| 1. |
- Lundin, Kristina, et al.
(författare)
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Patterns and Frequencies of Acquired and Constitutional Uniparental Isodisomies in Pediatric and Adult B-Cell Precursor Acute Lymphoblastic Leukemia.
- 2016
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Ingår i: Genes, Chromosomes and Cancer. - : Wiley. - 1045-2257. ; 55:5, s. 472-479
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Tidskriftsartikel (refereegranskat)abstract
- Single nucleotide polymorphism (SNP) arrays are increasingly being used in clinical routine for genetic analysis of pediatric B-cell precursor acute lymphoblastic leukemias (BCP ALL). Because constitutional DNA is not readily available as a control at the time of diagnosis, it is important to be able to distinguish between acquired and constitutional aberrations in a diagnostic setting. In the present study we focused on uniparental isodisomies (UPIDs). SNP array analyses of 143 pediatric and 38 adult B-cell precursor acute lymphoblastic leukemias and matched remission samples revealed acquired whole chromosome or segmental UPIDs (wUPIDs, sUPIDs) in 32 cases (18%), without any age- or gender-related frequency differences. Acquired sUPIDs were larger than the constitutional ones (mean 35.3 Mb vs. 10.7 Mb; P<0.0001) and were more often terminally located in the chromosomes (69% vs. 4.5%; P<0.0001). Chromosomes 3, 5, and 9 were most often involved in acquired wUPIDs, whilst recurrent acquired sUPIDs targeted 6p, 9p, 9q, and 14q. The majority (56%) of sUPID9p was associated with homozygous CDKN2A deletions. In pediatric ALL, all wUPIDs were found in high hyperdiploid (51-67 chromosomes) cases and an extended analysis, also including unmatched diagnostic samples, revealed a higher frequency of wUPID-positivity in higher modal number (56-67 chromosomes) than in lower modal number (51-55 chromosomes) high hyperdiploid cases (34% versus 11%; P=0.04), suggesting different underlying mechanisms of formation of these subtypes of high hyperdiploidy. This article is protected by copyright. All rights reserved.
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| 2. |
- Safavi, Setareh, et al.
(författare)
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Genetic and epigenetic characterization of hypodiploid acute lymphoblastic leukemia
- 2015
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Ingår i: Oncotarget. - : IMPACT JOURNALS LLC. - 1949-2553. ; 6:40, s. 42793-42802
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: To investigate the genetic and epigenetic landscape of hypodiploid (<45 chromosomes) acute lymphoblastic leukemia (ALL). Methods: Single nucleotide polymorphism array, whole exome sequencing, RNA sequencing, and methylation array analyses were performed on eleven hypodiploid ALL cases. Results: In line with previous studies, mutations in IKZF3 and FLT3 were detected in near-haploid (25-30 chromosomes) cases. Low hypodiploidy (31-39 chromosomes) was associated with somatic TP53 mutations. Notably, mutations of this gene were also found in 3/3 high hypodiploid (40-44 chromosomes) cases, suggesting that the mutational patterns are similar in low hypodiploid and high hypodiploid ALL. The high hypodiploid ALLs frequently displayed substantial cell-to-cell variability in chromosomal content, indicative of chromosomal instability; a rare phenomenon in ALL. Gene expression analysis showed that genes on heterodisomic chromosomes were more highly expressed in hypodiploid cases. Cases clustered according to hypodiploid subtype in the unsupervised methylation analyses, but there was no association between chromosomal copy number and methylation levels. A comparison between samples obtained at diagnosis and relapse showed that the relapse did not arise from the major diagnostic clone in 3/4 cases. Conclusion: Taken together, our data support the conclusion that near-haploid and low hypodiploid ALL are different with regard to mutational profiles and also suggest that ALL cases with high hypodiploidy may harbor chromosomal instability.
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| 3. |
- Safavi, Setareh, et al.
(författare)
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HSP90 inhibition blocks ERBB3 and RET phosphorylation in myxoid/round cell liposarcoma and causes massive cell death in vitro and in vivo
- 2016
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Ingår i: OncoTarget. - : Impact Journals, LLC. - 1949-2553. ; 7:1, s. 433-445
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Tidskriftsartikel (refereegranskat)abstract
- Myxoid sarcoma (MLS) is one of the most common types of malignant soft tissue tumors. MLS is characterized by the FUS-DDIT3 or EWSR1-DDIT3 fusion oncogenes that encode abnormal transcription factors. The receptor tyrosine kinase (RTK) encoding RET was previously identified as a putative downstream target gene to FUS-DDIT3 and here we show that cultured MLS cells expressed phosphorylated RET together with its ligand Persephin. Treatment with RET specific kinase inhibitor Vandetanib failed to reduce RET phosphorylation and inhibit cell growth, suggesting that other RTKs may phosphorylate RET. A screening pointed out EGFR and ERBB3 as the strongest expressed phosphorylated RTKs in MLS cells. We show that ERBB3 formed nuclear and cytoplasmic complexes with RET and both RTKs were previously reported to form complexes with EGFR. The formation of RTK hetero complexes could explain the observed Vandetanib resistence in MLS. EGFR and ERBB3 are clients of HSP90 that help complex formation and RTK activation. Treatment of cultured MLS cells with HSP90 inhibitor 17-DMAG, caused loss of RET and ERBB3 phosphorylation and lead to rapid cell death. Treatment of MLS xenograft carrying Nude mice resulted in massive necrosis, rupture of capillaries and hemorrhages in tumor tissues. We conclude that complex formation between RET and other RTKs may cause RTK inhibitor resistance. HSP90 inhibitors can overcome this resistance and are thus promising drugs for treatment of MLS/RCLS.
