1
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Luchetti A, Forni G, Martelossi J, Savojardo C, Martelli PL, Casadio R, Skaist AM, Wheelan SJ, Mantovani B. Comparative genomics of tadpole shrimps (Crustacea, Branchiopoda, Notostraca): Dynamic genome evolution against the backdrop of morphological stasis. Genomics 2021; 113:4163-4172. [PMID: 34748900 DOI: 10.1016/j.ygeno.2021.11.001] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 12/21/2022]
Abstract
This analysis presents five genome assemblies of four Notostraca taxa. Notostraca origin dates to the Permian/Upper Devonian and the extant forms show a striking morphological similarity to fossil taxa. The comparison of sequenced genomes with other Branchiopoda genomes shows that, despite the morphological stasis, Notostraca share a dynamic genome evolution with high turnover for gene families' expansion/contraction and a transposable elements content comparable to other branchiopods. While Notostraca substitutions rate appears similar or lower in comparison to other branchiopods, a subset of genes shows a faster evolutionary pace, highlighting the difficulty of generalizing about genomic stasis versus dynamism. Moreover, we found that the variation of Triops cancriformis transposable elements content appeared linked to reproductive strategies, in line with theoretical expectations. Overall, besides providing new genomic resources for the study of these organisms, which appear relevant for their ecology and evolution, we also confirmed the decoupling of morphological and molecular evolution.
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Affiliation(s)
- Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy.
| | - Giobbe Forni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Jacopo Martelossi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Castrense Savojardo
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Pier Luigi Martelli
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Pharmacy and Biotechnology, University of Bologna, Italy
| | - Alyza M Skaist
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sarah J Wheelan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bologna, Italy
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2
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Pham MT, Gupta H, Gupta A, Vaghasia A, Skaist AM, Garrison MA, Chikamarne R, Wheelan SJ, Nelson WG, Yegnasubramanian S. Abstract 2198: Allelic phasing of genomic alterations through linked read whole genome sequencing in human prostate cancer cell lines. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2198] [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
Prostate cancer research has relied on a limited number of prostate cancer cell lines despite decades of effort in establishing them from human prostate cancers. These cell lines thus represent precious resources for in vitro and in vivo preclinical studies of prostate cancer and have fueled many advances in the field. While there has been tremendous effort in characterizing their molecular profiles and genomic features, comprehensive whole genome sequencing with allelic phasing of genomic alterations has not been undertaken to date. Here, we utilized powerful whole genome linked-read sequencing of high molecular weight DNA (>60Kbp) from eight common prostate cancer cell lines as well as four castrate resistant (CR) subclones derived from three of those cell lines. Long range information enabled assembly of mutations (single nucleotide variants-SNVs and small indels) and structural variants (SVs) across the genome into large phased blocks. This allowed accounting of multiple mutations within a given gene to assess whether they were present on a single allele, or on opposite alleles, to assess the “allelic status” of phased mutations. Using this phased mutational analysis, we found that in cell lines with microsatellite instability (MSI; LNCaP, LAPC4, DU145, CWR22Rv1), 10-20% of a priori defined driver genes are inactivated by at least two heterozygous mutations on opposite alleles. Overall, MSI cell lines had higher levels of mutations and fewer SVs than those that were microsatellite stable (MSS; PC3, VCaP). The phased SV analysis allowed identification of complex rearrangement chains consistent with chromothripsis (PC3, DU145) and chromoplexy (VCAP, LnCAP-C42b), including reconstruction of the complex chained TMPRSS2-ERG rearrangement in VCaP. Additionally, comparison of parental and CR subclones revealed previously known as well as several novel genomic alterations that were associated with the CR subclones, including chromosome 8 amplification (in LNCaP-Abl and LAPC4-CR), further androgen receptor amplification amongst a host of increased complex SVs (in VCAP-CR), SWI/SNF mutations and increased complex SVs (in LNCAP-C42b), CDK12 biallelic loss and numerous tandem duplications (in LAPC4-CR). This study therefore comprehensively characterizes allelically phased genomic alterations in the commonly used prostate cancer cell lines and provides a useful resource for future cancer research.
