1
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Fouad FM, Eid JI. PAX5 fusion genes in acute lymphoblastic leukemia: A literature review. Medicine (Baltimore) 2023; 102:e33836. [PMID: 37335685 DOI: 10.1097/md.0000000000033836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is a common cancer affecting children worldwide. The development of ALL is driven by several genes, some of which can be targeted for treatment by inhibiting gene fusions. PAX5 is frequently mutated in ALL and is involved in chromosomal rearrangements and translocations. Mutations in PAX5 interact with other genes, such as ETV6 and FOXP1, which influence B-cell development. PAX5/ETV6 has been observed in both B-ALL patients and a mouse model. The interaction between PAX5 and FOXP1 negatively suppresses the Pax5 gene in B-ALL patients. Additionally, ELN and PML genes have been found to fuse with PAX5, leading to adverse effects on B-cell differentiation. ELN-PAX5 interaction results in the decreased expression of LEF1, MB1, and BLNK, while PML-PAX5 is critical in the early stages of leukemia. PAX5 fusion genes prevent the transcription of the PAX5 gene, making it an essential target gene for the study of leukemia progression and the diagnosis of B-ALL.
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Affiliation(s)
- Fatma Mohamed Fouad
- Biology Department, College of Science, Sultan Qaboos University, Muscat, Oman
- Chemistry Department, Biotechnology/Bimolecular Chemistry program, Faculty of Science, Cairo University, Giza, Egypt
| | - Jehane I Eid
- Zoology Department, Faculty of Science, Cairo University, Giza, Egypt
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2
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Jia Z, Gu Z. PAX5 alterations in B-cell acute lymphoblastic leukemia. Front Oncol 2022; 12:1023606. [PMID: 36387144 PMCID: PMC9640836 DOI: 10.3389/fonc.2022.1023606] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 10/13/2022] [Indexed: 12/01/2022] Open
Abstract
PAX5, a master regulator of B cell development and maintenance, is one of the most common targets of genetic alterations in B-cell acute lymphoblastic leukemia (B-ALL). PAX5 alterations consist of copy number variations (whole gene, partial, or intragenic), translocations, and point mutations, with distinct distribution across B-ALL subtypes. The multifaceted functional impacts such as haploinsufficiency and gain-of-function of PAX5 depending on specific variants have been described, thereby the connection between the blockage of B cell development and the malignant transformation of normal B cells has been established. In this review, we provide the recent advances in understanding the function of PAX5 in orchestrating the development of both normal and malignant B cells over the past decade, with a focus on the PAX5 alterations shown as the initiating or driver events in B-ALL. Recent large-scale genomic analyses of B-ALL have identified multiple novel subtypes driven by PAX5 genetic lesions, such as the one defined by a distinct gene expression profile and PAX5 P80R mutation, which is an exemplar leukemia entity driven by a missense mutation. Although altered PAX5 is shared as a driver in B-ALL, disparate disease phenotypes and clinical outcomes among the patients indicate further heterogeneity of the underlying mechanisms and disturbed gene regulation networks along the disease development. In-depth mechanistic studies in human B-ALL and animal models have demonstrated high penetrance of PAX5 variants alone or concomitant with other genetic lesions in driving B-cell malignancy, indicating the altered PAX5 and deregulated genes may serve as potential therapeutic targets in certain B-ALL cases.
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Affiliation(s)
- Zhilian Jia
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, United States
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, United States
| | - Zhaohui Gu
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA, United States
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, United States
- *Correspondence: Zhaohui Gu,
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3
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The Pleiotropy of PAX5 Gene Products and Function. Int J Mol Sci 2022; 23:ijms231710095. [PMID: 36077495 PMCID: PMC9456430 DOI: 10.3390/ijms231710095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/23/2022] [Accepted: 08/26/2022] [Indexed: 11/17/2022] Open
Abstract
PAX5, a member of the Paired Box (PAX) transcription factor family, is an essential factor for B-lineage identity during lymphoid differentiation. Mechanistically, PAX5 controls gene expression profiles, which are pivotal to cellular processes such as viability, proliferation, and differentiation. Given its crucial function in B-cell development, PAX5 aberrant expression also correlates with hallmark cancer processes leading to hematological and other types of cancer lesions. Despite the well-established association of PAX5 in the development, maintenance, and progression of cancer disease, the use of PAX5 as a cancer biomarker or therapeutic target has yet to be implemented. This may be partly due to the assortment of PAX5 expressed products, which layers the complexity of their function and role in various regulatory networks and biological processes. In this review, we provide an overview of the reported data describing PAX5 products, their regulation, and function in cellular processes, cellular biology, and neoplasm.
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4
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Matsumoto Y, Chinen Y, Shimura Y, Nagoshi H, Sasaki N, Muramatsu A, Kuriyama K, Ohshiro M, Hirakawa Y, Iwai T, Uchiyama H, Taki T, Horiike S, Kuroda J, Taniwaki M. Recurrent intragenic exon rearrangements of SOBP and AUTS2 in non-Hodgkin B-cell lymphoma. Int J Hematol 2019; 111:75-83. [PMID: 31686349 DOI: 10.1007/s12185-019-02766-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 11/28/2022]
Abstract
Expression of intragenic exon rearrangements (IERs) has reportedly been detected in both normal and cancer cells. However, there have been few reports of occurrence of these rearrangements specific to neoplasms including malignant lymphoma. In this study, we detected IERs of ten genes (NBPF8, SOBP, AUTS2, RAB21, SPATA13, ABCC4, WDR7, PHLPP1, NFATC1 and MAGED1) in non-Hodgkin B cell lymphoma (B-NHL) cell line KPUM-UH1 using a high-resolution single nucleotide polymorphism array and reverse transcription polymerase chain reaction using reversely directed divergent primers within exons involved in genomic intragenic gains followed by sequencing analysis. Among them, the IERs involved in SOBP (6q21) exon 2 and 3 and AUTS2 (7q11.22) exon 2-4 were the molecular lesions specific to tumors and were frequently detected in B-NHL samples. These IERs constitute novel genetic alterations of B-NHL, which might be associated with tumorigenesis and be useful as genetic biological markers.
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Affiliation(s)
- Yosuke Matsumoto
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan.
| | - Yoshiaki Chinen
- Department of Hematology, Fukuchiyama City Hospital, Fukuchiyama, Japan.,Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuji Shimura
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hisao Nagoshi
- Department of Hematology and Oncology, Hiroshima University, Hiroshima, Japan
| | - Nana Sasaki
- Department of Hematology, Japanese Red Cross Kyoto Daini Hospital, Kyoto, Japan
| | - Ayako Muramatsu
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Kodai Kuriyama
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Muneo Ohshiro
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Yoshiko Hirakawa
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Toshiki Iwai
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Hitoji Uchiyama
- Department of Hematology, Japanese Red Cross Kyoto Daiichi Hospital, 15-749, Honmachi, Higashiyama-ku, Kyoto, 605-8981, Japan
| | - Tomohiko Taki
- Department of Medical Technology, Kyorin University, Faculty of Health Science, Tokyo, Japan.,Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeo Horiike
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Junya Kuroda
- Division of Hematology and Oncology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masafumi Taniwaki
- Center for Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine, Kyoto, Japan
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5
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Berry NK, Scott RJ, Rowlings P, Enjeti AK. Clinical use of SNP-microarrays for the detection of genome-wide changes in haematological malignancies. Crit Rev Oncol Hematol 2019; 142:58-67. [PMID: 31377433 DOI: 10.1016/j.critrevonc.2019.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 12/17/2022] Open
Abstract
Single nucleotide polymorphism (SNP) microarrays are commonly used for the clinical investigation of constitutional genomic disorders; however, their adoption for investigating somatic changes is being recognised. With increasing importance being placed on defining the cancer genome, a shift in technology is imperative at a clinical level. Microarray platforms have the potential to become frontline testing, replacing or complementing standard investigations such as FISH or karyotype. This 'molecular karyotype approach' exemplified by SNP-microarrays has distinct advantages in the investigation of several haematological malignancies. A growing body of literature, including guidelines, has shown support for the use of SNP-microarrays in the clinical laboratory to aid in a more accurate definition of the cancer genome. Understanding the benefits of this technology along with discussing the barriers to its implementation is necessary for the development and incorporation of SNP-microarrays in a clinical laboratory for the investigation of haematological malignancies.
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Affiliation(s)
- Nadine K Berry
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology, Newcastle, New South Wales, Australia.
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, New South Wales, Australia; Department of Molecular Medicine, NSW Health Pathology, Newcastle, New South Wales, Australia
| | - Philip Rowlings
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia
| | - Anoop K Enjeti
- Department of Haematology, Calvary Mater Hospital, Newcastle, New South Wales, Australia; School of Medicine and Public Health, University Newcastle, New South Wales, Australia
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6
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Ha J, Kim B, Hahn S, Lee ST, Lyu CJ, Choi JR. A patient with B-cell acute lymphoblastic leukemia with PAX5-ETV6 rearrangement with dic(9;12)(p13;p13) identified by chromosomal microarray. Ann Hematol 2018; 97:1505-1507. [PMID: 29520434 DOI: 10.1007/s00277-018-3291-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 02/28/2018] [Indexed: 10/17/2022]
Affiliation(s)
- Jihye Ha
- Department of Laboratory Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Borahm Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
| | - Seungmin Hahn
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea
| | - Chuhl Joo Lyu
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Korea
| | - Jong Rak Choi
- Department of Laboratory Medicine, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Korea.
