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Jaeger-Ruckstuhl CA, Lo Y, Fulton E, Waltner OG, Shabaneh TB, Simon S, Muthuraman PV, Correnti CE, Newsom OJ, Engstrom IA, Kanaan SB, Bhise SS, Peralta JMC, Ruff R, Price JP, Stull SM, Stevens AR, Bugos G, Kluesner MG, Voillet V, Muhunthan V, Morrish F, Olson JM, Gottardo R, Sarthy JF, Henikoff S, Sullivan LB, Furlan SN, Riddell SR. Signaling via a CD27-TRAF2-SHP-1 axis during naive T cell activation promotes memory-associated gene regulatory networks. Immunity 2024; 57:287-302.e12. [PMID: 38354704 DOI: 10.1016/j.immuni.2024.01.011] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 09/26/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024]
Abstract
The interaction of the tumor necrosis factor receptor (TNFR) family member CD27 on naive CD8+ T (Tn) cells with homotrimeric CD70 on antigen-presenting cells (APCs) is necessary for T cell memory fate determination. Here, we examined CD27 signaling during Tn cell activation and differentiation. In conjunction with T cell receptor (TCR) stimulation, ligation of CD27 by a synthetic trimeric CD70 ligand triggered CD27 internalization and degradation, suggesting active regulation of this signaling axis. Internalized CD27 recruited the signaling adaptor TRAF2 and the phosphatase SHP-1, thereby modulating TCR and CD28 signals. CD27-mediated modulation of TCR signals promoted transcription factor circuits that induced memory rather than effector associated gene programs, which are induced by CD28 costimulation. CD27-costimulated chimeric antigen receptor (CAR)-engineered T cells exhibited improved tumor control compared with CD28-costimulated CAR-T cells. Thus, CD27 signaling during Tn cell activation promotes memory properties with relevance to T cell immunotherapy.
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Affiliation(s)
- Carla A Jaeger-Ruckstuhl
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
| | - Yun Lo
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Elena Fulton
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Olivia G Waltner
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Tamer B Shabaneh
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sylvain Simon
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Pranav V Muthuraman
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Colin E Correnti
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Oliver J Newsom
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Ian A Engstrom
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Sami B Kanaan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Shruti S Bhise
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jobelle M C Peralta
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Raymond Ruff
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Jason P Price
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Sylvia M Stull
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Andrew R Stevens
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Grace Bugos
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Mitchell G Kluesner
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Valentin Voillet
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Vishaka Muhunthan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Fionnuala Morrish
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - James M Olson
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Raphaël Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Statistics, University of Washington, Seattle, WA 98195, USA; Swiss Institute of Bioinformatics, University of Lausanne and Lausanne University Hospital, Lausanne 1011, Switzerland
| | - Jay F Sarthy
- Seattle Children's Hospital, Seattle, WA 98105, USA; Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Science Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Lucas B Sullivan
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Scott N Furlan
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Stanley R Riddell
- Translational Sciences and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA.
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2
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Janssens DH, Duran M, Otto DJ, Kirkey D, Yi JS, Meshinchi S, Sarthy JF, Ahmad K, Henikoff S. KMT2A oncoproteins induce epigenetic resistance to targeted therapies. bioRxiv 2023:2023.12.29.573681. [PMID: 38234854 PMCID: PMC10793413 DOI: 10.1101/2023.12.29.573681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Chromosomal translocations involving the Lysine-Methyl-Tansferase-2A ( KMT2A ) locus generate potent oncogenes that cause highly aggressive acute leukemias 1 . KMT2A and the most frequent translocation partners encode proteins that interact with DNA to regulate developmental gene expression 2 . KMT2A-oncogenic fusion proteins (oncoproteins) contribute to the epigenetic mechanisms that allow KMT2A -rearranged leukemias to evade targeted therapies. By profiling the oncoprotein-target sites of 34 KMT2A -rearranged leukemia samples, we find that the genomic enrichment of oncoprotein binding is highly variable between samples. At high levels of expression, the oncoproteins preferentially activate either the lymphoid or myeloid lineage program depending on the fusion partner. These fusion-partner-dependent binding sites correspond to the frequencies of each mutation in acute lymphoid leukemia versus acute myeloid leukemia. By profiling a sample that underwent a lymphoid-to-myeloid lineage switching event in response to lymphoid-directed treatment, we find the global oncoprotein levels are reduced and the oncoprotein-target gene network changes. At lower levels of expression, the oncoprotein shifts to a non-canonical regulatory program that favors the myeloid lineage, and in a subset of resistant patients, the Menin inhibitor Revumenib induces a similar response. The dynamic shifts in KMT2A oncoproteins we describe likely contribute to epigenetic resistance of KMT2A -rearranged leukemias to targeted therapies.
