Functional and in silico assessment of MAX variants of unknown significance

Iñaki Comino-Méndez; Luis J Leandro-García; Guillermo Montoya; Lucía Inglada-Pérez; Aguirre A de Cubas; María Currás-Freixes; Carolyn Tysoe; Louise Izatt; Rocío Letón; Álvaro Gómez-Graña; Veronika Mancikova; María Apellániz-Ruiz; Massimo Mannelli; Francesca Schiavi; Judith Favier; Anne-Paule Gimenez-Roqueplo; Henri J L M Timmers; Giovanna Roncador; Juan F Garcia; Cristina Rodríguez-Antona; Mercedes Robledo; Alberto Cascón

doi:10.1007/s00109-015-1306-y

Functional and in silico assessment of MAX variants of unknown significance

Iñaki Comino-Méndez, Luis J Leandro-García, Guillermo Montoya, Lucía Inglada-Pérez, Aguirre A de Cubas, María Currás-Freixes, Carolyn Tysoe, Louise Izatt, Rocío Letón, Álvaro Gómez-Graña, Veronika Mancikova, María Apellániz-Ruiz, Massimo Mannelli, Francesca Schiavi, Judith Favier, Anne-Paule Gimenez-Roqueplo, Henri J L M Timmers, Giovanna Roncador, Juan F Garcia, Cristina Rodríguez-AntonaMercedes Robledo, Alberto Cascón

14 Citations (Scopus)

Abstract

Abstract: The presence of germline mutations affecting the MYC-associated protein X (MAX) gene has recently been identified as one of the now 11 major genetic predisposition factors for the development of hereditary pheochromocytoma and/or paraganglioma. Little is known regarding how missense variants of unknown significance (VUS) in MAX affect its pivotal role in the regulation of the MYC/MAX/MXD axis. In the present study, we propose a consensus computational prediction based on five “state-of-the-art” algorithms. We also describe a PC12-based functional assay to assess the effects that 12 MAX VUS may have on MYC’s E-box transcriptional activation. For all but two of these 12 VUS, the functional assay and the consensus computational prediction gave consistent results; we classified seven variants as pathogenic and three as nonpathogenic. The introduction of wild-type MAX cDNA into PC12 cells significantly decreased MYC’s ability to bind to canonical E-boxes, while pathogenic MAX proteins were not able to fully repress MYC activity. Further clinical and molecular evaluation of variant carriers corroborated the results obtained with our functional assessment. In the absence of clear heritability, clinical information, and molecular data, consensus computational predictions and functional models are able to correctly classify VUS affecting MAX. Key messages: A functional assay assesses the effects of MAX VUS over MYC transcriptional activity.A consensus computational prediction and the functional assay show high concordance.Variant carriers’ clinical and molecular data support the functional assessment.

Original language	English
Journal	Journal of Molecular Medicine
Volume	93
Issue number	11
Pages (from-to)	1247-55
Number of pages	9
ISSN	0946-2716
DOIs	https://doi.org/10.1007/s00109-015-1306-y
Publication status	Published - 1 Nov 2015

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10.1007/s00109-015-1306-y

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Comino-Méndez, I., Leandro-García, L. J., Montoya, G., Inglada-Pérez, L., de Cubas, A. A., Currás-Freixes, M., Tysoe, C., Izatt, L., Letón, R., Gómez-Graña, Á., Mancikova, V., Apellániz-Ruiz, M., Mannelli, M., Schiavi, F., Favier, J., Gimenez-Roqueplo, A.-P., Timmers, H. J. L. M., Roncador, G., Garcia, J. F., ... Cascón, A. (2015). Functional and in silico assessment of MAX variants of unknown significance. Journal of Molecular Medicine, 93(11), 1247-55. https://doi.org/10.1007/s00109-015-1306-y

Comino-Méndez, I, Leandro-García, LJ, Montoya, G, Inglada-Pérez, L, de Cubas, AA, Currás-Freixes, M, Tysoe, C, Izatt, L, Letón, R, Gómez-Graña, Á, Mancikova, V, Apellániz-Ruiz, M, Mannelli, M, Schiavi, F, Favier, J, Gimenez-Roqueplo, A-P, Timmers, HJLM, Roncador, G, Garcia, JF, Rodríguez-Antona, C, Robledo, M & Cascón, A 2015, 'Functional and in silico assessment of MAX variants of unknown significance', Journal of Molecular Medicine, vol. 93, no. 11, pp. 1247-55. https://doi.org/10.1007/s00109-015-1306-y

@article{7ddf107f816f4858af0a82318e3d4fb9,

title = "Functional and in silico assessment of MAX variants of unknown significance",

abstract = "Abstract: The presence of germline mutations affecting the MYC-associated protein X (MAX) gene has recently been identified as one of the now 11 major genetic predisposition factors for the development of hereditary pheochromocytoma and/or paraganglioma. Little is known regarding how missense variants of unknown significance (VUS) in MAX affect its pivotal role in the regulation of the MYC/MAX/MXD axis. In the present study, we propose a consensus computational prediction based on five “state-of-the-art” algorithms. We also describe a PC12-based functional assay to assess the effects that 12 MAX VUS may have on MYC{\textquoteright}s E-box transcriptional activation. For all but two of these 12 VUS, the functional assay and the consensus computational prediction gave consistent results; we classified seven variants as pathogenic and three as nonpathogenic. The introduction of wild-type MAX cDNA into PC12 cells significantly decreased MYC{\textquoteright}s ability to bind to canonical E-boxes, while pathogenic MAX proteins were not able to fully repress MYC activity. Further clinical and molecular evaluation of variant carriers corroborated the results obtained with our functional assessment. In the absence of clear heritability, clinical information, and molecular data, consensus computational predictions and functional models are able to correctly classify VUS affecting MAX. Key messages: A functional assay assesses the effects of MAX VUS over MYC transcriptional activity.A consensus computational prediction and the functional assay show high concordance.Variant carriers{\textquoteright} clinical and molecular data support the functional assessment.",

