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1. Impact of methodological choices in comparative effectiveness studies: application in natalizumab versus fingolimod comparison among patients with multiple sclerosis

Author

Lefort, M, Sharmin, S, Andersen, JB, Vukusic, S, Casey, R, Debouverie, M, Edan, G, Ciron, J, Ruet, A, De Seze, J, Maillart, E, Zephir, H, Labauge, P, Defer, G, Lebrun-Frenay, C, Moreau, T, Berger, E, Clavelou, P, Pelletier, J, Stankoff, B, Gout, O, Thouvenot, E, Heinzlef, O, Al-Khedr, A, Bourre, B, Casez, O, Cabre, P, Montcuquet, A, Wahab, A, Camdessanche, JP, Maurousset, A, Ben Nasr, H, Hankiewicz, K, Pottier, C, Maubeuge, N, Nifle, C, Laplaud, DA, Horakova, D, Dimitri-Boulos, D, Havrdova, EK, Alroughani, R, Izquierdo, G, Eichau, S, Ozakbas, S, Patti, F, Onofrj, M, Lugaresi, A, Terzi, M, Grammond, P, Grand'Maison, F, Yamout, B, Prat, A, Girard, M, Duquette, P, Boz, C, Trojano, M, McCombe, P, Slee, M, Lechner-Scott, J, Turkoglu, R, Sola, P, Ferraro, D, Granella, F, Shaygannejad, V, Prevost, J, Maimone, D, Skibina, O, Buzzard, K, Van der Walt, A, Karabudak, R, Van Wijmeersch, B, Csepany, T, Spitaleri, D, Vucic, S, Koch-Henriksen, N, Sellebjerg, F, Soerensen, PS, Christensen, CCH, Rasmussen, P, Jensen, MB, Frederiksen, JL, Bramow, S, Mathiesen, HK, Schreiber, K, Butzkueven, H, Magyari, M, Kalincik, T, Leray, E, Lefort, M, Sharmin, S, Andersen, JB, Vukusic, S, Casey, R, Debouverie, M, Edan, G, Ciron, J, Ruet, A, De Seze, J, Maillart, E, Zephir, H, Labauge, P, Defer, G, Lebrun-Frenay, C, Moreau, T, Berger, E, Clavelou, P, Pelletier, J, Stankoff, B, Gout, O, Thouvenot, E, Heinzlef, O, Al-Khedr, A, Bourre, B, Casez, O, Cabre, P, Montcuquet, A, Wahab, A, Camdessanche, JP, Maurousset, A, Ben Nasr, H, Hankiewicz, K, Pottier, C, Maubeuge, N, Nifle, C, Laplaud, DA, Horakova, D, Dimitri-Boulos, D, Havrdova, EK, Alroughani, R, Izquierdo, G, Eichau, S, Ozakbas, S, Patti, F, Onofrj, M, Lugaresi, A, Terzi, M, Grammond, P, Grand'Maison, F, Yamout, B, Prat, A, Girard, M, Duquette, P, Boz, C, Trojano, M, McCombe, P, Slee, M, Lechner-Scott, J, Turkoglu, R, Sola, P, Ferraro, D, Granella, F, Shaygannejad, V, Prevost, J, Maimone, D, Skibina, O, Buzzard, K, Van der Walt, A, Karabudak, R, Van Wijmeersch, B, Csepany, T, Spitaleri, D, Vucic, S, Koch-Henriksen, N, Sellebjerg, F, Soerensen, PS, Christensen, CCH, Rasmussen, P, Jensen, MB, Frederiksen, JL, Bramow, S, Mathiesen, HK, Schreiber, K, Butzkueven, H, Magyari, M, Kalincik, T, and Leray, E

Abstract

BACKGROUND: Natalizumab and fingolimod are used as high-efficacy treatments in relapsing-remitting multiple sclerosis. Several observational studies comparing these two drugs have shown variable results, using different methods to control treatment indication bias and manage censoring. The objective of this empirical study was to elucidate the impact of methods of causal inference on the results of comparative effectiveness studies. METHODS: Data from three observational multiple sclerosis registries (MSBase, the Danish MS Registry and French OFSEP registry) were combined. Four clinical outcomes were studied. Propensity scores were used to match or weigh the compared groups, allowing for estimating average treatment effect for treated or average treatment effect for the entire population. Analyses were conducted both in intention-to-treat and per-protocol frameworks. The impact of the positivity assumption was also assessed. RESULTS: Overall, 5,148 relapsing-remitting multiple sclerosis patients were included. In this well-powered sample, the 95% confidence intervals of the estimates overlapped widely. Propensity scores weighting and propensity scores matching procedures led to consistent results. Some differences were observed between average treatment effect for the entire population and average treatment effect for treated estimates. Intention-to-treat analyses were more conservative than per-protocol analyses. The most pronounced irregularities in outcomes and propensity scores were introduced by violation of the positivity assumption. CONCLUSIONS: This applied study elucidates the influence of methodological decisions on the results of comparative effectiveness studies of treatments for multiple sclerosis. According to our results, there are no material differences between conclusions obtained with propensity scores matching or propensity scores weighting given that a study is sufficiently powered, models are correctly specified and positivity assumption is ful

Published
2022

2. Impact of methodological choices in comparative effectiveness studies:application in natalizumab versus fingolimod comparison among patients with multiple sclerosis

Author

Lefort, M., Sharmin, S., Andersen, J. B., Vukusic, S., Casey, R., Debouverie, M., Edan, G., Ciron, J., Ruet, A., De Sèze, J., Maillart, E., Zephir, H., Labauge, P., Defer, G., Lebrun-Frenay, C., Moreau, T., Berger, E., Clavelou, P., Pelletier, J., Stankoff, B., Gout, O., Thouvenot, E., Heinzlef, O., Al-Khedr, A., Bourre, B., Casez, O., Cabre, P., Montcuquet, A., Wahab, A., Camdessanché, J. P., Maurousset, A., Ben Nasr, H., Hankiewicz, K., Pottier, C., Maubeuge, N., Dimitri-Boulos, D., Nifle, C., Laplaud, D. A., Horakova, D., Havrdova, E. K., Alroughani, R., Izquierdo, G., Eichau, S., Ozakbas, S., Patti, F., Onofrj, M., Lugaresi, A., Terzi, M., Grammond, P., Grand’Maison, F., Yamout, B., Prat, A., Girard, M., Duquette, P., Boz, C., Trojano, M., McCombe, P., Slee, M., Lechner-Scott, J., Turkoglu, R., Sola, P., Ferraro, D., Granella, F., Shaygannejad, V., Prevost, J., Maimone, D., Skibina, O., Buzzard, K., Van der Walt, A., Karabudak, R., Van Wijmeersch, B., Csepany, T., Spitaleri, D., Vucic, S., Koch-Henriksen, N., Sellebjerg, F., Soerensen, P. S., Hilt Christensen, C. C., Rasmussen, P. V., Jensen, M. B., Frederiksen, J. L., Bramow, S., Mathiesen, H. K., Schreiber, K. I., Butzkueven, H., Magyari, M., Kalincik, T., Leray, E., Lefort, M., Sharmin, S., Andersen, J. B., Vukusic, S., Casey, R., Debouverie, M., Edan, G., Ciron, J., Ruet, A., De Sèze, J., Maillart, E., Zephir, H., Labauge, P., Defer, G., Lebrun-Frenay, C., Moreau, T., Berger, E., Clavelou, P., Pelletier, J., Stankoff, B., Gout, O., Thouvenot, E., Heinzlef, O., Al-Khedr, A., Bourre, B., Casez, O., Cabre, P., Montcuquet, A., Wahab, A., Camdessanché, J. P., Maurousset, A., Ben Nasr, H., Hankiewicz, K., Pottier, C., Maubeuge, N., Dimitri-Boulos, D., Nifle, C., Laplaud, D. A., Horakova, D., Havrdova, E. K., Alroughani, R., Izquierdo, G., Eichau, S., Ozakbas, S., Patti, F., Onofrj, M., Lugaresi, A., Terzi, M., Grammond, P., Grand’Maison, F., Yamout, B., Prat, A., Girard, M., Duquette, P., Boz, C., Trojano, M., McCombe, P., Slee, M., Lechner-Scott, J., Turkoglu, R., Sola, P., Ferraro, D., Granella, F., Shaygannejad, V., Prevost, J., Maimone, D., Skibina, O., Buzzard, K., Van der Walt, A., Karabudak, R., Van Wijmeersch, B., Csepany, T., Spitaleri, D., Vucic, S., Koch-Henriksen, N., Sellebjerg, F., Soerensen, P. S., Hilt Christensen, C. C., Rasmussen, P. V., Jensen, M. B., Frederiksen, J. L., Bramow, S., Mathiesen, H. K., Schreiber, K. I., Butzkueven, H., Magyari, M., Kalincik, T., and Leray, E.

