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Molecular characterization of the t(4;12)(q27~28;q14~15) chromosomal rearrangement in lipoma

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ABSTRACT

Lipomas are common benign soft tissue tumors whose genetic and cytogenetic features are well characterized. The karyotype is usually near- or pseudodiploid with characteristic structural chromosomal aberrations. The most common rearrangements target the high mobility group AT-hook 2 (HMGA2) gene in 12q14.3, with breakpoints occurring within or outside of the gene locus leading to deregulation of HMGA2. The most common fusion partner for HMGA2 in lipoma is lipoma-preferred partner (3q27), but also other genes frequently recombine with HMGA2. Furthermore, truncated HMGA2 transcripts are recurrently observed in lipomas. The present study describes 5 lipomas carrying the translocation t(4;12)(q27~28;q14~15) as the sole chromosomal anomaly, as well as 1 lipoma in which the three-way translocation t(1;4;12)(q21;q27~28;q14~15) was identified. Molecular analyses performed on 4 of these cases detected 4 truncated forms of HMGA2. In 3 tumors, the HMGA2 truncated transcripts included sequences originating from the chromosomal sub-band 4q28.1. Notably, in 2 of these cases, the fourth exon of HMGA2 was fused to transposable elements located in 4q28.1.

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Truncated HMGA2 transcripts identified in lipomas with t(4;12)(q27~28;q14~15). Chromatograms of the 3′-rapid amplification of complementary DNA ends products. (A) Fusion between HMGA2 exon 3 and a chromosome 4 long interspersed element sequence was noticed in case 1. (B) Transcript observed in case 2; junction between HMGA2 exon 3 and chromosome 4. (C) Truncated transcript observed in case 3; junction between the third exon and the first intronic fragment of HMGA2. (D) Case 4. Junction between HMGA2 exon 4 and the first chromosome 4 Alu sequence. HMGA2, high mobility group AT-hook 2.
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f2-ol-0-0-4834: Truncated HMGA2 transcripts identified in lipomas with t(4;12)(q27~28;q14~15). Chromatograms of the 3′-rapid amplification of complementary DNA ends products. (A) Fusion between HMGA2 exon 3 and a chromosome 4 long interspersed element sequence was noticed in case 1. (B) Transcript observed in case 2; junction between HMGA2 exon 3 and chromosome 4. (C) Truncated transcript observed in case 3; junction between the third exon and the first intronic fragment of HMGA2. (D) Case 4. Junction between HMGA2 exon 4 and the first chromosome 4 Alu sequence. HMGA2, high mobility group AT-hook 2.

Mentions: 3′-RACE on the lipomas of cases 1–4 (Table I) amplified fragments which were revealed to be chimeric HMGA2-cDNA fragments by Sanger sequencing analysis (Fig. 2). In lipomas 1, 2 and 4, HMGA2 was fused with sequences from intergenic regions of 4q28.1. In lipoma 1, the exon 4 of HMGA2 was fused with the transposable elements long interspersed element L2a and mammalian interspersed repetitive located in 4q28.1 (Fig. 3), whereas lipoma 2 exhibited HMGA2 exon 3 fused with a circa 750-bp fragment from band 4q28.1. In lipoma 4, HMGA2 exon 4 was fused with two Alu sequences from chromosome band 4q28.1 (Fig. 3). In lipoma 3, the third exon of HMGA2 was fused with two HMGA2 intron 3 sequences of 469 and 305 bp, respectively, with a distance between them of ~75 kbp.


Molecular characterization of the t(4;12)(q27~28;q14~15) chromosomal rearrangement in lipoma
Truncated HMGA2 transcripts identified in lipomas with t(4;12)(q27~28;q14~15). Chromatograms of the 3′-rapid amplification of complementary DNA ends products. (A) Fusion between HMGA2 exon 3 and a chromosome 4 long interspersed element sequence was noticed in case 1. (B) Transcript observed in case 2; junction between HMGA2 exon 3 and chromosome 4. (C) Truncated transcript observed in case 3; junction between the third exon and the first intronic fragment of HMGA2. (D) Case 4. Junction between HMGA2 exon 4 and the first chromosome 4 Alu sequence. HMGA2, high mobility group AT-hook 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4998094&req=5

f2-ol-0-0-4834: Truncated HMGA2 transcripts identified in lipomas with t(4;12)(q27~28;q14~15). Chromatograms of the 3′-rapid amplification of complementary DNA ends products. (A) Fusion between HMGA2 exon 3 and a chromosome 4 long interspersed element sequence was noticed in case 1. (B) Transcript observed in case 2; junction between HMGA2 exon 3 and chromosome 4. (C) Truncated transcript observed in case 3; junction between the third exon and the first intronic fragment of HMGA2. (D) Case 4. Junction between HMGA2 exon 4 and the first chromosome 4 Alu sequence. HMGA2, high mobility group AT-hook 2.
Mentions: 3′-RACE on the lipomas of cases 1–4 (Table I) amplified fragments which were revealed to be chimeric HMGA2-cDNA fragments by Sanger sequencing analysis (Fig. 2). In lipomas 1, 2 and 4, HMGA2 was fused with sequences from intergenic regions of 4q28.1. In lipoma 1, the exon 4 of HMGA2 was fused with the transposable elements long interspersed element L2a and mammalian interspersed repetitive located in 4q28.1 (Fig. 3), whereas lipoma 2 exhibited HMGA2 exon 3 fused with a circa 750-bp fragment from band 4q28.1. In lipoma 4, HMGA2 exon 4 was fused with two Alu sequences from chromosome band 4q28.1 (Fig. 3). In lipoma 3, the third exon of HMGA2 was fused with two HMGA2 intron 3 sequences of 469 and 305 bp, respectively, with a distance between them of ~75 kbp.

View Article: PubMed Central - PubMed

ABSTRACT

Lipomas are common benign soft tissue tumors whose genetic and cytogenetic features are well characterized. The karyotype is usually near- or pseudodiploid with characteristic structural chromosomal aberrations. The most common rearrangements target the high mobility group AT-hook 2 (HMGA2) gene in 12q14.3, with breakpoints occurring within or outside of the gene locus leading to deregulation of HMGA2. The most common fusion partner for HMGA2 in lipoma is lipoma-preferred partner (3q27), but also other genes frequently recombine with HMGA2. Furthermore, truncated HMGA2 transcripts are recurrently observed in lipomas. The present study describes 5 lipomas carrying the translocation t(4;12)(q27~28;q14~15) as the sole chromosomal anomaly, as well as 1 lipoma in which the three-way translocation t(1;4;12)(q21;q27~28;q14~15) was identified. Molecular analyses performed on 4 of these cases detected 4 truncated forms of HMGA2. In 3 tumors, the HMGA2 truncated transcripts included sequences originating from the chromosomal sub-band 4q28.1. Notably, in 2 of these cases, the fourth exon of HMGA2 was fused to transposable elements located in 4q28.1.

No MeSH data available.


Related in: MedlinePlus