MitoDiag network coordination:
2023 - COMMI project
Fighting Diagnostic Odyssey in Mitochondrial Diseases.
Project for the Establishment of a Cohort of Patients with Mitochondrial Diseases.
Mitochondrial diseases are a group of disorders, most often hereditary, characterized by mitochondrial dysfunction. Mitochondria are organelles present in all cells and play an essential role in cellular function by enabling energy production through the process of cellular respiration. Mitochondrial diseases are caused by mutations in genes involved in mitochondrial functions, impacting the cells' energy production. Understanding the causes of mitochondrial diseases is particularly complex because the mitochondrial genome alone is not sufficient to ensure proper mitochondrial function, as it is also linked to the nuclear genome. Thus, mitochondrial diseases can be caused by mutations in either the mitochondrial or nuclear genome. These are the most common metabolic diseases, highly heterogeneous in clinical, biochemical, and genetic aspects.
The diagnosis of mitochondrial diseases has been completely transformed by the emergence of Next-Generation Sequencing (NGS) technologies, which have rapidly increased the genetic diagnosis rate from 10-20% to over 50% in some cohorts, revealing numerous variants (either pathogenic or of currently unknown significance). The French Network of Mitochondrial Disease Diagnostic Laboratories, MITODIAG, collaborates closely with the two National Reference Centers, CARAMMEL and CALISSON, as well as the FILNEMUS network, to improve patient diagnosis and care.
The COMMI project aims to assemble a cohort of 400 patients tested by high-throughput sequencing, with clinical and genetic descriptions, within the MITODIAG network laboratories. This patient group has a confirmed molecular diagnosis through the identification of one or more pathogenic variants in nuclear genes. The study data will be anonymized. The objective of this project is to better define the clinical spectrum associated with the different nuclear genes, establish genotype-phenotype correlations, and thus improve the interpretation of increasingly complex genetic analyses, given the growing number of genetic variants of unknown significance.
The challenge is to reduce the diagnostic odyssey and achieve a reliable diagnosis by interpreting the clinical impact of these new rare variants. This will also help improve patient care, facilitate access to clinical trials, and refine molecular diagnostic strategies. Additional information is available upon request from the coordinator. Likewise, patients are free to refuse the use of their data for this project on mitochondrial diseases and may change their decision at any time.
Project for the Establishment of a Cohort of Patients with Mitochondrial Diseases.
Mitochondrial diseases are a group of disorders, most often hereditary, characterized by mitochondrial dysfunction. Mitochondria are organelles present in all cells and play an essential role in cellular function by enabling energy production through the process of cellular respiration. Mitochondrial diseases are caused by mutations in genes involved in mitochondrial functions, impacting the cells' energy production. Understanding the causes of mitochondrial diseases is particularly complex because the mitochondrial genome alone is not sufficient to ensure proper mitochondrial function, as it is also linked to the nuclear genome. Thus, mitochondrial diseases can be caused by mutations in either the mitochondrial or nuclear genome. These are the most common metabolic diseases, highly heterogeneous in clinical, biochemical, and genetic aspects.
The diagnosis of mitochondrial diseases has been completely transformed by the emergence of Next-Generation Sequencing (NGS) technologies, which have rapidly increased the genetic diagnosis rate from 10-20% to over 50% in some cohorts, revealing numerous variants (either pathogenic or of currently unknown significance). The French Network of Mitochondrial Disease Diagnostic Laboratories, MITODIAG, collaborates closely with the two National Reference Centers, CARAMMEL and CALISSON, as well as the FILNEMUS network, to improve patient diagnosis and care.
The COMMI project aims to assemble a cohort of 400 patients tested by high-throughput sequencing, with clinical and genetic descriptions, within the MITODIAG network laboratories. This patient group has a confirmed molecular diagnosis through the identification of one or more pathogenic variants in nuclear genes. The study data will be anonymized. The objective of this project is to better define the clinical spectrum associated with the different nuclear genes, establish genotype-phenotype correlations, and thus improve the interpretation of increasingly complex genetic analyses, given the growing number of genetic variants of unknown significance.
