Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis

Linda M. Polfus; Rajiv K. Khajuria; Ursula M. Schick; Nathan Pankratz; Raha Pazoki; Jennifer A. Brody; Ming Huei Chen; Paul L. Auer; James S. Floyd; Jie Huang; Leslie Lange; Frank J A van Rooij; Richard A. Gibbs; Ginger Metcalf; Donna Muzny; Narayanan Veeraraghavan; Klaudia Walter; Lu Chen; Lisa Yanek; Lewis C. Becker; Gina M. Peloso; Aoi Wakabayashi; Mart Kals; Andres Metspalu; Tõnu Esko; Keolu Fox; Robert Wallace; Nora Franceshini; Nena Matijevic; Kenneth M. Rice; Traci M. Bartz; Leo Pekka Lyytikäinen; Mika Kähönen; Terho Lehtimäki; Olli T. Raitakari; Ruifang Li-Gao; Dennis O. Mook-Kanamori; Guillaume Lettre; Cornelia M. van Duijn; Oscar H. Franco; Stephen S. Rich; Fernando Rivadeneira; Albert Hofman; André G. Uitterlinden; James G. Wilson; Bruce M. Psaty; Nicole Soranzo; Abbas Dehghan; Eric Boerwinkle; Xiaoling Zhang; Andrew D. Johnson; Christopher J. O'Donnell; Jill M. Johnsen; Alexander P. Reiner; Santhi K. Ganesh; Vijay G. Sankaran

doi:10.1016/j.ajhg.2016.06.016

Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis

Linda M. Polfus, Rajiv K. Khajuria, Ursula M. Schick, Nathan Pankratz, Raha Pazoki, Jennifer A. Brody, Ming Huei Chen, Paul L. Auer, James S. Floyd, Jie Huang, Leslie Lange, Frank J A van Rooij, Richard A. Gibbs, Ginger Metcalf, Donna Muzny, Narayanan Veeraraghavan, Klaudia Walter, Lu Chen, Lisa Yanek, Lewis C. BeckerGina M. Peloso, Aoi Wakabayashi, Mart Kals, Andres Metspalu, Tõnu Esko, Keolu Fox, Robert Wallace, Nora Franceshini, Nena Matijevic, Kenneth M. Rice, Traci M. Bartz, Leo Pekka Lyytikäinen, Mika Kähönen, Terho Lehtimäki, Olli T. Raitakari, Ruifang Li-Gao, Dennis O. Mook-Kanamori, Guillaume Lettre, Cornelia M. van Duijn, Oscar H. Franco, Stephen S. Rich, Fernando Rivadeneira, Albert Hofman, André G. Uitterlinden, James G. Wilson, Bruce M. Psaty, Nicole Soranzo, Abbas Dehghan, Eric Boerwinkle, Xiaoling Zhang, Andrew D. Johnson, Christopher J. O'Donnell, Jill M. Johnsen, Alexander P. Reiner, Santhi K. Ganesh, Vijay G. Sankaran

Laboratory Medicine and Pathology

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

34 Scopus citations

Abstract

Circulating blood cell counts and indices are important indicators of hematopoietic function and a number of clinical parameters, such as blood oxygen-carrying capacity, inflammation, and hemostasis. By performing whole-exome sequence association analyses of hematologic quantitative traits in 15,459 community-dwelling individuals, followed by in silico replication in up to 52,024 independent samples, we identified two previously undescribed coding variants associated with lower platelet count: a common missense variant in CPS1 (rs1047891, MAF = 0.33, discovery + replication p = 6.38 × 10⁻¹⁰) and a rare synonymous variant in GFI1B (rs150813342, MAF = 0.009, discovery + replication p = 1.79 × 10⁻²⁷). By performing CRISPR/Cas9 genome editing in hematopoietic cell lines and follow-up targeted knockdown experiments in primary human hematopoietic stem and progenitor cells, we demonstrate an alternative splicing mechanism by which the GFI1B rs150813342 variant suppresses formation of a GFI1B isoform that preferentially promotes megakaryocyte differentiation and platelet production. These results demonstrate how unbiased studies of natural variation in blood cell traits can provide insight into the regulation of human hematopoiesis.

