1
|
Nakamura M, Verboon JM, Allen TE, Abreu-Blanco MT, Liu R, Dominguez ANM, Delrow JJ, Parkhurst SM. Autocrine insulin pathway signaling regulates actin dynamics in cell wound repair. PLoS Genet 2020; 16:e1009186. [PMID: 33306674 PMCID: PMC7758051 DOI: 10.1371/journal.pgen.1009186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/23/2020] [Revised: 12/23/2020] [Accepted: 10/09/2020] [Indexed: 01/13/2023] Open
Abstract
Cells are exposed to frequent mechanical and/or chemical stressors that can compromise the integrity of the plasma membrane and underlying cortical cytoskeleton. The molecular mechanisms driving the immediate repair response launched to restore the cell cortex and circumvent cell death are largely unknown. Using microarrays and drug-inhibition studies to assess gene expression, we find that initiation of cell wound repair in the Drosophila model is dependent on translation, whereas transcription is required for subsequent steps. We identified 253 genes whose expression is up-regulated (80) or down-regulated (173) in response to laser wounding. A subset of these genes were validated using RNAi knockdowns and exhibit aberrant actomyosin ring assembly and/or actin remodeling defects. Strikingly, we find that the canonical insulin signaling pathway controls actin dynamics through the actin regulators Girdin and Chickadee (profilin), and its disruption leads to abnormal wound repair. Our results provide new insight for understanding how cell wound repair proceeds in healthy individuals and those with diseases involving wound healing deficiencies. Organisms are constantly subject to damage by physiological and environmental stresses at the cell, tissue, and organ levels. While organisms have robust repair systems to survive from such damage, the underlying molecular mechanisms for these different scales of repair are different. Using microarray analyses and pharmacological assays with the Drosophila model, we examined the requirements for transcription and translation during cell wound repair. We find that translation, rather than transcription, is needed for the initial steps of cell wound repair. Transcription is required for the later steps of the repair process. We have successfully identified and verified 80 up-regulated and 173 down-regulated genes, most of which are new players in cell wound repair. A number of these genes function to regulate cytoskeleton dynamics at different steps of cell repair process. Interestingly, a subset of these genes encode components of the insulin signaling pathway. While insulin signaling is required for tissue and organ wound repair, we find that a canonical insulin pathway is activated upon wounding in the repair of individual cells as well. Our results provide new insight for understanding how cell wound repair proceeds in healthy individuals and those with diseases involving wound healing deficiencies.
Collapse
Affiliation(s)
- Mitsutoshi Nakamura
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Jeffrey M. Verboon
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Tessa E. Allen
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Maria Teresa Abreu-Blanco
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Raymond Liu
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Andrew N. M. Dominguez
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Jeffrey J. Delrow
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Susan M. Parkhurst
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- * E-mail:
| |
Collapse
|
2
|
Kuppers DA, Arora S, Lim Y, Lim AR, Carter LM, Corrin PD, Plaisier CL, Basom R, Delrow JJ, Wang S, Hansen He H, Torok-Storb B, Hsieh AC, Paddison PJ. N 6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis. Nat Commun 2019; 10:4596. [PMID: 31601799 PMCID: PMC6787028 DOI: 10.1038/s41467-019-12518-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [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: 09/18/2018] [Accepted: 08/26/2019] [Indexed: 12/30/2022] Open
Abstract
Many of the regulatory features governing erythrocyte specification, maturation, and associated disorders remain enigmatic. To identify new regulators of erythropoiesis, we utilize a functional genomic screen for genes affecting expression of the erythroid marker CD235a/GYPA. Among validating hits are genes coding for the N6-methyladenosine (m6A) mRNA methyltransferase (MTase) complex, including, METTL14, METTL3, and WTAP. We demonstrate that m6A MTase activity promotes erythroid gene expression programs through selective translation of ~300 m6A marked mRNAs, including those coding for SETD histone methyltransferases, ribosomal components, and polyA RNA binding proteins. Remarkably, loss of m6A marks results in dramatic loss of H3K4me3 marks across key erythroid-specific KLF1 transcriptional targets (e.g., Heme biosynthesis genes). Further, each m6A MTase subunit and a subset of their mRNAs targets are required for human erythroid specification in primary bone-marrow derived progenitors. Thus, m6A mRNA marks promote the translation of a network of genes required for human erythropoiesis.
