117 results on '"Migliavacca E"'
Search Results
2. A gene expression signature that distinguishes desmoid tumours from nodular fasciitis
- Author
-
Bacac, M, Migliavacca, E, Stehle, J-C, McKee, T, Delorenzi, M, Coindre, J-M, Guillou, L, and Stamenkovic, I
- Published
- 2006
- Full Text
- View/download PDF
3. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes
- Author
-
Loviglio MN, Leleu M, Männik K, Passeggeri M, Giannuzzi G, van der Werf I, Waszak SM, Zazhytska M, Roberts-Caldeira I, Gheldof N, Migliavacca E, Alfaiz AA, Hippolyte L, Maillard AM, 2p15 Consortium, 16p112 Consortium, Merla G, Van Dijck A, Kooy RF, Sanlaville D, Rosenfeld JA, Shaffer LG, Andrieux J, Marshall C, Scherer SW, Shen Y, Gusella JF, Thorsteinsdottir U, Thorleifsson G, Dermitzakis ET, Deplancke B, Beckmann JS, Rougemont J, Jacquemont S, Reymond A, Loviglio, Mn, Leleu, M, Männik, K, Passeggeri, M, Giannuzzi, G, van der Werf, I, Waszak, Sm, Zazhytska, M, Roberts-Caldeira, I, Gheldof, N, Migliavacca, E, Alfaiz, Aa, Hippolyte, L, Maillard, Am, 2p15, Consortium, 16p112, Consortium, Merla, G, Van Dijck, A, Kooy, Rf, Sanlaville, D, Rosenfeld, Ja, Shaffer, Lg, Andrieux, J, Marshall, C, Scherer, Sw, Shen, Y, Gusella, Jf, Thorsteinsdottir, U, Thorleifsson, G, Dermitzakis, Et, Deplancke, B, Beckmann, J, Rougemont, J, Jacquemont, S, and Reymond, A
- Abstract
Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.
- Published
- 2017
4. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes
- Author
-
Loviglio, M. N, Leleu, M., Männik, K., Passeggeri, M., Giannuzzi, G., van der Werf, I., Waszak, S. M., Zazhytska, M., Roberts Caldeira, I., Gheldof, N., Migliavacca, E., Alfaiz, A. A., Hippolyte, L., Maillard, A. M., van Dijck, A., Kooy, R. F., Sanlaville, D., Rosenfeld, J. A., Shaffer, L. G., Andrieux, J., Marshall, C., Scherer, S. W., Shen, Y., Gusella, J. F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E. T., Deplancke, B., Beckmann, J. S., Rougemont, J., Jacquemont, S., Reymond, A., Collaborators: Loviglio MN, Männik, K, van der Werf, I, Giannuzzi, G, Zazhytska, M, Gheldof, N, Migliavacca, E, Alfaiz, Aa, Roberts Caldeira, I, Hippolyte, L, Maillard, Am, Ferrarini, A, Butschi, Fn, Conrad, B, Addor, Mc, Belfiore, M, Roetzer, K, Dijck, Av, Blaumeiser, B, Kooy, F, Roelens, F, Dheedene, A, Chiaie, Bd, Menten, B, Oostra, A, Caberg, Jh, Carter, M, Kellam, B, Stavropoulos, Dj, Marshall, C, Scherer, Sw, Weksberg, R, Cytrynbaum, C, Bassett, A, Lowther, C, Gillis, J, Mackay, S, Bache, I, Ousager, Lb, Smerdel, Mp, Graakjaer, J, Kjaergaard, S, Metspalu, A, Mathieu, M, Bonneau, D, Guichet, A, Parent, P, Férec, C, Gerard, M, Plessis, G, Lespinasse, J, Masurel, A, Marle, N, Faivre, L, Callier, P, Layet, V, Meur, Nl, Le Goff, C, Duban Bedu, B, Sukno, S, Boute, O, Andrieux, J, Blanchet, P, Geneviève, D, Puechberty, J, Schneider, A, Leheup, B, Jonveaux, P, Mercier, S, David, A, Le Caignec, C, de Pontual, L, Pipiras, E, Jacquette, A, Keren, B, Gilbert Dussardier, B, Bilan, F, Goldenberg, A, Chambon, P, Toutain, A, Till, M, Sanlaville, D, Leube, B, Royer Pokora, B, Grabe, Hj, Schmidt, Co, Schurmann, C, Homuth, G, Thorleifsson, G, Thorsteinsdottir, U, Bernardini, L, Novelli, A, Micale, L, Merla, G, Zollino, M, Mari, Francesca, Rizzo, Cl, Renieri, Alessandra, Silengo, M, Vulto van Silfhout AT, Schouten, M, Pfundt, R, de Leeuw, N, Vansenne, F, Maas, Sm, Barge Schaapveld DQ, Knegt, Ac, Stadheim, B, Rodningen, O, Houge, G, Price, S, Hawkes, L, Campbell, C, Kini, U, Vogt, J, Walters, R, Blakemore, A, Gusella, Jf, Shen, Y, Scott, D, Bacino, Ca, Tsuchiya, K, Ladda, R, Sell, S, Asamoah, A, Hamati, Ai, Rosenfeld, Ja, Shaffer, Lg, Mitchell, E, Hodge, Jc, Beckmann, Js, Jacquemont, S, Reymond, A, Ewans, Lj, Mowat, D, Walker, J, Amor, Dj, Esch, Hv, Leroy, P, Bamforth, Js, Babu, D, Isidor, B, Didonato, N, Hackmann, K, Passeggeri, M, Haeringen, Av, Smith, R, Ellingwood, S, Farber, Dm, Puri, V, Zadeh, N, Weaver, Dd, Miller, M, Wilks, T, Jorgez, Cj, Lafayette, D, Blaumeiser, Bettina, 2p15 Consortium, 16p11.2 Consortium, Loviglio, M.N., Männik, K., van der Werf, I., Giannuzzi, G., Zazhytska, M., Gheldof, N., Migliavacca, E., Alfaiz, A.A., Roberts-Caldeira, I., Hippolyte, L., Maillard, A.M., Ferrarini, A., Butschi, F.N., Conrad, B., Addor, M.C., Belfiore, M., Roetzer, K., Dijck, A.V., Blaumeiser, B., Kooy, F., Roelens, F., Dheedene, A., Chiaie, B.D., Menten, B., Oostra, A., Caberg, J.H., Carter, M., Kellam, B., Stavropoulos, D.J., Marshall, C., Scherer, S.W., Weksberg, R., Cytrynbaum, C., Bassett, A., Lowther, C., Gillis, J., MacKay, S., Bache, I., Ousager, L.B., Smerdel, M.P., Graakjaer, J., Kjaergaard, S., Metspalu, A., Mathieu, M., Bonneau, D., Guichet, A., Parent, P., Férec, C., Gerard, M., Plessis, G., Lespinasse, J., Masurel, A., Marle, N., Faivre, L., Callier, P., Layet, V., Meur, N.L., Le Goff, C., Duban-Bedu, B., Sukno, S., Boute, O., Andrieux, J., Blanchet, P., Geneviève, D., Puechberty, J., Schneider, A., Leheup, B., Jonveaux, P., Mercier, S., David, A., Le Caignec, C., de Pontual, L., Pipiras, E., Jacquette, A., Keren, B., Gilbert-Dussardier, B., Bilan, F., Goldenberg, A., Chambon, P., Toutain, A., Till, M., Sanlaville, D., Leube, B., Royer-Pokora, B., Grabe, H.J., Schmidt, C.O., Schurmann, C., Homuth, G., Thorleifsson, G., Thorsteinsdottir, U., Bernardini, L., Novelli, A., Micale, L., Merla, G., Zollino, M., Mari, F., Rizzo, C.L., Renieri, A., Silengo, M., Vulto-van Silfhout, A.T., Schouten, M., Pfundt, R., de Leeuw, N., Vansenne, F., Maas, S.M., Barge-Schaapveld, D.Q., Knegt, A.C., Stadheim, B., Rodningen, O., Houge, G., Price, S., Hawkes, L., Campbell, C., Kini, U., Vogt, J., Walters, R., Blakemore, A., Gusella, J.F., Shen, Y., Scott, D., Bacino, C.A., Tsuchiya, K., Ladda, R., Sell, S., Asamoah, A., Hamati, A.I., Rosenfeld, J.A., Shaffer, L.G., Mitchell, E., Hodge, J.C., Beckmann, J.S., Jacquemont, S., Reymond, A., Ewans, L.J., Mowat, D., Walker, J., Amor, D.J., Esch, H.V., Leroy, P., Bamforth, J.S., Babu, D., Isidor, B., DiDonato, N., Hackmann, K., Passeggeri, M., Haeringen, A.V., Smith, R., Ellingwood, S., Farber, D.M., Puri, V., Zadeh, N., Weaver, D.D., Miller, M., Wilks, T., Jorgez, C.J., Lafayette, D., Other departments, and Human Genetics
- Subjects
0301 basic medicine ,Male ,Microcephaly ,Autism Spectrum Disorder ,Obesity/genetics ,Settore MED/03 - GENETICA MEDICA ,Body Mass Index ,Microcephaly/genetics ,Gene duplication ,Chromosome Duplication ,ddc:576.5 ,Copy-number variation ,Child ,In Situ Hybridization ,In Situ Hybridization, Fluorescence ,Genetics ,medicine.diagnostic_test ,Chromosome Mapping ,Middle Aged ,Phenotype ,Chromatin ,Chemistry ,Psychiatry and Mental Health ,Child, Preschool ,Female ,Original Article ,Chromosomes, Human, Pair 16/genetics ,Megalencephaly/genetics ,Chromosome Deletion ,Autistic Disorder/genetics ,Molecular Biology ,Cellular and Molecular Neuroscience ,Human ,Rare cancers Radboud Institute for Health Sciences [Radboudumc 9] ,Adult ,Adolescent ,DNA Copy Number Variations ,Locus (genetics) ,DNA Copy Number Variations/genetics ,Biology ,Aged ,Autistic Disorder ,Chromosomes, Human, Pair 16 ,Humans ,Infant ,Intellectual Disability ,Megalencephaly ,Obesity ,Chromosomes ,Fluorescence ,Chromatin/metabolism ,03 medical and health sciences ,medicine ,Preschool ,Gene ,Neurodevelopmental disorders Donders Center for Medical Neuroscience [Radboudumc 7] ,Pair 16 ,medicine.disease ,Intellectual Disability/genetics ,Autism Spectrum Disorder/genetics ,030104 developmental biology ,Human medicine ,Chromosome Mapping/methods ,Fluorescence in situ hybridization - Abstract
Contains fulltext : 174530.pdf (Publisher’s version ) (Open Access) Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.
- Published
- 2015
- Full Text
- View/download PDF
5. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes
- Author
-
Loviglio, M.N., Leleu, M., Mannik, K., Passeggeri, M., Giannuzzi, G., Werf, I. van der, Waszak, S.M., Zazhytska, M., Roberts-Caldeira, I., Gheldof, N., Migliavacca, E., Alfaiz, A.A., Hippolyte, L., Maillard, A.M., Dijck, A. Van, Kooy, R.F., Sanlaville, D., Rosenfeld, J.A., Shaffer, L.G., Andrieux, J., Marshall, C., Scherer, S.W., Shen, Y., Gusella, J.F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E.T., Deplancke, B., Beckmann, J.S., Rougemont, J., Jacquemont, S., Reymond, A., Vulto-van Silfhout, A.T., Schouten, M.I., Pfundt, R.P., Leeuw, N. de, et al., Loviglio, M.N., Leleu, M., Mannik, K., Passeggeri, M., Giannuzzi, G., Werf, I. van der, Waszak, S.M., Zazhytska, M., Roberts-Caldeira, I., Gheldof, N., Migliavacca, E., Alfaiz, A.A., Hippolyte, L., Maillard, A.M., Dijck, A. Van, Kooy, R.F., Sanlaville, D., Rosenfeld, J.A., Shaffer, L.G., Andrieux, J., Marshall, C., Scherer, S.W., Shen, Y., Gusella, J.F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E.T., Deplancke, B., Beckmann, J.S., Rougemont, J., Jacquemont, S., Reymond, A., Vulto-van Silfhout, A.T., Schouten, M.I., Pfundt, R.P., Leeuw, N. de, and et al.
- Abstract
Contains fulltext : 174530.pdf (publisher's version ) (Open Access), Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.