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3
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Trouth A, Ravichandran K, Gafken PR, Martire S, Namciu SJ, Banaszynski LA, Sarthy JF, Ramachandran I. G1 length dictates heterochromatin landscape. bioRxiv 2023:2023.12.05.570186. [PMID: 38106207 PMCID: PMC10723301 DOI: 10.1101/2023.12.05.570186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Stem cells have lower facultative heterochromatin as defined by trimethylation of histone H3 lysine 27 (H3K27me3) compared to differentiated cells, however, the underlying mechanism for this observation has been unknown. Because H3K27me3 levels are diluted two-fold in every round of replication and then restored through the rest of the cycle, we reasoned that the cell cycle length could determine the time available for setting total H3K27me3 levels. Here, we demonstrate that a fast cell cycle sets low levels of H3K27me3 in serum-grown murine embryonic stem cells (mESCs). Extending the G1 phase leads to an increase in global H3K27me3 in mESCs due to the formation of de novo Polycomb domains, and the length of the G1/S block correlates with the extent of gain in H3K27me3, arguing that levels of the modification depend on the time available between successive rounds of replication. Similarly, accelerating the cell cycle in HEK293 cells decreases H3K27me3 levels. Finally, we applied this principle in tumor cells that, due to the dominant negative effect of the sub-stoichiometric H3K27M mutant, have reduced H3K27me3. Here, extending G1 using Palbociclib increased H3K27me3 levels, pointing to an unexpected means to rescue the effect of oncohistones. Our results suggest cell cycle length as a universal mechanism to modulate heterochromatin formation and, thus, cellular identity.
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4
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Kaonis S, Smith JL, Katiyar N, Merrill M, Hyelkma T, Namciu S, Le Q, Babaeva E, Ishida T, Morris SM, Girard E, Furuyama S, Ries R, Bernstein I, Meshinchi S, Henikoff S, Meers M, Hadland B, Sarthy JF. Chromatin Profiling of CBFA2T3-GLIS2 AMLs Identifies Key Transcription Factor Dependencies and BRG1 Inhibition as a Novel Therapeutic Strategy. bioRxiv 2023:2023.08.30.555598. [PMID: 37693371 PMCID: PMC10491196 DOI: 10.1101/2023.08.30.555598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Oncogenic fusions involving transcription factors are present in the majority of pediatric leukemias; however, the context-specific mechanisms they employ to drive cancer remain poorly understood. CBFA2T3-GLIS2 (C/G) fusions occur in treatment-refractory acute myeloid leukemias and are restricted to young children. To understand how the C/G fusion drives oncogenesis we applied CUT&RUN chromatin profiling to an umbilical cord blood/endothelial cell (EC) co-culture model of C/G AML that recapitulates the biology of this malignancy. We find C/G fusion binding is mediated by its zinc finger domains. Integration of fusion binding sites in C/G- transduced cells with Polycomb Repressive Complex 2 (PRC2) sites in control cord blood cells identifies MYCN, ZFPM1, ZBTB16 and LMO2 as direct C/G targets. Transcriptomic analysis of a large pediatric AML cohort shows that these genes are upregulated in C/G patient samples. Single cell RNA-sequencing of umbilical cord blood identifies a population of megakaryocyte precursors that already express many of these genes despite lacking the fusion. By integrating CUT&RUN data with CRISPR dependency screens we identify BRG1/SMARCA4 as a vulnerability in C/G AML. BRG1 profiling in C/G patient-derived cell lines shows that the CBFA2T3 locus is a binding site, and treatment with clinically-available BRG1 inhibitors reduces fusion levels and downstream C/G targets including N-MYC, resulting in C/G leukemia cell death and extending survival in a murine xenograft model.
