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Department of Pediatrics, Graduate School of Medicine, University of Tokyo, Tokyo, 113-8655 [R. O., T. Taki, T. Take, H. K., M. K., Y. H.]; Third Department of Internal Medicine, Kyoto Prefectural University of Medicine, Kyoto, 602-8655 [M. T.]; Department of Pediatrics, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, 594-1101 [T. O., K. K.]; and Division of Hematology and Oncology, Saitama Childrens Medical Center, Saitama, 339-8551 [R. H.] Japan
| ABSTRACT |
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2.3-, 3.1-, and 4.6-kb SEPTIN6 transcripts was simultaneously detected in fetal lung, liver, and brain, in all of the adult tissues except brain, and in acute lymphoblastic leukemia and AML cell lines. However, the expression of an
2.7-kb transcript was detected alone in fetal heart and adult brain. The SEPTIN6 protein is homologous to septin family members including CDCREL1 and AF17q25/MSF, which generate fusion products with MLL. The MLL-SEPTIN6 fusion proteins contain almost the entire septin protein, similar to MLL-CDCREL1 and MLL-AF17q25/MSF. Notably, all three of the patients were diagnosed with M1 or M2. Combined present results and literatures suggest that AML with the MLL-SEPTIN6 fusion gene is a subset of infant AML, which differentiate into the myeloid lineage, although AML with other MLL fusion genes is capable of differentiating into the myelomonocytic or monocytic lineage. | Introduction |
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| Materials and Methods |
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Leukemic Cell Lines.
B-precursor ALL (REH and NALM26), B-ALL (BALM14, BALM9, BJAB, and A4/FUK), and AML (SN-1) cell lines were analyzed by Northern blot analysis. Acute monocytic leukemia (THP-1, CTS, P31/FUJ, IMS/M1, and KOCL-48), AML (YNH-1, ML-1, Kasumi-3, KG-1, P39/TSU, inv-3, NB-4, and HEL) and acute megakaryoblastic leukemia (CMS and CMY) cell lines were also analyzed by RT-PCR.
Southern Blot Analysis.
High molecular weight DNA was extracted from either BM or PB at diagnosis, and 10 µg of DNA was analyzed with a 0.9-kb BamHI fragment (MLL probe), as reported previously (9)
.
cDNA Panhandle PCR.
Total RNA was extracted from either BM or PB cells at diagnosis using Isogen (Wako Pure Chemical Industries, Ltd., Osaka, Japan) and analyzed by modified cDNA panhandle PCR method as described previously (10
, 11)
. In brief, first-strand cDNAs were synthesized with MLL-random hexamer oligonucleotides, MLL-N. After primer 1 extension with MLL-1, and extension in stem-loop templates, the sample was amplified by first PCR with ALL-6A and MLL-1. Then, one-twenty fifth of the products were used for nested PCR with MLL-3 and ALL-8S. The products (5 µl) were electrophoresed in a 3% agarose gel. The MLL-random hexamer oligonucleotides and primers used were as follows: MLL-N, 5'-TCGAGGAAAAGAGTGAAGAAGGGAATGTCTCNNNNNN-3'; MLL-1, 5'-TGAAGAACGTGGTGGACTCT-3'; ALL-6A, 5'-GTCCAGAGCAGAGCAAACAGA-3'; MLL-3, 5'-GTCAGAAACCTACCCCATCA-3'; and ALL-8S, 5'-TGTGAAGCAGAA AATGTGTGG-3'.
RT-PCR.
Total RNA (4 µg) was reverse transcribed to cDNA in a total volume of 33 µl with random hexamers by using the Ready-To-Go You-Prime First-Strand Beads (Pharmacia Biotech, Tokyo, Japan). Conditions and reagents for PCR have been already described (9)
. The primers used were as follows: ALL-7S, 5'-TCCTCAGCACTCTCTCCAAT-3'; SEP62A, 5'-GGGATGAGCACAGAAGTCCA-3'; ALL-9A, 5'-GGAAGGGCTCACAACAGAC-3'; SEP6-S, 5'-TGTGCAGTAGCTCCCGTTG-3'; SEP68SS, 5'-GAGGAGATGAGACAGATGTTCGT-3'; SEP64A, 5'-GGTCCAGAGAC TTCAGGGAATG-3'; SEP611KA, 5'-CTGTTGCGCAGGAAAAGGGTGT-3'; and 24RA1, 5'-TAGGAACCTCGGCTTAAAAGGCTAA-3'.
Nucleotide Sequencing.
Nucleotide sequences of phage clones, PCR products, and, if necessary, subcloned PCR products, were analyzed as described previously (9)
.
Screening of the cDNA Library.
The 556-bp SEPTIN6 cDNA probe spanning exons 14 (nucleotides 230765) was used for screening a cDNA library derived from human placenta (Ref. 9
; Clontech Laboratories, Inc., Palo Alto, CA).