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7
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Ji Q, Qi D, Xu X, Xu Y, Goodman SB, Kang L, Song Q, Fan Z, Maloney WJ, Wang Y. Cryptotanshinone Protects Cartilage against Developing Osteoarthritis through the miR-106a-5p/GLIS3 Axis. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 11:170-179. [PMID: 29858052 PMCID: PMC5992348 DOI: 10.1016/j.omtn.2018.02.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/05/2018] [Accepted: 02/05/2018] [Indexed: 02/06/2023]
Abstract
Cryptotanshinone (CTS) has emerged as an anti-inflammatory agent in osteoarthritis (OA). However, the molecular mechanism underlying its potent therapeutic effect on OA remains largely unknown. MicroRNAs (miRNAs) act as crucial regulators in maintaining cartilage homeostasis. To investigate whether CTS protects against developing OA through regulation of miRNAs, we examined the potential CTS-mediated miRNA molecules using microarray analysis. We found that CTS significantly promoted miR-106a-5p expression in chondrocytes. Using the OA mouse model created by anterior cruciate ligament transection, we revealed that intra-articular injection of miR-106a-5p agomir attenuated OA. In addition, miR-106a-5p inhibited GLI-similar 3 (GLIS3) production by directly targeting the 3′ untranslated region. CTS promoted miR-106a-5p expression through recruitment of a member of the paired box (PAX) family of transcription factors, PAX5, to the miR-106a-5p promoter. Inhibition of PAX5 mimicked the effect of miR-106a-5p and abolished the CTS ability to regulate miR-106a-5p expression. In OA patients, miR-106-5p is downregulated which is accompanied by downregulation of PAX5 and upregulation of GLIS3. Collectively, these data highlight that the PAX5/miR-106a-5p/GLIS3 axis acts as a novel pleiotropic regulator in CTS-mediated OA cartilage protection, suggesting that miR-106a-5p and PAX5 activation and GLIS3 inhibition might be useful and attractive for therapeutic strategies to treat OA patients.
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Affiliation(s)
- Quanbo Ji
- Department of Orthopaedics, General Hospital of Chinese People's Liberation Army, Beijing 100853, China; Department of Orthopaedic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Dengbin Qi
- Department of Orthopaedics, General Hospital of Chinese People's Liberation Army, Beijing 100853, China
| | - Xiaojie Xu
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology, Beijing 100850, China
| | - Yameng Xu
- Department of Traditional Chinese Medicine, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Stuart B Goodman
- Department of Orthopaedic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Lei Kang
- Department of Nuclear Medicine, Peking University First Hospital, Beijing 100034, China
| | - Qi Song
- Department of Oncology, General Hospital of Chinese People's Liberation Army, Beijing 100853, China
| | - Zhongyi Fan
- Department of Oncology, General Hospital of Chinese People's Liberation Army, Beijing 100853, China
| | - William J Maloney
- Department of Orthopaedic Surgery, Stanford University, Stanford, CA 94305, USA.
| | - Yan Wang
- Department of Orthopaedics, General Hospital of Chinese People's Liberation Army, Beijing 100853, China.
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8
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Deregulation of polycomb repressor complex 1 modifier AUTS2 in T-cell leukemia. Oncotarget 2018; 7:45398-45413. [PMID: 27322685 PMCID: PMC5216730 DOI: 10.18632/oncotarget.9982] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/29/2016] [Indexed: 11/25/2022] Open
Abstract
Recently, we identified deregulated expression of the B-cell specific transcription factor MEF2C in T-cell acute lymphoid leukemia (T-ALL). Here, we performed sequence analysis of a regulatory upstream section of MEF2C in T-ALL cell lines which, however, proved devoid of mutations. Unexpectedly, we found strong conservation between the regulatory upstream region of MEF2C (located at chromosomal band 5q14) and an intergenic stretch at 7q11 located between STAG3L4 and AUTS2, covering nearly 20 kb. While the non-coding gene STAG3L4 was inconspicuously expressed, AUTS2 was aberrantly upregulated in 6% of T-ALL patients (public dataset GSE42038) and in 3/24 T-ALL cell lines, two of which represented very immature differentiation stages. AUTS2 expression was higher in normal B-cells than in T-cells, indicating lineage-specific activity in lymphopoiesis. While excluding chromosomal aberrations, examinations of AUTS2 transcriptional regulation in T-ALL cells revealed activation by IL7-IL7R-STAT5-signalling and MEF2C. AUTS2 protein has been shown to interact with polycomb repressor complex 1 subtype 5 (PRC1.5), transforming this particular complex into an activator. Accordingly, expression profiling and functional analyses demonstrated that AUTS2 activated while PCGF5 repressed transcription of NKL homeobox gene MSX1 in T-ALL cells. Forced expression and pharmacological inhibition of EZH2 in addition to H3K27me3 analysis indicated that PRC2 repressed MSX1 as well. Taken together, we found that AUTS2 and MEF2C, despite lying on different chromosomes, share strikingly similar regulatory upstream regions and aberrant expression in T-ALL subsets. Our data implicate chromatin complexes PRC1/AUTS2 and PRC2 in a gene network in T-ALL regulating early lymphoid differentiation.
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9
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Imoto N, Hayakawa F, Kurahashi S, Morishita T, Kojima Y, Yasuda T, Sugimoto K, Tsuzuki S, Naoe T, Kiyoi H. B Cell Linker Protein (BLNK) Is a Selective Target of Repression by PAX5-PML Protein in the Differentiation Block That Leads to the Development of Acute Lymphoblastic Leukemia. J Biol Chem 2015; 291:4723-31. [PMID: 26703467 DOI: 10.1074/jbc.m115.637835] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Indexed: 11/06/2022] Open
Abstract
PAX5 is a transcription factor that is required for the development and maintenance of B cells. Promyelocytic leukemia (PML) is a tumor suppressor and proapoptotic factor. The fusion gene PAX5-PML has been identified in acute lymphoblastic leukemia with chromosomal translocation t(9;15)(p13;q24). We have reported previously that PAX5-PML dominant-negatively inhibited PAX5 transcriptional activity and impaired PML function by disrupting PML nuclear bodies (NBs). Here we demonstrated the leukemogenicity of PAX5-PML by introducing it into normal mouse pro-B cells. Arrest of differentiation was observed in PAX5-PML-introduced pro-B cells, resulting in the development of acute lymphoblastic leukemia after a long latency in mice. Among the transactivation targets of PAX5, B cell linker protein (BLNK) was repressed selectively in leukemia cells, and enforced BLNK expression abrogated the differentiation block and survival induced by PAX5-PML, indicating the importance of BLNK repression for the formation of preleukemic state. We also showed that PML NBs were intact in leukemia cells and attributed this to the low expression of PAX5-PML, indicating that the disruption of PML NBs was not required for the PAX5-PML-induced onset of leukemia. These results provide novel insights into the molecular mechanisms underlying the onset of leukemia by PAX5 mutations.
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Affiliation(s)
- Naoto Imoto
- From the Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Fumihiko Hayakawa
- From the Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan,
| | - Shingo Kurahashi
- the Division of Hematology and Oncology, Toyohashi Municipal Hospital, Toyohashi, 441-8570, Japan
| | - Takanobu Morishita
- From the Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Yuki Kojima
- From the Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Takahiko Yasuda
- the Department of Cellular Signaling, Graduate School of Medicine, University of Tokyo, 113-8654, Tokyo, Japan
| | - Keiki Sugimoto
- the Fujii Memorial Research Institute, Otsuka Pharmaceutical Co., Ltd., Otsu, 520-0106, Japan
| | - Shinobu Tsuzuki
- the Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, 464-8681, Japan, and
| | - Tomoki Naoe
- the National Hospital Organization Nagoya Medical Center, Nagoya, 460-0001, Japan
| | - Hitoshi Kiyoi
- From the Department of Hematology and Oncology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
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10
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Schneider A, Puechberty J, Ng BL, Coubes C, Gatinois V, Tournaire M, Girard M, Dumont B, Bouret P, Magnetto J, Baghdadli A, Pellestor F, Geneviève D. Identification of disrupted AUTS2 and EPHA6 genes by array painting in a patient carrying a de novo balanced translocation t(3;7) with intellectual disability and neurodevelopment disorder. Am J Med Genet A 2015; 167A:3031-7. [PMID: 26333717 DOI: 10.1002/ajmg.a.37350] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 08/12/2015] [Indexed: 11/09/2022]
Abstract
Intellectual disability (ID) is a frequent feature but is highly clinically and genetically heterogeneous. The establishment of the precise diagnosis in patients with ID is challenging due to this heterogeneity but crucial for genetic counseling and appropriate care for the patients. Among the etiologies of patients with ID, apparently balanced de novo rearrangements represent 0.6%. Several mechanisms explain the ID in patients with apparently balanced de novo rearrangement. Among them, disruption of a disease gene at the breakpoint, is frequently evoked. In this context, technologies recently developed are used to characterize precisely such chromosomal rearrangements. Here, we report the case of a boy with ID, facial features and autistic behavior who is carrying a de novo balanced reciprocal translocation t(3;7)(q11.2;q11.22)dn. Using microarray analysis, array painting (AP) technology combined with molecular study, we have identified the interruption of the autism susceptibility candidate 2 gene (AUTS2) and EPH receptor A6 gene (EPHA6). We consider that the disruption of AUTS2 explains the phenotype of the patient; the exact role of EPHA6 in human pathology is not well defined. Based on the observation of recurrent germinal and somatic translocations involving AUTS2 and the molecular environment content, we put forward the hypothesis that the likely chromosomal mechanism responsible for the translocation could be due either to replicative stress or to recombination-based mechanisms.
