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Fang EX, Ning Y, Liu H. Testing and Confidence Intervals for High Dimensional Proportional Hazards Model. J R Stat Soc Series B Stat Methodol 2017; 79:1415-1437. [PMID: 37854943 PMCID: PMC10584375 DOI: 10.1111/rssb.12224] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This paper proposes a decorrelation-based approach to test hypotheses and construct confidence intervals for the low dimensional component of high dimensional proportional hazards models. Motivated by the geometric projection principle, we propose new decorrelated score, Wald and partial likelihood ratio statistics. Without assuming model selection consistency, we prove the asymptotic normality of these test statistics, establish their semiparametric optimality. We also develop new procedures for constructing pointwise confidence intervals for the baseline hazard function and baseline survival function. Thorough numerical results are provided to back up our theory.
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Affiliation(s)
- Ethan X. Fang
- Department of Operations Research and Financial Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Yang Ning
- Department of Operations Research and Financial Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Han Liu
- Department of Operations Research and Financial Engineering, Princeton University, Princeton, NJ 08544, USA
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Hotspots of MLV integration in the hematopoietic tumor genome. Oncogene 2016; 36:1169-1175. [PMID: 27721401 PMCID: PMC5340798 DOI: 10.1038/onc.2016.285] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 06/15/2016] [Accepted: 07/08/2016] [Indexed: 01/16/2023]
Abstract
Extensive research has been performed regarding the integration sites of murine leukemia retrovirus (MLV) for the identification of proto-oncogenes. To date, the overlap of mutations within specific oligonucleotides across different tumor genomes has been regarded as a rare event; however, a recent study of MLV integration into the oncogene Zfp521 suggested the existence of a hotspot oligonucleotide for MLV integration. In the current review, we discuss the hotspots of MLV integration into several genes: c-Myc, Stat5a and N-myc, as well as ZFP521, as examined in tumor genomes. From this, MLV integration convergence within specific oligonucleotides is not necessarily a rare event. This short review aims to promote re-consideration of MLV integration within the tumor genome, which involves both well-known and potentially newly identified and novel mechanisms and specifications.
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Tsuruyama T, Hiratsuka T, Aini W, Nakamura T. STAT5A Modulates Chemokine Receptor CCR6 Expression and Enhances Pre-B Cell Growth in a CCL20-Dependent Manner. J Cell Biochem 2016; 117:2630-42. [PMID: 27018255 DOI: 10.1002/jcb.25558] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 03/24/2016] [Indexed: 12/15/2022]
Abstract
Signal transducer and activator of transcription 5A (STAT5A) contributes to B-cell responses to cytokines through suppressor of cytokine signaling (Socs) genes in innate immunity. However, its direct roles in B-cell responses to chemokines are poorly understood. In this study, we examined the role of STAT5A in the innate immune response. We found that STAT5A upregulated the transcription of C-C motif receptor 6 (Ccr6) to induce responses to its ligand, CCL20. STAT5A transcriptional activity proceeded through binding to the interferon-γ activation site (GAS) element in the CCR6 promoter in the genome of pre-B cells. High levels of STAT5A and CCR6 increased CCL20-dependent colony growth of pre-B cells. In human B-lymphoblastic lymphoma with inflammation, STAT5A phosphorylation was correlated with CCR6 expression (P > 0.05 compared with that in cases without inflammation). In conclusion, our data supported our hypothesis that STAT5A enhanced the response of pre-B cells to CCL20 to promote their growth. J. Cell. Biochem. 117: 2630-2642, 2016. © 2016 Wiley Periodicals, Inc.
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MESH Headings
- Animals
- Apoptosis
- Blotting, Western
- Cell Proliferation
- Cells, Cultured
- Chemokine CCL20/genetics
- Chemokine CCL20/metabolism
- Cytokines/genetics
- Cytokines/metabolism
- Humans
- Immunoenzyme Techniques
- Inflammation/genetics
- Inflammation/metabolism
- Inflammation/pathology
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/metabolism
- Lymphoma, B-Cell/pathology
- Mice
- Phosphorylation
- Precursor Cells, B-Lymphoid/cytology
- Precursor Cells, B-Lymphoid/metabolism
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Receptors, CCR6/genetics
- Receptors, CCR6/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- STAT5 Transcription Factor/genetics
- STAT5 Transcription Factor/metabolism
- Signal Transduction
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Affiliation(s)
- Tatsuaki Tsuruyama
- Department of Diagnostic Pathology, Kyoto University Hospital, 54 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8397, Japan.
