Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations

J. Pei; M. Schuldt; E. Nagyova; Z. Gu; S. el Bouhaddani; L. Yiangou; M. Jansen; J. J.A. Calis; L. M. Dorsch; C. Snijders Blok; N. A.M. van den Dungen; N. Lansu; B. J. Boukens; I. R. Efimov; M. Michels; M. C. Verhaar; R. de Weger; A. Vink; F. G. van Steenbeek; A. F. Baas; R. P. Davis; H. W. Uh; D. W.D. Kuster; C. Cheng; M. Mokry; J. van der Velden; F. W. Asselbergs; M. Harakalova

doi:10.1186/s13148-021-01043-3

Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations

J. Pei, M. Schuldt, E. Nagyova, Z. Gu, S. el Bouhaddani, L. Yiangou, M. Jansen, J. J.A. Calis, L. M. Dorsch, C. Snijders Blok, N. A.M. van den Dungen, N. Lansu, B. J. Boukens, I. R. Efimov, M. Michels, M. C. Verhaar, R. de Weger, A. Vink, F. G. van Steenbeek, A. F. BaasR. P. Davis, H. W. Uh, D. W.D. Kuster, C. Cheng, M. Mokry, J. van der Velden, F. W. Asselbergs^*, M. Harakalova

^*Corresponding author for this work

Biomedical Engineering

Research output: Contribution to journal › Article › peer-review

18 Scopus citations

Abstract

Background: Hypertrophic cardiomyopathy (HCM) is the most common genetic disease of the cardiac muscle, frequently caused by mutations in MYBPC3. However, little is known about the upstream pathways and key regulators causing the disease. Therefore, we employed a multi-omics approach to study the pathomechanisms underlying HCM comparing patient hearts harboring MYBPC3 mutations to control hearts. Results: Using H3K27ac ChIP-seq and RNA-seq we obtained 9310 differentially acetylated regions and 2033 differentially expressed genes, respectively, between 13 HCM and 10 control hearts. We obtained 441 differentially expressed proteins between 11 HCM and 8 control hearts using proteomics. By integrating multi-omics datasets, we identified a set of DNA regions and genes that differentiate HCM from control hearts and 53 protein-coding genes as the major contributors. This comprehensive analysis consistently points toward altered extracellular matrix formation, muscle contraction, and metabolism. Therefore, we studied enriched transcription factor (TF) binding motifs and identified 9 motif-encoded TFs, including KLF15, ETV4, AR, CLOCK, ETS2, GATA5, MEIS1, RXRA, and ZFX. Selected candidates were examined in stem cell-derived cardiomyocytes with and without mutated MYBPC3. Furthermore, we observed an abundance of acetylation signals and transcripts derived from cardiomyocytes compared to non-myocyte populations. Conclusions: By integrating histone acetylome, transcriptome, and proteome profiles, we identified major effector genes and protein networks that drive the pathological changes in HCM with mutated MYBPC3. Our work identifies 38 highly affected protein-coding genes as potential plasma HCM biomarkers and 9 TFs as potential upstream regulators of these pathomechanisms that may serve as possible therapeutic targets.

Original language	English (US)
Article number	61
Journal	Clinical Epigenetics
Volume	13
Issue number	1
DOIs	https://doi.org/10.1186/s13148-021-01043-3
State	Published - Dec 2021

Funding

We would like to thank Pedro Espinosa for performing immunohistochemistry and immunofluorescent stainings. Grateful thanks to Cris dos Remedios and the Sydney Heart Bank for providing non-failing donor tissue. This work was supported by the Netherlands Foundation for Cardiovascular Excellence (to C.C.), the NWO VENI Grant (No. 016.176.136 to M.H.), three NWO VIDI Grants (No. 91714302 to C.C., No. 016096359 to M.C.V and No. 91715303 to R.P.D.), ZonMW-NWO VICI Grant 91818902 (to J.V.), the Erasmus MC fellowship grant (to C.C.), the RM fellowship grant of the UMC Utrecht (to C.C.), Wilhelmina Children’s Hospital research funding (No. OZF/14 to M.H.), the Netherlands Cardiovascular Research Initiative: An initiative with the support of the Dutch Heart Foundation (CVON2014-40 DOSIS to J.V., M.H., F.W.A., CVON2014-11 RECONNECT to C.C., M.C.V., Dekker 2015T041 to A.F.B. and Queen of Heart to C.C. and M.C.V.), UCL Hospitals NIHR Biomedical Research Centre (to F.W.A.), and the Starting Grant (STEMCARDIORISK) from the European Research Council under the European Union’s Horizon 2020 Research and Innovation Program (H2020 European Research Council; Grant Agreement 638030) to R.P.D.