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De Sarkar N, Patton RD, Doebley AL, Hanratty B, Adil M, Kreitzman AJ, Sarthy JF, Ko M, Brahma S, Meers MP, Janssens DH, Ang LS, Coleman IM, Bose A, Dumpit RF, Lucas JM, Nunez TA, Nguyen HM, McClure HM, Pritchard CC, Schweizer MT, Morrissey C, Choudhury AD, Baca SC, Berchuck JE, Freedman ML, Ahmad K, Haffner MC, Montgomery RB, Corey E, Henikoff S, Nelson PS, Ha G. Nucleosome Patterns in Circulating Tumor DNA Reveal Transcriptional Regulation of Advanced Prostate Cancer Phenotypes. Cancer Discov 2023; 13:632-653. [PMID: 36399432 PMCID: PMC9976992 DOI: 10.1158/2159-8290.cd-22-0692] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [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: 06/16/2022] [Revised: 10/01/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
Abstract
Advanced prostate cancers comprise distinct phenotypes, but tumor classification remains clinically challenging. Here, we harnessed circulating tumor DNA (ctDNA) to study tumor phenotypes by ascertaining nucleosome positioning patterns associated with transcription regulation. We sequenced plasma ctDNA whole genomes from patient-derived xenografts representing a spectrum of androgen receptor active (ARPC) and neuroendocrine (NEPC) prostate cancers. Nucleosome patterns associated with transcriptional activity were reflected in ctDNA at regions of genes, promoters, histone modifications, transcription factor binding, and accessible chromatin. We identified the activity of key phenotype-defining transcriptional regulators from ctDNA, including AR, ASCL1, HOXB13, HNF4G, and GATA2. To distinguish NEPC and ARPC in patient plasma samples, we developed prediction models that achieved accuracies of 97% for dominant phenotypes and 87% for mixed clinical phenotypes. Although phenotype classification is typically assessed by IHC or transcriptome profiling from tumor biopsies, we demonstrate that ctDNA provides comparable results with diagnostic advantages for precision oncology. SIGNIFICANCE This study provides insights into the dynamics of nucleosome positioning and gene regulation associated with cancer phenotypes that can be ascertained from ctDNA. New methods for classification in phenotype mixtures extend the utility of ctDNA beyond assessments of somatic DNA alterations with important implications for molecular classification and precision oncology. This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Navonil De Sarkar
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pathology and Prostate Cancer Center of Excellence, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Robert D. Patton
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Anna-Lisa Doebley
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington
- Medical Scientist Training Program, University of Washington, Seattle, Washington
| | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Mohamed Adil
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Adam J. Kreitzman
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jay F. Sarthy
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Minjeong Ko
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Sandipan Brahma
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Michael P. Meers
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Derek H. Janssens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Lisa S. Ang
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ilsa M. Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Arnab Bose
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ruth F. Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jared M. Lucas
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Talina A. Nunez
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Holly M. Nguyen
- Department of Urology, University of Washington, Seattle, Washington
| | | | - Colin C. Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Michael T. Schweizer
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Atish D. Choudhury
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sylvan C. Baca
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Matthew L. Freedman
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kami Ahmad
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - R. Bruce Montgomery
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Urology, University of Washington, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
- Corresponding Authors: Gavin Ha, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-2802; E-mail: ; and Peter S. Nelson, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-3377; E-mail:
