Alternative titles; symbols
Other entities represented in this entry:
HGNC Approved Gene Symbol: HMGA2
Cytogenetic location: 12q14.3 Genomic coordinates (GRCh38): 12:65,824,460-65,966,291 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 12q14.3 | Silver-Russell syndrome 5 | 618908 | Autosomal dominant | 3 |
The mammalian HMGIC/Y (HMGA; also see 600701) nonhistone chromosomal proteins, which are often referred to as architectural proteins, participate in a wide variety of cellular processes including regulation of inducible gene transcription, integration of retroviruses into chromosomes, and the induction of neoplastic transformation and promotion of metastatic progression of cancer cells. They are characterized by the presence of 3 copies of a conserved DNA-binding peptide motif (AT-hook) that preferentially binds with the minor groove of many AT-rich promoter and enhancer DNA regulatory elements. Although they possess no substantial secondary structure while free in solution, they organize the framework of the nucleoprotein-DNA transcriptional complex through protein-protein and protein-DNA interactions. These interactions induce both structural changes in chromatin substrates and the formation of stereospecific complexes called 'enhanceosomes' on the promoter/enhancer regions of genes whose transcription they regulate (Grosschedl et al., 1994; Reeves and Beckerbauer, 2001).
Using a segment of mouse Hmgic to screen a human hepatoma cDNA library, followed by RT-PCR, Patel et al. (1994) cloned HMGIC (HMGA2). The deduced 109-amino acid has 3 basic segments of 9 amino acids each and a highly acidic C terminus, with multiple phosphorylation sites. It has only 5 amino acid differences with the mouse homolog. Two-dimensional gel electrophoresis showed expression of HMGIC in 3 hepatoma cell lines, but not in 5 hematopoietic cell lines.
By Northern blot analysis, Zhou et al. (1995) found no expression of mouse Hmgic in 18 adult tissues tested. However, Hmgic expression was observed during mouse embryogenesis as early as 10.5 days postcoitum and essentially disappeared by day 15.5 postcoitum. Hmgic is expressed almost exclusively in undifferentiated mesenchymal cells.
Hauke et al. (2005) identified several alternative HMGA2 transcripts in human cell lines, cultured tissues, and primary normal tissues. Northern blot analysis of a human lipoma cell line revealed the expression of full-length HMGA2 and 5 additional transcripts consisting of exons 1-3 and part of intron 3, but not exons 4-5.
Using comparative genome analysis, von Ahsen et al. (2008) identified a highly conserved region within intron 3 of the HMGA2 gene in human, mouse, and other mammalian species. In mouse, this region produces a microRNA, Mir763.
Chau et al. (1995) demonstrated that the HMGIC gene consists of 5 exons, the first and last of which include long untranslated regions. The 5-prime UTR includes a (CA/T)n tract and a polymorphic (CT)n tract. Exons 1-3 separately encode the 3 basic DNA-binding domains (A-T hooks), exon 4 encodes an 11-amino acid sequence characteristic of HMGIC and absent from HMGIY, and exon 5 encodes the acidic C-terminal domain. Ashar et al. (1996) also characterized the gene and showed that it spans at least 60 kb, with intron 3 extending at least 25 kb.
Manfioletti et al. (1995) found that the Hmgic gene in the mouse has 5 exons; it is longer than 50 kb. A highly homologous Hmgic pseudogene was also identified in the mouse.
Zhou et al. (1995) identified mutation in the mouse Hmgic gene as the cause of the 'pygmy' phenotype (see ANIMAL MODEL), which maps to a region of mouse chromosome 10 that shares syntenic homology with human 12q14-q15.
Both Ashar et al. (1995) and Schoenmakers et al. (1995) identified HMGIC as a candidate gene within the 1.7-Mb multiple aberration region on 12q15 that harbors recurrent breakpoints found in many types of benign tumors such as uterine leiomyoma, lipomas, and pleomorphic adenomas of the salivary glands (Rohen et al., 1995).
By linkage analysis in CEPH pedigrees, Ishwad et al. (1997) localized the HMGIC gene to 12q13-q15 with no recombination observed between HMGIC and markers D12S102 and D12S8.
The finding of a mutation in the Hmgic gene in the 'pygmy' mouse indicated that HMGIC has a role in aberrant growth and development. Because body fat is disproportionately reduced in weight in the 'pygmy' mouse, Ashar et al. (1995) suggested that HMGIC may normally play a role in adipogenesis.