- Published
- 2017
6. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes
- Author
-
Loviglio, M. N., Leleu, M., Männik, K., Passeggeri, M., Giannuzzi, G., Van Der Werf, I., Waszak, S. M., Zazhytska, M., Roberts-Caldeira, I., Gheldof, N., Migliavacca, E., Alfaiz, A. A., Hippolyte, L., Maillard, A. M., Zollino, Marcella, Van Dijck, A., Kooy, R. F., Sanlaville, D., Rosenfeld, J. A., Shaffer, L. G., Andrieux, J., Marshall, C., Scherer, S. W., Shen, Y., Gusella, J. F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E. T., Deplancke, B., Beckmann, J. S., Rougemont, J., Jacquemont, S., Reymond, A., Zollino, M. (ORCID:0000-0003-4871-9519), Loviglio, M. N., Leleu, M., Männik, K., Passeggeri, M., Giannuzzi, G., Van Der Werf, I., Waszak, S. M., Zazhytska, M., Roberts-Caldeira, I., Gheldof, N., Migliavacca, E., Alfaiz, A. A., Hippolyte, L., Maillard, A. M., Zollino, Marcella, Van Dijck, A., Kooy, R. F., Sanlaville, D., Rosenfeld, J. A., Shaffer, L. G., Andrieux, J., Marshall, C., Scherer, S. W., Shen, Y., Gusella, J. F., Thorsteinsdottir, U., Thorleifsson, G., Dermitzakis, E. T., Deplancke, B., Beckmann, J. S., Rougemont, J., Jacquemont, S., Reymond, A., and Zollino, M. (ORCID:0000-0003-4871-9519)
- Abstract
Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.
- Published
- 2017
7. Elevated levels of MIC-1/GDF15 in the cerebrospinal fluid of patients are associated with glioblastoma and worse outcome
- Author
-
Shnaper S., Desbaillets I., Brown D. A., Murat A., Migliavacca E., Schluep M., Ostermann S., Hamou M. F., Stupp R., Breit S. N., de Tribolet N., and Hegi M. E.
- Abstract
For patients with brain tumors identification of diagnostic and prognostic markers in easy accessible biological material such as plasma or cerebrospinal fluid (CSF) would greatly facilitate patient management. MIC 1/GDF15 (growth differentiation factor 15) is a secreted protein of the TGF beta superfamily and emerged as a candidate marker exhibiting increasing mRNA expression during malignant progression of glioma. Determination of MIC 1/GDF15 protein levels by ELISA in the CSF of a cohort of 94 patients with intracranial tumors including gliomas meningioma and metastasis revealed significantly increased concentrations in glioblastoma patients (median 229 pg/ml) when compared with control cohort of patients treated for non neoplastic diseases (median below limit of detection of 156 pg/ml p < 0.0001 Mann Whitney test). However plasma MIC 1/GDF15 levels were not elevated in the matching plasma samples from these patients. Most interestingly patients with glioblastoma and increased CSF MIC 1/GDF15 had a shorter survival (p = 0.007 log rank test). In conclusion MIC 1/GDF15 protein measured in the CSF may have diagnostic and prognostic value in patients with intracranial tumors.
- Published
- 2009
- Full Text
- View/download PDF
8. A robust neuromuscular system protects rat and human skeletal muscle from sarcopenia.
- Author
-
Pannérec, A, Springer, M, Migliavacca, E, Ireland, A, Piasecki, M, Karaz, S, Jacot, G, Métairon, S, Danenberg, E, Raymond, F, Descombes, P, McPhee, JS, Feige, JN, Pannérec, A, Springer, M, Migliavacca, E, Ireland, A, Piasecki, M, Karaz, S, Jacot, G, Métairon, S, Danenberg, E, Raymond, F, Descombes, P, McPhee, JS, and Feige, JN
- Abstract
Declining muscle mass and function is one of the main drivers of loss of independence in the elderly. Sarcopenia is associated with numerous cellular and endocrine perturbations, and it remains challenging to identify those changes that play a causal role and could serve as targets for therapeutic intervention. In this study, we uncovered a remarkable differential susceptibility of certain muscles to age-related decline. Aging rats specifically lose muscle mass and function in the hindlimbs, but not in the forelimbs. By performing a comprehensive comparative analysis of these muscles, we demonstrate that regional susceptibility to sarcopenia is dependent on neuromuscular junction fragmentation, loss of motoneuron innervation, and reduced excitability. Remarkably, muscle loss in elderly humans also differs in vastus lateralis and tibialis anterior muscles in direct relation to neuromuscular dysfunction. By comparing gene expression in susceptible and non-susceptible muscles, we identified a specific transcriptomic signature of neuromuscular impairment. Importantly, differential molecular profiling of the associated peripheral nerves revealed fundamental changes in cholesterol biosynthetic pathways. Altogether our results provide compelling evidence that susceptibility to sarcopenia is tightly linked to neuromuscular decline in rats and humans, and identify dysregulation of sterol metabolism in the peripheral nervous system as an early event in this process.
- Published
- 2016
9. A Potential Contributory Role for Ciliary Dysfunction in the 16p11.2 600 kb BP4-BP5 Pathology
- Author
-
Migliavacca, E., Golzio, C., Mannik, K., Blumenthal, I., Oh, E.C., Harewood, L., Kosmicki, J.A., Loviglio, M.N., Giannuzzi, G., Hippolyte, L., Maillard, A.M., Alfaiz, A.A., Haelst, M.M. van, Andrieux, J., Gusella, J.F., Daly, M.J., Beckmann, J.S., Jacquemont, S., Talkowski, M.E., Katsanis, N., Reymond, A., Vulto-van Silfhout, A.T., Vries, B. de, Binsbergen, E. van, et al., Migliavacca, E., Golzio, C., Mannik, K., Blumenthal, I., Oh, E.C., Harewood, L., Kosmicki, J.A., Loviglio, M.N., Giannuzzi, G., Hippolyte, L., Maillard, A.M., Alfaiz, A.A., Haelst, M.M. van, Andrieux, J., Gusella, J.F., Daly, M.J., Beckmann, J.S., Jacquemont, S., Talkowski, M.E., Katsanis, N., Reymond, A., Vulto-van Silfhout, A.T., Vries, B. de, Binsbergen, E. van, and et al.
- Abstract
Item does not contain fulltext, The 16p11.2 600 kb copy-number variants (CNVs) are associated with mirror phenotypes on BMI, head circumference, and brain volume and represent frequent genetic lesions in autism spectrum disorders (ASDs) and schizophrenia. Here we interrogated the transcriptome of individuals carrying reciprocal 16p11.2 CNVs. Transcript perturbations correlated with clinical endophenotypes and were enriched for genes associated with ASDs, abnormalities of head size, and ciliopathies. Ciliary gene expression was also perturbed in orthologous mouse models, raising the possibility that ciliary dysfunction contributes to 16p11.2 pathologies. In support of this hypothesis, we found structural ciliary defects in the CA1 hippocampal region of 16p11.2 duplication mice. Moreover, by using an established zebrafish model, we show genetic interaction between KCTD13, a key driver of the mirrored neuroanatomical phenotypes of the 16p11.2 CNV, and ciliopathy-associated genes. Overexpression of BBS7 rescues head size and neuroanatomical defects of kctd13 morphants, whereas suppression or overexpression of CEP290 rescues phenotypes induced by KCTD13 under- or overexpression, respectively. Our data suggest that dysregulation of ciliopathy genes contributes to the clinical phenotypes of these CNVs.
- Published
- 2015
10. The 16p11.2 locus modulates brain structures common to autism, schizophrenia and obesity
- Author
-
Maillard, AM, Ruef, A, Pizzagalli, F, Migliavacca, E, Hippolyte, L, Adaszewski, S, Dukart, J, Ferrari, C, Conus, P, Maennik, K, Zazhytska, M, Siffredi, V, Maeder, P, Kutalik, Z, Kherif, F, Hadjikhani, N, Beckmann, JS, Reymond, A, Draganski, B, Jacquemont, S, Maillard, AM, Ruef, A, Pizzagalli, F, Migliavacca, E, Hippolyte, L, Adaszewski, S, Dukart, J, Ferrari, C, Conus, P, Maennik, K, Zazhytska, M, Siffredi, V, Maeder, P, Kutalik, Z, Kherif, F, Hadjikhani, N, Beckmann, JS, Reymond, A, Draganski, B, and Jacquemont, S
- Abstract
Anatomical structures and mechanisms linking genes to neuropsychiatric disorders are not deciphered. Reciprocal copy number variants at the 16p11.2 BP4-BP5 locus offer a unique opportunity to study the intermediate phenotypes in carriers at high risk for autism spectrum disorder (ASD) or schizophrenia (SZ). We investigated the variation in brain anatomy in 16p11.2 deletion and duplication carriers. Beyond gene dosage effects on global brain metrics, we show that the number of genomic copies negatively correlated to the gray matter volume and white matter tissue properties in cortico-subcortical regions implicated in reward, language and social cognition. Despite the near absence of ASD or SZ diagnoses in our 16p11.2 cohort, the pattern of brain anatomy changes in carriers spatially overlaps with the well-established structural abnormalities in ASD and SZ. Using measures of peripheral mRNA levels, we confirm our genomic copy number findings. This combined molecular, neuroimaging and clinical approach, applied to larger datasets, will help interpret the relative contributions of genes to neuropsychiatric conditions by measuring their effect on local brain anatomy.
- Published
- 2015
11. The complex SNP and CNV genetic architecture of the increased risk of congenital heart defects in Down syndrome
- Author
-
Sailani, M.R. Makrythanasis, P. Valsesia, A. Santoni, F.A. Deutsch, S. Popadin, K. Borel, C. Migliavacca, E. Sharp, A.J. Sail, G.D. Falconnet, E. Rabionet, K. Serra-Juhé, C. Vicari, S. Laux, D. Grattau, Y. Dembour, G. Megarbane, A. Touraine, R. Stora, S. Kitsiou, S. Fryssira, H. Chatzisevastou-Loukidou, C. Kanavakis, E. Merla, G. Bonnet, D. Pérez-Jurado, L.A. Estivill, X. Delabar, J.M. Antonarakis, S.E.
- Subjects
cardiovascular diseases - Abstract
Congenital heart defect (CHD) occurs in 40% of Down syndrome (DS) cases. While carrying three copies of chromosome 21 increases the risk for CHD, trisomy 21 itself is not sufficient to cause CHD. Thus, additional genetic variation and/or environmental factors could contribute to the CHD risk. Here we report genomic variations that in oncert with trisomy 21, determine the risk for CHD in DS. This case-control GWAS includes 187 DS with CHD (AVSD = 69, ASD = 53, VSD = 65) as cases, and 151 DS without CHD as controls. Chromosome 21-specific association studies revealed rs2832616 and rs1943950 as CHD risk alleles (adjusted genotypic P-values < 0.05). These signals were confirmed in a replication cohort of 92 DS-CHD cases and 80 DS-without CHD (nominal P-value 0.0022). Furthermore, CNV analyses using a customized chromosome 21 aCGH of 135K probes in 55 DS-AVSD and 53 DS-without CHD revealed three CNV regions associated with AVSD risk (FDR ≤ 0.05). Two of these regions that are located within the previously identified CHD region on chromosome 21 were further confirmed in a replication study of 49 DS-AVSD and 45 DS- without CHD (FDR ≤ 0.05). One of these CNVs maps near the RIPK4 gene, and the second includes the ZBTB21 (previously ZNF295) gene, highlighting the potential role of these genes in the pathogenesis of CHD in DS. We propose that the genetic architecture of the CHD risk of DS is complex and includes trisomy 21, and SNP and CNV variations in chromosome 21. In addition, a yetunidentified genetic variation in the rest of the genome may contribute to this complex genetic architecture. © 2013, Published by Cold Spring Harbor Laboratory Press.
- Published
- 2013
12. Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
- Author
-
Bonhoure, N, Bounova, G, Bernasconi, D, Praz, V, Lammers, F, Canella, D, Willis, I M, Herr, W, Hernandez, N, Delorenzi, M, Deplancke, B, Desvergne, B, Guex, N, Naef, F, Rougemont, J, Schibler, U, Andersin, T, Cousin, P, Gilardi, F, Gos, P, Raghav, S, Villeneuve, D, Fabbretti, R, Vlegel, V, Xenarios, I, Migliavacca, E, David, F, Jarosz, Y, Kuznetsov, D, Liechti, R, Martin, O, Delafontaine, J, Cajan, J, Gustafson, K, Krier, I, Leleu, M, Molina, N, Naldi, A, Rib, L, Symul, L, Bonhoure, N, Bounova, G, Bernasconi, D, Praz, V, Lammers, F, Canella, D, Willis, I M, Herr, W, Hernandez, N, Delorenzi, M, Deplancke, B, Desvergne, B, Guex, N, Naef, F, Rougemont, J, Schibler, U, Andersin, T, Cousin, P, Gilardi, F, Gos, P, Raghav, S, Villeneuve, D, Fabbretti, R, Vlegel, V, Xenarios, I, Migliavacca, E, David, F, Jarosz, Y, Kuznetsov, D, Liechti, R, Martin, O, Delafontaine, J, Cajan, J, Gustafson, K, Krier, I, Leleu, M, Molina, N, Naldi, A, Rib, L, and Symul, L
- Published
- 2014
13. Metal speciation in contaminated marine sediments after liming
- Author
-
Bambara, W., DE PROPRIS, L., Gabellini, M., Gente, Vincenzo, Geraldini, S., LA MARCA, Floriana, Massacci, Paolo, and Migliavacca, E.
- Subjects
METAL SPECIATION ,liming ,MARINE SEDIMENTS - Published
- 2005
14. Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15.