- Center for Anatomical, Pathological, Forensic Medical Research, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
| | - Takuya Hiratsuka
- Department of Pathology and Biology of Diseases, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Wulamujiang Aini
- Center for Anatomical, Pathological, Forensic Medical Research, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Takuro Nakamura
- Cancer Institute, Laboratory of Carcinogenesis, Ariake 3-8021, Koto-ku, Tokyo, 135-8550, Japan
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ZFP521 contributes to pre-B-cell lymphomagenesis through modulation of the pre-B-cell receptor signaling pathway. Oncogene 2015; 35:3227-38. [PMID: 26522721 DOI: 10.1038/onc.2015.385] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 08/10/2015] [Accepted: 08/14/2015] [Indexed: 11/08/2022]
Abstract
ZFP521 was previously identified as a putative gene involved in induction of B-cell lymphomagenesis. However, the contribution of ZFP521 to lymphomagenesis has not been confirmed. In this study, we sought to elucidate the role of ZFP521 in B-cell lymphomagenesis. To this end, we used a retroviral insertion method to show that ZFP521 was a target of mutagenesis in pre-B-lymphoblastic lymphoma cells. The pre-B-cell receptor (pre-BCR) signaling molecules BLNK, BTK and BANK1 were positively regulated by the ZFP521 gene, leading to enhancement of the pre-BCR signaling pathway. In addition, c-myc and c-jun were upregulated following activation of ZFP521. Stimulation of pre-BCR signaling using anti-Vpreb antibodies caused aberrant upregulation of c-myc and c-jun and of Ccnd3, which encodes cyclin D3, thereby inducing the growth of pre-B cells. Stimulation with Vpreb affected the growth of pre-B cells, and addition of interleukin (IL)-7 receptor exerted competitive effects on pre-B-cell growth. Knockdown of BTK and BANK1, targets of ZFP521, suppressed the effects of Vpreb stimulation on cell growth. Furthermore, in human lymphoblastic lymphoma, analogous to pre-B-cell lymphoma in mice, the expression of ZNF521, the homolog of ZFP521 in humans, was upregulated. In conclusion, our data showed that the ZFP521 gene comprehensively induced pre-B-cell lymphomagenesis by modulating the pre-B-cell receptor signaling pathway.
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Kaszynski RH, Akatsuka S, Hiratsuka T, Jin G, Ozeki M, Okuno T, Nakamura T, Manabe T, Takakuwa T, Hiai H, Toyokuni S, Tamaki K, Tsuruyama T. A quantitative trait locus responsible for inducing B-cell lymphoblastic lymphoma is a hotspot for microsatellite instability. Cancer Sci 2010; 101:800-5. [PMID: 20353532 PMCID: PMC11159001 DOI: 10.1111/j.1349-7006.2009.01437.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Revised: 11/02/2009] [Accepted: 11/04/2009] [Indexed: 01/16/2023] Open
Abstract
While the molecular mechanisms underlying microsatellite instability (MSI) have been exhaustively investigated, identifying the patterns of MSI distribution within diverse cancer genomes has remained an elusive issue. In the present study, we conducted genome-wide MSI screening in B-cell lymphoblastic lymphomas (B-LBL) which spontaneously develop in the SL/Kh strain of mice. Tumor samples harvested from 16 mice were investigated using a framework map consisting of 150 microsatellite markers spaced at increments of roughly 0.5-3.0 centimorgans, spanning the entirety of mouse chromosomes (mus musculus chromosomes [MMU]) 3-6. MMU3 contains a quantitative trait locus (QTL), Bomb1 (bone marrow pre-B1), known to induce an aberrant expansion of pre-B cells in bone marrow prior to the onset of B-LBL in SL/Kh mice. The remaining chromosomes were selected on the basis of those most closely resembling MMU3 in terms of total estimated length (maximum variance 10 Mb). MSI was confirmed at 2
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Affiliation(s)
- Richard H Kaszynski
- Department of Forensic Medicine and Molecular Pathology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Hiratsuka T, Tsuruyama T, Kaszynski R, Kometani K, Minato N, Nakamura T, Tamaki K, Hiai H. Bone marrow pre-B expansion by SL/Kh-Bomb1 locus: Not sufficient for lymphomagenesis. Leuk Res 2008; 32:309-14. [PMID: 17617450 DOI: 10.1016/j.leukres.2007.05.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2007] [Revised: 05/15/2007] [Accepted: 05/18/2007] [Indexed: 11/22/2022]
Abstract
The pre-B lymphoma in SL/Kh mice is a polygenic trait involving a number of host genes. In prelymphoma-stage bone marrow, transient pre-B cell expansion is induced by a host locus, Bomb1, and later followed by the emergence of a monoclonal population with a similar phenotype. To determine whether these pre-B cells represent precursors of lymphomas, we generated a congenic strain, NFS.SL/Kh-Bomb1 mice, by marker-assisted backcrossing to NFS. The congenic mice showed pre-B cell expansion, but pre-B lymphomas were not observed, even after 1 year of observation, irrespective of murine leukemia virus inoculation. Disturbed early B cell differentiation per se is not sufficient for SL/Kh lymphomagenesis.
