De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia

Hanneke A. Haijes, Maria J.E. Koster, Holger Rehmann, Dong Li, H. Hakonarson, Gerarda Cappuccio, Miroslava Hancarova, Daphne Lehalle, Willie Reardon, G. Bradley Schaefer, Anna Lehman, Ingrid M.B.H. van de Laar, Coranne D. Tesselaar, Clesson Turner, A. Goldenberg, Sophie Patrier, Julien Thevenon, Michele Pinelli, Nicola Brunetti-Pierri, Darina PrchalováMarkéta Havlovicová, Markéta Vlckova, Zdeněk Sedláček, E. Lopez, Vassilis Ragoussis, Alistair T. Pagnamenta, Usha Kini, Harmjan R. Vos, Robert M. van Es, Richard F.M.A. van Schaik, Ton A.J. van Essen, M. Kibaek, Jenny C. Taylor, Jennifer Sullivan, Vandana Shashi, S. Petrovski, Christina Fagerberg, Donna M. Martin, Koen L.I. van Gassen, R. Pfundt, Marni J. Falk, Elizabeth M. McCormick, H. T.Marc Timmers, Peter M. van Hasselt*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

The RNA polymerase II complex (pol II) is responsible for transcription of all ∼21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly disease-causing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.

Original languageEnglish
JournalAmerican Journal of Human Genetics
Volume105
Issue number2
Pages (from-to)283-301
ISSN0002-9297
DOIs
Publication statusPublished - 1. Aug 2019

Fingerprint

Muscle Hypotonia
RNA Polymerase II
HeLa Cells
Saccharomyces cerevisiae
Cell Survival
Alleles
DNA
Enzymes
Proteins

Keywords

  • de novo variants
  • desert regions
  • desert Z score
  • dominant-negative effect
  • haplo-insufficiency
  • infantile-onset hypotonia
  • neurodevelopmental syndrome
  • POLR2A
  • RNA polymerase II complex
  • RPB1

Cite this

Haijes, H. A., Koster, M. J. E., Rehmann, H., Li, D., Hakonarson, H., Cappuccio, G., ... van Hasselt, P. M. (2019). De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia. American Journal of Human Genetics, 105(2), 283-301. https://doi.org/10.1016/j.ajhg.2019.06.016
Haijes, Hanneke A. ; Koster, Maria J.E. ; Rehmann, Holger ; Li, Dong ; Hakonarson, H. ; Cappuccio, Gerarda ; Hancarova, Miroslava ; Lehalle, Daphne ; Reardon, Willie ; Schaefer, G. Bradley ; Lehman, Anna ; van de Laar, Ingrid M.B.H. ; Tesselaar, Coranne D. ; Turner, Clesson ; Goldenberg, A. ; Patrier, Sophie ; Thevenon, Julien ; Pinelli, Michele ; Brunetti-Pierri, Nicola ; Prchalová, Darina ; Havlovicová, Markéta ; Vlckova, Markéta ; Sedláček, Zdeněk ; Lopez, E. ; Ragoussis, Vassilis ; Pagnamenta, Alistair T. ; Kini, Usha ; Vos, Harmjan R. ; van Es, Robert M. ; van Schaik, Richard F.M.A. ; van Essen, Ton A.J. ; Kibaek, M. ; Taylor, Jenny C. ; Sullivan, Jennifer ; Shashi, Vandana ; Petrovski, S. ; Fagerberg, Christina ; Martin, Donna M. ; van Gassen, Koen L.I. ; Pfundt, R. ; Falk, Marni J. ; McCormick, Elizabeth M. ; Timmers, H. T.Marc ; van Hasselt, Peter M. / De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia. In: American Journal of Human Genetics. 2019 ; Vol. 105, No. 2. pp. 283-301.
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abstract = "The RNA polymerase II complex (pol II) is responsible for transcription of all ∼21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly disease-causing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.",
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author = "Haijes, {Hanneke A.} and Koster, {Maria J.E.} and Holger Rehmann and Dong Li and H. Hakonarson and Gerarda Cappuccio and Miroslava Hancarova and Daphne Lehalle and Willie Reardon and Schaefer, {G. Bradley} and Anna Lehman and {van de Laar}, {Ingrid M.B.H.} and Tesselaar, {Coranne D.} and Clesson Turner and A. Goldenberg and Sophie Patrier and Julien Thevenon and Michele Pinelli and Nicola Brunetti-Pierri and Darina Prchalov{\'a} and Mark{\'e}ta Havlovicov{\'a} and Mark{\'e}ta Vlckova and Zdeněk Sedl{\'a}ček and E. Lopez and Vassilis Ragoussis and Pagnamenta, {Alistair T.} and Usha Kini and Vos, {Harmjan R.} and {van Es}, {Robert M.} and {van Schaik}, {Richard F.M.A.} and {van Essen}, {Ton A.J.} and M. Kibaek and Taylor, {Jenny C.} and Jennifer Sullivan and Vandana Shashi and S. Petrovski and Christina Fagerberg and Martin, {Donna M.} and {van Gassen}, {Koen L.I.} and R. Pfundt and Falk, {Marni J.} and McCormick, {Elizabeth M.} and Timmers, {H. T.Marc} and {van Hasselt}, {Peter M.}",
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Haijes, HA, Koster, MJE, Rehmann, H, Li, D, Hakonarson, H, Cappuccio, G, Hancarova, M, Lehalle, D, Reardon, W, Schaefer, GB, Lehman, A, van de Laar, IMBH, Tesselaar, CD, Turner, C, Goldenberg, A, Patrier, S, Thevenon, J, Pinelli, M, Brunetti-Pierri, N, Prchalová, D, Havlovicová, M, Vlckova, M, Sedláček, Z, Lopez, E, Ragoussis, V, Pagnamenta, AT, Kini, U, Vos, HR, van Es, RM, van Schaik, RFMA, van Essen, TAJ, Kibaek, M, Taylor, JC, Sullivan, J, Shashi, V, Petrovski, S, Fagerberg, C, Martin, DM, van Gassen, KLI, Pfundt, R, Falk, MJ, McCormick, EM, Timmers, HTM & van Hasselt, PM 2019, 'De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia', American Journal of Human Genetics, vol. 105, no. 2, pp. 283-301. https://doi.org/10.1016/j.ajhg.2019.06.016