Abstract

Background: Natalizumab and fingolimod are used as high-efficacy treatments in relapsing–remitting multiple sclerosis. Several observational studies comparing these two drugs have shown variable results, using different methods to control treatment indication bias and manage censoring. The objective of this empirical study was to elucidate the impact of methods of causal inference on the results of comparative effectiveness studies. Methods: Data from three observational multiple sclerosis registries (MSBase, the Danish MS Registry and French OFSEP registry) were combined. Four clinical outcomes were studied. Propensity scores were used to match or weigh the compared groups, allowing for estimating average treatment effect for treated or average treatment effect for the entire population. Analyses were conducted both in intention-to-treat and per-protocol frameworks. The impact of the positivity assumption was also assessed. Results: Overall, 5,148 relapsing–remitting multiple sclerosis patients were included. In this well-powered sample, the 95% confidence intervals of the estimates overlapped widely. Propensity scores weighting and propensity scores matching procedures led to consistent results. Some differences were observed between average treatment effect for the entire population and average treatment effect for treated estimates. Intention-to-treat analyses were more conservative than per-protocol analyses. The most pronounced irregularities in outcomes and propensity scores were introduced by violation of the positivity assumption. Conclusions: This applied study elucidates the influence of methodological decisions on the results of comparative effectiveness studies of treatments for multiple sclerosis. According to our results, there are no material differences between conclusions obtained with propensity scores matching or propensity scores weighting given that a study is sufficiently powered, models are correctly specified and positivity assumption is

Published
2022

3. Impact of methodological choices in comparative effectiveness studies:application in natalizumab versus fingolimod comparison among patients with multiple sclerosis

Author

Lefort, M., Sharmin, S., Andersen, J. B., Vukusic, S., Casey, R., Debouverie, M., Edan, G., Ciron, J., Ruet, A., De Sèze, J., Maillart, E., Zephir, H., Labauge, P., Defer, G., Lebrun-Frenay, C., Moreau, T., Berger, E., Clavelou, P., Pelletier, J., Stankoff, B., Gout, O., Thouvenot, E., Heinzlef, O., Al-Khedr, A., Bourre, B., Casez, O., Cabre, P., Montcuquet, A., Wahab, A., Camdessanché, J. P., Maurousset, A., Ben Nasr, H., Hankiewicz, K., Pottier, C., Maubeuge, N., Dimitri-Boulos, D., Nifle, C., Laplaud, D. A., Horakova, D., Havrdova, E. K., Alroughani, R., Izquierdo, G., Eichau, S., Ozakbas, S., Patti, F., Onofrj, M., Lugaresi, A., Terzi, M., Grammond, P., Grand’Maison, F., Yamout, B., Prat, A., Girard, M., Duquette, P., Boz, C., Trojano, M., McCombe, P., Slee, M., Lechner-Scott, J., Turkoglu, R., Sola, P., Ferraro, D., Granella, F., Shaygannejad, V., Prevost, J., Maimone, D., Skibina, O., Buzzard, K., Van der Walt, A., Karabudak, R., Van Wijmeersch, B., Csepany, T., Spitaleri, D., Vucic, S., Koch-Henriksen, N., Sellebjerg, F., Soerensen, P. S., Hilt Christensen, C. C., Rasmussen, P. V., Jensen, M. B., Frederiksen, J. L., Bramow, S., Mathiesen, H. K., Schreiber, K. I., Butzkueven, H., Magyari, M., Kalincik, T., Leray, E., Lefort, M., Sharmin, S., Andersen, J. B., Vukusic, S., Casey, R., Debouverie, M., Edan, G., Ciron, J., Ruet, A., De Sèze, J., Maillart, E., Zephir, H., Labauge, P., Defer, G., Lebrun-Frenay, C., Moreau, T., Berger, E., Clavelou, P., Pelletier, J., Stankoff, B., Gout, O., Thouvenot, E., Heinzlef, O., Al-Khedr, A., Bourre, B., Casez, O., Cabre, P., Montcuquet, A., Wahab, A., Camdessanché, J. P., Maurousset, A., Ben Nasr, H., Hankiewicz, K., Pottier, C., Maubeuge, N., Dimitri-Boulos, D., Nifle, C., Laplaud, D. A., Horakova, D., Havrdova, E. K., Alroughani, R., Izquierdo, G., Eichau, S., Ozakbas, S., Patti, F., Onofrj, M., Lugaresi, A., Terzi, M., Grammond, P., Grand’Maison, F., Yamout, B., Prat, A., Girard, M., Duquette, P., Boz, C., Trojano, M., McCombe, P., Slee, M., Lechner-Scott, J., Turkoglu, R., Sola, P., Ferraro, D., Granella, F., Shaygannejad, V., Prevost, J., Maimone, D., Skibina, O., Buzzard, K., Van der Walt, A., Karabudak, R., Van Wijmeersch, B., Csepany, T., Spitaleri, D., Vucic, S., Koch-Henriksen, N., Sellebjerg, F., Soerensen, P. S., Hilt Christensen, C. C., Rasmussen, P. V., Jensen, M. B., Frederiksen, J. L., Bramow, S., Mathiesen, H. K., Schreiber, K. I., Butzkueven, H., Magyari, M., Kalincik, T., and Leray, E.

Abstract

Background: Natalizumab and fingolimod are used as high-efficacy treatments in relapsing–remitting multiple sclerosis. Several observational studies comparing these two drugs have shown variable results, using different methods to control treatment indication bias and manage censoring. The objective of this empirical study was to elucidate the impact of methods of causal inference on the results of comparative effectiveness studies. Methods: Data from three observational multiple sclerosis registries (MSBase, the Danish MS Registry and French OFSEP registry) were combined. Four clinical outcomes were studied. Propensity scores were used to match or weigh the compared groups, allowing for estimating average treatment effect for treated or average treatment effect for the entire population. Analyses were conducted both in intention-to-treat and per-protocol frameworks. The impact of the positivity assumption was also assessed. Results: Overall, 5,148 relapsing–remitting multiple sclerosis patients were included. In this well-powered sample, the 95% confidence intervals of the estimates overlapped widely. Propensity scores weighting and propensity scores matching procedures led to consistent results. Some differences were observed between average treatment effect for the entire population and average treatment effect for treated estimates. Intention-to-treat analyses were more conservative than per-protocol analyses. The most pronounced irregularities in outcomes and propensity scores were introduced by violation of the positivity assumption. Conclusions: This applied study elucidates the influence of methodological decisions on the results of comparative effectiveness studies of treatments for multiple sclerosis. According to our results, there are no material differences between conclusions obtained with propensity scores matching or propensity scores weighting given that a study is sufficiently powered, models are correctly specified and positivity assumption is

Published
2022

4. The effectiveness of natalizumab vs fingolimod-A comparison of international registry studies

Author

Andersen, JB, Sharmin, S, Lefort, M, Koch-Henriksen, N, Sellebjerg, F, Sorensen, PS, Christensen, CCH, Rasmussen, P, Jensen, MB, Frederiksen, JL, Bramow, S, Mathiesen, HK, Schreiber, K, Horakova, D, Havrdova, EK, Alroughani, R, Izquierdo, G, Eichau, S, Ozakbas, S, Patti, F, Onofrj, M, Lugaresi, A, Terzi, M, Grammond, P, Maison, FG, Yamout, B, Prat, A, Girard, M, Duquette, P, Boz, C, Trojano, M, McCombe, P, Slee, M, Lechner-Scott, J, Turkoglu, R, Sola, P, Ferraro, D, Granella, F, Shaygannejad, V, Prevost, J, Skibina, O, Solaro, C, Karabudak, R, Wijmeersch, B, Csepany, T, Spitaleri, D, Vucic, S, Casey, R, Debouverie, M, Edan, G, Ciron, J, Ruet, A, Seze, JD, Maillart, E, Zephir, H, Labauge, P, Defer, G, Lebrun, C, Moreau, T, Berger, E, Clavelou, P, Pelletier, J, Stankoff, B, Gout, O, Thouvenot, E, Heinzlef, O, Al-Khedr, A, Bourre, B, Casez, O, Cabre, P, Montcuquet, A, Wahab, A, Camdessanche, J-P, Marousset, A, Patry, I, Hankiewicz, K, Pottier, C, Maubeuge, N, Labeyrie, C, Nifle, C, Leray, E, Laplaud, DA, Butzkueven, H, Kalincik, T, Vukusic, S, Magyari, M, Andersen, JB, Sharmin, S, Lefort, M, Koch-Henriksen, N, Sellebjerg, F, Sorensen, PS, Christensen, CCH, Rasmussen, P, Jensen, MB, Frederiksen, JL, Bramow, S, Mathiesen, HK, Schreiber, K, Horakova, D, Havrdova, EK, Alroughani, R, Izquierdo, G, Eichau, S, Ozakbas, S, Patti, F, Onofrj, M, Lugaresi, A, Terzi, M, Grammond, P, Maison, FG, Yamout, B, Prat, A, Girard, M, Duquette, P, Boz, C, Trojano, M, McCombe, P, Slee, M, Lechner-Scott, J, Turkoglu, R, Sola, P, Ferraro, D, Granella, F, Shaygannejad, V, Prevost, J, Skibina, O, Solaro, C, Karabudak, R, Wijmeersch, B, Csepany, T, Spitaleri, D, Vucic, S, Casey, R, Debouverie, M, Edan, G, Ciron, J, Ruet, A, Seze, JD, Maillart, E, Zephir, H, Labauge, P, Defer, G, Lebrun, C, Moreau, T, Berger, E, Clavelou, P, Pelletier, J, Stankoff, B, Gout, O, Thouvenot, E, Heinzlef, O, Al-Khedr, A, Bourre, B, Casez, O, Cabre, P, Montcuquet, A, Wahab, A, Camdessanche, J-P, Marousset, A, Patry, I, Hankiewicz, K, Pottier, C, Maubeuge, N, Labeyrie, C, Nifle, C, Leray, E, Laplaud, DA, Butzkueven, H, Kalincik, T, Vukusic, S, and Magyari, M

