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Neelamraju Y, Gjini E, Chhangawala S, Fan H, He S, Jing CB, Nguyen AT, Prajapati S, Sheridan C, Houvras Y, Melnick A, Look AT, Garrett-Bakelman FE. Depletion of tet2 results in age-dependent changes in DNA methylation and gene expression in a zebrafish model of myelodysplastic syndrome. Front Hematol 2023; 2:1235170. [PMID: 37937078 PMCID: PMC10629367 DOI: 10.3389/frhem.2023.1235170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Introduction Myelodysplastic syndrome (MDS) is a heterogeneous group of clonal hematopoietic disorders characterized by ineffective hematopoiesis, cytopenias, and dysplasia. The gene encoding ten-eleven translocation 2 (tet2), a dioxygenase enzyme that catalyzes the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine, is a recurrently mutated tumor suppressor gene in MDS and other myeloid malignancies. Previously, we reported a stable zebrafish line with a loss-of-function mutation in the tet2 gene. The tet2m/m-mutant zebrafish developed a pre-MDS state with kidney marrow dysplasia, but normal circulating blood counts by 11 months of age and accompanying anemia, signifying the onset of MDS, by 24 months of age. Methods In the current study, we collected progenitor cells from the kidney marrows of the adult tet2m/m and tet2wt/wt fish at 4 and 15 months of age and conducted enhanced reduced representation of bisulfite sequencing (ERRBS) and bulk RNA-seq to measure changes in DNA methylation and gene expression of hematopoietic stem and progenitor cells (HSPCs). Results and discussion A global increase in DNA methylation of gene promoter regions and CpG islands was observed in tet2m/m HSPCs at 4 months of age when compared with the wild type. Furthermore, hypermethylated genes were significantly enriched for targets of SUZ12 and the metal-response-element-binding transcription factor 2 (MTF2)-involved in the polycomb repressive complex 2 (PRC2). However, between 4 and 15 months of age, we observed a paradoxical global decrease in DNA methylation in tet2m/m HSPCs. Gene expression analyses identified upregulation of genes associated with mTORC1 signaling and interferon gamma and alpha responses in tet2m/m HSPCs at 4 months of age when compared with the wild type. Downregulated genes in HSPCs of tet2-mutant fish at 4 months of age were enriched for cell cycle regulation, heme metabolism, and interleukin 2 (IL2)/signal transducer and activator of transcription 5 (STAT5) signaling, possibly related to increased self-renewal and clonal advantage in HSPCs with tet2 loss of function. Finally, there was an overall inverse correlation between overall increased promoter methylation and gene expression.
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Affiliation(s)
- Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Evisa Gjini
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | | | - Hao Fan
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Shuning He
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | | | - Ashley T. Nguyen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
| | - Subhash Prajapati
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Caroline Sheridan
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | | | - Ari Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - A. Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
| | - Francine E. Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
- Department of Medicine, University of Virginia, Charlottesville, VA, United States
- University of Virginia Cancer Center, Charlottesville, VA, United States
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2
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Rapaport F, Seier K, Neelamraju Y, Hassane D, Baslan T, Gildea DT, Haddox S, Lee T, Murdock HM, Sheridan C, Thurmond A, Wang L, Carroll M, Cripe LD, Fernandez H, Mason CE, Paietta E, Roboz GJ, Sun Z, Tallman MS, Zhang Y, Gönen M, Levine R, Melnick AM, Kleppe M, Garrett-Bakelman FE. Correction: Integrative analysis identifies an older female-linked AML patient group with better risk in ECOG-ACRIN Cancer Research Group's clinical trial E3999. Blood Cancer J 2023; 13:103. [PMID: 37407550 PMCID: PMC10322919 DOI: 10.1038/s41408-023-00862-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023] Open
Affiliation(s)
- Franck Rapaport
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Clinical and Translational Science, The Rockefeller University, New York, NY, USA
| | - Kenneth Seier
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Duane Hassane
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel T Gildea
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Samuel Haddox
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Tak Lee
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - H Moses Murdock
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Caroline Sheridan
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexis Thurmond
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Ling Wang
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Larry D Cripe
- Simon Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Hugo Fernandez
- Department of Malignant Hematology & Cellular Therapy, Moffitt Cancer Center, Tampa, FL, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, USA
| | | | - Gail J Roboz
- Weill Cornell Medicine and The New York Presbyterian Hospital, New York, NY, USA
| | - Zhuoxin Sun
- Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Yanming Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mithat Gönen
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ross Levine
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ari M Melnick
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Maria Kleppe
- Human Oncology and Pathogenesis Program, Molecular Cancer Medicine Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Department of Medicine, University of Virginia, Charlottesville, VA, USA.
- University of Virginia Cancer Center, Charlottesville, VA, USA.