| | - Gavin Ha
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Corresponding Authors: Gavin Ha, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-2802; E-mail: ; and Peter S. Nelson, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-3377; E-mail:
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6
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Apfelbaum AA, Wu F, Hawkins AG, Magnuson B, Jiménez JA, Taylor SD, Wrenn ED, Waltner O, Pfaltzgraff ER, Song JY, Hall C, Wellik DM, Ljungman M, Furlan SN, Ryan RJ, Sarthy JF, Lawlor ER. EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma. Clin Cancer Res 2022; 28:4466-4478. [PMID: 35653119 PMCID: PMC9588607 DOI: 10.1158/1078-0432.ccr-22-0384] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/05/2022] [Accepted: 05/25/2022] [Indexed: 01/28/2023]
Abstract
PURPOSE Propagation of Ewing sarcoma requires precise regulation of EWS::FLI1 transcriptional activity. Determining the mechanisms of fusion regulation will advance our understanding of tumor progression. Here we investigated whether HOXD13, a developmental transcription factor that promotes Ewing sarcoma metastatic phenotypes, influences EWS::FLI1 transcriptional activity. EXPERIMENTAL DESIGN Existing tumor and cell line datasets were used to define EWS::FLI1 binding sites and transcriptional targets. Chromatin immunoprecipitation and CRISPR interference were employed to identify enhancers. CUT&RUN and RNA sequencing defined binding sites and transcriptional targets of HOXD13. Transcriptional states were investigated using bulk and single-cell transcriptomic data from cell lines, patient-derived xenografts, and patient tumors. Mesenchymal phenotypes were assessed by gene set enrichment, flow cytometry, and migration assays. RESULTS We found that EWS::FLI1 creates a de novo GGAA microsatellite enhancer in a developmentally conserved regulatory region of the HOXD locus. Knockdown of HOXD13 led to widespread changes in expression of developmental gene programs and EWS::FLI1 targets. HOXD13 binding was enriched at established EWS::FLI1 binding sites where it influenced expression of EWS::FLI1-activated genes. More strikingly, HOXD13 bound and activated EWS::FLI1-repressed genes, leading to adoption of mesenchymal and migratory cell states that are normally suppressed by the fusion. Single-cell analysis confirmed that direct transcriptional antagonism between HOXD13-mediated gene activation and EWS::FLI1-dependent gene repression defines the state of Ewing sarcoma cells along a mesenchymal axis. CONCLUSIONS Ewing sarcoma tumors are comprised of tumor cells that exist along a mesenchymal transcriptional continuum. The identity of cells along this continuum is, in large part, determined by the competing activities of EWS::FLI1 and HOXD13. See related commentary by Weiss and Bailey, p. 4360.
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Affiliation(s)
- April A. Apfelbaum
- Cancer Biology PhD Program, University of Michigan, Ann Arbor, MI, 48109, USA,Seattle Children’s Research Institute, Seattle, WA, 98101, USA
| | - Feinan Wu
- Genomics and Bioinformatics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Allegra G. Hawkins
- Childhood Cancer Data Lab Alex’s Lemonade Stand Foundation, Philadelphia, PA, USA
| | - Brian Magnuson
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jennifer A. Jiménez
- Cancer Biology PhD Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sean D. Taylor
- Seattle Children’s Research Institute, Seattle, WA, 98101, USA
| | - Emma D. Wrenn
- Seattle Children’s Research Institute, Seattle, WA, 98101, USA
| | - Olivia Waltner
- Fred Hutch Cancer Research Center, Seattle, WA, 98109, USA
| | | | - Jane Y. Song
- Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Cody Hall
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Deneen M. Wellik
- Department of Cell and Regenerative Biology, University of Wisconsin, Madison, WI, 53705
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Scott N. Furlan
- Fred Hutch Cancer Research Center, Seattle, WA, 98109, USA,Department of Pediatrics, University of Washington, Seattle, WA, 98105, USA
| | - Russell J.H. Ryan
- Immunology Discovery, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jay F. Sarthy
- Fred Hutch Cancer Research Center, Seattle, WA, 98109, USA,Department of Pediatrics, University of Washington, Seattle, WA, 98105, USA
| | - Elizabeth R. Lawlor
- Seattle Children’s Research Institute, Seattle, WA, 98101, USA,Department of Pediatrics, University of Washington, Seattle, WA, 98105, USA.,Correspondence: Elizabeth R. Lawlor MD, PhD, Seattle Children’s Research Institute, Olive Lab, 1100 Olive Way, Suite 100 Seattle, WA 98101,
