Periodic Reporting for period 1 - MITO (The function and biomarker potential of mitochondrial microRNAs in hypertension)
Période du rapport: 2020-08-03 au 2022-08-02
Hypertension is a complex disease resulting from dynamic interactions between genetic, lifestyle and environmental factors. Due to this multifaceted pathogenesis, aetiology of hypertension is unknown in 90-95% of patients. A significant proportion of patients are not aware that they have hypertension since this disease can remain silent for years without triggering any symptoms.
Although it is straightforward to diagnose hypertension and relatively easy to treat the condition with low-cost drugs, recent hypertension prevalence data pinpointed that significant gaps in diagnosis and treatment remain. Thus, there is an unmet need for novel biomarkers for primordial prevention, better control, and decrease in morbidity and mortality associated with hypertension.
Over the years, multiple candidate circulating protein-coding RNAs and noncoding RNAs (ncRNAs) have been identified in various hypertension phenotypes. Among them microRNAs (miRNAs), short ncRNA transcripts, appeared as attractive biomarkers for essential hypertension. Due to the fact that miRNAs participate in disease evolution and response to anti-hypertensive therapy, they represent promising diagnostic, prognostic and surrogate end-point biomarkers for follow-up of hypertension control.
The main objective of the project was to discover clinically-translatable novel miRNA-based methods to improve healthcare of hypertensive patients. In line with that, the MITO project delivered a machine learning based model to predict essential hypertension using miRNA signature from whole blood. In addition, the project allowed a high-quality training of the MSCA fellow, covering three interlinked domains: biomarker discovery, biomarker validation and functional association. This training provided the MSCA fellow with with a strong knowledge of state-of-the-art technologies (WP1) which allowed to achieve the following scientific goals:
(i) Discover novel circulating miRNAs associated with hypertension (WP2) – seven miRNAs and eight piwi-interacting RNAs (piRNAs) were identified as potential biomarkers for hypertension.
(ii) Validate candidate miRNAs and explore gender differences (WP3) – the association with hypertension of six miRNAs was validated in a cohort of 572 participants.
(iii) Determine functional associations between miRNAs and hypertension (WP4) - two lead miRNAs were selected for functional characterisation.
Although it is straightforward to diagnose hypertension and relatively easy to treat the condition with low-cost drugs, recent hypertension prevalence data pinpointed that significant gaps in diagnosis and treatment remain. Thus, there is an unmet need for novel biomarkers for primordial prevention, better control, and decrease in morbidity and mortality associated with hypertension.
Over the years, multiple candidate circulating protein-coding RNAs and noncoding RNAs (ncRNAs) have been identified in various hypertension phenotypes. Among them microRNAs (miRNAs), short ncRNA transcripts, appeared as attractive biomarkers for essential hypertension. Due to the fact that miRNAs participate in disease evolution and response to anti-hypertensive therapy, they represent promising diagnostic, prognostic and surrogate end-point biomarkers for follow-up of hypertension control.
The main objective of the project was to discover clinically-translatable novel miRNA-based methods to improve healthcare of hypertensive patients. In line with that, the MITO project delivered a machine learning based model to predict essential hypertension using miRNA signature from whole blood. In addition, the project allowed a high-quality training of the MSCA fellow, covering three interlinked domains: biomarker discovery, biomarker validation and functional association. This training provided the MSCA fellow with with a strong knowledge of state-of-the-art technologies (WP1) which allowed to achieve the following scientific goals:
(i) Discover novel circulating miRNAs associated with hypertension (WP2) – seven miRNAs and eight piwi-interacting RNAs (piRNAs) were identified as potential biomarkers for hypertension.
(ii) Validate candidate miRNAs and explore gender differences (WP3) – the association with hypertension of six miRNAs was validated in a cohort of 572 participants.
(iii) Determine functional associations between miRNAs and hypertension (WP4) - two lead miRNAs were selected for functional characterisation.
The MITO project was delineated into five work packages (WPs). WP1 included project management and advanced training of the MSCA fellow in state of the art techniques relevant to RNA biomarkers discovery and validation. This training was conducted at Luxembourg Institute of Health and at three partner institutions. Advanced training in biomarker validation including various biostatistics tests and bioinformatics methods was conducted by supervisor (Yvan Devaux), research engineer, bioinformatician, and biostatistician at the LIH. The MSCA fellow attended advanced bioinformatics training entitled ‘’Multiomics data analysis’’ organized by LIH from 2 to 24 October 2021. Besides this training, the MSCA fellow attended an advanced excel training organized in collaboration between LIH and KeyJob, a training & support agency. The MSCA fellow attended the online seminar ‘’Unleash the power of digital PCR in gene expression analysis’’, on 16 February 2021, provided by Qiagen. The MSCA fellow successfully completed 4 institutionally organized trainings in transferable soft skills. She coordinated the preparation of 5 grant applications and submitted 2 follow up grant applications as principal investigator and 2 awards for women in research.
