1
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Miyajima T, Onozawa M, Yoshida S, Miyashita N, Kimura H, Takahashi S, Yokoyama S, Matsukawa T, Goto H, Sugita J, Fujisawa S, Hidaka D, Ogasawara R, Mori A, Matsuoka S, Shigematsu A, Wakasa K, Kasahara I, Saga T, Hashiguchi J, Takeda Y, Ibata M, Yutaka T, Fujimoto K, Kondo T, Teshima T. Clinical implications of NUP98::NSD1 fusion at diagnosis in adult FLT3-ITD positive AML. Eur J Haematol 2023; 111:620-627. [PMID: 37465857 DOI: 10.1111/ejh.14055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023]
Abstract
OBJECTIVES The cryptic fusion oncogene NUP98::NSD1 is known to be associated with FLT3-ITD mutation in acute myeloid leukemia (AML), and an independent poor prognostic factor in pediatric AML. However, there are little data regarding the clinical significance of NUP98::NSD1 in adult cohort. METHODS We conducted a multicenter retrospective study to investigate the prevalence, clinical characteristics, and prognostic impact of NUP98::NSD1 in adult FLT3-ITD-positive AML patients. RESULTS In a total of 97 FLT3-ITD-positive AML patients, six cases (6.2%) were found to harbor the NUP98::NSD1 fusion transcript. NUP98::NSD1 positive cases had significantly higher platelet counts and a higher frequency of FAB-M4 morphology than NUP98::NSD1 negative cases. NUP98::NSD1 was found to be mutually exclusive with NPM1 mutation, and was accompanied by the WT1 mutation in three of the six cases. The presence of NUP98::NSD1 fusion at the time of diagnosis predicted poor response to cytarabine-anthracycline-based intensive induction chemotherapy (induction failure rate: 83% vs. 36%, p = .038). Five of the six cases with NUP98::NSD1 underwent allogeneic hematopoietic stem cell transplantation (HSCT). Two of the five cases have successfully maintained remission, with one of them being rescued through a second HSCT. CONCLUSIONS Detecting NUP98::NSD1 in adult FLT3-ITD-positive AML is crucial to recognizing chemotherapy-resistant group.
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Affiliation(s)
- Toru Miyajima
- Department of Hematology, Graduate School of Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Masahiro Onozawa
- Department of Hematology, Graduate School of Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Shota Yoshida
- Department of Hematology, Graduate School of Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Naoki Miyashita
- Department of Hematology, Graduate School of Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Hiroyuki Kimura
- Department of Hematology, Graduate School of Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Shogo Takahashi
- Department of Hematology, Graduate School of Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Shota Yokoyama
- Department of Hematology, Graduate School of Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Toshihiro Matsukawa
- Department of Hematology, Graduate School of Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
| | - Hideki Goto
- Department of Hematology, Graduate School of Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Junichi Sugita
- Department of Hematology, Graduate School of Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
- Department of Hematology, Sapporo Hokuyu Hospital, Sapporo, Japan
| | - Shinichi Fujisawa
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Daisuke Hidaka
- Department of Hematology, Sapporo Hokuyu Hospital, Sapporo, Japan
| | - Reiki Ogasawara
- Department of Hematology, Sapporo Hokuyu Hospital, Sapporo, Japan
| | - Akio Mori
- Blood Disorders Center, Aiiku Hospital, Sapporo, Japan
| | - Satomi Matsuoka
- Department of Hematology, Asahikawa City Hospital, Asahikawa, Japan
| | - Akio Shigematsu
- Department of Hematology, Kushiro Rosai Hospital, Kushiro, Japan
| | - Kentaro Wakasa
- Department of Hematology, Obihiro Kosei Hospital, Obihiro, Japan
| | - Ikumi Kasahara
- Department of Hematology, Sapporo City General Hospital, Sapporo, Japan
| | - Tomoyuki Saga
- Department of Hematology, Kin-Ikyo Chuo Hospital, Sapporo, Japan
| | - Junichi Hashiguchi
- Department of Internal Medicine/General Medicine, Kitami Red Cross Hospital, Kitami, Japan
| | - Yukari Takeda
- Department of Hematology, Tonan Hospital, Sapporo, Japan
| | - Makoto Ibata
- Department of Hematology, Sapporo Kosei General Hospital, Sapporo, Japan
| | - Tsutsumi Yutaka
- Department of Hematology, Hakodate Municipal Hospital, Hakodate, Japan
| | - Katsuya Fujimoto
- Department of Hematology, National Hospital Organization Hokkaido Cancer Center, Sapporo, Japan
| | - Takeshi Kondo
- Blood Disorders Center, Aiiku Hospital, Sapporo, Japan
| | - Takanori Teshima
- Department of Hematology, Graduate School of Medicine, Hokkaido University Faculty of Medicine, Sapporo, Japan
- Division of Laboratory and Transfusion Medicine, Hokkaido University Hospital, Sapporo, Japan
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2
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Michmerhuizen NL, Klco JM, Mullighan CG. Mechanistic insights and potential therapeutic approaches for NUP98-rearranged hematologic malignancies. Blood 2020; 136:2275-2289. [PMID: 32766874 PMCID: PMC7702474 DOI: 10.1182/blood.2020007093] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Nucleoporin 98 (NUP98) fusion oncoproteins are observed in a spectrum of hematologic malignancies, particularly pediatric leukemias with poor patient outcomes. Although wild-type full-length NUP98 is a member of the nuclear pore complex, the chromosomal translocations leading to NUP98 gene fusions involve the intrinsically disordered and N-terminal region of NUP98 with over 30 partner genes. Fusion partners include several genes bearing homeodomains or having known roles in transcriptional or epigenetic regulation. Based on data in both experimental models and patient samples, NUP98 fusion oncoprotein-driven leukemogenesis is mediated by changes in chromatin structure and gene expression. Multiple cofactors associate with NUP98 fusion oncoproteins to mediate transcriptional changes possibly via phase separation, in a manner likely dependent on the fusion partner. NUP98 gene fusions co-occur with a set of additional mutations, including FLT3-internal tandem duplication and other events contributing to increased proliferation. To improve the currently dire outcomes for patients with NUP98-rearranged malignancies, therapeutic strategies have been considered that target transcriptional and epigenetic machinery, cooperating alterations, and signaling or cell-cycle pathways. With the development of more faithful experimental systems and continued study, we anticipate great strides in our understanding of the molecular mechanisms and therapeutic vulnerabilities at play in NUP98-rearranged models. Taken together, these studies should lead to improved clinical outcomes for NUP98-rearranged leukemia.