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7
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Wu SJ, Furlan SN, Mihalas AB, Kaya-Okur HS, Feroze AH, Emerson SN, Zheng Y, Carson K, Cimino PJ, Keene CD, Sarthy JF, Gottardo R, Ahmad K, Henikoff S, Patel AP. Single-cell CUT&Tag analysis of chromatin modifications in differentiation and tumor progression. Nat Biotechnol 2021; 39:819-824. [PMID: 33846646 DOI: 10.1038/s41587-021-00865-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/18/2021] [Indexed: 12/12/2022]
Abstract
Methods for quantifying gene expression1 and chromatin accessibility2 in single cells are well established, but single-cell analysis of chromatin regions with specific histone modifications has been technically challenging. In this study, we adapted the CUT&Tag method3 to scalable nanowell and droplet-based single-cell platforms to profile chromatin landscapes in single cells (scCUT&Tag) from complex tissues and during the differentiation of human embryonic stem cells. We focused on profiling polycomb group (PcG) silenced regions marked by histone H3 Lys27 trimethylation (H3K27me3) in single cells as an orthogonal approach to chromatin accessibility for identifying cell states. We show that scCUT&Tag profiling of H3K27me3 distinguishes cell types in human blood and allows the generation of cell-type-specific PcG landscapes from heterogeneous tissues. Furthermore, we used scCUT&Tag to profile H3K27me3 in a patient with a brain tumor before and after treatment, identifying cell types in the tumor microenvironment and heterogeneity in PcG activity in the primary sample and after treatment.
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Affiliation(s)
- Steven J Wu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA
| | - Scott N Furlan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA.,Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Anca B Mihalas
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Hatice S Kaya-Okur
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Howard Hughes Medical Institute, Seattle, WA, USA.,Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - Abdullah H Feroze
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Samuel N Emerson
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Ye Zheng
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kalee Carson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Patrick J Cimino
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Jay F Sarthy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Raphael Gottardo
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Howard Hughes Medical Institute, Seattle, WA, USA.
| | - Anoop P Patel
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA. .,Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA. .,Department of Neurological Surgery, University of Washington, Seattle, WA, USA.
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8
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Sarthy JF, Meers MP, Janssens DH, Henikoff JG, Feldman H, Paddison PJ, Lockwood CM, Vitanza NA, Olson JM, Ahmad K, Henikoff S. Histone deposition pathways determine the chromatin landscapes of H3.1 and H3.3 K27M oncohistones. eLife 2020; 9:61090. [PMID: 32902381 PMCID: PMC7518889 DOI: 10.7554/elife.61090] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/08/2020] [Indexed: 12/16/2022] Open
Abstract
Lysine 27-to-methionine (K27M) mutations in the H3.1 or H3.3 histone genes are characteristic of pediatric diffuse midline gliomas (DMGs). These oncohistone mutations dominantly inhibit histone H3K27 trimethylation and silencing, but it is unknown how oncohistone type affects gliomagenesis. We show that the genomic distributions of H3.1 and H3.3 oncohistones in human patient-derived DMG cells are consistent with the DNAreplication-coupled deposition of histone H3.1 and the predominant replication-independent deposition of histone H3.3. Although H3K27 trimethylation is reduced for both oncohistone types, H3.3K27M-bearing cells retain some domains, and only H3.1K27M-bearing cells lack H3K27 trimethylation. Neither oncohistone interferes with PRC2 binding. Using Drosophila as a model, we demonstrate that inhibition of H3K27 trimethylation occurs only when H3K27M oncohistones are deposited into chromatin and only when expressed in cycling cells. We propose that oncohistones inhibit the H3K27 methyltransferase as chromatin patterns are being duplicated in proliferating cells, predisposing them to tumorigenesis.