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Affiliation(s)
- Anouck Schneider
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | | | - Bee Ling Ng
- Cytometry Core Facility, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | | | - Vincent Gatinois
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Magali Tournaire
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Manon Girard
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Bruno Dumont
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Pauline Bouret
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - Julia Magnetto
- CRA, Département de Psychiatrie de l'Enfant et de l'Adolescent, Centre de Ressources Autisme, CHRU de Montpellier, France
| | - Amaria Baghdadli
- CRA, Département de Psychiatrie de l'Enfant et de l'Adolescent, Centre de Ressources Autisme, CHRU de Montpellier, France
| | - Franck Pellestor
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France
| | - David Geneviève
- Laboratoire de Génétique Chromosomique, Plateforme de puces à ADN, CHRU de Montpellier, France.,Département de Génétique Médicale, CHRU de Montpellier, France
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11
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Unpeaceful roles of mutant PAX proteins in cancer. Semin Cell Dev Biol 2015; 44:126-34. [DOI: 10.1016/j.semcdb.2015.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 09/10/2015] [Accepted: 09/16/2015] [Indexed: 01/07/2023]
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12
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Anderl S, König M, Attarbaschi A, Strehl S. PAX5-KIAA1549L: a novel fusion gene in a case of pediatric B-cell precursor acute lymphoblastic leukemia. Mol Cytogenet 2015; 8:48. [PMID: 26157485 PMCID: PMC4495688 DOI: 10.1186/s13039-015-0138-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/25/2015] [Indexed: 12/11/2022] Open
Abstract
Background In B-cell precursor acute lymphoblastic leukemia (BCP-ALL) PAX5, a transcription factor pivotal for B-cell commitment and maintenance, is frequently affected by genetic alterations. In 2-3 % of the cases PAX5 rearrangements result in the expression of oncogenic fusion genes. The encoded chimeric proteins consist of the N-terminal PAX5 DNA-binding paired domain, which is fused to the C-terminal domains of a remarkable heterogeneous group of partner proteins. Results Employing fluorescence in situ hybridization and molecular methods PAX5-KIAA1549L was identified as novel fusion gene in a case of pediatric BCP-ALL. Conclusion Our report underlines the high diversity of PAX5 fusion partners in BCP-ALL and we describe the second involvement of KIAA1549L in a genetic rearrangement in acute leukemia. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0138-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefanie Anderl
- CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung e.V., Vienna, Austria
| | - Margit König
- CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung e.V., Vienna, Austria
| | - Andishe Attarbaschi
- Department of Pediatrics, St. Anna Children's Hospital, Vienna, Austria ; Medical University of Vienna, Vienna, Austria
| | - Sabine Strehl
- CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung e.V., Vienna, Austria
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13
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The role of the Janus-faced transcription factor PAX5-JAK2 in acute lymphoblastic leukemia. Blood 2014; 125:1282-91. [PMID: 25515960 DOI: 10.1182/blood-2014-04-570960] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PAX5-JAK2 has recently been identified as a novel recurrent fusion gene in B-cell precursor acute lymphoblastic leukemia, but the function of the encoded chimeric protein has not yet been characterized in detail. Herein we show that the PAX5-JAK2 chimera, which consists of the DNA-binding paired domain of PAX5 and the active kinase domain of JAK2, is a nuclear protein that has the ability to bind to wild-type PAX5 target loci. Moreover, our data provide compelling evidence that PAX5-JAK2 functions as a nuclear catalytically active kinase that autophosphorylates and in turn phosphorylates and activates downstream signal transducers and activators of transcription (STATs) in an apparently noncanonical mode. The chimeric protein also enables cytokine-independent growth of Ba/F3 cells and therefore possesses transforming potential. Importantly, the kinase activity of PAX5-JAK2 can be efficiently blocked by JAK2 inhibitors, rendering it a potential target for therapeutic intervention. Together, our data show that PAX5-JAK2 simultaneously deregulates the PAX5 downstream transcriptional program and activates the Janus kinase-STAT signaling cascade and thus, by interfering with these two important pathways, may promote leukemogenesis.
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The role of Pax5 in leukemia: diagnosis and prognosis significance. Med Oncol 2014; 32:360. [PMID: 25428382 DOI: 10.1007/s12032-014-0360-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/12/2014] [Indexed: 12/12/2022]
Abstract
Pax5 transcription factor, also known as B-cell specific activator protein (BSAP), plays a dual role in the hematopoietic system. Pax5 expression is essential in B-cell precursors for normal differentiation and maturation of B-cells. On the other hand, it inhibits the differentiation and progress toward other lineages. The expression of this factor is involved in several aspects of B-cell differentiation, including commitment, immunoglobulin gene rearrangement, BCR signal transduction and B-cell survival, so that the deletion or inactivating mutations of Pax5 cause cell arrest in Pro-B-cell stage. In recent years, point mutations, deletions and various rearrangements in Pax5 gene have been reported in several types of human cancers. However, no clear relationship has been found between these aberrations and disease prognosis. Specific expression of Pax5 in B-cells can raise it as a marker for the diagnosis and differentiation of B-cell leukemias and lymphomas as well as account for remission or relapse. Extensive studies on Pax5 along with other genes and immunomarkers are necessary for decisive results in this regard.
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Denk D, Bradtke J, König M, Strehl S. PAX5 fusion genes in t(7;9)(q11.2;p13) leukemia: a case report and review of the literature. Mol Cytogenet 2014; 7:13. [PMID: 24507461 PMCID: PMC3937052 DOI: 10.1186/1755-8166-7-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/29/2014] [Indexed: 11/17/2022] Open
Abstract
Background B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is characterized by recurrent genetic alterations including chromosomal translocations. The transcription factor PAX5, which is pivotal for B-cell commitment and maintenance, is affected by rearrangements, which lead to the expression of in-frame fusion genes in about 2.5% of the cases. Results Using conventional cytogenetics, fluorescence in situ hybridization (FISH), and molecular methods, an additional case with a der(9)t(7;9)(q11.23;p13) resulting in the expression of a PAX5-ELN fusion gene was identified. Furthermore, a general review of leukemia harboring a t(7;9)(q11.2;p13) or der(9)t(7;9)(q11.2;p13), which occurs more often in children than in adults and shows a remarkably high male preponderance, is given. These cytogenetically highly similar translocations lead to the expression of one of three different in frame PAX5-fusions, namely with AUTS2 (7q11.22), ELN (7q11.23), or POM121 (7q11.23), which constitute the only currently known cluster of PAX5 partner genes. Conclusion Our report underlines the recurrent involvement of PAX5 in different fusion genes resulting either from t(7;9)(q11.2;p13) or der(9)t(7;9)(q11.2;p13), which cannot be distinguished cytogenetically and whose discrimination requires molecular analysis.
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Affiliation(s)
| | | | | | - Sabine Strehl
- CCRI, Children's Cancer Research Institute, St, Anna Kinderkrebsforschung e,V,, Zimmermannplatz 10, 1090 Vienna, Austria.
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Fortschegger K, Anderl S, Denk D, Strehl S. Functional heterogeneity of PAX5 chimeras reveals insight for leukemia development. Mol Cancer Res 2014; 12:595-606. [PMID: 24435167 DOI: 10.1158/1541-7786.mcr-13-0337] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED PAX5, a transcription factor pivotal for B-cell commitment and maintenance, is one of the most frequent targets of somatic mutations in B-cell precursor acute lymphoblastic leukemia. A number of PAX5 rearrangements result in the expression of in-frame fusion genes encoding chimeric proteins, which at the N-terminus consistently retain the PAX5 DNA-binding paired domain fused to the C-terminal domains of a markedly heterogeneous group of fusion partners. PAX5 fusion proteins are thought to function as aberrant transcription factors, which antagonize wild-type PAX5 activity. To gain mechanistic insight into the role of PAX5 fusion proteins in leukemogenesis, the biochemical and functional properties of uncharacterized fusions: PAX5-DACH1, PAX5-DACH2, PAX5-ETV6, PAX5-HIPK1, and PAX5-POM121 were ascertained. Independent of the subcellular distribution of the wild-type partner proteins, ectopic expression of all PAX5 fusion proteins showed a predominant nuclear localization, and by chromatin immunoprecipitation all of the chimeric proteins exhibited binding to endogenous PAX5 target sequences. Furthermore, consistent with the presence of potential oligomerization motifs provided by the partner proteins, the self-interaction capability of several fusion proteins was confirmed. Remarkably, a subset of the PAX5 fusion proteins conferred CD79A promoter activity; however, in contrast with wild-type PAX5, the fusion proteins were unable to induce Cd79a transcription in a murine plasmacytoma cell line. These data show that leukemia-associated PAX5 fusion proteins share some dominating characteristics such as nuclear localization and DNA binding but also show distinctive features. IMPLICATIONS This comparative study of multiple PAX5 fusion proteins demonstrates both common and unique properties, which likely dictate their function and impact on leukemia development.
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Affiliation(s)
- Klaus Fortschegger
- Children's Cancer Research Institute (CCRI), St. Anna Kinderkrebsforschung e.V. Zimmermannplatz 10, 1090 Vienna, Austria.
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Gu DL, Chen YH, Shih JH, Lin CH, Jou YS, Chen CF. Target genes discovery through copy number alteration analysis in human hepatocellular carcinoma. World J Gastroenterol 2013; 19:8873-8879. [PMID: 24379610 PMCID: PMC3870538 DOI: 10.3748/wjg.v19.i47.8873] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 12/06/2013] [Indexed: 02/06/2023] Open
Abstract
High-throughput short-read sequencing of exomes and whole cancer genomes in multiple human hepatocellular carcinoma (HCC) cohorts confirmed previously identified frequently mutated somatic genes, such as TP53, CTNNB1 and AXIN1, and identified several novel genes with moderate mutation frequencies, including ARID1A, ARID2, MLL, MLL2, MLL3, MLL4, IRF2, ATM, CDKN2A, FGF19, PIK3CA, RPS6KA3, JAK1, KEAP1, NFE2L2, C16orf62, LEPR, RAC2, and IL6ST. Functional classification of these mutated genes suggested that alterations in pathways participating in chromatin remodeling, Wnt/β-catenin signaling, JAK/STAT signaling, and oxidative stress play critical roles in HCC tumorigenesis. Nevertheless, because there are few druggable genes used in HCC therapy, the identification of new therapeutic targets through integrated genomic approaches remains an important task. Because a large amount of HCC genomic data genotyped by high density single nucleotide polymorphism arrays is deposited in the public domain, copy number alteration (CNA) analyses of these arrays is a cost-effective way to reveal target genes through profiling of recurrent and overlapping amplicons, homozygous deletions and potentially unbalanced chromosomal translocations accumulated during HCC progression. Moreover, integration of CNAs with other high-throughput genomic data, such as aberrantly coding transcriptomes and non-coding gene expression in human HCC tissues and rodent HCC models, provides lines of evidence that can be used to facilitate the identification of novel HCC target genes with the potential of improving the survival of HCC patients.