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3
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Wang Z, Neelamraju Y, Meydan C, Dunham N, Gandara J, Lee T, Prajapati S, Rapaport F, Sheridan C, Zumbo P, Becker M, Bullinger L, Carroll M, D’Andrea R, Dillon R, Levine R, Mason CE, Melnick A, Neuberg D, Bekiranov S, Zang C, Garrett-Bakelman FE. Abstract 3155: Gene expression profiles reveal distinct regulatory activities of transcription factors GATA1 and TAL1 upon AML relapse. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
The purpose of this study is to identify key regulatory pathways that potentially drive abnormal gene expression program in relapsed Acute Myeloid Leukemia (AML) patients, by integrative computational analyses on multi-omics molecular profiles. Relapsed AML remains a clinical challenge. Epigenetic heterogeneity may contribute to transcriptional dysregulation and disease progression in AML. However, what specific transcriptional programs and potential regulatory mechanisms contribute to disease relapse are not yet well understood. To characterize the global transcriptional landscapes in relapsed AML, we integrated genomics data from two cohorts of matched diagnosis and relapse patient specimens. We identified 5,416 differentially expressed genes (DEGs) between diagnosis and relapse in Cohort I. Unsupervised clustering yielded three distinct DEG groups: group A, B and C genes that were predominantly (88%) down-regulated, divergently regulated, or predominantly (65%) up-regulated, respectively, upon relapse. The expression pattern of all DEGs separated the patients into two clusters, most robustly by Group B genes. Interestingly, the majority of DEGs did not associate with changes in gene promoter methylation. Similar patterns were observed in Cohort II. We used Binding Analysis for Regulation of Transcription (BART) to identify transcriptional regulators (TRs) that potentially regulated the DEGs not associated with DNA methylation changes, and assessed the differential expression of identified TRs during disease progression. PU.1 was identified as a potential TR for Group A genes and was down-regulated upon relapse. GATA1 and TAL1 were identified as regulating Group B genes and were up-regulated in patient cluster1 and down-regulated in cluster2, consistent with the expression pattern of Group B genes. RBBP5 was a top predicted TR for Group C genes and was up-regulated upon relapse. We next validated the potential functionality of those predicted factors. In NSG mice transplanted with a human AML specimen, TAL1 and GATA1 were downregulated in AML cells collected four weeks after chemotherapy treatment, and were inferred as TRs for the down-regulated genes, similar to the patient data. PU.1 was inferred as regulating the up-regulated genes. Furthermore, we found that the level of differential expression of TAL1, GATA1, and PU.1 in each patient specimen associated with the correlation of DEG profiles between the patient specimen and TR perturbation in human-derived hematopoietic cell lines. Our results support the possibility that in some AML patients, TRs with roles in hematopoiesis and leukemia might contribute to disease relapse. Further mechanistic studies deciphering the molecular and phenotypic events facilitated by these TRs will yield significant insight into disease biology and possible therapeutic targeting approaches in relapsed AML.
Citation Format: Zhenjia Wang, Yaseswini Neelamraju, Cem Meydan, Nicholas Dunham, Jorge Gandara, Tak Lee, Subhash Prajapati, Franck Rapaport, Caroline Sheridan, Paul Zumbo, Michael Becker, Lars Bullinger, Martin Carroll, Richard D’Andrea, Richard Dillon, Ross Levine, Christopher E. Mason, Ari Melnick, Donna Neuberg, Stefan Bekiranov, Chongzhi Zang, Francine E. Garrett-Bakelman. Gene expression profiles reveal distinct regulatory activities of transcription factors GATA1 and TAL1 upon AML relapse [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3155.
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Affiliation(s)
| | | | | | | | | | - Tak Lee
- 2Weill Cornell Medicine, New York, NY
| | | | | | | | | | | | | | | | - Richard D’Andrea
- 7University of South Australia and SA Pathology, Adelaide, Australia
| | | | - Ross Levine
- 3Memorial Sloan Kettering Cancer Center, New York, NY
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Barreyro L, Sampson AM, Ishikawa C, Hueneman KM, Choi K, Pujato MA, Chutipongtanate S, Wyder M, Haffey WD, O'Brien E, Wunderlich M, Ramesh V, Kolb EM, Meydan C, Neelamraju Y, Bolanos LC, Christie S, Smith MA, Niederkorn M, Muto T, Kesari S, Garrett-Bakelman FE, Bartholdy B, Will B, Weirauch MT, Mulloy JC, Gul Z, Medlin S, Kovall RA, Melnick AM, Perentesis JP, Greis KD, Nurmemmedov E, Seibel WL, Starczynowski DT. Blocking UBE2N abrogates oncogenic immune signaling in acute myeloid leukemia. Sci Transl Med 2022; 14:eabb7695. [PMID: 35263148 DOI: 10.1126/scitranslmed.abb7695] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Dysregulation of innate immune signaling pathways is implicated in various hematologic malignancies. However, these pathways have not been systematically examined in acute myeloid leukemia (AML). We report that AML hematopoietic stem and progenitor cells (HSPCs) exhibit a high frequency of dysregulated innate immune-related and inflammatory pathways, referred to as oncogenic immune signaling states. Through gene expression analyses and functional studies in human AML cell lines and patient-derived samples, we found that the ubiquitin-conjugating enzyme UBE2N is required for leukemic cell function in vitro and in vivo by maintaining oncogenic immune signaling states. It is known that the enzyme function of UBE2N can be inhibited by interfering with thioester formation between ubiquitin and the active site. We performed in silico structure-based and cellular-based screens and identified two related small-molecule inhibitors UC-764864/65 that targeted UBE2N at its active site. Using these small-molecule inhibitors as chemical probes, we further revealed the therapeutic efficacy of interfering with UBE2N function. This resulted in the blocking of ubiquitination of innate immune- and inflammatory-related substrates in human AML cell lines. Inhibition of UBE2N function disrupted oncogenic immune signaling by promoting cell death of leukemic HSPCs while sparing normal HSPCs in vitro. Moreover, baseline oncogenic immune signaling states in leukemic cells derived from discrete subsets of patients with AML exhibited a selective dependency on UBE2N function in vitro and in vivo. Our study reveals that interfering with UBE2N abrogates leukemic HSPC function and underscores the dependency of AML cells on UBE2N-dependent oncogenic immune signaling states.
