Periodic Reporting for period 3 - DIAMONDS (Diagnosis and Management of Febrile Illness using RNA Personalised Molecular Signature Diagnosis)
Periodo di rendicontazione: 2023-01-01 al 2023-12-31
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. However, amongst them are a small proportion with serious life-threatening bacterial infections 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 relies first on exclusion of severe bacterial infection using microbiological approaches including bacterial cultures. Bacterial culture results may not be available for 24-48 hours, and patients with suspected significant infection are first treated with broad-spectrum antibiotics, pending the microbiological results, which in many cases fail to confidently identify the cause. Thus, many patients undergo unnecessary investigation and treatment with broad-spectrum antibiotics. 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 discovered 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 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 has undertaken RNA-Seq and bioinformatic analyses to identify the RNA profile of common infectious and inflammatory diseases. DIAMONDS is establishing a European Diagnostic Transcriptomic Library which will be available to researchers and clinicians worldwide as a resource for understanding infectious and inflammatory diseases.
Using bioinformatic methods we have selected the smallest number of genes that enable individual infectious and inflammatory diseases to be distinguished – an approach called Personalised Molecular Signature Diagnosis (PMSD). We are developing diagnostic devices to rapidly detect the genes required to distinguish common diseases, and are testing these prospectively. By the end of the study, we aim to have validated the concept of diagnosis of infectious and inflammatory diseases using PMSD, established the accuracy of a PMSD detection device, and provided evidence on cost-effectiveness and clinical value of PMSD.
The current approach to infectious and inflammatory diseases relies first on exclusion of severe bacterial infection using microbiological approaches including bacterial cultures. Bacterial culture results may not be available for 24-48 hours, and patients with suspected significant infection are first treated with broad-spectrum antibiotics, pending the microbiological results, which in many cases fail to confidently identify the cause. Thus, many patients undergo unnecessary investigation and treatment with broad-spectrum antibiotics. 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 discovered 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 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 has undertaken RNA-Seq and bioinformatic analyses to identify the RNA profile of common infectious and inflammatory diseases. DIAMONDS is establishing a European Diagnostic Transcriptomic Library which will be available to researchers and clinicians worldwide as a resource for understanding infectious and inflammatory diseases.
Using bioinformatic methods we have selected the smallest number of genes that enable individual infectious and inflammatory diseases to be distinguished – an approach called Personalised Molecular Signature Diagnosis (PMSD). We are developing diagnostic devices to rapidly detect the genes required to distinguish common diseases, and are testing these prospectively. By the end of the study, we aim to have validated the concept of diagnosis of infectious and inflammatory diseases using PMSD, established the accuracy of a PMSD detection device, and provided evidence on cost-effectiveness and clinical value of PMSD.
Since January 2020, the DIAMONDS consortium has recruited over 12000 patients and 2000 control subjects. Detailed clinical data are available on the secure online database, and samples for diagnostic studies are stored in a sample biobank. Quality control and sample handling procedures have been implemented to ensure integrity of research data. To improve accuracy of phenotyping, molecular pathogen detection has been completed on 2953 throat swabs and 3999 blood samples. In response to the COVID-19 pandemic, DIAMONDS included over 1500 patients affected by COVID-19 and multisystem inflammatory syndrome in children (MIS-C). DIAMONDS has also identified the cause of the newly emerged post-pandemic childhood hepatitis of unknown cause.
RNA-Seq has been completed on 1400 patient samples to add to the existing RNA expression data bank. The bioinformatic team developed and applied a novel computational pipeline to identify RNA signatures of the pandemic-associated 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 diagnostic that distinguishes 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 has confirmed accurate diagnosis of the major disease classes. Large-scale manufacture of a V1 prototype pouch is enabling evaluation on independent cohorts.
Bioinformatic analysis of RNA-Seq data has also identified smaller PMSD signatures based on 10-20 transcripts that have utility for specific clinical settings. Development of small signature PMSD tests for specific clinical indications using CMOS technology has been achieved and development of the first multiclass test using lab-on-chip technology is underway to distinguish bacterial infection, viral infection and malaria or TB. This will be evaluated on DIAMONDS samples during 2024. A pilot demonstration to evaluate the technical performance, clinical utility, cost-effectiveness and user acceptability of PMSD has commenced and will conclude in October 2024. Large-scale validation of an optimised PMSD using nanostring technology will commence in Summer 2024.
RNA-Seq has been completed on 1400 patient samples to add to the existing RNA expression data bank. The bioinformatic team developed and applied a novel computational pipeline to identify RNA signatures of the pandemic-associated 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 diagnostic that distinguishes 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 has confirmed accurate diagnosis of the major disease classes. Large-scale manufacture of a V1 prototype pouch is enabling evaluation on independent cohorts.
Bioinformatic analysis of RNA-Seq data has also identified smaller PMSD signatures based on 10-20 transcripts that have utility for specific clinical settings. Development of small signature PMSD tests for specific clinical indications using CMOS technology has been achieved and development of the first multiclass test using lab-on-chip technology is underway to distinguish bacterial infection, viral infection and malaria or TB. This will be evaluated on DIAMONDS samples during 2024. A pilot demonstration to evaluate the technical performance, clinical utility, cost-effectiveness and user acceptability of PMSD has commenced and will conclude in October 2024. Large-scale validation of an optimised PMSD using nanostring technology will commence in Summer 2024.
DIAMONDS has recruited and phenotyped a large cohort of patients with a range of infectious and inflammatory diseases, despite the constraints of the COVID-19 pandemic. 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 PMSD test has been manufactured by bioMérieux and showed good cross-platform performance. Large-scale manufacture of Version 1 PMSD using the FilmArray platform enabled the Pilot Demonstration of PMSD to commence in Summer 2023. This large-scale evaluation 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.