Collapse
Affiliation(s)
- Daniel A Kuppers
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Yiting Lim
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Andrea R Lim
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98195, USA
| | - Lucas M Carter
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Philip D Corrin
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Christopher L Plaisier
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, 85281, USA
| | - Ryan Basom
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Jeffrey J Delrow
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Shiyan Wang
- Princess Margaret Cancer Centre/University Health Network, Toronto, ON, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre/University Health Network, Toronto, ON, Canada
| | - Beverly Torok-Storb
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Andrew C Hsieh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
- School of Medicine, University of Washington, Seattle, WA, 98195, USA.
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| |
Collapse
|
3
|
Galipeau PC, Oman KM, Paulson TG, Sanchez CA, Zhang Q, Marty JA, Delrow JJ, Kuhner MK, Vaughan TL, Reid BJ, Li X. Correction to: NSAID use and somatic exomic mutations in Barrett's esophagus. Genome Med 2019; 11:14. [PMID: 30867038 PMCID: PMC6417226 DOI: 10.1186/s13073-019-0625-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 11/25/2022] Open
Affiliation(s)
- Patricia C Galipeau
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA
| | - Kenji M Oman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA
| | - Thomas G Paulson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA
| | - Carissa A Sanchez
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA
| | - Qing Zhang
- Bioinformatics Shared Resource, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Jerry A Marty
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Mary K Kuhner
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle, WA, 98195-5065, USA
| | - Thomas L Vaughan
- Department of Epidemiology, University of Washington, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Brian J Reid
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA.,Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle, WA, 98195-5065, USA.,Department of Medicine, University of Washington, Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Xiaohong Li
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA.
| |
Collapse
|
4
|
OhAinle M, Helms L, Vermeire J, Roesch F, Humes D, Basom R, Delrow JJ, Overbaugh J, Emerman M. A virus-packageable CRISPR screen identifies host factors mediating interferon inhibition of HIV. eLife 2018; 7:e39823. [PMID: 30520725 PMCID: PMC6286125 DOI: 10.7554/elife.39823] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [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: 07/04/2018] [Accepted: 11/13/2018] [Indexed: 12/14/2022] Open
Abstract
Interferon (IFN) inhibits HIV replication by inducing antiviral effectors. To comprehensively identify IFN-induced HIV restriction factors, we assembled a CRISPR sgRNA library of Interferon Stimulated Genes (ISGs) into a modified lentiviral vector that allows for packaging of sgRNA-encoding genomes in trans into budding HIV-1 particles. We observed that knockout of Zinc Antiviral Protein (ZAP) improved the performance of the screen due to ZAP-mediated inhibition of the vector. A small panel of IFN-induced HIV restriction factors, including MxB, IFITM1, Tetherin/BST2 and TRIM5alpha together explain the inhibitory effects of IFN on the CXCR4-tropic HIV-1 strain, HIV-1LAI, in THP-1 cells. A second screen with a CCR5-tropic primary strain, HIV-1Q23.BG505, described an overlapping, but non-identical, panel of restriction factors. Further, this screen also identifies HIV dependency factors. The ability of IFN-induced restriction factors to inhibit HIV strains to replicate in human cells suggests that these human restriction factors are incompletely antagonized. Editorial note This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
Collapse
Affiliation(s)
- Molly OhAinle
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Louisa Helms
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Jolien Vermeire
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Ferdinand Roesch
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Daryl Humes
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Ryan Basom
- Genomics and Bioinformatics Shared ResourceFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared ResourceFred Hutchinson Cancer Research CenterSeattleUnited States
