Genomic and Genic Deletions of the FOX Gene Cluster on 16q24.1 and Inactivating Mutations of FOXF1 Cause Alveolar Capillary Dysplasia and Other Malformations

Paweł Stankiewicz, Partha Sen, Samarth S. Bhatt, Mekayla Storer, Zhilian Xia, Bassem A. Bejjani, Zhishuo Ou, Joanna Wiszniewska, Daniel J. Driscoll, Juan Bolivar, Mislen Bauer, Elaine H. Zackai, Donna McDonald-McGinn, Małgorzata M.J. Nowaczyk, Mitzi Murray, Tamim H. Shaikh, Vicki Martin, Matthew Tyreman, Ingrid Simonic, Lionel WillattJoan Paterson, Sarju Mehta, Diana Rajan, Tomas Fitzgerald, Susan Gribble, Elena Prigmore, Ankita Patel, Lisa G. Shaffer, Nigel P. Carter, Sau Wai Cheung, Claire Langston, Charles Shaw-Smith

Research output: Contribution to journalArticle

243 Citations (Scopus)

Abstract

Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a rare, neonatally lethal developmental disorder of the lung with defining histologic abnormalities typically associated with multiple congenital anomalies (MCA). Using array CGH analysis, we have identified six overlapping microdeletions encompassing the FOX transcription factor gene cluster in chromosome 16q24.1q24.2 in patients with ACD/MPV and MCA. Subsequently, we have identified four different heterozygous mutations (frameshift, nonsense, and no-stop) in the candidate FOXF1 gene in unrelated patients with sporadic ACD/MPV and MCA. Custom-designed, high-resolution microarray analysis of additional ACD/MPV samples revealed one microdeletion harboring FOXF1 and two distinct microdeletions upstream of FOXF1, implicating a position effect. DNA sequence analysis revealed that in six of nine deletions, both breakpoints occurred in the portions of Alu elements showing eight to 43 base pairs of perfect microhomology, suggesting replication error Microhomology-Mediated Break-Induced Replication (MMBIR)/Fork Stalling and Template Switching (FoSTeS) as a mechanism of their formation. In contrast to the association of point mutations in FOXF1 with bowel malrotation, microdeletions of FOXF1 were associated with hypoplastic left heart syndrome and gastrointestinal atresias, probably due to haploinsufficiency for the neighboring FOXC2 and FOXL1 genes. These differences reveal the phenotypic consequences of gene alterations in cis.

Original languageEnglish (US)
Pages (from-to)780-791
Number of pages12
JournalAmerican Journal of Human Genetics
Volume84
Issue number6
DOIs
StatePublished - Jun 12 2009
Externally publishedYes

Fingerprint

Persistent Fetal Circulation Syndrome
Multigene Family
Mutation
Alu Elements
Hypoplastic Left Heart Syndrome
Genes
Haploinsufficiency
Frameshift Mutation
Nonsense Codon
Microarray Analysis
DNA Sequence Analysis
Point Mutation
Base Pairing
Transcription Factors
Chromosomes
Lung
Alveolar capillary dysplasia

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Genomic and Genic Deletions of the FOX Gene Cluster on 16q24.1 and Inactivating Mutations of FOXF1 Cause Alveolar Capillary Dysplasia and Other Malformations. / Stankiewicz, Paweł; Sen, Partha; Bhatt, Samarth S.; Storer, Mekayla; Xia, Zhilian; Bejjani, Bassem A.; Ou, Zhishuo; Wiszniewska, Joanna; Driscoll, Daniel J.; Bolivar, Juan; Bauer, Mislen; Zackai, Elaine H.; McDonald-McGinn, Donna; Nowaczyk, Małgorzata M.J.; Murray, Mitzi; Shaikh, Tamim H.; Martin, Vicki; Tyreman, Matthew; Simonic, Ingrid; Willatt, Lionel; Paterson, Joan; Mehta, Sarju; Rajan, Diana; Fitzgerald, Tomas; Gribble, Susan; Prigmore, Elena; Patel, Ankita; Shaffer, Lisa G.; Carter, Nigel P.; Cheung, Sau Wai; Langston, Claire; Shaw-Smith, Charles.

In: American Journal of Human Genetics, Vol. 84, No. 6, 12.06.2009, p. 780-791.