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Affiliation(s)
- Laura Barreyro
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Avery M Sampson
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Chiharu Ishikawa
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kathleen M Hueneman
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mario A Pujato
- Center for Autoimmune Genetics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Somchai Chutipongtanate
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA.,Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Michael Wyder
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Wendy D Haffey
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Eric O'Brien
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Vighnesh Ramesh
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ellen M Kolb
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY, USA
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Lyndsey C Bolanos
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Susanne Christie
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Molly A Smith
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Madeline Niederkorn
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Tomoya Muto
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Santosh Kesari
- Saint John's Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.,Department of Medicine, University of Virginia, Charlottesville, VA, USA.,Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA.,University of Virginia Cancer Center, Charlottesville, VA, USA
| | - Boris Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genetics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Division of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - James C Mulloy
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Zartash Gul
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Stephen Medlin
- Department of Internal Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Rhett A Kovall
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ari M Melnick
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY, USA
| | - John P Perentesis
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kenneth D Greis
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
| | - Elmar Nurmemmedov
- Saint John's Cancer Institute at Providence St. John's Health Center, Santa Monica, CA, USA
| | - William L Seibel
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Daniel T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
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5
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Olson TL, Cheon H, Xing JC, Olson KC, Paila U, Hamele CE, Neelamraju Y, Shemo BC, Schmachtenberg M, Sundararaman SK, Toro MF, Keller CA, Farber EA, Onengut-Gumuscu S, Garrett-Bakelman FE, Hardison RC, Feith DJ, Ratan A, Loughran TP. Frequent somatic TET2 mutations in chronic NK-LGL leukemia with distinct patterns of cytopenias. Blood 2021; 138:662-673. [PMID: 33786584 PMCID: PMC8394905 DOI: 10.1182/blood.2020005831] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 03/30/2021] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic natural killer large granular lymphocyte (NK-LGL) leukemia, also referred to as chronic lymphoproliferative disorder of NK cells, is a rare disorder defined by prolonged expansion of clonal NK cells. Similar prevalence of STAT3 mutations in chronic T-LGL and NK-LGL leukemia is suggestive of common pathogenesis. We undertook whole-genome sequencing to identify mutations unique to NK-LGL leukemia. The results were analyzed to develop a resequencing panel that was applied to 58 patients. Phosphatidylinositol 3-kinase pathway gene mutations (PIK3CD/PIK3AP1) and TNFAIP3 mutations were seen in 5% and 10% of patients, respectively. TET2 was exceptional in that mutations were present in 16 (28%) of 58 patient samples, with evidence that TET2 mutations can be dominant and exclusive to the NK compartment. Reduced-representation bisulfite sequencing revealed that methylation patterns were significantly altered in TET2 mutant samples. The promoter of TET2 and that of PTPRD, a negative regulator of STAT3, were found to be methylated in additional cohort samples, largely confined to the TET2 mutant group. Mutations in STAT3 were observed in 19 (33%) of 58 patient samples, 7 of which had concurrent TET2 mutations. Thrombocytopenia and resistance to immunosuppressive agents were uniquely observed in those patients with only TET2 mutation (Games-Howell post hoc test, P = .0074; Fisher's exact test, P = .00466). Patients with STAT3 mutation, inclusive of those with TET2 comutation, had lower hematocrit, hemoglobin, and absolute neutrophil count compared with STAT3 wild-type patients (Welch's t test, P ≤ .015). We present the discovery of TET2 mutations in chronic NK-LGL leukemia and evidence that it identifies a unique molecular subtype.
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Affiliation(s)
- Thomas L Olson
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - HeeJin Cheon
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
- Medical Scientist Training Program, University of Virginia School of Medicine, Charlottesville, VA
| | - Jeffrey C Xing
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
- Medical Scientist Training Program, University of Virginia School of Medicine, Charlottesville, VA
| | - Kristine C Olson
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Umadevi Paila
- Center for Public Health Genomics, University of Virginia, Charlottesville; VA
| | - Cait E Hamele
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA
| | - Bryna C Shemo
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Matt Schmachtenberg
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Shriram K Sundararaman
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Mariella F Toro
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Cheryl A Keller
- Department of Biochemistry and Molecular Biology, Center for Computational Biology & Bioinformatics, The Pennsylvania State University, State College, PA; and
| | - Emily A Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville; VA
| | | | - Francine E Garrett-Bakelman
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Center for Computational Biology & Bioinformatics, The Pennsylvania State University, State College, PA; and
| | - David J Feith
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
| | - Aakrosh Ratan
- Center for Public Health Genomics, University of Virginia, Charlottesville; VA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA
| | - Thomas P Loughran
- University of Virginia Cancer Center, Charlottesville, VA
- Division of Hematology/Oncology, Department of Medicine, and
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6
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Rapaport F, Neelamraju Y, Baslan T, Hassane D, Gruszczynska A, Robert de Massy M, Farnoud N, Haddox S, Lee T, Medina-Martinez J, Sheridan C, Thurmond A, Becker M, Bekiranov S, Carroll M, Moses Murdock H, Valk PJM, Bullinger L, D'Andrea R, Lowe SW, Neuberg D, Levine RL, Melnick A, Garrett-Bakelman FE. Genomic and evolutionary portraits of disease relapse in acute myeloid leukemia. Leukemia 2021; 35:2688-2692. [PMID: 33580203 PMCID: PMC8357838 DOI: 10.1038/s41375-021-01153-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/23/2020] [Accepted: 01/22/2021] [Indexed: 11/12/2022]
Affiliation(s)
- Franck Rapaport
