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1. A mitochondria-specific mutational signature of aging: increased rate of A>G substitutions on a heavy chain

Author

Mikhaylova, A. G., primary, Mikhailova, A. A., additional, Ushakova, K., additional, Tretiakov, E.O., additional, Iliushchenko, D., additional, Shamansky, V., additional, Iurchenko, A., additional, Zazhytska, M., additional, Kozenkova, E., additional, Zdobnov, E., additional, Makeev, V., additional, Yurov, V., additional, Tanaka, M., additional, Gostimskaya, I., additional, Fleischmann, Z., additional, Annis, S., additional, Franco, M., additional, Wasko, K., additional, Kunz, W.S, additional, Knorre, D.A., additional, Mazunin, I., additional, Nikolaev, S., additional, Fellay, J., additional, Reymond, A., additional, Khrapko, K., additional, Gunbin, K., additional, and Popadin, K., additional

Published
2021
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4. Mitochondrial mutational spectrum provides an universal marker of cellular and organismal longevity

Author

Mikhaylova, A. G., Mikhailova, A. A., Ushakova, K., Tretiakov, E., Yurchenko, A., Zazhytska, M., Knorre, D.A., Zdobnov, E., Fleischmann, Z., Annis, S., Franco, M., Wasko, K., Kunz, W.S., Mazunin, I., Nikolaev, S., Reymond, A., Khrapko, K., Gunbin, K., and Popadin, K.

Abstract

It has been shown recently that mitochondrial (mtDNA) somatic variants are numerous enough to trace cellular lineages in our body. Here we extend this statement and demonstrate that mtDNA variants can be interpreted not only as neutral markers of cell divisions but the relative frequency of different mtDNA substitutions (i.e. mtDNA mutational spectrum) can inform us about important biological properties such as cell longevity. Analysing 7611 somatic mtDNA mutations from 37 types of human cancers and more than 2000 somatic mtDNA mutations from 25 healthy human tissues we observed that mtDNA mutational spectrum is associated with cell turnover rate: the ratio of T>C to G>A is increasing with cell longevity. To extend this logic we considered that, if universal, the discovered mutation bias may drive the differences in mtDNA mutational spectrum between mammalian species with short-(‘mice’) and long-(‘elephants’) lived oocytes. Based on presumably neutral polymorphisms in MT-CYB we reconstructed mutational spectra for 424 mammalian species and obtained that the fraction of T>C positively correlated with the species-specific generation length, which is a good proxy for oocyte longevity. Next, comparing complete mitochondrial genomes of 650 mammalian species we confirmed that exactly the same process shapes the nucleotide content of the most neutral sites in the whole mitochondrial genomes of short-(high T, low C) versus long-(low T, high C) lived mammals. Altogether analysing mtDNA mutations in time interval from dozens of years (somatic mutations) through the hundreds of thousands of years (within species polymorphisms) to millions of years (between species substitutions) we demonstrated that T>C/G>A positively correlates with cellular and organismal longevity. We hypothesize that the discovered mtDNA signature presents a chemical damage which is associated with the level of oxidative metabolism which, in turn, correlates with cellular and organismal longevity. The described properties of mtDNA mutational spectrum shed light on mtDNA replication, mtDNA evolution of mammals and can be used as a marker of cell longevity in single-cell analyses of heterogeneous samples.

Published
2019
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5. 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

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., 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

7. Chromatin three-dimensional interactions mediate genetic effects on gene expression

Author

Delaneau, O., primary, Zazhytska, M., additional, Borel, C., additional, Giannuzzi, G., additional, Rey, G., additional, Howald, C., additional, Kumar, S., additional, Ongen, H., additional, Popadin, K., additional, Marbach, D., additional, Ambrosini, G., additional, Bielser, D., additional, Hacker, D., additional, Romano, L., additional, Ribaux, P., additional, Wiederkehr, M., additional, Falconnet, E., additional, Bucher, P., additional, Bergmann, S., additional, Antonarakis, S. E., additional, Reymond, A., additional, and Dermitzakis, E. T., additional

Published
2019
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8. Mammalian mitochondrial mutational spectrum as a hallmark of cellular and organismal aging