Abstract

BACKGROUND: Natalizumab and fingolimod were the first preparations recommended for disease breakthrough in priorly treated relapsing-remitting multiple sclerosis. Of three published head-to-head studies two showed that natalizumab is the more effective to prevent relapses and EDSS worsening. METHODS: By re-analyzing original published results from MSBase, France, and Denmark using uniform methodologies, we aimed at identifying the effects of differences in methodology, in the MS-populations, and at re-evaluating the differences in effectiveness between the two drugs. We gained access to copies of the individual amended databases and pooled all data. We used uniform inclusion/exclusion criteria and statistical methods with Inverse Probability Treatment Weighting. RESULTS: The pooled analyses comprised 968 natalizumab- and 1479 fingolimod treated patients. The on-treatment natalizumab/fingolimod relapse rate ratio was 0.77 (p=0.004). The hazard ratio (HR) for a first relapse was 0.82 (p=0.030), and the HR for sustained EDSS improvement was 1.4 (p=0.009). There were modest differences between each of the original published studies and the replication study, but the conclusions of the three original studies remained unchanged: in two of them natalizumab was more effective, but in the third there was no difference between natalizumab and fingolimod. CONCLUSION: The results were largely invariant to the epidemiological and statistical methods but differed between the MS populations. Generally, the advantage of natalizumab was confirmed.

Published
2021

5. Underlying genetic variation in familial frontotemporal dementia: sequencing of 198 patients

Author

Mol, Merel, van Rooij, Jeroen, Wong, Tse, Melhem, Shamiram, Verkerk, Annemieke, Kievit, Anneke, van Minkelen, Rick, Rademakers, R, Pottier, C, Donker Kaat, Laura, Seelaar, Harro, van Swieten, J.C., Dopper, Elise, Mol, Merel, van Rooij, Jeroen, Wong, Tse, Melhem, Shamiram, Verkerk, Annemieke, Kievit, Anneke, van Minkelen, Rick, Rademakers, R, Pottier, C, Donker Kaat, Laura, Seelaar, Harro, van Swieten, J.C., and Dopper, Elise

Abstract

Frontotemporal dementia (FTD) presents with a wide variability in clinical syndromes, genetic etiologies, and underlying pathologies. Despite the discovery of pathogenic variants in several genes, many familial cases remain unsolved. In a large FTD cohort of 198 familial patients, we aimed to determine the types and frequencies of variants in genes related to FTD. Pathogenic or likely pathogenic variants were revealed in 74 (37%) patients, including 4 novel variants. The repeat expansion in C9orf72 was most common (21%), followed by variants in MAPT (6%), GRN (4.5%), and TARDBP (3.5%). Other pathogenic variants were found in VCP, TBK1, PSEN1, and a novel homozygous variant in OPTN. Furthermore, we identified 15 variants of uncertain significance, including a promising variant in TUBA4A and a frameshift in VCP, for which additional research is needed to confirm pathogenicity. The patients without identified genetic cause demonstrated a wide clinical and pathological variety. Our study contributes to the clinical characterization of the genetic subtypes and confirms the value of whole-exome sequencing in identifying novel genetic variants.

Published
2021

6. Underlying genetic variation in familial frontotemporal dementia: sequencing of 198 patients

Author

Mol, M.O., Rooij, J.G.J. (Jeroen) van, Wong, T.H. (Tsz Hang), Melhem, S. (Shamiram), Verkerk, A., Kievit, A.J.A. (Anneke J.A.), Thornton, A.S. (Andrew), Rademakers, S. (Suzanne), Pottier, C. (Cyril), Donker Kaat, L. (Laura), Seelaar, H. (Harro), Swieten, J.C. (John) van, Dopper, E.G.P. (Elise), Mol, M.O., Rooij, J.G.J. (Jeroen) van, Wong, T.H. (Tsz Hang), Melhem, S. (Shamiram), Verkerk, A., Kievit, A.J.A. (Anneke J.A.), Thornton, A.S. (Andrew), Rademakers, S. (Suzanne), Pottier, C. (Cyril), Donker Kaat, L. (Laura), Seelaar, H. (Harro), Swieten, J.C. (John) van, and Dopper, E.G.P. (Elise)

Abstract

Frontotemporal dementia (FTD) presents with a wide variability in clinical syndromes, genetic etiologies, and underlying pathologies. Despite the discovery of pathogenic variants in several genes, many familial cases remain unsolved. In a large FTD cohort of 198 familial patients, we aimed to determine the types and frequencies of variants in genes related to FTD. Pathogenic or likely pathogenic variants were revealed in 74 (37%) patients, including 4 novel variants. The repeat expansion in C9orf72 was most common (21%), followed by variants in MAPT (6%), GRN (4.5%), and TARDBP (3.5%). Other pathogenic variants were found in VCP, TBK1, PSEN1, and a novel homozygous variant in OPTN. Furthermore, we identified 15 variants of uncertain significance, including a promising variant in TUBA4A and a frameshift in VCP, for which additional research is needed to confirm pathogenicity. The patients without identified genetic cause demonstrated a wide clinical and pathological variety. Our study contributes to the clinical characterization of the genetic subtypes and confirms the value of whole-exome sequencing in identifying novel genetic variants.

Published
2020
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7. LifeTime and improving European healthcare through cell-based interceptive medicine