Keywords

HCM
Histone acetylome
MYBPC3
Proteome
Transcription factors
Transcriptome

ASJC Scopus subject areas

Molecular Biology
Genetics
Developmental Biology
Genetics(clinical)

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10.1186/s13148-021-01043-3

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Pei, J., Schuldt, M., Nagyova, E., Gu, Z., el Bouhaddani, S., Yiangou, L., Jansen, M., Calis, J. J. A., Dorsch, L. M., Blok, C. S., van den Dungen, N. A. M., Lansu, N., Boukens, B. J., Efimov, I. R., Michels, M., Verhaar, M. C., de Weger, R., Vink, A., van Steenbeek, F. G., ... Harakalova, M. (2021). Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations. Clinical Epigenetics, 13(1), Article 61. https://doi.org/10.1186/s13148-021-01043-3

@article{bc01d91cc1484ce2b182f3490b80513a,

title = "Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations",

abstract = "Background: Hypertrophic cardiomyopathy (HCM) is the most common genetic disease of the cardiac muscle, frequently caused by mutations in MYBPC3. However, little is known about the upstream pathways and key regulators causing the disease. Therefore, we employed a multi-omics approach to study the pathomechanisms underlying HCM comparing patient hearts harboring MYBPC3 mutations to control hearts. Results: Using H3K27ac ChIP-seq and RNA-seq we obtained 9310 differentially acetylated regions and 2033 differentially expressed genes, respectively, between 13 HCM and 10 control hearts. We obtained 441 differentially expressed proteins between 11 HCM and 8 control hearts using proteomics. By integrating multi-omics datasets, we identified a set of DNA regions and genes that differentiate HCM from control hearts and 53 protein-coding genes as the major contributors. This comprehensive analysis consistently points toward altered extracellular matrix formation, muscle contraction, and metabolism. Therefore, we studied enriched transcription factor (TF) binding motifs and identified 9 motif-encoded TFs, including KLF15, ETV4, AR, CLOCK, ETS2, GATA5, MEIS1, RXRA, and ZFX. Selected candidates were examined in stem cell-derived cardiomyocytes with and without mutated MYBPC3. Furthermore, we observed an abundance of acetylation signals and transcripts derived from cardiomyocytes compared to non-myocyte populations. Conclusions: By integrating histone acetylome, transcriptome, and proteome profiles, we identified major effector genes and protein networks that drive the pathological changes in HCM with mutated MYBPC3. Our work identifies 38 highly affected protein-coding genes as potential plasma HCM biomarkers and 9 TFs as potential upstream regulators of these pathomechanisms that may serve as possible therapeutic targets.",

keywords = "HCM, Histone acetylome, MYBPC3, Proteome, Transcription factors, Transcriptome",

author = "J. Pei and M. Schuldt and E. Nagyova and Z. Gu and {el Bouhaddani}, S. and L. Yiangou and M. Jansen and Calis, {J. J.A.} and Dorsch, {L. M.} and Blok, {C. Snijders} and {van den Dungen}, {N. A.M.} and N. Lansu and Boukens, {B. J.} and Efimov, {I. R.} and M. Michels and Verhaar, {M. C.} and {de Weger}, R. and A. Vink and {van Steenbeek}, {F. G.} and Baas, {A. F.} and Davis, {R. P.} and Uh, {H. W.} and Kuster, {D. W.D.} and C. Cheng and M. Mokry and {van der Velden}, J. and Asselbergs, {F. W.} and M. Harakalova",