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| 4. |
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| 5. |
- Safavi, Setareh
(författare)
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Molecular Genetic Characterization of Acute Lymphoblastic Leukemia with a Poor Prognosis
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Acute lymphoblastic leukemia (ALL) affects individuals at all ages, with peak incidences in children <4 years and adults >50 years. ALL is broadly categorized into B-cell precursor (BCP) and T-cell ALL with specific clinical features associated with outcome. In contrast to pediatric ALL, which has a favorable prognosis, adult ALL is associated with a much poorer outcome with less than 40% overall survival rates, decreasing with higher age. The presence of specific acquired genetic abnormalities is important for diagnosis, prognostication, and treatment stratification. ALL can be further categorized into subgroups defined by structural or ploidy abnormalities. One such subgroup, hypodiploid ALL (<46 chromosomes) is seen in 5-8% of all cases, and associated with a very dismal prognosis. It can be further subdivided into two distinct genetic and clinical subgroups, namely near-haploidy (24-31 chromosomes) and low hypodiploidy (32-39 chromosomes), and, comprising cases with a more heterogenous background, high hypodiploidy (40-43 chromosomes) and cases with 44 and 45 chromosomes. Near-haploid and low hypodiploid ALL are very rare, comprising less than 1% of BCP ALL, with overall survival rates of <30%. The general aim of my PhD project has been to characterize ALL patients with a poor prognosis, including adult ALL (article I) and hypodiploid ALL (article II-IV). To investigate the genetic landscape of adult ALL, we performed SNP array analysis on 126 ALL cases. Characteristic deletions seen in pediatric ALL were detected, furthermore, comparison of diagnostic and relapse clonal relationship showed evolution from an ancestral clone in the majority of cases, highlighting similarities in childhood and adult disease. In addition, the analysis revealed several recurrent cryptic genetic events not previously implicated with adult ALL, including the BCAT1, BTLA, NR3C1, PIK3AP1 and SERP2 genes. In articles II-IV the genetic and epigenetic background of hypodiploid ALL was further investigated using SNP array analysis, exome and RNA sequencing, methylation array analysis and FISH analysis. Characteristic chromosomal patterns were confirmed and subtype specific alterations targeting IKZF3, NF1, FLT3 and TP53 were identified near-haploid and low hypodiploid respectively. Furthermore, due to the specific pattern of CDKN2A deletions in one case, we could conclude that chromosomal loss was the primary event with further microdeletions occurring after the near-haploidization. Combining SNP array and FISH analysis, a sublconal pattern was detected in three cases harboring >79 chromosomes, showing a possible hypodiploid origin due to the extensive loss of heterozygosity identified in such cases. That all three cases harbored TP53 mutations emphasized similarities to low hypodiploid ALL. In conclusion, screening for specific genetic abnormalities routinely in the clinic may improve prognostication and treatment stratification in cases with a poor prognosis.
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| 6. |
- Safavi, Setareh, et al.
(författare)
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Near-haploid and low hypodiploid acute lymphoblastic leukemia - two distinct subtypes but consistently poor prognosis
- 2017
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Ingår i: Blood. - : American Society of Hematology. - 1528-0020 .- 0006-4971. ; 129:4, s. 420-423
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Tidskriftsartikel (refereegranskat)abstract
- Hypodiploidy <40 chromosomes is an uncommon genetic feature of acute lymphoblastic leukemia (ALL) in both children and adults. It has long been clear by cytogenetic analyses, and recently confirmed by mutational profiling, that these cases may be further subdivided into two subtypes: near-haploid ALL with 24-30 chromosomes and low hypodiploid ALL with 31-39 chromosomes. Both groups are associated with a very poor prognosis and these patients are among those who could benefit most from novel treatments.
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| 7. |
- Safavi, Setareh, et al.