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Center for Clinical and Translational Science, The Rockefeller University, New York, NY, USA.,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Timour Baslan
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Duane Hassane
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Agata Gruszczynska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Marc Robert de Massy
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Noushin Farnoud
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samuel Haddox
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Tak Lee
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Juan Medina-Martinez
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Caroline Sheridan
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Alexis Thurmond
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Michael Becker
- Department of Medicine, University of Rochester, Rochester, NY, USA
| | - Stefan Bekiranov
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Heardly Moses Murdock
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Peter J M Valk
- Department of Hematology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Lars Bullinger
- Department of Internal Medicine III, University Hospital of Ulm, Ulm, Germany.,Department of Hematology, Oncology and Tumor Immunology, Charité University Medicine Berlin, Berlin, Germany
| | - Richard D'Andrea
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Scott W Lowe
- Cancer Biology and Genetics Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Donna Neuberg
- Department of Data Science, Dana Farber Cancer Institute, Boston, MA, USA
| | - Ross L Levine
- Molecular Cancer Medicine Service, Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ari Melnick
- Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA
| | - Francine E Garrett-Bakelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA. .,Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA. .,Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA. .,University of Virginia Cancer Center, Charlottesville, VA, USA.
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7
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Abshiru NA, Sikora JW, Camarillo JM, Morris JA, Compton PD, Lee T, Neelamraju Y, Haddox S, Sheridan C, Carroll M, Cripe LD, Tallman MS, Paietta EM, Melnick AM, Thomas PM, Garrett-Bakelman FE, Kelleher NL. Targeted detection and quantitation of histone modifications from 1,000 cells. PLoS One 2020; 15:e0240829. [PMID: 33104722 PMCID: PMC7588077 DOI: 10.1371/journal.pone.0240829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/02/2020] [Indexed: 01/30/2023] Open
Abstract
Histone post-translational modifications (PTMs) create a powerful regulatory mechanism for maintaining chromosomal integrity in cells. Histone acetylation and methylation, the most widely studied histone PTMs, act in concert with chromatin-associated proteins to control access to genetic information during transcription. Alterations in cellular histone PTMs have been linked to disease states and have crucial biomarker and therapeutic potential. Traditional bottom-up mass spectrometry of histones requires large numbers of cells, typically one million or more. However, for some cell subtype-specific studies, it is difficult or impossible to obtain such large numbers of cells and quantification of rare histone PTMs is often unachievable. An established targeted LC-MS/MS method was used to quantify the abundance of histone PTMs from cell lines and primary human specimens. Sample preparation was modified by omitting nuclear isolation and reducing the rounds of histone derivatization to improve detection of histone peptides down to 1,000 cells. In the current study, we developed and validated a quantitative LC-MS/MS approach tailored for a targeted histone assay of 75 histone peptides with as few as 10,000 cells. Furthermore, we were able to detect and quantify 61 histone peptides from just 1,000 primary human stem cells. Detection of 37 histone peptides was possible from 1,000 acute myeloid leukemia patient cells. We anticipate that this revised method can be used in many applications where achieving large cell numbers is challenging, including rare human cell populations.
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Affiliation(s)
- Nebiyu A. Abshiru
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Jacek W. Sikora
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Jeannie M. Camarillo
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Juliette A. Morris
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Philip D. Compton
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Tak Lee
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
| | - Samuel Haddox
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
| | - Caroline Sheridan
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Martin Carroll
- Division of Hematology and Oncology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States of America
| | - Larry D. Cripe
- Indiana University/Melvin and Bren Simon Cancer Center, Indianapolis, IN, United States of America
| | - Martin S. Tallman
- Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | | | - Ari M. Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
| | - Paul M. Thomas
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
| | - Francine E. Garrett-Bakelman
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States of America
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States of America
- Division of Hematology/Medical Oncology, Department of Medicine, University of Virginia, Charlottesville, VA, United States of America
- * E-mail: (FEGB); (NLK)
| | - Neil L. Kelleher
- Departments of Chemistry, Molecular Biosciences, and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, United States of America
- * E-mail: (FEGB); (NLK)
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8
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Gökmen-Polar Y, Neelamraju Y, Goswami CP, Gu Y, Gu X, Nallamothu G, Vieth E, Janga SC, Ryan M, Badve SS. Splicing factor ESRP1 controls ER-positive breast cancer by altering metabolic pathways. EMBO Rep 2019; 20:embr.201846078. [PMID: 30665944 DOI: 10.15252/embr.201846078] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 12/04/2018] [Accepted: 12/11/2018] [Indexed: 12/12/2022] Open
Abstract
The epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2) control the epithelial-to-mesenchymal transition (EMT) splicing program in cancer. However, their role in breast cancer recurrence is unclear. In this study, we report that high levels of ESRP1, but not ESRP2, are associated with poor prognosis in estrogen receptor positive (ER+) breast tumors. Knockdown of ESRP1 in endocrine-resistant breast cancer models decreases growth significantly and alters the EMT splicing signature, which we confirm using TCGA SpliceSeq data of ER+ BRCA tumors. However, these changes are not accompanied by the development of a mesenchymal phenotype or a change in key EMT-transcription factors. In tamoxifen-resistant cells, knockdown of ESRP1 affects lipid metabolism and oxidoreductase processes, resulting in the decreased expression of fatty acid synthase (FASN), stearoyl-CoA desaturase 1 (SCD1), and phosphoglycerate dehydrogenase (PHGDH) at both the mRNA and protein levels. Furthermore, ESRP1 knockdown increases the basal respiration and spare respiration capacity. This study reports a novel role for ESRP1 that could form the basis for the prevention of tamoxifen resistance in ER+ breast cancer.
