve costly hospital investigations and many children are treated based on clinical suspicion where a diagnosis of TB cannot be confirmed or excluded. A better test for childhood TB that enables earlier diagnosis will enable treatment to be started before the disease has spread to the brain and other organs, improving outcome and reducing costs. Furthermore, an accurate test for TB would prevent unnecessary TB treatment being given to many thousands of children who are treated for TB each year worldwide, but who actually have other diseases.
This study has provided evidence that gene expression signatures can be used to identify children with TB on a single blood sample. Biotechnology and industrial expertise is now needed to turn these promising findings into a simple cheap test that can be used in hospitals and clinics, and also in resource-poor regions of the world, where the burden of TB is greatest.
Professor Michael Levin, from Imperial College London, who led the study said: “The findings reported today are the result of a 7 year collaborative effort of clinicians and scientists in Africa working closely with investigators in the UK and Singapore, to apply sophisticated new molecular methods to the global problem of TB in childhood. The gene “signature of childhood TB”that our study has identified, provides a new approach to the difficult problem of diagnosing TB in children. What is now needed is collaboration from biotechnology and industrial partners to translate these exciting findings into a simple, rapid and affordable test for TB that can be used in hospitals world wide”.
Prof Brian Eley, who led the clinical study in Cape Town said: “Childhood TB is a major problem in African hospitals. Thousands of children are investigated for TB, and treated without proof that they have TB, because our current tests are unable to confirm TB in the vast majority of children who present with strong clinical and chest X-ray evidence of TB. An accurate test for childhood TB would be an enormous breakthrough, enabling earlier diagnosis, reducing long hospital admissions for investigation of TB suspects, and limiting the number of children treated inappropriately.”
Dr Suzanne Anderson who led the study in Malawi said “The study highlights the importance of collaboration between academic institutions in affluent countries, with those in resource poor regions of the world. This study has enabled the sophisticated molecular and informatics methods to be used to help improve diagnosis of TB which predominantly affects the resource poor regions of the world.”
The study was funded by an EU Action for Diseases of Poverty program grant. The Kenyan component was supported by a Wellcome Trust Training Fellowship to Dr Andrew Brent; and recruitment in Malawi and Kenya and analysis in London took place at research centers supported by the Wellcome Trust.
To Read the full study Click here