note = "Funding Information: We would like to thank Pedro Espinosa for performing immunohistochemistry and immunofluorescent stainings. Grateful thanks to Cris dos Remedios and the Sydney Heart Bank for providing non-failing donor tissue. Funding Information: This work was supported by the Netherlands Foundation for Cardiovascular Excellence (to C.C.), the NWO VENI Grant (No. 016.176.136 to M.H.), three NWO VIDI Grants (No. 91714302 to C.C., No. 016096359 to M.C.V and No. 91715303 to R.P.D.), ZonMW-NWO VICI Grant 91818902 (to J.V.), the Erasmus MC fellowship grant (to C.C.), the RM fellowship grant of the UMC Utrecht (to C.C.), Wilhelmina Children{\textquoteright}s Hospital research funding (No. OZF/14 to M.H.), the Netherlands Cardiovascular Research Initiative: An initiative with the support of the Dutch Heart Foundation (CVON2014-40 DOSIS to J.V., M.H., F.W.A., CVON2014-11 RECONNECT to C.C., M.C.V., Dekker 2015T041 to A.F.B. and Queen of Heart to C.C. and M.C.V.), UCL Hospitals NIHR Biomedical Research Centre (to F.W.A.), and the Starting Grant (STEMCARDIORISK) from the European Research Council under the European Union{\textquoteright}s Horizon 2020 Research and Innovation Program (H2020 European Research Council; Grant Agreement 638030) to R.P.D. Publisher Copyright: {\textcopyright} 2021, The Author(s).",

year = "2021",

month = dec,

doi = "10.1186/s13148-021-01043-3",

language = "English (US)",

volume = "13",

journal = "Clinical Epigenetics",

issn = "1868-7075",

publisher = "Springer Verlag",

number = "1",

}

Pei, J, Schuldt, M, Nagyova, E, Gu, Z, el Bouhaddani, S, Yiangou, L, Jansen, M, Calis, JJA, Dorsch, LM, Blok, CS, van den Dungen, NAM, Lansu, N, Boukens, BJ, Efimov, IR, Michels, M, Verhaar, MC, de Weger, R, Vink, A, van Steenbeek, FG, Baas, AF, Davis, RP, Uh, HW, Kuster, DWD, Cheng, C, Mokry, M, van der Velden, J, Asselbergs, FW & Harakalova, M 2021, 'Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations', Clinical Epigenetics, vol. 13, no. 1, 61. https://doi.org/10.1186/s13148-021-01043-3

TY - JOUR

T1 - Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations

AU - Pei, J.

AU - Schuldt, M.

AU - Nagyova, E.

AU - Gu, Z.

AU - el Bouhaddani, S.

AU - Yiangou, L.

AU - Jansen, M.

AU - Calis, J. J.A.

AU - Dorsch, L. M.

AU - Blok, C. Snijders

AU - van den Dungen, N. A.M.

AU - Lansu, N.

AU - Boukens, B. J.

AU - Efimov, I. R.

AU - Michels, M.

AU - Verhaar, M. C.

AU - de Weger, R.

AU - Vink, A.

AU - van Steenbeek, F. G.

AU - Baas, A. F.

AU - Davis, R. P.

AU - Uh, H. W.

AU - Kuster, D. W.D.

AU - Cheng, C.

AU - Mokry, M.

AU - van der Velden, J.

AU - Asselbergs, F. W.

AU - Harakalova, M.

N1 - Funding Information: We would like to thank Pedro Espinosa for performing immunohistochemistry and immunofluorescent stainings. Grateful thanks to Cris dos Remedios and the Sydney Heart Bank for providing non-failing donor tissue. Funding Information: This work was supported by the Netherlands Foundation for Cardiovascular Excellence (to C.C.), the NWO VENI Grant (No. 016.176.136 to M.H.), three NWO VIDI Grants (No. 91714302 to C.C., No. 016096359 to M.C.V and No. 91715303 to R.P.D.), ZonMW-NWO VICI Grant 91818902 (to J.V.), the Erasmus MC fellowship grant (to C.C.), the RM fellowship grant of the UMC Utrecht (to C.C.), Wilhelmina Children’s Hospital research funding (No. OZF/14 to M.H.), the Netherlands Cardiovascular Research Initiative: An initiative with the support of the Dutch Heart Foundation (CVON2014-40 DOSIS to J.V., M.H., F.W.A., CVON2014-11 RECONNECT to C.C., M.C.V., Dekker 2015T041 to A.F.B. and Queen of Heart to C.C. and M.C.V.), UCL Hospitals NIHR Biomedical Research Centre (to F.W.A.), and the Starting Grant (STEMCARDIORISK) from the European Research Council under the European Union’s Horizon 2020 Research and Innovation Program (H2020 European Research Council; Grant Agreement 638030) to R.P.D. Publisher Copyright: © 2021, The Author(s).