- Author
-
Sharp, A.J., Migliavacca, E., Dupre, Y., Stathaki, E., Sailani, M.R., Baumer, A., Schinzel, A., Mackay, D.J., Robinson, D.O., Cobellis, G., Cobellis, L., Brunner, H.G., Steiner, B., Antonarakis, S.E., Sharp, A.J., Migliavacca, E., Dupre, Y., Stathaki, E., Sailani, M.R., Baumer, A., Schinzel, A., Mackay, D.J., Robinson, D.O., Cobellis, G., Cobellis, L., Brunner, H.G., Steiner, B., and Antonarakis, S.E.
- Abstract
1 september 2010, Contains fulltext : 87767.pdf (publisher's version ) (Open Access), The maternal and paternal genomes possess distinct epigenetic marks that distinguish them at imprinted loci. In order to identify imprinted loci, we used a novel method, taking advantage of the fact that uniparental disomy (UPD) provides a system that allows the two parental chromosomes to be studied independently. We profiled the paternal and maternal methylation on chromosome 15 using immunoprecipitation of methylated DNA and hybridization to tiling oligonucleotide arrays. Comparison of six individuals with maternal versus paternal UPD15 revealed 12 differentially methylated regions (DMRs). Putative DMRs were validated by bisulfite sequencing, confirming the presence of parent-of-origin-specific methylation marks. We detected DMRs associated with known imprinted genes within the Prader-Willi/Angelman syndrome region, such as SNRPN and MAGEL2, validating this as a method of detecting imprinted loci. Of the 12 DMRs identified, eight were novel, some of which are associated with genes not previously thought to be imprinted. These include a site within intron 2 of IGF1R at 15q26.3, a gene that plays a fundamental role in growth, and an intergenic site upstream of GABRG3 that lies within a previously defined candidate region conferring an increased maternal risk of psychosis. These data provide a map of parent-of-origin-specific epigenetic modifications on chromosome 15, identifying DNA elements that may play a functional role in the imprinting process. Application of this methodology to other chromosomes for which UPD has been reported will allow the systematic identification of imprinted sites throughout the genome.
- Published
- 2010
15. Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15
- Author
-
Sharp, A J, Migliavacca, E, Dupre, Y, Stathaki, E, Sailani, M R, Baumer, A, Schinzel, A, Mackay, D J, Robinson, D O, Cobellis, G, Cobellis, L, Brunner, H G, Steiner, B, Antonarakis, S E, Sharp, A J, Migliavacca, E, Dupre, Y, Stathaki, E, Sailani, M R, Baumer, A, Schinzel, A, Mackay, D J, Robinson, D O, Cobellis, G, Cobellis, L, Brunner, H G, Steiner, B, and Antonarakis, S E
- Abstract
The maternal and paternal genomes possess distinct epigenetic marks that distinguish them at imprinted loci. In order to identify imprinted loci, we used a novel method, taking advantage of the fact that uniparental disomy (UPD) provides a system that allows the two parental chromosomes to be studied independently. We profiled the paternal and maternal methylation on chromosome 15 using immunoprecipitation of methylated DNA and hybridization to tiling oligonucleotide arrays. Comparison of six individuals with maternal versus paternal UPD15 revealed 12 differentially methylated regions (DMRs). Putative DMRs were validated by bisulfite sequencing, confirming the presence of parent-of-origin-specific methylation marks. We detected DMRs associated with known imprinted genes within the Prader-Willi/Angelman syndrome region, such as SNRPN and MAGEL2, validating this as a method of detecting imprinted loci. Of the 12 DMRs identified, eight were novel, some of which are associated with genes not previously thought to be imprinted. These include a site within intron 2 of IGF1R at 15q26.3, a gene that plays a fundamental role in growth, and an intergenic site upstream of GABRG3 that lies within a previously defined candidate region conferring an increased maternal risk of psychosis. These data provide a map of parent-of-origin-specific epigenetic modifications on chromosome 15, identifying DNA elements that may play a functional role in the imprinting process. Application of this methodology to other chromosomes for which UPD has been reported will allow the systematic identification of imprinted sites throughout the genome.
- Published
- 2010
16. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes
- Author
-
Loviglio, M N, Leleu, M, Männik, K, Passeggeri, M, Giannuzzi, G, van der Werf, I, Waszak, S M, Zazhytska, M, Roberts-Caldeira, I, Gheldof, N, Migliavacca, E, Alfaiz, A A, Hippolyte, L, Maillard, A M, Van Dijck, A, Kooy, R F, Sanlaville, D, Rosenfeld, J A, Shaffer, L G, Andrieux, J, Marshall, C, Scherer, S W, Shen, Y, Gusella, J F, Thorsteinsdottir, U, Thorleifsson, G, Dermitzakis, E T, Deplancke, B, Beckmann, J S, Rougemont, J, Jacquemont, S, and Reymond, A
- Abstract
Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts’ maps could uncover functionally and clinically related genes.
- Published
- 2017
- Full Text
- View/download PDF
17. A recurrent 14q32.2 microdeletion mediated by expanded TGG repeats
- Author
-
Bena, F., primary, Gimelli, S., additional, Migliavacca, E., additional, Brun-Druc, N., additional, Buiting, K., additional, Antonarakis, S. E., additional, and Sharp, A. J., additional
- Published
- 2010
- Full Text
- View/download PDF
18. 114 INVITED Malignant glioma: molecular pathways, mechanisms of disease and resistance to chemoradiotherapy
- Author
-
Hegi, M.E., primary, Migliavacca, E., additional, Gorlia, T., additional, Lambiv, W.L., additional, Shay, T., additional, Domany, E., additional, Delorenzi, M., additional, Stupp, R., additional, and Murat, A., additional
- Published
- 2007
- Full Text
- View/download PDF
19. MULTIVARIATE REGRESSION APPLIED TO THE PERFORMANCE OTIMIZATION OF A COUNTERCURRENT ULTRACENTRIFUGE - A PRELIMINARY STUDY
- Author
-
Migliavacca, E., primary
- Published
- 2006
- Full Text
- View/download PDF
20. 24 Molecular profiles of gliomas, mechanistic insights and associations with outcome
- Author
-
Murat, A., primary, Migliavacca, E., additional, Shay, T., additional, Stupp, R., additional, Domany, E., additional, Delorenzi, M., additional, and Hegi, M.E., additional
- Published
- 2006
- Full Text
- View/download PDF
21. Établissement de profils moléculaires de glioblastomes. Étude transversale dans le cadre d’une étude clinique randomisée de l’organisation européenne de recherche et traitement du cancer (EORTC) et du National Cancer Institute du Canada (NCIC) qui avait pour but de tester l’addition de temozolomide à la radiothérapie
- Author
-
Hegi, M., primary, Murat, A., additional, Migliavacca, E., additional, Shay, T., additional, Diserens, A.C., additional, Hamou, M.F., additional, Weller, M., additional, Kros, J., additional, Hainfellner, J., additional, Janzer, R., additional, Cairncross, G., additional, Descombes, P., additional, De Tribolet, N., additional, Delorenzi, M., additional, Domany, E., additional, and Stupp, R., additional
- Published
- 2004
- Full Text
- View/download PDF
22. Simultaneous bio-sorption of heavy metals by marine sea-weeds
- Author
-
Massacci, P., primary, Ferrini, M., additional, and Migliavacca, E., additional
- Published
- 2003
- Full Text
- View/download PDF
23. Stem cell-related "self-renewal" signature and high epidermal growth factor receptor expression associated with resistance to concomitant chemoradiotherapy in glioblastoma.
- Author
-
Murat A, Migliavacca E, Gorlia T, Lambiv WL, Shay T, Hamou MF, de Tribolet N, Regli L, Wick W, Kouwenhoven MC, Hainfellner JA, Heppner FL, Dietrich PY, Zimmer Y, Cairncross JG, Janzer RC, Domany E, Delorenzi M, Stupp R, and Hegi ME
- Published
- 2008
- Full Text
- View/download PDF
24. MDB: a database system utilizing automatic construction of modules and STAR-derived universal language.
- Author
-
Migliavacca, E, Adzhubei, A A, and Peitsch, M C
- Abstract
The value of information greatly increases if stored in databases. The objective was to construct a multi-purpose database system primarily designed to store and provide access to three-dimensional structures of biological molecules including theoretical models.
- Published
- 2001
- Full Text
- View/download PDF
25. Structure-property Relationships of Trimetazidine Derivatives and Model Compounds as Potential Antioxidants
- Author
-
Ancerewicz, J., Migliavacca, E., Carrupt, P.-A., Testa, B., Bree, F., Zini, R., Tillement, J.-P., Labidalle, S., Guyot, D., and Chauvet-Monges, A.-M.
- Published
- 1998
- Full Text
- View/download PDF
26. A mathematical model of the circulation in the presence of the bidirectional cavopulmonary anastomosis in children with a univentricular heart
- Author
-
Pennati, G., Migliavacca, E., Dubini, G., Pietrabissa, R., and Leval, M. R. De
- Published
- 1997
- Full Text
- View/download PDF
27. Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes
- Author
-
Loviglio, M N, Leleu, M, Männik, K, Passeggeri, M, Giannuzzi, G, Van Der Werf, I, Waszak, S M, Zazhytska, M, Roberts-Caldeira, I, Gheldof, N, Migliavacca, E, Alfaiz, A A, Hippolyte, L, Maillard, A M, Loviglio, Maria Nicla, Männik, Katrin, Van Der Werf, Ilse, Giannuzzi, Giuliana, Zazhytska, Marianna, Gheldof, Nele, Migliavacca, Eugenia, Alfaiz, Ali A, Roberts-Caldeira, Inês, Hippolyte, Loyse, Maillard, Anne M, Ferrarini, Alessandra, Butschi, Florence Niel, Conrad, Bernard, Addor, Marie-Claude, Belfiore, Marco, Roetzer, Katharina, Dijck, Anke Van, Blaumeiser, Bettina, Kooy, Frank, Roelens, Filip, Dheedene, Annelies, Chiaie, Barbara Delle, Menten, Björn, Oostra, Ann, Caberg, Jean-Hubert, Carter, Melissa, Kellam, Barbara, Stavropoulos, Dimitri J, Marshall, Christian, Scherer, Stephen W, Weksberg, Rosanna, Cytrynbaum, Cheryl, Bassett, Anne, Lowther, Chelsea, Gillis, Jane, Mackay, Sara, Bache, Iben, Ousager, Lilian B, Smerdel, Maja Patricia, Graakjaer, Jesper, Kjaergaard, Susanne, Metspalu, Andres, Mathieu, Michele, Bonneau, Dominique, Guichet, Agnes, Parent, Philippe, Férec, Claude, Gerard, Marion, Plessis, Ghislaine, Lespinasse, James, Masurel, Alice, Marle, Nathalie, Faivre, Laurence, Callier, Patrick, Layet, Valerie, Meur, Nathalie Le, Le Goff, Céline, Duban-Bedu, Bénédicte, Sukno, Sylvie, Boute, Odile, Andrieux, Joris, Blanchet, Patricia, Geneviève, David, Puechberty, Jacques, Schneider, Anouck, Leheup, Bruno, Jonveaux, Philippe, Mercier, Sandra, David, Albert, Le Caignec, Cédric, De Pontual, Loic, Pipiras, Eva, Jacquette, Aurelia, Keren, Boris, Gilbert-Dussardier, Brigitte, Bilan, Frederic, Goldenberg, Alice, Chambon, Pascal, Toutain, Annick, Till, Marianne, Sanlaville, Damien, Leube, Barbara, Royer-Pokora, Brigitte, Grabe, Hans Jörgen, Schmidt, Carsten Oliver, Schurmann, Claudia, Homuth, Georg, Thorleifsson, Gudmar, Thorsteinsdottir, Unnur, Bernardini, Laura, Novelli, Antonio, Micale, Lucia, Merla, Giuseppe, Zollino, Marcella, Mari, Francesca, Rizzo, Caterina Lo, Renieri, Alessandra, Silengo, Margherita, Vulto-Van Silfhout, Anneke T, Schouten, Meyke, Pfundt, Rolph, De Leeuw, Nicole, Vansenne, Fleur, Maas, Saskia M, Barge-Schaapveld, Daniela Qcm, Knegt, Alida C, Stadheim, Barbro, Rodningen, Olaug, Houge, Gunnar, Price, Sue, Hawkes, Lara, Campbell, Carolyn, Kini, Usha, Vogt, Julie, Walters, Robin, Blakemore, Alexandra, Gusella, James F, Shen, Yiping, Scott, Daryl, Bacino, Carlos A, Tsuchiya, Karen, Ladda, Roger, Sell, Susan, Asamoah, Alexander, Hamati, Aline I, Rosenfeld, Jill A, Shaffer, Lisa G, Mitchell, Elyse, Hodge, Jennelle C, Beckmann, Jacques S, Jacquemont, Sébastien, Reymond, Alexandre, Ewans, Lisa J, Mowat, David, Walker, Jan, Amor, David J, Esch, Hilde Van, Leroy, Patricia, Bamforth, John-Steven, Babu, Deepti, Isidor, Bertrand, Didonato, Nataliya, Hackmann, Karl, Passeggeri, Marzia, Haeringen, Arie Van, Smith, Rosemarie, Ellingwood, Sara, Farber, Darren M, Puri, Vinay, Zadeh, Neda, Weaver, David D, Miller, Mandy, Wilks, Timothy, Jorgez, Carolina J, Lafayette, Deedee, Van Dijck, A, Kooy, R F, Sanlaville, D, Rosenfeld, J A, Shaffer, L G, Andrieux, J, Marshall, C, Scherer, S W, Shen, Y, Gusella, J F, Thorsteinsdottir, U, Thorleifsson, G, Dermitzakis, E T, Deplancke, B, Beckmann, J S, Rougemont, J, Jacquemont, S, Reymond, A, 2p15 Consortium, and 16p11 2 Consortium
- Abstract
Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts’ maps could uncover functionally and clinically related genes.
