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Awarded Amount$285,937DiseaseNTD (Mycetoma)InterventionDiagnosticDevelopment StageConcept DevelopmentCollaboration PartnersRIKEN , Hospital General de Mexico , Mycetoma Research Centre (MRC), University of Khartoum , Erasmus University Medical Center
Introduction and Background of the Project
Mycetoma is a neglected tropical disease of the subcutaneous tissue and is characterized by large tumor-like lesions. It is caused by more than 70 different causative agents, but four of these are responsible for 79.5% of all mycetoma cases world-wide. Appropriate treatment outcome depends on proper identification of the causative organism. The current mycetoma diagnostics tools are tedious, invasive of low sensitivity and specificity and expensive. Presently there is no point-of-care diagnostic test for mycetoma.
To identify species-specific markers for the 4 most common causative agents of mycetoma in urine and plasma of mycetoma patients
In order to identify species-specific markers a five step-approach will be taken
- Urine and plasma will be isolated from patients with mycetoma
- The causative agent will be identified by PCR
- Exosomes will be isolated from urine and plasma, as they will most likely contain species specific markers
- RNA will be isolated from the exosomes and sequenced
- The transcriptomes will be profiled and markers identified
The markers identified in MycEXomics can later be used to develop Point-of-Care diagnostic tools to detect early cases of mycetoma.
How can your partnership (project) address global health challenges?
Mycetoma is a debilitating disease and many patients become dependent on their relatives and society. Treatment of mycetoma is expensive and of long duration. On top of that for fungal mycetoma surgery or even amputation are needed. Higher therapeutic success rates are obtained when mycetoma is diagnosed early. Currently, there is no point-of-care test for mycetoma and screening for early (subclinical) cases is impossible. As a result, the disease is often only identified at a late stage. By identifying markers which in the future can be developed in point-of-care diagnostic tools we hope to identify mycetoma as early as possible in order to prevent the need for amputations.
What sort of innovation are you bringing in your project?
Since for mycetoma currently no diagnostic markers are available, we will be the first to identify these markers directly in urine and plasma. By isolating RNA from exosomes we will maximize the likelihood of not only identifying host-associated markers but also pathogen-associated markers.
Role and Responsibility of Each Partner
Manage GHIT investment & will sequence the RNA isolated from the exosomes and characterize the expression profile of the individual markers.
Mycetoma Research Centre (MRC) & Hospital General de México “Dr. Eduardo Liceaga”
Mycetoma Research Centre and Hospital General de México will be responsible for collecting blood and urine from mycetoma patients. They will also diagnose the patients according to the protocols used in their institutes.
Erasmus University Medical Center
ErasmusMC will verify the species identification by sequencing and isolate the exosomes and purify RNA from them.
Together the four partners will identify diagnostic markers for each of the four causative agents of mycetoma.
1. Project objective
The main objective of MycEXomics was to identify pathogen-specific markers for common mycetoma causative agents in exosomes isolated from urine and plasma which can be used to identify the causative agent to the species-level and to monitor the mycetoma patient therapeutic response during treatment. The identified marker will be used to develop POC diagnostic test. MycEXomics POC test, will enable identification of mycetoma subclinical cases, case identification in large screening campaigns thus allowing a more precise burden estimation. Finally, enable identifying early cases, thus allows treatment in early stage which most in its turn will eradicate the need for amputations.
2. Project design
MycEXomics workflow based on recruitment of discovery cohort, samples collection, pathogen identification and typing, and transcriptomics profiling. We recruited discovery cohort (consists of patients and controls). From each subject in the discovery cohort, plasma and urine samples were collected. For patients, mycetoma grains are collected and cultured and molecularly identified. The isolates were typed. Patients are selected and included in the sequencing cohort based on the molecular typing result. Exosomes isolated from plasma and urine of the patients and controls followed by RNA extraction. For each sample, we prepared smallRNA and microRNA sequencing libraries. Resulting sequencing profiles, were analyzed using statistical methods.
3. Results, lessons learned
MycEXomics was implemented as Target Research Platform (TRP), with five activities. In the first activity (discovery cohort recruitment), we recruited discovery cohort (n=139). The second activity, Identify and type pathogens molecularly, we verified pathogen ID by sequencing by the Internally Transcribed Spacer (ITS) barcoding gene for Eumycetoma causative agents or the hsp65 barcoding gene for Actinomycetoma. To determine the genetic diversity of M. mycetomatis, a Short-Tandem-Repeat Assay (MmySTR) was used to determine the genetic diversity of the samples (genotyping). The third activity, Exosomes isolation and RNA extraction from the plasma and urine samples from the discovery cohort. In the fourth activity, Exosomal RNA profiling was completed by preparing RNA sequencing and microRNA sequencing libraries. The fifth and final activity in MycEXomics, was the marker discovery. In this activity, raw sequencing reads from the transcriptomic profiles were mapped against human genome / pathogen genome. This process enabled us to identify three types of molecular diagnostic markers (Pathogen specific markers, host specific markers annotated in miRbase 22.1, and host specific marker annotated in human GENCODE 42). Based on the above workflow, we created search space for three types of molecular diagnostic markers. We are planning to perform further analysis using the list of markers genes to understand the biology behind these genes by conducting Gene set enrichment analysis (GSEA).
- Due the pandemic in Mexico City during the project years, the collaboration partner in this project, was not able to contribute to the discovery cohort, therefore, the current discovery cohort recruited from one geographical region (Sudan).
- We demonstrated the feasibility of MycEXomics approach to identify circulated pathogen markers in the (extracellular vesicles) EV of urine and plasma of mycetoma patient.
- To our knowledge this is the first research of its type in NTDs. And the concept could be applied for other NTDs to identify potential diagnostic and therapeutic markers for other NTDs.
In summary, at this stage of MycEXomics, we successfully developed and implemented TRP. The concept development was initiated, completed, and reported to GHIT Fund.