Marta Brunetti
Kristin Andersen
Ingvild Lobmaier2- 1Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- 2Department of Pathology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
Background/Aim: Lipomas are benign tumors of adipocytic origin. The most frequent chromosome rearrangement in lipomas involves the high-mobility group AT-hook 2 gene (HMGA2), which maps to 12q14. We investigated two lipomas showing rearrangements of chromosomal bands 8q22 and 12q14 in their karyotypes, with the aim of identifying the gene products affected by these aberrations.
Materials and Methods: The two lipomas were selected because their karyotype showed an 8;12-rearrangement with the very same breakpoint position. The cases were investigated using RNA sequencing, reverse transcription polymerase chain reaction (RT-PCR), Sanger sequencing techniques, Fluorescence in situ hybridization (FISH), and array comparative genomic hybridization (aCGH).
Results: RNA sequencing and RT-PCR of the two lipomas showed the presence of the HMGA2::CIBAR1-DT chimera.
Conclusions: The HMGA2::CIBAR1-DT fusion, identified here for the first time, is a recurrent transcript in lipomas.
Introduction
According to the World Health Organization (WHO), lipomas are classified as benign adipocytic tumors composed of mature fat tissue (1). They are the most common mesenchymal neoplasm in adults, more frequently seen in men (2, 3). The most common chromosomal rearrangement in lipomas involves chromosomal band 12q14, targeting the high mobility group A2 (HMGA2) gene (1). HMGA2 has an important role in tumor pathogenesis. In lipomas, the gene is most frequently found truncated; however, its involvement in fusion transcripts with different partners is also well documented (4, 5). In both scenarios, the molecular product is the loss of the 3’ untranslated region (3’ UTR) of HMGA2, which normally contains binding sites for microRNAs such as let-7, leading to overexpression of the protein (4, 6). In some cases, gene fusions are formed. The most frequent translocation, t(3;12)(q27~28;q13~15), generates an HMGA2::LPP fusion (7), however, other common partners are Phospholipid Phosphatase 3 (PLPP3; mapping on1p32.2), Atypical Chemokine Receptor 3 (ACKR3; on 2q37), EBF Transcription Factor 1 (EBF1; on 5q33), Nuclear Factor I B (NFIB; on 9p22), Glutamate Receptor Interacting Protein 1 (GRIP1; on 12q14.3), LHFPL Tetraspan Subfamily Member 6 (LHFP; on 13q12), SET Binding Protein 1 (SETPB1; on 18q12.3), and Gelsolin (GSN; on 9q33.2) (5, 8–14). In these fusion transcripts, the DNA-binding AT-hook domains of HMGA2 are retained and fused with the transcriptional regulatory domains of the fusion partner.
Here, we describe a novel, recurrent aberration of chromosome bands 8q22 and 12q14 in lipomas and their molecular product.
Materials and methods
Patients
The two lipoma samples were surgically removed at the Radium Hospital, Oslo University Hospital, in the years 2016 and 2021. They were cytogenetically investigated as part of our diagnostic routine. They were located on the flank (case 1) and on the thigh (case 2; Table 1). The study was approved by the Regional Ethics Committee (Regional komité for medisinsk forskningsetikk Sør-Øst, Norge). All patients’ information has been de-identified.
Table 1. Clinical and karyotypic data for the two lipoma samples investigated.
G-banding and karyotyping
Samples from the surgical specimens were short-term cultured, stained for G-banding analysis, and cytogenetically characterized as previously described (15, 16). The karyotypic description followed the International System of Cytogenomic Nomenclature (17).
