Periodic Reporting for period 2 - DIAMONDS (Diagnosis and Management of Febrile Illness using RNA Personalised Molecular Signature Diagnosis)
Okres sprawozdawczy: 2021-07-01 do 2022-12-31
Infectious and inflammatory diseases are amongst the most common conditions for which patients consult medical care in the community and hospitals. A large proportion of patients attending medical care with fever or inflammation have self-resolving viral or other conditions which only require symptomatic treatments. However, hidden amongst them are a small proportion of patients with serious life-threatening bacterial infections including sepsis and meningitis or serious inflammatory diseases. The major problem facing clinicians is how to rapidly identify and distinguish the serious conditions that require specific treatments.
The current approach to infectious and inflammatory diseases is to first exclude the possibility of severe bacterial infection through conventional microbiological investigation including blood cultures and cultures from other sites. As results of cultures may not be available for 24-48 hours, patients suspected of having significant infections are first treated with broad-spectrum antibiotics while awaiting the culture results. Current diagnostic approaches fail to identify the cause in a high proportion of cases and many patients undergo extensive investigation and treatment with broad-spectrum antibiotics because the possibility of infection cannot be excluded. A small proportion of patients with fever and inflammation do not have infections but have serious and persistent inflammatory disorders that require specific treatments. These are often only diagnosed after a lengthy process of first excluding infection and then stepwise exclusion of other conditions.
DIAMONDS aims to revolutionise the diagnostic process for infectious and inflammatory diseases by demonstrating and bringing into clinical use diagnostic approaches based on host molecular signatures. The underlying hypothesis in DIAMONDS is that individual infectious and inflammatory conditions are associated with unique patterns of genes that are activated or repressed in the patient’s blood in response to the individual disease. These unique molecular patterns can be identified through genome-wide RNA sequencing (RNA-Seq) and can be used as a “molecular signature” or “fingerprint” specific for each disease process. DIAMONDS builds on our previous EU-funded EUCLIDS and PERFORM studies which have recruited over 10,000 patients with fever and inflammation at multiple hospitals in Europe, Africa, and Asia. We have established proof of principle that individual diseases, such as tuberculosis, bacterial infections, viral infections, or inflammatory diseases like Kawasaki disease and rheumatoid arthritis, are characterised by unique RNA signatures. DIAMONDS will move the concept of diagnosis of infection and inflammatory disease by RNA molecular signatures a step closer to clinical introduction by first expanding the range of infectious and inflammatory diseases for which we have gene expression data, to cover a wide range of infectious and inflammatory diseases. Using samples from carefully phenotyped patients, DIAMONDS will undertake RNA-Seq and bioinformatic analyses to identify the RNA profile of common infectious and inflammatory diseases. DIAMONDS will establish a European RNA transcriptomic library which will be available to researchers and clinicians worldwide as a resource for understanding infectious and inflammatory diseases.
Using bioinformatic methods we will select the smallest number of genes that enable individual infectious and inflammatory diseases to be distinguished from each other. We will develop a diagnostic device to rapidly detect the genes required to distinguish common diseases, and test the device to measure personalised molecular signatures in a prospective cohort. By the end of the study, we aim to have validated the concept of diagnosis of infectious and inflammatory diseases using personalised molecular signatures, established the accuracy of a diagnostic device to detect personalised molecular signatures, and provided evidence on cost-effectiveness and clinical value of a new diagnostic approach through RNA molecular signature diagnosis.
The current approach to infectious and inflammatory diseases is to first exclude the possibility of severe bacterial infection through conventional microbiological investigation including blood cultures and cultures from other sites. As results of cultures may not be available for 24-48 hours, patients suspected of having significant infections are first treated with broad-spectrum antibiotics while awaiting the culture results. Current diagnostic approaches fail to identify the cause in a high proportion of cases and many patients undergo extensive investigation and treatment with broad-spectrum antibiotics because the possibility of infection cannot be excluded. A small proportion of patients with fever and inflammation do not have infections but have serious and persistent inflammatory disorders that require specific treatments. These are often only diagnosed after a lengthy process of first excluding infection and then stepwise exclusion of other conditions.