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Affiliation(s)
- Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Chirayu P Goswami
- Department of Bioinformatics, Thomas Jefferson University Hospitals, Philadelphia, PA, USA
| | - Yuan Gu
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xiaoping Gu
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gouthami Nallamothu
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Edyta Vieth
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sarath C Janga
- Department of BioHealth Informatics, School of Informatics and Computing, IUPUI, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.,Centre for Computational Biology and Bioinformatics Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael Ryan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,In Silico Solutions, Falls Church, VA, USA
| | - Sunil S Badve
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA .,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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9
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Badve SS, Neelamraju Y, Goswami CP, Gu X, Nallamothu G, Gu Y, Vieth E, Janga SC, Ryan M, Gokmen-Polar Y. Abstract P5-04-03: Aggressiveness of epithelial cancers is independent of epithelial-to-mesenchymal transition. Cancer Res 2018. [DOI: 10.1158/1538-7445.sabcs17-p5-04-03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Epithelial-to-Mesenchymal Transition (EMT)is postulated to be an important step in cancer progression and controlled by multiple mechanisms including EMT transcription factors (EMT-TFs) and splicing factors such as Epithelial Splicing Regulatory Proteins (ESRP1 and ESRP2). We previously have shown that the expression of ESRP1 and ESRP2 have significantly elevated in cases with high Oncotype DX scores and in ERα-positive cells with acquired endocrine resistance (SABCS 2013). This study seeks to identify the role of EMT-TFs and ESRP1s in the determination of outcomes of patients with ER+ breast cancer.
Patients and Methods: The expression of EMT-TFs and ESRP1 was analyzed in the Affymetrix microarray and TCGA BRCA databases. Next, we generated genetically engineered knockdown models of ESRP1 to understand its functional role in endocrine resistance. We performed RNA-seq and MATS analysis to identify alternative splicing events (ASEs) between ESRP1 knockdown and control cell lines [(2C3 vs 2-control (LCC2 set) and 9C2 vs 9-control(LCC9 set)]. Validation of the ASEs was performed using a probe-based platform [Human Transcriptome Array 2.0 (HTA)] and TCGA SpliceSeq from breast tumors.
Results: High levels of ESRP1 mRNA, but not EMT-TFs, are associated with poor prognosis in human ER+ breast tumors (Affymetrix; P=2.8e-07 and TCGA; P=0.00011). Knockdown of ESRP1 in ER+ endocrine resistant breast cancer induced glandular differentiation, rather than mesenchymal features. This was associated with significant reduction in cell and tumor growth in mammary fat pad orthotopic xenograft mice models of LCC2 and LCC9. No alterations in EMT-TFs were observed in these cells. Transcriptome profiling of ESRP1 knockdown cells further revealed altered ASEs in EMT splicing gene signature, but not at the gene level. These alterations (SE-skipped exon) were further validated for ARHGEF11, ENAH, FNIP1, SCRIB, and SLK using probe based HTA platform for ESRP1 knockdown cells and TCGA-SpliceSeq ER+ BRCA tumors in ER+ ESRP1low versus ESRP1high breast tumors.
Conclusions: Our data demonstrates for the first time that high ESRP1 is associated with poor prognosis in ER+ breast cancer. Despite its involvement in regulation of EMT splicing signature, low levels (or knockdown) of ESRP1 were not associated with EMT phenotype in tumors or in endocrine-resistant ER+ cells. Taken together, our findings indicate that EMT is not important in determining prognosis in ER+ breast cancer and that ESRP1 exerts a different role in aggressive ER+ breast cancers.
Citation Format: Badve SS, Neelamraju Y, Goswami CP, Gu X, Nallamothu G, Gu Y, Vieth E, Janga SC, Ryan M, Gokmen-Polar Y. Aggressiveness of epithelial cancers is independent of epithelial-to-mesenchymal transition [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-04-03.
