Full text
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| Author(s): |
Ana Carolina dos Santos Fonseca
Total Authors: 1
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| Document type: | Master's Dissertation |
| Press: | São Paulo. |
| Institution: | Universidade de São Paulo (USP). Instituto de Biociências (IBIOC/SB) |
| Defense date: | 2011-10-17 |
| Examining board members: |
Angela Maria Vianna Morgante;
Fernando Kok;
Carla Rosenberg
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| Advisor: | Angela Maria Vianna Morgante |
| Abstract | |
This study aimed at identifying mechanisms that lead to phenotypic abnormalities in carriers of balanced chromosomal rearrangements. We studied six apparently balanced chromosomal translocations detected in patients with congenital malformations, intellectual impairment or neuropsychomotor delay. Breakpoint mapping of apparently balanced chromosomal rearrangements was performed by fluorescence in situ hybridization (FISH), and cryptic genomic imbalances were investigated by array comparative genomic hybridization (a-CGH). We studied two sporadic translocations, t(7;17) (p13;q24) and t(17;20) (q24.3,q11.2). The breakpoints were located on chromosome 17, respectively, 917-855 kb and 624-585 kb upstream the SOX9 gene. There are no genes mapped to these segments. Patients had skeletal abnormalities that led to the diagnosis of acampomelic campomelic dysplasia. No submicroscopic chromosomal imbalances were detected by a-CGH. These translocations can alter gene expression by directly disrupting regulatory elements or by a position effect. The translocation t(7;17) and (17;20) provided additional information regarding the regulatory region of SOX9. The clinical manifestations associated with the translocation t(17;20) allowed the redefining of the limits of the distal breakpoint cluster of rearrangements on chromosome 17, which are associated with SOX9-related disorders. A conserved element was identified as a candidate SOX9 enhancer for testis development. Two additional sporadic translocations were associated with submicroscopic imbalances in cis to the breakpoints: t(10;21) and t(X;22). The translocation t(10;21)(p13;q22) was present in a girl with delayed motor development, microcephaly and generalized spasticity. The breakpoints on chromosomes 10 and 21 were mapped to 440 kb and 172 kb segments, respectively. Among the genes mapped to these breakpoint regions, only CDNF on chromossome 10, is highly expressed in the nervous system. Four de novo deletions on chromosome 10 were identified by a-CGH, revealing the complexity of the rearrangement. Two deletions were located at the vicinity of the translocation breakpoint: a 973 kb deletion on 10p14 and a 1.15 Mb deletion on 10p13 located, respectively, 3.27 Mb and 210 kb distal to the translocation breakpoint. Two other deletions were detected on the long arm of chromosome 10: a 700 kb deletion on 10q26.13, located 110.10 Mb distal to the translocation breakpoint, which we could not mapped by FISH; and a 1.66 Mb deletion on 10q26.2-q26.3, located 114.68 Mb distal to the translocation breakpoint. Fourteen genes are mapped to the microdeletion regions. Among these genes, GPR26, OPTN, CUGBP2 are highly expressed in the nervous system and, together with CNDF, are candidates for having clinical effects. The chromothripsis model, in which rearrangements result from a series of simultaneous double-stranded breaks followed by random joining of chromosomal fragments, might explain the formation of this t(10,21) translocation. Applying a-CGH to the apparently balanced translocation t(X;22)(q22;q13) carried by a girl, we detected duplicated segments on 22q13 and Xq22, encompassing 490 kb and 570 kb, respectively. FISH analysis revealed that the additional copies were located to the breakpoints of the derivative X chromosome (22q13 duplicated segment) and of the derivative 22 chromosome (Xq22 duplicated segment). No genes are mapped to the duplicated segment of chromosome 22. One of the 14 duplicated genes on the X chromosome is PLP1 (proteolipid protein 1). PLP1 point mutations and duplications cause Pelizaeus-Merzbacher disease, characterized by hypomyelination of the central nervous system, and affecting almost exclusively males. Neurological examination of the patient, including MRI showed that her clinical manifestations were compatible with Pelizaeus-Merzbacher disease. The pattern of X chromosome inactivation was determined in peripheral blood lymphocytes, based on the AR gene methylation, and cytologically, in metaphases spreads, after 5-BrdU incorporation, and showed that the normal X chromosome was the inactive one in the majority of cells. This pattern of X inactivation makes cells functionally balanced for the translocated segments. A copy of the PLP1 gene, however, is present on chromosome 22, in addition to the copies located on the chromosomes X and der(X). Thus, two active copies of the gene are present in the cells, irrespective of the X-inactivation pattern. A mechanism based on replication bubbles can explain the formation of translocations with duplication at the breakpoints, such as this t(X;22). An apparently balanced familial translocation t(2;22)(p13;q12.2) was detected in association with learning disability and craniofacial and hand dysmorphisms. The combination of a-CGH and FISH revealed that the rearrangement, identified by Gbanding as a two-break balanced translocation, was a more complex three-chromosome rearrangement: a segment from chromosome 2 was inserted into chromosome 5 short arm, an event that probably caused a 5p15.1 deletion; on chromosome 22 a segment from 5q23.2-23.3 was inserted into the breakpoint. Chromosomes der(2) and der(22) were present in all affected individuals. However, the der(5) did not segregate with the clinical phenotype, and was detected in a phenotypically normal individual. The 6.6 Mb duplication of the long arm of chromosome 5 was the imbalance common to all affected individuals. The 17 genes in this region are candidates for the clinical phenotypes through dosage effect. In addition, common to all affected individuals is the haploinsufficiency of SLC1A4, a gene highly expressed in the nervous system, which is encompassed by the deletion on chromosome 2. Interestingly, learning disabilities were more pronounced in those patients who also carried chromosome 2 deletion. CEP68, RAB1A, ACTR2 and SPRED2, mapped to this deleted segment, might contribute to the variability of the clinical phenotype in the family. The translocation t(2;5;22) might have originated from a series of simultaneously occurring brakes, two on the short arm of chromosome 2, four breaks on the short arm and two on the long arm of chromosome 5, and one break on the long arm of chromosome 22. We also investigated by a-CGH a sporadic translocation t(2;16)(q35;q24.1) whose carrier had hand and feet defects. Submicroscopic imbalances were not detected. Previously performed FISH delimited the breakpoints segments on chromosomes 2 and 16, which encompassed no genes. The IHH gene, which is involved in limb development, is located approximately 1 Mb upstream chromosome 2 breakpoint. Therefore, the translocation might have disrupted a regulatory element of IHH or, alternatively, separated the gene from a regulatory region, thus altering IHH expression. This study provides further evidence for the occurrence of submicroscopic chromosomal imbalances in association with apparently balanced rearrangements. In three out of six translocations - t(10,21), t(2;5;22), t(X;22) - cryptic duplications/deletions in cis to the breakpoints were detected, which might account for the clinical manifestations of the patients. This study also highlights the importance of FISH in the analysis of genomic imbalances detected by array in determining how losses and gains of submicroscopic segments relate to the rearranged chromosomes. The characterization of the balanced translocations in this study also contributed to suggest mechanisms for their formation (AU) | |
| FAPESP's process: | 09/03480-8 - Characterization of apparently balanced chromosomal rearrangements associated with clinical phenotypes: breakpoint mapping and screening for submicroscopic deletions and duplications |
| Grantee: | Ana Carolina dos Santos Fonseca |
| Support Opportunities: | Scholarships in Brazil - Master |