DNA and RNA extraction
Fresh-frozen material from a representative area of the tumors was used to extract DNA and RNA. DNA was extracted using the Maxwell 16 extractor (Promega, Madison, WI, USA) and purified using a Maxwell 16 Cell DNA Purification kit (Promega) according to the manufacturer’s recommendations. RNA was extracted using a miRNeasy kit (QIAGEN, Hilden, Germany). The concentrations were measured using a QIAxel microfluidic UV/VIS spectrophotometer (QIAGEN) and a Quantus fluorometer (Promega). RNA quality was assessed with an Agilent RNA 6000 Nano total kit on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA sequencing
Each tumor’s total RNA (200 ng) was sent to the Genomics Core Facility at the Norwegian Radium Hospital, Oslo University Hospital, https://oslo.genomics.no/, for high-throughput paired-end RNA sequencing. The FusionCatcher (18) and DeFuse software package (version 0.6.1) was utilized to identify putative fusion transcripts by analyzing the output generated from RNA-Sequencing (19).
Reverse transcription polymerase chain reaction
The transcripts identified by RNA sequencing were tested by reverse transcription (RT), polymerase chain reaction (PCR), and Cycle sequencing. In brief, 200 ng total RNA was reverse-transcribed in a 20 μL reaction volume using iScript Advanced cDNA Synthesis Kit for RT-qPCR according to the manufacturer’s instructions (Bio-Rad, Hercules, CA, USA). cDNA was used as a template in subsequent PCR amplification using the primers combination HMGA2-947FW (5’-AGGCAGCAAAAACAAGAGTCCC-3’) and 8q22-intron-SEQ3-94333290-rev3 (5’-GACATTCTGGACCAGGTAGAAGAGA-3’). The quality of cDNA synthesis was assessed by amplification of a cDNA fragment from the ABL proto-oncogene 1, non-receptor tyrosine kinase (ABL1) gene using the primer combination ABL1-185F1 (5’-ATGACCCCAACCTTTTCGTTGCA- 3’) and ABL1-325R1 (5’-TAGTTGCTTGGGACCCAGCCTTG-3’). Four μl of the PCR products were stained with GelRed (Biotium, Hayward, CA, USA), analyzed by electrophoresis through a 1.0% agarose gel, and photographed. The remaining PCR products were purified with the MinElute PCR Purification Kit (Qiagen) and sequenced using the BigDye™ Terminator v1.1 Cycle Sequencing Kit according to the company’s recommendations (ThermoFisher Scientific, Waltham, MA, United States). The basic local alignment search tool software (BLAST; https://blast.ncbi.nlm.nih.gov/Blast.cgi) was used for computer analysis of sequence data (20). The BLAT alignment tool and the human genome browser at the University of California, Santa Cruz (UCSC) were also used to map the sequences on the Human GRCh37/hg19 assembly (BLAT; http://genome.ucsc.edu/cgi-bin/hgBlat) (21).
Fluorescent in situ hybridization
FISH analysis was performed on tumor cells from cases 1 and 2 using an HMGA2 Break-apart Probe MPP16360 (CytoCell, Milton, Cambridge, UK) with the target chromosomal region of 12q14.3, encompassing the HMGA2 gene. Chromosome preparations were counterstained with 0.2 μg/ml DAPI and overlaid with a 24×50 mm2 coverslip. Fluorescent signals were captured and analyzed using the CytoVision system (Leica Biosystems, Newcastle, UK).
Array comparative genomic hybridization
Array Comparative Genomic Hybridization (aCGH) was used to examine imbalances in the genome. The CytoSure Consortium Cancer + SNP arrays (Oxford Gene Technology, Oxford, UK) were used according to the manufacturer’s recommendations. The slide (CytoSure Cancer +SNP array, 4 × 180k) was scanned in an Agilent SureScan Dx microarray scanner using Agilent Feature Extraction Software (version 12.2.0.7), and data were analyzed using CytoSure Interpret Software (version 4.11.39, Oxford Gene Technology). The copy number aberrations were identified using the Circular Binary Segmentation (CBS) algorithm. A custom-made aberration filter defining imbalances was added. Copy number aberrations (CNA) were defined as a region with a minimum of five gained/lost probes. The cut-off value for the mean log ratio was set to a minimum of absolute 0.5, and only genomic imbalances larger than 0, 5 Mb were investigated as CNA. Annotations were based on the human reference sequence GRCh37/hg19.