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Affiliation(s)
- SS Badve
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - Y Neelamraju
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - CP Goswami
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - X Gu
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - G Nallamothu
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - Y Gu
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - E Vieth
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - SC Janga
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - M Ryan
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
| | - Y Gokmen-Polar
- Pathology and Lab Medicine, Indiana University, Indianapolis, IN; School of Informatics and Computing, Indiana University, Indianapolis, IN; In Silico Solutions, Falls Church, VA
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10
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Abstract
RNA Binding Proteins (RBPs) are a class of post-transcriptional regulatory molecules which are increasingly documented to be dysfunctional in cancer genomes. However, our current understanding of these alterations is limited. Here, we delineate the mutational landscape of ∼1300 RBPs in ∼6000 cancer genomes. Our analysis revealed that RBPs have an average of ∼3 mutations per Mb across 26 cancer types. We identified 281 RBPs to be enriched for mutations (GEMs) in at least one cancer type. GEM RBPs were found to undergo frequent frameshift and inframe deletions as well as missense, nonsense and silent mutations when compared to those that are not enriched for mutations. Functional analysis of these RBPs revealed the enrichment of pathways associated with apoptosis, splicing and translation. Using the OncodriveFM framework, we also identified more than 200 candidate driver RBPs that were found to accumulate functionally impactful mutations in at least one cancer. Expression levels of 15% of these driver RBPs exhibited significant difference, when transcriptome groups with and without deleterious mutations were compared. Functional interaction network of the driver RBPs revealed the enrichment of spliceosomal machinery, suggesting a plausible mechanism for tumorogenesis while network analysis of the protein interactions between RBPs unambiguously revealed the higher degree, betweenness and closeness centrality for driver RBPs compared to non-drivers. Analysis to reveal cancer-specific Ribonucleoprotein (RNP) mutational hotspots showed extensive rewiring even among common drivers between cancer types. Knockdown experiments on pan-cancer drivers such as SF3B1 and PRPF8 in breast cancer cell lines, revealed cancer subtype specific functions like selective stem cell features, indicating a plausible means for RBPs to mediate cancer-specific phenotypes. Hence, this study would form a foundation to uncover the contribution of the mutational spectrum of RBPs in dysregulating the post-transcriptional regulatory networks in different cancer types.
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Affiliation(s)
- Yaseswini Neelamraju
- a Department of Bio Health Informatics, School of Informatics and Computing , Indiana University Purdue University , Indianapolis , Indiana , USA
| | - Abel Gonzalez-Perez
- b Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences , Universitat Pompeu Fabra , Barcelona , Spain
| | - Poornima Bhat-Nakshatri
- c Department of Surgery , Indiana University School of Medicine , Indianapolis , Indiana , USA
| | - Harikrishna Nakshatri
- c Department of Surgery , Indiana University School of Medicine , Indianapolis , Indiana , USA.,d Department of Biochemistry & Molecular Biology , Indiana University School of Medicine , Indianapolis , Indiana , USA.,e VA Roudebush Medical Center , Indianapolis , Indiana , USA
| | - Sarath Chandra Janga
- a Department of Bio Health Informatics, School of Informatics and Computing , Indiana University Purdue University , Indianapolis , Indiana , USA.,f Centre for Computational Biology and Bioinformatics , Indiana University School of Medicine , 5021 Health Information and Translational Sciences (HITS), Indianapolis , Indiana , USA.,g Department of Medical and Molecular Genetics , Indiana University School of Medicine , Medical Research and Library Building, Indianapolis , Indiana , USA
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11
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Gökmen-Polar Y, Neelamraju Y, Gu X, Nallamothu G, Janga SC, Badve S. Abstract 1097: Knockdown of splicing factor ESRP1 affects multiple splicing factors. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: Tissue-specific alternative splicing (AS) is an important mechanism for regulating gene expression. Epithelial Splicing Regulatory Proteins 1 and 2 (ESRP1 and ESRP2), two RNA-binding proteins (RBPs) that promote splicing, are potential candidates that contribute to breast cancer recurrence and resistance to therapies. In our prior studies, we have shown that ESRPs are associated with endocrine resistance. In this study, we seek to investigate the impact of the ESRP1 knockdown in endocrine resistant breast cancer cells. Methods: Expression of ESRP1 was analyzed in endocrine resistant-LCC2 and LCC9 cells. Knockdown of ESRP1 expression in LCC2 and LCC9 cells was achieved using lenti-viral based shRNA approach (Mission TRC human shRNA constructs, Sigma). We next performed paired-end RNA-sequencing of LCC2 and LCC9 cells transfected with control and two clones representative of shRNA knockdown (Illumina HiSeq platform, SeqWright Genomic Services) according to the manufacturer's instructions. After processing and quality check of raw FASTQ data (Illumina CASAVA, FASTQ and FASTX toolkits), reads were aligned, and quantified using bioinformatics software tools (Tophat/Cufflinks and Sailfish). Results: Expression of ESRP1 is significantly elevated in ERα-positive endocrine -resistant cells (LCC2 and LCC9 cells). ESRP1 knockdown was confirmed using qRT-PCR analysis in LCC2 cell lines (clone1 - 80% reduction and clone 3- 95% reduction) and in LCC9 cells (clone 2- 90% reduction and clone 3- 50% reduction). RNA-seq analysis identified 5153 differentially regulated genes between ESRP1 knockdown and control LCC2 cell lines. Of the 5153 genes, 1117 and 2109 genes were unique to clone 1 and clone 3, respectively, while 1927 genes were common in both clones. Targeted RNA-seq analysis also revealed that ESRP1 regulates the expression of several genes including other splicing factors. Furthermore, a functional enrichment analysis of these genes revealed a possible role of altering important pathways such as cell-cell adhesion and cell signaling. Additionally, it was observed that neither ESR1 nor any of its downstream genes were affected by the knockdown of ESRP1. This data was similar to that obtained in knockdown of LCC9 cells. Conclusions: ESRP1 regulates splicing of multiple genes in ER+ breast cancer. The process is independent of ER pathway. Targeting splicing could be a novel modality for treating endocrine therapy resistant breast cancer.