Citation Format: Minh-Tam Pham, Harshath Gupta, Anuj Gupta, Ajay Vaghasia, Alyza M. Skaist, McKinzie A. Garrison, Roshan Chikamarne, Sarah J. Wheelan, William G. Nelson, Srinivasan Yegnasubramanian. Allelic phasing of genomic alterations through linked read whole genome sequencing in human prostate cancer cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2198.
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Affiliation(s)
| | | | - Anuj Gupta
- Johns Hopkins School of Medicine, Baltimore, MD
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3
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Freeman ZT, Nirschl TR, Hovelson DH, Johnston RJ, Engelhardt JJ, Selby MJ, Kochel CM, Lan RY, Zhai J, Ghasemzadeh A, Gupta A, Skaist AM, Wheelan SJ, Jiang H, Pearson AT, Snyder LA, Korman AJ, Tomlins SA, Yegnasubramanian S, Drake CG. A conserved intratumoral regulatory T cell signature identifies 4-1BB as a pan-cancer target. J Clin Invest 2020; 130:1405-1416. [PMID: 32015231 DOI: 10.1172/jci128672] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [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: 03/11/2019] [Accepted: 11/13/2019] [Indexed: 12/19/2022] Open
Abstract
Despite advancements in targeting the immune checkpoints program cell death protein 1 (PD-1), programmed death ligand 1 (PD-L1), and cytotoxic T lymphocyte-associated protein 4 (CTLA-4) for cancer immunotherapy, a large number of patients and cancer types remain unresponsive. Current immunotherapies focus on modulating an antitumor immune response by directly or indirectly expanding antitumor CD8 T cells. A complementary strategy might involve inhibition of Tregs that otherwise suppress antitumor immune responses. Here, we sought to identify functional immune molecules preferentially expressed on tumor-infiltrating Tregs. Using genome-wide RNA-Seq analysis of purified Tregs sorted from multiple human cancer types, we identified a conserved Treg immune checkpoint signature. Using immunocompetent murine tumor models, we found that antibody-mediated depletion of 4-1BB-expressing cells (4-1BB is also known as TNFRSF9 or CD137) decreased tumor growth without negatively affecting CD8 T cell function. Furthermore, we found that the immune checkpoint 4-1BB had a high selectivity for human tumor Tregs and was associated with worse survival outcomes in patients with multiple tumor types. Thus, antibody-mediated depletion of 4-1BB-expressing Tregs represents a strategy with potential activity across cancer types.
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Affiliation(s)
- Zachary T Freeman
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Unit for Laboratory Animal Medicine, Medical School.,Rogel Cancer Center, and
| | - Thomas R Nirschl
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Daniel H Hovelson
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | | | | | - Mark J Selby
- Bristol-Myers Squibb, Redwood City, California, USA
| | - Christina M Kochel
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ruth Y Lan
- Bristol-Myers Squibb, Redwood City, California, USA
| | - Jingyi Zhai
- Department of Biostatistics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Ali Ghasemzadeh
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Anuj Gupta
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Alyza M Skaist
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sarah J Wheelan
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hui Jiang
- Rogel Cancer Center, and.,Department of Biostatistics, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Alexander T Pearson
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Linda A Snyder
- Oncology Discovery, Janssen R&D, Spring House, Pennsylvania, USA
| | | | - Scott A Tomlins
- Rogel Cancer Center, and.,Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Michigan Center for Translational Pathology, Department of Pathology, and.,Department of Urology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Srinivasan Yegnasubramanian
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Charles G Drake
- Department of Oncology and.,Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA.,Division of Hematology and Oncology, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, New York, USA
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4
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Jackson CM, Dinalankara W, Choi J, Nirschl TR, Kochel CM, Pant A, Routkevitch D, Saleh L, Jackson C, Skaist AM, Gupta A, Snyder LA, Schaeffer EM, Ross AE, Carter B, Allaf ME, Bivalacqua TJ, DeMarzo AM, Weingart JD, Bettegowda C, Brem H, Pardoll DM, Marchionni L, Drake CG, Lim M. Abstract A32: Characterizing patterns of cytokine coexpression with immune checkpoint markers in CD4 and CD8 tumor-infiltrating lymphocytes. Cancer Immunol Res 2020. [DOI: 10.1158/2326-6074.tumimm19-a32] [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