Results
The karyotype of both lipomas showed aberrations involving chromosomes 8 and 12 (Figure 1), among other rearrangements. In case 1, an insertion of 12q13–q14 into 8q22 was observed, whereas in case 2, a translocation between 8q22 and 12q14 was identified. A complete description of the karyotypes is reported in Table 1.
Figure 1. Partial karyograms of cases 1 (A) and 2 (B) showing normal and derivative (der) chromosomes 8 and 12. Arrows are pointing to the breakpoints position.
Using the deFuse software on the fastq files of the RNA sequencing data, two HMGA2::CIBAR1-DT(previously known as LINC00535) chimeric transcripts were found for case 1 and three for case 2. In case 1, the two transcripts involved the exon 3 of the HMGA2 with introns 4 and 5, respectively, of the CIBAR1-DT transcript (ENST00000520096.5). In case 2, the chimeric transcripts involved different breakpoints within the HMGA2 gene (NM_003483.6), located in intron 2 and exon 3, respectively, and were fused to intron 4 of the CIBAR1-DT transcript (Figure 2). RT-PCR followed by cycling Sanger sequencing confirmed the presence of the fusion between exon 3 of the HMGA2 gene and intron 4 of CIBAR1 Divergent Transcript (CIBAR1-DT), previously known as Long Intergenic Non-Protein Coding RNA 535 (LINC00535)(Figure 2), in both cases. The cases were also analyzed with FusionCatcher software, but no fusion transcripts were identified.
Figure 2. Overview of the sequences found by RNA- and Sanger sequencing. (A) The fusion transcripts obtained after analysis using the deFuse software package for cases 1 and 2. In bold: sequence of the high-mobility group AT-hook 2 (HMGA2). In red |: the junction of HMGA2 with a sequence from CIBAR1-DT. (B) Partial chromatogram of case 1 using the HMGA2-947F and 8q22seq3-rev3 primers. Breakpoint of the fusion transcript is shown between exon 3 in HMGA2 and intron 4 in CIBAR1-DT.
Examination of metaphase spreads and interphase nuclei, hybridized with the HMGA2 break-apart probe, showed a split in HMGA2 (Figure 3). The aCGH analysis for cases 1 and 2 revealed no imbalances in the genome when applying the cut-off values routinely used (data not shown).
Figure 3. FISH analysis of interphase nuclei from case 1 (A) and 2 (B) with the HMGA2 break-apart probe showing the intact HMGA2 gene (yellow signal) on one of the homologous chromosomes and a disrupted gene in the other (separate red and green signals). FISH analysis on metaphase spread from case 2 (C) shows red and green fluorescence signals on derivative chromosome 12 and derivative chromosome 8, respectively, and a yellow signal in the normal chromosome 12.
Discussion
We present here, for the first time, two lipomas with two 8q22;12q14-rearrangements, leading to the formation of an HMGA2::CIBAR1-DT fusion transcript.
The “Mitelman Database Chromosome Aberrations and Gene Fusions in Cancer” database (last updated 10th of July 2025) (22) displays 33 entries of “lipoma” with the involvement of the 12q14/HMGA2 gene (22). In only 11 entries, the aberration leads to fusion genes involving HMGA2 with different partners or intergenic sequences. Different types of aberrations were reported; however, no 8q22 involvement has been described. In all types of rearrangement, the sequence of the HMGA2 gene (exons 1 to 3), coding for the AT-hook domains, is separated from the 3’-untranslated region, which regulates HMGA2 transcription, resulting in altered expression and leading to tumorigenesis in these tissues (23, 24).
The CIBAR1 Divergent Transcript(CIBAR1-DT) is a long non-coding RNA (lncRNA) that maps to chromosome band 8q22.1. It has been reported that lncRNAs are susceptible to form fusion transcripts with gene/mRNA, as it is the case here, as well as with other lncRNAs (25). However, the biological significance of fusions involving lncRNAs in the tumor phenotype remains uncertain (25).