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Affiliation(s)
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
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3
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Masetti R, Bertuccio SN, Guidi V, Cerasi S, Lonetti A, Pession A. Uncommon cytogenetic abnormalities identifying high-risk acute myeloid leukemia in children. Future Oncol 2020; 16:2747-2762. [DOI: 10.2217/fon-2020-0505] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Pediatric acute myeloid leukemia (AML) represents an aggressive disease and is the leading cause of childhood leukemic mortality. The genomic landscape of pediatric AML has been recently mapped and redefined thanks to large-scale sequencing efforts. Today, understanding how to incorporate the growing list of genetic lesions into a risk stratification algorithm for pediatric AML is increasingly challenging given the uncertainty regarding the prognostic impact of rare lesions. Here we review some uncommon cytogenetic lesions to be considered for inclusion in the high-risk groups of the next pediatric AML treatment protocols. We describe their main clinical characteristics, biological background and outcome. We also provide some suggestions for the management of these rare but challenging patients and some novel targeted therapeutic options.
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Affiliation(s)
- Riccardo Masetti
- Pediatric Hematology-Oncology Unit, Department of Medical & Surgical Sciences DIMEC, University of Bologna, Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Salvatore Nicola Bertuccio
- Pediatric Hematology-Oncology Unit, Department of Medical & Surgical Sciences DIMEC, University of Bologna, Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Vanessa Guidi
- Pediatric Hematology-Oncology Unit, Department of Medical & Surgical Sciences DIMEC, University of Bologna, Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Sara Cerasi
- Pediatric Hematology-Oncology Unit, Department of Medical & Surgical Sciences DIMEC, University of Bologna, Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Annalisa Lonetti
- Giorgio Prodi Interdepartmental Cancer Research Centre, University of Bologna, Sant'Orsola-Malpighi Hospital, Bologna, Italy
| | - Andrea Pession
- Pediatric Hematology-Oncology Unit, Department of Medical & Surgical Sciences DIMEC, University of Bologna, Sant'Orsola-Malpighi Hospital, Bologna, Italy
- Giorgio Prodi Interdepartmental Cancer Research Centre, University of Bologna, Sant'Orsola-Malpighi Hospital, Bologna, Italy
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4
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Mitani Y, Hiwatari M, Seki M, Hangai M, Takita J. Successful treatment of acute myeloid leukemia co-expressing NUP98/NSD1 and FLT3/ITD with preemptive donor lymphocyte infusions. Int J Hematol 2019; 110:512-516. [PMID: 31134509 DOI: 10.1007/s12185-019-02665-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/11/2019] [Accepted: 05/14/2019] [Indexed: 12/17/2022]
Abstract
Patients with acute myeloid leukemia (AML) co-expressing NUP98/NSD1 and FLT3/ITD have a dismal prognosis despite undergoing hematopoietic stem cell transplantation (HSCT). There are a few studies on successful treatment of relapsed AML co-expressing NUP98/NSD1 and FLT3/ITD. We report a refractory case of molecular relapse of AML co-expressing NUP98/NSD1 and FLT3/ITD post-matched sibling HSCT. Donor lymphocyte infusion (DLI) at an early stage of post-transplantation resulted in complete molecular remission for 29 months with durable chronic graft-versus-host disease. Our case suggests the clinical efficacy of preemptive DLI following minimal residual disease analysis for the treatment of refractory AML.
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Affiliation(s)
- Yuichi Mitani
- Department of Pediatrics, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Mitsuteru Hiwatari
- Department of Pediatrics, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Masafumi Seki
- Department of Pediatrics, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Mayumi Hangai
- Department of Pediatrics, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Junko Takita
- Department of Pediatrics, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.,Department of Pediatrics, Kyoto University, Kyoto, Japan
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5
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Goto H, Kimura M, Hirano N, Suenobu S, Ihara K. NUP98-HOXC13 fusion gene in acute myeloid leukemia: Pediatric case. Pediatr Int 2017; 59:1105-1106. [PMID: 28960734 DOI: 10.1111/ped.13376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 06/21/2017] [Accepted: 07/20/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Hironori Goto
- Department of Pediatrics, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Makoto Kimura
- Department of Pediatrics, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Naoki Hirano
- Department of Pediatrics, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Souichi Suenobu
- Department of Pediatrics, Oita University Faculty of Medicine, Yufu, Oita, Japan.,Division of General Pediatrics and Emergency Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Kenji Ihara
- Department of Pediatrics, Oita University Faculty of Medicine, Yufu, Oita, Japan
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6
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Zhang X, Yang C, Peng X, Chen X, Feng Y. Acute WT1-positive promyelocytic leukemia with hypogranular variant morphology, bcr-3 isoform of PML-RARα and Flt3-ITD mutation: a rare case report. SAO PAULO MED J 2017; 135:179-184. [PMID: 28125133 PMCID: PMC9977332 DOI: 10.1590/1516-3180.2016.020104102016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 10/04/2016] [Indexed: 12/18/2022] Open
Abstract
CONTEXT: Acute promyelocytic leukemia (APL) accounts for 8% to 10% of cases of acute myeloid leukemia (AML). Remission in cases of high-risk APL is still difficult to achieve, and relapses occur readily. CASE REPORT: Here, we describe a case of APL with high white blood cell counts in blood tests and hypogranular variant morphology in bone marrow, together with fms-like tyrosine kinase-3 with internal tandem duplication mutations (FLT3-ITD), and bcr-3 isoform of PML-RARα. Most importantly, we detected high level of Wilms' tumor gene (WT1) in marrow blasts, through the reverse transcription polymerase chain reaction (RT-PCR). To date, no clear conclusions about an association between WT1 expression levels and APL have been reached. This patient successively received a combined treatment regimen consisting of hydroxycarbamide, arsenic trioxide and idarubicin plus cytarabine, which ultimately enabled complete remission. Unfortunately, he subsequently died of sudden massive hemoptysis because of pulmonary infection. CONCLUSION: Based on our findings and a review of the literature, abnormal functioning of WT1 may be a high-risk factor in cases of APL. Further studies aimed towards evaluating the impact of WT1 expression on the prognosis for APL patients are of interest.