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Affiliation(s)
- Jay F Sarthy
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Cancer and Blood Disorders, Seattle, United States
| | - Michael P Meers
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Derek H Janssens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Jorja G Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Heather Feldman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, United States
| | - Nicholas A Vitanza
- Cancer and Blood Disorders, Seattle, United States.,Clinical Research Division Fred Hutchinson Cancer Research Center, Seattle, United States
| | - James M Olson
- Cancer and Blood Disorders, Seattle, United States.,Clinical Research Division Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
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9
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Woerner A, Shin DS, Chick JFB, Smith CA, Sarthy JF, Monroe EJ. Endolymphatic exclusion for the treatment of pediatric chylous ascites secondary to neuroblastoma resection: report of two cases. Radiol Case Rep 2020; 15:1044-1049. [PMID: 32461775 PMCID: PMC7240057 DOI: 10.1016/j.radcr.2020.04.060] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 04/27/2020] [Accepted: 04/27/2020] [Indexed: 11/24/2022] Open
Abstract
Chylous ascites is a rare, but highly morbid complication of oncologic resection, often associated with retroperitoneal lymphadenectomy. Conservative measures with total parenteral nutrition or lipid-reduced formulas constitute the initial mainstay therapy, but not without risks and failures. This report describes 2 endolymphatic treatment strategies for iatrogenic chylous ascites following neuroblastoma resection. Lymphatic leaks were identified using intranodal lymphangiography, targeted with cone-beam computed tomographic guidance, and embolized with n-butyl cyanoacrylate. There were no adverse outcomes, with complete resolution of chylous ascites and a mean follow-up of 26 months.
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Affiliation(s)
- Andrew Woerner
- Interventional Radiology Section, Department of Radiology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA 98195, USA
| | - David S Shin
- Interventional Radiology Section, Department of Radiology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA 98195, USA
| | - Jeffrey Forris Beecham Chick
- Interventional Radiology Section, Department of Radiology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA 98195, USA.,Division of Vascular and Interventional Radiology, Department of Radiology, Seattle Children's Hospital, 4800 Sand Point Way Northeast, Seattle, WA 98105, USA
| | - Caitlin A Smith
- Department of General Surgery, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Jay F Sarthy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Cancer and Blood Disorders Center, Seattle Children's Hospital, Seattle, WA, USA
| | - Eric J Monroe
- Interventional Radiology Section, Department of Radiology, University of Washington, 1959 Northeast Pacific Street, Seattle, WA 98195, USA.,Division of Vascular and Interventional Radiology, Department of Radiology, Seattle Children's Hospital, 4800 Sand Point Way Northeast, Seattle, WA 98105, USA
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10
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Zeineldin M, Federico S, Chen X, Fan Y, Xu B, Stewart E, Zhou X, Jeon J, Griffiths L, Nguyen R, Norrie J, Easton J, Mulder H, Yergeau D, Liu Y, Wu J, Van Ryn C, Naranjo A, Hogarty MD, Kamiński MM, Valentine M, Pruett-Miller SM, Pappo A, Zhang J, Clay MR, Bahrami A, Vogel P, Lee S, Shelat A, Sarthy JF, Meers MP, George RE, Mardis ER, Wilson RK, Henikoff S, Downing JR, Dyer MA. MYCN amplification and ATRX mutations are incompatible in neuroblastoma. Nat Commun 2020; 11:913. [PMID: 32060267 PMCID: PMC7021759 DOI: 10.1038/s41467-020-14682-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 01/23/2020] [Indexed: 12/31/2022] Open
Abstract
Aggressive cancers often have activating mutations in growth-controlling oncogenes and inactivating mutations in tumor-suppressor genes. In neuroblastoma, amplification of the MYCN oncogene and inactivation of the ATRX tumor-suppressor gene correlate with high-risk disease and poor prognosis. Here we show that ATRX mutations and MYCN amplification are mutually exclusive across all ages and stages in neuroblastoma. Using human cell lines and mouse models, we found that elevated MYCN expression and ATRX mutations are incompatible. Elevated MYCN levels promote metabolic reprogramming, mitochondrial dysfunction, reactive-oxygen species generation, and DNA-replicative stress. The combination of replicative stress caused by defects in the ATRX-histone chaperone complex, and that induced by MYCN-mediated metabolic reprogramming, leads to synthetic lethality. Therefore, ATRX and MYCN represent an unusual example, where inactivation of a tumor-suppressor gene and activation of an oncogene are incompatible. This synthetic lethality may eventually be exploited to improve outcomes for patients with high-risk neuroblastoma.
