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Raf Sciot - One of the best experts on this subject based on the ideXlab platform.
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comprehensive genetic analysis identifies a pathognomonic nab2 stat6 fusion gene nonrandom secondary genomic imbalances and a characteristic gene expression profile in solitary fibrous tumor
Genes Chromosomes and Cancer, 2013Co-Authors: Arezoo Mohajeri, Henryk A Domanski, Johnbosco Tayebwa, Anna Collin, Jenny Nilsson, Linda Magnusson, Otte Brosjo, Olle Larsson, Fredrik Vult Von Steyern, Raf SciotAbstract:Solitary fibrous tumor (SFT) is a mesenchymal neoplasm displaying variable morphologic and clinical features. To identify pathogenetically important genetic rearrangements, 44 SFTs were analyzed using a variety of techniques. Chromosome Banding and fluorescence in situ hybridization (FISH) showed recurrent breakpoints in 12q13, clustering near the NAB2 and STAT6 genes, and single nucleotide polymorphism array analysis disclosed frequent deletions affecting STAT6. Quantitative real-time PCR revealed high expression levels of the 5'-end of NAB2 and the 3'-end of STAT6, which at deep sequencing of enriched DNA corresponded to NAB2/STAT6 fusions. Subsequent reverse-transcriptase PCR (RT-PCR) analysis identified a NAB2/STAT6 fusion in 37/41 cases, confirming that this fusion gene underlies the pathogenesis of SFT. The hypothesis that the NAB2/STAT6 fusions will result in altered properties of the transcriptional co-repressor NAB2 - a key regulator of the early growth response 1 (EGR1) transcription factor - was corroborated by global gene expression analysis; SFTs showed deregulated expression of EGR1 target genes, as well as of other, developmentally important genes. We also identified several nonrandom secondary changes, notably loss of material from 13q and 14q. As neither Chromosome Banding nor FISH analysis identify more than a minor fraction of the fusion-positive cases, and because multiple primer combinations are required to identify all possible fusion transcripts by RT-PCR, alternative diagnostic markers might instead be found among deregulated genes identified at global gene expression analysis. Indeed, using immunohistochemistry on tissue microarrays, the top up-regulated gene, GRIA2, was found to be differentially expressed also at the protein level. © 2013 Wiley Periodicals, Inc. (Less)
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comprehensive genetic analysis identifies a pathognomonic nab2 stat6 fusion gene nonrandom secondary genomic imbalances and a characteristic gene expression profile in solitary fibrous tumor
Genes Chromosomes and Cancer, 2013Co-Authors: Arezoo Mohajeri, Henryk A Domanski, Fredrik Vult Von Steyern, Johnbosco Tayebwa, Anna Collin, Jenny Nilsson, Linda Magnusson, Otte Brosjo, Olle Larsson, Raf SciotAbstract:Solitary fibrous tumor (SFT) is a mesenchymal neoplasm displaying variable morphologic and clinical features. To identify pathogenetically important genetic rearrangements, 44 SFTs were analyzed using a variety of techniques. Chromosome Banding and fluorescence in situ hybridization (FISH) showed recurrent breakpoints in 12q13, clustering near the NAB2 and STAT6 genes, and single nucleotide polymorphism array analysis disclosed frequent deletions affecting STAT6. Quantitative real-time PCR revealed high expression levels of the 5'-end of NAB2 and the 3'-end of STAT6, which at deep sequencing of enriched DNA corresponded to NAB2/STAT6 fusions. Subsequent reverse-transcriptase PCR (RT-PCR) analysis identified a NAB2/STAT6 fusion in 37/41 cases, confirming that this fusion gene underlies the pathogenesis of SFT. The hypothesis that the NAB2/STAT6 fusions will result in altered properties of the transcriptional co-repressor NAB2--a key regulator of the early growth response 1 (EGR1) transcription factor - was corroborated by global gene expression analysis; SFTs showed deregulated expression of EGR1 target genes, as well as of other, developmentally important genes. We also identified several nonrandom secondary changes, notably loss of material from 13q and 14q. As neither Chromosome Banding nor FISH analysis identify more than a minor fraction of the fusion-positive cases, and because multiple primer combinations are required to identify all possible fusion transcripts by RT-PCR, alternative diagnostic markers might instead be found among deregulated genes identified at global gene expression analysis. Indeed, using immunohistochemistry on tissue microarrays, the top up-regulated gene, GRIA2, was found to be differentially expressed also at the protein level.