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Acute lymphoblastic leukemia (ALL). Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Oksenberg N, Ahituv N. The role of AUTS2 in neurodevelopment and human evolution. Trends Genet 2013; 29:600-8. [PMID: 24008202 DOI: 10.1016/j.tig.2013.08.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/05/2013] [Accepted: 08/06/2013] [Indexed: 12/31/2022]
Abstract
The autism susceptibility candidate 2 (AUTS2) gene is associated with multiple neurological diseases, including autism, and has been implicated as an important gene in human-specific evolution. Recent functional analysis of this gene has revealed a potential role in neuronal development. Here, we review the literature regarding AUTS2, including its discovery, expression, association with autism and other neurological and non-neurological traits, implication in human evolution, function, regulation, and genetic pathways. Through progress in clinical genomic analysis, the medical importance of this gene is becoming more apparent, as highlighted in this review, but more work needs to be done to discover the precise function and the genetic pathways associated with AUTS2.
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Affiliation(s)
- Nir Oksenberg
- Department of Bioengineering and Therapeutic Sciences, and Institute for Human Genetics, University of California, San Francisco (UCSF), 1550 4th Street, San Francisco, CA 94158, USA
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Zachariadis V, Schoumans J, Ofverholm I, Barbany G, Halvardsson E, Forestier E, Johansson B, Nordenskjöld M, Nordgren A. Detecting dic(9;20)(p13.2;p11.2)-positive B-cell precursor acute lymphoblastic leukemia in a clinical setting using fluorescence in situ hybridization. Leukemia 2013; 28:196-8. [PMID: 23787394 DOI: 10.1038/leu.2013.189] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- V Zachariadis
- 1] Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden [2] Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden [3] Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - J Schoumans
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - I Ofverholm
- 1] Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden [2] Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden [3] Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - G Barbany
- 1] Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden [2] Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden [3] Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - E Halvardsson
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - E Forestier
- Department of Clinical Sciences, Pediatrics, University of Umeå, Umeå, Sweden
| | - B Johansson
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, Lund, Sweden
| | - M Nordenskjöld
- 1] Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden [2] Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden [3] Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - A Nordgren
- 1] Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden [2] Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden [3] Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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Abstract
The t(12;21) chromosomal translocation, targeting the gene encoding the RUNX1 transcription factor, is observed in 25% of pediatric acute lymphoblastic leukemia (ALL) and is an initiating event in the disease. To elucidate the mechanism by which RUNX1 disruption initiates leukemogenesis, we investigated its normal role in murine B-cell development. This study revealed 2 critical functions of Runx1: (1) to promote survival and development of progenitors specified to the B-cell lineage, a function that can be substituted by ectopic Bcl2 expression, and (2) to enable the developmental transition through the pre-B stage triggered by the pre-B-cell antigen receptor (pre-BCR). Gene expression analysis and genomewide Runx1 occupancy studies support the hypothesis that Runx1 reinforces the transcription factor network governing early B-cell survival and development and specifically regulates genes encoding members of the Lyn kinase subfamily (key integrators of interleukin-7 and pre-BCR signaling) and the stage-specific transcription factors SpiB and Aiolos (critical downstream effectors of pre-BCR signaling). Interrogation of expression databases of 257 ALL samples demonstrated the specific down-regulation of the SPIB and IKZF3 genes (the latter encoding AIOLOS) in t(12;21) ALL, providing novel insight into the mechanism by which the translocation blocks B-cell development and promotes leukemia.
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22
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Giacomini CP, Sun S, Varma S, Shain AH, Giacomini MM, Balagtas J, Sweeney RT, Lai E, Del Vecchio CA, Forster AD, Clarke N, Montgomery KD, Zhu S, Wong AJ, van de Rijn M, West RB, Pollack JR. Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types. PLoS Genet 2013; 9:e1003464. [PMID: 23637631 PMCID: PMC3636093 DOI: 10.1371/journal.pgen.1003464] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/05/2013] [Indexed: 02/07/2023] Open
Abstract
Gene fusions, like BCR/ABL1 in chronic myelogenous leukemia, have long been recognized in hematologic and mesenchymal malignancies. The recent finding of gene fusions in prostate and lung cancers has motivated the search for pathogenic gene fusions in other malignancies. Here, we developed a “breakpoint analysis” pipeline to discover candidate gene fusions by tell-tale transcript level or genomic DNA copy number transitions occurring within genes. Mining data from 974 diverse cancer samples, we identified 198 candidate fusions involving annotated cancer genes. From these, we validated and further characterized novel gene fusions involving ROS1 tyrosine kinase in angiosarcoma (CEP85L/ROS1), SLC1A2 glutamate transporter in colon cancer (APIP/SLC1A2), RAF1 kinase in pancreatic cancer (ATG7/RAF1) and anaplastic astrocytoma (BCL6/RAF1), EWSR1 in melanoma (EWSR1/CREM), CDK6 kinase in T-cell acute lymphoblastic leukemia (FAM133B/CDK6), and CLTC in breast cancer (CLTC/VMP1). Notably, while these fusions involved known cancer genes, all occurred with novel fusion partners and in previously unreported cancer types. Moreover, several constituted druggable targets (including kinases), with therapeutic implications for their respective malignancies. Lastly, breakpoint analysis identified new cell line models for known rearrangements, including EGFRvIII and FIP1L1/PDGFRA. Taken together, we provide a robust approach for gene fusion discovery, and our results highlight a more widespread role of fusion genes in cancer pathogenesis. Gene fusions represent an important class of cancer genes, created by rearrangements of the genome that bring together two different genes. Because they are unique to cancer cells, gene fusions are ideal diagnostic markers and therapeutic targets. While gene fusions were once thought restricted mainly to blood cancers, recent discoveries suggest they are more widespread. Here, we have developed an approach for mining DNA microarray data to detect the tell-tale signatures of gene fusions, as “breakpoints” occurring within the encoding DNA or expressed transcripts. We apply this approach to a large collection of nearly 1,000 human cancer specimens. From this analysis, we discover and verify twelve new gene fusions occurring in diverse cancer types. We verify that some of these rearrangements recur in other samples of the same cancer type (supporting a causal role) and that the cancers show dependency on the fusion for cancer cell growth. Notably, some of these fusions (e.g. CEP85L/ROS1 in angiosarcoma) represent the first for that cancer type and thus provide important new biological insight. Some are also good drug targets (including rearrangements of ROS1, RAF1, and CDK6 kinases), with clear implications for therapy.
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Affiliation(s)
- Craig P. Giacomini
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Steven Sun
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - A. Hunter Shain
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Marilyn M. Giacomini
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Jay Balagtas
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert T. Sweeney
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Everett Lai
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Catherine A. Del Vecchio
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Andrew D. Forster
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nicole Clarke
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kelli D. Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shirley Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Albert J. Wong
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert B. West
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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Zachariadis V, Schoumans J, Barbany G, Heyman M, Forestier E, Johansson B, Nordenskjöld M, Nordgren A. Homozygous deletions of CDKN2A are present in all dic(9;20)(p13·2;q11·2)-positive B-cell precursor acute lymphoblastic leukaemias and may be important for leukaemic transformation. Br J Haematol 2012; 159:488-91. [PMID: 22994152 DOI: 10.1111/bjh.12051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Hao JJ, Shi ZZ, Zhao ZX, Zhang Y, Gong T, Li CX, Zhan T, Cai Y, Dong JT, Fu SB, Zhan QM, Wang MR. Characterization of genetic rearrangements in esophageal squamous carcinoma cell lines by a combination of M-FISH and array-CGH: further confirmation of some split genomic regions in primary tumors. BMC Cancer 2012; 12:367. [PMID: 22920630 PMCID: PMC3561653 DOI: 10.1186/1471-2407-12-367] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 08/17/2012] [Indexed: 01/29/2023] Open
Abstract
Background Chromosomal and genomic aberrations are common features of human cancers. However, chromosomal numerical and structural aberrations, breakpoints and disrupted genes have yet to be identified in esophageal squamous cell carcinoma (ESCC). Methods Using multiplex-fluorescence in situ hybridization (M-FISH) and oligo array-based comparative hybridization (array-CGH), we identified aberrations and breakpoints in six ESCC cell lines. Furthermore, we detected recurrent breakpoints in primary tumors by dual-color FISH. Results M-FISH and array-CGH results revealed complex numerical and structural aberrations. Frequent gains occurred at 3q26.33-qter, 5p14.1-p11, 7pter-p12.3, 8q24.13-q24.21, 9q31.1-qter, 11p13-p11, 11q11-q13.4, 17q23.3-qter, 18pter-p11, 19 and 20q13.32-qter. Losses were frequent at 18q21.1-qter. Breakpoints that clustered within 1 or 2 Mb were identified, including 9p21.3, 11q13.3-q13.4, 15q25.3 and 3q28. By dual-color FISH, we observed that several recurrent breakpoint regions in cell lines were also present in ESCC tumors. In particular, breakpoints clustered at 11q13.3-q13.4 were identified in 43.3% (58/134) of ESCC tumors. Both 11q13.3-q13.4 splitting and amplification were significantly correlated with lymph node metastasis (LNM) (P = 0.004 and 0.022) and advanced stages (P = 0.004 and 0.039). Multivariate logistic regression analysis revealed that only 11q13.3-q13.4 splitting was an independent predictor for LNM (P = 0.026). Conclusions The combination of M-FISH and array-CGH helps produce more accurate karyotypes. Our data provide significant, detailed information for appropriate uses of these ESCC cell lines for cytogenetic and molecular biological studies. The aberrations and breakpoints detected in both the cell lines and primary tumors will contribute to identify affected genes involved in the development and progression of ESCC.