The challenge is to reduce the diagnostic odyssey and achieve a reliable diagnosis by interpreting the clinical impact of these new rare variants. This will also help improve patient care, facilitate access to clinical trials, and refine molecular diagnostic strategies. Additional information is available upon request from the coordinator. Likewise, patients are free to refuse the use of their data for this project on mitochondrial diseases and may change their decision at any time.
2022 - MITOMICS project
Mitochondrial Disease database: An integrated multi-OMICS approach
Mitochondrial diseases are rare, clinically and genetically extremely heterogeneous, caused by a deficit of energy production via the mitochondria. Mitochondria are dependent on 2 genomes mitochondrial DNA (mtDNA) and nuclear DNA, and many pathogenic variants carried by these 2 genomes are responsible for mitochondrial diseases. There is a cross talk and regulatory mechanisms between both genomes, which are still poorly understood, involved in the control and maintenance of mitochondrial biogenesis. All of these mechanisms play an important role in the clinical and genetic heterogeneities presented by patients suffering from mitochondrial disease and are difficult to identify by "classical" high-throughput mtDNA, whole exome (WES) or genome (WGS) sequencing approaches.
Mitomatcher is the first French database collecting genetic and clinical data for patients with mitochondrial diseases, implemented by the national mitochondrial laboratory network MITODIAG in conjunction with the reference centres (CARAMMEL and CALISSON) and FILNEMUS the rare disease network.
Mitomatcher comprises 3 different modules:
i) HPO related phenotypic data module
ii) genetic module currently containing mtDNA variants from more than 5000 patients with mitochondrial disease
iii) query and cross-reference module for the clinical-biological data.
The MITOMICS project aims to better understand the molecular mechanisms responsible for the clinical-genetic heterogeneity of mitochondrial diseases. The integration of multi-OMICS data (transcriptomics/proteomics/metabolomics) combined with clinical and genomic data (WES, WGS) in the Mitomatcher database should help to unravel the complexity of these diseases. Societal implications (ethics, juridics) of genomics research will be investigated and guidelines will be defined.
The cross analysis of these data requires the development of in silico tools. Different approaches will be developed to :i) identify co-occurrences of mtDNA and/or nuclear DNA variants responsible for mitochondrial diseases in order to reveal new genotype/phenotype correlations
ii) characterise the mitochondrial and nuclear crosstalk
iii) identify OMICS signatures specific to mitochondrial dysfunction.
The study will be divided into 4 WPs starting with data collection and mitomatcher implementation (WP1) and from WP2-4 with the development of algorithms and data integration with increasing complexity with sequential data implementation starting with mtDNA variants alone, then combined with nuclear variants and finally multi-OMICs.
Innovative machine learning, neural networks and artificial intelligence approaches will be developed such as Ruche a multi-layeR mUlti-omics maCHine learning intEgration tool or ABEILLE (ABerrant Expression Identification empLoying machine LEarning), an autoencoder-based method for the identification of aberrant gene expression from RNA-seq which will be applied to other OMICs. The identification of combinations of variants or affected signaling pathways from homogeneous groups of patients will be further verified by laboratory experiments. This project will also allow further development of in silico tools for the analysis of mtDNA variants such as Eklipse to detect mtDNA rearrangements.
Mitomatcher database will be accessible, already following international standards (Fast Healthcare Interoperability Resources, HPO), interoperable with other national or international databases and reusable for the development of ancillary studies for these disorders.
In the long term, the results obtained will allow the identification of new genotype/phenotype correlations and a better understanding of the pathophysiological mechanisms of mitochondrial diseases. The identification of specific signatures via an integrated multi-OMICs approach through Mitomics should also target specific pathways, thus enabling the development of new therapeutic strategies for mitochondrial diseases.