Citation Format: Yesim Gökmen-Polar, Yaseswini Neelamraju, Xiaoping Gu, Gouthami Nallamothu, Sarath C. Janga, Sunil Badve. Knockdown of splicing factor ESRP1 affects multiple splicing factors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1097. doi:10.1158/1538-7445.AM2015-1097
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Affiliation(s)
- Yesim Gökmen-Polar
- 1Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Yaseswini Neelamraju
- 2Department of Biohealth Informatics, School of Informatics and Computing, IUPUI, Indianapolis, IN
| | - Xiaoping Gu
- 1Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Gouthami Nallamothu
- 1Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Sarath C. Janga
- 2Department of Biohealth Informatics, School of Informatics and Computing, IUPUI, Indianapolis, IN
| | - Sunil Badve
- 1Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN
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12
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Abstract
RNA Binding Protein (RBP) Expression and Disease Dynamics database (READ DB) is a non-redundant, curated database of human RBPs. RBPs curated from different experimental studies are reported with their annotation, tissue-wide RNA and protein expression levels, evolutionary conservation, disease associations, protein-protein interactions, microRNA predictions, their known RNA recognition sequence motifs as well as predicted binding targets and associated functional themes, providing a one stop portal for understanding the expression, evolutionary trajectories and disease dynamics of RBPs in the context of post-transcriptional regulatory networks.
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Affiliation(s)
- Seyedsasan Hashemikhabir
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN, 46202, USA
| | - Yaseswini Neelamraju
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN, 46202, USA
| | - Sarath Chandra Janga
- Department of Biohealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN, 46202, USA, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN, 46202, USA, and Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN, 46202, USA
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13
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Neelamraju Y, Hashemikhabir S, Janga SC. The human RBPome: from genes and proteins to human disease. J Proteomics 2015; 127:61-70. [PMID: 25982388 DOI: 10.1016/j.jprot.2015.04.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Revised: 04/07/2015] [Accepted: 04/28/2015] [Indexed: 12/29/2022]
Abstract
RNA binding proteins (RBPs) play a central role in mediating post transcriptional regulation of genes. However less is understood about them and their regulatory mechanisms. In this study, we construct a catalogue of 1344 experimentally confirmed RBPs. The domain architecture of RBPs enabled us to classify them into three groups - Classical (29%), Non-classical (19%) and unclassified (52%). A higher percentage of proteins with unclassified domains reveals the presence of various uncharacterised motifs that can potentially bind RNA. RBPs were found to be highly disordered compared to Non-RBPs (p<2.2e-16, Fisher's exact test), suggestive of a dynamic regulatory role of RBPs in cellular signalling and homeostasis. Evolutionary analysis in 62 different species showed that RBPs are highly conserved compared to Non-RBPs (p<2.2e-16, Wilcox-test), reflecting the conservation of various biological processes like mRNA splicing and ribosome biogenesis. The expression patterns of RBPs from human proteome map revealed that ~40% of them are ubiquitously expressed and ~60% are tissue-specific. RBPs were also seen to be highly associated with several neurological disorders, cancer and inflammatory diseases. Anatomical contexts like B cells, T-cells, foetal liver and foetal brain were found to be strongly enriched for RBPs, implying a prominent role of RBPs in immune responses and different developmental stages. The catalogue and meta-analysis presented here should form a foundation for furthering our understanding of RBPs and the cellular networks they control, in years to come. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Yaseswini Neelamraju
- Department of Biohealth Informatics School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Seyedsasan Hashemikhabir
- Department of Biohealth Informatics School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States
| | - Sarath Chandra Janga
- Department of Biohealth Informatics School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, IN 46202, United States; Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, IN 46202, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, IN 46202, United States.
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14
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Gokmen-Polar Y, Neelamraju Y, Goswami CP, Nakshatri H, Janga SC, Badve S. Abstract P3-05-20: ESRP1 adds sp(l)ice to endocrine resistance. Cancer Res 2015. [DOI: 10.1158/1538-7445.sabcs14-p3-05-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction:
De novo or acquired resistance to endocrine therapy limits its utility in a significant number of estrogen receptor (ER) breast cancers. An increasing number of molecular assays predict the likelihood of distant recurrence in tamoxifen-treated patients with node-negative, ER+ breast cancer. However, these do not provide the mechanistic basis for endocrine resistance. It is crucial to identify novel targets and improve the success of endocrine therapies. We previously shown that epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2), RNA binding proteins that promote splicing, are significantly elevated in cases with high Oncotype DX scores (innate resistance) and in ERα-positive cells with acquired tamoxifen resistance (MCF-7 LCC2 cells) and fulvestrant and tamoxifen resistance (MCF-7/LCC9 cells). The aim of this study was to investigate the ESRP1/ESRP2-regulated alternative splicing events leading to innate and acquired endocrine resistance.
Methods:
A combinatorial bioinformatics approach was employed to identify genes altered through alternative splicing by ESRP1/ESRP2 in endocrine resistance. Briefly, genes with ESRP1/ESRP2 motifs were screened in the human genome. This data was integrated with tamoxifen-treated datasets, and filtered using protein-protein interactions (PPI; BIOGRID) and clinical outcome (KM plotter. Potential target gene transcripts were further narrowed down using an algorithm based on motif binding location and the Cancer Genome Atlas (TCGA) breast cancer datasets with low and high ESRP1 cases. The alternative transcripts were further validated using splice variant specific-custom qRT-PCR in low and high RS Oncotype cases as surrogate for endocrine sensitivity and resistance.