Chromosomal translocations involving the HMGA2 gene often lead to its truncation. In particular, the coding region of HMGA2 is disrupted, resulting in the loss of critical functional domains required for its architectural role in chromatin remodeling and transcriptional regulation (26). Consequently, the fusion is predicted to cause a loss of function of HMGA2, which may contribute to the pathogenesis of the tumor by impairing its normal gene regulatory functions (27). Since HMGA2 is important in numerous biological processes, such as cell proliferation and cell cycle progression, the acquisition of sub-microscopic alterations in HMGA2 can define the pathogenesis of different disease phenotypes (25).
The aCGH analysis did not detect any copy number changes in any of the present cases. This may be due to the log ratio threshold of 0.5 that we chose to score imbalances (28), which may be too stringent to identify low-level mosaic or subclonal copy number changes, as well as lack of good coverage by the platform used. This limitation could be overcome using other type of approach such as chromosomal microarray (CMA) platforms that target high-resolution arrays for the chromosomes in general and the chromosomal sub-band 12q14.3 specifically in the present case, with dense probe coverage of the 3’ UTR region of HMGA2 (29) and long-read sequencing (30). Both technologies can identify additional cases with cryptic HMGA2 alterations that remain undetected with conventional FISH or standard aCGH (29, 30). This is the first time rearranged chromosomes 8 and 12 in two lipomas are found to lead to the HMGA2::CIBAR1-DT fusion transcript, though with cytogenetically different aberrations, but with the same breakpoints. Cytogenetically abnormal adipocytic tumors with involvement of 8q22 and 12q14, as well as the identification of the HMGA2::CIBAR1-DT, can help subclassify these tumors, distinguishing lipomas from malignant adipocytic tumors. The patients with benign lipogenic tumors undergo only a surgical removal of the tumor with no need for further treatment (1).
Conclusion
In conclusion, aberrations involving the 8q22 and 12q14 chromosomal bands were found to be recurrent in lipomas. The aberrations led to the formation of an HMGA2::CIBAR1-DT fusion transcript, which has not been previously identified. The identification of the fusion transcript with involvement of HMGA2 could be valuable in making a differential diagnosis.
Data availability statement
The original contributions presented in the study are included in the article/supplementary material. Further inquiries can be directed to the corresponding author.
Ethics statement
The studies involving humans were approved by (Regional komité for medisinsk forskningsetikk Sør-Øst, Norge). The studies were conducted in accordance with the local legislation and institutional requirements. The participants provided their written informed consent to participate in this study. Written informed consent was obtained from the individual(s) for the publication of any potentially identifiable images or data included in this article.
Author contributions
MB: Conceptualization, Methodology, Software, Validation, Visualization, Writing – original draft, Writing – review & editing, Supervision. KA: Methodology, Writing – original draft, Writing – review & editing. IL: Data curation, Writing – original draft, Writing – review & editing. FM: Conceptualization, Funding acquisition, Project administration, Writing – original draft, Writing – review & editing, Resources.
Funding
The author(s) declared that financial support was received for this work and/or its publication. This research was funded by The Norwegian Radium Hospital Foundation (Radiumhospitalets legater).
Acknowledgments
The authors wish to thank the diagnostic group and the student Inger Kjønnøy at the Section for Cancer Cytogenetics for technical assistance and support.
Conflict of interest
The authors declared that this work was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Generative AI statement
The authors declare that no Gen AI was used in the creation of this manuscript.
Any alternative text (alt text) provided alongside figures in this article has been generated by Frontiers with the support of artificial intelligence and reasonable efforts have been made to ensure accuracy, including review by the authors wherever possible. If you identify any issues, please contact us.
Publisher’s note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
References
1. Antonescu CR, B. JA, Cunha IW, Dei Tos AP, Fletcher CDM, Folpe AL, et al. Soft tissue tumours. In: WHO Classification of Tumours Editorial Board. International Agency for Research on Cancer., Lyon, France (2020). p. 6–318.
2. Kolb L, Yarrarapu SNS, Ameer MA, and Rosario-Collazo JA. Lipoma. In: StatPearls. StatPearls Publishing LLC, Treasure Island (FL (2025).
3. Charifa A, Azmat CE, and Badri T. Lipoma Pathology. In: StatPearls. StatPearls Publishing LLC, Treasure Island (FL (2025).