This current work resulted in a publication:
["Mitochondrial medicine" in the light of the fourth national plan for rare diseases (PNMR4): The example of the MITOMICS project] Clémence Guillermain, Stéphane Tirard, Sylvie Bannwarth, Vincent Procaccio médecine/sciences 2025 ; 41 : 000-000 PubMed
Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders. Bannwarth S, Procaccio V, Lebre AS, Jardel C, Chaussenot A, Hoarau C, Maoulida H, Charrier N, Gai X, Xie HM, Ferre M, Fragaki K, Hardy G, Mousson de Camaret B, Marlin S, Dhaenens CM, Slama A, Rocher C, Paul Bonnefont J, Rotig A, Aoutil N, Gilleron M, Desquiret-Dumas V, Reynier P, Ceresuela J, Jonard L, Devos A, Espil-Taris C, Martinez D, Gaignard P, Le Quan Sang KH, Amati-Bonneau P, Falk MJ, Florentz C, Chabrol B, Durand-Zaleski I, and Paquis-Flucklinger V. (2013). J Med Genet 50: 704-714. PubMed
This work resulted in a publication:
Whole mitochondrial genome screening in maternally inherited non-syndromic hearing impairment using a microarray resequencing mitochondrial DNA chip. Lévêque M, Marlin S, Jonard L, Procaccio V, Reynier P, Amati-Bonneau P, Baulande S, Pierron D, Lacombe D, Duriez F, Francannet C, Mom T, Journel H, Catros H, Drouin-Garraud V, Obstoy MF, Dollfus H, Eliot MM, Faivre L, Duvillard C, Couderc R, Garabedian EN, Petit C, Feldmann D, Denoyelle F.. Eur J Hum Genet 2007;15:1145-55. PubMed
This work resulted in consensual protocols and an article of recommendations.
Development and implementation of standardized respiratory chain spectrophotometric assays for clinical diagnosis. Medja F, Allouche S, Frachon P, Jardel C, Malgat M, Mousson de Camaret B, Slama A, Lunardi J, Mazat JP, Lombès A. Mitochondrion 2009;9:331-9. PubMed
New evidence of a mitochondrial genetic background paradox: impact of the J haplogroup on the A3243G mutation. Pierron D, Rocher C, Amati-Bonneau P, Reynier P, Martin-Négrier ML, Allouche S, Batandier C, Mousson de Camaret B, Godinot C, Rotig A, Feldmann D, Bellanne-Chantelot C, Arveiler B, Pennarun E, Rossignol R, Crouzet M, Murail P, Thoraval D, Letellier T. BMC Med Genet. 2008 May 7;9:41. PubMed
This workshop was aimed at people wishing to learn and acquire basic skills in molecular biology and molecular anthropology for the observation and analysis of population genetics including pathology. Participants were given the opportunity to perform basic molecular biology techniques (mtDNA extraction, PCR, library preparations and NGS sequencing), which allowed them to determine their own mitochondrial haplogroup and initiate bioinformatic analysis of mitochondrial DNA sequences.
livret_Atelier_2017.pdf
livret_Atelier_2014.pdf
Mitochondrial diseases are rare, clinically and genetically extremely heterogeneous, caused by a deficit of energy production via the mitochondria. Mitochondria are dependent on 2 genomes mitochondrial DNA (mtDNA) and nuclear DNA, and many pathogenic variants carried by these 2 genomes are responsible for mitochondrial diseases. There is a cross talk and regulatory mechanisms between both genomes, which are still poorly understood, involved in the control and maintenance of mitochondrial biogenesis. All of these mechanisms play an important role in the clinical and genetic heterogeneities presented by patients suffering from mitochondrial disease and are difficult to identify by "classical" high-throughput mtDNA, whole exome (WES) or genome (WGS) sequencing approaches.
Mitomatcher is the first French database collecting genetic and clinical data for patients with mitochondrial diseases, implemented by the national mitochondrial laboratory network MITODIAG in conjunction with the reference centres (CARAMMEL and CALISSON) and FILNEMUS the rare disease network.
Mitomatcher comprises 3 different modules:
The MITOMICS project aims to better understand the molecular mechanisms responsible for the clinical-genetic heterogeneity of mitochondrial diseases. The integration of multi-OMICS data (transcriptomics/proteomics/metabolomics) combined with clinical and genomic data (WES, WGS) in the Mitomatcher database should help to unravel the complexity of these diseases. Societal implications (ethics, juridics) of genomics research will be investigated and guidelines will be defined.