To study the role of HMGIC in adipogenesis and obesity, Anand and Chada (2000) examined Hmgic expression in the adipose tissue of adult obese mice. Mice with a partial or complete deficiency of Hmgic resisted diet-induced obesity. Disruption of Hmgic caused a reduction in obesity induced by leptin deficiency (ob/ob; see 164160) in a gene dose-dependent manner. Anand and Chada (2000) concluded that their studies implicate a role for HMGIC in fat cell proliferation, indicating that it may be an adipose-specific target for the treatment of obesity. Commenting on the work of Anand and Chada (2000), Danforth (2000) reported observations suggesting that too few adipocytes predisposes to type II diabetes mellitus (see 125853). He suggested that this could explain the lower prevalence of type II diabetes in the generalized and more hypercellular obese than in the centrally obese, who for genetic or environmental reasons have lost the ability to accommodate excess energy by differentiating new adipocytes.
To evaluate the role of the HMGIC component in the development of lipoma (151900), Arlotta et al. (2000) expressed the 3 DNA-binding domains of Hmgic in transgenic mice. Despite the ubiquitous expression of the truncated Hmgic protein, the transgenic mice developed a selective abundance of fat tissue early in life, showed marked adipose tissue inflammation, and had an abnormally high incidence of lipomas. These findings demonstrated that the DNA-binding domain of HMGIC, in the absence of a C-terminal fusion partner, are sufficient to perturb adipogenesis and predispose to lipomas.
Ferguson et al. (2003) showed that inhibition of histone deacetylase reduced transient Hmga2 promoter activity in mouse and human cells and significantly reduced the steady-state level of endogenous Hmga2 mRNA in mouse fibroblasts. Crosslinked chromatin immunoprecipitation analysis revealed decreased binding of Sp1 (189906), Sp3 (601804), and acetylated H3 and H4 on the Hmga2 promoter.
The HMGA2-LPP (600700) fusion protein contains the N-terminal DNA-binding domains of HMGA2 fused to the C-terminal LIM domains of LPP. In addition to its role in adipogenesis, Kubo et al. (2006) showed that HMGA2-LPP may promote chondrogenesis. Reporter gene assays demonstrated that HMGA2-LPP, full-length wildtype HMGA2, and an N-terminal fragment of HMGA2 transactivated the Col11a2 (120290) promoter in transfected HeLa cells, but the C-terminal fragment of LPP alone did not.
Mayr et al. (2007) reported that chromosomal translocations associated with human tumors disrupt repression of HMGA2 by LET7 (see 605386) miRNA. This disrupted repression promotes anchorage-independent growth, a characteristic of oncogenic transformation. Thus, losing miRNA-directed repression of an oncogene provides a mechanism for tumorigenesis, and disrupting a single miRNA-target interaction can produce an observable phenotype in mammalian cells.
Using database analysis, luciferase reporter assays, and mutagenesis, Lee and Dutta (2007) identified 6 functional LET7 target sites in the 3-prime UTR of HMGA2. Combined ectopic expression of LET7B (MIRNLET7B; 611249) and LET7E (MIRNLET7E; 611250), which the authors used to represent all LET7 miRNAs, reduced HMGA2 expression and cell proliferation in a lung cancer cell line. In contrast, inhibition of LET7 induced HMGA2 mRNA and protein. Overexpression of the HMGA2 ORF without the 3-prime UTR rescued the growth-suppressive effect of LET7 on lung cancer cells.
Using quantitative RT-PCR, knockdown, and microarray analyses, Li et al. (2007) identified HMGA2 as a regulator of genes linked to mesenchymal cell differentiation, adipogenesis, and cell proliferation in human embryonic stem cells.
Nonhomologous end joining (NHEJ) of DNA double-strand breaks (DSBs) requires a DNA-dependent protein kinase complex (DNA-PK) that is composed of a Ku70 (XRCC6; 152690)-Ku80 (XRCC5; 194364) heterodimer and the catalytic subunit DNA-PKcs (PRKDC; 600899). Using several mammalian cell lines, Li et al. (2009) found that HMGA2 modulated NHEJ processing during the repair of DSBs, and that its overexpression resulted in accumulation of chromosomal aberrations and aneuploidy. Overexpression of HMGA2 in HeLa cells caused hyperphosphorylation of DNA-PKcs at ser2056 and thr2609 and accumulation of gamma-H2AX (H2AFX; 601772) both before and after induction of DSBs. Conversely, knockdown of HMGA2 decreased hyperphosphorylation of DNA-PKcs both before and after induction of DSBs. Real-time imaging showed prolonged presence of DNA-PKcs and delayed clearance of gamma-H2AX at DSB sites following irradiation. Li et al. (2009) concluded that HMGA2 overexpression can impede NHEJ and cause genomic instability.