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Affiliation(s)
- Maged Zeineldin
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Sara Federico
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project, St. Louis, MO, USA
| | - Yiping Fan
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Beisi Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Elizabeth Stewart
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Xin Zhou
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jongrye Jeon
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Lyra Griffiths
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Rosa Nguyen
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jackie Norrie
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Heather Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Donald Yergeau
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jianrong Wu
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Collin Van Ryn
- Children's Oncology Group Statistics and Data Center, Department of Biostatistics, University of Florida, Gainesville, FlL, 32607, USA
| | - Arlene Naranjo
- Children's Oncology Group Statistics and Data Center, Department of Biostatistics, University of Florida, Gainesville, FlL, 32607, USA
| | - Michael D Hogarty
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Marcin M Kamiński
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Marc Valentine
- Cytogenetics Shared Resource, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Alberto Pappo
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Michael R Clay
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Armita Bahrami
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Peter Vogel
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Seungjae Lee
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Anang Shelat
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jay F Sarthy
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Michael P Meers
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Rani E George
- Department of Hematology/Oncology, Dana Farber Cancer Institute, Boston, MA, 02215, USA
| | - Elaine R Mardis
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Richard K Wilson
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Steven Henikoff
- Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Michael A Dyer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- St. Jude Children's Research Hospital-Washington University Pediatric Cancer Genome Project, St. Louis, MO, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
- Department of Ophthalmology, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
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11
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Abstract
Identification of cancer-associated mutations in core histone genes has proved challenging due to these genes' highly conserved nature and presence in large arrays. Recent analyses of cancer genomes, including one in this issue of Cancer Discovery, show that mutations in the histone fold can affect nucleosome stability, providing a novel mechanism by which oncohistones contribute to tumorigenesis.See related article by Bennett et al., p. 1438.
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Affiliation(s)
- Jay F Sarthy
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Cancer and Blood Disorders, Seattle Children's Hospital, Seattle, Washington
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington. .,Howard Hughes Medical Institute, Chevy Chase, Maryland
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12
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Steineck A, Krumm N, Sarthy JF, Pritchard CC, Chapman T, Stacey AW, Vitanza NA, Cole B. Response to Pembrolizumab in a Patient With Xeroderma Pigmentosum and Advanced Squamous Cell Carcinoma. JCO Precis Oncol 2019; 3:PO.19.00028. [PMID: 32923855 PMCID: PMC7446378 DOI: 10.1200/po.19.00028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/13/2019] [Indexed: 12/15/2022] Open
Affiliation(s)
| | | | - Jay F. Sarthy
- Seattle Children’s Hospital, Seattle, WA
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | - Nicholas A. Vitanza
- Seattle Children’s Hospital, Seattle, WA
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Bonnie Cole
- Seattle Children’s Hospital, Seattle, WA
- University of Washington School of Medicine, Seattle, WA
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13
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Janssens DH, Wu SJ, Sarthy JF, Meers MP, Myers CH, Olson JM, Ahmad K, Henikoff S. Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs. Epigenetics Chromatin 2018; 11:74. [PMID: 30577869 PMCID: PMC6302505 DOI: 10.1186/s13072-018-0243-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 12/03/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Our understanding of eukaryotic gene regulation is limited by the complexity of protein-DNA interactions that comprise the chromatin landscape and by inefficient methods for characterizing these interactions. We recently introduced CUT&RUN, an antibody-targeted nuclease cleavage method that profiles DNA-binding proteins, histones and chromatin-modifying proteins in situ with exceptional sensitivity and resolution. RESULTS Here, we describe an automated CUT&RUN platform and apply it to characterize the chromatin landscapes of human cells. We find that automated CUT&RUN profiles of histone modifications crisply demarcate active and repressed chromatin regions, and we develop a continuous metric to identify cell-type-specific promoter and enhancer activities. We test the ability of automated CUT&RUN to profile frozen tumor samples and find that our method readily distinguishes two pediatric glioma xenografts by their subtype-specific gene expression programs. CONCLUSIONS The easy, cost-effective workflow makes automated CUT&RUN an attractive tool for high-throughput characterization of cell types and patient samples.