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FOSL1 as a candidate target gene for 11q12 rearrangements in desmoplastic fibroblastoma.
Laboratory investigation; a journal of technical methods and pathology, 2012Co-Authors: Gemma Macchia, Fredrik Mertens, Domenico Trombetta, Emely Möller, Clelia Tiziana Storlazzi, Maria Debiec-rychter, Raf Sciot, Karolin Hansén NordAbstract:Desmoplastic fibroblastoma (DF) is a benign fibroblastic/myofibroblastic tumor. Cytogenetic analyses have revealed consistent rearrangement of Chromosome band 11q12, strongly suggesting that this region harbors a gene of pathogenetic importance. To identify the target gene of the 11q12 rearrangements, we analyzed six cases diagnosed as DF using Chromosome Banding, fluorescence in situ hybridization (FISH), single-nucleotide polymorphism array and gene expression approaches. Different structural rearrangements involving 11q12 were found in five of the six cases. Metaphase FISH analyses in two of them mapped the 11q12 breakpoints to an B20-kb region, harboring FOSL1. Global gene expression profiling followed by quantitative real-time PCR showed that FOSL1 was expressed at higher levels in DF with 11q12 rearrangements than in desmoid-type fibromatoses. Furthermore, FOSL1 was not upregulated in the single case of DF that did not show cytogenetic involvement of 11q12; instead this tumor was found to display a hemizygous loss on 5q, including the APC (adenomatous polyposis coli) locus, raising the possibility that it actually was a misdiagnosed Gardner fibroma. 5 0 RACE-PCR in two 11q12-positive DF did not identify any fusion transcripts. Thus, in agreement with the finding at Chromosome Banding analysis that varying translocation partners are involved in the 11q12 rearrangement, the molecular data suggest that the functional outcome of the 11q12 rearrangements is deregulated expression of FOSL1.
Fredrik Mertens - One of the best experts on this subject based on the ideXlab platform.
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comprehensive genetic analysis of a pediatric pleomorphic myxoid liposarcoma reveals near haploidization and loss of the rb1 gene
Histopathology, 2016Co-Authors: Jakob Hofvander, Iman Ghanei, Emma Martensson, David Gisselsson, Vickie Y Jo, Fredrik MertensAbstract:Pleomorphic myxoid liposarcoma (PML) is an exceptionally rare and poorly studied subtype of liposarcoma, typically occurring in children and adolescents. The few previous genetic studies have shown that PML lacks the gene fusions and amplifications that characterize myxoid liposarcoma, atypical lipomatous tumor, and dedifferentiated liposarcoma. To learn more about its pathogenesis, we performed a comprehensive genetic analysis, including Chromosome Banding, fluorescence in situ hybridization, single nucleotide polymorphism (SNP) array analysis, deep sequencing of the exome (WES) complemented by targeted sequencing of hotspot regions of selected cancer-associated genes, and transcriptome sequencing (RNA-seq), of a PML in a 10-year-old boy.
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FOSL1 as a candidate target gene for 11q12 rearrangements in desmoplastic fibroblastoma.