The cross analysis of these data requires the development of in silico tools. Different approaches will be developed to :
Innovative machine learning, neural networks and artificial intelligence approaches will be developed such as Ruche a multi-layeR mUlti-omics maCHine learning intEgration tool or ABEILLE (ABerrant Expression Identification empLoying machine LEarning), an autoencoder-based method for the identification of aberrant gene expression from RNA-seq which will be applied to other OMICs. The identification of combinations of variants or affected signaling pathways from homogeneous groups of patients will be further verified by laboratory experiments. This project will also allow further development of in silico tools for the analysis of mtDNA variants such as Eklipse to detect mtDNA rearrangements.
Mitomatcher database will be accessible, already following international standards (Fast Healthcare Interoperability Resources, HPO), interoperable with other national or international databases and reusable for the development of ancillary studies for these disorders.
In the long term, the results obtained will allow the identification of new genotype/phenotype correlations and a better understanding of the pathophysiological mechanisms of mitochondrial diseases. The identification of specific signatures via an integrated multi-OMICs approach through Mitomics should also target specific pathways, thus enabling the development of new therapeutic strategies for mitochondrial diseases.
This current work resulted in a publication:
["Mitochondrial medicine" in the light of the fourth national plan for rare diseases (PNMR4): The example of the MITOMICS project] Clémence Guillermain, Stéphane Tirard, Sylvie Bannwarth, Vincent Procaccio médecine/sciences 2025 ; 41 : 000-000 PubMed
Past Projects
2008-2012 : STIC implementation and medico-economic evaluation of the exhaustive mtDNA analysis by Surveyor and Mitochips techniques
BACKGROUND :
Mitochondrial DNA (mtDNA) diseases are rare disorders whose prevalence is estimated around 1 in 5000. Patients are usually tested only for deletions and for common mutations of mtDNA which account for 5-40% of cases, depending on the study. However, the prevalence of rare mtDNA mutations is not known.
Mitochondrial DNA (mtDNA) diseases are rare disorders whose prevalence is estimated around 1 in 5000. Patients are usually tested only for deletions and for common mutations of mtDNA which account for 5-40% of cases, depending on the study. However, the prevalence of rare mtDNA mutations is not known.
METHODS :
We analysed the whole mtDNA in a cohort of 743 patients suspected of manifesting a mitochondrial disease, after excluding deletions and common mutations. Both heteroplasmic and homoplasmic variants were identified using two complementary strategies (Surveyor and MitoChip). Multiple correspondence analyses followed by hierarchical ascendant cluster process were used to explore relationships between clinical spectrum, age at onset and localisation of mutations.
We analysed the whole mtDNA in a cohort of 743 patients suspected of manifesting a mitochondrial disease, after excluding deletions and common mutations. Both heteroplasmic and homoplasmic variants were identified using two complementary strategies (Surveyor and MitoChip). Multiple correspondence analyses followed by hierarchical ascendant cluster process were used to explore relationships between clinical spectrum, age at onset and localisation of mutations.
RESULTS :
7.4% of deleterious mutations and 22.4% of novel putative mutations were identified. Pathogenic heteroplasmic mutations were more frequent than homoplasmic mutations (4.6% vs 2.8%). Patients carrying deleterious mutations showed symptoms before 16 years of age in 67% of cases. Early onset disease (< 1 year) was significantly associated with mutations in protein coding genes (mainly in complex I) while late onset disorders (>16 years) were associated with mutations in tRNA genes. MTND5 and MTND6 genes were identified as 'hotspots' of mutations, with Leigh syndrome accounting for the large majority of associated phenotypes.
7.4% of deleterious mutations and 22.4% of novel putative mutations were identified. Pathogenic heteroplasmic mutations were more frequent than homoplasmic mutations (4.6% vs 2.8%). Patients carrying deleterious mutations showed symptoms before 16 years of age in 67% of cases. Early onset disease (< 1 year) was significantly associated with mutations in protein coding genes (mainly in complex I) while late onset disorders (>16 years) were associated with mutations in tRNA genes. MTND5 and MTND6 genes were identified as 'hotspots' of mutations, with Leigh syndrome accounting for the large majority of associated phenotypes.
CONCLUSIONS :
Rare mitochondrial DNA mutations probably account for more than 7.4% of patients with respiratory chain deficiency. This study shows that a comprehensive analysis of mtDNA is essential, and should include young children, for an accurate diagnosis that is now accessible with the development of next generation sequencing technology.