Results:
Motif analysis in combination with tamoxifen-treated datasets identified 2212 differentially expressed genes. Further collective analysis of number of PPI (>50) and survival data from KM plotter (P<0.001) narrowed down 79 candidate genes that are associated with tamoxifen resistance. TCGA data confirmed presence of distinct transcripts (splicing variants) based on ESPR1 expression levels. Splice specific RT-PCR confirmed alternative splicing events involving cycle related genes such as AURKA, FZR1, and MDM2 in low ESRP1 (and low RS) and high ESRP1 (high RS) cases.
Conclusion:
ESRP1/ESRP2 by inducing alternative splicing play an important role in tamoxifen resistance and recurrence of ER+ breast cancer. Targeting alternative splicing may offer novel avenues for combating endocrine-resistance in breast cancer.
Citation Format: Yesim Gokmen-Polar, Yaseswini Neelamraju, Chirayu Pankaj Goswami, Harikrishna Nakshatri, Sarath Chandra Janga, Sunil Badve. ESRP1 adds sp(l)ice to endocrine resistance [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P3-05-20.
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15
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Chaturvedi P, Neelamraju Y, Arif W, Kalsotra A, Janga SC. Uncovering RNA binding proteins associated with age and gender during liver maturation. Sci Rep 2015; 5:9512. [PMID: 25824884 PMCID: PMC4379467 DOI: 10.1038/srep09512] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/09/2015] [Indexed: 11/09/2022] Open
Abstract
In the present study, we perform an association analysis focusing on the expression changes of 1344 RNA Binding proteins (RBPs) as a function of age and gender in human liver. We identify 88 and 45 RBPs to be significantly associated with age and gender respectively. Experimental verification of several of the predicted associations in mice confirmed our findings. Our results suggest that a small fraction of the gender-associated RBPs (~40%) are expressed higher in males than females. Altogether, these observations show that several of these RBPs are important and conserved regulators in maintaining liver function. Further analysis of the protein interaction network of RBPs associated with age and gender based on the centrality measures like degree, betweenness and closeness revealed that several of these RBPs might be prominent players in aging liver and impart gender specific alterations in gene expression via the formation of protein complexes. Indeed, both age and gender-associated RBPs in liver were found to show significantly higher clustering coefficients and network centrality measures compared to non-associated RBPs. The compendium of RBPs and this study will help us gain insight into the role of post-transcriptional regulatory molecules in aging and gender specific expression of genes.
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Affiliation(s)
- Praneet Chaturvedi
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202
| | - Yaseswini Neelamraju
- Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202
| | - Waqar Arif
- Departments of Biochemistry and Medical Biochemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - Auinash Kalsotra
- Departments of Biochemistry and Medical Biochemistry, University of Illinois, Urbana-Champaign, Illinois 61801, USA
| | - Sarath Chandra Janga
- 1] Department of BioHealth Informatics, School of Informatics and Computing, Indiana University Purdue University, 719 Indiana Ave Ste 319, Walker Plaza Building, Indianapolis, Indiana 46202 [2] Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 5021 Health Information and Translational Sciences (HITS), 410 West 10th Street, Indianapolis, Indiana, 46202 [3] Department of Medical and Molecular Genetics, Indiana University School of Medicine, Medical Research and Library Building, 975 West Walnut Street, Indianapolis, Indiana, 46202
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Gökmen-Polar Y, Vladislav IT, Neelamraju Y, Janga SC, Badve S. Prognostic impact of HOTAIR expression is restricted to ER-negative breast cancers. Sci Rep 2015; 5:8765. [PMID: 25739705 PMCID: PMC4350112 DOI: 10.1038/srep08765] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/27/2015] [Indexed: 12/26/2022] Open
Abstract
Expression of HOX transcript antisense intergenic RNA (HOTAIR), a large intergenic noncoding RNA (lincRNA), has been described as a metastases-associated lincRNA in various cancers including breast, liver and colon cancer cancers. We sought to determine if expression of HOTAIR could be used as a surrogate for assessing nodal metastases and evaluated RNA in situ hybridization (RNA-ISH) assay in a tissue microarray constructed from 133 breast cancer patients. The prognostic value of HOTAIR was further validated in large cohorts using The Cancer Genome Atlas (TCGA) breast cancer subjects. RNA-ISH analysis was successful in 94 cases (17% cases scored 0, 32.9% scored 1, 30.8% scored 2, and 19.1% scored 3). The expression of HOTAIR did not correlate with nodal metastasis regardless of the scoring intensity or with other study parameters (age, tumor size and grade, expression status). Further analysis of TCGA dataset showed that HOTAIR expression was lower in ductal carcinomas but higher in ER-negative tumors. Overexpression of HOTAIR was not associated with nodal metastases or prognosis in ER-positive patients. Its function as a poor prognostic indicator in ER-negative patients was restricted to node-positive patients. HOTAIR appears to be a marker for lymphatic metastases rather than hematogenous metastases in ER-negative patients.
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Affiliation(s)
- Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - I Tudor Vladislav
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN
| | - Yaseswini Neelamraju
- Department of Biohealth Informatics, School of Informatics and Computing, IUPUI, Indianapolis, IN
| | - Sarath C Janga
- Department of Biohealth Informatics, School of Informatics and Computing, IUPUI, Indianapolis, IN
| | - Sunil Badve
- 1] Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN [2] Department of Medicine, Indiana University School of Medicine, Indianapolis, IN [3] Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN
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