author = "I{\~n}aki Comino-M{\'e}ndez and Leandro-Garc{\'i}a, {Luis J} and Guillermo Montoya and Luc{\'i}a Inglada-P{\'e}rez and {de Cubas}, {Aguirre A} and Mar{\'i}a Curr{\'a}s-Freixes and Carolyn Tysoe and Louise Izatt and Roc{\'i}o Let{\'o}n and {\'A}lvaro G{\'o}mez-Gra{\~n}a and Veronika Mancikova and Mar{\'i}a Apell{\'a}niz-Ruiz and Massimo Mannelli and Francesca Schiavi and Judith Favier and Anne-Paule Gimenez-Roqueplo and Timmers, {Henri J L M} and Giovanna Roncador and Garcia, {Juan F} and Cristina Rodr{\'i}guez-Antona and Mercedes Robledo and Alberto Casc{\'o}n",

year = "2015",

month = nov,

day = "1",

doi = "10.1007/s00109-015-1306-y",

language = "English",

volume = "93",

pages = "1247--55",

journal = "Journal of Molecular Medicine",

issn = "0946-2716",

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TY - JOUR

T1 - Functional and in silico assessment of MAX variants of unknown significance

AU - Comino-Méndez, Iñaki

AU - Leandro-García, Luis J

AU - Montoya, Guillermo

AU - Inglada-Pérez, Lucía

AU - de Cubas, Aguirre A

AU - Currás-Freixes, María

AU - Tysoe, Carolyn

AU - Izatt, Louise

AU - Letón, Rocío

AU - Gómez-Graña, Álvaro

AU - Mancikova, Veronika

AU - Apellániz-Ruiz, María

AU - Mannelli, Massimo

AU - Schiavi, Francesca

AU - Favier, Judith

AU - Gimenez-Roqueplo, Anne-Paule

AU - Timmers, Henri J L M

AU - Roncador, Giovanna

AU - Garcia, Juan F

AU - Rodríguez-Antona, Cristina

AU - Robledo, Mercedes

AU - Cascón, Alberto

PY - 2015/11/1

Y1 - 2015/11/1

N2 - Abstract: The presence of germline mutations affecting the MYC-associated protein X (MAX) gene has recently been identified as one of the now 11 major genetic predisposition factors for the development of hereditary pheochromocytoma and/or paraganglioma. Little is known regarding how missense variants of unknown significance (VUS) in MAX affect its pivotal role in the regulation of the MYC/MAX/MXD axis. In the present study, we propose a consensus computational prediction based on five “state-of-the-art” algorithms. We also describe a PC12-based functional assay to assess the effects that 12 MAX VUS may have on MYC’s E-box transcriptional activation. For all but two of these 12 VUS, the functional assay and the consensus computational prediction gave consistent results; we classified seven variants as pathogenic and three as nonpathogenic. The introduction of wild-type MAX cDNA into PC12 cells significantly decreased MYC’s ability to bind to canonical E-boxes, while pathogenic MAX proteins were not able to fully repress MYC activity. Further clinical and molecular evaluation of variant carriers corroborated the results obtained with our functional assessment. In the absence of clear heritability, clinical information, and molecular data, consensus computational predictions and functional models are able to correctly classify VUS affecting MAX. Key messages: A functional assay assesses the effects of MAX VUS over MYC transcriptional activity.A consensus computational prediction and the functional assay show high concordance.Variant carriers’ clinical and molecular data support the functional assessment.

AB - Abstract: The presence of germline mutations affecting the MYC-associated protein X (MAX) gene has recently been identified as one of the now 11 major genetic predisposition factors for the development of hereditary pheochromocytoma and/or paraganglioma. Little is known regarding how missense variants of unknown significance (VUS) in MAX affect its pivotal role in the regulation of the MYC/MAX/MXD axis. In the present study, we propose a consensus computational prediction based on five “state-of-the-art” algorithms. We also describe a PC12-based functional assay to assess the effects that 12 MAX VUS may have on MYC’s E-box transcriptional activation. For all but two of these 12 VUS, the functional assay and the consensus computational prediction gave consistent results; we classified seven variants as pathogenic and three as nonpathogenic. The introduction of wild-type MAX cDNA into PC12 cells significantly decreased MYC’s ability to bind to canonical E-boxes, while pathogenic MAX proteins were not able to fully repress MYC activity. Further clinical and molecular evaluation of variant carriers corroborated the results obtained with our functional assessment. In the absence of clear heritability, clinical information, and molecular data, consensus computational predictions and functional models are able to correctly classify VUS affecting MAX. Key messages: A functional assay assesses the effects of MAX VUS over MYC transcriptional activity.A consensus computational prediction and the functional assay show high concordance.Variant carriers’ clinical and molecular data support the functional assessment.

U2 - 10.1007/s00109-015-1306-y

DO - 10.1007/s00109-015-1306-y

M3 - Journal article

C2 - 26070438

SN - 0946-2716

VL - 93

SP - 1247

EP - 1255

JO - Journal of Molecular Medicine

JF - Journal of Molecular Medicine

IS - 11

ER -

Functional and in silico assessment of MAX variants of unknown significance

Abstract

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