In recent years, immunotherapy has become one of the most exciting and promising avenues to cancer treatment. Treatment with immune checkpoint inhibitors has managed to produce long-term remission of solid tumors in many patients. However, patients who respond well to such treatment are often a minority; this is particularly the case with some cancers such as renal cell carcinoma, non-small cell lung cancer, and glioblastoma, where many patients either derive no benefit or only a short-term benefit. In this analysis, we examined gene expression data from RNA sequencing experiments that compared tumor-infiltrating lymphocytes (TIL) with paired circulating lymphocytes from patients with renal cell carcinoma (RCC), bladder cancer (BLCA), prostate cancer (PRAD), and glioblastoma (GBM). Our analysis helped to characterize global CD4 and CD8 TIL gene expression patterns among these four cohorts. Further, using the expression profiles for known immune checkpoint markers PD-1, TIM-3, and LAG-3 in CD8 cells, we dichotomized the patient samples into potential checkpoint inhibitor responder and nonresponder groups. This model was then used to identify other genes that are associated with CD8 TIL exhaustion, which may lead to the identification of cytokines useful in discovering specific therapeutic targets.
Citation Format: Christopher M. Jackson, Wikum Dinalankara, John Choi, Thomas R. Nirschl, Christina M. Kochel, Ayush Pant, Denis Routkevitch, Laura Saleh, Christina Jackson, Alyza M. Skaist, Anuj Gupta, Linda A. Snyder, Edward M. Schaeffer, Ashley E. Ross, Ballentine Carter, Mohamad E. Allaf, Trinity J. Bivalacqua, Angelo M. DeMarzo, Jon D. Weingart, Chetan Bettegowda, Henry Brem, Drew M. Pardoll, Luigi Marchionni, Charles G. Drake, Michael Lim. Characterizing patterns of cytokine coexpression with immune checkpoint markers in CD4 and CD8 tumor-infiltrating lymphocytes [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2019 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(3 Suppl):Abstract nr A32.
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Affiliation(s)
| | | | - John Choi
- 1Johns Hopkins University School of Medicine, Baltimore, MD,
| | | | | | - Ayush Pant
- 1Johns Hopkins University School of Medicine, Baltimore, MD,
| | | | - Laura Saleh
- 1Johns Hopkins University School of Medicine, Baltimore, MD,
| | | | - Alyza M. Skaist
- 1Johns Hopkins University School of Medicine, Baltimore, MD,
| | - Anuj Gupta
- 1Johns Hopkins University School of Medicine, Baltimore, MD,
| | | | | | - Ashley E. Ross
- 1Johns Hopkins University School of Medicine, Baltimore, MD,
| | | | | | | | | | - Jon D. Weingart
- 1Johns Hopkins University School of Medicine, Baltimore, MD,
| | | | - Henry Brem
- 1Johns Hopkins University School of Medicine, Baltimore, MD,
| | - Drew M. Pardoll
- 1Johns Hopkins University School of Medicine, Baltimore, MD,
| | | | | | - Michael Lim
- 1Johns Hopkins University School of Medicine, Baltimore, MD,
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5
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Luchetti A, Forni G, Skaist AM, Wheelan SJ, Mantovani B. Mitochondrial genome diversity and evolution in Branchiopoda (Crustacea). Zoological Lett 2019; 5:15. [PMID: 31149346 PMCID: PMC6537178 DOI: 10.1186/s40851-019-0131-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/19/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The crustacean class Branchiopoda includes fairy shrimps, clam shrimps, tadpole shrimps, and water fleas. Branchiopods, which are well known for their great variety of reproductive strategies, date back to the Cambrian and extant taxa can be mainly found in freshwater habitats, also including ephemeral ponds. Mitochondrial genomes of the notostracan taxa Lepidurus apus lubbocki (Italy), L. arcticus (Iceland) and Triops cancriformis (an Italian and a Spanish population) are here characterized for the first time and analyzed together with available branchiopod mitogenomes. RESULTS Overall, branchiopod mitogenomes share the basic structure congruent with the ancestral Pancrustacea model. On the other hand, rearrangements involving tRNAs and the control region are observed among analyzed taxa. Remarkably, an unassigned region in the L. apus lubbocki mitogenome showed a chimeric structure, likely resulting from a non-homologous recombination