28. PPAR gamma Controls Ectopic Adipogenesis and Cross-Talks with Myogenesis During Skeletal Muscle Regeneration
- Author
-
Dammone, G, Karaz, S, Lukjanenko, L, Winkler, C, Sizzano, F, Jacot, G, Migliavacca, E, Palini, A, Desvergne, B, Gilardi, F, and Feige, JN
29. Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock
- Author
-
Bart Deplancke, Frédéric Schütz, Nouria Hernandez, Federica Gilardi, Nicolas GUEX, Leonor Rib, Ian Willis, Beatrice Desvergne, CycliX Consortium, Hernandez, N., Delorenzi, M., Deplancke, B., Desvergne, B., Guex, N., Herr, W., Naef, F., Rougemont, J., Schibler, U., Andersin, T., Cousin, P., Gilardi, F., Lammers, F., Mange, F., Villeneuve, D., David, F., Fabbretti, R., Jacquet, P., Krier, I., Kuznetsov, D., Leleu, M., Liechti, R., Martin, O., Migliavacca, E., Naldi, A., Praz, V., Rib, L., Sobel, J., Vlegel, V., and Xenarios, I.
- Subjects
0301 basic medicine ,Transcription, Genetic ,Circadian clock ,ARNTL Transcription Factors/deficiency ,ARNTL Transcription Factors/genetics ,Animals ,Circadian Clocks/genetics ,Circadian Rhythm/genetics ,Eating/genetics ,Fasting/metabolism ,Gene Expression Profiling ,Gene Expression Regulation ,Liver/metabolism ,Mice ,Mice, Knockout ,Oligonucleotide Array Sequence Analysis ,Protein Binding ,RNA Polymerase III/genetics ,RNA Polymerase III/metabolism ,Repressor Proteins/deficiency ,Repressor Proteins/genetics ,Signal Transduction ,Repressor ,Biology ,RNA polymerase III ,Eating ,03 medical and health sciences ,0302 clinical medicine ,Transcription (biology) ,Circadian Clocks ,Gene expression ,Genetics ,Circadian rhythm ,Genetics (clinical) ,Regulation of gene expression ,Research ,ARNTL Transcription Factors ,RNA Polymerase III ,Fasting ,Circadian Rhythm ,Cell biology ,Repressor Proteins ,ARNTL ,030104 developmental biology ,Liver ,030217 neurology & neurosurgery - Abstract
RNA polymerase III (Pol III) synthesizes short noncoding RNAs, many of which are essential for translation. Accordingly, Pol III activity is tightly regulated with cell growth and proliferation by factors such as MYC, RB1, TRP53, and MAF1. MAF1 is a repressor of Pol III transcription whose activity is controlled by phosphorylation; in particular, it is inactivated through phosphorylation by the TORC1 kinase complex, a sensor of nutrient availability. Pol III regulation is thus sensitive to environmental cues, yet a diurnal profile of Pol III transcription activity is so far lacking. Here, we first use gene expression arrays to measure mRNA accumulation during the diurnal cycle in the livers of (1) wild-type mice, (2) arrhythmic Arntl knockout mice, (3) mice fed at regular intervals during both night and day, and (4) mice lacking the Maf1 gene, and so provide a comprehensive view of the changes in cyclic mRNA accumulation occurring in these different systems. We then show that Pol III occupancy of its target genes rises before the onset of the night, stays high during the night, when mice normally ingest food and when translation is known to be increased, and decreases in daytime. Whereas higher Pol III occupancy during the night reflects a MAF1-dependent response to feeding, the rise of Pol III occupancy before the onset of the night reflects a circadian clock-dependent response. Thus, Pol III transcription during the diurnal cycle is regulated both in response to nutrients and by the circadian clock, which allows anticipatory Pol III transcription.
- Published
- 2017
- Full Text
- View/download PDF
30. Differential regulation of RNA polymerase III genes during liver regeneration
- Author
-
Meghdad Yeganeh, Cristian Carmeli, Dominic Villeneuve, Mauro Delorenzi, Winship Herr, Leonor Rib, Nouria Hernandez, Viviane Praz, Nicolas Guex, CycliX consortium, Hernandez, N., Delorenzi, M., Deplancke, B., Desvergne, B., Guex, N., Herr, W., Naef, F., Rougemont, J., Schibler, U., Andersin, T., Cousin, P., Gilardi, F., Gos, P., Lammers, F., Lopes, M., Mange, F., Minocha, S., Raghav, S., Villeneuve, D., Fabbretti, R., Vlegel, V., Xenarios, I., Migliavacca, E., Praz, V., David, F., Jarosz, Y., Kuznetsov, D., Liechti, R., Martin, O., Delafontaine, J., Cajan, J., Carmeli, C., Gustafson, K., Krier, I., Leleu, M., Molina, N., Naldi, A., Rib, L., Sobel, J., Symul, L., Bounova, G., and Jacquet, P.
- Subjects
Chromatin Immunoprecipitation ,Transcription, Genetic ,DNA polymerase ,DNA polymerase II ,viruses ,RNA polymerase II ,RNA polymerase III ,Histones ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Transcription (biology) ,Genetics ,Animals ,Hepatectomy ,Humans ,Gene ,030304 developmental biology ,0303 health sciences ,biology ,Cell Cycle ,Gene regulation, Chromatin and Epigenetics ,Gene Expression Regulation, Developmental ,RNA Polymerase III ,Histone-Lysine N-Methyltransferase ,Liver regeneration ,Liver Regeneration ,Housekeeping gene ,Cell biology ,Liver ,biology.protein ,RNA Polymerase II ,Cell Division ,030217 neurology & neurosurgery ,Protein Binding - Abstract
Mouse liver regeneration after partial hepatectomy involves cells in the remaining tissue synchronously entering the cell division cycle. We have used this system and H3K4me3, Pol II and Pol III profiling to characterize adaptations in Pol III transcription. Our results broadly define a class of genes close to H3K4me3 and Pol II peaks, whose Pol III occupancy is high and stable, and another class, distant from Pol II peaks, whose Pol III occupancy strongly increases after partial hepatectomy. Pol III regulation in the liver thus entails both highly expressed housekeeping genes and genes whose expression can adapt to increased demand.
- Published
- 2019
31. A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver
- Author
-
Mauro Delorenzi, Irina Krier, Teemu Andersin, Li Long, Nicolas Guex, Arnaud Fortier, David Bernasconi, Marion Leleu, Guillaume Rey, Julia Cajan, Fabrice P. A. David, Winship Herr, Fabienne Lammers, Sunil K. Raghav, Olivier Martin, Jacques Rougemont, Aurélien Naldi, Roberto Fabbretti, Eugenia Migliavacca, Pascal Gos, Viviane Praz, Robin Liechti, Ueli Schibler, Gwendal LeMartelot, Nouria Hernandez, Laura Symul, Pascal Cousin, Frederick J. Ross, Yohan Jarosz, Béatrice Desvergne, Donatella Canella, Nacho Molina, Ioannis Xenarios, Felix Naef, Lucas Sinclair, Volker Vlegel, Federica Gilardi, Gwendal Le Martelot, Bart Deplancke, Dmitry Kuznetsov, University of Zurich, Delorenzi, Mauro, CycliX Consortium, Hernandez, N., Delorenzi, M., Deplancke, B., Desvergne, B., Guex, N., Herr, W., Naef, F., Rougemont, J., Schibler, U., Andersin, T., Cousin, P., Gilardi, F., Gos, P., Le Martelot, G., Lammers, F., Canella, D., Raghav, S., Fabbretti, R., Fortier, A., Long, L., Vlegel, V., Xenarios, I., Migliavacca, E., Praz, V., David, F., Jarosz, Y., Kuznetsov, D., Liechti, R., Martin, O., Ross, F., Sinclair, L., Cajan, J., Krier, I., Leleu, M., Molina, N., Naldi, A., Rey, G., Symul, L., and Bernasconi, D.
- Subjects
Male ,Chromatin Immunoprecipitation ,2716 Genetics (clinical) ,Pseudogene ,genetic processes ,Biology ,RNA polymerase III ,Mice ,chemistry.chemical_compound ,RNA, Transfer ,SX00 SystemsX.ch ,1311 Genetics ,Transcription (biology) ,RNA polymerase ,Gene expression ,Genetics ,Animals ,Humans ,SX04 CycliX ,Gene ,Genetics (clinical) ,Oligonucleotide Array Sequence Analysis ,Models, Genetic ,Gene Expression Profiling ,Research ,RNA Polymerase III ,RNA ,Genomics ,Sequence Analysis, DNA ,Molecular biology ,Mice, Inbred C57BL ,enzymes and coenzymes (carbohydrates) ,Liver ,chemistry ,Transfer RNA ,570 Life sciences ,biology ,bacteria ,Chromatin Immunoprecipitation/methods ,Genomics/methods ,Liver/metabolism ,RNA Polymerase III/genetics ,RNA Polymerase III/metabolism ,RNA, Transfer/genetics ,RNA, Transfer/metabolism ,Sequence Analysis, DNA/methods - Abstract
The genomic loci occupied by RNA polymerase (RNAP) III have been characterized in human culture cells by genome-wide chromatin immunoprecipitations, followed by deep sequencing (ChIP-seq). These studies have shown that only ∼40% of the annotated 622 human tRNA genes and pseudogenes are occupied by RNAP-III, and that these genes are often in open chromatin regions rich in active RNAP-II transcription units. We have used ChIP-seq to characterize RNAP-III-occupied loci in a differentiated tissue, the mouse liver. Our studies define the mouse liver RNAP-III-occupied loci including a conserved mammalian interspersed repeat (MIR) as a potential regulator of an RNAP-III subunit-encoding gene. They reveal that synteny relationships can be established between a number of human and mouse RNAP-III genes, and that the expression levels of these genes are significantly linked. They establish that variations within the A and B promoter boxes, as well as the strength of the terminator sequence, can strongly affect RNAP-III occupancy of tRNA genes. They reveal correlations with various genomic features that explain the observed variation of 81% of tRNA scores. In mouse liver, loci represented in the NCBI37/mm9 genome assembly that are clearly occupied by RNAP-III comprise 50 Rn5s (5S RNA) genes, 14 known non-tRNA RNAP-III genes, nine Rn4.5s (4.5S RNA) genes, and 29 SINEs. Moreover, out of the 433 annotated tRNA genes, half are occupied by RNAP-III. Transfer RNA gene expression levels reflect both an underlying genomic organization conserved in dividing human culture cells and resting mouse liver cells, and the particular promoter and terminator strengths of individual genes.