4. Agostini A, Brunetti M, Davidson B, Trope CG, Heim S, Panagopoulos I, et al. Expressions of miR-30c and let-7a are inversely correlated with HMGA2 expression in squamous cell carcinoma of the vulva. Oncotarget. (2016) 7:85058–62. doi: 10.18632/oncotarget.13187
5. Nilsson M, Mertens F, Höglund M, Mandahl N, and Panagopoulos I. Truncation and fusion of HMGA2 in lipomas with rearrangements of 5q32–>q33 and 12q14–>q15. Cytogenet Genome Res. (2006) 112:60–6. doi: 10.1159/000087514
6. Agostini A, Gorunova L, Bjerkehagen B, Lobmaier I, Heim S, and Panagopoulos I. Molecular characterization of the t(4;12)(q27~28;q14~15) chromosomal rearrangement in lipoma. Oncol Lett. (2016) 12:1701–4. doi: 10.3892/ol.2016.4834
7. Petit MM, Swarts S, Bridge JA, and Van de Ven WJ. Expression of reciprocal fusion transcripts of the HMGIC and LPP genes in parosteal lipoma. Cancer Genet Cytogenet. (1998) 106:18–23. doi: 10.1016/S0165-4608(98)00038-7
8. Italiano A, Ebran N, Attias R, Chevallier A, Monticelli I, Mainguené C, et al. NFIB rearrangement in superficial, retroperitoneal, and colonic lipomas with aberrations involving chromosome band 9p22. Genes Chromosomes Cancer. (2008) 47:971–7. doi: 10.1002/gcc.20602
9. Panagopoulos I, Gorunova L, Bjerkehagen B, Lobmaier I, and Heim S. The recurrent chromosomal translocation t(12;18)(q14~15;q12~21) causes the fusion gene HMGA2-SETBP1 and HMGA2 expression in lipoma and osteochondrolipoma. Int J Oncol. (2015) 47:884–90. doi: 10.3892/ijo.2015.3099
10. Petit MM, Schoenmakers EF, Huysmans C, Geurts JM, Mandahl N, and Van de Ven WJ. LHFP, a novel translocation partner gene of HMGIC in a lipoma, is a member of a new family of LHFP-like genes. Genomics. (1999) 57:438–41. doi: 10.1006/geno.1999.5778
11. Bianchini L, Birtwisle L, Saâda E, Bazin A, Long E, Roussel JF, et al. Identification of PPAP2B as a novel recurrent translocation partner gene of HMGA2 in lipomas. Genes Chromosomes Cancer. (2013) 52:580–90. doi: 10.1002/gcc.22055
12. Broberg K, Zhang M, Strömbeck B, Isaksson M, Nilsson M, Mertens F, et al. Fusion of RDC1 with HMGA2 in lipomas as the result of chromosome aberrations involving 2q35–37 and 12q13-15. Int J Oncol. (2002) 21:321–6. doi: 10.3892/ijo.21.2.321
13. Nilsson M, Panagopoulos I, Mertens F, and Mandahl N. Fusion of the HMGA2 and NFIB genes in lipoma. Virchows Arch. (2005) 447:855–8. doi: 10.1007/s00428-005-0037-9
14. Panagopoulos I, Andersen K, Brunetti M, Gorunova L, Lund-Iversen M, Micci F, et al. Fusion of the high-mobility group AT-hook 2 (HMGA2) and the gelsolin (GSN) genes in lipomas with t(9;12)(q33;q14) chromosomal translocation. In Vivo. (2023) 37:524–30. doi: 10.21873/invivo.13110
15. Polito P, Dal Cin P, Debiec-Rychter M, and Hagemeijer A. Human solid tumors: cytogenetic techniques. Methods Mol Biol. (2003) 220:135–50. doi: 10.1385/1-59259-363-1:135
16. Lukeis R and Suter M. Cytogenetics of solid tumours. Methods Mol Biol. (2011) 730:173–87. doi: 10.1007/978-1-61779-074-4-13
17. McGowan-Jordan J HR and Moore S. ISCN 2020: An International system for human cytogenomic nomenclature. Karger: Basel, Switzerland. (2020). 164.