event between the two flanking trnC and trnY genes. Notably, Anostraca and Onychocaudata mitogenomes showed increased GC content compared to both Notostraca and the common ancestor, and a significantly higher substitution rate, which does not correlate with selective pressures, as suggested by dN/dS values. CONCLUSIONS Branchiopod mitogenomes appear rather well-conserved, although gene rearrangements have occurred. For the first time, it is reported a putative non-homologous recombination event involving a mitogenome, which produced a pseudogenic tRNA sequence. In addition, in line with data in the literature, we explain the higher substitution rate of Anostraca and Onychocaudata with the inferred GC substitution bias that occurred during their evolution.
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Affiliation(s)
- Andrea Luchetti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bolgna, Italy
| | - Giobbe Forni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bolgna, Italy
| | - Alyza M. Skaist
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Sarah J. Wheelan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Barbara Mantovani
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi 3, 40126 Bolgna, Italy
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6
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Kelley DZ, Flam EL, Izumchenko E, Danilova LV, Wulf HA, Guo T, Singman DA, Afsari B, Skaist AM, Considine M, Welch JA, Stavrovskaya E, Bishop JA, Westra WH, Khan Z, Koch WM, Sidransky D, Wheelan SJ, Califano JA, Favorov AV, Fertig EJ, Gaykalova DA. Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks. Cancer Res 2017; 77:6538-6550. [PMID: 28947419 DOI: 10.1158/0008-5472.can-17-0833] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 08/22/2017] [Accepted: 09/20/2017] [Indexed: 11/16/2022]
Abstract
Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus-related (HPV+) head and neck squamous cell carcinoma (HNSCC) samples. We further associated chromatin aberrations with gene expression changes from a larger cohort of the tumor and normal samples with RNA-Seq data. We detect differential histone enrichment associated with tumor-specific gene expression variation, sites of HPV integration in the human genome, and HPV-associated histone enrichment sites upstream of cancer driver genes, which play central roles in cancer-associated pathways. These comprehensive analyses enable unprecedented characterization of the complex network of molecular changes resulting from chromatin alterations that drive HPV-related tumorigenesis. Cancer Res; 77(23); 6538-50. ©2017 AACR.
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Affiliation(s)
- Dylan Z Kelley
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Emily L Flam
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Evgeny Izumchenko
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ludmila V Danilova
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Hildegard A Wulf
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Theresa Guo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Dzov A Singman
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bahman Afsari
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alyza M Skaist
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Michael Considine
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jane A Welch
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Pathology, Johns Hopkins Medical School of Medicine, Baltimore, Maryland
| | - Elena Stavrovskaya
- Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia.,Institute for Information Transmission Problems, RAS, Moscow, Russia
| | - Justin A Bishop
- Department of Pathology, Johns Hopkins Medical School of Medicine, Baltimore, Maryland
| | - William H Westra
- Department of Pathology, Johns Hopkins Medical School of Medicine, Baltimore, Maryland
| | - Zubair Khan
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Wayne M Koch
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sarah J Wheelan
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joseph A Califano
- Head and Neck Cancer Center, Moores Cancer Center, University of California, San Diego, La Jolla, California.,Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of California, San Diego, La Jolla, California
| | - Alexander V Favorov
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Laboratory of Bioinformatics, Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia
| | - Elana J Fertig
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Daria A Gaykalova