Author

Rajewsky, N., Almouzni, G., Gorski, S. A., Aerts, S., Amit, I., Bertero, M. G., Bock, C., Bredenoord, A. L., Cavalli, G., Chiocca, S., Clevers, H., De Strooper, B., Eggert, A., Ellenberg, J., Fernández, X. M., Figlerowicz, M., Gasser, S. M., Hubner, N., Kjems, J., Knoblich, J. A., Krabbe, G., Lichter, P., Linnarsson, S., Marine, J. -C, Marioni, J., Marti-Renom, M. A., Netea, M. G., Nickel, D., Nollmann, M., Novak, H. R., Parkinson, H., Piccolo, S., Pinheiro, I., Pombo, A., Popp, C., Reik, W., Roman-Roman, S., Rosenstiel, P., Schultze, J. L., Stegle, O., Tanay, A., Testa, G., Thanos, D., Theis, F. J., Torres-Padilla, M. -E, Valencia, A., Vallot, C., van Oudenaarden, A., Vidal, M., Voet, T., Alberi, L., Alexander, S., Alexandrov, T., Arenas, E., Bagni, C., Balderas, R., Bandelli, A., Becher, B., Becker, M., Beerenwinkel, N., Benkirame, M., Beyer, M., Bickmore, W., Biessen, E. E. A. L., Blomberg, N., Blumcke, I., Bodenmiller, B., Borroni, B., Boumpas, D. T., Bourgeron, T., Bowers, S., Braeken, D., Brooksbank, C., Brose, N., Bruining, H., Bury, J., Caporale, N., Cattoretti, G., Chabane, N., Chneiweiss, H., Cook, S. A., Curatolo, P., de Jonge, M. I., Deplancke, B., de Witte, P., Dimmeler, S., Draganski, B., Drews, A. -D, Dumbrava, C., Engelhardt, S., Gasser, T., Giamarellos-Bourboulis, E. J., Graff, C., Grün, D., Gut, I., Hansson, O., Henshall, D. C., Herland, Anna, Heutink, P., Heymans, S. R. B., Heyn, H., Huch, M., Huitinga, I., Jackowiak, P., Jongsma, K. R., Journot, L., Junker, J. P., Katz, S., Kehren, J., Kempa, S., Kirchhof, P., Klein, C., Koralewska, N., Korbel, J. O., Kühnemund, M., Lamond, A. I., Lauwers, E., Le Ber, I., Leinonen, V., Tobon, A. L., Lundberg, E., Lunkes, A., Maatz, H., Mann, M., Marelli, L., Matser, V., Matthews, P. M., Mechta-Grigoriou, F., Menon, R., Nielsen, A. F., Pagani, M., Pasterkamp, R. J., Pitkanen, A., Popescu, V., Pottier, C., Puisieux, A., Rademakers, R., Reiling, D., Reiner, O., Remondini, D., Ritchie, C., Rohrer, J. D., Saliba, A. -E, Sanchez-Valle, R., Santosuosso, A., Sauter, A., Scheltema, R. A., Scheltens, P., Schiller, H. B., Schneider, A., Seibler, P., Sheehan-Rooney, K., Shields, D., Sleegers, K., Smit, G., Smith, K. G. C., Smolders, I., Synofzik, M., Tam, W. L., Teichmann, S., Thom, M., Turco, M. Y., van Beusekom, H. M. M., Vandenberghe, R., den Hoecke, S. V., Van de Poel, I., der Ven, A., van der Zee, J., van Lunzen, J., van Minnebruggen, G., Van Paesschen, W., van Swieten, J., van Vught, R., Verhage, M., Verstreken, P., Villa, C. E., Vogel, J., von Kalle, C., Walter, J., Weckhuysen, S., Weichert, W., Wood, L., Ziegler, A. -G, Zipp, F., Community, LifeTime, Rajewsky, N., Almouzni, G., Gorski, S. A., Aerts, S., Amit, I., Bertero, M. G., Bock, C., Bredenoord, A. L., Cavalli, G., Chiocca, S., Clevers, H., De Strooper, B., Eggert, A., Ellenberg, J., Fernández, X. M., Figlerowicz, M., Gasser, S. M., Hubner, N., Kjems, J., Knoblich, J. A., Krabbe, G., Lichter, P., Linnarsson, S., Marine, J. -C, Marioni, J., Marti-Renom, M. A., Netea, M. G., Nickel, D., Nollmann, M., Novak, H. R., Parkinson, H., Piccolo, S., Pinheiro, I., Pombo, A., Popp, C., Reik, W., Roman-Roman, S., Rosenstiel, P., Schultze, J. L., Stegle, O., Tanay, A., Testa, G., Thanos, D., Theis, F. J., Torres-Padilla, M. -E, Valencia, A., Vallot, C., van Oudenaarden, A., Vidal, M., Voet, T., Alberi, L., Alexander, S., Alexandrov, T., Arenas, E., Bagni, C., Balderas, R., Bandelli, A., Becher, B., Becker, M., Beerenwinkel, N., Benkirame, M., Beyer, M., Bickmore, W., Biessen, E. E. A. L., Blomberg, N., Blumcke, I., Bodenmiller, B., Borroni, B., Boumpas, D. T., Bourgeron, T., Bowers, S., Braeken, D., Brooksbank, C., Brose, N., Bruining, H., Bury, J., Caporale, N., Cattoretti, G., Chabane, N., Chneiweiss, H., Cook, S. A., Curatolo, P., de Jonge, M. I., Deplancke, B., de Witte, P., Dimmeler, S., Draganski, B., Drews, A. -D, Dumbrava, C., Engelhardt, S., Gasser, T., Giamarellos-Bourboulis, E. J., Graff, C., Grün, D., Gut, I., Hansson, O., Henshall, D. C., Herland, Anna, Heutink, P., Heymans, S. R. B., Heyn, H., Huch, M., Huitinga, I., Jackowiak, P., Jongsma, K. R., Journot, L., Junker, J. P., Katz, S., Kehren, J., Kempa, S., Kirchhof, P., Klein, C., Koralewska, N., Korbel, J. O., Kühnemund, M., Lamond, A. I., Lauwers, E., Le Ber, I., Leinonen, V., Tobon, A. L., Lundberg, E., Lunkes, A., Maatz, H., Mann, M., Marelli, L., Matser, V., Matthews, P. M., Mechta-Grigoriou, F., Menon, R., Nielsen, A. F., Pagani, M., Pasterkamp, R. J., Pitkanen, A., Popescu, V., Pottier, C., Puisieux, A., Rademakers, R., Reiling, D., Reiner, O., Remondini, D., Ritchie, C., Rohrer, J. D., Saliba, A. -E, Sanchez-Valle, R., Santosuosso, A., Sauter, A., Scheltema, R. A., Scheltens, P., Schiller, H. B., Schneider, A., Seibler, P., Sheehan-Rooney, K., Shields, D., Sleegers, K., Smit, G., Smith, K. G. C., Smolders, I., Synofzik, M., Tam, W. L., Teichmann, S., Thom, M., Turco, M. Y., van Beusekom, H. M. M., Vandenberghe, R., den Hoecke, S. V., Van de Poel, I., der Ven, A., van der Zee, J., van Lunzen, J., van Minnebruggen, G., Van Paesschen, W., van Swieten, J., van Vught, R., Verhage, M., Verstreken, P., Villa, C. E., Vogel, J., von Kalle, C., Walter, J., Weckhuysen, S., Weichert, W., Wood, L., Ziegler, A. -G, Zipp, F., and Community, LifeTime

Abstract

LifeTime aims to track, understand and target human cells during the onset and progression of complex diseases and their response to therapy at single-cell resolution. This mission will be implemented through the development and integration of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during progression from health to disease. Analysis of such large molecular and clinical datasets will discover molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. Timely detection and interception of disease embedded in an ethical and patient-centered vision will be achieved through interactions across academia, hospitals, patient-associations, health data management systems and industry. Applying this strategy to key medical challenges in cancer, neurological, infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade., QC 20201117Correction in: Nature, Volume 587, Issue 7834, Pages 377 - 386, 19 November 2020. DOI: 10.1038/s41586-021-03287-8, Scopus ID: 2-s2.0-85102698588

Published
2020
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8. Underlying genetic variation in familial frontotemporal dementia: sequencing of 198 patients

Author

Mol, M.O., Rooij, J.G.J. (Jeroen) van, Wong, T.H. (Tsz Hang), Melhem, S. (Shamiram), Verkerk, A., Kievit, A.J.A. (Anneke J.A.), Thornton, A.S. (Andrew), Rademakers, S. (Suzanne), Pottier, C. (Cyril), Donker Kaat, L. (Laura), Seelaar, H. (Harro), Swieten, J.C. (John) van, Dopper, E.G.P. (Elise), Mol, M.O., Rooij, J.G.J. (Jeroen) van, Wong, T.H. (Tsz Hang), Melhem, S. (Shamiram), Verkerk, A., Kievit, A.J.A. (Anneke J.A.), Thornton, A.S. (Andrew), Rademakers, S. (Suzanne), Pottier, C. (Cyril), Donker Kaat, L. (Laura), Seelaar, H. (Harro), Swieten, J.C. (John) van, and Dopper, E.G.P. (Elise)

Abstract

Frontotemporal dementia (FTD) presents with a wide variability in clinical syndromes, genetic etiologies, and underlying pathologies. Despite the discovery of pathogenic variants in several genes, many familial cases remain unsolved. In a large FTD cohort of 198 familial patients, we aimed to determine the types and frequencies of variants in genes related to FTD. Pathogenic or likely pathogenic variants were revealed in 74 (37%) patients, including 4 novel variants. The repeat expansion in C9orf72 was most common (21%), followed by variants in MAPT (6%), GRN (4.5%), and TARDBP (3.5%). Other pathogenic variants were found in VCP, TBK1, PSEN1, and a novel homozygous variant in OPTN. Furthermore, we identified 15 variants of uncertain significance, including a promising variant in TUBA4A and a frameshift in VCP, for which additional research is needed to confirm pathogenicity. The patients without identified genetic cause demonstrated a wide clinical and pathological variety. Our study contributes to the clinical characterization of the genetic subtypes and confirms the value of whole-exome sequencing in identifying novel genetic variants.

Published
2020
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9. LifeTime and improving European healthcare through cell-based interceptive medicine