DIAMONDS aims to revolutionise the diagnostic process for infectious and inflammatory diseases by demonstrating and bringing into clinical use diagnostic approaches based on host molecular signatures. The underlying hypothesis in DIAMONDS is that individual infectious and inflammatory conditions are associated with unique patterns of genes that are activated or repressed in the patient’s blood in response to the individual disease. These unique molecular patterns can be identified through genome-wide RNA sequencing (RNA-Seq) and can be used as a “molecular signature” or “fingerprint” specific for each disease process. DIAMONDS builds on our previous EU-funded EUCLIDS and PERFORM studies which have recruited over 10,000 patients with fever and inflammation at multiple hospitals in Europe, Africa, and Asia. We have established proof of principle that individual diseases, such as tuberculosis, bacterial infections, viral infections, or inflammatory diseases like Kawasaki disease and rheumatoid arthritis, are characterised by unique RNA signatures. DIAMONDS will move the concept of diagnosis of infection and inflammatory disease by RNA molecular signatures a step closer to clinical introduction by first expanding the range of infectious and inflammatory diseases for which we have gene expression data, to cover a wide range of infectious and inflammatory diseases. Using samples from carefully phenotyped patients, DIAMONDS will undertake RNA-Seq and bioinformatic analyses to identify the RNA profile of common infectious and inflammatory diseases. DIAMONDS will establish a European RNA transcriptomic library which will be available to researchers and clinicians worldwide as a resource for understanding infectious and inflammatory diseases.
Using bioinformatic methods we will select the smallest number of genes that enable individual infectious and inflammatory diseases to be distinguished from each other. We will develop a diagnostic device to rapidly detect the genes required to distinguish common diseases, and test the device to measure personalised molecular signatures in a prospective cohort. By the end of the study, we aim to have validated the concept of diagnosis of infectious and inflammatory diseases using personalised molecular signatures, established the accuracy of a diagnostic device to detect personalised molecular signatures, and provided evidence on cost-effectiveness and clinical value of a new diagnostic approach through RNA molecular signature diagnosis.
Since commencing DIAMONDS in January 2020, the consortium obtained ethical and regulatory approvals to commence recruitment of patients at all partner sites. Despite delays caused by the COVID-19 pandemic, DIAMONDS has successfully recruited over 10,500 subjects by December 2022. Detailed clinical are available on the secure online database, and samples for both diagnostic studies are stored in a sample biobank. Quality control and sample handling procedures have been implemented to ensure integrity of research data. In response to the COVID-19 pandemic, DIAMONDS included over 1500 patients affected by COVID-19 and the multisystem inflammatory syndrome in children (MIS-C), and also newly emerging post pandemic conditions including the Childhood hepatitis of unknown cause. RNA-Seq has been completed on an initial cohort and the bioinformatic team has applied our novel computational pipeline to identify RNA signatures of MIS-C-which enable distinction of this disease from bacterial and viral infections, and Kawasaki disease. Bioinformatic analysis has identified our first personalised molecular signature for diagnosis (PMSD) to distinguish the major disease categories. This “version 1 PMSD” has been converted to an RT-qPCR assay by partner bioMérieux, for implementation using their Filmarray-platform. The prototype v1 PMSD assay has been manufactured, and cross platform evaluation of the performance of this first assay is underway. Bioinformatic analysis of the RNA-Seq data has identified smaller PMSD signatures based on 10-20 transcripts that have clinical utility for specific situations. Development of small signature PMSD tests for specific clinical indications using CSMOS technology, and evaluation of alternative platforms for detection of PMSD is underway and the data will be used to select the optimal approaches for validation of PMSD a Pilot demonstration commencing October 2023.
DIAMONDS has progressed well despite the constraints of the COVID-19 pandemic in recruiting and phenotyping a large cohort of patients with a range of infectious and inflammatory diseases. RNA-Seq followed by bioinformatic analysis has confirmed our hypothesis that unique molecular signatures can be used to distinguish individual infectious and inflammatory diseases. The first personalised molecular signature diagnostic test has been manufactured by bioMérieux , and will undergo evaluation early in 2023, enabling large scale manufacture of a PMSD test for clinical evaluation in the Pilot demonstration in Autumn 2023. This large scale evaluation of the PMSD device will include evaluation of health care costs, acceptability to users and stake holders, and will provide proof of concept for the introduction of a new approach to diagnosing infectious and inflammatory diseases by personalised molecular signatures.