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RUNX1-mutated families show phenotype heterogeneity and a somatic mutation profile unique to germline predisposed AML

Brown, Anna L., Arts, Peer, Carmichael, Catherine L., Babic, Milena, Dobbins, Julia, Chong, Chan-Eng, Schreiber, Andreas W., Feng, Jinghua, Phillips, Kerry, Wang, Paul P. S., Ha, Thuong, Homan, Claire C., King-Smith, Sarah L., Rawlings, Lesley, Vakulin, Cassandra, Dubowsky, Andrew, Burdett, Jessica, Moore, Sarah, McKavanagh, Grace, Henry, Denae, Wells, Amanda, Mercorella, Belinda, Nicola, Mario, Suttle, Jeffrey, Wilkins, Ella, Li, Xiao-Chun, Michaud, Joelle, Brautigan, Peter, Cannon, Ping, Altree, Meryl, Jaensch, Louise, Fine, Miriam, Butcher, Carolyn, D’Andrea, Richard J., Lewis, Ian D., Hiwase, Devendra K., Papaemmanuil, Elli, Horwitz, Marshall S., Natsoulis, Georges, Rienhoff, Hugh Y., Patton, Nigel, Mapp, Sally, Susman, Rachel, Morgan, Susan, Cooney, Julian, Currie, Mark, Popat, Uday, Bochtler, Tilmann, Izraeli, Shai, Bradstock, Kenneth, Godley, Lucy A., Krämer, Alwin, Fröhling, Stefan, Wei, Andrew H., Forsyth, Cecily, Mar Fan, Helen, Poplawski, Nicola K., Hahn, Christopher N., Scott, Hamish S.·2020·Blood Advances
DOI 10.1182/bloodadvances.2019000901
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Abstract

First reported in 1999, germline runt-related transcription factor 1 (RUNX1) mutations are a well-established cause of familial platelet disorder with predisposition to myeloid malignancy (FPD-MM). We present the clinical phenotypes and genetic mutations detected in 10 novel RUNX1-mutated FPD-MM families. Genomic analyses on these families detected 2 partial gene deletions, 3 novel mutations, and 5 recurrent mutations as the germline RUNX1 alterations leading to FPD-MM. Combining genomic data from the families reported herein with aggregated published data sets resulted in 130 germline RUNX1 families, which allowed us to investigate whether specific germline mutation characteristics (type, location) could explain the large phenotypic heterogeneity between patients with familial platelet disorder and different HMs. Comparing the somatic mutational signatures between the available familial (n = 35) and published sporadic (n = 137) RUNX1-mutated AML patients showed enrichment for somatic mutations affecting the second RUNX1 allele and GATA2. Conversely, we observed a decreased number of somatic mutations affecting NRAS, SRSF2, and DNMT3A and the collective genes associated with CHIP and epigenetic regulation. This is the largest aggregation and analysis of germline RUNX1 mutations performed to date, providing a unique opportunity to examine the factors underlying phenotypic differences and disease progression from FPD to MM.