Original language	English (US)
Pages (from-to)	481-488
Number of pages	8
Journal	American Journal of Human Genetics
Volume	99
Issue number	2
DOIs	https://doi.org/10.1016/j.ajhg.2016.06.016
State	Published - Aug 4 2016

Bibliographical note

Funding Information:
The work described in this manuscript was supported in part by NIH grants HL122684 to S.K.G. and DK103794 and HL120791 to V.G.S. N.S. is supported by the Wellcome Trust (grant codes WT098051 and WT091310), the EU 7 th Framework Programme (EPIGENESYS grant code 257082 and BLUEPRINT grant code HEALTH-F5-2011-282510) and the NIH Research (NIHR) Blood and Transplant Research Unit (BTRU) in Donor Health and Genomics at the University of Cambridge in partnership with NHS Blood and Transplant (NHSBT).

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© 2016 American Society of Human Genetics

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10.1016/j.ajhg.2016.06.016

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Polfus, L. M., Khajuria, R. K., Schick, U. M., Pankratz, N., Pazoki, R., Brody, J. A., Chen, M. H., Auer, P. L., Floyd, J. S., Huang, J., Lange, L., van Rooij, F. J. A., Gibbs, R. A., Metcalf, G., Muzny, D., Veeraraghavan, N., Walter, K., Chen, L., Yanek, L., ... Sankaran, V. G. (2016). Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis. American Journal of Human Genetics, 99(2), 481-488. https://doi.org/10.1016/j.ajhg.2016.06.016

Polfus, LM, Khajuria, RK, Schick, UM, Pankratz, N, Pazoki, R, Brody, JA, Chen, MH, Auer, PL, Floyd, JS, Huang, J, Lange, L, van Rooij, FJA, Gibbs, RA, Metcalf, G, Muzny, D, Veeraraghavan, N, Walter, K, Chen, L, Yanek, L, Becker, LC, Peloso, GM, Wakabayashi, A, Kals, M, Metspalu, A, Esko, T, Fox, K, Wallace, R, Franceshini, N, Matijevic, N, Rice, KM, Bartz, TM, Lyytikäinen, LP, Kähönen, M, Lehtimäki, T, Raitakari, OT, Li-Gao, R, Mook-Kanamori, DO, Lettre, G, van Duijn, CM, Franco, OH, Rich, SS, Rivadeneira, F, Hofman, A, Uitterlinden, AG, Wilson, JG, Psaty, BM, Soranzo, N, Dehghan, A, Boerwinkle, E, Zhang, X, Johnson, AD, O'Donnell, CJ, Johnsen, JM, Reiner, AP, Ganesh, SK & Sankaran, VG 2016, 'Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis', American Journal of Human Genetics, vol. 99, no. 2, pp. 481-488. https://doi.org/10.1016/j.ajhg.2016.06.016

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title = "Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis",

abstract = "Circulating blood cell counts and indices are important indicators of hematopoietic function and a number of clinical parameters, such as blood oxygen-carrying capacity, inflammation, and hemostasis. By performing whole-exome sequence association analyses of hematologic quantitative traits in 15,459 community-dwelling individuals, followed by in silico replication in up to 52,024 independent samples, we identified two previously undescribed coding variants associated with lower platelet count: a common missense variant in CPS1 (rs1047891, MAF = 0.33, discovery + replication p = 6.38 × 10−10) and a rare synonymous variant in GFI1B (rs150813342, MAF = 0.009, discovery + replication p = 1.79 × 10−27). By performing CRISPR/Cas9 genome editing in hematopoietic cell lines and follow-up targeted knockdown experiments in primary human hematopoietic stem and progenitor cells, we demonstrate an alternative splicing mechanism by which the GFI1B rs150813342 variant suppresses formation of a GFI1B isoform that preferentially promotes megakaryocyte differentiation and platelet production. These results demonstrate how unbiased studies of natural variation in blood cell traits can provide insight into the regulation of human hematopoiesis.",