18. Nicorici D, Şatalan M, Edgren H, Kangaspeska S, Murumägi A, Kallioniemi O, et al. FusionCatcher – a tool for finding somatic fusion genes in paired-end RNA-sequencing data. bioRxiv. (2014), 011650. doi: 10.1101/011650
19. McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, et al. deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PloS Comput Biol. (2011) 7:e1001138. doi: 10.1371/journal.pcbi.1001138
20. Altschul SF, Gish W, Miller W, Myers EW, and Lipman DJ. Basic local alignment search tool. J Mol Biol. (1990) 215:403–10. doi: 10.1016/S0022-2836(05)80360-2
21. Kent WJ. BLAT–the BLAST-like alignment tool. Genome Res. (2002) 12:656–64. doi: 10.1101gr.229202
22. Mitelman F. JB and Mertens F. Mitelman database of chromosome aberrations and gene fusions in cancer. (2025).
23. Borrmann L, Wilkening S, and Bullerdiek J. The expression of HMGA genes is regulated by their 3UTR. Oncogene. (2001) 20:4537–41. doi: 10.1038/sj.onc.1204577
24. Kristjánsdóttir K, Fogarty EA, and Grimson A. Systematic analysis of the Hmga2 3 UTR identifies many independent regulatory sequences and a novel interaction between distal sites. Rna. (2015) 21:1346–60. doi: 10.1261/rna.051177.115
25. Sánchez-Marín D, Silva-Cázares MB, Porras-Reyes FI, García-Román R, and Campos-Parra AD. Breaking paradigms: Long non-coding RNAs forming gene fusions with potential implications in cancer. Genes Dis. (2024) 11:101136. doi: 10.1016/j.gendis.2023.101136
26. Vignali R and Marracci S. HMGA genes and proteins in development and evolution. Int J Mol Sci. (2020) 21:E654. doi: 10.3390/ijms21020654
27. Mansoori B, Mohammadi A, Ditzel HJ, Duijf PHG, Khaze V, Gjerstorff MF, et al. HMGA2 as a critical regulator in cancer development. Genes (Basel). (2021) 12(2):269. doi: 10.3390/genes12020269
28. Schoumans J, Suela J, Hastings R, Muehlematter D, Rack K, van den Berg E, et al. Guidelines for genomic array analysis in acquired haematological neoplastic disorders. Genes Chromosomes Cancer. (2016) 55:480–91. doi: 10.1002/gcc.22350
29. Handa S, Schaniel C, Tripodi J, Ahire D, Mia MB, Klingborg S, et al. HMGA2 overexpression with specific chromosomal abnormalities predominate in CALR and ASXL1 mutated myelofibrosis. Leukemia. (2025) 39:663–74. doi: 10.1038/s41375-024-02496-0
Keywords: CIBAR1 divergent transcript (CIBAR1-DT), cytogenetics, fluorescence in situ hybridization, fusion gene, high mobility group AT-hook 2 (HMGA2) gene
Citation: Brunetti M, Andersen K, Lobmaier I and Micci F (2026) Identification of the HMGA2::CIBAR1-DT fusion transcript in two lipomas with chromosomal rearrangements involving chromosomes 8 and 12. Front. Oncol. 15:1717031. doi: 10.3389/fonc.2025.1717031
Received: 01 October 2025; Accepted: 08 December 2025; Revised: 02 December 2025;
Published: 06 January 2026.
Edited by:
Christoph Schaniel, Icahn School of Medicine at Mount Sinai, United StatesReviewed by:
Patrick Gonzales, University of Kansas Medical Center, United StatesJoseph Tripodi, Icahn School of Medicine at Mount Sinai, United States
Copyright © 2026 Brunetti, Andersen, Lobmaier and Micci. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Marta Brunetti, YnJ1bmV0dGkubWFydGE5MEBnbWFpbC5jb20=; bWJydW5lQG91cy1oZi5ubw==