Author

Rajewsky, N. (Nikolaus), Almouzni, G. (Geneviève), Gorski, S.A. (Stanislaw A.), Aerts, S. (Stein), Amit, I. (Ido), Bertero, M.G. (Michela G.), Bock, C. (Christoph), Bredenoord, A.L. (Annelien L.), Cavalli, G. (Giacomo), Chiocca, S. (Susanna), Clevers, H.C. (Hans), Strooper, B. (Bart) de, Eggert, A. (Angelika), Ellenberg, J. (Jan), Fernández, X.M. (Xosé M.), Figlerowicz, M. (Marek), Gasser, S.M. (Susan M.), Hübner, N. (Norbert), Kjems, J. (Jørgen), Knoblich, J.A. (Jürgen A.), Krabbe, G. (Grietje), Lichter, P. (Peter), Linnarsson, S. (Sten), Marine, J.-C. (J.), Marioni, J. (John), Marti-Renom, M.A. (Marc A.), Netea, M.G. (Mihai), Nickel, D. (Dörthe), Nollmann, M. (Marcelo), Novak, H.R. (Halina R.), Parkinson, H. (Helen), Piccolo, S. (Stefano), Pinheiro, I. (Inês), Pombo, A. (Ana), Popp, C. (Christian), Reik, W. (Wolf), Roman-Roman, S. (Sergio), Rosenstiel, P. (Philip), Schultze, J.L. (Joachim), Stegle, O. (Oliver), Tanay, A. (Amos), Testa, G. (Giuseppe), Thanos, D. (Dimitris), Theis, F. (Fabian), Torres-Padilla, M.-E. (Maria-Elena), Valencia, A. (Alfonso), Vallot, C. (Céline), van Oudenaarden, A. (Alexander), Vidal, M. (Marie), Voet, T. (Thierry), Alberi, L. (Lavinia), Alexander, S. (Stephanie), Alexandrov, T. (Theodore), Arenas, E. (Ernest), Bagni, C. (Claudia), Balderas, R. (Robert), Bandelli, A. (Andrea), Becher, B. (Burkhard), Becker, M. (Matthias), Beerenwinkel, N. (Niko), Benkirame, M. (Monsef), Beyer, M. (Marc), Bickmore, W. (Wendy), Biessen, E.E.A.L. (Erik E.A.L.), Blomberg, N. (Niklas), Blumcke, I. (Ingmar), Bodenmiller, B. (Bernd), Borroni, B. (Barbara), Boumpas, D.T. (Dimitrios T.), Bourgeron, T. (Thomas), Bowers, S. (Sarion), Braeken, D. (Dries), Brooksbank, C. (Catherine), Brose, N. (Nils), Bruining, J. (Hans), Bury, J. (Jo), Caporale, N. (Nicolo), Cattoretti, G. (Giorgio), Chabane, N. (Nadia), Chneiweiss, H. (Hervé), Cook, S.A. (Stuart A.), Curatolo, P. (Paolo), Jonge, M.I. (Marien) de, Deplancke, B. (Bart), De Strooper, B. (Bart), de Witte, P. (Peter), Dimmeler, S. (Stefanie), Draganski, B. (Bogdan), Drews, A.-D. (Anna-Dorothee), Dumbrava, C. (Costica), Engelhardt, S. (Stefan), Gasser, T. (Thomas), Giamarellos-Bourboulis, E. (Evangelos), Graff, C. (Caroline), Grün, D. (Dominic), Gut, I. (Ivo), Hansson, O. (Oskar), Henshall, D.C. (David C.), Herland, A. (Anna), Heutink, P. (Peter), Heymans, S. (Stephane), Heyn, H. (Holger), Huch, M. (Meritxell), Huitinga, I. (Inge), Jackowiak, P. (Paulina), Jongsma, K.R. (Karin), Journot, L. (Laurent), Junker, J.P. (Jan Philipp), Katz, S. (Shauna), Kehren, J. (Jeanne), Kempa, S. (Stefan), Kirchhof, P. (Paulus), Klein, C. (Christoph), Koralewska, N. (Natalia), Korbel, J.O. (Jan), Kühnemund, M. (Malte), Lamond, A.I. (Angus I.), Lauwers, E. (Elsa), Le Ber, I. (Isabelle), Leinonen, V. (Ville), Tobon, A.L. (Alejandro Lopez), Lundberg, E. (Emma), Lunkes, A. (Astrid), Maatz, H. (Henrike), Mann, M. (Mathias), Marelli, L. (Luca), Matser, V. (Vera), Matthews, P.M. (P.), Mechta-Grigoriou, F. (Fatima), Menon, R. (Radhika), Nielsen, A.F. (Anne F.), Pagani, M. (Massimiliano), Pasterkamp, R.J. (Jeroen), Pitkanen, A. (Asla), Popescu, V. (Valentin), Pottier, C. (Cyril), Puisieux, A. (Alain), Rademakers, R. (Rosa), Reiling, D. (Dory), Reiner, O. (Orly), Remondini, D. (Daniel), Ritchie, C. (Craig), Rohrer, J.D. (Jonathan D.), Saliba, A.-E. (Antione-Emmanuel), Sánchez-Valle, R. (Raquel), Santosuosso, A. (Amedeo), Sauter, A. (Arnold), Scheltema, R.A. (Richard A.), Scheltens, P. (Philip), Schiller, H.B. (Herbert B.), Schneider, A. (Anja), Seibler, P. (Philip), Sheehan-Rooney, K. (Kelly), Shields, D. (David), Sleegers, K. (Kristel), Smit, G. (Guus), Smith, K.G.C. (Kenneth G. C.), Smolders, I. (Ilse), Synofzik, M. (Matthis), Tam, W.L. (Wai Long), Teichmann, S. (Sarah), Thom, M. (Maria), Turco, M.Y. (Margherita Y.), Beusekom, H.M.M. (Heleen) van, Vandenberghe, R. (Rik), den Hoecke, S.V. (Silvie Van), Van de Poel, E. (Ellen), der Ven, A. (Andre van), van der Zee, J. (Julie), van Lunzen, J. (Jan), van Minnebruggen, G. (Geert), Van Paesschen, W. (Wim), Swieten, J.C. (John) van, van Vught, R. (Remko), Verhage, M. (Matthijs), Verstreken, P. (Patrik), Villa, C.E. (Carlo Emanuele), Vogel, J. (Jörg), Kalle, C. (Christof) von, Walter, J. (Jörn), Weckhuysen, S. (Sarah), Weichert, W. (Wilko), Wood, L. (Louisa), Ziegler, A.-G. (Anette-Gabriele), Zipp, F. (Frauke), Rajewsky, N. (Nikolaus), Almouzni, G. (Geneviève), Gorski, S.A. (Stanislaw A.), Aerts, S. (Stein), Amit, I. (Ido), Bertero, M.G. (Michela G.), Bock, C. (Christoph), Bredenoord, A.L. (Annelien L.), Cavalli, G. (Giacomo), Chiocca, S. (Susanna), Clevers, H.C. (Hans), Strooper, B. (Bart) de, Eggert, A. (Angelika), Ellenberg, J. (Jan), Fernández, X.M. (Xosé M.), Figlerowicz, M. (Marek), Gasser, S.M. (Susan M.), Hübner, N. (Norbert), Kjems, J. (Jørgen), Knoblich, J.A. (Jürgen A.), Krabbe, G. (Grietje), Lichter, P. (Peter), Linnarsson, S. (Sten), Marine, J.-C. (J.), Marioni, J. (John), Marti-Renom, M.A. (Marc A.), Netea, M.G. (Mihai), Nickel, D. (Dörthe), Nollmann, M. (Marcelo), Novak, H.R. (Halina R.), Parkinson, H. (Helen), Piccolo, S. (Stefano), Pinheiro, I. (Inês), Pombo, A. (Ana), Popp, C. (Christian), Reik, W. (Wolf), Roman-Roman, S. (Sergio), Rosenstiel, P. (Philip), Schultze, J.L. (Joachim), Stegle, O. (Oliver), Tanay, A. (Amos), Testa, G. (Giuseppe), Thanos, D. (Dimitris), Theis, F. (Fabian), Torres-Padilla, M.-E. (Maria-Elena), Valencia, A. (Alfonso), Vallot, C. (Céline), van Oudenaarden, A. (Alexander), Vidal, M. (Marie), Voet, T. (Thierry), Alberi, L. (Lavinia), Alexander, S. (Stephanie), Alexandrov, T. (Theodore), Arenas, E. (Ernest), Bagni, C. (Claudia), Balderas, R. (Robert), Bandelli, A. (Andrea), Becher, B. (Burkhard), Becker, M. (Matthias), Beerenwinkel, N. (Niko), Benkirame, M. (Monsef), Beyer, M. (Marc), Bickmore, W. (Wendy), Biessen, E.E.A.L. (Erik E.A.L.), Blomberg, N. (Niklas), Blumcke, I. (Ingmar), Bodenmiller, B. (Bernd), Borroni, B. (Barbara), Boumpas, D.T. (Dimitrios T.), Bourgeron, T. (Thomas), Bowers, S. (Sarion), Braeken, D. (Dries), Brooksbank, C. (Catherine), Brose, N. (Nils), Bruining, J. (Hans), Bury, J. (Jo), Caporale, N. (Nicolo), Cattoretti, G. (Giorgio), Chabane, N. (Nadia), Chneiweiss, H. (Hervé), Cook, S.A. (Stuart A.), Curatolo, P. (Paolo), Jonge, M.I. (Marien) de, Deplancke, B. (Bart), De Strooper, B. (Bart), de Witte, P. (Peter), Dimmeler, S. (Stefanie), Draganski, B. (Bogdan), Drews, A.-D. (Anna-Dorothee), Dumbrava, C. (Costica), Engelhardt, S. (Stefan), Gasser, T. (Thomas), Giamarellos-Bourboulis, E. (Evangelos), Graff, C. (Caroline), Grün, D. (Dominic), Gut, I. (Ivo), Hansson, O. (Oskar), Henshall, D.C. (David C.), Herland, A. (Anna), Heutink, P. (Peter), Heymans, S. (Stephane), Heyn, H. (Holger), Huch, M. (Meritxell), Huitinga, I. (Inge), Jackowiak, P. (Paulina), Jongsma, K.R. (Karin), Journot, L. (Laurent), Junker, J.P. (Jan Philipp), Katz, S. (Shauna), Kehren, J. (Jeanne), Kempa, S. (Stefan), Kirchhof, P. (Paulus), Klein, C. (Christoph), Koralewska, N. (Natalia), Korbel, J.O. (Jan), Kühnemund, M. (Malte), Lamond, A.I. (Angus I.), Lauwers, E. (Elsa), Le Ber, I. (Isabelle), Leinonen, V. (Ville), Tobon, A.L. (Alejandro Lopez), Lundberg, E. (Emma), Lunkes, A. (Astrid), Maatz, H. (Henrike), Mann, M. (Mathias), Marelli, L. (Luca), Matser, V. (Vera), Matthews, P.M. (P.), Mechta-Grigoriou, F. (Fatima), Menon, R. (Radhika), Nielsen, A.F. (Anne F.), Pagani, M. (Massimiliano), Pasterkamp, R.J. (Jeroen), Pitkanen, A. (Asla), Popescu, V. (Valentin), Pottier, C. (Cyril), Puisieux, A. (Alain), Rademakers, R. (Rosa), Reiling, D. (Dory), Reiner, O. (Orly), Remondini, D. (Daniel), Ritchie, C. (Craig), Rohrer, J.D. (Jonathan D.), Saliba, A.-E. (Antione-Emmanuel), Sánchez-Valle, R. (Raquel), Santosuosso, A. (Amedeo), Sauter, A. (Arnold), Scheltema, R.A. (Richard A.), Scheltens, P. (Philip), Schiller, H.B. (Herbert B.), Schneider, A. (Anja), Seibler, P. (Philip), Sheehan-Rooney, K. (Kelly), Shields, D. (David), Sleegers, K. (Kristel), Smit, G. (Guus), Smith, K.G.C. (Kenneth G. C.), Smolders, I. (Ilse), Synofzik, M. (Matthis), Tam, W.L. (Wai Long), Teichmann, S. (Sarah), Thom, M. (Maria), Turco, M.Y. (Margherita Y.), Beusekom, H.M.M. (Heleen) van, Vandenberghe, R. (Rik), den Hoecke, S.V. (Silvie Van), Van de Poel, E. (Ellen), der Ven, A. (Andre van), van der Zee, J. (Julie), van Lunzen, J. (Jan), van Minnebruggen, G. (Geert), Van Paesschen, W. (Wim), Swieten, J.C. (John) van, van Vught, R. (Remko), Verhage, M. (Matthijs), Verstreken, P. (Patrik), Villa, C.E. (Carlo Emanuele), Vogel, J. (Jörg), Kalle, C. (Christof) von, Walter, J. (Jörn), Weckhuysen, S. (Sarah), Weichert, W. (Wilko), Wood, L. (Louisa), Ziegler, A.-G. (Anette-Gabriele), and Zipp, F. (Frauke)