This work resulted in a publication:Rare mitochondrial DNA mutations probably account for more than 7.4% of patients with respiratory chain deficiency. This study shows that a comprehensive analysis of mtDNA is essential, and should include young children, for an accurate diagnosis that is now accessible with the development of next generation sequencing technology.
Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders. Bannwarth S, Procaccio V, Lebre AS, Jardel C, Chaussenot A, Hoarau C, Maoulida H, Charrier N, Gai X, Xie HM, Ferre M, Fragaki K, Hardy G, Mousson de Camaret B, Marlin S, Dhaenens CM, Slama A, Rocher C, Paul Bonnefont J, Rotig A, Aoutil N, Gilleron M, Desquiret-Dumas V, Reynier P, Ceresuela J, Jonard L, Devos A, Espil-Taris C, Martinez D, Gaignard P, Le Quan Sang KH, Amati-Bonneau P, Falk MJ, Florentz C, Chabrol B, Durand-Zaleski I, and Paquis-Flucklinger V. (2013). J Med Genet 50: 704-714. PubMed
2004-2007 : Evaluation of Mitochips Technology (Affymetrix) for complete resequencing of mtDNA: 133 patients were tested in collaboration with PartnerChip (support GIS-MR).
Mitochondrial DNA (mtDNA) mutations have been implicated in non-syndromic hearing loss either as primary or as predisposing factors. As only a part of the mitochondrial genome is usually explored in deafness, its prevalence is probably under-estimated. Among 1350 families with non-syndromic sensorineural hearing loss collected through a French collaborative network, we selected 29 large families with a clear maternal lineage and screened them for known mtDNA mutations in 12S rRNA, tRNASer(UCN) and tRNALeu(UUR) genes. When no mutation could be identified, a whole mitochondrial genome screening was performed, using a microarray resequencing chip: the MitoChip version 2.0 developed by Affymetrix Inc. Known mtDNA mutations was found in nine of the 29 families, which are described in the article: five with A1555G, two with the T7511C, one with 7472insC and one with A3243G mutation. In the remaining 20 families, the resequencing Mitochip detected 258 mitochondrial homoplasmic variants and 107 potentially heteroplasmic variants. Controls were made by direct sequencing on selected fragments and showed a high sensibility of the MitoChip but a low specificity, especially for heteroplasmic variations. An original analysis on the basis of species conservation, frequency and phylogenetic investigation was performed to select the more probably pathogenic variants. The entire genome analysis allowed us to identify five additional families with a putatively pathogenic mitochondrial variant: T669C, C1537T, G8078A, G12236A and G15077A. These results indicate that the new MitoChip platform is a rapid and valuable tool for identification of new mtDNA mutations in deafness.This work resulted in a publication:
Whole mitochondrial genome screening in maternally inherited non-syndromic hearing impairment using a microarray resequencing mitochondrial DNA chip. Lévêque M, Marlin S, Jonard L, Procaccio V, Reynier P, Amati-Bonneau P, Baulande S, Pierron D, Lacombe D, Duriez F, Francannet C, Mom T, Journel H, Catros H, Drouin-Garraud V, Obstoy MF, Dollfus H, Eliot MM, Faivre L, Duvillard C, Couderc R, Garabedian EN, Petit C, Feldmann D, Denoyelle F.. Eur J Hum Genet 2007;15:1145-55. PubMed
2000-2009 : Inter-laboratory coordination work on enzymatic assays of the respiratory chain.
Diversity of respiratory chain spectrophotometric assays may lead to difficult comparison of results between centers. The French network of mitochondrial diseases diagnostic centers undertook comparison of the results obtained with different protocols in the French diagnostic centers. The diversity of protocols was shown to have striking consequences, which prompted the network to undertake standardization and optimization of the protocols with respect to clinical diagnosis, i.e. high velocity while maintaining linear kinetics relative to time and enzyme concentration. Assays were set up on animal tissues and verified on control human muscle and fibroblasts. Influence of homogenization buffer and narrow range of optimal concentration of phosphate, substrate and tissue were shown. Experimental data and proposed protocols have been posted on a free access website. Their subsequent use in several diagnostic centers has improved consistency for all assays.This work resulted in consensual protocols and an article of recommendations.