Chromosomal Rearrangements
By FISH, Schoenmakers et al. (1995) showed that most of the breakpoints in benign tumors of 8 different types (lipoma, pleomorphic salivary adenoma, and uterine leiomyoma) fall within the HMGIC gene. Most of the breaks were within the 140-kb third intron. They described isolation of cDNA clones of the chromosome 3-derived lipoma-preferred partner LPP (600700), which was fused with the HMGIC gene by the t(3;12) translocation found in benign lipoma (151900).
In FISH studies, Ashar et al. (1995) found apparent deletion of the 3-prime end of the HMGIC gene in translocations associated with lipoma. Chimeric transcripts were isolated from 2 other lipomas in which HMGIC DNA-binding domains (AT-hook motifs) were fused to either a LIM or an acidic transactivator domain.
In a case of pericentric inversion inv(12)(p11.2q15), Kazmierczak et al. (1998) cloned part of a then unknown gene in 12p11.2 that was fused to the third exon of HMGIC. Using FISH with PAC clones, they showed that the same region was involved in 12p11.2 aberrations in lipomas, aggressive angiomyxomas, and pulmonary chondroid hamartomas. The original fusion transcript came from an aggressive angiomyxoma with the above-noted inversion. Nucci et al. (2001) studied the aberrant HMGIC expression accompanying translocation t(8;12) in aggressive angiomyxoma of the vulva.
Ashar et al. (2003) reported the expression of truncated HMGA2 transcripts that gained no functional domains. The highly polymorphic region in the 5-prime untranslated region (UTR) of HMGA2 was used to determine the allele-specific expression of HMGA2 in lipomas. Microsatellite PCR revealed a monoallelic expression pattern, and only the translocated allele was expressed when the DNA-binding domains of the rearranged allele were fused with transcription activation domains. Surprisingly, a diallelic expression pattern of HMGA2 was observed in lipoma ST91-198, and the wildtype allele was also expressed. In conjunction with studies involving rearrangement of HMGA genes in other benign mesenchymal tumors, the results of Ashar et al. (2003) supported a model in which the expression of the wildtype HMGA allele is critical for the pathogenesis of mesenchymal tumors and in which rearrangements of HMGA do not lead to a gain of function in the chimeric HMGA protein.
Ligon et al. (2005) described an 8-year-old boy who had a de novo pericentric inversion of chromosome 12, with breakpoints at p11.22 and q14.3, and a phenotype including extreme somatic overgrowth, advanced endochondral bone and dental ages, a cerebellar tumor, and multiple lipomas. His chromosomal inversion was found to truncate HMGA2, which maps to the 12q14.3 breakpoint. Similar truncations of mouse Hmga2 in transgenic mice result in somatic overgrowth and, in particular, increased abundance of fat and lipomas (Arlotta et al., 2000), features strikingly similar to those observed in the child. This represented the first report of a constitutional rearrangement affecting HMGA2 and demonstrated the role of this gene in human growth and development.
Petit et al. (1999) identified the LHFP gene (606710) as the fusion partner of HMGIC in a lipoma with t(12;13). The expressed HMGIC/LHFP fusion transcript encodes the 3 DNA-binding domains of HMGIC followed by 69 amino acids encoded by frameshifted LHFP sequences.
In 2 pulmonary chondroid hamartomas from different patients and 1 uterine leiomyoma (150699) with apparently normal karyotypes, Kazmierczak et al. (1996) found identical RTVL-H 3-prime LTRs (see 190080) fused as ectopic sequences to exon 3 of HMGIC. Screening of genomic cosmid and plasmid clones derived from intron 3 of HMGIC for the presence of these RTVL-H sequences showed a cluster of these retrotransposon-like sequences in this region. Because some RTVL-H LTRs are able to promote the expression of upstream and downstream genes, they may act as transcriptional promoters of HMGIC. These findings suggested to Kazmierczak et al. (1996) that the reexpression of HMGIC exons 1 to 3, rather than the formation of particular fusion genes, is the critical event in the genesis of the tumors.
Schoenmakers et al. (1999) demonstrated that an unusual isoform of the RAD51L1 (RAD51B; 602948) gene on 14q23-q24 is the preferential translocation partner of HMGIC in uterine leiomyomas with a translocation t(12;14).