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Affiliation(s)
- Jia-Jie Hao
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Science, 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
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Iacobucci I, Iraci N, Messina M, Lonetti A, Chiaretti S, Valli E, Ferrari A, Papayannidis C, Paoloni F, Vitale A, Storlazzi CT, Ottaviani E, Guadagnuolo V, Durante S, Vignetti M, Soverini S, Pane F, Foà R, Baccarani M, Müschen M, Perini G, Martinelli G. IKAROS deletions dictate a unique gene expression signature in patients with adult B-cell acute lymphoblastic leukemia. PLoS One 2012; 7:e40934. [PMID: 22848414 PMCID: PMC3405023 DOI: 10.1371/journal.pone.0040934] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 06/15/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Deletions of IKAROS (IKZF1) frequently occur in B-cell precursor acute lymphoblastic leukemia (B-ALL) but the mechanisms by which they influence pathogenesis are unclear. To address this issue, a cohort of 144 adult B-ALL patients (106 BCR-ABL1-positive and 38 B-ALL negative for known molecular rearrangements) was screened for IKZF1 deletions by single nucleotide polymorphism (SNP) arrays; a sub-cohort of these patients (44%) was then analyzed for gene expression profiling. PRINCIPAL FINDINGS Total or partial deletions of IKZF1 were more frequent in BCR-ABL1-positive than in BCR-ABL1-negative B-ALL cases (75% vs 58%, respectively, p = 0.04). Comparison of the gene expression signatures of patients carrying IKZF1 deletion vs those without showed a unique signature featured by down-regulation of B-cell lineage and DNA repair genes and up-regulation of genes involved in cell cycle, JAK-STAT signalling and stem cell self-renewal. Through chromatin immunoprecipitation and luciferase reporter assays we corroborated these findings both in vivo and in vitro, showing that Ikaros deleted isoforms lacked the ability to directly regulate a large group of the genes in the signature, such as IGLL1, BLK, EBF1, MSH2, BUB3, ETV6, YES1, CDKN1A (p21), CDKN2C (p18) and MCL1. CONCLUSIONS Here we identified and validated for the first time molecular pathways specifically controlled by IKZF1, shedding light into IKZF1 role in B-ALL pathogenesis.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Hematology and Oncological Sciences “L. and A. Seràgnoli”, S. Orsola Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Nunzio Iraci
- Department of Biology, University of Bologna, Bologna, Italy
| | - Monica Messina
- Division of Hematology, Department of Cellular Biotechnologies and Hematology, “Sapienza” University of Rome, Rome, Italy
| | - Annalisa Lonetti
- Cellular Signalling Laboratory, Department of Human Anatomy, University of Bologna, Bologna, Italy
| | - Sabina Chiaretti
- Division of Hematology, Department of Cellular Biotechnologies and Hematology, “Sapienza” University of Rome, Rome, Italy
| | - Emanuele Valli
- Department of Biology, University of Bologna, Bologna, Italy
| | - Anna Ferrari
- Department of Hematology and Oncological Sciences “L. and A. Seràgnoli”, S. Orsola Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Cristina Papayannidis
- Department of Hematology and Oncological Sciences “L. and A. Seràgnoli”, S. Orsola Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Francesca Paoloni
- Gruppo Italiano Malattie Ematologiche Maligne dell’Adulto (GIMEMA) Data Center, GIMEMA Foundation, Rome, Italy
| | - Antonella Vitale
- Division of Hematology, Department of Cellular Biotechnologies and Hematology, “Sapienza” University of Rome, Rome, Italy
| | | | - Emanuela Ottaviani
- Department of Hematology and Oncological Sciences “L. and A. Seràgnoli”, S. Orsola Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Viviana Guadagnuolo
- Department of Hematology and Oncological Sciences “L. and A. Seràgnoli”, S. Orsola Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Sandra Durante
- Department of Hematology and Oncological Sciences “L. and A. Seràgnoli”, S. Orsola Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Marco Vignetti
- Gruppo Italiano Malattie Ematologiche Maligne dell’Adulto (GIMEMA) Data Center, GIMEMA Foundation, Rome, Italy
| | - Simona Soverini
- Department of Hematology and Oncological Sciences “L. and A. Seràgnoli”, S. Orsola Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Fabrizio Pane
- CEINGE Biotecnologie Avanzate and Department of Biochemistry and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Robin Foà
- Division of Hematology, Department of Cellular Biotechnologies and Hematology, “Sapienza” University of Rome, Rome, Italy
| | - Michele Baccarani
- Department of Hematology and Oncological Sciences “L. and A. Seràgnoli”, S. Orsola Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Markus Müschen
- Leukemia Research Program, Childrens Hospital Los Angeles, University of Southern California, Los Angeles, California, United States of America
| | - Giovanni Perini
- Department of Biology, University of Bologna, Bologna, Italy
| | - Giovanni Martinelli
- Department of Hematology and Oncological Sciences “L. and A. Seràgnoli”, S. Orsola Malpighi Hospital, University of Bologna, Bologna, Italy
- * E-mail:
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Montero-Ruíz O, Alcántara-Ortigoza MA, Betancourt M, Juárez-Velázquez R, González-Márquez H, Pérez-Vera P. Expression of RUNX1 isoforms and its target gene BLK in childhood acute lymphoblastic leukemia. Leuk Res 2012; 36:1105-11. [PMID: 22748822 DOI: 10.1016/j.leukres.2012.05.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 05/16/2012] [Accepted: 05/22/2012] [Indexed: 12/11/2022]
Abstract
Bone marrow samples from children with acute lymphoblastic leukemia were analyzed for the expression of RUNX1a/b/c isoforms. Obtained patterns were associated with genetic abnormalities and the expression of the RUNX1 regulated gene BLK. RUNX1c was present in all patients, but the expected over-expression of RUNX1a was not observed. Over-expression of total RUNT domain isoforms was detected in patients with extra RUNX1 copies, and unexpectedly, in those with t(4;11). Only expression of the total RUNT domain-containing isoforms and BLK presented positive correlation. Results suggest a more complex role of RUNX1 in leukemogenesis than the proposed antagonism between the isoforms.
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Affiliation(s)
- Oreth Montero-Ruíz
- Laboratorio de Cultivo de Tejidos, Instituto Nacional de Pediatría, México, DF, Mexico
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Denk D, Nebral K, Bradtke J, Pass G, Möricke A, Attarbaschi A, Strehl S. PAX5-AUTS2: a recurrent fusion gene in childhood B-cell precursor acute lymphoblastic leukemia. Leuk Res 2012; 36:e178-81. [PMID: 22578776 PMCID: PMC3389344 DOI: 10.1016/j.leukres.2012.04.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 03/15/2012] [Accepted: 04/16/2012] [Indexed: 01/14/2023]
Abstract
PAX5 rearrangements resulting in the expression of fusion transcripts account for 2–3% of childhood B-cell precursor acute lymphoblastic leukemia. Most PAX5 fusions are rare and many of them have only been described in a couple of, or even only in single, cases. We have identified the third case with a PAX5-AUTS2 fusion, which results from unbalanced t(7;9)(q11.2;p13.2) rearrangements. Our findings substantiate that PAX5-AUTS2 is a recurrent fusion gene in pediatric B-cell precursor acute lymphoblastic leukemia, and we summarize the clinical characteristics of such patients.
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Affiliation(s)
- Dagmar Denk
- CCRI, Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
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Sato-Otsubo A, Sanada M, Ogawa S. Single-nucleotide polymorphism array karyotyping in clinical practice: where, when, and how? Semin Oncol 2012; 39:13-25. [PMID: 22289488 DOI: 10.1053/j.seminoncol.2011.11.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Single-nucleotide polymorphism array (SNP-A) karyotyping is a new technology that has enabled genome-wide detection of genetic lesions in human cancers, including hematopoietic neoplasms. Taking advantage of very large numbers of allele-specific probes synthesized on microarrays at high density, copy number alterations as well as allelic imbalances can be sensitively detected in a genome-wide manner at unprecedented resolutions. Most importantly, SNP-A karyotyping represents the only platform currently available for genome-scale detection of copy neutral loss of heterozygosity (CN-LOH) or uniparental disomy (UPD), which is widely observed in cancer genomes. Although not applicable to detection of balanced translocations, which are commonly found in hematopoietic malignancies, SNP-A karyotyping technology complements and even outperforms conventional metaphase karyotyping, potentially allowing for more accurate genetic diagnosis of hematopoietic neoplasms in clinical practice. Here, we review the current status of SNP-A karyotyping and its application to hematopoietic neoplasms.
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Affiliation(s)
- Aiko Sato-Otsubo
- Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Sequential array comparative genomic hybridization analysis identifies copy number changes during blastic transformation of chronic myeloid leukemia. Leuk Res 2012; 36:418-21. [PMID: 22309891 DOI: 10.1016/j.leukres.2011.12.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Revised: 12/20/2011] [Accepted: 12/24/2011] [Indexed: 02/07/2023]
Abstract
The present study was performed to provide direct evidence on copy number changes during progression from chronic phase (CP) to blastic phase (BP) in chronic myeloid leukemia (CML) through a longitudinal follow-up study. Matched CP and BP samples in three patients were analyzed using high-resolution array comparative genomic hybridization (aCGH) chips. During blastic transformation, loss of large genomic segments including 6q14.1-q22.31, chromosome 7 and 9p13.2-p21.3 were noted. Furthermore, small-sized copy number changes involving cancer-associated genes were observed. In addition, we identified a novel fusion gene consisted of PAX5 and MLLT3 (AF9). It is likely that blastic transformation of CML is a multi-step process associated accumulation of several genomic events which may largely overlap with those found in acute leukemias.