Laboratory investigation; a journal of technical methods and pathology, 2012Co-Authors: Gemma Macchia, Fredrik Mertens, Domenico Trombetta, Emely Möller, Clelia Tiziana Storlazzi, Maria Debiec-rychter, Raf Sciot, Karolin Hansén NordAbstract:Desmoplastic fibroblastoma (DF) is a benign fibroblastic/myofibroblastic tumor. Cytogenetic analyses have revealed consistent rearrangement of Chromosome band 11q12, strongly suggesting that this region harbors a gene of pathogenetic importance. To identify the target gene of the 11q12 rearrangements, we analyzed six cases diagnosed as DF using Chromosome Banding, fluorescence in situ hybridization (FISH), single-nucleotide polymorphism array and gene expression approaches. Different structural rearrangements involving 11q12 were found in five of the six cases. Metaphase FISH analyses in two of them mapped the 11q12 breakpoints to an B20-kb region, harboring FOSL1. Global gene expression profiling followed by quantitative real-time PCR showed that FOSL1 was expressed at higher levels in DF with 11q12 rearrangements than in desmoid-type fibromatoses. Furthermore, FOSL1 was not upregulated in the single case of DF that did not show cytogenetic involvement of 11q12; instead this tumor was found to display a hemizygous loss on 5q, including the APC (adenomatous polyposis coli) locus, raising the possibility that it actually was a misdiagnosed Gardner fibroma. 5 0 RACE-PCR in two 11q12-positive DF did not identify any fusion transcripts. Thus, in agreement with the finding at Chromosome Banding analysis that varying translocation partners are involved in the 11q12 rearrangement, the molecular data suggest that the functional outcome of the 11q12 rearrangements is deregulated expression of FOSL1.
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Chromosome Banding analysis of cells from fine needle aspiration biopsy samples from soft tissue and bone tumors is it clinically meaningful
Cancer Genetics and Cytogenetics, 2011Co-Authors: Charles Walther, Nils Mandahl, Henryk A Domanski, Fredrik Vult Von Steyern, Fredrik MertensAbstract:Morphologic evaluation of samples from fine-needle aspiration (FNA) and core needle (CN) biopsies is an important part of the pretreatment diagnosis of bone and soft tissue tumors. Because most such tumors have characteristic, sometimes even specific, chromosomal rearrangements, ancillary genetic analyses could provide important diagnostic information. Whereas directed analyses, such as fluorescence in situ hybridization or reverse transcriptase–polymerase chain reaction, for specific genetic aberrations are well suited for the relatively small cell numbers obtained with FNA biopsies, the possibility to obtain tumor karyotypes after cell culturing has been less well studied. In the present study, karyotypes from 114 FNA biopsy samples were compared to those in corresponding surgical tumor samples; in addition, results on 31 CN samples and their corresponding tumor samples were available. Of the 138 surgical tumor samples, 88 (64%) showed clonal acquired Chromosome aberrations, 42 (30%) displayed a normal karyotype, and 8 (6%) did not yield any karyotype as a result of infection or poor cell growth. The corresponding figures for the 114 FNA samples were 27 (24%), 28 (25%), and 59 (52%), and for the 31 CN samples 15 (48%), 10 (32%), and 6 (19%). The relatively low success rate, with the possible exception of primitive round cell/Ewing sarcomas (abnormal karyotype in 6 of 11 FNA samples), strongly indicates that it is not meaningful to attempt cell culturing and Chromosome Banding analysis on FNA biopsy sample cells in patients with suspected bone or soft tissue tumors. The use of ancillary techniques such as fluorescence in situ hybridization might improve the diagnostic value from FNA. Our preliminary data suggest that if a pretreatment karyotype is wanted, the cytogenetic analysis should be made on cells from CN samples, close to half of which showed an aberrant karyotype.
