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Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies.

Ayoglu B, Chaouch A, Lochmüller H, Politano L, Bertini E, Spitali P, Hiller M, Niks EH, Gualandi F, Pontén F, Bushby K, Aartsma-Rus A, Schwartz E, Le Priol Y, Straub V, Uhlén M, Cirak S, 't Hoen PA, Muntoni F, Ferlini A, Schwenk JM, Nilsson P, Al-Khalili Szigyarto C - EMBO Mol Med (2014)

Bottom Line: We addressed this challenge by combining samples collected within the BIO-NMD consortium from four geographically dispersed clinical sites to identify protein markers associated with muscular dystrophy using an antibody bead array platform with 384 antibodies.Based on concordance in statistical significance and confirmatory results obtained from analysis of both serum and plasma, we identified eleven proteins associated with muscular dystrophy, among which four proteins were elevated in blood from muscular dystrophy patients: carbonic anhydrase III (CA3) and myosin light chain 3 (MYL3), both specifically expressed in slow-twitch muscle fibers and mitochondrial malate dehydrogenase 2 (MDH2) and electron transfer flavoprotein A (ETFA).Using age-matched sub-cohorts, 9 protein profiles correlating with disease progression and severity were identified, which hold promise for the development of new clinical tools for management of dystrophinopathies.

View Article: PubMed Central - PubMed

Affiliation: Affinity Proteomics, SciLifeLab, School of Biotechnology KTH-Royal Institute of Technology, Stockholm, Sweden.

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Association of protein profiles with ambulation status and respiratory insufficiencyA, C Venn diagrams illustrate the number of proteins revealing significant differences (P value < 0.01) in group comparisons between ambulant (AMB) and non-ambulant (Non-AMB) DMD patients (A) and in ventilated and non-ventilated DMD patients (C).B, D ROC curves represent the classification power of a panel composed of CA3, ENO3, ETFA, MDH2, MYL3, and TNNT3 profiles between ambulant and non-ambulant DMD patients in UCL plasma cohort and UNEW plasma and serum cohorts (B). Classification of UNEW ventilated and non-ventilated patients was based on a panel including MDH2, PPM1F, ETFA, and TNNT3 for plasma and a panel including MDH2, PPM1F, COL6A1, and LCP1 for serum (D).
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fig06: Association of protein profiles with ambulation status and respiratory insufficiencyA, C Venn diagrams illustrate the number of proteins revealing significant differences (P value < 0.01) in group comparisons between ambulant (AMB) and non-ambulant (Non-AMB) DMD patients (A) and in ventilated and non-ventilated DMD patients (C).B, D ROC curves represent the classification power of a panel composed of CA3, ENO3, ETFA, MDH2, MYL3, and TNNT3 profiles between ambulant and non-ambulant DMD patients in UCL plasma cohort and UNEW plasma and serum cohorts (B). Classification of UNEW ventilated and non-ventilated patients was based on a panel including MDH2, PPM1F, ETFA, and TNNT3 for plasma and a panel including MDH2, PPM1F, COL6A1, and LCP1 for serum (D).

Mentions: Besides patient age, there are other hallmarks of disease progression and deterioration of muscular function that are rigorously monitored and used to assess health status of DMD patients. These include loss of ambulation, respiratory insufficiency, and cardiac dysfunction. Analyzing the protein profiles within the DMD cohorts by hierarchical clustering showed that the ambulant and non-ambulant DMD patients could be separated from each other (Supplementary Fig S9). Five of the seven previously mentioned proteins, CA3, MDH2, MYL3, ETFA, and TNNT3, contributed to the statistically significant discrimination of ambulant and non-ambulant DMD patients, both in serum and in plasma (Fig 6A). Additionally, a cytoplasmic protein, beta-enolase (ENO3), expressed in striated muscle tissue, revealed significantly different profiles between non-ambulant and ambulant DMD patients. The signal intensity levels for all of these six protein targets were decreased in non-ambulant patients in comparison with ambulant patients (Supplementary Fig S10A). Since the age distribution in the DMD cohorts was broad, we have defined and compared two smaller age-matched sub-groups of DMD patients from the UNEW cohort; one for ambulant patients and one for non-ambulant patients with mean age of 11.6 and 13.8, respectively. This comparison revealed the same trends for the six proteins, namely that the signal intensity levels decreased within the DMD patient group with loss of ambulation (Supplementary Fig S11). Next, the classification performance of these six proteins in serum and plasma samples of ambulant and non-ambulant UNEW and UCL cohorts was assessed. As indicated by the AUC values ≥ 0.91, sub-panels consisting of the seven antibodies targeting these six proteins allowed a good classification between ambulant and non-ambulant DMD patients (Fig 6B). Within the ambulant patient group from UNEW, the protein profiles showed little correlation with the NorthStar Ambulatory Assessment (NSAA) score (data not shown) (Mazzone et al, 2013). The limited number of patients (27) included in the analysis, and the complexity of the NSAA scoring system, which comprises assessment of 17 different activities related to gross motor function, might obscure subtle differences in protein profiles and highlights the need of detailed patient data recording in connection with sample retrieval.


Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies.