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Put N, Deeren D, Michaux L, Vandenberghe P. FOXP1 and PAX5 are rare but recurrent translocations partners in acute lymphoblastic leukemia. Cancer Genet 2011; 204:462-4. [PMID: 21962897 DOI: 10.1016/j.cancergen.2011.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 07/11/2011] [Accepted: 07/14/2011] [Indexed: 11/29/2022]
Abstract
Here, we report the case of a 57-year-old man, who was diagnosed with B-cell acute lymphoblastic leukemia (B-ALL). His diagnostic workup identified a translocation t(3;9)(p13;p13). This is the fifth case reported to date that involved the forkhead box P1 gene (FOXP1) and paired box gene 5 (PAX5). The PAX5-FOXP1 translocation is a nonrandom aberration, which is recurrent in both childhood and in adult B-ALL, and may contribute to leukemogenesis by blocking differentiation of hematopoietic cells into mature B-cells.
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Affiliation(s)
- Natalie Put
- Department of Human Genetics, Universitaire Ziekenhuizen Leuven, Katholieke Universiteit Leuven, Leuven, Belgium
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Mackinnon RN, Campbell LJ. The role of dicentric chromosome formation and secondary centromere deletion in the evolution of myeloid malignancy. GENETICS RESEARCH INTERNATIONAL 2011; 2011:643628. [PMID: 22567363 PMCID: PMC3335544 DOI: 10.4061/2011/643628] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 07/20/2011] [Indexed: 01/16/2023]
Abstract
Dicentric chromosomes have been identified as instigators of the genome instability associated with cancer, but this instability is often resolved by one of a number of different secondary events. These include centromere inactivation, inversion, and intercentromeric deletion. Deletion or excision of one of the centromeres may be a significant occurrence in myeloid malignancy and other malignancies but has not previously been widely recognized, and our reports are the first describing centromere deletion in cancer cells. We review what is known about dicentric chromosomes and the mechanisms by which they can undergo stabilization in both constitutional and cancer genomes. The failure to identify centromere deletion in cancer cells until recently can be partly explained by the standard approaches to routine diagnostic cancer genome analysis, which do not identify centromeres in the context of chromosome organization. This hitherto hidden group of primary dicentric, secondary monocentric chromosomes, together with other unrecognized dicentric chromosomes, points to a greater role for dicentric chromosomes in cancer initiation and progression than is generally acknowledged. We present a model that predicts and explains a significant role for dicentric chromosomes in the formation of unbalanced translocations in malignancy.
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Affiliation(s)
- Ruth N Mackinnon
- Victorian Cancer Cytogenetics Service, St Vincent's Hospital (Melbourne) Ltd., P.O. Box 2900, Fitzroy, VIC 3065, Australia
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Chromosomal aberrations in solid tumors. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 95:55-94. [PMID: 21075329 DOI: 10.1016/b978-0-12-385071-3.00004-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Ever since the identification of the exact number of human chromosomes in 1956, several cancer-specific chromosomal abnormalities have been identified in different tumors. Among the various genetic changes, such as alterations in oncogenes, tumor suppressor genes, and microRNA genes, recurrent chromosome translocations have been identified as an important class of mutations in hematological malignancies, soft tissue sarcomas, and more recently in prostate cancer and lung cancer. Recurrent gene fusions are used for cancer classification and as diagnostic markers, and some have been successfully targeted for drug development. Recent advances in high-throughput sequencing technology and the ambitious undertaking of "The Cancer Genome Atlas" (TCGA) project will help drive the identification of the underlying genetic aberrations in most of the solid cancers. This chapter presents an overview on the current status of the knowledge on chromosome aberrations in solid cancers, cytogenetic and noncytogenetic methods for the characterization of changes at the DNA and RNA levels, technological advancements in high-throughput characterization of the cancer genome and transcriptome, and the current understanding of the molecular mechanism involved in the formation of gene fusions in solid cancer.
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Tao J, Deng NT, Ramnarayanan K, Huang B, Oh HK, Leong SH, Lim SS, Tan IB, Ooi CH, Wu J, Lee M, Zhang S, Rha SY, Chung HC, Smoot DT, Ashktorab H, Kon OL, Cacheux V, Yap C, Palanisamy N, Tan P. CD44-SLC1A2 gene fusions in gastric cancer. Sci Transl Med 2011; 3:77ra30. [PMID: 21471434 DOI: 10.1126/scitranslmed.3001423] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fusion genes are chimeric genes formed in cancers through genomic aberrations such as translocations, amplifications, and rearrangements. To identify fusion genes in gastric cancer, we analyzed regions of chromosomal imbalance in a cohort of 106 primary gastric cancers and 27 cell lines derived from gastric cancers. Multiple samples exhibited genomic breakpoints in the 5' region of SLC1A2/EAAT2, a gene encoding a glutamate transporter. Analysis of a breakpoint-positive SNU16 cell line revealed expression of a CD44-SLC1A2 fusion transcript caused by a paracentric chromosomal inversion, which was predicted to produce a truncated but functional SLC1A2 protein. In primary tumors, CD44-SLC1A2 gene fusions were detected in 1 to 2% of gastric cancers, but not in adjacent matched normal gastric tissues. When we specifically silenced CD44-SLC1A2, cellular proliferation, invasion, and anchorage-independent growth were significantly reduced. Conversely, CD44-SLC1A2 overexpression in gastric cells stimulated these pro-oncogenic traits. CD44-SLC1A2 silencing caused significant reductions in intracellular glutamate concentrations and sensitized SNU16 cells to cisplatin, a commonly used chemotherapeutic agent in gastric cancer. We conclude that fusion of the SLC1A2 gene coding region to CD44 regulatory elements likely causes SLC1A2 transcriptional dysregulation, because tumors expressing high SLC1A2 levels also tended to be CD44-SLC1A2-positive. CD44-SLC1A2 may represent a class of gene fusions in cancers that establish a pro-oncogenic metabolic milieu favoring tumor growth and survival.
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Affiliation(s)
- Jiong Tao
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 119074, Singapore
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Abstract
PAX5 encodes a master regulator of B-cell development. It fuses to other genes associated with acute lymphoblastoid leukemia (ALL). These fusion products are potent dominant-negative (DN) inhibitors of wild-type PAX5 resulting in a blockade of B-cell differentiation. Here, we show that multimerization of PAX5 DNA-binding domain (DBD) is necessary and sufficient to cause extremely stable chromatin binding and DN-activity. ALL-associated PAX5-C20S results from fusion of the N-terminal region of PAX5 including its paired DBD, to the C-terminus of C20orf112, a protein of unknown function. We report that PAX5-C20S is a tetramer which interacts extraordinarily stably with chromatin as determined by fluorescence recovery after photobleaching (FRAP) in living cells. Tetramerization, stable chromatin-binding and DN-activity all require a putative five-turn amphipathic α-helix at the C-terminus of C20orf112, and does not require potential co-repressor binding peptides elsewhere in the sequence. In vitro, the monomeric PAX5 DBD and PAX5-C20S binds a PAX5-binding site with equal affinity when it is at the center of an oligonucleotide too short to bind to more than one PAX5 DBD. But PAX5-C20S binds the same sequence with tenfold higher affinity than the monomeric PAX5 DBD when it is in a long DNA molecule. We suggest that the increased affinity results from interactions of one or more of the additional DBDs with neighboring non-specific sites in a long DNA molecule, and that this can account for the increased stability of PAX5-C20S chromatin binding compared to wt PAX5, resulting in DN-activity by competition for binding to PAX5-target sites. Consistent with this model, the ALL-associated PAX5 fused to ETV6 or the multimerization domain of ETV6 SAM results in stable chromatin binding and DN-activity. In addition, PAX5 DBD fused to artificial dimerization, trimerization, and tetramerization domains result in parallel increases in the stability of chromatin binding and DN-activity. Our studies suggest that oncogenic fusion proteins that retain the DBD of the transcription factor and the multimerization sequence of the partner protein can act in a DN fashion by multimerizing and binding avidly to gene targets preventing the normal transcription factor from binding and inducing expression of its target genes. Inhibition of this multimeriztion may provide a novel therapeutic approach for cancers with this or similar fusion proteins.
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Przybytkowski E, Ferrario C, Basik M. The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome. BMC Med Genomics 2011; 4:16. [PMID: 21272361 PMCID: PMC3041991 DOI: 10.1186/1755-8794-4-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 01/27/2011] [Indexed: 01/28/2023] Open
Abstract
Background Molecular alterations critical to development of cancer include mutations, copy number alterations (amplifications and deletions) as well as genomic rearrangements resulting in gene fusions. Massively parallel next generation sequencing, which enables the discovery of such changes, uses considerable quantities of genomic DNA (> 5 ug), a serious limitation in ever smaller clinical samples. However, a commonly available microarray platforms such as array comparative genomic hybridization (array CGH) allows the characterization of gene copy number at a single gene resolution using much smaller amounts of genomic DNA. In this study we evaluate the sensitivity of ultra-dense array CGH platforms developed by Agilent, especially that of the 1 million probe array (1 M array), and their application when whole genome amplification is required because of limited sample quantities. Methods We performed array CGH on whole genome amplified and not amplified genomic DNA from MCF-7 breast cancer cells, using 244 K and 1 M Agilent arrays. The ADM-2 algorithm was used to identify micro-copy number alterations that measured less than 1 Mb in genomic length. Results DNA from MCF-7 breast cancer cells was analyzed for micro-copy number alterations, defined as measuring less than 1 Mb in genomic length. The 4-fold extra resolution of the 1 M array platform relative to the less dense 244 K array platform, led to the improved detection of copy number variations (CNVs) and micro-CNAs. The identification of intra-genic breakpoints in areas of DNA copy number gain signaled the possible presence of gene fusion events. However, the ultra-dense platforms, especially the densest 1 M array, detect artifacts inherent to whole genome amplification and should be used only with non-amplified DNA samples. Conclusions This is a first report using 1 M array CGH for the discovery of cancer genes and biomarkers. We show the remarkable capacity of this technology to discover CNVs, micro-copy number alterations and even gene fusions. However, these platforms require excellent genomic DNA quality and do not tolerate relatively small imperfections related to the whole genome amplification.