Abstract

LifeTime aims to track, understand and target human cells during the onset and progression of complex diseases and their response to therapy at single-cell resolution. This mission will be implemented through the development and integration of single-cell multi-omics and imaging, artificial intelligence and patient-derived experimental disease models during progression from health to disease. Analysis of such large molecular and clinical datasets will discover molecular mechanisms, create predictive computational models of disease progression, and reveal new drug targets and therapies. Timely detection and interception of disease embedded in an ethical and patient-centered vision will be achieved through interactions across academia, hospitals, patient-associations, health data management systems and industry. Applying this strategy to key medical challenges in cancer, neurological, infectious, chronic inflammatory and cardiovascular diseases at the single-cell level will usher in cell-based interceptive medicine in Europe over the next decade.

Published
2020
Full Text
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10. The demise of Angkor: Systemic vulnerability of urban infrastructure to climatic variations

Author

Penny, D, Zachreson, C, Fletcher, R, Lau, D, Lizier, JT, Fischer, N, Evans, D, Pottier, C, Prokopenko, M, Penny, D, Zachreson, C, Fletcher, R, Lau, D, Lizier, JT, Fischer, N, Evans, D, Pottier, C, and Prokopenko, M

Abstract

Complex infrastructural networks provide critical services to cities but can be vulnerable to external stresses, including climatic variability. This vulnerability has also challenged past urban settlements, but its role in cases of historic urban demise has not been precisely documented. We transform archeological data from the medieval Cambodian city of Angkor into a numerical model that allows us to quantify topological damage to critical urban infrastructure resulting from climatic variability. Our model reveals unstable behavior in which extensive and cascading damage to infrastructure occurs in response to flooding within Angkor's urban water management system. The likelihood and extent of the cascading failure abruptly grow with the magnitude of flooding relative to normal flows in the system. Our results support the hypothesis that systemic infrastructural vulnerability, coupled with abrupt climatic variation, contributed to the demise of the city. The factors behind Angkor's demise are analogous to challenges faced by modern urban communities struggling with complex critical infrastructure.

Published
2018

11. CCNF mutations in amyotrophic lateral sclerosis and frontotemporal dementia

Author

Williams, KL, Topp, S, Yang, S, Smith, B, Fifita, JA, Warraich, ST, Zhang, KY, Farrawell, N, Vance, C, Hu, X, Chesi, A, Leblond, CS, Lee, A, Rayner, SL, Sundaramoorthy, V, Dobson-Stone, C, Molloy, MP, Van Blitterswijk, M, Dickson, DW, Petersen, RC, Graff-Radford, NR, Boeve, BF, Murray, ME, Pottier, C, Don, E, Winnick, C, McCann, EP, Hogan, A, Daoud, H, Levert, A, Dion, PA, Mitsui, J, Ishiura, H, Takahashi, Y, Goto, J, Kost, J, Gellera, C, Gkazi, AS, Miller, J, Stockton, J, Brooks, WS, Boundy, K, Polak, M, Muñoz-Blanco, JL, Esteban-Pérez, J, Rábano, A, Hardiman, O, Morrison, KE, Ticozzi, N, Silani, V, De Belleroche, J, Glass, JD, Kwok, JBJ, Guillemin, GJ, Chung, RS, Tsuji, S, Brown, RH, García-Redondo, A, Rademakers, R, Landers, JE, Gitler, AD, Rouleau, GA, Cole, NJ, Yerbury, JJ, Atkin, JD, Shaw, CE, Nicholson, GA, Blair, IP, Williams, KL, Topp, S, Yang, S, Smith, B, Fifita, JA, Warraich, ST, Zhang, KY, Farrawell, N, Vance, C, Hu, X, Chesi, A, Leblond, CS, Lee, A, Rayner, SL, Sundaramoorthy, V, Dobson-Stone, C, Molloy, MP, Van Blitterswijk, M, Dickson, DW, Petersen, RC, Graff-Radford, NR, Boeve, BF, Murray, ME, Pottier, C, Don, E, Winnick, C, McCann, EP, Hogan, A, Daoud, H, Levert, A, Dion, PA, Mitsui, J, Ishiura, H, Takahashi, Y, Goto, J, Kost, J, Gellera, C, Gkazi, AS, Miller, J, Stockton, J, Brooks, WS, Boundy, K, Polak, M, Muñoz-Blanco, JL, Esteban-Pérez, J, Rábano, A, Hardiman, O, Morrison, KE, Ticozzi, N, Silani, V, De Belleroche, J, Glass, JD, Kwok, JBJ, Guillemin, GJ, Chung, RS, Tsuji, S, Brown, RH, García-Redondo, A, Rademakers, R, Landers, JE, Gitler, AD, Rouleau, GA, Cole, NJ, Yerbury, JJ, Atkin, JD, Shaw, CE, Nicholson, GA, and Blair, IP

Abstract

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are overlapping, fatal neurodegenerative disorders in which the molecular and pathogenic basis remains poorly understood. Ubiquitinated protein aggregates, of which TDP-43 is a major component, are a characteristic pathological feature of most ALS and FTD patients. Here we use genome-wide linkage analysis in a large ALS/FTD kindred to identify a novel disease locus on chromosome 16p13.3. Whole-exome sequencing identified a CCNF missense mutation at this locus. Interrogation of international cohorts identified additional novel CCNF variants in familial and sporadic ALS and FTD. Enrichment of rare protein-altering CCNF variants was evident in a large sporadic ALS replication cohort. CCNF encodes cyclin F, a component of an E3 ubiquitin-protein ligase complex (SCFCyclin F). Expression of mutant CCNF in neuronal cells caused abnormal ubiquitination and accumulation of ubiquitinated proteins, including TDP-43 and a SCFCyclin F substrate. This implicates common mechanisms, linked to protein homeostasis, underlying neuronal degeneration.