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Affiliation(s)
- Xi Zhang
- MD, PhD. Professor, Department of Hematology, Xinqiao Hospital, Third Military Medical University, Chongqing, China.
| | - Cheng Yang
- MD. Attending Physician, Department of Hematology, Xinqiao Hospital, Third Military Medical University, Chongqing, China.
| | - Xiangui Peng
- MD. Affiliated Professor, Department of Hematology, Xinqiao Hospital, Third Military Medical University, Chongqing, China.
| | - Xinghua Chen
- MD, PhD. Full Professor, Department of Hematology, Xinqiao Hospital, Third Military Medical University, Chongqing, China.
| | - Yimei Feng
- MD, PhD. Assistant Professor, Department of Hematology, Xinqiao Hospital, Third Military Medical University, Chongqing, China.
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7
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Hara Y, Shiba N, Ohki K, Tabuchi K, Yamato G, Park MJ, Tomizawa D, Kinoshita A, Shimada A, Arakawa H, Saito AM, Kiyokawa N, Tawa A, Horibe K, Taga T, Adachi S, Taki T, Hayashi Y. Prognostic impact of specific molecular profiles in pediatric acute megakaryoblastic leukemia in non-Down syndrome. Genes Chromosomes Cancer 2017; 56:394-404. [DOI: 10.1002/gcc.22444] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 12/19/2016] [Accepted: 12/30/2016] [Indexed: 12/17/2022] Open
Affiliation(s)
- Yusuke Hara
- Department of Hematology and Oncology; Gunma Children's Medical Center; Shibukawa Japan
- Department of Pediatrics; Gunma University Graduate School of Medicine; Maebashi Japan
- Clinical Research Center, National Hospital Organization Nagoya Medical Center; Nagoya Japan
| | - Norio Shiba
- Department of Hematology and Oncology; Gunma Children's Medical Center; Shibukawa Japan
- Department of Pediatrics; Gunma University Graduate School of Medicine; Maebashi Japan
- Clinical Research Center, National Hospital Organization Nagoya Medical Center; Nagoya Japan
| | - Kentaro Ohki
- Department of Hematology and Oncology; Gunma Children's Medical Center; Shibukawa Japan
- Department of Pediatric Hematology and Oncology Research; National Research Institute for Child Health and Development; Tokyo Japan
| | - Ken Tabuchi
- Department of Pediatrics; Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital; Tokyo Japan
| | - Genki Yamato
- Department of Hematology and Oncology; Gunma Children's Medical Center; Shibukawa Japan
- Department of Pediatrics; Gunma University Graduate School of Medicine; Maebashi Japan
- Clinical Research Center, National Hospital Organization Nagoya Medical Center; Nagoya Japan
| | - Myoung-ja Park
- Department of Hematology and Oncology; Gunma Children's Medical Center; Shibukawa Japan
| | - Daisuke Tomizawa
- Division of Leukemia and Lymphoma; Children's Cancer Center, National Center for Child Health and Development; Tokyo Japan
| | - Akitoshi Kinoshita
- Department of Pediatrics; St Marianna University School of Medicine; Kawasaki Japan
| | - Akira Shimada
- Department of Pediatrics; Okayama University Hospital; Okayama Japan
| | - Hirokazu Arakawa
- Department of Pediatrics; Gunma University Graduate School of Medicine; Maebashi Japan
| | - Akiko M. Saito
- Clinical Research Center, National Hospital Organization Nagoya Medical Center; Nagoya Japan
| | - Nobutaka Kiyokawa
- Department of Pediatric Hematology and Oncology Research; National Research Institute for Child Health and Development; Tokyo Japan
| | - Akio Tawa
- Department of Pediatrics; National Hospital Organization Osaka National Hospital; Osaka Japan
| | - Keizo Horibe
- Clinical Research Center, National Hospital Organization Nagoya Medical Center; Nagoya Japan
| | - Takashi Taga
- Department of Pediatrics; Shiga University of Medical Science; Otsu Japan
| | - Souichi Adachi
- Department of Human Health Sciences Kyoto University Graduate School of Medicine; Kyoto Japan
| | - Tomohiko Taki
- Department of Molecular Diagnostics and Therapeutics; Kyoto Prefectural University of Medicine Graduate School of Medical Science; Kyoto Japan
| | - Yasuhide Hayashi
- Department of Hematology and Oncology; Gunma Children's Medical Center; Shibukawa Japan
- Clinical Research Center, National Hospital Organization Nagoya Medical Center; Nagoya Japan
- Gunma Red Cross Blood Center; Maebashi Japan
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8
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Struski S, Lagarde S, Bories P, Puiseux C, Prade N, Cuccuini W, Pages MP, Bidet A, Gervais C, Lafage-Pochitaloff M, Roche-Lestienne C, Barin C, Penther D, Nadal N, Radford-Weiss I, Collonge-Rame MA, Gaillard B, Mugneret F, Lefebvre C, Bart-Delabesse E, Petit A, Leverger G, Broccardo C, Luquet I, Pasquet M, Delabesse E. NUP98 is rearranged in 3.8% of pediatric AML forming a clinical and molecular homogenous group with a poor prognosis. Leukemia 2016; 31:565-572. [PMID: 27694926 DOI: 10.1038/leu.2016.267] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 08/25/2016] [Accepted: 08/30/2016] [Indexed: 01/21/2023]
Abstract
Pediatric acute myeloid leukemia (AML) is a rare disease whose prognosis is highly variable according to factors such as chromosomal abnormalities. Recurrent genomic rearrangements are detected in half of pediatric AML by karyotype. NUcleoPorin 98 (NUP98) gene is rearranged with 31 different fusion partner genes. These rearrangements are frequently undetected by conventional cytogenetics, as the NUP98 gene is located at the end of the chromosome 11 short arm (11p15). By screening a series of 574 pediatric AML, we detected a NUP98 rearrangement in 22 cases (3.8%), a frequency similar to CBFB-MYH11 fusion gene (4.0%). The most frequent NUP98 fusion gene partner is NSD1. These cases are homogeneous regarding their biological and clinical characteristics, and associated with bad prognosis only improved by bone marrow transplantation. We detailed the biological characteristics of these AML by exome sequencing which demonstrated few recurrent mutations (FLT3 ITD, WT1, CEBPA, NBPF14, BCR and ODF1). The analysis of the clonal structure in these cases suggests that the mutation order in the NUP98-rearranged pediatric AML begins with the NUP98 rearrangement leading to epigenetic dysregulations then followed by mutations of critical hematopoietic transcription factors and finally, activation of the FLT3 signaling pathway.