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spectral karyotyping and Chromosome Banding studies of primary breast carcinomas and their lymph node metastases
International Journal of Molecular Medicine, 2000Co-Authors: Adewale Adeyinka, Fredrik Mertens, S Kytola, Nikos Pandis, C LarssonAbstract:Three primary breast tumors and their lymph node metastases were characterized by G-Banding, spectral karyotyping (SKY), and fluorescence in situ hybridization (FISH). In each case, the karyotypic abnormalities detected were similar in the primary tumor and its matched metastasis. Two of the pairs had near-diploid karyotypes with three to four chromosomal aberrations, whereas the third pair had a near-pentaploid Chromosome content and many marker Chromosomes in the primary tumor and a near-tetraploid Chromosome number with almost the same marker Chromosomes in the metastasis. SKY and FISH confirmed the karyotypic similarities between the primary tumors and their metastases and, in addition, improved the identification and characterization of marker Chromosomes. One of the tumor pairs with near-diploid karyotypes had gain of 8q, 16q, and 17q, whereas the other had gain of 1q and Chromosome 8 material in the form of ring Chromosomes. The third pair had more complex chromosomal translocations and numerical changes resulting in net gain of material from Chromosomes X, 1, 2, 6, 7, 14, 16, 19, and 20, and Chromosome arms 8q and 11q, as well as net loss of material from Chromosomes 3, 13, 18, 21, and 22. The present study underscores the need to combine conventional Chromosome Banding and molecular cytogenetic techniques in the cytogenetic analysis of solid tumors.
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unique cytological features and Chromosome aberrations in chondroid lipoma a case report based on fine needle aspiration cytology histopathology electron microscopy Chromosome Banding and molecular cytogenetics
The American Journal of Surgical Pathology, 1999Co-Authors: David Gisselsson, Fredrik Mertens, Henryk A Domanski, Mattias Hoglund, Birgitta Carlen, Helena Willen, Nils MandahlAbstract:Chondroid lipoma is a rare, benign tumor that may mimic soft-tissue sarcoma clinically. Its histopathologic features may resemble hibernoma, myxoid liposarcoma, myxoid chondrosarcoma, and other lipomatous or chondroid neoplasms. In this study, a chondroid lipoma was analyzed by fine-needle aspiration cytology, histopathology, electron microscopy, Chromosome Banding, and metaphase fluorescence in situ hybridization. The results demonstrate that chondroid lipoma exhibits a characteristic pattern by fine-needle aspiration cytology, including a mixture of benign adipose tissue with lipoblastlike cells, and chondroblastlike cells with a fibrochondroid matrix. Cytogenetically, a three-way rearrangement between Chromosomes 1, 2, and 5 was found, together with an 11;16 translocation with a breakpoint in 11q13, approximately 1 Mb proximal to the MEN1 region shown to be rearranged frequently in hibernoma. The presence of a karyotype of low complexity, but without any of the genetic aberrations characteristic for other types of soft-tissue tumors, indicate that chondroid lipoma develops along a unique pathogenetic pathway.
Henryk A Domanski - One of the best experts on this subject based on the ideXlab platform.
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comprehensive genetic analysis identifies a pathognomonic nab2 stat6 fusion gene nonrandom secondary genomic imbalances and a characteristic gene expression profile in solitary fibrous tumor
Genes Chromosomes and Cancer, 2013Co-Authors: Arezoo Mohajeri, Henryk A Domanski, Fredrik Vult Von Steyern, Johnbosco Tayebwa, Anna Collin, Jenny Nilsson, Linda Magnusson, Otte Brosjo, Olle Larsson, Raf SciotAbstract:Solitary fibrous tumor (SFT) is a mesenchymal neoplasm displaying variable morphologic and clinical features. To identify pathogenetically important genetic rearrangements, 44 SFTs were analyzed using a variety of techniques. Chromosome Banding and fluorescence in situ hybridization (FISH) showed recurrent breakpoints in 12q13, clustering near the NAB2 and STAT6 genes, and single nucleotide polymorphism array analysis disclosed frequent deletions affecting STAT6. Quantitative real-time PCR revealed high expression levels of the 5'-end of NAB2 and the 3'-end of STAT6, which at deep sequencing of enriched DNA corresponded to NAB2/STAT6 fusions. Subsequent reverse-transcriptase PCR (RT-PCR) analysis identified a NAB2/STAT6 fusion in 37/41 cases, confirming that this fusion gene underlies the pathogenesis of SFT. The hypothesis that the NAB2/STAT6 fusions will result in altered properties of the transcriptional co-repressor NAB2--a key regulator of the early growth response 1 (EGR1) transcription factor - was corroborated by global gene expression analysis; SFTs showed deregulated expression of EGR1 target genes, as well as of other, developmentally important genes. We also identified several nonrandom secondary changes, notably loss of material from 13q and 14q. As neither Chromosome Banding nor FISH analysis identify more than a minor fraction of the fusion-positive cases, and because multiple primer combinations are required to identify all possible fusion transcripts by RT-PCR, alternative diagnostic markers might instead be found among deregulated genes identified at global gene expression analysis. Indeed, using immunohistochemistry on tissue microarrays, the top up-regulated gene, GRIA2, was found to be differentially expressed also at the protein level.