FISH Analysis.
Chromosomal mapping of the BAC clone RP13163A20 was performed by the FISH method (12)
. FISH analysis of the patients leukemic cells using a YAC clone specific to 11q23 (13HH4) and RP13163A20 was carried out as described previously (12)
.
Northern Blot Analysis.
An aliquot (1 µg) of mRNA derived from each cell line and multiple human tissue Northern blots (Clontech Laboratories, Inc.) were analyzed with the 32P-labeled same SEPTIN6 cDNA probe as used for screening a cDNA library (9)
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| Results |
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The overlapping clones and the PCR product were assembled into two types of contiguous sequences resulting in total cDNA sizes of 2059 nt (type I; GenBank accession no. AF403058) and 2695 nt (type II; AF403059). They were then compared with known genomic sequences in public databases and found to contain at least nine common exons at the 5' region in addition to some additional exons at the 3' region (Fig. 2A)
.
To study the expression of fusion transcripts in leukemic cells from patient 1, we performed RT-PCR analysis for RNA from the leukemic cells using primers ALL-7S and one of the antisense primers, SEP611KA and 24RA1, which corresponded to chimeric transcripts fused to type I and II. However, no PCR product was obtained, suggesting that the quality of mRNA from the leukemic cells of patient 1 was not good. We next preformed RT-PCR using primers SEP68SS and one of the same antisense primers, and detected a 346-bp product only when primers SEP68SS and SEP611KA were used, suggesting that a fusion transcript was formed by type I (data not shown).
Computer analysis indicated a type I encoding a 427-amino acid protein, and a type II encoding a 434-amino acid protein with an estimated molecular mass of 48.8 kDa and 49.7 kDa. Each product contained different amino acid sequences at the COOH-terminus. Sequence comparison of the predicted proteins using the FASTA file revealed highly significant homology to mouse Septin6 protein (95.8% identity; Fig. 2B
). Therefore, we designated this gene SEPTIN6 as a human homologue of mouse Septin6. Motif analysis using the PSORT II and Pfam database revealed a coiled-coil region at the COOH region and a GTP-binding domain, which is highly conserved among septin family proteins. This domain was conserved in each isoform. The fusion partner genes of MLL, CDCREL1, and AF17q25/MSF, which also belong to the septin family, were homologous to this novel gene (Fig. 2C)
.
Chromosomal Assignment of the SEPTIN6 Gene.
To assign the chromosomal location of the SEPTIN6 gene, we found a BAC clone (RP13163A20) after comparing SEPTIN6 with known genomic sequences in public databases. Surprisingly, the BAC clone showed specific signals at Xq24 but not at 5q13 in all of the metaphase male cells tested (Fig. 3, A and B)
. We next performed a FISH analysis of leukemic interphase cells of patient 1 using a YAC clone specific to 11q23 (13HH4) and RP13163A20, and detected three signals of 13HH4 and RP13163A20, respectively (Fig. 3C)
. Only one of the three signals was found to be fused. These results suggest that the chromosome aberration in patient 1 was not a reciprocal t(5;11)(q13;q23) but a complex chromosome abnormality including t(X;11)(q24;q23).
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We also performed FISH analyses of leukemic metaphase cells of patient 2 and leukemic interphase cells of patient 3 using a YAC clone 13HH4 and RP13163A20. Three signals of 13HH4 and RP13163A20 were detected in patient 3, similarly to patient 1 (data not shown). However, no split signals of RP13163A20 were detected, despite 3 signals of 13HH4, in patient 2 (Fig. 3D)
. One signal of RP13163A20 was found to be fused to a split signal of 13HH4 on der(X), suggesting that the split signals were too close to discriminate by FISH analysis or that one of the split signals of RP13163A20 on der(X) was deleted.
Expression of the SEPTIN6 Gene.
To examine the expression of SEPTIN6, we performed Northern blot analysis on poly(A)+ RNA from various human tissues and detected four types of transcripts,
2.3-kb, 3.1-kb, 4.6-kb, and 2.7-kb (Fig. 4)
. Expression of the 2.3-kb, 3.1-kb, and 4.6-kb transcripts was detected almost simultaneously in fetal lung, liver, and brain, and in all of the adult tissues tested except brain. On the other hand, expression of the 2.7-kb transcript was detected alone in fetal heart and adult brain. We also performed Northern blot analysis of RNAs of leukemic cell lines. The SEPTIN6 gene was expressed in six leukemic cell lines, including three B-ALL (BALM14, BALM9, and A4/FUK), two B-precursor ALL (REH and NALM26), and one AML cell lines (SN-1). In addition, we examined the expression of SEPTIN6 in 10 AML including 2 acute megakaryoblastic leukemia cell lines and in 5 acute monocytic leukemia cell lines by RT-PCR using primers SEP6-S and SEP64A. The expression of SEPTIN6 was found in all of the cell lines.