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Affiliation(s)
- S Struski
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France.,Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France
| | - S Lagarde
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France
| | - P Bories
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France
| | - C Puiseux
- Department of Pediatric Oncology, University Hospital of Toulouse, Toulouse, France
| | - N Prade
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France
| | - W Cuccuini
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, University Hospital of Saint-Louis, Paris, France
| | - M-P Pages
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, Hospices Civils de Lyon, Lyon, France
| | - A Bidet
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, University Hospital of Haut-Leveque, Bordeaux, France
| | - C Gervais
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, University Hospital of Hautepierre, Strasbourg, France
| | - M Lafage-Pochitaloff
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Medical Genetic, University Hospital of La Timone, Marseille, France
| | - C Roche-Lestienne
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Medical Genetic, University Hospital Jeanne de Flandre, University of Lille 2, Lille, France
| | - C Barin
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Genetic, University Hospital Bretonneau, Tours, France
| | - D Penther
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Oncology Genetic, Cancer Institute Henri Becquerel, Rouen, France
| | - N Nadal
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, University Hospital of Saint-Étienne, Saint-Etienne, France
| | - I Radford-Weiss
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Genetic, University Hospital Necker, Paris, France
| | - M-A Collonge-Rame
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Genetic, University Hospital Saint-Jacques, Besancon, France
| | - B Gaillard
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, University Hospital Robert Debré, Reims, France
| | - F Mugneret
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Cytogenetic, University Hospital of Dijon, Dijon, France
| | - C Lefebvre
- Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France.,Department of Haematology, Oncology and Immunology, University Hospital of Grenoble, Grenoble, France
| | - E Bart-Delabesse
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France
| | - A Petit
- Department of Pediatric Oncology, University Hospital of Trousseau, Paris, France
| | - G Leverger
- Department of Pediatric Oncology, University Hospital of Trousseau, Paris, France
| | - C Broccardo
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France
| | - I Luquet
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France.,Groupe Francophone de Cytogénétique Hématologique (GFCH), Paris, France
| | - M Pasquet
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France.,Department of Pediatric Oncology, University Hospital of Toulouse, Toulouse, France
| | - E Delabesse
- Department of Haematology, University Hospital of Toulouse, University of Toulouse, Centre of Research on Cancer of Toulouse (CRCT), Toulouse, France
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9
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Lavallée VP, Lemieux S, Boucher G, Gendron P, Boivin I, Girard S, Hébert J, Sauvageau G. Identification of MYC mutations in acute myeloid leukemias with NUP98–NSD1 translocations. Leukemia 2016; 30:1621-4. [DOI: 10.1038/leu.2016.19] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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10
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Hu J, Hong X, Li Z, Lu Q. Acute monocytic leukaemia with t(11; 12) (p15; q13) chromosomal changes: A case report and literature review. Oncol Lett 2015; 10:2307-2310. [PMID: 26622840 DOI: 10.3892/ol.2015.3511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 06/16/2015] [Indexed: 01/21/2023] Open
Abstract
Acute myeloid leukaemia (AML) is a type of heterogeneous disease derived from haematopoietic stem cells. Cytogenetic characterisation is essential for diagnosis and prognosis stratification. Here, we present the case of a 43-year-old female diagnosed with leukaemia, who demonstrated a rare chromosomal change of t(11; 12) (p15; q13) along with a positive FLT3-ITD mutation. The patient had a white blood cell count of 76.41×109/l. Bone marrow morphology revealed that monoblasts accounted for 25.5% of cells, and premonocytes accounted for 49.0%. This patient strongly responded to idarubicin and Ara-c (cytarabine) chemotherapy, which rapidly eliminated the leukaemia cell clones. However, the proliferation rate of the leukaemia cells was high during the intermission of chemotherapy. Subsequently, following two courses of chemotherapy, full haematological remission could not be attained. AML patients with t(11; 12) (p15; q13) combined with FLT3-ITD mutations are expected to have a short life expectancy; however, early haematopoietic stem cell transplantation therapy may improve the treatment outcome for these patients.