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Affiliation(s)
- Takuya Hiratsuka
- Department of Pathology and Biology of Diseases, Kyoto University Graduate School of Medicine, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Hendriks RW, Kersseboom R. Involvement of SLP-65 and Btk in tumor suppression and malignant transformation of pre-B cells. Semin Immunol 2006; 18:67-76. [PMID: 16300960 DOI: 10.1016/j.smim.2005.10.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Signals from the precursor-B cell receptor (pre-BCR) are essential for selection and clonal expansion of pre-B cells that have performed productive immunoglobulin heavy chain V(D)J recombination. In the mouse, the downstream signaling molecules SLP-65 and Btk cooperate to limit proliferation and induce differentiation of pre-B cells, thereby acting as tumor suppressors to prevent pre-B cell leukemia. In contrast, recent observations in human BCR-ABL1(+) pre-B lymphoblastic leukemia cells demonstrate that Btk is constitutively phosphorylated and activated by the BCR-ABL1 fusion protein. As a result, activated Btk transmits survival signals that are essential for the transforming activity of oncogenic Abl tyrosine kinase.
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Affiliation(s)
- Rudi W Hendriks
- Department of Immunology, Erasmus MC Rotterdam, P.O. Box 1738, NL-3000 DR Rotterdam, The Netherlands.
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Warming S, Suzuki T, Yamaguchi TP, Jenkins NA, Copeland NG. Early B-cell factor-associated zinc-finger gene is a frequent target of retroviral integration in murine B-cell lymphomas. Oncogene 2004; 23:2727-31. [PMID: 15048087 DOI: 10.1038/sj.onc.1207452] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The early B-cell factor (EBF)-associated zinc-finger protein (EBFAZ) binds to and negatively regulates EBF, a basic helix-loop-helix transcription factor required for B-cell lineage commitment and development of the olfactory epithelium. It also binds to SMA- and MAD-related protein 1 (SMAD1) and SMAD4 in response to bone morphogenic protein 2 (BMP2) signaling. It is highly related to ecotropic viral integration site 3 (EVI3), a protein that, like EBFAZ, contains 30 Krüppel-like zinc-finger repeats. In previous studies, we showed that Evi3 is a frequent target of retroviral integration in AKXD27 B-cell lymphomas. Here, we show that EBFAZ is also a frequent target. Integrations at Ebfaz and Evi3 are mutually exclusive, suggesting that they function in the same tumor pathway. Lymphomas with integrations at Ebfaz or Evi3 express the pre-B-cell-specific marker immunoglobulin lambda chain 5, and contain immunoglobulin heavy-chain rearrangements, suggesting that they are blocked at an early B-cell stage. Unlike Evi3, which is expressed at low levels in normal B cells, or Ebfaz, which is not expressed in B cells, both genes are highly expressed following viral integration. Collectively, our results suggest that ectopic expression of Ebfaz can substitute for the upregulated expression of Evi3 in B-cell disease and highlight the importance of this gene family in hematopoietic cancer.
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Affiliation(s)
- Søren Warming
- Mouse Cancer Genetics Program, National Cancer Institute, Center for Cancer Research, West 7th Street at Fort Detrick, Frederick, MD 21702, USA
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