author = "Polfus, {Linda M.} and Khajuria, {Rajiv K.} and Schick, {Ursula M.} and Nathan Pankratz and Raha Pazoki and Brody, {Jennifer A.} and Chen, {Ming Huei} and Auer, {Paul L.} and Floyd, {James S.} and Jie Huang and Leslie Lange and {van Rooij}, {Frank J A} and Gibbs, {Richard A.} and Ginger Metcalf and Donna Muzny and Narayanan Veeraraghavan and Klaudia Walter and Lu Chen and Lisa Yanek and Becker, {Lewis C.} and Peloso, {Gina M.} and Aoi Wakabayashi and Mart Kals and Andres Metspalu and T{\~o}nu Esko and Keolu Fox and Robert Wallace and Nora Franceshini and Nena Matijevic and Rice, {Kenneth M.} and Bartz, {Traci M.} and Lyytik{\"a}inen, {Leo Pekka} and Mika K{\"a}h{\"o}nen and Terho Lehtim{\"a}ki and Raitakari, {Olli T.} and Ruifang Li-Gao and Mook-Kanamori, {Dennis O.} and Guillaume Lettre and {van Duijn}, {Cornelia M.} and Franco, {Oscar H.} and Rich, {Stephen S.} and Fernando Rivadeneira and Albert Hofman and Uitterlinden, {Andr{\'e} G.} and Wilson, {James G.} and Psaty, {Bruce M.} and Nicole Soranzo and Abbas Dehghan and Eric Boerwinkle and Xiaoling Zhang and Johnson, {Andrew D.} and O'Donnell, {Christopher J.} and Johnsen, {Jill M.} and Reiner, {Alexander P.} and Ganesh, {Santhi K.} and Sankaran, {Vijay G.}",

note = "Funding Information: The work described in this manuscript was supported in part by NIH grants HL122684 to S.K.G. and DK103794 and HL120791 to V.G.S. N.S. is supported by the Wellcome Trust (grant codes WT098051 and WT091310), the EU 7 th Framework Programme (EPIGENESYS grant code 257082 and BLUEPRINT grant code HEALTH-F5-2011-282510) and the NIH Research (NIHR) Blood and Transplant Research Unit (BTRU) in Donor Health and Genomics at the University of Cambridge in partnership with NHS Blood and Transplant (NHSBT). Publisher Copyright: {\textcopyright} 2016 American Society of Human Genetics",

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month = aug,

day = "4",

doi = "10.1016/j.ajhg.2016.06.016",

language = "English (US)",

volume = "99",

pages = "481--488",

journal = "American Journal of Human Genetics",

issn = "0002-9297",

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T1 - Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis

AU - Polfus, Linda M.

AU - Khajuria, Rajiv K.

AU - Schick, Ursula M.

AU - Pankratz, Nathan

AU - Pazoki, Raha

AU - Brody, Jennifer A.

AU - Chen, Ming Huei

AU - Auer, Paul L.

AU - Floyd, James S.

AU - Huang, Jie

AU - Lange, Leslie

AU - van Rooij, Frank J A

AU - Gibbs, Richard A.

AU - Metcalf, Ginger

AU - Muzny, Donna

AU - Veeraraghavan, Narayanan

AU - Walter, Klaudia

AU - Chen, Lu

AU - Yanek, Lisa

AU - Becker, Lewis C.

AU - Peloso, Gina M.

AU - Wakabayashi, Aoi

AU - Kals, Mart

AU - Metspalu, Andres

AU - Esko, Tõnu

AU - Fox, Keolu

AU - Wallace, Robert

AU - Franceshini, Nora

AU - Matijevic, Nena

AU - Rice, Kenneth M.

AU - Bartz, Traci M.