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Affiliation(s)
- Jiasheng Hu
- Department of Haematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Xiuli Hong
- Department of Haematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Zhe Li
- Department of Pediatrics, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
| | - Quanyi Lu
- Department of Haematology, Zhongshan Hospital of Xiamen University, Xiamen, Fujian 361004, P.R. China
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11
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NUP98/NSD1 and FLT3/ITD coexpression is more prevalent in younger AML patients and leads to induction failure: a COG and SWOG report. Blood 2014; 124:2400-7. [PMID: 25145343 DOI: 10.1182/blood-2014-04-570929] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
NUP98/NSD1 has recently been reported in association with poor outcome in acute myeloid leukemia (AML). Previous studies also observed a high overlap between NUP98/NSD1 and FLT3/ITD, raising the question as to whether the reported poor outcome is due to NUP98/NSD1 or caused by the co-occurrence of these 2 genetic lesions. We aimed to determine the prognostic significance of NUP98/NSD1 in the context of FLT3/ITD AML. A total of 1421 patients enrolled in 5 consecutive Children's Oncology Group/Children's Cancer Group and SWOG trials were evaluated. NUP98/NSD1 was found in 15% of FLT3/ITD and 7% of cytogenetically normal (CN)-AML. Those with dual FLT3/ITD and NUP98/NSD1 (82% of NUP98/NSD1 patients) had a complete remission rate of 27% vs 69% in FLT3/ITD without NUP98/NSD1 (P < .001). The corresponding 3-year overall survival was 31% vs 48% (P = .011), respectively. In CN-AML, patients with concomitant NUP98/NSD1 and FLT3/ITD had a worse outcome than those harboring NUP98/NSD1 only. In multivariate analysis, the dual NUP98/NSD1 and FLT3/ITD remained an independent predictor of poor outcome, and NUP98/NSD1 without FLT3/ITD lost its prognostic significance. Our study demonstrates that it is the interaction between NUP98/NSD1 and FLT3/ITD that determines the poor outcome of patients with NUP98/NSD1 disease.
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12
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Abstract
Nuclear pore complexes (NPCs) are the sole gateways between the nucleus and the cytoplasm of eukaryotic cells and they mediate all macromolecular trafficking between these cellular compartments. Nucleocytoplasmic transport is highly selective and precisely regulated and as such an important aspect of normal cellular function. Defects in this process or in its machinery have been linked to various human diseases, including cancer. Nucleoporins, which are about 30 proteins that built up NPCs, are critical players in nucleocytoplasmic transport and have also been shown to be key players in numerous other cellular processes, such as cell cycle control and gene expression regulation. This review will focus on the three nucleoporins Nup98, Nup214, and Nup358. Common to them is their significance in nucleocytoplasmic transport, their multiple other functions, and being targets for chromosomal translocations that lead to haematopoietic malignancies, in particular acute myeloid leukaemia. The underlying molecular mechanisms of nucleoporin-associated leukaemias are only poorly understood but share some characteristics and are distinguished by their poor prognosis and therapy outcome.
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13
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Takeda A, Yaseen NR. Nucleoporins and nucleocytoplasmic transport in hematologic malignancies. Semin Cancer Biol 2014; 27:3-10. [PMID: 24657637 DOI: 10.1016/j.semcancer.2014.02.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 11/19/2022]
Abstract
Hematologic malignancies are often associated with chromosomal rearrangements that lead to the expression of chimeric fusion proteins. Rearrangements of the genes encoding two nucleoporins, NUP98 and NUP214, have been implicated in the pathogenesis of several types of hematologic malignancies, particularly acute myeloid leukemia. NUP98 rearrangements result in fusion of an N-terminal portion of NUP98 to one of numerous proteins. These rearrangements often follow treatment with topoisomerase II inhibitors and tend to occur in younger patients. They have been shown to induce leukemia in mice and to enhance proliferation and disrupt differentiation in primary human hematopoietic precursors. NUP214 has only a few fusion partners. DEK-NUP214 is the most common NUP214 fusion in AML; it tends to occur in younger patients and is usually associated with FLT3 internal tandem duplications. The leukemogenic activity of NUP214 fusions is less well characterized. Normal nucleoporins, including NUP98 and NUP214, have important functions in nucleocytoplasmic transport, transcription, and mitosis. These functions and their disruptions by oncogenic nucleoporin fusions are discussed.
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Affiliation(s)
- Akiko Takeda
- Department of Pathology and Immunology, Washington University in St. Louis, United States.
| | - Nabeel R Yaseen
- Department of Pathology and Immunology, Washington University in St. Louis, United States.
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14
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Salsi V, Ferrari S, Gorello P, Fantini S, Chiavolelli F, Mecucci C, Zappavigna V. NUP98 fusion oncoproteins promote aneuploidy by attenuating the mitotic spindle checkpoint. Cancer Res 2013; 74:1079-90. [PMID: 24371226 DOI: 10.1158/0008-5472.can-13-0912] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
NUP98 is a recurrent fusion partner in chromosome translocations that cause acute myelogenous leukemia. NUP98, a nucleoporin, and its interaction partner Rae1, have been implicated in the control of chromosome segregation, but their mechanistic contributions to tumorigenesis have been unclear. Here, we show that expression of NUP98 fusion oncoproteins causes mitotic spindle defects and chromosome missegregation, correlating with the capability of NUP98 fusions to cause premature securin degradation and slippage from an unsatisfied spindle assembly checkpoint (SAC). NUP98 fusions, unlike wild-type NUP98, were found to physically interact with the anaphase promoting complex/cyclosome (APC/C)(Cdc20) and to displace the BubR1 SAC component, suggesting a possible mechanistic basis for their interference with SAC function. In addition, NUP98 oncoproteins displayed a prolonged half-life in cells. We found that NUP98 stability is controlled by a PEST sequence, absent in NUP98 oncoproteins, whose deletion reproduced the aberrant SAC-interfering activity of NUP98 oncoproteins. Together, our findings suggest that NUP98 oncoproteins predispose myeloid cells to oncogenic transformation or malignant progression by promoting whole chromosome instability.