Mine et al. (2001) systematically examined the tumors of 45 Japanese patients for all possible types of gene fusions involving HMGIC, by means of 3-prime RACE and RT-PCR experiments. HMGIC gene fusions were found in 16 (36%) of the tumors. Aberrant splicings to 5 cryptic sequences located in introns of the HMGIC gene were found in 11 of these cases, and translocations causing juxtaposition to other genes, such as COX6C (124090) and RAD51B, were found in 5. In all fusion transcripts, the first 2 or 3 exons of HMGIC were fused to ectopic sequences. The results suggested that a fusion event, resulting in the separation of the DNA-binding domains of HMGIC from the spacer and the acidic carboxy-terminal regulatory domain, is a common tumorigenic mechanism in the development of uterine myomas. Other fusion partners in uterine leiomyoma include the ALDH2 (100650) gene (Kazmierczak et al., 1995) and the HEI10 (608249) gene.
In a 4-year-old Romanian boy with severe pre- and postnatal growth restriction, Mari et al. (2009) identified heterozygosity for a de novo 1.8-Mb deletion on chromosome 12q14.3 that encompassed 6 genes, including HMGA2. The authors stated that the phenotype was similar to that of primordial dwarfism or severe Silver-Russell syndrome (see SRS5, 618908).
Heldt et al. (2018) reported a mother and her son and daughter with intrauterine growth retardation, postnatal feeding difficulties, and short stature, in whom they identified heterozygosity for a 1.67-MB deletion on chromosome 12q14.3 (chr12:65,863,186_67,528,640, GRCh37) encompassing 7 genes, including HMGA2.
Silver-Russell Syndrome 5
In an Italian mother and daughter with Silver-Russell syndrome (SRS5; 618908), De Crescenzo et al. (2015) identified heterozygosity for a 7-bp deletion in the HMGA2 gene (600698.0001). Functional analysis indicated that the mutation severely affected splicing efficiency of HMGA2.
From a cohort of 192 patients with a suspected diagnosis of SRS, Abi Habib et al. (2018) identified 2 unrelated patients with heterozygous de novo mutations in the HMGA2 gene (600698.0002 and 600698.0003). Experiments in Hep3b cells demonstrated that HMGA2 positively regulates expression of the IGF2 promoter P3, both independently and via an HMGA2-PLAG1 (603026)-IGF2 (147470) pathway. The authors noted that disruption of any gene in the pathway results in a decrease in IGF2 expression and produces an SRS phenotype similar to that of patients carrying 11p15.5 epigenetic defects (see SRS1, 180860).
In a 10.5-year-old boy with intrauterine growth retardation, short stature, and learning difficulties, Costain et al. (2018) identified heterozygosity for a 1-bp deletion in the HMGA2 gene (600698.0004) that was inherited from his similarly affected mother.
In a 4-year-old girl with SRS, Leszinski et al. (2018) identified heterozygosity for a de novo 7.3-kb deletion on chromosome 12q14.3, including exons 1 and 2 of the HMGA2 gene.
Polymorphisms
Ishwad et al. (1997) identified a highly informative dinucleotide repeat polymorphism in the 5-prime flanking region of the HMGIC gene. The polymorphism consisted of 18 to 37 copies of a (CT)n repeat with an observed heterozygosity of 82 to 83% in African Americans and Caucasians.
Associations Pending Confirmation
For discussion of a possible association between variation in the HMGA2 gene and stature, see STQTL9 (611547).
For discussion of a possible association between variation in the HMGA2 gene and uterine leiomyomata, see 150699.
For discussion of a possible association between variation in the HMGA2 gene and familial multiple lipomatosis, see 151900.
The viable pygmy (pg) mutation on chromosome 10 of the mouse gives rise to small stature owing to disruptions of growth and development. An insertional mutation facilitated cloning of the locus (Xiang et al., 1990). Subsequently, it was shown that expression of the HMGIC gene is abrogated in 3 pygmy alleles (Zhou et al., 1995). Among the 4 viable spontaneous mouse mutants which disrupt growth, 'pygmy' is unique because its phenotype cannot be explained by aberrations in the growth hormone-insulin-like growth factor endocrine pathway. Zhou et al. (1995) showed that the cause is inactivation of the Hmgic gene, a member of the Hmgi family of proteins which function as architectural factors in the nuclear scaffold and are critical in the assembly of stereospecific transcriptional complexes. Hmgic and another Hmgi family member, Hmgi(y), are expressed predominantly during embryogenesis. The HMGI proteins are known to be regulated by cell cycle-dependent phosphorylation which alters their DNA binding affinity. Zhou et al. (1995) suggested that identification of the 'pygmy' gene as Hmgic may suggest new avenues of research into the biochemical nature of the African pygmy phenotype (265850) and the numerous growth hormone-resistant human dwarf syndromes.