- Published
- 2012
- Full Text
- View/download PDF
32. Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
- Author
-
Bonhoure, Nicolas, Bounova, Gergana, Bernasconi, David, Praz, Viviane, Lammers, Fabienne, Canella, Donatella, Willis, Ian M., Herr, Winship, Hernandez, Nouria, Delorenzi, Mauro, Deplancke, Bart, Desvergne, Béatrice, Guex, Nicolas, Naef, Felix, Rougemont, Jacques, Schibler, Ueli, Andersin, Teemu, Cousin, Pascal, Gilardi, Federica, Gos, Pascal, Raghav, Sunil, Villeneuve, Dominic, Fabbretti, Roberto, Vlegel, Volker, Xenarios, Ioannis, Migliavacca, Eugenia, David, Fabrice, Jarosz, Yohan, Kuznetsov, Dmitry, Liechti, Robin, Martin, Olivier, Delafontaine, Julien, Cajan, Julia, Gustafson, Kyle, Krier, Irina, Leleu, Marion, Molina, Nacho, Naldi, Aurélien, Rib, Leonor, Symul, Laura, CycliX Consortium, Hernandez, N., Delorenzi, M., Deplancke, B., Desvergne, B., Guex, N., Herr, W., Naef, F., Rougemont, J., Schibler, U., Andersin, T., Cousin, P., Gilardi, F., Gos, P., Lammers, F., Raghav, S., Villeneuve, D., Fabbretti, R., Vlegel, V., Xenarios, I., Migliavacca, E., Praz, V., David, F., Jarosz, Y., Kuznetsov, D., Liechti, R., Martin, O., Delafontaine, J., Cajan, J., Gustafson, K., Krier, I., Leleu, M., Molina, N., Naldi, A., Rib, L., Symul, L., Bounova, G., University of Zurich, and Hernandez, N
- Subjects
Quality Control ,Normalization (statistics) ,2716 Genetics (clinical) ,Chromatin Immunoprecipitation ,Occupancy ,SX20 Research, Technology and Development Projects ,Immunoprecipitation ,Sample (material) ,Method ,Biology ,Mice ,03 medical and health sciences ,0302 clinical medicine ,SX00 SystemsX.ch ,1311 Genetics ,Genetics ,Animals ,Humans ,Genetics(clinical) ,SX04 CycliX ,Genetics (clinical) ,030304 developmental biology ,Quantile normalization ,0303 health sciences ,Computational Biology ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,Reference Standards ,Chromatin ,570 Life sciences ,biology ,Spike (software development) ,Biological system ,Chromatin immunoprecipitation ,030217 neurology & neurosurgery - Abstract
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments are widely used to determine, within entire genomes, the occupancy sites of any protein of interest, including, for example, transcription factors, RNA polymerases, or histones with or without various modifications. In addition to allowing the determination of occupancy sites within one cell type and under one condition, this method allows, in principle, the establishment and comparison of occupancy maps in various cell types, tissues, and conditions. Such comparisons require, however, that samples be normalized. Widely used normalization methods that include a quantile normalization step perform well when factor occupancy varies at a subset of sites, but may miss uniform genome-wide increases or decreases in site occupancy. We describe a spike adjustment procedure (SAP) that, unlike commonly used normalization methods intervening at the analysis stage, entails an experimental step prior to immunoprecipitation. A constant, low amount from a single batch of chromatin of a foreign genome is added to the experimental chromatin. This “spike” chromatin then serves as an internal control to which the experimental signals can be adjusted. We show that the method improves similarity between replicates and reveals biological differences including global and largely uniform changes.
- Published
- 2014
- Full Text
- View/download PDF
33. Rhythmic Changes in Gene Activation Power the Circadian Clock
- Author
-
Gwendal Le Martelot, Donatella Canella, Laura Symul, Eugenia Migliavacca, Federica Gilardi, Robin Liechti, Olivier Martin, Keith Harshman, Mauro Delorenzi, Béatrice Desvergne, Winship Herr, Bart Deplancke, Ueli Schibler, Jacques Rougemont, Nicolas Guex, Nouria Hernandez, Felix Naef, CycliX Consortium, University of Zurich, Hernandez, Nouria, CycliX Consortium, Hernandez, N., Delorenzi, M., Deplancke, B., Desvergne, B., Guex, N., Herr, W., Naef, F., Rougemont, J., Schibler, U., Andersin, T., Cousin, P., Gilardi, F., Gos, P., Le Martelot, G., Lammers, F., Canella, D., Raghav, S., Fabbretti, R., Fortier, A., Long, L., Vlegel, V., Xenarios, I., Migliavacca, E., Praz, V., David, F., Jarosz, Y., Kuznetsov, D., Liechti, R., Martin, O., Delafontaine, J., Sinclair, L., Cajan, J., Krier, I., Leleu, M., Molina, N., Naldi, A., Rey, G., Symul, L., and Bernasconi, D.
- Subjects
Male ,Time Factors ,Transcription, Genetic ,Circadian clock ,RNA polymerase II ,Biochemistry ,Epigenesis, Genetic ,Histones ,Mice ,0302 clinical medicine ,SX00 SystemsX.ch ,Transcription (biology) ,2400 General Immunology and Microbiology ,Gene expression ,Molecular Cell Biology ,Transcriptional regulation ,RNA Processing, Post-Transcriptional ,Biology (General) ,Promoter Regions, Genetic ,Regulation of gene expression ,Genetics ,0303 health sciences ,Reverse Transcriptase Polymerase Chain Reaction ,General Neuroscience ,Systems Biology ,2800 General Neuroscience ,Genomics ,Chromatin ,Circadian Rhythm ,Liver ,DNA methylation ,Synopsis ,RNA Polymerase II ,Transcription Initiation Site ,General Agricultural and Biological Sciences ,Half-Life ,Research Article ,Chromatin Immunoprecipitation ,SX20 Research, Technology and Development Projects ,QH301-705.5 ,E-box ,1100 General Agricultural and Biological Sciences ,Biology ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Rhythm ,1300 General Biochemistry, Genetics and Molecular Biology ,Animals ,Circadian rhythm ,RNA, Messenger ,SX04 CycliX ,Gene ,Post-transcriptional regulation ,030304 developmental biology ,Chromatin Assembly and Disassembly ,DNA Methylation ,Histones/genetics ,Histones/metabolism ,Kinetics ,Liver/cytology ,Liver/metabolism ,Mice, Inbred C57BL ,Models, Genetic ,RNA Polymerase II/genetics ,RNA Polymerase II/metabolism ,RNA, Messenger/analysis ,RNA, Messenger/metabolism ,Transcriptome ,General Immunology and Microbiology ,Computational Biology ,Promoter ,biology.protein ,570 Life sciences ,biology ,Chromatin immunoprecipitation ,Neuroscience ,030217 neurology & neurosurgery - Abstract
Genome-wide rhythms in RNA polymerase II loading and dynamic chromatin remodeling underlie periodic gene expression during diurnal cycles in the mouse liver., Interactions of cell-autonomous circadian oscillators with diurnal cycles govern the temporal compartmentalization of cell physiology in mammals. To understand the transcriptional and epigenetic basis of diurnal rhythms in mouse liver genome-wide, we generated temporal DNA occupancy profiles by RNA polymerase II (Pol II) as well as profiles of the histone modifications H3K4me3 and H3K36me3. We used these data to quantify the relationships of phases and amplitudes between different marks. We found that rhythmic Pol II recruitment at promoters rather than rhythmic transition from paused to productive elongation underlies diurnal gene transcription, a conclusion further supported by modeling. Moreover, Pol II occupancy preceded mRNA accumulation by 3 hours, consistent with mRNA half-lives. Both methylation marks showed that the epigenetic landscape is highly dynamic and globally remodeled during the 24-hour cycle. While promoters of transcribed genes had tri-methylated H3K4 even at their trough activity times, tri-methylation levels reached their peak, on average, 1 hour after Pol II. Meanwhile, rhythms in tri-methylation of H3K36 lagged transcription by 3 hours. Finally, modeling profiles of Pol II occupancy and mRNA accumulation identified three classes of genes: one showing rhythmicity both in transcriptional and mRNA accumulation, a second class with rhythmic transcription but flat mRNA levels, and a third with constant transcription but rhythmic mRNAs. The latter class emphasizes widespread temporally gated posttranscriptional regulation in the mouse liver., Author Summary In mammalian organs such as the liver, many metabolic and physiological processes occur preferentially at specific times during the 24-hour daily cycle. The timing of these rhythmic functions depends on a complex interplay between the endogenous circadian clock and environmental timing cues relayed through the master circadian clock in the suprachiasmatic nucleus, or via feeding rhythms. These rhythms can be implemented on several regulatory levels, and here we aimed at a better understanding of the transcriptional and epigenetic changes that regulate diurnal rhythms. We performed genome-wide analysis of the locations of RNA polymerase II (Pol II) and the epigenetic histone modifications H3K4me3 and H3K36me3 at specific times of day, relating these data to mRNA expression levels. Our analyses show that Pol II transcriptional rhythms are biphasic in mouse liver, having predominant peak activities in the morning and evening. Moreover, dynamic changes in histone marks lag transcription rhythms genome-wide, indicating that the epigenetic landscape can be remodeled during the 24-hour cycle. Finally, a quantitative analysis of temporal Pol II and mRNA accumulation profiles indicates that posttranscriptional regulation significantly contributes to the amplitude and phase of mRNA accumulation profiles. While many studies have analyzed how transcription and chromatin states are modified during irreversible cell differentiation processes, our work highlights how these states can evolve reversibly in a system exhibiting periodicity in time.
- Published
- 2012
34. Protein phosphorylation as intracellular target in the action of MAO-A inhibitors and other antidepressants
- Author
-
Perez, J., Cagnoli, C., Mori, S., Tinelli, D., Migliavacca, E., Brunello, N., and Racagni, G.
- Published
- 1993
- Full Text
- View/download PDF
35. Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15
- Author
-
Elisavet Stathaki, Andrew J. Sharp, Albert Schinzel, Alessandra Baumer, David O. Robinson, Yann Dupré, Deborah J G Mackay, Stylianos E. Antonarakis, Bernhard Steiner, Eugenia Migliavacca, Luigi Cobellis, Han G. Brunner, Mohammad Reza Sailani, Gilda Cobellis, University of Zurich, Sharp, A., Migliavacca, E., Dupre, Y., Stathaki, E., Sailani, M., Baumer, A., Schinzel, A., Mackay, D., Robinson, D., Cobellis, G., Cobellis, Luigi, Brunner, H., Steiner, B., and Antonarakis, S.
- Subjects
2716 Genetics (clinical) ,10039 Institute of Medical Genetics ,Bisulfite sequencing ,DNA Methylation ,Method ,610 Medicine & health ,Biology ,Chromosomes, Human, Pair 15/*genetics ,snRNP Core Proteins ,Genomic disorders and inherited multi-system disorders [IGMD 3] ,03 medical and health sciences ,Chromosome 15 ,1311 Genetics ,Angelman syndrome ,Genetics ,medicine ,DNA/metabolism ,Humans ,ddc:576.5 ,Epigenetics ,Genetics (clinical) ,030304 developmental biology ,0303 health sciences ,Chromosomes, Human, Pair 15 ,snRNP Core Protein ,Gene Expression Profiling ,Protein ,030305 genetics & heredity ,Uniparental Disomy/*genetics ,Proteins ,DNA ,Uniparental Disomy ,Angelman Syndrome/genetics ,medicine.disease ,Prader-Willi Syndrome/genetics ,Uniparental disomy ,Differentially methylated regions ,SnRNP Core Proteins/genetics ,Proteins/genetics ,DNA methylation ,570 Life sciences ,biology ,Angelman Syndrome ,Genomic imprinting ,Prader-Willi Syndrome ,Human - Abstract
The maternal and paternal genomes possess distinct epigenetic marks that distinguish them at imprinted loci. In order to identify imprinted loci, we used a novel method, taking advantage of the fact that uniparental disomy (UPD) provides a system that allows the two parental chromosomes to be studied independently. We profiled the paternal and maternal methylation on chromosome 15 using immunoprecipitation of methylated DNA and hybridization to tiling oligonucleotide arrays. Comparison of six individuals with maternal versus paternal UPD15 revealed 12 differentially methylated regions (DMRs). Putative DMRs were validated by bisulfite sequencing, confirming the presence of parent-of-origin-specific methylation marks. We detected DMRs associated with known imprinted genes within the Prader-Willi/Angelman syndrome region, such as SNRPN and MAGEL2, validating this as a method of detecting imprinted loci. Of the 12 DMRs identified, eight were novel, some of which are associated with genes not previously thought to be imprinted. These include a site within intron 2 of IGF1R at 15q26.3, a gene that plays a fundamental role in growth, and an intergenic site upstream of GABRG3 that lies within a previously defined candidate region conferring an increased maternal risk of psychosis. These data provide a map of parent-of-origin-specific epigenetic modifications on chromosome 15, identifying DNA elements that may play a functional role in the imprinting process. Application of this methodology to other chromosomes for which UPD has been reported will allow the systematic identification of imprinted sites throughout the genome.