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Affiliation(s)
- Valentina Salsi
- Authors' Affiliations: Department of Life Sciences, University of Modena and Reggio Emilia, Modena; and Department of Hematology, University of Perugia, University Hospital S. Maria della Misericordia, Perugia, Italy
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15
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Akiki S, Dyer SA, Grimwade D, Ivey A, Abou-Zeid N, Borrow J, Jeffries S, Caddick J, Newell H, Begum S, Tawana K, Mason J, Velangi M, Griffiths M. NUP98-NSD1 fusion in association with FLT3-ITD mutation identifies a prognostically relevant subgroup of pediatric acute myeloid leukemia patients suitable for monitoring by real time quantitative PCR. Genes Chromosomes Cancer 2013; 52:1053-64. [PMID: 23999921 DOI: 10.1002/gcc.22100] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/10/2013] [Indexed: 12/26/2022] Open
Abstract
The cytogenetically cryptic t(5;11)(q35;p15) leading to the NUP98-NSD1 fusion is a rare but recurrent gene rearrangement recently reported to identify a group of young AML patients with poor prognosis. We used reverse transcription polymerase chain reaction (PCR) to screen retrospectively diagnostic samples from 54 unselected pediatric AML patients and designed a real time quantitative PCR assay to track individual patient response to treatment. Four positive cases (7%) were identified; three arising de novo and one therapy related AML. All had intermediate risk cytogenetic markers and a concurrent FLT3-ITD but lacked NPM1 and CEBPA mutations. The patients had a poor response to therapy and all proceeded to hematopoietic stem cell transplant. These data lend support to the adoption of screening for NUP98-NSD1 in pediatric AML without otherwise favorable genetic markers. The role of quantitative PCR is also highlighted as a potential tool for managing NUP98-NSD1 positive patients post-treatment.
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Affiliation(s)
- Susanna Akiki
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS foundation Trust, Birmingham, UK; School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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16
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The Impact of FLT3 Mutations on the Development of Acute Myeloid Leukemias. LEUKEMIA RESEARCH AND TREATMENT 2013; 2013:275760. [PMID: 23936658 PMCID: PMC3725705 DOI: 10.1155/2013/275760] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 04/30/2013] [Accepted: 05/14/2013] [Indexed: 11/17/2022]
Abstract
The development of the genetic studies on acute myeloid leukemias (AMLs) has led to the identification of some recurrent genetic abnormalities. Their discovery was of fundamental importance not only for a better understanding of the molecular pathogenesis of AMLs, but also for the identification of new therapeutic targets. In this context, it is essential to identify AML-associated “driver” mutations, which have a causative role in leukemogenesis. Evidences accumulated during the last years indicate that activating internal tandem duplication mutations in FLT3 (FLT3-ITD), detected in about 20% of AMLs, represents driver mutations and valid therapeutic targets in AMLs. Furthermore, the screening of FLT3-ITD mutations has also considerably helped to improve the identification of more accurate prognostic criteria and of the therapeutic selection of patients.
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17
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Shiba N, Ichikawa H, Taki T, Park MJ, Jo A, Mitani S, Kobayashi T, Shimada A, Sotomatsu M, Arakawa H, Adachi S, Tawa A, Horibe K, Tsuchida M, Hanada R, Tsukimoto I, Hayashi Y. NUP98-NSD1 gene fusion and its related gene expression signature are strongly associated with a poor prognosis in pediatric acute myeloid leukemia. Genes Chromosomes Cancer 2013; 52:683-93. [PMID: 23630019 DOI: 10.1002/gcc.22064] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 03/15/2013] [Indexed: 12/17/2022] Open
Abstract
The cryptic t(5;11)(q35;p15.5) creates a fusion gene between the NUP98 and NSD1 genes. To ascertain the significance of this gene fusion, we explored its frequency, clinical impact, and gene expression pattern using DNA microarray in pediatric acute myeloid leukemia (AML) patients. NUP98-NSD1 fusion transcripts were detected in 6 (4.8%) of 124 pediatric AML patients. Supervised hierarchical clustering analyses using probe sets that were differentially expressed in these patients detected a characteristic gene expression pattern, including 18 NUP98-NSD1-negative patients (NUP98-NSD1-like patients). In total, a NUP98-NSD1-related gene expression signature (NUP98-NSD1 signature) was found in 19% (24/124) and in 58% (15/26) of cytogenetically normal cases. Their 4-year overall survival (OS) and event-free survival (EFS) were poor (33.3% in NUP98-NSD1-positive and 38.9% in NUP98-NSD1-like patients) compared with 100 NUP98-NSD1 signature-negative patients (4-year OS: 86.0%, 4-year EFS: 72.0%). Interestingly, t(7;11)(p15;p15)/NUP98-HOXA13, t(6;11)(q27;q23)/MLL-MLLT4 and t(6;9)(p22;q34)/DEK-NUP214, which are known as poor prognostic markers, were found in NUP98-NSD1-like patients. Furthermore, another type of NUP98-NSD1 fusion transcript was identified by additional RT-PCR analyses using other primers in a NUP98-NSD1-like patient, revealing the significance of this signature to detect NUP98-NSD1 gene fusions and to identify a new poor prognostic subgroup in AML.
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Affiliation(s)
- Norio Shiba
- Department of Hematology/Oncology, Gunma Children's Medical Center, Shibukawa, Japan
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18
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NUP98/JARID1A is a novel recurrent abnormality in pediatric acute megakaryoblastic leukemia with a distinct HOX gene expression pattern. Leukemia 2013; 27:2280-8. [PMID: 23531517 DOI: 10.1038/leu.2013.87] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 03/15/2013] [Indexed: 12/11/2022]
Abstract
Cytogenetic abnormalities and early response to treatment are the main prognostic factors in acute myeloid leukemia (AML). Recently, NUP98/NSD1 (t(5; 11)(q35; p15)), a cytogenetically cryptic fusion, was described as recurrent event in AML, characterized by dismal prognosis and HOXA/B gene overexpression. Using split-signal fluorescence in situ hybridization, other NUP98-rearranged pediatric AML cases were identified, including several acute megakaryoblastic leukemia (AMKL) cases with a cytogenetically cryptic fusion of NUP98 to JARID1A (t(11;15)(p15;q35)). In this study we screened 105 pediatric AMKL cases to analyze the frequency of NUP98/JARID1A and other recurrent genetic abnormalities. NUP98/JARID1A was identified in 11/105 patients (10.5%). Other abnormalities consisted of RBM15/MKL1 (n=16), CBFA2T3/GLIS2 (n=13) and MLL-rearrangements (n=13). Comparing NUP98/JARID1A-positive patients with other pediatric AMKL patients, no significant differences in sex, age and white blood cell count were found. NUP98/JARID1A was not an independent prognostic factor for 5-year overall (probability of overall survival (pOS)) or event-free survival (probability of event-free survival (pEFS)), although the 5-year pOS for the entire AMKL cohort was poor (42 ± 6%). Cases with RBM15/MLK1 fared significantly better in terms of pOS and pEFS, although this was not independent from other risk factors in multivariate analysis. NUP98/JARID1A cases were characterized by HOXA/B gene overexpression, which is a potential druggable pathway. In conclusion, NUP98/JARID1A is a novel recurrent genetic abnormality in pediatric AMKL.