Development and implementation of standardized respiratory chain spectrophotometric assays for clinical diagnosis. Medja F, Allouche S, Frachon P, Jardel C, Malgat M, Mousson de Camaret B, Slama A, Lunardi J, Mazat JP, Lombès A. Mitochondrion 2009;9:331-9. PubMed
2006-2008 : Role of mitochondrial haplogoups in MELAS.
BACKGROUND :
The A3243G mutation in the tRNALeu gene (UUR), is one of the most common pathogenic mitochondrial DNA (mtDNA) mutations in France, and is associated with highly variable and heterogeneous disease phenotypes. To define the relationships between the A3243G mutation and mtDNA backgrounds, we determined the haplogroup affiliation of 142 unrelated French patients - diagnosed as carriers of the A3243G mutation - by control-region sequencing and RFLP survey of their mtDNAs.
The A3243G mutation in the tRNALeu gene (UUR), is one of the most common pathogenic mitochondrial DNA (mtDNA) mutations in France, and is associated with highly variable and heterogeneous disease phenotypes. To define the relationships between the A3243G mutation and mtDNA backgrounds, we determined the haplogroup affiliation of 142 unrelated French patients - diagnosed as carriers of the A3243G mutation - by control-region sequencing and RFLP survey of their mtDNAs.
RESULTS :
The analysis revealed 111 different haplotypes encompassing all European haplogroups, indicating that the 3243 site might be a mutational hot spot. However, contrary to previous findings, we observed a statistically significant underepresentation of the A3243G mutation on haplogroup J in patients (p = 0.01, OR = 0.26, C.I. 95%: 0.08-0.83), suggesting that might be due to a strong negative selection at the embryo or germ line stages.
CONCLUSION :
Thus, our study supports the existence of mutational hotspot on mtDNA and a "haplogroup J paradox," a haplogroup that may increase the expression of mtDNA pathogenic mutations, but also be beneficial in certain environmental contexts.
This work resulted in a publication:New evidence of a mitochondrial genetic background paradox: impact of the J haplogroup on the A3243G mutation. Pierron D, Rocher C, Amati-Bonneau P, Reynier P, Martin-Négrier ML, Allouche S, Batandier C, Mousson de Camaret B, Godinot C, Rotig A, Feldmann D, Bellanne-Chantelot C, Arveiler B, Pennarun E, Rossignol R, Crouzet M, Murail P, Thoraval D, Letellier T. BMC Med Genet. 2008 May 7;9:41. PubMed
2004-2006 : Epidemiology of mitochondrial diseases.
Reynier P; Réseau "Maladies Mitochondriales". [Epidemiology of mitochondrial cytopathies: contribution from the French mitochondrial diseases network]. Ann Biol Clin (Paris) 2006; 64:584-6. French. PubMed2017 : Workshop Meetochondrie
The Association Network "MeetOchondrie" organized from 8 to 10 March 2017, in Angers, a workshop entitled "La Génétique mitochondriale dans tous ses états".This workshop was aimed at people wishing to learn and acquire basic skills in molecular biology and molecular anthropology for the observation and analysis of population genetics including pathology. Participants were given the opportunity to perform basic molecular biology techniques (mtDNA extraction, PCR, library preparations and NGS sequencing), which allowed them to determine their own mitochondrial haplogroup and initiate bioinformatic analysis of mitochondrial DNA sequences.
livret_Atelier_2017.pdf
2014 : Workshop Meetochondrie
The Association Network "MeetOchondrie" organized from 25 to 27 June 2014, in Angers, a workshop entitled "La Génétique mitochondriale dans tous ses états". This workshop was aimed at people wishing to learn and acquire basic skills in molecular biology and molecular anthropology for the observation and analysis of population genetics including pathology. Participants were given the opportunity to perform basic molecular biology techniques (mtDNA extraction, PCR, library preparations and NGS sequencing), which allowed them to determine their own mitochondrial haplogroup and initiate bioinformatic analysis of mitochondrial DNA sequences.livret_Atelier_2014.pdf