Published
2016

12. CCNF mutations in amyotrophic lateral sclerosis and frontotemporal dementia

Author

Williams, KL, Topp, S, Yang, S, Smith, B, Fifita, JA, Warraich, ST, Zhang, KY, Farrawell, N, Vance, C, Hu, X, Chesi, A, Leblond, CS, Lee, A, Rayner, SL, Sundaramoorthy, V, Dobson-Stone, C, Molloy, MP, Van Blitterswijk, M, Dickson, DW, Petersen, RC, Graff-Radford, NR, Boeve, BF, Murray, ME, Pottier, C, Don, E, Winnick, C, McCann, EP, Hogan, A, Daoud, H, Levert, A, Dion, PA, Mitsui, J, Ishiura, H, Takahashi, Y, Goto, J, Kost, J, Gellera, C, Gkazi, AS, Miller, J, Stockton, J, Brooks, WS, Boundy, K, Polak, M, Muñoz-Blanco, JL, Esteban-Pérez, J, Rábano, A, Hardiman, O, Morrison, KE, Ticozzi, N, Silani, V, De Belleroche, J, Glass, JD, Kwok, JBJ, Guillemin, GJ, Chung, RS, Tsuji, S, Brown, RH, García-Redondo, A, Rademakers, R, Landers, JE, Gitler, AD, Rouleau, GA, Cole, NJ, Yerbury, JJ, Atkin, JD, Shaw, CE, Nicholson, GA, Blair, IP, Williams, KL, Topp, S, Yang, S, Smith, B, Fifita, JA, Warraich, ST, Zhang, KY, Farrawell, N, Vance, C, Hu, X, Chesi, A, Leblond, CS, Lee, A, Rayner, SL, Sundaramoorthy, V, Dobson-Stone, C, Molloy, MP, Van Blitterswijk, M, Dickson, DW, Petersen, RC, Graff-Radford, NR, Boeve, BF, Murray, ME, Pottier, C, Don, E, Winnick, C, McCann, EP, Hogan, A, Daoud, H, Levert, A, Dion, PA, Mitsui, J, Ishiura, H, Takahashi, Y, Goto, J, Kost, J, Gellera, C, Gkazi, AS, Miller, J, Stockton, J, Brooks, WS, Boundy, K, Polak, M, Muñoz-Blanco, JL, Esteban-Pérez, J, Rábano, A, Hardiman, O, Morrison, KE, Ticozzi, N, Silani, V, De Belleroche, J, Glass, JD, Kwok, JBJ, Guillemin, GJ, Chung, RS, Tsuji, S, Brown, RH, García-Redondo, A, Rademakers, R, Landers, JE, Gitler, AD, Rouleau, GA, Cole, NJ, Yerbury, JJ, Atkin, JD, Shaw, CE, Nicholson, GA, and Blair, IP

Abstract

Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are overlapping, fatal neurodegenerative disorders in which the molecular and pathogenic basis remains poorly understood. Ubiquitinated protein aggregates, of which TDP-43 is a major component, are a characteristic pathological feature of most ALS and FTD patients. Here we use genome-wide linkage analysis in a large ALS/FTD kindred to identify a novel disease locus on chromosome 16p13.3. Whole-exome sequencing identified a CCNF missense mutation at this locus. Interrogation of international cohorts identified additional novel CCNF variants in familial and sporadic ALS and FTD. Enrichment of rare protein-altering CCNF variants was evident in a large sporadic ALS replication cohort. CCNF encodes cyclin F, a component of an E3 ubiquitin-protein ligase complex (SCFCyclin F). Expression of mutant CCNF in neuronal cells caused abnormal ubiquitination and accumulation of ubiquitinated proteins, including TDP-43 and a SCFCyclin F substrate. This implicates common mechanisms, linked to protein homeostasis, underlying neuronal degeneration.

Published
2016

13. Whole-genome sequencing reveals important role for TBK1 and OPTN mutations in frontotemporal lobar degeneration without motor neuron disease

Author

Pottier, C., Bieniek, K.F., Finch, N., Vorst, M. van de, Baker, M., Perkersen, R., Brown, P., Ravenscroft, T., Blitterswijk, M. van, Nicholson, A.M., DeTure, M., Knopman, D.S., Josephs, K.A., Parisi, J.E., Petersen, R.C., Boylan, K.B., Boeve, B.F., Graff-Radford, N.R., Veltman, J.A., Gilissen, C., Murray, M.E., Dickson, D.W., Rademakers, R., Pottier, C., Bieniek, K.F., Finch, N., Vorst, M. van de, Baker, M., Perkersen, R., Brown, P., Ravenscroft, T., Blitterswijk, M. van, Nicholson, A.M., DeTure, M., Knopman, D.S., Josephs, K.A., Parisi, J.E., Petersen, R.C., Boylan, K.B., Boeve, B.F., Graff-Radford, N.R., Veltman, J.A., Gilissen, C., Murray, M.E., Dickson, D.W., and Rademakers, R.

Abstract

Contains fulltext : 154461.pdf (publisher's version ) (Closed access), Frontotemporal lobar degeneration with TAR DNA-binding protein 43 inclusions (FTLD-TDP) is the most common pathology associated with frontotemporal dementia (FTD). Repeat expansions in chromosome 9 open reading frame 72 (C9ORF72) and mutations in progranulin (GRN) are the major known genetic causes of FTLD-TDP; however, the genetic etiology in the majority of FTLD-TDP remains unexplained. In this study, we performed whole-genome sequencing in 104 pathologically confirmed FTLD-TDP patients from the Mayo Clinic brain bank negative for C9ORF72 and GRN mutations and report on the contribution of rare single nucleotide and copy number variants in 21 known neurodegenerative disease genes. Interestingly, we identified 5 patients (4.8 %) with variants in optineurin (OPTN) and TANK-binding kinase 1 (TBK1) that are predicted to be highly pathogenic, including two double mutants. Case A was a compound heterozygote for mutations in OPTN, carrying the p.Q235* nonsense and p.A481V missense mutation in trans, while case B carried a deletion of OPTN exons 13-15 (p.Gly538Glufs*27) and a loss-of-function mutation (p.Arg117*) in TBK1. Cases C-E carried heterozygous missense mutations in TBK1, including the p.Glu696Lys mutation which was previously reported in two amyotrophic lateral sclerosis (ALS) patients and is located in the OPTN binding domain. Quantitative mRNA expression and protein analysis in cerebellar tissue showed a striking reduction of OPTN and/or TBK1 expression in 4 out of 5 patients supporting pathogenicity in these specific patients and suggesting a loss-of-function disease mechanism. Importantly, neuropathologic examination showed FTLD-TDP type A in the absence of motor neuron disease in 3 pathogenic mutation carriers. In conclusion, we highlight TBK1 as an important cause of pure FTLD-TDP, identify the first OPTN mutations in FTLD-TDP, and suggest a potential oligogenic basis for at least a subset of FTLD-TDP patients. Our data further add to the growing body of ev

Published
2015

14. Whole-genome sequencing reveals important role for TBK1 and OPTN mutations in frontotemporal lobar degeneration without motor neuron disease

Author

Pottier, C., Bieniek, K.F., Finch, N., Vorst, M. van de, Baker, M., Perkersen, R., Brown, P., Ravenscroft, T., Blitterswijk, M. van, Nicholson, A.M., DeTure, M., Knopman, D.S., Josephs, K.A., Parisi, J.E., Petersen, R.C., Boylan, K.B., Boeve, B.F., Graff-Radford, N.R., Veltman, J.A., Gilissen, C., Murray, M.E., Dickson, D.W., Rademakers, R., Pottier, C., Bieniek, K.F., Finch, N., Vorst, M. van de, Baker, M., Perkersen, R., Brown, P., Ravenscroft, T., Blitterswijk, M. van, Nicholson, A.M., DeTure, M., Knopman, D.S., Josephs, K.A., Parisi, J.E., Petersen, R.C., Boylan, K.B., Boeve, B.F., Graff-Radford, N.R., Veltman, J.A., Gilissen, C., Murray, M.E., Dickson, D.W., and Rademakers, R.

Abstract

Contains fulltext : 154461.pdf (publisher's version ) (Closed access), Frontotemporal lobar degeneration with TAR DNA-binding protein 43 inclusions (FTLD-TDP) is the most common pathology associated with frontotemporal dementia (FTD). Repeat expansions in chromosome 9 open reading frame 72 (C9ORF72) and mutations in progranulin (GRN) are the major known genetic causes of FTLD-TDP; however, the genetic etiology in the majority of FTLD-TDP remains unexplained. In this study, we performed whole-genome sequencing in 104 pathologically confirmed FTLD-TDP patients from the Mayo Clinic brain bank negative for C9ORF72 and GRN mutations and report on the contribution of rare single nucleotide and copy number variants in 21 known neurodegenerative disease genes. Interestingly, we identified 5 patients (4.8 %) with variants in optineurin (OPTN) and TANK-binding kinase 1 (TBK1) that are predicted to be highly pathogenic, including two double mutants. Case A was a compound heterozygote for mutations in OPTN, carrying the p.Q235* nonsense and p.A481V missense mutation in trans, while case B carried a deletion of OPTN exons 13-15 (p.Gly538Glufs*27) and a loss-of-function mutation (p.Arg117*) in TBK1. Cases C-E carried heterozygous missense mutations in TBK1, including the p.Glu696Lys mutation which was previously reported in two amyotrophic lateral sclerosis (ALS) patients and is located in the OPTN binding domain. Quantitative mRNA expression and protein analysis in cerebellar tissue showed a striking reduction of OPTN and/or TBK1 expression in 4 out of 5 patients supporting pathogenicity in these specific patients and suggesting a loss-of-function disease mechanism. Importantly, neuropathologic examination showed FTLD-TDP type A in the absence of motor neuron disease in 3 pathogenic mutation carriers. In conclusion, we highlight TBK1 as an important cause of pure FTLD-TDP, identify the first OPTN mutations in FTLD-TDP, and suggest a potential oligogenic basis for at least a subset of FTLD-TDP patients. Our data further add to the growing body of ev

Published
2015

15. Whole-genome sequencing reveals important role for TBK1 and OPTN mutations in frontotemporal lobar degeneration without motor neuron disease

Author

Pottier, C., Bieniek, K.F., Finch, N., Vorst, M. van de, Baker, M., Perkersen, R., Brown, P., Ravenscroft, T., Blitterswijk, M. van, Nicholson, A.M., DeTure, M., Knopman, D.S., Josephs, K.A., Parisi, J.E., Petersen, R.C., Boylan, K.B., Boeve, B.F., Graff-Radford, N.R., Veltman, J.A., Gilissen, C., Murray, M.E., Dickson, D.W., Rademakers, R., Pottier, C., Bieniek, K.F., Finch, N., Vorst, M. van de, Baker, M., Perkersen, R., Brown, P., Ravenscroft, T., Blitterswijk, M. van, Nicholson, A.M., DeTure, M., Knopman, D.S., Josephs, K.A., Parisi, J.E., Petersen, R.C., Boylan, K.B., Boeve, B.F., Graff-Radford, N.R., Veltman, J.A., Gilissen, C., Murray, M.E., Dickson, D.W., and Rademakers, R.