AU - Lyytikäinen, Leo Pekka

AU - Kähönen, Mika

AU - Lehtimäki, Terho

AU - Raitakari, Olli T.

AU - Li-Gao, Ruifang

AU - Mook-Kanamori, Dennis O.

AU - Lettre, Guillaume

AU - van Duijn, Cornelia M.

AU - Franco, Oscar H.

AU - Rich, Stephen S.

AU - Rivadeneira, Fernando

AU - Hofman, Albert

AU - Uitterlinden, André G.

AU - Wilson, James G.

AU - Psaty, Bruce M.

AU - Soranzo, Nicole

AU - Dehghan, Abbas

AU - Boerwinkle, Eric

AU - Zhang, Xiaoling

AU - Johnson, Andrew D.

AU - O'Donnell, Christopher J.

AU - Johnsen, Jill M.

AU - Reiner, Alexander P.

AU - Ganesh, Santhi K.

AU - Sankaran, Vijay G.

N1 - Funding Information: The work described in this manuscript was supported in part by NIH grants HL122684 to S.K.G. and DK103794 and HL120791 to V.G.S. N.S. is supported by the Wellcome Trust (grant codes WT098051 and WT091310), the EU 7 th Framework Programme (EPIGENESYS grant code 257082 and BLUEPRINT grant code HEALTH-F5-2011-282510) and the NIH Research (NIHR) Blood and Transplant Research Unit (BTRU) in Donor Health and Genomics at the University of Cambridge in partnership with NHS Blood and Transplant (NHSBT). Publisher Copyright: © 2016 American Society of Human Genetics

PY - 2016/8/4

Y1 - 2016/8/4

N2 - Circulating blood cell counts and indices are important indicators of hematopoietic function and a number of clinical parameters, such as blood oxygen-carrying capacity, inflammation, and hemostasis. By performing whole-exome sequence association analyses of hematologic quantitative traits in 15,459 community-dwelling individuals, followed by in silico replication in up to 52,024 independent samples, we identified two previously undescribed coding variants associated with lower platelet count: a common missense variant in CPS1 (rs1047891, MAF = 0.33, discovery + replication p = 6.38 × 10−10) and a rare synonymous variant in GFI1B (rs150813342, MAF = 0.009, discovery + replication p = 1.79 × 10−27). By performing CRISPR/Cas9 genome editing in hematopoietic cell lines and follow-up targeted knockdown experiments in primary human hematopoietic stem and progenitor cells, we demonstrate an alternative splicing mechanism by which the GFI1B rs150813342 variant suppresses formation of a GFI1B isoform that preferentially promotes megakaryocyte differentiation and platelet production. These results demonstrate how unbiased studies of natural variation in blood cell traits can provide insight into the regulation of human hematopoiesis.

AB - Circulating blood cell counts and indices are important indicators of hematopoietic function and a number of clinical parameters, such as blood oxygen-carrying capacity, inflammation, and hemostasis. By performing whole-exome sequence association analyses of hematologic quantitative traits in 15,459 community-dwelling individuals, followed by in silico replication in up to 52,024 independent samples, we identified two previously undescribed coding variants associated with lower platelet count: a common missense variant in CPS1 (rs1047891, MAF = 0.33, discovery + replication p = 6.38 × 10−10) and a rare synonymous variant in GFI1B (rs150813342, MAF = 0.009, discovery + replication p = 1.79 × 10−27). By performing CRISPR/Cas9 genome editing in hematopoietic cell lines and follow-up targeted knockdown experiments in primary human hematopoietic stem and progenitor cells, we demonstrate an alternative splicing mechanism by which the GFI1B rs150813342 variant suppresses formation of a GFI1B isoform that preferentially promotes megakaryocyte differentiation and platelet production. These results demonstrate how unbiased studies of natural variation in blood cell traits can provide insight into the regulation of human hematopoiesis.

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Whole-Exome Sequencing Identifies Loci Associated with Blood Cell Traits and Reveals a Role for Alternative GFI1B Splice Variants in Human Hematopoiesis

Abstract

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