Author

Mikhaylova, A. G., primary, Mikhailova, A. A., additional, Ushakova, K., additional, Tretiakov, E.O., additional, Shamansky, V., additional, Yurchenko, A., additional, Zazhytska, M., additional, Zdobnov, E., additional, Makeev, V., additional, Yurov, V., additional, Tanaka, M., additional, Gostimskaya, I., additional, Fleischmann, Z., additional, Annis, S., additional, Franco, M., additional, Wasko, K., additional, Kunz, W.S, additional, Knorre, D.A., additional, Mazunin, I., additional, Nikolaev, S., additional, Fellay, J., additional, Reymond, A., additional, Khrapko, K., additional, Gunbin, K., additional, and Popadin, K., additional

Published
2019
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9. 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

10. 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

11. Intra- and inter-chromosomal chromatin interactions mediate genetic effects on regulatory networks

Author

Delaneau, O., primary, Zazhytska, M., additional, Borel, C., additional, Howald, C., additional, Kumar, S., additional, Ongen, H., additional, Popadin, K., additional, Marbach, D., additional, Ambrosini, G., additional, Bielser, D., additional, Hacker, D., additional, Romano-Palumbo, L., additional, Ribaux, P., additional, Wiederkehr, M., additional, Falconnet, E., additional, Bucher, P., additional, Bergmann, S., additional, Antonarakis, S. E., additional, Reymond, A., additional, and Dermitzakis, E. T., additional

Published
2017
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12. 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

14. 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
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16. Chromatin 3D interactions mediate genetic effects on gene expression

Author

Delaneau, O., Zazhytska, M., Borel, C., Giannuzzi, G., Rey, G., Howald, C., Ongen, H., Popadin, K., Marbach, D., Ambrosini, G., Bielser, D., Hacker, D., Romano-Palumbo, L., Ribaux, P., Falconnet, E., Bucher, P., Bergmann, S., Antonarakis, S., Reymond, A., and Dermitzakis, E.

17. 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.

19. Noninvasive Diagnostic Method to Objectively Measure Olfaction and Diagnose Smell Disorders by a Molecularly Targeted Fluorescence Imaging Agent.

Author

Adilbay D, Gonzales J, Zazhytska M, Demetrio de Souza Franca P, Roberts S, Viray TD, Artschwager R, Patel S, Kodra A, Overdevest JB, Chow CY, King GF, Jain SK, Ordonez AA, Carroll LS, Lomvardas S, Reiner T, and Pillarsetty N

Subjects
Animals, Humans, Optical Imaging methods, Smell, Fluorescent Dyes chemistry, Mice, COVID-19 diagnostic imaging, Male, Olfaction Disorders diagnostic imaging
Abstract

Despite the recent advances in understanding the mechanisms of olfaction, no tools are currently available to noninvasively identify loss of smell. Because of the substantial increase in patients presenting with coronavirus disease 2019-related loss of smell, the pandemic has highlighted the urgent need to develop quantitative methods. Methods: Our group investigated the use of a novel fluorescent probe named Tsp1a-IR800 P as a tool to diagnose loss of smell. Tsp1a-IR800 P targets sodium channel 1.7, which plays a critical role in olfaction by aiding the signal propagation to the olfactory bulb. Results: Intuitively, we have identified that conditions leading to loss of smell, including chronic inflammation and coronavirus disease 2019, correlate with the downregulation of sodium channel 1.7 expression in the olfactory epithelium, both at the transcript and at the protein levels. We demonstrated that lower Tsp1a-IR800 P fluorescence emissions significantly correlate with loss of smell in live animals-thus representing a potential tool for its semiquantitative assessment. Currently available methods rely on delayed subjective behavioral studies. Conclusion: This method could aid in significantly improving preclinical and clinical studies by providing a way to objectively diagnose loss of smell and therefore aid the development of therapeutic interventions., (© 2024 by the Society of Nuclear Medicine and Molecular Imaging.)

Published
2024
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20. Non-invasive diagnostic method to objectively measure olfaction and diagnose smell disorders by molecularly targeted fluorescent imaging agent.