PY - 2021/12

Y1 - 2021/12

N2 - Background: Hypertrophic cardiomyopathy (HCM) is the most common genetic disease of the cardiac muscle, frequently caused by mutations in MYBPC3. However, little is known about the upstream pathways and key regulators causing the disease. Therefore, we employed a multi-omics approach to study the pathomechanisms underlying HCM comparing patient hearts harboring MYBPC3 mutations to control hearts. Results: Using H3K27ac ChIP-seq and RNA-seq we obtained 9310 differentially acetylated regions and 2033 differentially expressed genes, respectively, between 13 HCM and 10 control hearts. We obtained 441 differentially expressed proteins between 11 HCM and 8 control hearts using proteomics. By integrating multi-omics datasets, we identified a set of DNA regions and genes that differentiate HCM from control hearts and 53 protein-coding genes as the major contributors. This comprehensive analysis consistently points toward altered extracellular matrix formation, muscle contraction, and metabolism. Therefore, we studied enriched transcription factor (TF) binding motifs and identified 9 motif-encoded TFs, including KLF15, ETV4, AR, CLOCK, ETS2, GATA5, MEIS1, RXRA, and ZFX. Selected candidates were examined in stem cell-derived cardiomyocytes with and without mutated MYBPC3. Furthermore, we observed an abundance of acetylation signals and transcripts derived from cardiomyocytes compared to non-myocyte populations. Conclusions: By integrating histone acetylome, transcriptome, and proteome profiles, we identified major effector genes and protein networks that drive the pathological changes in HCM with mutated MYBPC3. Our work identifies 38 highly affected protein-coding genes as potential plasma HCM biomarkers and 9 TFs as potential upstream regulators of these pathomechanisms that may serve as possible therapeutic targets.

AB - Background: Hypertrophic cardiomyopathy (HCM) is the most common genetic disease of the cardiac muscle, frequently caused by mutations in MYBPC3. However, little is known about the upstream pathways and key regulators causing the disease. Therefore, we employed a multi-omics approach to study the pathomechanisms underlying HCM comparing patient hearts harboring MYBPC3 mutations to control hearts. Results: Using H3K27ac ChIP-seq and RNA-seq we obtained 9310 differentially acetylated regions and 2033 differentially expressed genes, respectively, between 13 HCM and 10 control hearts. We obtained 441 differentially expressed proteins between 11 HCM and 8 control hearts using proteomics. By integrating multi-omics datasets, we identified a set of DNA regions and genes that differentiate HCM from control hearts and 53 protein-coding genes as the major contributors. This comprehensive analysis consistently points toward altered extracellular matrix formation, muscle contraction, and metabolism. Therefore, we studied enriched transcription factor (TF) binding motifs and identified 9 motif-encoded TFs, including KLF15, ETV4, AR, CLOCK, ETS2, GATA5, MEIS1, RXRA, and ZFX. Selected candidates were examined in stem cell-derived cardiomyocytes with and without mutated MYBPC3. Furthermore, we observed an abundance of acetylation signals and transcripts derived from cardiomyocytes compared to non-myocyte populations. Conclusions: By integrating histone acetylome, transcriptome, and proteome profiles, we identified major effector genes and protein networks that drive the pathological changes in HCM with mutated MYBPC3. Our work identifies 38 highly affected protein-coding genes as potential plasma HCM biomarkers and 9 TFs as potential upstream regulators of these pathomechanisms that may serve as possible therapeutic targets.

KW - HCM

KW - Histone acetylome

KW - MYBPC3

KW - Proteome

KW - Transcription factors

KW - Transcriptome

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U2 - 10.1186/s13148-021-01043-3

DO - 10.1186/s13148-021-01043-3

M3 - Article

C2 - 33757590

AN - SCOPUS:85103192155

SN - 1868-7075

VL - 13

JO - Clinical Epigenetics

JF - Clinical Epigenetics

IS - 1

M1 - 61

ER -

Multi-omics integration identifies key upstream regulators of pathomechanisms in hypertrophic cardiomyopathy due to truncating MYBPC3 mutations

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