Brants et al. (2004) showed that Imp2 (IGF2BP2; 608289) expression was downregulated in Hmga2-null mouse embryos, but that Hmga2 deletion had no effect on the expression of Imp1 (IGF2BP1; 608288) or Imp3 (IGF2BP3; 608259).
In humans, hundreds of loci with small effects control the heritable proportion of height variability. In domestic animals, breeding and selection has typically resulted in only a few loci with comparatively large effects on height. Using a genomewide association study, fine mapping, and sequence analysis, Frischknecht et al. (2015) identified an 83G-A transition in the Hmga2 gene that was possibly linked to short stature in Shetland ponies. Resequencing a larger cohort of Shetland ponies, 2 other pony breeds, and 11 horse breeds confirmed that the mutation occurred exclusively in ponies and not in full-sized horses. A correlation plot revealed a largely additive mode of inheritance, with a mean reduction in height at withers of 9.5 cm per copy of the mutant A allele in ponies. The mutation caused a gly28-to-glu (G28E) substitution in the first AT-hook domain of the 109-amino acid Hmga2 protein. This G28E substitution affects the critical RGR motif that binds the minor groove of DNA. EMSA showed that Hmga2 with the G28E mutation exhibited reduced binding to an Hmga2-binding site in double-stranded DNA.
Chung et al. (2018) found that homozygous loss of Hmga2 resulted in fetal lethality in pig. Hmga2 -/- fetuses were smaller and lighter with abnormal placentas compared with wildtype. Hmga2 +/- pigs were about 80% lighter than wildtype, with dramatic reductions in length, height, and circumference measurements compared with wildtype. In gilts, disruption of 1 Hmga2 allele led to a 35% reduction in growth parameters. Hmga2 -/- pigs generated by gene editing showed significant size reduction, ranging from 35 to 85% of wildtype depending on age. Additionally, Hmga2 -/- pigs had a greater weight-to-size ratio, suggesting a leaner phenotype. Organ sizes were also affected in both Hmga2 +/- and Hmga2 -/- pigs. Both male and female Hmga2 +/- pigs displayed normal reproductive development, but Hmga2 -/- males were sterile due to cryptorchidism. Testis-specific expression of Hmga2 did not rescue cryptorchidism.
The article by Kumar et al. (2014) reporting that HMGA2 functions as a competing endogenous RNA for the LET7 microRNA family (see 605386) to promote lung cancer progression was retracted.
In an Italian mother and daughter with Silver-Russell syndrome (SRS5; 618908), De Crescenzo et al. (2015) identified heterozygosity for a 7-bp deletion (GTTCCAG) within intron 4 of the HMGA2 gene, which eliminated the 3-prime AG acceptor site. Other family members were unavailable for segregation analysis, but the mutation was not found in 50 Italian controls. A minigene splicing assay in transfected cells demonstrated that the 7-bp deletion severely affects splicing efficiency of HMGA2, with no fragment corresponding to wildtype transcript observed in the mutant construct lanes on gel electrophoresis.
In a female patient with Silver-Russell syndrome (SRS5; 618908), Abi Habib et al. (2018) identified heterozygosity for a de novo c.193C-T transition (c.193C-T, NM_003483.4) in the HMGA2 gene, resulting in a gln65-to-ter (Q65X) substitution.
In a male patient with Silver-Russell syndrome (SRS5; 618908), Abi Habib et al. (2018) identified heterozygosity for a 1-bp deletion (c.189del, NM_003483.4) in the HMGA2 gene, causing a frameshift predicted to result in elongation of the protein (Ala64LeufsExt102). Parental DNA was unavailable for study, but the father's short stature suggested that the deletion was paternally inherited.
In a 10.5-year-old boy (case 1096) with Silver-Russell syndrome (SRS5; 618908), Costain et al. (2018) identified heterozygosity for a 1-bp deletion (c.303delC) in exon 5 of the HMGA2 gene, causing a frameshift predicted to result in a premature termination codon (Ser102HisfsTer64). The mutation was inherited from his affected mother.
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