Structural characterization of SIL, a gene frequently disrupted in T-cell acute lymphoblastic leukemia.

Abstract

The SIL (SCL interrupting locus) gene was initially discovered at the site of a genomic rearrangement in a T-cell acute lymphoblastic leukemia cell line. This rearrangement, which occurs in a remarkably site-specific fashion, is present in the leukemic cells of 16 to 26% of patients with T-cell acute lymphoblastic leukemia. We have now cloned a normal SIL cDNA from a cell line which does not carry the rearrangement. The SIL cDNA has a long open reading frame of 1,287 amino acids, with a predicted molecular size of 143 kDa. The predicted protein is not homologous with any previously described protein; however, a potential eukaryotic topoisomerase I active site was identified. Cross-species hybridization using a SIL cDNA probe indicated that the SIL gene was conserved in mammals. A survey of human and murine cell lines and tissues demonstrated SIL mRNA to be ubiquitously expressed, at low levels, in hematopoietic cell lines and tissues. With the exception of 11.5-day-old mouse embryos, SIL mRNA was not detected in nonhematopoietic tissues. The genomic structure of SIL was also analyzed. The gene consists of 18 exons distributed over 70 kb, with the 5' portion of the gene demonstrating alternate exon utilization.Nonrandom chromosomal translocations or deletions present in specific malignancies have been recognized for the past 30 years, since the association of the Ph chromosome with chronic myelogenous leukemia (20). The analysis of these recurring chromosomal abnormalities at a molecular level has identified numerous proto-oncogenes and growthaffecting genes (for a review, see reference 23). These rearrangements often occur at the sites of transcriptionally active DNA, which may be in a more open chromatin configuration and thus more susceptible to chromosomal breakage and rejoining (17). Chromosomal breakpoints often involve genes that are important for the growth or development of the cell that undergoes the translocation; the classic example is seen in Burkitt's lymphoma, in which the c-myc and immunoglobulin genes are disrupted and brought into chromosomal contiguity (18).Traditionally, these chromosomal abnormalities have been identified cytogenetically on preparations of metaphase chromosomes. Recently, while investigating the genomic structure of the newly described SCL (TCL5, tal-J) gene (6, 7, 9, 13), a member of the basic helix-loop-helix family of transcription factors, we identified a frequent, site-specific chromosomal deletion that involved SCL and a previously unidentified locus that we called SIL (for SCL interrupting locus) (4). This interstitial deletion is the first known instance whereby two genes, neither one of which is an antigen receptor gene, are joined through the action of the V(D)J recombinase system. The deletion occurs below the level of conventional cytogenetic detection and leads to a fusion mRNA between SIL and SCL. A 5.5-kb SIL transcript, distinct from SCL, was identified in normal tissues by Northern (RNA) blot hybridization (4). To better understand how disruption of the SIL g...

Regulation of the stem cell leukemia ( SCL ) gene: A tale of two fishes

“…The highly conserved pattern of SCL expression implies the existence of functionally homologous regulatory elements. In human, mouse, and chicken, the SCL gene is flanked upstream by the SCl interrupting locus (SIL) gene and downstream by the membrane-associated protein (MAP)17 gene (28,54,55). By contrast, no homologue of SIL or MAP17 was identified flanking the pufferfish SCL gene, which instead is flanked by a PDZ domain gene and a Saccular Collagen gene (Fig.…”

Split-signal FISH for detection of chromosome aberrations in acute lymphoblastic leukemia

“…As the SIL gene is ubiquitously expressed, the SIL-TAL1 fusion gene transcript results in ectopic TAL1 expression in T cells. 123 In the SIL gene, three deletion breakpoints (sildb1-3) have been identified, of which sildb1 is most frequently used (95%). 119,121,124 The TAL1 gene contains seven deletion breakpoints (taldb1-7), with two being involved in 98% of cases (taldb1 and 2).…”

“…129 The SIL gene consists of 18 exons spanning 65 kb and is located just upstream of the TAL1 gene. 123 Two probes are required for the detection of both types of TAL1 gene aberrations, that is, the SIL-TAL1 fusion gene (microscopic deletion) and TAL1 translocations, in a single FISH test. The upstream FISH probe is positioned in the B90 kb region that is deleted during a SIL-TAL1 fusion, whereas the downstream probe is positioned downstream of the TAL1 breakpoints (Figure 8a).…”

Standardization and quality control studies of ‘real-time’ quantitative reverse transcriptase polymerase chain reaction of fusion gene transcripts for residual disease detection in leukemia – A Europe Against Cancer Program

“…[136][137][138] The SIL gene is a member of the immediateearly gene family, but its function in hematopoietic cells is not yet well defined. 129,139 Although both the SIL and TAL1 genes contain several conserved deletion breakpoints, most cases (X95%) involve the sildb1 breakpoint in combination with the taldb1 or taldb2 breakpoint. 131,132,140 By alternative splicing, three different SIL-TAL1 transcripts can be formed, of which the type II transcript is the most predominant one.…”