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comprehensive genetic analysis identifies a pathognomonic nab2 stat6 fusion gene nonrandom secondary genomic imbalances and a characteristic gene expression profile in solitary fibrous tumor
Genes Chromosomes and Cancer, 2013Co-Authors: Arezoo Mohajeri, Henryk A Domanski, Johnbosco Tayebwa, Anna Collin, Jenny Nilsson, Linda Magnusson, Otte Brosjo, Olle Larsson, Fredrik Vult Von Steyern, Raf SciotAbstract:Solitary fibrous tumor (SFT) is a mesenchymal neoplasm displaying variable morphologic and clinical features. To identify pathogenetically important genetic rearrangements, 44 SFTs were analyzed using a variety of techniques. Chromosome Banding and fluorescence in situ hybridization (FISH) showed recurrent breakpoints in 12q13, clustering near the NAB2 and STAT6 genes, and single nucleotide polymorphism array analysis disclosed frequent deletions affecting STAT6. Quantitative real-time PCR revealed high expression levels of the 5'-end of NAB2 and the 3'-end of STAT6, which at deep sequencing of enriched DNA corresponded to NAB2/STAT6 fusions. Subsequent reverse-transcriptase PCR (RT-PCR) analysis identified a NAB2/STAT6 fusion in 37/41 cases, confirming that this fusion gene underlies the pathogenesis of SFT. The hypothesis that the NAB2/STAT6 fusions will result in altered properties of the transcriptional co-repressor NAB2 - a key regulator of the early growth response 1 (EGR1) transcription factor - was corroborated by global gene expression analysis; SFTs showed deregulated expression of EGR1 target genes, as well as of other, developmentally important genes. We also identified several nonrandom secondary changes, notably loss of material from 13q and 14q. As neither Chromosome Banding nor FISH analysis identify more than a minor fraction of the fusion-positive cases, and because multiple primer combinations are required to identify all possible fusion transcripts by RT-PCR, alternative diagnostic markers might instead be found among deregulated genes identified at global gene expression analysis. Indeed, using immunohistochemistry on tissue microarrays, the top up-regulated gene, GRIA2, was found to be differentially expressed also at the protein level. © 2013 Wiley Periodicals, Inc. (Less)
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Chromosome Banding analysis of cells from fine needle aspiration biopsy samples from soft tissue and bone tumors is it clinically meaningful
Cancer Genetics and Cytogenetics, 2011Co-Authors: Charles Walther, Nils Mandahl, Henryk A Domanski, Fredrik Vult Von Steyern, Fredrik MertensAbstract:Morphologic evaluation of samples from fine-needle aspiration (FNA) and core needle (CN) biopsies is an important part of the pretreatment diagnosis of bone and soft tissue tumors. Because most such tumors have characteristic, sometimes even specific, chromosomal rearrangements, ancillary genetic analyses could provide important diagnostic information. Whereas directed analyses, such as fluorescence in situ hybridization or reverse transcriptase–polymerase chain