Author

Adilbay D, Gonzales J, Zazhytska M, Demetrio de Souza Franca P, Roberts S, Viray T, Artschwager R, Patel S, Kodra A, Overdevest JB, Chow CY, King GF, Jain SK, Ordonez AA, Carroll LS, Reiner T, and Pillarsetty N

Abstract

The sense of smell (olfaction) is one of the most important senses for animals including humans. Despite significant advances in the understanding mechanism of olfaction, currently, there are no objective non-invasive methods that can identify loss of smell. Covid-19-related loss of smell has highlighted the need to develop methods that can identify loss of olfaction. Voltage-gated sodium channel 1.7 (Na V 1.7) plays a critical role in olfaction by aiding the signal propagation to the olfactory bulb. We have identified several conditions such as chronic inflammation and viral infections such as Covid-19 that lead to loss of smell correlate with downregulation of Na V 1.7 expression at transcript and protein levels in the olfactory epithelium. Leveraging this knowledge, we have developed a novel fluorescent probe Tsp1a-IR800 that targets Na V 1.7. Using fluorescence imaging we can objectively measure the loss of sense of smell in live animals non-invasively. We also demonstrate that our non-invasive method is semiquantitative because the loss of fluorescence intensity correlates with the level of smell loss. Our results indicate, that our probe Tsp1a-IR800, can objectively diagnose anosmia in animal and human subjects using infrared fluorescence. We believe this method to non-invasively diagnose loss of smell objectively is a significant advancement in relation to current methods that rely on highly subjective behavioral studies and can aid in studying olfaction loss and the development of therapeutic interventions., Competing Interests: Disclosure of Potential Conflicts of Interest S.P. and T.R. are shareholders of Summit Biomedical Imaging, T.R. is now an executive of and shareholder in Novartis AG. J.G., P.D.S.F., G.K. and T.R. are co-inventors on a Tsp1a-related patent application. All other authors have no conflicts to declare.

Published
2022
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21. SARS-CoV-2 infection in hamsters and humans results in lasting and unique systemic perturbations after recovery.

Author

Frere JJ, Serafini RA, Pryce KD, Zazhytska M, Oishi K, Golynker I, Panis M, Zimering J, Horiuchi S, Hoagland DA, Møller R, Ruiz A, Kodra A, Overdevest JB, Canoll PD, Borczuk AC, Chandar V, Bram Y, Schwartz R, Lomvardas S, Zachariou V, and tenOever BR

Subjects
Animals, Cricetinae, Humans, Interferons, Mesocricetus, SARS-CoV-2, Post-Acute COVID-19 Syndrome, COVID-19 complications
Abstract

The host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection can result in prolonged pathologies collectively referred to as post-acute sequalae of COVID-19 (PASC) or long COVID. To better understand the mechanism underlying long COVID biology, we compared the short- and long-term systemic responses in the golden hamster after either SARS-CoV-2 or influenza A virus (IAV) infection. Results demonstrated that SARS-CoV-2 exceeded IAV in its capacity to cause permanent injury to the lung and kidney and uniquely affected the olfactory bulb (OB) and olfactory epithelium (OE). Despite a lack of detectable infectious virus, the OB and OE demonstrated myeloid and T cell activation, proinflammatory cytokine production, and an interferon response that correlated with behavioral changes extending a month after viral clearance. These sustained transcriptional changes could also be corroborated from tissue isolated from individuals who recovered from COVID-19. These data highlight a molecular mechanism for persistent COVID-19 symptomology and provide a small animal model to explore future therapeutics.

Published
2022
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22. Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia.

Author

Zazhytska M, Kodra A, Hoagland DA, Frere J, Fullard JF, Shayya H, McArthur NG, Moeller R, Uhl S, Omer AD, Gottesman ME, Firestein S, Gong Q, Canoll PD, Goldman JE, Roussos P, tenOever BR, Jonathan B Overdevest, and Lomvardas S

Subjects
Animals, Cricetinae, Down-Regulation, Humans, Receptors, Odorant, SARS-CoV-2, Smell, Anosmia, COVID-19
Abstract

SARS-CoV-2 infects less than 1% of cells in the human body, yet it can cause severe damage in a variety of organs. Thus, deciphering the non-cell-autonomous effects of SARS-CoV-2 infection is imperative for understanding the cellular and molecular disruption it elicits. Neurological and cognitive defects are among the least understood symptoms of COVID-19 patients, with olfactory dysfunction being their most common sensory deficit. Here, we show that both in humans and hamsters, SARS-CoV-2 infection causes widespread downregulation of olfactory receptors (ORs) and of their signaling components. This non-cell-autonomous effect is preceded by a dramatic reorganization of the neuronal nuclear architecture, which results in dissipation of genomic compartments harboring OR genes. Our data provide a potential mechanism by which SARS-CoV-2 infection alters the cellular morphology and the transcriptome of cells it cannot infect, offering insight to its systemic effects in olfaction and beyond., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Published
2022
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23. Disruption of nuclear architecture as a cause of COVID-19 induced anosmia.