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| Discussion |
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3 years. Two of the three patients reported in the literature were long-term survivors. However, the cases reported in the literature may not have the same molecular abnormality described in this work; therefore, the prognosis is unknown at this time and will have to await the identification of large numbers of cases through molecular analysis. None of the three patients were characterized as simple reciprocal t(X;11)(q24;q23). Patient 1 may have a three-way chromosome translocation among 5q13, 11q23, and Xq24. Patient 2 had an insertion of 11q23 at Xq2224. t(10;11) is strongly associated with complex translocations, because the direction of transcription of AF10 is opposite to that of MLL, and t(10;11)(p12;q23) cannot form regular head to tail fusion transcripts (14 ,15) . This may explain why t(X;11)(q24;q23) is often complex and associated with 11q insertions. These results may suggest that the orientation of the SEPTIN6 gene is reversed, telomere to centromere at Xq24.
SEPTIN6 is homologous to septin proteins. The septins are a family of nucleotide-binding proteins originally found in the yeast Saccharomyces cerevisiae as cell division cycle regulatory proteins. These proteins possess a well-conserved central core domain that binds GTP. To date, several genes have been identified as coding septin family proteins, for example, CDC3, CDC10, CDC11, and CDC12 in yeast; Pnut, Sep1, and Sep2 in Drosophila; Nedd5, H5, Diff6, E-septin, and G-septin in mouse; and CDCREL1, AF17q25/MSF, and septin 2-like cell division control protein in human (16) . Recently, it was shown that Septin6 was associated with synaptic vesicles in various brain regions, including glomeruli of the olfactory bulb in mice. CDCREL1 and AF17q25/MSF were also identified as the fusion partners of MLL (17, 18, 19, 20) . Septin proteins are associated with actin stress fibers in interphase cells, the cleavage furrow of dividing cells, and the bud neck of budding yeast. In addition, the functions of the septin proteins are considered to be related to the organization of specialized domains within the cells (16) .
SEPTIN6 was expressed almost ubiquitously in this study, being similar to AF17q25/MSF and Nedd5, but different from CDCREL1 (17, 18, 19, 20, 21, 22) . Recently, functional subgroups of the septin family were proposed (16) ; thus, this expressional difference may reflect a functional difference. Several isoforms were detected, compatible with other septin family genes, for example, AF17q25/MSF (16 , 19) , which were considered to correspond to the results of Northern blot analysis.
In the leukemic cells of patients, two types of MLL-SEPTIN6 fusion transcripts were detected. By sequencing analysis, we found in-frame fusion of exon 7 or 8 of MLL to exon 2 of SEPTIN6. However, we could not detect SEPTIN6-MLL fusion transcripts by RT-PCR. Therefore, the 5'-MLL-SEPTIN6 -3' transcript is considered critical to the leukemogenesis of t(X;11)-AML.
The MLL-SEPTIN6 fusion proteins contain almost the entire septin protein as well as the NH2 terminus of MLL, including the DNA-binding regions, similar to MLL-CDCREL1 and MLL-AF17q25/MSF (Fig. 2B
; Refs. 17, 18, 19, 20
). Therefore, a common region, e.g., the GTP-binding domain, might be crucial for the leukemogenesis associated with MLL-SEPTIN fusion proteins. The function of the MLL fusion protein remains unknown, although a few interesting reports have been published. It was shown that Mll-lacZ fusion gene was sufficient to cause leukemia in mice, and it seemed that lacZ could contribute to leukemogenesis through oligomerization of the MLL-lacZ fusion protein (23)
. Similarly, the coiled-coil region, which is found in CDCREL1 as well as AF1p/Eps15, and AF6 located at the COOH-terminus of SEPTIN6 might also contribute to leukemogenesis. Functional analyses of MLL-SEPTIN6 fusion proteins in addition to MLL-CDCREL1 and MLL-AF17q25/MSF may provide new insights into the leukemogenesis of AML with 11q23 translocations.
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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1 Supported by a grant-in-aid for Cancer Research from the Ministry of Health and Welfare of Japan, a grant-in-aid for Scientific Research on Priority Areas, and grant-in-aid for Scientific Research (B) and (C) from the Ministry of Education, Culture, Sports, Science and Technology, Japan. ![]()
2 To whom requests for reprints should be addressed, at Department of Pediatrics, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan. Phone: 81-3-3815-5411, extension 33462; Fax: 81-3-3816-4108; E-mail: hayashiy-tky{at}umin.ac.jp ![]()
3 The abbreviations used are: AML, acute myeloid leukemia; ALL, acute lymphoblastic leukemia; BM, bone marrow; PB, peripheral blood; RT-PCR, reverse transcription-PCR; FISH, fluorescence in situ hybridization; ORF, open reading frame. ![]()
Received 7/27/01. Accepted 11/30/01.
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