reaction, for specific genetic aberrations are well suited for the relatively small cell numbers obtained with FNA biopsies, the possibility to obtain tumor karyotypes after cell culturing has been less well studied. In the present study, karyotypes from 114 FNA biopsy samples were compared to those in corresponding surgical tumor samples; in addition, results on 31 CN samples and their corresponding tumor samples were available. Of the 138 surgical tumor samples, 88 (64%) showed clonal acquired Chromosome aberrations, 42 (30%) displayed a normal karyotype, and 8 (6%) did not yield any karyotype as a result of infection or poor cell growth. The corresponding figures for the 114 FNA samples were 27 (24%), 28 (25%), and 59 (52%), and for the 31 CN samples 15 (48%), 10 (32%), and 6 (19%). The relatively low success rate, with the possible exception of primitive round cell/Ewing sarcomas (abnormal karyotype in 6 of 11 FNA samples), strongly indicates that it is not meaningful to attempt cell culturing and Chromosome Banding analysis on FNA biopsy sample cells in patients with suspected bone or soft tissue tumors. The use of ancillary techniques such as fluorescence in situ hybridization might improve the diagnostic value from FNA. Our preliminary data suggest that if a pretreatment karyotype is wanted, the cytogenetic analysis should be made on cells from CN samples, close to half of which showed an aberrant karyotype.
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unique cytological features and Chromosome aberrations in chondroid lipoma a case report based on fine needle aspiration cytology histopathology electron microscopy Chromosome Banding and molecular cytogenetics
The American Journal of Surgical Pathology, 1999Co-Authors: David Gisselsson, Fredrik Mertens, Henryk A Domanski, Mattias Hoglund, Birgitta Carlen, Helena Willen, Nils MandahlAbstract:Chondroid lipoma is a rare, benign tumor that may mimic soft-tissue sarcoma clinically. Its histopathologic features may resemble hibernoma, myxoid liposarcoma, myxoid chondrosarcoma, and other lipomatous or chondroid neoplasms. In this study, a chondroid lipoma was analyzed by fine-needle aspiration cytology, histopathology, electron microscopy, Chromosome Banding, and metaphase fluorescence in situ hybridization. The results demonstrate that chondroid lipoma exhibits a characteristic pattern by fine-needle aspiration cytology, including a mixture of benign adipose tissue with lipoblastlike cells, and chondroblastlike cells with a fibrochondroid matrix. Cytogenetically, a three-way rearrangement between Chromosomes 1, 2, and 5 was found, together with an 11;16 translocation with a breakpoint in 11q13, approximately 1 Mb proximal to the MEN1 region shown to be rearranged frequently in hibernoma. The presence of a karyotype of low complexity, but without any of the genetic aberrations characteristic for other types of soft-tissue tumors, indicate that chondroid lipoma develops along a unique pathogenetic pathway.
Arezoo Mohajeri - One of the best experts on this subject based on the ideXlab platform.