Research output: Contribution to journalArticle

Stankiewicz, P, Sen, P, Bhatt, SS, Storer, M, Xia, Z, Bejjani, BA, Ou, Z, Wiszniewska, J, Driscoll, DJ, Bolivar, J, Bauer, M, Zackai, EH, McDonald-McGinn, D, Nowaczyk, MMJ, Murray, M, Shaikh, TH, Martin, V, Tyreman, M, Simonic, I, Willatt, L, Paterson, J, Mehta, S, Rajan, D, Fitzgerald, T, Gribble, S, Prigmore, E, Patel, A, Shaffer, LG, Carter, NP, Cheung, SW, Langston, C & Shaw-Smith, C 2009, 'Genomic and Genic Deletions of the FOX Gene Cluster on 16q24.1 and Inactivating Mutations of FOXF1 Cause Alveolar Capillary Dysplasia and Other Malformations', American Journal of Human Genetics, vol. 84, no. 6, pp. 780-791. https://doi.org/10.1016/j.ajhg.2009.05.005
Stankiewicz, Paweł ; Sen, Partha ; Bhatt, Samarth S. ; Storer, Mekayla ; Xia, Zhilian ; Bejjani, Bassem A. ; Ou, Zhishuo ; Wiszniewska, Joanna ; Driscoll, Daniel J. ; Bolivar, Juan ; Bauer, Mislen ; Zackai, Elaine H. ; McDonald-McGinn, Donna ; Nowaczyk, Małgorzata M.J. ; Murray, Mitzi ; Shaikh, Tamim H. ; Martin, Vicki ; Tyreman, Matthew ; Simonic, Ingrid ; Willatt, Lionel ; Paterson, Joan ; Mehta, Sarju ; Rajan, Diana ; Fitzgerald, Tomas ; Gribble, Susan ; Prigmore, Elena ; Patel, Ankita ; Shaffer, Lisa G. ; Carter, Nigel P. ; Cheung, Sau Wai ; Langston, Claire ; Shaw-Smith, Charles. / Genomic and Genic Deletions of the FOX Gene Cluster on 16q24.1 and Inactivating Mutations of FOXF1 Cause Alveolar Capillary Dysplasia and Other Malformations. In: American Journal of Human Genetics. 2009 ; Vol. 84, No. 6. pp. 780-791.
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abstract = "Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a rare, neonatally lethal developmental disorder of the lung with defining histologic abnormalities typically associated with multiple congenital anomalies (MCA). Using array CGH analysis, we have identified six overlapping microdeletions encompassing the FOX transcription factor gene cluster in chromosome 16q24.1q24.2 in patients with ACD/MPV and MCA. Subsequently, we have identified four different heterozygous mutations (frameshift, nonsense, and no-stop) in the candidate FOXF1 gene in unrelated patients with sporadic ACD/MPV and MCA. Custom-designed, high-resolution microarray analysis of additional ACD/MPV samples revealed one microdeletion harboring FOXF1 and two distinct microdeletions upstream of FOXF1, implicating a position effect. DNA sequence analysis revealed that in six of nine deletions, both breakpoints occurred in the portions of Alu elements showing eight to 43 base pairs of perfect microhomology, suggesting replication error Microhomology-Mediated Break-Induced Replication (MMBIR)/Fork Stalling and Template Switching (FoSTeS) as a mechanism of their formation. In contrast to the association of point mutations in FOXF1 with bowel malrotation, microdeletions of FOXF1 were associated with hypoplastic left heart syndrome and gastrointestinal atresias, probably due to haploinsufficiency for the neighboring FOXC2 and FOXL1 genes. These differences reveal the phenotypic consequences of gene alterations in cis.",
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T1 - Genomic and Genic Deletions of the FOX Gene Cluster on 16q24.1 and Inactivating Mutations of FOXF1 Cause Alveolar Capillary Dysplasia and Other Malformations

AU - Stankiewicz, Paweł

AU - Sen, Partha

AU - Bhatt, Samarth S.

AU - Storer, Mekayla

AU - Xia, Zhilian

AU - Bejjani, Bassem A.

AU - Ou, Zhishuo

AU - Wiszniewska, Joanna

AU - Driscoll, Daniel J.

AU - Bolivar, Juan

AU - Bauer, Mislen

AU - Zackai, Elaine H.

AU - McDonald-McGinn, Donna

AU - Nowaczyk, Małgorzata M.J.

AU - Murray, Mitzi

AU - Shaikh, Tamim H.

AU - Martin, Vicki

AU - Tyreman, Matthew

AU - Simonic, Ingrid

AU - Willatt, Lionel

AU - Paterson, Joan

AU - Mehta, Sarju

AU - Rajan, Diana

AU - Fitzgerald, Tomas

AU - Gribble, Susan

AU - Prigmore, Elena

AU - Patel, Ankita

AU - Shaffer, Lisa G.

AU - Carter, Nigel P.

AU - Cheung, Sau Wai

AU - Langston, Claire

AU - Shaw-Smith, Charles

PY - 2009/6/12

Y1 - 2009/6/12

N2 - Alveolar capillary dysplasia with misalignment of pulmonary veins (ACD/MPV) is a rare, neonatally lethal developmental disorder of the lung with defining histologic abnormalities typically associated with multiple congenital anomalies (MCA). Using array CGH analysis, we have identified six overlapping microdeletions encompassing the FOX transcription factor gene cluster in chromosome 16q24.1q24.2 in patients with ACD/MPV and MCA. Subsequently, we have identified four different heterozygous mutations (frameshift, nonsense, and no-stop) in the candidate FOXF1 gene in unrelated patients with sporadic ACD/MPV and MCA. Custom-designed, high-resolution microarray analysis of additional ACD/MPV samples revealed one microdeletion harboring FOXF1 and two distinct microdeletions upstream of FOXF1, implicating a position effect. DNA sequence analysis revealed that in six of nine deletions, both breakpoints occurred in the portions of Alu elements showing eight to 43 base pairs of perfect microhomology, suggesting replication error Microhomology-Mediated Break-Induced Replication (MMBIR)/Fork Stalling and Template Switching (FoSTeS) as a mechanism of their formation. In contrast to the association of point mutations in FOXF1 with bowel malrotation, microdeletions of FOXF1 were associated with hypoplastic left heart syndrome and gastrointestinal atresias, probably due to haploinsufficiency for the neighboring FOXC2 and FOXL1 genes. These differences reveal the phenotypic consequences of gene alterations in cis.

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