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Affiliation(s)
- Derek H Janssens
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - Steven J Wu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, 98195, USA
| | - Jay F Sarthy
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
- Cancer and Blood Disorder Center, Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA, 98105, USA
| | - Michael P Meers
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - Carrie H Myers
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - James M Olson
- Cancer and Blood Disorder Center, Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA, 98105, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 N. Fairview Ave, Seattle, WA, 98109, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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14
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Sarthy JF, Reddivalla N, Radhi M, Chastain K. Pediatric 8p11 eosinophilic myeloproliferative syndrome (EMS): A case report and review of the literature. Pediatr Blood Cancer 2017; 64. [PMID: 27808462 DOI: 10.1002/pbc.26310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 09/05/2016] [Accepted: 09/21/2016] [Indexed: 01/05/2023]
Abstract
The 8p11 eosinophilic myeloproliferative syndrome (EMS) is an aggressive neoplasm driven by translocation of the fibroblast growth factor receptor 1 and often transforms to leukemias and lymphomas that are refractory to treatment. The first case was identified in 1983, and to date over 70 cases have been reported in the literature. Despite those reports, no consensus exists on management of this condition, and inconsistency in treatment regimens is even more pronounced in the pediatric literature. We report a case of a male infant with the 8p11 EMS, review the published pediatric experience with EMS, and discuss treatment strategies for this enigmatic hematological disorder.
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Affiliation(s)
- Jay F Sarthy
- Children's Mercy Hospitals and Clinics, Kansas City, Missouri 64113
| | | | - Mohamed Radhi
- Children's Mercy Hospitals and Clinics, Kansas City, Missouri 64113
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15
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Abstract
The single-stranded overhangs at the ends of telomeres are thought to be critical for telomere maintenance, but how they are generated has been largely unclear. Two studies (one in this issue of Molecular Cell, Wu et al., 2010) have now implicated the Apollo nuclease in maintaining the overhang specifically at those telomeres generated by leading-strand DNA synthesis.
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Affiliation(s)
- Jay F Sarthy
- Howard Hughes Medical Institute and Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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16
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Shieh CC, Trumbull JD, Sarthy JF, McKenna DG, Parihar AS, Zhang XF, Faltynek CR, Gopalakrishnan M. Automated Parallel Oocyte Electrophysiology Test Station (POETs™): A Screening Platform for Identification of Ligand-Gated Ion Channel Modulators. Assay Drug Dev Technol 2003; 1:655-63. [PMID: 15090238 DOI: 10.1089/154065803770381011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ligand-gated ion channels (LGICs) play important roles in the regulation of cellular function and signaling and serve as excellent drug targets. However, fast desensitization of most LGICs limits the choice of reliable methods to identify agonists, antagonists, and/or modulators in a high throughput manner. In this study, automated Parallel Oocyte Electrophysiology Test station (POETs) was used to screen a directed compound library against a rapidly desensitizing LGIC and to characterize further the pharmacological properties of the hits. POETs allows up to six two-electrode voltage-clamp experiments to be performed in parallel by automatically loading of the oocytes into flowcells, assessing individual oocyte behavior prior to initiating experiments. Oocytes injected with cRNA were transferred from a chilled 96-well plate into flowcells by the instrument, where they were impaled under software control by two independent electrodes. Expression was tested by measuring current responses to rapid application of agonists. Compounds, prepared in a 96-well format, were tested for effects by coapplication with agonist at a single concentration of 30 microM over 2 s. After compound application, oocytes were washed for a minimum of 30 s, and used repeatedly if the test compounds had no significant effect on the control response. Typical throughput could reach approximately 14 plates/day depending on the protocol. Pilot library screening revealed a hit rate of 0.06%, with active compounds having IC(50) values of 4-40 microM. Hits were also confirmed in native neurons using patch-clamp techniques. We conclude that automated POETs serves as a suitable platform for screening and expedient identification of LGIC modulators.
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Affiliation(s)
- Char-Chang Shieh
- Neuroscience Research, Global Pharmaceutical Research Division, Abbott Laboratories, Abbott Park, IL 60064, USA.
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