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comprehensive genetic analysis identifies a pathognomonic nab2 stat6 fusion gene nonrandom secondary genomic imbalances and a characteristic gene expression profile in solitary fibrous tumor
Genes Chromosomes and Cancer, 2013Co-Authors: Arezoo Mohajeri, Henryk A Domanski, Fredrik Vult Von Steyern, Johnbosco Tayebwa, Anna Collin, Jenny Nilsson, Linda Magnusson, Otte Brosjo, Olle Larsson, Raf SciotAbstract:Solitary fibrous tumor (SFT) is a mesenchymal neoplasm displaying variable morphologic and clinical features. To identify pathogenetically important genetic rearrangements, 44 SFTs were analyzed using a variety of techniques. Chromosome Banding and fluorescence in situ hybridization (FISH) showed recurrent breakpoints in 12q13, clustering near the NAB2 and STAT6 genes, and single nucleotide polymorphism array analysis disclosed frequent deletions affecting STAT6. Quantitative real-time PCR revealed high expression levels of the 5'-end of NAB2 and the 3'-end of STAT6, which at deep sequencing of enriched DNA corresponded to NAB2/STAT6 fusions. Subsequent reverse-transcriptase PCR (RT-PCR) analysis identified a NAB2/STAT6 fusion in 37/41 cases, confirming that this fusion gene underlies the pathogenesis of SFT. The hypothesis that the NAB2/STAT6 fusions will result in altered properties of the transcriptional co-repressor NAB2--a key regulator of the early growth response 1 (EGR1) transcription factor - was corroborated by global gene expression analysis; SFTs showed deregulated expression of EGR1 target genes, as well as of other, developmentally important genes. We also identified several nonrandom secondary changes, notably loss of material from 13q and 14q. As neither Chromosome Banding nor FISH analysis identify more than a minor fraction of the fusion-positive cases, and because multiple primer combinations are required to identify all possible fusion transcripts by RT-PCR, alternative diagnostic markers might instead be found among deregulated genes identified at global gene expression analysis. Indeed, using immunohistochemistry on tissue microarrays, the top up-regulated gene, GRIA2, was found to be differentially expressed also at the protein level.
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comprehensive genetic analysis identifies a pathognomonic nab2 stat6 fusion gene nonrandom secondary genomic imbalances and a characteristic gene expression profile in solitary fibrous tumor
Genes Chromosomes and Cancer, 2013Co-Authors: Arezoo Mohajeri, Henryk A Domanski, Johnbosco Tayebwa, Anna Collin, Jenny Nilsson, Linda Magnusson, Otte Brosjo, Olle Larsson, Fredrik Vult Von Steyern, Raf SciotAbstract:Solitary fibrous tumor (SFT) is a mesenchymal neoplasm displaying variable morphologic and clinical features. To identify pathogenetically important genetic rearrangements, 44 SFTs were analyzed using a variety of techniques. Chromosome Banding and fluorescence in situ hybridization (FISH) showed recurrent breakpoints in 12q13, clustering near the NAB2 and STAT6 genes, and single nucleotide polymorphism array analysis disclosed frequent deletions affecting STAT6. Quantitative real-time PCR revealed high expression levels of the 5'-end of NAB2 and the 3'-end of STAT6, which at deep sequencing of enriched DNA corresponded to NAB2/STAT6 fusions. Subsequent reverse-transcriptase PCR (RT-PCR) analysis identified a NAB2/STAT6 fusion in 37/41 cases, confirming that this fusion gene underlies the pathogenesis of SFT. The hypothesis that the NAB2/STAT6 fusions will result in altered properties of the transcriptional co-repressor NAB2 - a key regulator of the early growth response 1 (EGR1) transcription factor - was corroborated by global gene expression analysis; SFTs showed deregulated expression of EGR1 target genes, as well as of other, developmentally important genes. We also identified several nonrandom secondary changes, notably loss of material from 13q and 14q. As neither Chromosome Banding nor FISH analysis identify more than a minor fraction of the fusion-positive cases, and because multiple primer combinations are required to identify all possible fusion transcripts by RT-PCR, alternative diagnostic markers might instead be found among deregulated genes identified at global gene expression analysis. Indeed, using immunohistochemistry on tissue microarrays, the top up-regulated gene, GRIA2, was found to be differentially expressed also at the protein level. © 2013 Wiley Periodicals, Inc. (Less)
Takashi R. Endo - One of the best experts on this subject based on the ideXlab platform.
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Chromosome Arm Locations of Barley Sucrose Transporter Gene in Transgenic Winter Wheat Lines.