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Figure 1 CC-BY-NC-ND · From the PDF
Figure 2 Schematic representation of RUNX1 showing the known germline genetic alterations associated with FPD-MM spectrum phenotypes. Shown are all mutations reported in this study, combined with published RUNX1 single-nucleotide variants (SNVs), small insertions and deletions (Indels), and CNVs annotated to RUNX1C; NM_001754.4; LRG_482. Full-mutation annotations can be found in supplemental Table 1. The numbers of the coding exons and known functional domains are shown within the protein, and the number of amino acids are shown below the diagram. The frequency of recurrent mutations is indicated by (N). For all mutations, the protein changes (p.) are shown, unless specified as splice-site variants (SA or SD). SA, splice acceptor; SD, splice donor.
Figure 2 Schematic representation of RUNX1 showing the known germline genetic alterations associated with FPD-MM spectrum phenotypes. Shown are all mutations reported in this study, combined with published RUNX1 single-nucleotide variants (SNVs), small insertions and deletions (Indels), and CNVs annotated to RUNX1C; NM_001754.4; LRG_482. Full-mutation annotations can be found in supplemental Table 1. The numbers of the coding exons and known functional domains are shown within the protein, and the number of amino acids are shown below the diagram. The frequency of recurrent mutations is indicated by (N). For all mutations, the protein changes (p.) are shown, unless specified as splice-site variants (SA or SD). SA, splice acceptor; SD, splice donor.CC-BY-NC-ND · From the PDF
Figure 3 Somatic mutation differences in inherited (germline) and sporadic (somatic) RUNX1 mutated AML. Aggregation of somatic mutations in germline RUNX1 carriers who developed AML as identified through literature review (right). Comparison of the frequency of somatic mutation in myeloid genes in individuals with inherited or sporadic AML (left). *Somatic mutations identified in samples from this study.
Figure 3 Somatic mutation differences in inherited (germline) and sporadic (somatic) RUNX1 mutated AML. Aggregation of somatic mutations in germline RUNX1 carriers who developed AML as identified through literature review (right). Comparison of the frequency of somatic mutation in myeloid genes in individuals with inherited or sporadic AML (left). *Somatic mutations identified in samples from this study.CC-BY-NC-ND · From the PDF
Figure 4 The spectrum of hematological phenotypes reported with different germline RUNX1 mutations. The protein (p.) changes are shown, for frameshift (fs), stop-gain (*), and missense variants. Splice-site variants are shown with the cDNA change (c.), and (partial) gene deletions are abbreviated. CLL/SLL, chronic lymphocytic leukemia/small lymphocytic lymphoma; CMMoL, chronic myelomonocytic leukemia; Del, deletion; DLBCL, diffuse large B-cell lymphoma; Dup, duplication; Ex, Exon; HCL, hairy cell leukemia; MF, myelofibrosis; SCC, squamous cell carcinoma.
Figure 4 The spectrum of hematological phenotypes reported with different germline RUNX1 mutations. The protein (p.) changes are shown, for frameshift (fs), stop-gain (*), and missense variants. Splice-site variants are shown with the cDNA change (c.), and (partial) gene deletions are abbreviated. CLL/SLL, chronic lymphocytic leukemia/small lymphocytic lymphoma; CMMoL, chronic myelomonocytic leukemia; Del, deletion; DLBCL, diffuse large B-cell lymphoma; Dup, duplication; Ex, Exon; HCL, hairy cell leukemia; MF, myelofibrosis; SCC, squamous cell carcinoma.CC-BY-NC-ND · From the PDF

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Metadata

Authors
Brown, A. L., Arts, P., Carmichael, C. L., Babic, M., Dobbins, J., Chong, C.-E., Schreiber, A. W., Feng, J., Phillips, K., Wang, P. P. S., Ha, T., Homan, C. C., King-Smith, S. L., Rawlings, L., Vakulin, C., Dubowsky, A., Burdett, J., Moore, S., McKavanagh, G., Henry, D., Wells, A., Mercorella, B., Nicola, M., Suttle, J., Wilkins, E., Li, X.-C., Michaud, J., Brautigan, P., Cannon, P., Altree, M., Jaensch, L., Fine, M., Butcher, C., D’Andrea, R. J., Lewis, I. D., Hiwase, D. K., Papaemmanuil, E., Horwitz, M. S., Natsoulis, G., Rienhoff, H. Y., Patton, N., Mapp, S., Susman, R., Morgan, S., Cooney, J., Currie, M., Popat, U., Bochtler, T., Izraeli, S., Bradstock, K., Godley, L. A., Krämer, A., Fröhling, S., Wei, A. H., Forsyth, C., Mar Fan, H., Poplawski, N. K., Hahn, C. N., & Scott, H. S.
Venue
Blood Advances
Publisher
American Society of Hematology
Published
2020-03-24
Volume
4
Issue
6
Pages
1131-1144
ISSN
  • 2473-9529
  • 2473-9537
DOI
10.1182/bloodadvances.2019000901
Cited by
155
References
3
Language
en

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Brown, A. L., Arts, P., Carmichael, C. L., Babic, M., Dobbins, J., Chong, C.-E., Schreiber, A. W., Feng, J., Phillips, K., Wang, P. P. S., Ha, T., Homan, C. C., King-Smith, S. L., Rawlings, L., Vakulin, C., Dubowsky, A., Burdett, J., Moore, S., McKavanagh, G., . . . Scott, H. S. (2020). RUNX1-mutated families show phenotype heterogeneity and a somatic mutation profile unique to germline predisposed AML. Blood Advances. https://doi.org/10.1182/bloodadvances.2019000901