Abstract

Contains fulltext : 154461.pdf (publisher's version ) (Closed access), Frontotemporal lobar degeneration with TAR DNA-binding protein 43 inclusions (FTLD-TDP) is the most common pathology associated with frontotemporal dementia (FTD). Repeat expansions in chromosome 9 open reading frame 72 (C9ORF72) and mutations in progranulin (GRN) are the major known genetic causes of FTLD-TDP; however, the genetic etiology in the majority of FTLD-TDP remains unexplained. In this study, we performed whole-genome sequencing in 104 pathologically confirmed FTLD-TDP patients from the Mayo Clinic brain bank negative for C9ORF72 and GRN mutations and report on the contribution of rare single nucleotide and copy number variants in 21 known neurodegenerative disease genes. Interestingly, we identified 5 patients (4.8 %) with variants in optineurin (OPTN) and TANK-binding kinase 1 (TBK1) that are predicted to be highly pathogenic, including two double mutants. Case A was a compound heterozygote for mutations in OPTN, carrying the p.Q235* nonsense and p.A481V missense mutation in trans, while case B carried a deletion of OPTN exons 13-15 (p.Gly538Glufs*27) and a loss-of-function mutation (p.Arg117*) in TBK1. Cases C-E carried heterozygous missense mutations in TBK1, including the p.Glu696Lys mutation which was previously reported in two amyotrophic lateral sclerosis (ALS) patients and is located in the OPTN binding domain. Quantitative mRNA expression and protein analysis in cerebellar tissue showed a striking reduction of OPTN and/or TBK1 expression in 4 out of 5 patients supporting pathogenicity in these specific patients and suggesting a loss-of-function disease mechanism. Importantly, neuropathologic examination showed FTLD-TDP type A in the absence of motor neuron disease in 3 pathogenic mutation carriers. In conclusion, we highlight TBK1 as an important cause of pure FTLD-TDP, identify the first OPTN mutations in FTLD-TDP, and suggest a potential oligogenic basis for at least a subset of FTLD-TDP patients. Our data further add to the growing body of ev

Published
2015

17. Uncovering archaeological landscapes at Angkor using lidar

Author

Evans, D. H., Fletcher, R. J., Pottier, C., Chevance, J.-B., Soutif, D., Tan, B. S., Im, S., Ea, D., Tin, T., Kim, S., Cromarty, Fiona, De Greef, Stephane, Hanus, K., Baty, P., Kuszinger, R., Shimoda, I., Boornazian, G., Evans, D. H., Fletcher, R. J., Pottier, C., Chevance, J.-B., Soutif, D., Tan, B. S., Im, S., Ea, D., Tin, T., Kim, S., Cromarty, Fiona, De Greef, Stephane, Hanus, K., Baty, P., Kuszinger, R., Shimoda, I., and Boornazian, G.

Abstract

info:eu-repo/semantics/published

Published
2013

18. Merging SeaWiFS and MODIS/Aqua Ocean Color Data in North and Equatorial Atlantic Using Weighted Averaging and Objective Analysis

Author

Pottier, C, Garcon, V, Larnicol, G, Sudre, J, Schaeffer, P, Le Traon, Pierre-yves, Pottier, C, Garcon, V, Larnicol, G, Sudre, J, Schaeffer, P, and Le Traon, Pierre-yves

Abstract

Two approaches of ocean color data merging were tested and compared in the North and Equatorial Atlantic Basin: the weighted averaging and the objective analysis. The datasets used were the daily level-3 binned data of chlorophyll-a from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) and Moderate Resolution Imaging Spectroradiometer on the Aqua satellite over the year 2003, which is the first common full year of operation. Since they represent input for both approaches, matchups between the satellite and the in situ data from the SeaWiFS Bio-optical Archive and Storage System and the Atlantic Meridional Transect were first studied to compute a spatial map of the root mean-square error and of the bias. Because of the log distribution of the chlorophyll fields, each approach was applied to untransformed and log-transformed values. The application of the weighted averaging to log-transformed values does not show significant differences in comparison to its application to untransformed values. This is not the case, however, for the objective analysis that gives better results when applied to logtransformed values. Both approaches give combined chlorophyll data of equivalent quality, although the objective analysis could be improved with a better statistical characterization of noise and signal covariance. The main advantage of the objective analysis is its ability to interpolate in space (and time) by taking into account the characteristic scales of chlorophyll-a. As a result, the spatial coverage of the combined data is at least twice as large in the case of objective analysis than weighted averaging. OCR NOT CONTROLLED

Published
2006
Full Text
View/download PDF

19. Merging SeaWiFS and MODIS/Aqua Ocean Color Data in North and Equatorial Atlantic Using Weighted Averaging and Objective Analysis

Author

Pottier, C, Garcon, V, Larnicol, G, Sudre, J, Schaeffer, P, Le Traon, Pierre-yves, Pottier, C, Garcon, V, Larnicol, G, Sudre, J, Schaeffer, P, and Le Traon, Pierre-yves

Abstract

Two approaches of ocean color data merging were tested and compared in the North and Equatorial Atlantic Basin: the weighted averaging and the objective analysis. The datasets used were the daily level-3 binned data of chlorophyll-a from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) and Moderate Resolution Imaging Spectroradiometer on the Aqua satellite over the year 2003, which is the first common full year of operation. Since they represent input for both approaches, matchups between the satellite and the in situ data from the SeaWiFS Bio-optical Archive and Storage System and the Atlantic Meridional Transect were first studied to compute a spatial map of the root mean-square error and of the bias. Because of the log distribution of the chlorophyll fields, each approach was applied to untransformed and log-transformed values. The application of the weighted averaging to log-transformed values does not show significant differences in comparison to its application to untransformed values. This is not the case, however, for the objective analysis that gives better results when applied to logtransformed values. Both approaches give combined chlorophyll data of equivalent quality, although the objective analysis could be improved with a better statistical characterization of noise and signal covariance. The main advantage of the objective analysis is its ability to interpolate in space (and time) by taking into account the characteristic scales of chlorophyll-a. As a result, the spatial coverage of the combined data is at least twice as large in the case of objective analysis than weighted averaging. OCR NOT CONTROLLED

Published
2006
Full Text
View/download PDF

20. Merging SeaWiFS and MODIS/Aqua Ocean Color Data in North and Equatorial Atlantic Using Weighted Averaging and Objective Analysis

Author

Pottier, C, Garcon, V, Larnicol, G, Sudre, J, Schaeffer, P, Le Traon, Pierre-yves, Pottier, C, Garcon, V, Larnicol, G, Sudre, J, Schaeffer, P, and Le Traon, Pierre-yves

Abstract

Two approaches of ocean color data merging were tested and compared in the North and Equatorial Atlantic Basin: the weighted averaging and the objective analysis. The datasets used were the daily level-3 binned data of chlorophyll-a from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) and Moderate Resolution Imaging Spectroradiometer on the Aqua satellite over the year 2003, which is the first common full year of operation. Since they represent input for both approaches, matchups between the satellite and the in situ data from the SeaWiFS Bio-optical Archive and Storage System and the Atlantic Meridional Transect were first studied to compute a spatial map of the root mean-square error and of the bias. Because of the log distribution of the chlorophyll fields, each approach was applied to untransformed and log-transformed values. The application of the weighted averaging to log-transformed values does not show significant differences in comparison to its application to untransformed values. This is not the case, however, for the objective analysis that gives better results when applied to logtransformed values. Both approaches give combined chlorophyll data of equivalent quality, although the objective analysis could be improved with a better statistical characterization of noise and signal covariance. The main advantage of the objective analysis is its ability to interpolate in space (and time) by taking into account the characteristic scales of chlorophyll-a. As a result, the spatial coverage of the combined data is at least twice as large in the case of objective analysis than weighted averaging. OCR NOT CONTROLLED

Published
2006
Full Text
View/download PDF

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