Frontiers in plant science, 2019Co-Authors: Shotaro Takenaka, Winfriede Weschke, Bettina Brückner, Minoru Murata, Takashi R. EndoAbstract:Three transgenic HOSUT lines of winter wheat, HOSUT12, HOSUT20, and HOSUT24, each harbor a single copy of the cDNA for the barley sucrose transporter gene HvSUT1 (SUT), which was fused to the barley endosperm-specific Hordein B1 promoter (HO; the HOSUT transgene). Previously, flow cytometry combined with PCR analysis demonstrated that the HOSUT transgene had been integrated into different wheat Chromosomes: 7A, 5D, and 4A in HOSUT12, HOSUT20, and HOSUT24, respectively. In order to confirm the chromosomal location of the HOSUT transgene by a cytological approach using wheat aneuploid stocks, we crossed corresponding nullisomic-tetrasomic lines with the three HOSUT lines, namely nullisomic 7A-tetrasomic 7B with HOSUT12, nullisomic 5D-tetrasomic 5B with HOSUT20, and nullisomic 4A-tetrasomic 4B with HOSUT24. We examined the resulting chromosomal constitutions and the presence of the HOSUT transgene in the F2 progeny by means of Chromosome Banding and PCR. The Chromosome Banding patterns of the critical Chromosomes in the original HOSUT lines showed no difference from those of the corresponding wild type Chromosomes. The presence or absence of the critical Chromosomes completely corresponded to the presence or absence of the HOSUT transgene in the F2 plants. Investigating telocentric Chromosomes occurred in the F2 progeny, which were derived from the respective critical HOSUT Chromosomes, we found that the HOSUT transgene was individually integrated on the long arms of Chromosomes 4A, 7A, and 5D in the three HOSUT lines. Thus, in this study we verified the chromosomal locations of the transgene, which had previously been determined by flow cytometry, and moreover revealed the Chromosome-arm locations of the HOSUT transgene in the HOSUT lines.
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Data_Sheet_1_Chromosome Arm Locations of Barley Sucrose Transporter Gene in Transgenic Winter Wheat Lines.PDF
2019Co-Authors: Shotaro Takenaka, Winfriede Weschke, Bettina Brückner, Minoru Murata, Takashi R. EndoAbstract:Three transgenic HOSUT lines of winter wheat, HOSUT12, HOSUT20, and HOSUT24, each harbor a single copy of the cDNA for the barley sucrose transporter gene HvSUT1 (SUT), which was fused to the barley endosperm-specific Hordein B1 promoter (HO; the HOSUT transgene). Previously, flow cytometry combined with PCR analysis demonstrated that the HOSUT transgene had been integrated into different wheat Chromosomes: 7A, 5D, and 4A in HOSUT12, HOSUT20, and HOSUT24, respectively. In order to confirm the chromosomal location of the HOSUT transgene by a cytological approach using wheat aneuploid stocks, we crossed corresponding nullisomic-tetrasomic lines with the three HOSUT lines, namely nullisomic 7A-tetrasomic 7B with HOSUT12, nullisomic 5D-tetrasomic 5B with HOSUT20, and nullisomic 4A-tetrasomic 4B with HOSUT24. We examined the resulting chromosomal constitutions and the presence of the HOSUT transgene in the F2 progeny by means of Chromosome Banding and PCR. The Chromosome Banding patterns of the critical Chromosomes in the original HOSUT lines showed no difference from those of the corresponding wild type Chromosomes. The presence or absence of the critical Chromosomes completely corresponded to the presence or absence of the HOSUT transgene in the F2 plants. Investigating telocentric Chromosomes occurred in the F2 progeny, which were derived from the respective critical HOSUT Chromosomes, we found that the HOSUT transgene was individually integrated on the long arms of Chromosomes 4A, 7A, and 5D in the three HOSUT lines. Thus, in this study we verified the chromosomal locations of the transgene, which had previously been determined by flow cytometry, and moreover revealed the Chromosome-arm locations of the HOSUT transgene in the HOSUT lines.