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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7
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Ho H, Skaist AM, Pallavajjala A, Yonescu R, Batista D, Wheelan SJ, Ning Y. NUP98-PHF23 fusion is recurrent in acute myeloid leukemia and shares gene expression signature of leukemic stem cells. Leuk Res 2016; 45:1-7. [PMID: 27060678 DOI: 10.1016/j.leukres.2016.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/24/2016] [Accepted: 03/29/2016] [Indexed: 11/17/2022]
Abstract
Chromosome translocations involving nucleoporin 98 gene (NUP98) have been identified in a wide array of hematologic malignancies, and the resulting NUP98-associated fusions are known to play a critical role in leukemogensis through dysregulation of gene expression. Although NUP98-associated fusions were initially thought to be rare, application of molecular technologies has revealed that cryptic translocations involving NUP98 are more frequent than previously appreciated. We report an additional case of t(11;17)(p15;p13) resulting in the fusion of NUP98 and plant homeodomain finger 23 (PHF23) in a pediatric patient with acute myeloid leukemia (AML). Using RNA sequencing, we determined in-frame fusion points and also analyzed the gene expression profile of NUP98-PHF23 positive AML. Gene set enrichment analysis (GSEA) demonstrates that NUP98-PHF23 fusion shares gene expression signature of NUP98-HOXA9 fusion, the prototype of the NUP98-associated fusions, as well as the signature of leukemic stem cells. To our knowledge this is the first transcriptome analysis of human samples with NUP98-PHF23 positive AML. Our findings are in support of the gene expression study of NUP98-PHF23 mouse model and validate the usefulness of the mouse model in developing therapeutic strategies for the treatment of subsets of AML.
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Affiliation(s)
- Hao Ho
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Alyza M Skaist
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Aparna Pallavajjala
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Raluca Yonescu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Denise Batista
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Sarah J Wheelan
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yi Ning
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
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8
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Hong S, Skaist AM, Wheelan SJ, Friedman AD. AP-1 protein induction during monopoiesis favors C/EBP: AP-1 heterodimers over C/EBP homodimerization and stimulates FosB transcription. J Leukoc Biol 2011; 90:643-51. [PMID: 21543584 DOI: 10.1189/jlb.0111043] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
AP-1 proteins heterodimerize via their LZ domains to bind TGACGTCA or TGACTCA, whereas C/EBPs dimerize to bind ATTGCGCAAT. We demonstrate that intact C/EBPα also heterodimerizes with c-Jun or c-Fos to bind a hybrid DNA element, TGACGCAA, or more weakly to TGATGCAA. A 2:1 ratio of c-Jun:C/EBPα or c-Fos:C/EBPα was sufficient for preferential binding. Semiquantitative Western blot analysis indicates that the summation of c-Jun, JunB, and c-Fos levels in differentiating myeloid cells is similar to or exceeds the entirety of C/EBPα and C/EBPβ, indicating the feasibility of heterodimer formation. Induction of AP-1 proteins during monocytic differentiation favored formation of C/EBP:AP-1 heterodimers, with C/EBPα homodimers more evident during granulopoiesis. Approximately 350 human and 300 murine genes contain the TGACGCAA motif between -2 kb and +1 kb of their transcription start sites. We focused on the murine Fosb promoter, which contains a C/EBP:AP-1 cis element at -56 and -253, with the hFOSB gene containing an identical site at -253 and a 1-bp mismatch at -56. C/EBPα:AP-1 heterodimers bound either site preferentially in a gel-shift assay, C/EBPα:c-Fos ER fusion proteins induced endogenous Fosb mRNA but not in the presence of CHX, C/EBP and AP-1 proteins bound the endogenous Fosb promoter, mutation of the -56 cis element reduced reporter activity fivefold, and endogenous FosB protein was expressed preferentially during monopoiesis versus granulopoiesis. Increased expression of Jun/Fos proteins elevates C/EBP:AP-1 heterodimer formation to potentially activate novel sets of genes during monopoiesis and potentially during other biologic processes.
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Affiliation(s)
- SunHwa Hong
- Division of Pediatric Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
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