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Affiliation(s)
- Ewa Przybytkowski
- Department of Oncology, Lady Davis Institute, Sir Mortimer B, Davis Jewish General Hospital, McGill University, Montreal, Quebec, Canada
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37
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Collins-Underwood JR, Mullighan CG. Genetic Alterations Targeting Lymphoid Development in Acute Lymphoblastic Leukemia. Curr Top Dev Biol 2011; 94:171-96. [DOI: 10.1016/b978-0-12-380916-2.00006-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Qiu JJ, Chu H, Lu X, Jiang X, Dong S. The reduced and altered activities of PAX5 are linked to the protein-protein interaction motif (coiled-coil domain) of the PAX5-PML fusion protein in t(9;15)-associated acute lymphocytic leukemia. Oncogene 2010; 30:967-77. [PMID: 20972455 DOI: 10.1038/onc.2010.473] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The paired box domain of PAX5 was reported to fuse with the sequence of promyelocytic leukemia (PML) to produce PAX5-PML chimeric protein in two patients with B-cell acute lymphoblastic leukemia. In the present studies, we found, by gel shift assays, that PAX5-PML bound to a panel of PAX5-consensus sequence acts as a homodimer with reduction of its DNA-binding affinities in comparison with wild-type PAX5. In transient transfection assays using 293T and HeLa cells, and retrovirus transduction of murine hematopoietic stem/progenitor cells together with quantitative real-time polymerase chain reaction analysis, PAX5-PML inhibited wild-type PAX5 target gene transcriptional activity. Studies comparing PAX5-PML with PAX5-PML(ΔCC) demonstrated that the coiled-coil (CC) protein interaction domain located within the PML moiety was required for PAX5-PML homodimer complex formation and partial transcriptional repression of genes controlled by PAX5. Fluorescent microscopic examination of transiently expressed YFP-tagged proteins in HeLa and 293T cells demonstrated that YFP-PAX5-PML and YFP-PAX5-PML(ΔCC) exhibited a diffuse granular pattern within the nucleus, similar to PAX5 but not PML. By fluorescent recovery after photobleach (FRAP), we have shown that PAX5-PML fusion protein has reduced intranuclear mobility compared with wild-type PAX5. Furthermore, the dimerization domain (CC) of PML was responsible for the reduced intranuclear mobility of PAX5-PML. These results indicate that the CC domain of PAX5-PML is important for each of the known activities of PAX5-PML fusion proteins.
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Affiliation(s)
- J J Qiu
- Department of Medicine and Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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Abstract
Genomic aberrations are of predominant importance to the biology and clinical outcome of patients with acute myelogenous leukemia (AML), and conventional karyotype-based risk classifications are routinely used in clinical decision making in AML. One of the known limitations of cytogenetic analysis is the inability to detect genomic abnormalities less than 5 Mb in size, and it is currently unclear whether overcoming this limitation with high-resolution genomic single-nucleotide polymorphism (SNP) array analysis would be clinically relevant. Furthermore, given the heterogeneity of molecular mechanisms/aberrations that underlie the conventional karyotype-based risk classifications, it is likely that further refinements in genomic risk prognostication can be achieved. In this study, we analyzed flow cytometer-sorted, AML blast-derived, and paired, buccal DNA from 114 previously untreated prospectively enrolled AML patients for acquired genomic copy number changes and loss of heterozygosity using Affymetrix SNP 6.0 arrays, and we correlated genomic lesion load and specific chromosomal abnormalities with patient survival. Using multivariate analyses, we found that having ≥ 2 genomic lesions detected through SNP 6.0 array profiling approximately doubles the risk of death when controlling for age- and karyotype-based risk. Finally, we identified an independent negative prognostic impact of p53 mutations, or p53 mutations and 17p-loss of heterozygosity combined on survival in AML.
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Coyaud E, Struski S, Dastugue N, Brousset P, Broccardo C, Bradtke J. PAX5-AUTS2 fusion resulting from t(7;9)(q11.2;p13.2) can now be classified as recurrent in B cell acute lymphoblastic leukemia. Leuk Res 2010; 34:e323-5. [PMID: 20723977 DOI: 10.1016/j.leukres.2010.07.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2010] [Revised: 07/21/2010] [Accepted: 07/26/2010] [Indexed: 10/19/2022]
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Izraeli S. Application of genomics for risk stratification of childhood acute lymphoblastic leukaemia: from bench to bedside? Br J Haematol 2010; 151:119-31. [DOI: 10.1111/j.1365-2141.2010.08312.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Iacobucci I, Lonetti A, Paoloni F, Papayannidis C, Ferrari A, Storlazzi CT, Vignetti M, Cilloni D, Messa F, Guadagnuolo V, Paolini S, Elia L, Messina M, Vitale A, Meloni G, Soverini S, Pane F, Baccarani M, Foà R, Martinelli G. The PAX5 gene is frequently rearranged in BCR-ABL1-positive acute lymphoblastic leukemia but is not associated with outcome. A report on behalf of the GIMEMA Acute Leukemia Working Party. Haematologica 2010; 95:1683-90. [PMID: 20534699 DOI: 10.3324/haematol.2009.020792] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Recently, in genome-wide analyses of DNA copy number abnormalities using single nucleotide polymorphism microarrays, genetic alterations targeting PAX5 were identified in over 30% of pediatric patients with acute lymphoblastic leukemia. So far the occurrence of PAX5 alterations and their clinical correlation have not been investigated in adults with BCR-ABL1-positive acute lymphoblastic leukemia. DESIGN AND METHODS The aim of this study was to characterize the rearrangements on 9p involving PAX5 and their clinical significance in adults with BCR-ABL1-positive acute lymphoblastic leukemia. Eighty-nine adults with de novo BCR-ABL1-positive acute lymphoblastic leukemia were enrolled into institutional (n=15) or GIMEMA (Gruppo Italiano Malattie EMatologiche dell'Adulto) (n=74) clinical trials and, after obtaining informed consent, their genome was analyzed by single nucleotide polymorphism arrays (Affymetrix 250K NspI and SNP 6.0), genomic polymerase chain reaction analysis and re-sequencing. RESULTS PAX5 genomic deletions were identified in 29 patients (33%) with the extent of deletions ranging from a complete loss of chromosome 9 to the loss of a subset of exons. In contrast to BCR-ABL1-negative acute lymphoblastic leukemia, no point mutations were found, suggesting that deletions are the main mechanism of inactivation of PAX5 in BCR-ABL1-positive acute lymphoblastic leukemia. The deletions were predicted to result in PAX5 haploinsufficiency or expression of PAX5 isoforms with impaired DNA-binding. Deletions of PAX5 were not significantly correlated with overall survival, disease-free survival or cumulative incidence of relapse, suggesting that PAX5 deletions are not associated with outcome. CONCLUSIONS PAX5 deletions are frequent in adult BCR-ABL1-positive acute lymphoblastic leukemia and are not associated with a poor outcome.
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Affiliation(s)
- Ilaria Iacobucci
- Molecular Biology Unit, Department of Hematology/Oncology Seràgnoli, University of Bologna, Via Massarenti 9, Bologna, Italy
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Guastadisegni MC, Lonoce A, Impera L, Di Terlizzi F, Fugazza G, Aliano S, Grasso R, Cluzeau T, Raynaud S, Rocchi M, Storlazzi CT. CBFA2T2 and C20orf112: two novel fusion partners of RUNX1 in acute myeloid leukemia. Leukemia 2010; 24:1516-9. [DOI: 10.1038/leu.2010.106] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Parkin B, Ouillette P, Wang Y, Liu Y, Wright W, Roulston D, Purkayastha A, Dressel A, Karp J, Bockenstedt P, Al-Zoubi A, Talpaz M, Kujawski L, Liu Y, Shedden K, Shakhan S, Li C, Erba H, Malek SN. NF1 inactivation in adult acute myelogenous leukemia. Clin Cancer Res 2010; 16:4135-47. [PMID: 20505189 DOI: 10.1158/1078-0432.ccr-09-2639] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE This study was conducted to identify novel genes with importance to the biology of adult acute myelogenous leukemia (AML). EXPERIMENTAL DESIGN We analyzed DNA from highly purified AML blasts and paired buccal cells from 95 patients for recurrent genomic microdeletions using ultra-high density Affymetrix single nucleotide polymorphism 6.0 array-based genomic profiling. RESULTS Through fine mapping of microdeletions on 17q, we derived a minimal deleted region of approximately 0.9-Mb length that harbors 11 known genes; this region includes Neurofibromin 1 (NF1). Sequence analysis of all NF1 coding exons in the 11 AML cases with NF1 copy number changes identified acquired truncating frameshift mutations in two patients. These NF1 mutations were already present in the hematopoetic stem cell compartment. Subsequent expression analysis of NF1 mRNA in the entire AML cohort using fluorescence-activated cell sorting sorted blasts as a source of RNA identified six patients (one with a NF1 mutation) with absent NF1 expression. The NF1 null states were associated with increased Ras-bound GTP, and short hairpin RNA-mediated NF1 suppression in primary AML blasts with wild-type NF1 facilitated colony formation in methylcellulose. Primary AML blasts without functional NF1, unlike blasts with functional NF1, displayed sensitivity to rapamycin-induced apoptosis, thus identifying a dependence on mammalian target of rapamycin (mTOR) signaling for survival. Finally, colony formation in methylcellulose ex vivo of NF1 null CD34+/CD38- cells sorted from AML bone marrow samples was inhibited by low-dose rapamycin. CONCLUSIONS NF1 null states are present in 7 of 95 (7%) of adult AML and delineate a disease subset that could be preferentially targeted by Ras or mammalian target of rapamycin-directed therapeutics.