Ayoglu B, Chaouch A, Lochmüller H, Politano L, Bertini E, Spitali P, Hiller M, Niks EH, Gualandi F, Pontén F, Bushby K, Aartsma-Rus A, Schwartz E, Le Priol Y, Straub V, Uhlén M, Cirak S, 't Hoen PA, Muntoni F, Ferlini A, Schwenk JM, Nilsson P, Al-Khalili Szigyarto C - EMBO Mol Med (2014)

Association of protein profiles with ambulation status and respiratory insufficiencyA, C Venn diagrams illustrate the number of proteins revealing significant differences (P value < 0.01) in group comparisons between ambulant (AMB) and non-ambulant (Non-AMB) DMD patients (A) and in ventilated and non-ventilated DMD patients (C).B, D ROC curves represent the classification power of a panel composed of CA3, ENO3, ETFA, MDH2, MYL3, and TNNT3 profiles between ambulant and non-ambulant DMD patients in UCL plasma cohort and UNEW plasma and serum cohorts (B). Classification of UNEW ventilated and non-ventilated patients was based on a panel including MDH2, PPM1F, ETFA, and TNNT3 for plasma and a panel including MDH2, PPM1F, COL6A1, and LCP1 for serum (D).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4119355&req=5

fig06: Association of protein profiles with ambulation status and respiratory insufficiencyA, C Venn diagrams illustrate the number of proteins revealing significant differences (P value < 0.01) in group comparisons between ambulant (AMB) and non-ambulant (Non-AMB) DMD patients (A) and in ventilated and non-ventilated DMD patients (C).B, D ROC curves represent the classification power of a panel composed of CA3, ENO3, ETFA, MDH2, MYL3, and TNNT3 profiles between ambulant and non-ambulant DMD patients in UCL plasma cohort and UNEW plasma and serum cohorts (B). Classification of UNEW ventilated and non-ventilated patients was based on a panel including MDH2, PPM1F, ETFA, and TNNT3 for plasma and a panel including MDH2, PPM1F, COL6A1, and LCP1 for serum (D).
Mentions: Besides patient age, there are other hallmarks of disease progression and deterioration of muscular function that are rigorously monitored and used to assess health status of DMD patients. These include loss of ambulation, respiratory insufficiency, and cardiac dysfunction. Analyzing the protein profiles within the DMD cohorts by hierarchical clustering showed that the ambulant and non-ambulant DMD patients could be separated from each other (Supplementary Fig S9). Five of the seven previously mentioned proteins, CA3, MDH2, MYL3, ETFA, and TNNT3, contributed to the statistically significant discrimination of ambulant and non-ambulant DMD patients, both in serum and in plasma (Fig 6A). Additionally, a cytoplasmic protein, beta-enolase (ENO3), expressed in striated muscle tissue, revealed significantly different profiles between non-ambulant and ambulant DMD patients. The signal intensity levels for all of these six protein targets were decreased in non-ambulant patients in comparison with ambulant patients (Supplementary Fig S10A). Since the age distribution in the DMD cohorts was broad, we have defined and compared two smaller age-matched sub-groups of DMD patients from the UNEW cohort; one for ambulant patients and one for non-ambulant patients with mean age of 11.6 and 13.8, respectively. This comparison revealed the same trends for the six proteins, namely that the signal intensity levels decreased within the DMD patient group with loss of ambulation (Supplementary Fig S11). Next, the classification performance of these six proteins in serum and plasma samples of ambulant and non-ambulant UNEW and UCL cohorts was assessed. As indicated by the AUC values ≥ 0.91, sub-panels consisting of the seven antibodies targeting these six proteins allowed a good classification between ambulant and non-ambulant DMD patients (Fig 6B). Within the ambulant patient group from UNEW, the protein profiles showed little correlation with the NorthStar Ambulatory Assessment (NSAA) score (data not shown) (Mazzone et al, 2013). The limited number of patients (27) included in the analysis, and the complexity of the NSAA scoring system, which comprises assessment of 17 different activities related to gross motor function, might obscure subtle differences in protein profiles and highlights the need of detailed patient data recording in connection with sample retrieval.

Bottom Line: We addressed this challenge by combining samples collected within the BIO-NMD consortium from four geographically dispersed clinical sites to identify protein markers associated with muscular dystrophy using an antibody bead array platform with 384 antibodies.Based on concordance in statistical significance and confirmatory results obtained from analysis of both serum and plasma, we identified eleven proteins associated with muscular dystrophy, among which four proteins were elevated in blood from muscular dystrophy patients: carbonic anhydrase III (CA3) and myosin light chain 3 (MYL3), both specifically expressed in slow-twitch muscle fibers and mitochondrial malate dehydrogenase 2 (MDH2) and electron transfer flavoprotein A (ETFA).Using age-matched sub-cohorts, 9 protein profiles correlating with disease progression and severity were identified, which hold promise for the development of new clinical tools for management of dystrophinopathies.

View Article: PubMed Central - PubMed

Affiliation: Affinity Proteomics, SciLifeLab, School of Biotechnology KTH-Royal Institute of Technology, Stockholm, Sweden.

Show MeSH
Related in: MedlinePlus