The main objective of WP2 was to discover novel miRNAs biomarkers for essential hypertension. Using small deep RNA sequencing, seven miRNAs and eight piRNAs were identified as biomarkers for hypertension. Six candidate miRNAs were validated by RT-qPCR in 572 samples of the MITO cohort. Five miRNAs were significantly deregulated between patients and healthy controls. Since blood samples were collected during COVID-19 pandemic, an in house PCR test was developed to test the presence of Sars-CoV-2 genes in samples with unknown COVID-19 history. A significant proportion of blood samples were positive for two Sars-CoV-2 genes and were excluded from further analysis. The five significantly deregulated miRNAs together with clinical variables were integrated in a machine learning model for hypertension prediction. The features age, body mass index, current smoker, alcohol use, hypertension family history and two miRNAs were selected by Recursive Feature Elimination method. The k-nearest neighbour algorithm with selected features and optimal parameters could estimate the test dataset with 100% accuracy. The main results of WP2 and WP3 will be published in a scientific publication currently under preparation
The functional characterization of lead miRNA candidates in WP4 has not been carried out as initially planned due to the strong impact of COVID-19 pandemic on timely sample collection and transfer (WP1), delay of experiments planned in WP2 and WP3 as a consequence of delay in delivery of consumables and reorganization of group work according to COVID-19 restrictions. Although COVID-19 pandemic affected the organization and planning of experiments, the main objectives of the MITO project for WP2 and WP3 have been achieved and results will be published in an international peer-reviewed scientific journal.
In WP5, the MSCA fellow published 2 review articles and one position paper, one book chapter and one scientific brochure. One review paper and a guidelines paper for mitochondrial RNA expression profiling are under preparation. The MSCA fellow was appointed as review editor in Frontiers Molecular mechanism of Ageing Journal and delivered 7 public engagements to popularize Women in Research and hypertension prevention. As a management committee member of the CardioRNA COST Action CA17129, she participated in Core Group and Working Group meetings in Athens, Greece and Pavia, Italy. In addition, she has been invited as a speaker to The 47th FEBS Congress with the general topic “Together in bioscience for a better future”, session “RNA biology” (Tours, France, from 8 to 13 July 2023) and the 9th and final Management Committee – Working group meeting of CardioRNA COST Action (Nicosia, Cyprus, from 22 to 24 February 2023).
The main objective of WP2 was to discover novel miRNAs biomarkers for essential hypertension. Using small deep RNA sequencing, seven miRNAs and eight piRNAs were identified as biomarkers for hypertension. Six candidate miRNAs were validated by RT-qPCR in 572 samples of the MITO cohort. Five miRNAs were significantly deregulated between patients and healthy controls. Since blood samples were collected during COVID-19 pandemic, an in house PCR test was developed to test the presence of Sars-CoV-2 genes in samples with unknown COVID-19 history. A significant proportion of blood samples were positive for two Sars-CoV-2 genes and were excluded from further analysis. The five significantly deregulated miRNAs together with clinical variables were integrated in a machine learning model for hypertension prediction. The features age, body mass index, current smoker, alcohol use, hypertension family history and two miRNAs were selected by Recursive Feature Elimination method. The k-nearest neighbour algorithm with selected features and optimal parameters could estimate the test dataset with 100% accuracy. The main results of WP2 and WP3 will be published in a scientific publication currently under preparation
The functional characterization of lead miRNA candidates in WP4 has not been carried out as initially planned due to the strong impact of COVID-19 pandemic on timely sample collection and transfer (WP1), delay of experiments planned in WP2 and WP3 as a consequence of delay in delivery of consumables and reorganization of group work according to COVID-19 restrictions. Although COVID-19 pandemic affected the organization and planning of experiments, the main objectives of the MITO project for WP2 and WP3 have been achieved and results will be published in an international peer-reviewed scientific journal.
In WP5, the MSCA fellow published 2 review articles and one position paper, one book chapter and one scientific brochure. One review paper and a guidelines paper for mitochondrial RNA expression profiling are under preparation. The MSCA fellow was appointed as review editor in Frontiers Molecular mechanism of Ageing Journal and delivered 7 public engagements to popularize Women in Research and hypertension prevention. As a management committee member of the CardioRNA COST Action CA17129, she participated in Core Group and Working Group meetings in Athens, Greece and Pavia, Italy. In addition, she has been invited as a speaker to The 47th FEBS Congress with the general topic “Together in bioscience for a better future”, session “RNA biology” (Tours, France, from 8 to 13 July 2023) and the 9th and final Management Committee – Working group meeting of CardioRNA COST Action (Nicosia, Cyprus, from 22 to 24 February 2023).
Within the MITO project, we identified 6 miRNA biomarker candidates for essential hypertension. These prominent experimental results suggest that the integration of circulating miRNAs expression profiles and clinical data into machine learning model may serve as a useful tool to guide medical care providers for diagnosis and personalized patient management. In addition, the results generated in this project stimulate further experimental validations of the promising miRNA biomarker candidates identified as linked to essential hypertension.
For the applicant, the present project was a pivotal professional experience which allowed to gain the opportunity to learn from high-class researchers in the field and to raise her research performance to a high level. This allowed her to move to the industry (Biotech Company) since the middle of August 2022 and contribute as program leader to the development of new diagnostics, preventive strategies, innovative therapies and clinical applications that impact healthcare of cardiovascular patients.
For the applicant, the present project was a pivotal professional experience which allowed to gain the opportunity to learn from high-class researchers in the field and to raise her research performance to a high level. This allowed her to move to the industry (Biotech Company) since the middle of August 2022 and contribute as program leader to the development of new diagnostics, preventive strategies, innovative therapies and clinical applications that impact healthcare of cardiovascular patients.