(författare)
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Novel gene targets detected by genomic profiling in a consecutive series of 126 adults with acute lymphoblastic leukemia
- 2015
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Ingår i: Haematologica. - : Ferrata Storti Foundation (Haematologica). - 1592-8721 .- 0390-6078. ; 100:1, s. 55-61
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Tidskriftsartikel (refereegranskat)abstract
- In contrast to acute lymphoblastic leukemia in children, adult cases of this disease are associated with a very poor prognosis. In order to ascertain whether the frequencies and patterns of submicroscopic changes, identifiable with single nucleotide polymorphism array analysis, differ between childhood and adult acute lymphoblastic leukemia, we performed single nucleotide polymorphism array analyses of 126 adult cases, the largest series to date, including 18 paired diagnostic and relapse samples. Apart from identifying characteristic microdeletions of the CDKN2A, EBF1, ETV6, IKZF1, PAX5 and RB1 genes, the present study uncovered novel, focal deletions of the BCAT1, BTLA, NR3C1, PIK3AP1 and SERP2 genes in 2-6% of the adult cases. IKZF1 deletions were associated with B-cell precursor acute lymphoblastic leukemia (P=0.036), BCR-ABL1-positive acute lymphoblastic leukemia (P<0.001), and higher white blood cell counts (P=0.005). In addition, recurrent deletions of RASSF3 and TOX were seen in relapse samples. Comparing paired diagnostic/relapse samples revealed identical changes at diagnosis and relapse in 27%, clonal evolution in 22%, and relapses evolving from ancestral clones in 50%, akin to what has previously been reported in pediatric acute lymphoblastic leukemia and indicating that the mechanisms of relapse may be similar in adult and childhood cases. These findings provide novel insights into the leukemogenesis of adult acute lymphoblastic leukemia, showing similarities to childhood disease in the pattern of deletions and the clonal relationship between diagnostic and relapse samples, but with the adult cases harboring additional aberrations that have not been described in pediatric acute lymphoblastic leukemia.
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| 8. |
- Yang, Minjun, et al.
(författare)
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13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking
- 2020
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Ingår i: Blood. - : AMER SOC HEMATOLOGY. - 0006-4971 .- 1528-0020. ; 136:8, s. 946-956
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Tidskriftsartikel (refereegranskat)abstract
- Mutations in the FMS-like tyrosine kinase 3 (FLT3) gene in 13q12.2 are among the most common driver events in acute leukemia, leading to increased cell proliferation and survival through activation of the phosphatidylinositol 3-kinase/AKT-, RAS/MAPK-, and STAT5-signaling pathways. In this study, we examine the pathogenetic impact of somatic hemizygous 13q12.2 microdeletions in B-cell precursor (BCP) acute lymphoblastic leukemia (ALL) using 5 different patient cohorts (in total including 1418 cases). The 13q12.2 deletions occur immediately 59 of FLT3 and involve the PAN3 locus. By detailed analysis of the 13q12.2 segment, we show that the deletions lead to loss of a topologically associating domain border and an enhancer of FLT3. This results in increased cis interactions between the FLT3 promoter and another enhancer located distally to the deletion breakpoints, with subsequent allele-specific upregulation of FLT3 expression, expected to lead to ligand-independent activation of the receptor and downstream signaling. The 13q12.2 deletions are highly enriched in the high-hyperdiploid BCP ALL subtype (frequency 3.9% vs 0.5% in other BCP ALL) and in cases that subsequently relapsed. Taken together, our study describes a novel mechanism of FLT3 involvement in leukemogenesis by upregulation via chromatin remodeling and enhancer hijacking. These data further emphasize the role of FLT3 as a driver gene in BCP ALL.
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| 9. |
- Åman, Pierre, 1953, et al.
(författare)
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Regulatory mechanisms, expression levels and proliferation effects of the FUS-DDIT3 fusion oncogene in liposarcoma.
- 2016
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Ingår i: The Journal of pathology. - : Wiley. - 1096-9896 .- 0022-3417. ; 238:5, s. 689-99
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Tidskriftsartikel (refereegranskat)abstract
- Fusion oncogenes are among the most common types of oncogene in human cancers. The gene rearrangements result in new combinations of regulatory elements and functional protein domains. Here we studied a subgroup of sarcomas and leukaemias characterized by the FET (FUS, EWSR1, TAF15) family of fusion oncogenes, including FUS-DDIT3 in myxoid liposarcoma (MLS). We investigated the regulatory mechanisms, expression levels and effects of FUS-DDIT3 in detail. FUS-DDIT3 showed a lower expression than normal FUS at both the mRNA and protein levels, and single-cell analysis revealed a lack of correlation between FUS-DDIT3 and FUS expression. FUS-DDIT3 transcription was regulated by the FUS promotor, while its mRNA stability depended on the DDIT3 sequence. FUS-DDIT3 protein stability was regulated by protein interactions through the FUS part, rather than the leucine zipper containing DDIT3 part. In addition, in vitro as well as in vivo FUS-DDIT3 protein expression data displayed highly variable expression levels between individual MLS cells. Combined mRNA and protein analyses at the single-cell level showed that FUS-DDIT3 protein expression was inversely correlated to the expression of cell proliferation-associated genes. We concluded that FUS-DDIT3 is uniquely regulated at the transcriptional as well as the post-translational level and that its expression level is important for MLS tumour development. The FET fusion oncogenes are potentially powerful drug targets and detailed knowledge about their regulation and functions may help in the development of novel treatments. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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