- Published
- 2010
36. Genome-Wide Analysis of SREBP1 Activity around the Clock Reveals Its Combined Dependency on Nutrient and Circadian Signals
- Author
-
Felix Naef, Bart Deplancke, Laura Symul, Dmitry Kuznetsov, Aurélien Naldi, Winship Herr, Ioannis Xenarios, Nouria Hernandez, Federica Gilardi, Nicolas GUEX, Beatrice Desvergne, Guillaume Rey, CycliX Consortium, Hernandez, N., Delorenzi, M., Deplancke, B., Desvergne, B., Guex, N., Herr, W., Naef, F., Rougemont, J., Schibler, U., Andersin, T., Cousin, P., Gilardi, F., Gos, P., Martelot, G., Lammers, F., Canella, D., Raghav, S., Fabbretti, R., Fortier, A., Long, L., Vlegel, V., Xenarios, I., Migliavacca, E., Praz, V., David, F., Jarosz, Y., Kuznetsov, D., Liechti, R., Martin, O., Delafontaine, J., Sinclair, L., Cajan, J., Krier, I., Leleu, M., Molina, N., Naldi, A., Rey, G., Symul, L., Bernasconi, D., Baruchet, M., University of Zurich, and Guex, Nicolas
- Subjects
2716 Genetics (clinical) ,Cancer Research ,lcsh:QH426-470 ,SX20 Research, Technology and Development Projects ,Circadian clock ,CLOCK Proteins ,Biology ,Mice ,SX00 SystemsX.ch ,1311 Genetics ,Circadian Clocks ,1312 Molecular Biology ,Genetics ,Transcriptional regulation ,Animals ,Homeostasis ,1306 Cancer Research ,Circadian rhythm ,SX04 CycliX ,Molecular Biology ,Transcription factor ,Genetics (clinical) ,Ecology, Evolution, Behavior and Systematics ,Regulation of gene expression ,Binding Sites ,Genome ,Lipid Metabolism ,Bacterial circadian rhythms ,Circadian Rhythm ,Sterol regulatory element-binding protein ,Cell biology ,lcsh:Genetics ,1105 Ecology, Evolution, Behavior and Systematics ,Gene Expression Regulation ,Hepatocyte Nuclear Factor 4 ,570 Life sciences ,biology ,Sterol Regulatory Element Binding Protein 1 ,Protein Binding ,Research Article - Abstract
In mammals, the circadian clock allows them to anticipate and adapt physiology around the 24 hours. Conversely, metabolism and food consumption regulate the internal clock, pointing the existence of an intricate relationship between nutrient state and circadian homeostasis that is far from being understood. The Sterol Regulatory Element Binding Protein 1 (SREBP1) is a key regulator of lipid homeostasis. Hepatic SREBP1 function is influenced by the nutrient-response cycle, but also by the circadian machinery. To systematically understand how the interplay of circadian clock and nutrient-driven rhythm regulates SREBP1 activity, we evaluated the genome-wide binding of SREBP1 to its targets throughout the day in C57BL/6 mice. The recruitment of SREBP1 to the DNA showed a highly circadian behaviour, with a maximum during the fed status. However, the temporal expression of SREBP1 targets was not always synchronized with its binding pattern. In particular, different expression phases were observed for SREBP1 target genes depending on their function, suggesting the involvement of other transcription factors in their regulation. Binding sites for Hepatocyte Nuclear Factor 4 (HNF4) were specifically enriched in the close proximity of SREBP1 peaks of genes, whose expression was shifted by about 8 hours with respect to SREBP1 binding. Thus, the cross-talk between hepatic HNF4 and SREBP1 may underlie the expression timing of this subgroup of SREBP1 targets. Interestingly, the proper temporal expression profile of these genes was dramatically changed in Bmal1 −/− mice upon time-restricted feeding, for which a rhythmic, but slightly delayed, binding of SREBP1 was maintained. Collectively, our results show that besides the nutrient-driven regulation of SREBP1 nuclear translocation, a second layer of modulation of SREBP1 transcriptional activity, strongly dependent from the circadian clock, exists. This system allows us to fine tune the expression timing of SREBP1 target genes, thus helping to temporally separate the different physiological processes in which these genes are involved., Author Summary Circadian rhythmicity is part of our innate behavior and controls many physiological processes, such as sleeping and waking, activity, neurotransmitter production and a number of metabolic pathways. In mammals, the central circadian pacemaker in the hypothalamus is entrained on a daily basis by environmental cues (i.e. light), thus setting the period length and synchronizing the rhythms of all cells in the body. In the last decades, numerous investigations have highlighted the importance of the internal timekeeping mechanism for maintenance of organism health and longevity. Indeed, the reciprocal regulation of circadian clock and metabolism is now commonly accepted, although still poorly understood at the molecular level. Our global analysis of DNA binding along the day of Sterol Regulatory Element Binding Protein 1 (SREBP1), a key regulator of lipid biosynthesis, represents the first tool to comprehensively explore how its activity is connected to circadian-driven regulatory events. We show that the regulation of SREBP1 action by nutrients relies mainly on the control of its subcellular localization, while the circadian clock influences the promoter specific activity of SREBP1 within the nucleus. Furthermore, we identify the Hepatocyte Nuclear Factor 4 (HNF4) as a putative player in the cross-talk between molecular clock and metabolic regulation.
- Published
- 2014
- Full Text
- View/download PDF
37. Nicotinamide and pyridoxine stimulate muscle stem cell expansion and enhance regenerative capacity during aging.
- Author
-
Ancel S, Michaud J, Migliavacca E, Jomard C, Fessard A, Garcia P, Karaz S, Raja S, Jacot GE, Desgeorges T, Sánchez-García JL, Tauzin L, Ratinaud Y, Brinon B, Métairon S, Pinero L, Barron D, Blum S, Karagounis LG, Heshmat R, Ostovar A, Farzadfar F, Scionti I, Mounier R, Gondin J, Stuelsatz P, and Feige JN
- Abstract
Skeletal muscle relies on resident muscle stem cells (MuSCs) for growth and repair. Aging and muscle diseases impair MuSC function, leading to stem cell exhaustion and regenerative decline that contribute to the progressive loss of skeletal muscle mass and strength. In the absence of clinically available nutritional solutions specifically targeting MuSCs, we used a human myogenic progenitor (hMP) high-content imaging screen of natural molecules from food to identify nicotinamide (NAM) and pyridoxine (PN) as bioactive nutrients that stimulate MuSCs and have history of safe human use. NAM and PN synergize via CK1-mediated cytoplasmic β-catenin activation and AKT signaling to promote amplification and differentiation of MuSCs. Oral treatment with a combination of NAM/PN accelerates muscle regeneration in vivo by stimulating MuSCs, increases muscle strength during recovery, and overcomes MuSC dysfunction and regenerative failure during aging. Levels of NAM and bioactive PN spontaneously decline during aging in model organisms and inter-independently associate with muscle mass and walking speed in a human cohort of 186 aged people. Collectively, our results establish NAM/PN as a new nutritional intervention that stimulates MuSCs, enhances muscle regeneration, and alleviates age-related muscle decline with a direct opportunity for clinical translation.
- Published
- 2024
- Full Text
- View/download PDF
38. A dual-color PAX7 and MYF5 in vivo reporter to investigate muscle stem cell heterogeneity in regeneration and aging.
- Author
-
Ancel S, Michaud J, Sizzano F, Tauzin L, Oliveira M, Migliavacca E, Schüler SC, Raja S, Dammone G, Karaz S, Sánchez-García JL, Metairon S, Jacot G, Bentzinger CF, Feige JN, and Stuelsatz P
- Subjects
- Animals, Mice, Stem Cells metabolism, Stem Cells cytology, Cell Proliferation, Muscle, Skeletal metabolism, Muscle, Skeletal cytology, Cell Differentiation, Mice, Transgenic, Cell Self Renewal, PAX7 Transcription Factor metabolism, PAX7 Transcription Factor genetics, Myogenic Regulatory Factor 5 metabolism, Myogenic Regulatory Factor 5 genetics, Regeneration, Aging metabolism, Genes, Reporter
- Abstract
Increasing evidence suggests that the muscle stem cell (MuSC) pool is heterogeneous. In particular, a rare subset of PAX7-positive MuSCs that has never expressed the myogenic regulatory factor MYF5 displays unique self-renewal and engraftment characteristics. However, the scarcity and limited availability of protein markers make the characterization of these cells challenging. Here, we describe the generation of StemRep reporter mice enabling the monitoring of PAX7 and MYF5 proteins based on equimolar levels of dual nuclear fluorescence. High levels of PAX7 protein and low levels of MYF5 delineate a deeply quiescent MuSC subpopulation with an increased capacity for asymmetric division and distinct dynamics of activation, proliferation, and commitment. Aging primarily reduces the MYF5
Low MuSCs and skews the stem cell pool toward MYF5High cells with lower quiescence and self-renewal potential. Altogether, we establish the StemRep model as a versatile tool to study MuSC heterogeneity and broaden our understanding of mechanisms regulating MuSC quiescence and self-renewal in homeostatic, regenerating, and aged muscles., Competing Interests: Declaration of interests Except S.C.S., all authors are or were employees of Société des Produits Nestlé SA., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2024
- Full Text
- View/download PDF
39. The Mediating Role of Kynurenine Pathway Metabolites on the Relationship Between Inflammation and Muscle Mass in Oldest-Old Men.
- Author
-
Hetherington-Rauth M, Johnson E, Migliavacca E, Langsetmo L, Hepple RT, Ryan TE, Ferrucci L, Breuillé D, Corthesy J, Lane NE, Feige JN, Napoli N, Tramontana F, Orwoll ES, and Cawthon PM
- Subjects
- Humans, Male, Aged, 80 and over, C-Reactive Protein metabolism, Tumor Necrosis Factor-alpha metabolism, Sarcopenia metabolism, 3-Hydroxyanthranilic Acid metabolism, Cytokines metabolism, Xanthurenates metabolism, Kynurenine metabolism, Kynurenine analogs & derivatives, Inflammation metabolism, Biomarkers metabolism, Tryptophan metabolism, Muscle, Skeletal metabolism
- Abstract
Tryptophan (TRP) metabolites along the kynurenine (KYN) pathway (KP) have been found to influence muscle. Proinflammatory cytokines are known to stimulate the degradation of TRP down the KP. Given that both inflammation and KP metabolites have been connected with loss of muscle, we assessed the potential mediating role of KP metabolites on inflammation and muscle mass in older men. Five hundred and five men (85.0 ± 4.2 years) from the Osteoporotic Fractures in Men cohort study with measured D3-creatine dilution (D3Cr) muscle mass, KP metabolites, and inflammation markers (C-reactive protein [CRP], alpha-1-acid glycoprotein [AGP] and a subsample [n = 305] with interleukin [IL-6, IL-1β, IL-17A] and tumor necrosis factor-α [TNF-α]) were included in the analysis. KP metabolites and inflammatory markers were measured using liquid chromatography-tandem mass spectrometry and immunoassays, respectively. 23%-92% of the inverse relationship between inflammatory markers and D3Cr muscle mass was mediated by KP metabolites (indirect effect p < .05). 3-hydroxyanthranilic acid (3-HAA), quinolinic acid (QA), TRP, xanthurenic acid (XA), KYN/TRP, 3-hydroxykynurenine (3-HK)/3-HAA, QA/3-HAA, and nicotinamide (NAM)/QA mediated the AGP relationship. 3-HAA, QA, KYN/TRP, 3-HK/XA, HKr ratio, 3-HK/3-HAA, QA/3-HAA, and NAM/QA mediated the CRP. KYN/TRP, 3-HK/XA, and NAM/QA explained the relationship for IL-6 and 3-HK/XA and QA/3-HAA for TNF-α. No mediation effect was observed for the other cytokines (indirect effect p > .05). KP metabolites, particularly higher ratios of KYN/TRP, 3-HK/XA, 3-HK/3-HAA, QA/3-HAA, and a lower ratio of NAM/QA, mediated the relationship between inflammation and low muscle mass. Our preliminary cross-sectional data suggest that interventions to alter D3Cr muscle mass may focus on KP metabolites rather than inflammation per se., (© The Author(s) 2024. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)
- Published
- 2024
- Full Text
- View/download PDF
40. Trigonelline is an NAD + precursor that improves muscle function during ageing and is reduced in human sarcopenia.
- Author
-
Membrez M, Migliavacca E, Christen S, Yaku K, Trieu J, Lee AK, Morandini F, Giner MP, Stiner J, Makarov MV, Garratt ES, Vasiloglou MF, Chanvillard L, Dalbram E, Ehrlich AM, Sanchez-Garcia JL, Canto C, Karagounis LG, Treebak JT, Migaud ME, Heshmat R, Razi F, Karnani N, Ostovar A, Farzadfar F, Tay SKH, Sanders MJ, Lillycrop KA, Godfrey KM, Nakagawa T, Moco S, Koopman R, Lynch GS, Sorrentino V, and Feige JN
- Subjects
- Humans, Male, Mice, Animals, NAD metabolism, Caenorhabditis elegans, Aging, Muscle, Skeletal metabolism, Sarcopenia drug therapy, Sarcopenia prevention & control, Sarcopenia metabolism, Alkaloids pharmacology, Alkaloids therapeutic use, Alkaloids metabolism
- Abstract
Mitochondrial dysfunction and low nicotinamide adenine dinucleotide (NAD
+ ) levels are hallmarks of skeletal muscle ageing and sarcopenia1-3 , but it is unclear whether these defects result from local changes or can be mediated by systemic or dietary cues. Here we report a functional link between circulating levels of the natural alkaloid trigonelline, which is structurally related to nicotinic acid4 , NAD+ levels and muscle health in multiple species. In humans, serum trigonelline levels are reduced with sarcopenia and correlate positively with muscle strength and mitochondrial oxidative phosphorylation in skeletal muscle. Using naturally occurring and isotopically labelled trigonelline, we demonstrate that trigonelline incorporates into the NAD+ pool and increases NAD+ levels in Caenorhabditis elegans, mice and primary myotubes from healthy individuals and individuals with sarcopenia. Mechanistically, trigonelline does not activate GPR109A but is metabolized via the nicotinate phosphoribosyltransferase/Preiss-Handler pathway5,6 across models. In C. elegans, trigonelline improves mitochondrial respiration and biogenesis, reduces age-related muscle wasting and increases lifespan and mobility through an NAD+ -dependent mechanism requiring sirtuin. Dietary trigonelline supplementation in male mice enhances muscle strength and prevents fatigue during ageing. Collectively, we identify nutritional supplementation of trigonelline as an NAD+ -boosting strategy with therapeutic potential for age-associated muscle decline., (© 2024. The Author(s).)- Published