Author

Zazhytska M, Kodra A, Hoagland DA, Fullard JF, Shayya H, Omer A, Firestein S, Gong Q, Canoll PD, Goldman JE, Roussos P, tenOever BR, Overdevest JB, and Lomvardas S

Abstract

Olfaction relies on a coordinated partnership between odorant flow and neuronal communication. Disruption in our ability to detect odors, or anosmia, has emerged as a hallmark symptom of infection with SARS-CoV-2, yet the mechanism behind this abrupt sensory deficit remains elusive. Here, using molecular evaluation of human olfactory epithelium (OE) from subjects succumbing to COVID-19 and a hamster model of SARS-CoV-2 infection, we discovered widespread downregulation of olfactory receptors (ORs) as well as key components of their signaling pathway. OR downregulation likely represents a non-cell autonomous effect, since SARS-CoV-2 detection in OSNs is extremely rare both in human and hamster OEs. A likely explanation for the reduction of OR transcription is the striking reorganization of nuclear architecture observed in the OSN lineage, which disrupts multi-chromosomal compartments regulating OR expression in humans and hamsters. Our experiments uncover a novel molecular mechanism by which a virus with a very selective tropism can elicit persistent transcriptional changes in cells that evade it, contributing to the severity of COVID-19.

Published
2021
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24. DNA loop domain organization as revealed by single-cell gel electrophoresis.

Author

Afanasieva K, Chopei M, Zazhytska M, Vikhreva M, and Sivolob A

Subjects
Adult, Chloroquine pharmacology, Female, Humans, Intercalating Agents pharmacology, Kinetics, Male, Normal Distribution, Comet Assay methods, DNA chemistry, Nucleic Acid Conformation
Abstract

At higher order levels chromatin is organized into loops. This looping, which plays an important role in transcription regulation and other processes, remains poorly understood. We investigated the kinetics of DNA loop migration during single cell gel electrophoresis (the comet assay). The migration of a part of the loops was shown to be reversible after switching off electrophoresis and to be sensitive to intercalation-induced changes in supercoiling. Another group of the loops migrates rapidly, the rate being insensitive to the supercoiling level. The largest part of the loops cannot migrate at all, presumably because of their large size. The loop ends can be detached in the presence of high concentrations of intercalators or protein denaturants, thus increasing the fraction of DNA that cannot migrate in the gel. The distribution of the loop length up to 100kilobases appears to be consistent with the fractal globule organization., (© 2013.)

Published
2013
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25. Kinetics of comet formation in single-cell gel electrophoresis: loops and fragments.

Author

Afanasieva K, Zazhytska M, and Sivolob A

Subjects
Dose-Response Relationship, Drug, Dose-Response Relationship, Radiation, Humans, Kinetics, Chromatin drug effects, Chromatin metabolism, Chromatin radiation effects, Comet Assay, DNA drug effects, DNA metabolism, DNA radiation effects, DNA Breaks, Single-Stranded drug effects, DNA Breaks, Single-Stranded radiation effects, DNA Fragmentation drug effects, DNA Fragmentation radiation effects, Ethidium pharmacology, Lymphocytes drug effects, Lymphocytes metabolism, Lymphocytes radiation effects, X-Rays
Abstract

We investigated the mechanisms of DNA exit during single-cell gel electrophoresis (the comet assay) by measuring the kinetics of the comet tail formation. In the neutral comet assay, the rate of DNA exit was found to be dependent on the topological state of DNA, which was influenced by either ethidium bromide or a low radiation dose. The results clearly show that the comet tail is formed by extended DNA loops: the loop extension, being reversible when the DNA torsional constraint remains in the loops, is favored when the constraint is relaxed. The kinetics of the comet formation in the case of a high radiation dose points out that accumulation of the single-strand breaks causes DNA fragmentation. In contrast to the neutral comet assay, the alkaline comet assay is not related to the chromatin loops. Our results imply that the alkaline treatment induces detachment of the loops from the nuclear matrix, and the comet tail is formed by ssDNA fragments, the ends of which are pulled out from the comet head by electric force. We suggest that the kinetic approach can be considered as an important improvement of the comet assay.

Published
2010
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