1
|
Kuo PY, Leshchenko VV, Fazzari MJ, Perumal D, Gellen T, He T, Iqbal J, Baumgartner-Wennerholm S, Nygren L, Zhang F, Zhang W, Suh KS, Goy A, Yang DT, Chan WC, Kahl BS, Verma AK, Gascoyne RD, Kimby E, Sander B, Ye BH, Melnick AM, Parekh S. High-resolution chromatin immunoprecipitation (ChIP) sequencing reveals novel binding targets and prognostic role for SOX11 in mantle cell lymphoma. Oncogene 2014; 34:1231-40. [PMID: 24681958 DOI: 10.1038/onc.2014.44] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 01/07/2014] [Accepted: 01/19/2014] [Indexed: 12/18/2022]
Abstract
Sex determining region Y-box 11 (SOX11) expression is specific for mantle cell lymphoma (MCL) as compared with other non-Hodgkin's lymphomas. However, the function and direct-binding targets of SOX11 in MCL are largely unknown. We used high-resolution chromatin immunoprecipitation sequencing to identify the direct target genes of SOX11 in a genome-wide, unbiased manner and elucidate its functional significance. Pathway analysis identified WNT, PKA and TGF-beta signaling pathways as significantly enriched by SOX11-target genes. Quantitative chromatin immunoprecipitation sequencing and promoter reporter assays confirmed that SOX11 directly binds to individual genes and modulates their transcription activities in these pathways in MCL. Functional studies using RNA interference demonstrate that SOX11 directly regulates WNT in MCL. We analyzed SOX11 expression in three independent well-annotated tissue microarrays from the University of Wisconsin (UW), Karolinska Institute and British Columbia Cancer Agency. Our findings suggest that high SOX11 expression is associated with improved survival in a subset of MCL patients, particularly those treated with intensive chemotherapy. Transcriptional regulation of WNT and other biological pathways affected by SOX11-target genes may help explain the impact of SOX11 expression on patient outcomes.
Collapse
Affiliation(s)
- P-Y Kuo
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - V V Leshchenko
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M J Fazzari
- 1] Department of Population Health, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA [2] Department of Genetics, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA
| | - D Perumal
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - T Gellen
- Albert Einstein Cancer Center, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA
| | - T He
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - J Iqbal
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - S Baumgartner-Wennerholm
- Department of Medicine, Center for Haematology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - L Nygren
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - F Zhang
- Bioinformatics Laboratory, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - W Zhang
- Bioinformatics Laboratory, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - K S Suh
- Genomics and Biomarkers Program, John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, USA
| | - A Goy
- Genomics and Biomarkers Program, John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, USA
| | - D T Yang
- Department of Pathology, School of Medicine and Public Health, University of Wisconsin, Madison, WI, USA
| | - W-C Chan
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - B S Kahl
- Department of Medicine, School of Medicine and Public Health, and The UW Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - A K Verma
- Albert Einstein Cancer Center, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA
| | - R D Gascoyne
- Department of Pathology and Experimental Therapeutics, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - E Kimby
- Department of Medicine, Center for Haematology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - B Sander
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - B H Ye
- Department of Cell Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY, USA
| | - A M Melnick
- 1] Hematology and Oncology Division, Weill Cornell Medical College, New York, NY, USA [2] Department of Pharmacology, Weill Cornell Medical College, New York, NY, USA
| | - S Parekh
- Division of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
3
|
Islam TC, Asplund AC, Lindvall JM, Nygren L, Liden J, Kimby E, Christensson B, Smith CIE, Sander B. High level of cannabinoid receptor 1, absence of regulator of G protein signalling 13 and differential expression of Cyclin D1 in mantle cell lymphoma. Leukemia 2003; 17:1880-90. [PMID: 12970790 DOI: 10.1038/sj.leu.2403057] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mantle cell lymphoma (MCL) is a moderately aggressive B-cell lymphoma that responds poorly to currently used therapeutic protocols. In order to identify tumour characteristics that improve the understanding of biology of MCL, analysis of oligonucleotide microarrays were used to define specific gene expression profiles. Biopsy samples of MCL cases were compared to reactive lymphoid tissue. Among genes differentially expressed in MCL were genes that are involved in the regulation of proliferation, cell signalling, adhesion and homing. Furthermore, some genes with previously unknown function, such as C11orf32, C2orf10, TBC1D9 and ABCA6 were found to be differentially expressed in MCL compared to reactive lymphoid tissue. Of special interest was the high expression of the cannabinoid receptor 1 (CB1) gene in all MCL cases analysed. These results were further confirmed at the cellular and protein level by immunocytochemical staining and immunoblotting of MCL cells. Furthermore, there was a reduced expression of a regulator of G protein signalling, RGS13 in all MCLs, with a complete absence in the majority of cases while present in control lymphoid tissue. These results were further confirmed by PCR. Sequencing of the RGS13 gene revealed changes suggesting polymorphisms, indicating that downregulation of the expression of RGS13 is not related to mutations, but may serve as a new specific marker for MCL. Moreover, comparison between individual cases of MCL, revealed that the CCND1 gene appears to be differently expressed in MCL cases with high vs low proliferative activity.
Collapse
MESH Headings
- Adolescent
- Adult
- Aged
- Burkitt Lymphoma/genetics
- Burkitt Lymphoma/metabolism
- Burkitt Lymphoma/pathology
- Case-Control Studies
- Cell Division
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Child
- Cyclin D1/genetics
- Cyclin D1/metabolism
- DNA, Neoplasm/analysis
- DNA, Neoplasm/genetics
- Down-Regulation
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, B-Cell/genetics
- Leukemia, B-Cell/metabolism
- Leukemia, B-Cell/pathology
- Lymphoma, Mantle-Cell/genetics
- Lymphoma, Mantle-Cell/metabolism
- Lymphoma, Mantle-Cell/pathology
- Male
- Middle Aged
- Neoplasm Proteins/genetics
- Neoplasm Proteins/metabolism
- Oligonucleotide Array Sequence Analysis
- RGS Proteins/genetics
- RGS Proteins/metabolism
- RNA, Messenger/analysis
- RNA, Neoplasm/genetics
- Receptors, Cannabinoid
- Receptors, Drug/genetics
- Receptors, Drug/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
Collapse
Affiliation(s)
- T C Islam
- Clinical Research Center, Karolinska Institutet, Huddinge University Hospital, Stockholm, Sweden
| | | | | | | | | | | | | | | | | |
Collapse
|