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Affiliation(s)
- Brian Parkin
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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Okamoto R, Ogawa S, Nowak D, Kawamata N, Akagi T, Kato M, Sanada M, Weiss T, Haferlach C, Dugas M, Ruckert C, Haferlach T, Koeffler HP. Genomic profiling of adult acute lymphoblastic leukemia by single nucleotide polymorphism oligonucleotide microarray and comparison to pediatric acute lymphoblastic leukemia. Haematologica 2010; 95:1481-8. [PMID: 20435627 DOI: 10.3324/haematol.2009.011114] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Differences in survival have been reported between pediatric and adult acute lymphoblastic leukemia. The inferior prognosis in adult acute lymphoblastic leukemia is not fully understood but could be attributed, in part, to differences in genomic alterations found in adult as compared to in pediatric acute lymphoblastic leukemia. DESIGN AND METHODS We compared two different sets of high-density single nucleotide polymorphism array genotyping data from 75 new diagnostic adult and 399 previously published diagnostic pediatric acute lymphoblastic leukemia samples. The patients' samples were randomly acquired from among Caucasian and Asian populations and hybridized to either Affymetrix 50K or 250K single nucleotide polymorphism arrays. The array data were investigated with Copy Number Analysis for GeneChips (CNAG) software for allele-specific copy number analysis. RESULTS The high density single nucleotide polymorphism array analysis of 75 samples of adult acute lymphoblastic leukemia led to the identification of numerous cryptic and submicroscopic genomic lesions with a mean of 7.6 genomic alterations per sample. The patterns and frequencies of lesions detected in the adult samples largely reproduced known genomic hallmarks detected in previous single nucleotide polymorphism-array studies of pediatric acute lymphoblastic leukemia, such as common deletions of 3p14.2 (FHIT), 5q33.3 (EBF), 6q, 9p21.3 (CDKN2A/B), 9p13.2 (PAX5), 13q14.2 (RB1) and 17q11.2 (NF1). Some differences between adult and pediatric acute lymphoblastic leukemia were identified when the pediatric data set was partitioned into hyperdiploid and non-hyperdiploid cases and then compared to the nearly exclusively non-hyperdiploid adult samples. In this analysis, adult samples had a higher rate of deletions of chromosome 17p (TP53) and duplication of 17q. CONCLUSIONS Our analysis of adult acute lymphoblastic leukemia cases led to the identification of new potential target lesions relevant for the pathogenesis of acute lymphoblastic leukemia. However, no unequivocal pattern of submicroscopic genomic alterations was found to separate adult acute lymphoblastic leukemia from pediatric acute lymphoblastic leukemia. Therefore, apart from different therapy regimen, differences of prognosis between adult and pediatric acute lymphoblastic leukemia are probably based on genetic subgroups according to cytogenetically detectable lesions but not focal genomic copy number microlesions.
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Affiliation(s)
- Ryoko Okamoto
- Division of Hematology and Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, 8700, Beverly Blvd, Los Angeles, CA90048, USA.
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Wide diversity of PAX5 alterations in B-ALL: a Groupe Francophone de Cytogénétique Hématologique study. Blood 2010; 115:3089-97. [DOI: 10.1182/blood-2009-07-234229] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Abstract
PAX5 is the main target of somatic mutations in acute B lymphoblastic leukemia (B-ALL). We analyzed 153 adult and child B-ALL harboring karyotypic abnormalities at chromosome 9p, to determine the frequency and the nature of PAX5 alterations. We found PAX5 internal rearrangements in 21% of the cases. To isolate fusion partners, we used classic and innovative techniques (rolling circle amplification-rapid amplification of cDNA ends) and single nucleotide polymorphism-comparative genomic hybridization arrays. Recurrent and novel fusion partners were identified, including NCoR1, DACH2, GOLGA6, and TAOK1 genes showing the high variability of the partners. We noted that half the fusion genes can give rise to truncated PAX5 proteins. Furthermore, malignant cells carrying PAX5 fusion genes displayed a simple karyotype. These data strongly suggest that PAX5 fusion genes are early players in leukemogenesis. In addition, PAX5 deletion was observed in 60% of B-ALL with 9p alterations. Contrary to cases with PAX5 fusions, deletions were associated with complex karyotypes and common recurrent translocations. This supports the hypothesis of the secondary nature of the deletion. Our data shed more light on the high variability of PAX5 alterations in B-ALL. Therefore, it is probable that gene fusions occur early, whereas deletions should be regarded as a late/secondary event.
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Pichler H, Möricke A, Mann G, Teigler-Schlegel A, Niggli F, Nebral K, König M, Inthal A, Krehan D, Dworzak MN, Janousek D, Harbott J, Schrappe M, Gadner H, Strehl S, Haas OA, Panzer-Grümayer R, Attarbaschi A. Prognostic relevance of dic(9;20)(p11;q13) in childhood B-cell precursor acute lymphoblastic leukaemia treated with Berlin-Frankfurt-Münster (BFM) protocols containing an intensive induction and post-induction consolidation therapy. Br J Haematol 2010; 149:93-100. [DOI: 10.1111/j.1365-2141.2009.08059.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Familiades J, Bousquet M, Lafage-Pochitaloff M, Béné MC, Beldjord K, De Vos J, Dastugue N, Coyaud E, Struski S, Quelen C, Prade-Houdellier N, Dobbelstein S, Cayuela JM, Soulier J, Grardel N, Preudhomme C, Cavé H, Blanchet O, Lhéritier V, Delannoy A, Chalandon Y, Ifrah N, Pigneux A, Brousset P, Macintyre EA, Huguet F, Dombret H, Broccardo C, Delabesse E. PAX5 mutations occur frequently in adult B-cell progenitor acute lymphoblastic leukemia and PAX5 haploinsufficiency is associated with BCR-ABL1 and TCF3-PBX1 fusion genes: a GRAALL study. Leukemia 2009; 23:1989-98. [PMID: 19587702 DOI: 10.1038/leu.2009.135] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 03/17/2009] [Accepted: 05/05/2009] [Indexed: 11/12/2022]
Abstract
Adult and child B-cell progenitor acute lymphoblastic leukemia (BCP-ALL) differ in terms of incidence and prognosis. These disparities are mainly due to the molecular abnormalities associated with these two clinical entities. A genome-wide analysis using oligo SNP arrays recently demonstrated that PAX5 (paired-box domain 5) is the main target of somatic mutations in childhood BCP-ALL being altered in 38.9% of the cases. We report here the most extensive analysis of alterations of PAX5 coding sequence in 117 adult BCP-ALL patients in the unique clinical protocol GRAALL-2003/GRAAPH-2003. Our study demonstrates that PAX5 is mutated in 34% of adult BCP-ALL, mutations being partial or complete deletion, partial or complete amplification, point mutation or fusion gene. PAX5 alterations are heterogeneous consisting in complete loss in 17%, focal deletions in 10%, point mutations in 7% and translocations in 1% of the cases. PAX5 complete loss and PAX5 point mutations differ. PAX5 complete loss seems to be a secondary event and is significantly associated with BCR-ABL1 or TCF3-PBX1 fusion genes and a lower white blood cell count.
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Trageser D, Iacobucci I, Nahar R, Duy C, von Levetzow G, Klemm L, Park E, Schuh W, Gruber T, Herzog S, Kim YM, Hofmann WK, Li A, Storlazzi CT, Jäck HM, Groffen J, Martinelli G, Heisterkamp N, Jumaa H, Müschen M. Pre-B cell receptor-mediated cell cycle arrest in Philadelphia chromosome-positive acute lymphoblastic leukemia requires IKAROS function. ACTA ACUST UNITED AC 2009; 206:1739-53. [PMID: 19620627 PMCID: PMC2722172 DOI: 10.1084/jem.20090004] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
B cell lineage acute lymphoblastic leukemia (ALL) arises in virtually all cases from B cell precursors that are arrested at pre–B cell receptor–dependent stages. The Philadelphia chromosome–positive (Ph+) subtype of ALL accounts for 25–30% of cases of adult ALL, has the most unfavorable clinical outcome among all ALL subtypes and is defined by the oncogenic BCR-ABL1 kinase and deletions of the IKAROS gene in >80% of cases. Here, we demonstrate that the pre–B cell receptor functions as a tumor suppressor upstream of IKAROS through induction of cell cycle arrest in Ph+ ALL cells. Pre–B cell receptor–mediated cell cycle arrest in Ph+ ALL cells critically depends on IKAROS function, and is reversed by coexpression of the dominant-negative IKAROS splice variant IK6. IKAROS also promotes tumor suppression through cooperation with downstream molecules of the pre–B cell receptor signaling pathway, even if expression of the pre–B cell receptor itself is compromised. In this case, IKAROS redirects oncogenic BCR-ABL1 tyrosine kinase signaling from SRC kinase-activation to SLP65, which functions as a critical tumor suppressor downstream of the pre–B cell receptor. These findings provide a rationale for the surprisingly high frequency of IKAROS deletions in Ph+ ALL and identify IKAROS-mediated cell cycle exit as the endpoint of an emerging pathway of pre–B cell receptor–mediated tumor suppression.
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Affiliation(s)
- Daniel Trageser
- Leukemia and Lymphoma Program, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90027, USA
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