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19
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Lisboa S, Cerveira N, Bizarro S, Correia C, Vieira J, Torres L, Mariz JM, Teixeira MR. POU1F1 is a novel fusion partner of NUP98 in acute myeloid leukemia with t(3;11)(p11;p15). Mol Cancer 2013; 12:5. [PMID: 23332017 PMCID: PMC3567982 DOI: 10.1186/1476-4598-12-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 01/03/2013] [Indexed: 11/10/2022] Open
Abstract
Background NUP98 gene rearrangements have been reported in acute myeloid leukemia, giving rise to fusion proteins that seem to function as aberrant transcription factors, and are thought to be associated with poor prognosis. Findings A patient with treatment-related acute myeloid leukemia presented a t(3;11)(p11;p15) as the only cytogenetic abnormality. FISH and molecular genetic analyses identified a class 1 homeobox gene, POU1F1, located on chromosome 3p11, as the fusion partner of NUP98. In addition, we have found that the patient harbored an FLT3-ITD mutation, which most likely collaborated with the NUP98-POU1F1 fusion gene in malignant transformation. Conclusions We have identified POU1F1 as the NUP98 fusion partner in therapy-related AML with a t(3;11)(p11;p15). This is the first POU family member identified as a fusion partner in human cancer.
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Affiliation(s)
- Susana Lisboa
- Department of Genetics, Portuguese Oncology Institute, Rua Dr, António Bernardino de Almeida, 4200-072, Porto, Portugal
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20
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Fasan A, Haferlach C, Alpermann T, Kern W, Haferlach T, Schnittger S. A rare but specific subset of adult AML patients can be defined by the cytogenetically cryptic NUP98-NSD1 fusion gene. Leukemia 2012; 27:245-8. [PMID: 22945772 DOI: 10.1038/leu.2012.230] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Knock-in of a FLT3/ITD mutation cooperates with a NUP98-HOXD13 fusion to generate acute myeloid leukemia in a mouse model. Blood 2012; 119:2883-94. [PMID: 22323452 DOI: 10.1182/blood-2011-10-382283] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Constitutive activation of FLT3 by internal tandem duplication (ITD) is one of the most common molecular alterations in acute myeloid leukemia (AML). FLT3/ITD mutations have also been observed in myelodysplastic syndrome patients both before and during progression to AML. Previous work has shown that insertion of an FLT3/ITD mutation into the murine Flt3 gene induces a myeloproliferative neoplasm, but not progression to acute leukemia, suggesting that additional cooperating events are required. We therefore combined the FLT3/ITD mutation with a model of myelodysplastic syndrome involving transgenic expression of the Nup98-HoxD13 (NHD13) fusion gene. Mice expressing both the FLT3/ITD and NHD13 transgene developed AML with 100% penetrance and short latency. These leukemias were driven by mutant FLT3 expression and were susceptible to treatment with FLT3 tyrosine kinase inhibitors. We also observed a spontaneous loss of the wild-type Flt3 allele in these AMLs, further modeling the loss of the heterozygosity phenomenon that is seen in human AML with FLT3-activating mutations. Because resistance to FLT3 inhibitors remains an important clinical issue, this model may help identify new molecular targets in collaborative signaling pathways.
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Gosal G, Kochut KJ, Kannan N. ProKinO: an ontology for integrative analysis of protein kinases in cancer. PLoS One 2011; 6:e28782. [PMID: 22194913 PMCID: PMC3237543 DOI: 10.1371/journal.pone.0028782] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 11/15/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Protein kinases are a large and diverse family of enzymes that are genomically altered in many human cancers. Targeted cancer genome sequencing efforts have unveiled the mutational profiles of protein kinase genes from many different cancer types. While mutational data on protein kinases is currently catalogued in various databases, integration of mutation data with other forms of data on protein kinases such as sequence, structure, function and pathway is necessary to identify and characterize key cancer causing mutations. Integrative analysis of protein kinase data, however, is a challenge because of the disparate nature of protein kinase data sources and data formats. RESULTS Here, we describe ProKinO, a protein kinase-specific ontology, which provides a controlled vocabulary of terms, their hierarchy, and relationships unifying sequence, structure, function, mutation and pathway information on protein kinases. The conceptual representation of such diverse forms of information in one place not only allows rapid discovery of significant information related to a specific protein kinase, but also enables large-scale integrative analysis of protein kinase data in ways not possible through other kinase-specific resources. We have performed several integrative analyses of ProKinO data and, as an example, found that a large number of somatic mutations (∼288 distinct mutations) associated with the haematopoietic neoplasm cancer type map to only 8 kinases in the human kinome. This is in contrast to glioma, where the mutations are spread over 82 distinct kinases. We also provide examples of how ontology-based data analysis can be used to generate testable hypotheses regarding cancer mutations. CONCLUSION We present an integrated framework for large-scale integrative analysis of protein kinase data. Navigation and analysis of ontology data can be performed using the ontology browser available at: http://vulcan.cs.uga.edu/prokino.