- 2024
- Full Text
- View/download PDF
41. Nutrient Metabolites Associated With Low D3Cr Muscle Mass, Strength, and Physical Performance in Older Men.
- Author
-
Hetherington-Rauth M, Johnson E, Migliavacca E, Parimi N, Langsetmo L, Hepple RT, Grzywinski Y, Corthesy J, Ryan TE, Ferrucci L, Feige JN, Orwoll ES, and Cawthon PM
- Subjects
- Male, Humans, Aged, Cohort Studies, Hand Strength physiology, Physical Functional Performance, Muscles, Nutrients, Muscle, Skeletal, Creatine, Muscle Strength physiology
- Abstract
Background: The relationship between amino acids, B vitamins, and their metabolites with D3-creatine (D3Cr) dilution muscle mass, a more direct measure of skeletal muscle mass, has not been investigated. We aimed to assess associations of plasma metabolites with D3Cr muscle mass, as well as muscle strength and physical performance in older men from the Osteoporotic Fractures in Men cohort study., Methods: Out of 1 425 men (84.2 ± 4.1 years), men with the lowest D3Cr muscle mass (n = 100), slowest walking speed (n = 100), lowest grip strength (n = 100), and a random sample (n = 200) serving as a comparison group to the low groups were included. Metabolites were analyzed using liquid chromatography-tandem mass spectrometry. Metabolite differences between the low groups and random sample and their relationships with the muscle outcomes adjusted for confounders and multiple comparisons were assessed using t-test/Mann-Whitney-Wilcoxon and partial correlations, respectively., Results: For D3Cr muscle mass, significant biomarkers (p < .001) with ≥10% fold difference and largest partial correlations were tryptophan (Trp; r = 0.31), kynurenine (Kyn)/Trp; r = -0.27), nicotinamide (Nam)/quinolinic acid (Quin; r = 0.21), and alpha-hydroxy-5-methyl-tetrahydrofolate (hm-THF; r = -0.25). For walking speed, hm-THF, Nam/Quin, and Quin had the largest significance and fold difference, whereas valine (r = 0.17), Trp (r = 0.17), HKyn/Xant (r = -0.20), neopterin (r = -0.17), 5-methyl-THF (r = -0.20), methylated folate (r = -0.21), and thiamine (r = -0.18) had the strongest correlations. Only hm-THF was correlated with grip strength (r = -0.21) and differed between the low group and the random sample., Conclusions: Future interventions focusing on how the Trp metabolic pathway or hm-THF influences D3Cr muscle mass and physical performance declines in older adults are warranted., (© The Author(s) 2023. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
- Published
- 2024
- Full Text
- View/download PDF
42. Evidence for inefficient contraction and abnormal mitochondrial activity in sarcopenia using magnetic resonance spectroscopy.
- Author
-
Stephenson MC, Ho JXM, Migliavacca E, Kalimeri M, Karnani N, Banerji S, Totman JJ, Feige JN, Merchant RA, and Tay SKH
- Subjects
- Male, Humans, Aged, Energy Metabolism physiology, Adenosine Triphosphate metabolism, Magnetic Resonance Spectroscopy methods, Mitochondria metabolism, Adenosine Diphosphate metabolism, Muscle, Skeletal metabolism, Sarcopenia metabolism
- Abstract
Background: Mitochondrial dysfunction has been implicated in sarcopenia.
31 P magnetic resonance spectroscopy (MRS) enables non-invasive measurement of adenosine triphosphate (ATP) synthesis rates to probe mitochondrial function. Here, we assessed muscle energetics in older sarcopenic and non-sarcopenic men and compared with muscle biopsy-derived markers of mitochondrial function., Methods: Twenty Chinese men with sarcopenia (SARC, age = 73.1 ± 4.1 years) and 19 healthy aged and sex-matched controls (CON, age = 70.3 ± 4.2 years) underwent assessment of strength, physical performance, and magnetic resonance imaging. Concentrations of phosphocreatine (PCr), ATP and inorganic phosphate (Pi) as well as muscle pH were measured at rest and during an interleaved rest-exercise protocol to probe muscle mitochondrial function. Results were compared to biopsy-derived mitochondrial complex activity and expression to understand underlying metabolic perturbations., Results: Despite matched muscle contractile power (strength/cross-sectional area), the ATP contractile cost was higher in SARC compared with CON (low-intensity exercise: 1.06 ± 0.59 vs. 0.57 ± 0.22, moderate: 0.93 ± 0.43 vs. 0.58 ± 0.68, high: 0.70 ± 0.57 vs. 0.43 ± 0.51 mmol L-1 min-1 bar-1 cm-2 , P = 0.003, <0.0001 and <0.0001, respectively). Post-exercise mitochondrial oxidative synthesis rates (a marker of mitochondrial function) tended to be longer in SARC but did not reach significance (17.3 ± 6.4 vs. 14.6 ± 6.5 mmol L-1 min-1 , P = 0.2). However, relative increases in end-exercise ADP in SARC (31.8 ± 9.9 vs. 24.0 ± 7.3 mmol L-1 , P = 0.008) may have been a compensatory mechanism. Mitochondrial complex activity was found to be associated with exercise-induced drops in PCr [citrate synthetase activity (CS), Spearman correlation rho = -0.42, P = 0.03] and end-exercise ADP (complex III, rho = -0.52, P = 0.01; CS rho = -0.45, P = 0.02; SDH rho = -0.45, P = 0.03), with CS also being strongly associated with the PCr recovery rate following low intensity exercise (rho = -0.47, P = 0.02), and the cost of contraction at high intensity (rho = -0.54, P = 0.02). Interestingly, at high intensity, the fractional contribution of oxidative phosphorylation to exercise was correlated with activity in complex II (rho = 0.5, P = 0.03), CS (rho = 0.47, P = 0.02) and SDH (rho = 0.46, P = 0.03), linking increased mitochondrial complex activity with increased ability to generate energy through oxidative pathways., Conclusions: This study used31 P MRS to assess ATP utilization and resynthesis in sarcopenic muscle and demonstrated abnormal increases in the energy cost during exercise and perturbed mitochondrial energetics in recovery. Associations between mitochondrial complex activity and the fractional contribution to energy requirement during exercise indicate increased ability to generate energy oxidatively in those with better mitochondrial complex activity., (© 2023 The Authors. Journal of Cachexia, Sarcopenia and Muscle published by John Wiley & Sons Ltd on behalf of Society on Sarcopenia, Cachexia and Wasting Disorders.)- Published
- 2023
- Full Text
- View/download PDF
43. Statistical analysis of high-dimensional biomedical data: a gentle introduction to analytical goals, common approaches and challenges.
- Author
-
Rahnenführer J, De Bin R, Benner A, Ambrogi F, Lusa L, Boulesteix AL, Migliavacca E, Binder H, Michiels S, Sauerbrei W, and McShane L
- Subjects
- Humans, Research Design, Goals, Biomedical Research
- Abstract
Background: In high-dimensional data (HDD) settings, the number of variables associated with each observation is very large. Prominent examples of HDD in biomedical research include omics data with a large number of variables such as many measurements across the genome, proteome, or metabolome, as well as electronic health records data that have large numbers of variables recorded for each patient. The statistical analysis of such data requires knowledge and experience, sometimes of complex methods adapted to the respective research questions., Methods: Advances in statistical methodology and machine learning methods offer new opportunities for innovative analyses of HDD, but at the same time require a deeper understanding of some fundamental statistical concepts. Topic group TG9 "High-dimensional data" of the STRATOS (STRengthening Analytical Thinking for Observational Studies) initiative provides guidance for the analysis of observational studies, addressing particular statistical challenges and opportunities for the analysis of studies involving HDD. In this overview, we discuss key aspects of HDD analysis to provide a gentle introduction for non-statisticians and for classically trained statisticians with little experience specific to HDD., Results: The paper is organized with respect to subtopics that are most relevant for the analysis of HDD, in particular initial data analysis, exploratory data analysis, multiple testing, and prediction. For each subtopic, main analytical goals in HDD settings are outlined. For each of these goals, basic explanations for some commonly used analysis methods are provided. Situations are identified where traditional statistical methods cannot, or should not, be used in the HDD setting, or where adequate analytic tools are still lacking. Many key references are provided., Conclusions: This review aims to provide a solid statistical foundation for researchers, including statisticians and non-statisticians, who are new to research with HDD or simply want to better evaluate and understand the results of HDD analyses., (© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)
- Published
- 2023
- Full Text
- View/download PDF
44. Association of amino acid metabolites with osteoporosis, a metabolomic approach: Bushehr elderly health program.
- Author
-
Panahi N, Fahimfar N, Roshani S, Arjmand B, Gharibzadeh S, Shafiee G, Migliavacca E, Breuille D, Feige JN, Grzywinski Y, Corthesy J, Razi F, Heshmat R, Nabipour I, Farzadfar F, Soltani A, Larijani B, and Ostovar A
- Subjects
- Aged, Amino Acids, Chromatography, Liquid, Female, Humans, Male, Metabolomics, Prospective Studies, Tandem Mass Spectrometry, Bone Density, Osteoporosis diagnosis, Osteoporosis epidemiology
- Abstract
Introduction and Objectives: Amino acids are the most frequently reported metabolites associated with low bone mineral density (BMD) in metabolomics studies. We aimed to evaluate the association between amino acid metabolic profile and bone indices in the elderly population., Methods: 400 individuals were randomly selected from 2384 elderly men and women over 60 years participating in the second stage of the Bushehr elderly health (BEH) program, a population-based prospective cohort study that is being conducted in Bushehr, a southern province of Iran. Frozen plasma samples were used to measure 29 amino acid and derivatives metabolites using the UPLC-MS/MS-based targeted metabolomics platform. We conducted Elastic net regression analysis to detect the metabolites associated with BMD of different sites and lumbar spine trabecular bone score, and also to examine the ability of the measured metabolites to differentiate osteoporosis., Results: We adjusted the analysis for possible confounders (age, BMI, diabetes, smoking, physical activity, vitamin D level, and sex). Valine, leucine, isoleucine, and alanine in women and tryptophan in men were the most important amino acids inversely associated with osteoporosis (OR range from 0.77 to 0.89). Sarcosine, followed by tyrosine, asparagine, alpha aminobutyric acid, and ADMA in women and glutamine in men and when both women and men were considered together were the most discriminating amino acids detected in individuals with osteoporosis (OR range from 1.15 to 1.31)., Conclusion: We found several amino acid metabolites associated with possible bone status in elderly individuals. Further studies are required to evaluate the utility of these metabolites as clinical biomarkers for osteoporosis prediction and their effect on bone health as dietary supplements., (© 2022. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
- Published
- 2022
- Full Text
- View/download PDF
45. An engineered multicellular stem cell niche for the 3D derivation of human myogenic progenitors from iPSCs.
- Author
-
Mashinchian O, De Franceschi F, Nassiri S, Michaud J, Migliavacca E, Aouad P, Metairon S, Pruvost S, Karaz S, Fabre P, Molina T, Stuelsatz P, Hegde N, Le Moal E, Dammone G, Dumont NA, Lutolf MP, Feige JN, and Bentzinger CF
- Subjects
- Animals, Cell Differentiation, Endothelial Cells, Humans, Mice, Muscle Development, Phosphatidylinositol 3-Kinases metabolism, Stem Cell Niche, Induced Pluripotent Stem Cells metabolism
- Abstract
Fate decisions in the embryo are controlled by a plethora of microenvironmental interactions in a three-dimensional niche. To investigate whether aspects of this microenvironmental complexity can be engineered to direct myogenic human-induced pluripotent stem cell (hiPSC) differentiation, we here screened murine cell types present in the developmental or adult stem cell niche in heterotypic suspension embryoids. We identified embryonic endothelial cells and fibroblasts as highly permissive for myogenic specification of hiPSCs. After two weeks of sequential Wnt and FGF pathway induction, these three-component embryoids are enriched in Pax7-positive embryonic-like myogenic progenitors that can be isolated by flow cytometry. Myogenic differentiation of hiPSCs in heterotypic embryoids relies on a specialized structural microenvironment and depends on MAPK, PI3K/AKT, and Notch signaling. After transplantation in a mouse model of Duchenne muscular dystrophy, embryonic-like myogenic progenitors repopulate the stem cell niche, reactivate after repeated injury, and, compared to adult human myoblasts, display enhanced fusion and lead to increased muscle function. Altogether, we provide a two-week protocol for efficient and scalable suspension-based 3D derivation of Pax7-positive myogenic progenitors from hiPSCs., (© 2022 The Authors.)
- Published
- 2022
- Full Text
- View/download PDF
46. A Randomized Controlled Clinical Trial in Healthy Older Adults to Determine Efficacy of Glycine and N-Acetylcysteine Supplementation on Glutathione Redox Status and Oxidative Damage.