De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia. / Haijes, Hanneke A.; Koster, Maria J.E.; Rehmann, Holger; Li, Dong; Hakonarson, H.; Cappuccio, Gerarda; Hancarova, Miroslava; Lehalle, Daphne; Reardon, Willie; Schaefer, G. Bradley; Lehman, Anna; van de Laar, Ingrid M.B.H.; Tesselaar, Coranne D.; Turner, Clesson; Goldenberg, A.; Patrier, Sophie; Thevenon, Julien; Pinelli, Michele; Brunetti-Pierri, Nicola; Prchalová, Darina; Havlovicová, Markéta; Vlckova, Markéta; Sedláček, Zdeněk; Lopez, E.; Ragoussis, Vassilis; Pagnamenta, Alistair T.; Kini, Usha; Vos, Harmjan R.; van Es, Robert M.; van Schaik, Richard F.M.A.; van Essen, Ton A.J.; Kibaek, M.; Taylor, Jenny C.; Sullivan, Jennifer; Shashi, Vandana; Petrovski, S.; Fagerberg, Christina; Martin, Donna M.; van Gassen, Koen L.I.; Pfundt, R.; Falk, Marni J.; McCormick, Elizabeth M.; Timmers, H. T.Marc; van Hasselt, Peter M.

In: American Journal of Human Genetics, Vol. 105, No. 2, 01.08.2019, p. 283-301.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - De Novo Heterozygous POLR2A Variants Cause a Neurodevelopmental Syndrome with Profound Infantile-Onset Hypotonia

AU - Haijes, Hanneke A.

AU - Koster, Maria J.E.

AU - Rehmann, Holger

AU - Li, Dong

AU - Hakonarson, H.

AU - Cappuccio, Gerarda

AU - Hancarova, Miroslava

AU - Lehalle, Daphne

AU - Reardon, Willie

AU - Schaefer, G. Bradley

AU - Lehman, Anna

AU - van de Laar, Ingrid M.B.H.

AU - Tesselaar, Coranne D.

AU - Turner, Clesson

AU - Goldenberg, A.

AU - Patrier, Sophie

AU - Thevenon, Julien

AU - Pinelli, Michele

AU - Brunetti-Pierri, Nicola

AU - Prchalová, Darina

AU - Havlovicová, Markéta

AU - Vlckova, Markéta

AU - Sedláček, Zdeněk

AU - Lopez, E.

AU - Ragoussis, Vassilis

AU - Pagnamenta, Alistair T.

AU - Kini, Usha

AU - Vos, Harmjan R.

AU - van Es, Robert M.

AU - van Schaik, Richard F.M.A.

AU - van Essen, Ton A.J.

AU - Kibaek, M.

AU - Taylor, Jenny C.

AU - Sullivan, Jennifer

AU - Shashi, Vandana

AU - Petrovski, S.

AU - Fagerberg, Christina

AU - Martin, Donna M.

AU - van Gassen, Koen L.I.

AU - Pfundt, R.

AU - Falk, Marni J.

AU - McCormick, Elizabeth M.

AU - Timmers, H. T.Marc

AU - van Hasselt, Peter M.

PY - 2019/8/1

Y1 - 2019/8/1

N2 - The RNA polymerase II complex (pol II) is responsible for transcription of all ∼21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly disease-causing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.

AB - The RNA polymerase II complex (pol II) is responsible for transcription of all ∼21,000 human protein-encoding genes. Here, we describe sixteen individuals harboring de novo heterozygous variants in POLR2A, encoding RPB1, the largest subunit of pol II. An iterative approach combining structural evaluation and mass spectrometry analyses, the use of S. cerevisiae as a model system, and the assessment of cell viability in HeLa cells allowed us to classify eleven variants as probably disease-causing and four variants as possibly disease-causing. The significance of one variant remains unresolved. By quantification of phenotypic severity, we could distinguish mild and severe phenotypic consequences of the disease-causing variants. Missense variants expected to exert only mild structural effects led to a malfunctioning pol II enzyme, thereby inducing a dominant-negative effect on gene transcription. Intriguingly, individuals carrying these variants presented with a severe phenotype dominated by profound infantile-onset hypotonia and developmental delay. Conversely, individuals carrying variants expected to result in complete loss of function, thus reduced levels of functional pol II from the normal allele, exhibited the mildest phenotypes. We conclude that subtle variants that are central in functionally important domains of POLR2A cause a neurodevelopmental syndrome characterized by profound infantile-onset hypotonia and developmental delay through a dominant-negative effect on pol-II-mediated transcription of DNA.

KW - de novo variants

KW - desert regions

KW - desert Z score

KW - dominant-negative effect

KW - haplo-insufficiency

KW - infantile-onset hypotonia

KW - neurodevelopmental syndrome

KW - POLR2A

KW - RNA polymerase II complex

KW - RPB1

U2 - 10.1016/j.ajhg.2019.06.016

DO - 10.1016/j.ajhg.2019.06.016

M3 - Journal article

C2 - 31353023

AN - SCOPUS:85069833683

VL - 105

SP - 283

EP - 301

JO - American Journal of Human Genetics

JF - American Journal of Human Genetics

SN - 0002-9297

IS - 2

ER -