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Affiliation(s)
- Gurinder Gosal
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, United States of America
| | - Krys J. Kochut
- Department of Computer Science, University of Georgia, Athens, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, United States of America
- * E-mail: (NK); (KK)
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, United States of America
- * E-mail: (NK); (KK)
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Abstract
Structural chromosomal rearrangements of the Nucleoporin 98 gene (NUP98), primarily balanced translocations and inversions, are associated with a wide array of hematopoietic malignancies. NUP98 is known to be fused to at least 28 different partner genes in patients with hematopoietic malignancies, including acute myeloid leukemia, chronic myeloid leukemia in blast crisis, myelodysplastic syndrome, acute lymphoblastic leukemia, and bilineage/biphenotypic leukemia. NUP98 gene fusions typically encode a fusion protein that retains the amino terminus of NUP98; in this context, it is important to note that several recent studies have demonstrated that the amino-terminal portion of NUP98 exhibits transcription activation potential. Approximately half of the NUP98 fusion partners encode homeodomain proteins, and at least 5 NUP98 fusions involve known histone-modifying genes. Several of the NUP98 fusions, including NUP98-homeobox (HOX)A9, NUP98-HOXD13, and NUP98-JARID1A, have been used to generate animal models of both lymphoid and myeloid malignancy; these models typically up-regulate HOXA cluster genes, including HOXA5, HOXA7, HOXA9, and HOXA10. In addition, several of the NUP98 fusion proteins have been shown to inhibit differentiation of hematopoietic precursors and to increase self-renewal of hematopoietic stem or progenitor cells, providing a potential mechanism for malignant transformation.
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NUP98/NSD1 characterizes a novel poor prognostic group in acute myeloid leukemia with a distinct HOX gene expression pattern. Blood 2011; 118:3645-56. [PMID: 21813447 DOI: 10.1182/blood-2011-04-346643] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Translocations involving nucleoporin 98kD (NUP98) on chromosome 11p15 occur at relatively low frequency in acute myeloid leukemia (AML) but can be missed with routine karyotyping. In this study, high-resolution genome-wide copy number analyses revealed cryptic NUP98/NSD1 translocations in 3 of 92 cytogenetically normal (CN)-AML cases. To determine their exact frequency, we screened > 1000 well-characterized pediatric and adult AML cases using a NUP98/NSD1-specific RT-PCR. Twenty-three cases harbored the NUP98/NSD1 fusion, representing 16.1% of pediatric and 2.3% of adult CN-AML patients. NUP98/NSD1-positive AML cases had significantly higher white blood cell counts (median, 147 × 10⁹/L), more frequent FAB-M4/M5 morphology (in 63%), and more CN-AML (in 78%), FLT3/internal tandem duplication (in 91%) and WT1 mutations (in 45%) than NUP98/NSD1-negative cases. NUP98/NSD1 was mutually exclusive with all recurrent type-II aberrations. Importantly, NUP98/NSD1 was an independent predictor for poor prognosis; 4-year event-free survival was < 10% for both pediatric and adult NUP98/NSD1-positive AML patients. NUP98/NSD1-positive AML showed a characteristic HOX-gene expression pattern, distinct from, for example, MLL-rearranged AML, and the fusion protein was aberrantly localized in nuclear aggregates, providing insight into the leukemogenic pathways of these AMLs. Taken together, NUP98/NSD1 identifies a previously unrecognized group of young AML patients, with distinct characteristics and dismal prognosis, for whom new treatment strategies are urgently needed.
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25
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Balgobind BV, Hollink IHIM, Arentsen-Peters STCJM, Zimmermann M, Harbott J, Beverloo HB, von Bergh ARM, Cloos J, Kaspers GJL, de Haas V, Zemanova Z, Stary J, Cayuela JM, Baruchel A, Creutzig U, Reinhardt D, Pieters R, Zwaan CM, van den Heuvel-Eibrink MM. Integrative analysis of type-I and type-II aberrations underscores the genetic heterogeneity of pediatric acute myeloid leukemia. Haematologica 2011; 96:1478-87. [PMID: 21791472 DOI: 10.3324/haematol.2010.038976] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Several studies of pediatric acute myeloid leukemia have described the various type-I or type-II aberrations and their relationship with clinical outcome. However, there has been no recent comprehensive overview of these genetic aberrations in one large pediatric acute myeloid leukemia cohort. DESIGN AND METHODS We studied the different genetic aberrations, their associations and their impact on prognosis in a large pediatric acute myeloid leukemia series (n=506). Karyotypes were studied, and hotspot regions of NPM1, CEPBA, MLL, WT1, FLT3, N-RAS, K-RAS, PTPN11 and KIT were screened for mutations of available samples. The mutational status of all type-I and type-II aberrations was available in 330 and 263 cases, respectively. Survival analysis was performed in a subset (n=385) treated on consecutive acute myeloid leukemia Berlin-Frankfurt-Munster Study Group and Dutch Childhood Oncology Group treatment protocols. RESULTS Genetic aberrations were associated with specific clinical characteristics, e.g. significantly higher diagnostic white blood cell counts in MLL-rearranged, WT1-mutated and FLT3-ITD-positive acute myeloid leukemia. Furthermore, there was a significant difference in the distribution of these aberrations between children below and above the age of two years. Non-random associations, e.g. KIT mutations with core-binding factor acute myeloid leukemia, and FLT3-ITD with t(15;17)(q22;q21), NPM1- and WT1-mutated acute myeloid leukemia, respectively, were observed. Multivariate analysis revealed a 'favorable karyotype', i.e. t(15;17)(q22;q21), t(8;21)(q22;q22) and inv(16)(p13q22)/t(16;16)(p13;q22). NPM1 and CEBPA double mutations were independent factors for favorable event-free survival. WT1 mutations combined with FLT3-ITD showed the worst outcome for 5-year overall survival (22±14%) and 5-year event-free survival (20±13%), although it was not an independent factor in multivariate analysis. CONCLUSIONS Integrative analysis of type-I and type-II aberrations provides an insight into the frequencies, non-random associations and prognostic impact of the various aberrations, reflecting the heterogeneity of pediatric acute myeloid leukemia. These aberrations are likely to guide the stratification of pediatric acute myeloid leukemia and may direct the development of targeted therapies.
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Affiliation(s)
- Brian V Balgobind
- Department of Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
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