- Author
-
Lizzo G, Migliavacca E, Lamers D, Frézal A, Corthesy J, Vinyes-Parès G, Bosco N, Karagounis LG, Hövelmann U, Heise T, von Eynatten M, and Gut P
- Abstract
Glycine and cysteine are non-essential amino acids that are required to generate glutathione, an intracellular tripeptide that neutralizes reactive oxygen species and prevents tissue damage. During aging glutathione demand is thought to increase, but whether additional dietary intake of glycine and cysteine contributes towards the generation of glutathione in healthy older adults is not well understood. We investigated supplementation with glycine and n-acetylcysteine (GlyNAC) at three different daily doses for 2 weeks (low dose: 2.4 g, medium dose: 4.8 g, or high dose: 7.2 g/day, 1:1 ratio) in a randomized, controlled clinical trial in 114 healthy volunteers. Despite representing a cohort of healthy older adults (age mean = 65 years), we found significantly higher baseline levels of markers of oxidative stress, including that of malondialdehyde (MDA, 0.158 vs. 0.136 µmol/L, p < 0.0001), total cysteine (Cysteine-T, 314.8 vs. 276 µM, p < 0.0001), oxidized glutathione (GSSG, 174.5 vs. 132.3 µmol/L, p < 0.0001), and a lower ratio of reduced to oxidized glutathione (GSH-F:GSSG) (11.78 vs. 15.26, p = 0.0018) compared to a young reference group (age mean = 31.7 years, n = 20). GlyNAC supplementation was safe and well tolerated by the subjects, but did not increase levels of GSH-F:GSSG (end of study, placebo = 12.49 vs. 7.2 g = 12.65, p -value = 0.739) or that of total glutathione (GSH-T) (end of study, placebo = 903.5 vs. 7.2 g = 959.6 mg/L, p -value = 0.278), the primary endpoint of the study. Post-hoc analyses revealed that a subset of subjects characterized by high oxidative stress (above the median for MDA) and low baseline GSH-T status (below the median), who received the medium and high doses of GlyNAC, presented increased glutathione generation (end of study, placebo = 819.7 vs. 4.8g/7.2 g = 905.4 mg/L, p -value = 0.016). In summary GlyNAC supplementation is safe, well tolerated, and may increase glutathione levels in older adults with high glutathione demand. Clinical Trial Registration: https://clinicaltrials.gov/ct2/show/NCT05041179, NCT05041179., Competing Interests: GL, EM, AF, JC, NB, and PG are employees of Nestlé Institute of Health Sciences, Nestlé Research, Societé des Produits de Nestlé. GV-P, LK, and ME are employees of Nestlé Health Sciences, a subsidiary of Nestlé. Nestlé Health Sciences holds patents and licenses to patents and markets products for the use of glycine and n-acetylcysteine in conditions related to impaired mitochondrial functions. DL and UH are employees and TH is an employee and shareholder of Profil Institute for Metabolic Research GmbH, which has received research funding from Nestlé Health Sciences., (Copyright © 2022 Lizzo, Migliavacca, Lamers, Frézal, Corthesy, Vinyes-Parès, Bosco, Karagounis, Hövelmann, Heise, von Eynatten and Gut.)
- Published
- 2022
- Full Text
- View/download PDF
47. In vivo transcriptomic profiling using cell encapsulation identifies effector pathways of systemic aging.
- Author
-
Mashinchian O, Hong X, Michaud J, Migliavacca E, Lefebvre G, Boss C, De Franceschi F, Le Moal E, Collerette-Tremblay J, Isern J, Metairon S, Raymond F, Descombes P, Bouche N, Muñoz-Cánoves P, Feige JN, and Bentzinger CF
- Subjects
- Aging, Animals, Cell Differentiation, Cell Encapsulation, Mice, Muscle, Skeletal metabolism, Transcriptome, Satellite Cells, Skeletal Muscle, Stem Cells metabolism
- Abstract
Sustained exposure to a young systemic environment rejuvenates aged organisms and promotes cellular function. However, due to the intrinsic complexity of tissues it remains challenging to pinpoint niche-independent effects of circulating factors on specific cell populations. Here, we describe a method for the encapsulation of human and mouse skeletal muscle progenitors in diffusible polyethersulfone hollow fiber capsules that can be used to profile systemic aging in vivo independent of heterogeneous short-range tissue interactions. We observed that circulating long-range signaling factors in the old systemic environment lead to an activation of Myc and E2F transcription factors, induce senescence, and suppress myogenic differentiation. Importantly, in vitro profiling using young and old serum in 2D culture does not capture all pathways deregulated in encapsulated cells in aged mice. Thus, in vivo transcriptomic profiling using cell encapsulation allows for the characterization of effector pathways of systemic aging with unparalleled accuracy., Competing Interests: OM, XH, JM, GL, CB, FD, SM, FR, PD, NB, JF, CB Presently or previously employed by the Société des Produits Nestlé S.A., Switzerland, EM Presently or previously employed by the Société des Produits Nestlé; S.A., Switzerland, EL, JC, JI, PM No competing interests declared, (© 2022, Mashinchian et al.)
- Published
- 2022
- Full Text
- View/download PDF
48. Epigenome-wide association study of sarcopenia: findings from the Hertfordshire Sarcopenia Study (HSS).
- Author
-
Antoun E, Garratt ES, Taddei A, Burton MA, Barton SJ, Titcombe P, Westbury LD, Baczynska A, Migliavacca E, Feige JN, Sydall HE, Dennison E, Dodds R, Roberts HC, Richardson P, Sayer AA, Shaw S, Cooper C, Holbrook JD, Patel HP, Godfrey KM, and Lillycrop KA
- Subjects
- Aged, DNA Methylation, Epigenesis, Genetic, Hand Strength physiology, Humans, Male, Epigenome, Sarcopenia genetics
- Abstract
Background: Sarcopenia is the age-related loss of muscle mass, strength, and function. Epigenetic processes such as DNA methylation, which integrate both genetic and environmental exposures, have been suggested to contribute to the development of sarcopenia. This study aimed to determine whether differences in the muscle methylome are associated with sarcopenia and its component measures: grip strength, appendicular lean mass index (ALMi), and gait speed., Methods: Using the Infinium Human MethylationEPIC BeadChip, we measured DNA methylation in vastus lateralis muscle biopsies of 83 male participants (12 with sarcopenia) with a mean (standard deviation) age of 75.7 (3.6) years from the Hertfordshire Sarcopenia Study (HSS) and Hertfordshire Sarcopenia Study extension (HSSe) and examined associations with sarcopenia and its components. Pathway, histone mark, and transcription factor enrichment of the differentially methylated CpGs (dmCpGs) were determined, and sodium bisulfite pyrosequencing was used to validate the sarcopenia-associated dmCpGs. Human primary myoblasts (n = 6) isolated from vastus lateralis muscle biopsies from male individuals from HSSe were treated with the EZH2 inhibitor GSK343 to assess how perturbations in epigenetic processes may impact myoblast differentiation and fusion, measured by PAX7 and MYHC immunocytochemistry, and mitochondrial bioenergetics determined using the Seahorse XF96., Results: Sarcopenia was associated with differential methylation at 176 dmCpGs (false discovery rate ≤ 0.05) and 141 differentially methylated regions (Stouffer ≤ 0.05). The sarcopenia-associated dmCpGs were enriched in genes associated with myotube fusion (P = 1.40E-03), oxidative phosphorylation (P = 2.78E-02), and voltage-gated calcium channels (P = 1.59E-04). ALMi was associated with 71 dmCpGs, grip strength with 49 dmCpGs, and gait speed with 23 dmCpGs (false discovery rate ≤ 0.05). There was significant overlap between the dmCpGs associated with sarcopenia and ALMi (P = 3.4E-35), sarcopenia and gait speed (P = 4.78E-03), and sarcopenia and grip strength (P = 7.55E-06). There was also an over-representation of the sarcopenia, ALMi, grip strength, and gait speed-associated dmCpGs with sites of H3K27 trimethylation (all P ≤ 0.05) and amongst EZH2 target genes (all P ≤ 0.05). Furthermore, treatment of human primary myoblasts with the EZH2 inhibitor GSK343 inhibitor led to an increase in PAX7 expression (P ≤ 0.05), decreased myotube fusion (P = 0.043), and an increase in ATP production (P = 0.008), with alterations in the DNA methylation of genes involved in oxidative phosphorylation and myogenesis., Conclusions: These findings show that differences in the muscle methylome are associated with sarcopenia and individual measures of muscle mass, strength, and function in older individuals. This suggests that changes in the epigenetic regulation of genes may contribute to impaired muscle function in later life., (© 2021 The Authors. Journal of Cachexia, Sarcopenia and Muscle published by John Wiley & Sons Ltd on behalf of Society on Sarcopenia, Cachexia and Wasting Disorders.)
- Published
- 2022
- Full Text
- View/download PDF
49. Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia.
- Author
-
Börsch A, Ham DJ, Mittal N, Tintignac LA, Migliavacca E, Feige JN, Rüegg MA, and Zavolan M
- Subjects
- Age Factors, Aging genetics, Aging metabolism, Aging pathology, Animals, Body Composition, Disease Models, Animal, Disease Progression, Gene Expression Regulation, Humans, Male, Mice, Inbred C57BL, Muscle, Skeletal pathology, Muscle, Skeletal physiopathology, Phenotype, Rats, Sarcopenia pathology, Sarcopenia physiopathology, Signal Transduction, Species Specificity, Mice, Muscle, Skeletal metabolism, Sarcopenia genetics, Sarcopenia metabolism, Transcriptome
- Abstract
Sarcopenia, the age-related loss of skeletal muscle mass and function, affects 5-13% of individuals aged over 60 years. While rodents are widely-used model organisms, which aspects of sarcopenia are recapitulated in different animal models is unknown. Here we generated a time series of phenotypic measurements and RNA sequencing data in mouse gastrocnemius muscle and analyzed them alongside analogous data from rats and humans. We found that rodents recapitulate mitochondrial changes observed in human sarcopenia, while inflammatory responses are conserved at pathway but not gene level. Perturbations in the extracellular matrix are shared by rats, while mice recapitulate changes in RNA processing and autophagy. We inferred transcription regulators of early and late transcriptome changes, which could be targeted therapeutically. Our study demonstrates that phenotypic measurements, such as muscle mass, are better indicators of muscle health than chronological age and should be considered when analyzing aging-related molecular data.
- Published
- 2021
- Full Text
- View/download PDF
50. Mitochondrial oxidative capacity and NAD + biosynthesis are reduced in human sarcopenia across ethnicities.
- Author
-
Migliavacca E, Tay SKH, Patel HP, Sonntag T, Civiletto G, McFarlane C, Forrester T, Barton SJ, Leow MK, Antoun E, Charpagne A, Seng Chong Y, Descombes P, Feng L, Francis-Emmanuel P, Garratt ES, Giner MP, Green CO, Karaz S, Kothandaraman N, Marquis J, Metairon S, Moco S, Nelson G, Ngo S, Pleasants T, Raymond F, Sayer AA, Ming Sim C, Slater-Jefferies J, Syddall HE, Fang Tan P, Titcombe P, Vaz C, Westbury LD, Wong G, Yonghui W, Cooper C, Sheppard A, Godfrey KM, Lillycrop KA, Karnani N, and Feige JN
- Subjects
- Aged, Aged, 80 and over, Biopsy, Case-Control Studies, Energy Metabolism physiology, Humans, Jamaica, Male, Middle Aged, Mitochondria metabolism, Muscle, Skeletal cytology, Muscle, Skeletal metabolism, Oxidation-Reduction, Oxidative Phosphorylation, Oxidative Stress physiology, Proteostasis, Sarcopenia ethnology, Singapore, United Kingdom, Aging physiology, Mitochondria pathology, Muscle, Skeletal pathology, NAD biosynthesis, Sarcopenia pathology
- Abstract
The causes of impaired skeletal muscle mass and strength during aging are well-studied in healthy populations. Less is known on pathological age-related muscle wasting and weakness termed sarcopenia, which directly impacts physical autonomy and survival. Here, we compare genome-wide transcriptional changes of sarcopenia versus age-matched controls in muscle biopsies from 119 older men from Singapore, Hertfordshire UK and Jamaica. Individuals with sarcopenia reproducibly demonstrate a prominent transcriptional signature of mitochondrial bioenergetic dysfunction in skeletal muscle, with low PGC-1α/ERRα signalling, and downregulation of oxidative phosphorylation and mitochondrial proteostasis genes. These changes translate functionally into fewer mitochondria, reduced mitochondrial respiratory complex expression and activity, and low NAD
+ levels through perturbed NAD+ biosynthesis and salvage in sarcopenic muscle. We provide an integrated molecular profile of human sarcopenia across ethnicities, demonstrating a fundamental role of altered mitochondrial metabolism in the pathological loss of skeletal muscle mass and function in older people.- Published
- 2019
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.