| | - Julie Overbaugh
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| | - Michael Emerman
- Divisions of Human Biology and Basic SciencesFred Hutchinson Cancer Research CenterWashingtonUnited States
| |
Collapse
|
5
|
Ding Y, Herman JA, Toledo CM, Lang JM, Corrin P, Girard EJ, Basom R, Delrow JJ, Olson JM, Paddison PJ. ZNF131 suppresses centrosome fragmentation in glioblastoma stem-like cells through regulation of HAUS5. Oncotarget 2018; 8:48545-48562. [PMID: 28596487 PMCID: PMC5564707 DOI: 10.18632/oncotarget.18153] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 02/17/2017] [Accepted: 05/05/2017] [Indexed: 12/17/2022] Open
Abstract
Zinc finger domain genes comprise ∼3% of the human genome, yet many of their functions remain unknown. Here we investigated roles for the vertebrate-specific BTB domain zinc finger gene ZNF131 in the context of human brain tumors. We report that ZNF131 is broadly required for Glioblastoma stem-like cell (GSC) viability, but dispensable for neural progenitor cell (NPC) viability. Examination of gene expression changes after ZNF131 knockdown (kd) revealed that ZNF131 activity notably promotes expression of Joubert Syndrome ciliopathy genes, including KIF7, NPHP1, and TMEM237, as well as HAUS5, a component of Augmin/HAUS complex that facilitates microtubule nucleation along the mitotic spindle. Of these genes only kd of HAUS5 displayed GSC-specific viability loss. Critically, HAUS5 ectopic expression was sufficient to suppress viability defects of ZNF131 kd cells. Moreover, ZNF131 and HAUS5 kd phenocopied each other in GSCs, each causing: mitotic arrest, centrosome fragmentation, loss of Augmin/HAUS complex on the mitotic spindle, and loss of GSC self-renewal and tumor formation capacity. In control NPCs, we observed centrosome fragmentation and lethality only when HAUS5 kd was combined with kd of HAUS2 or HAUS4, demonstrating that the complex is essential in NPCs, but that GSCs have heightened requirement. Our results suggest that GSCs differentially rely on ZNF131-dependent expression of HAUS5 as well as the Augmin/HAUS complex activity to maintain the integrity of centrosome function and viability.
Collapse
Affiliation(s)
- Yu Ding
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Novartis Institute for Biomedical Research, Shanghai, China
| | - Jacob A Herman
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Chad M Toledo
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.,Nurix Inc., San Francisco, CA, USA
| | - Jackie M Lang
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| | - Philip Corrin
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Ryan Basom
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Patrick J Paddison
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA
| |
Collapse
|
6
|
Galipeau PC, Oman KM, Paulson TG, Sanchez CA, Zhang Q, Marty JA, Delrow JJ, Kuhner MK, Vaughan TL, Reid BJ, Li X. NSAID use and somatic exomic mutations in Barrett's esophagus. Genome Med 2018; 10:17. [PMID: 29486792 PMCID: PMC5830331 DOI: 10.1186/s13073-018-0520-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/09/2018] [Indexed: 12/18/2022] Open
Abstract
Background Use of aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs) has been shown to protect against tetraploidy, aneuploidy, and chromosomal alterations in the metaplastic condition Barrett’s esophagus (BE) and to lower the incidence and mortality of esophageal adenocarcinoma (EA). The esophagus is exposed to both intrinsic and extrinsic mutagens resulting from gastric reflux, chronic inflammation, and exposure to environmental carcinogens such as those found in cigarettes. Here we test the hypothesis that NSAID use inhibits accumulation of point mutations/indels during somatic genomic evolution in BE. Methods Whole exome sequences were generated from 82 purified epithelial biopsies and paired blood samples from a cross-sectional study of 41 NSAID users and 41 non-users matched by sex, age, smoking, and continuous time using or not using NSAIDs. Results NSAID use reduced overall frequency of point mutations across the spectrum of mutation types, lowered the frequency of mutations even when adjusted for both TP53 mutation and smoking status, and decreased the prevalence of clones with high variant allele frequency. Never smokers who consistently used NSAIDs had fewer point mutations in signature 17, which is commonly found in EA. NSAID users had, on average, a 50% reduction in functional gene mutations in nine cancer-associated pathways and also had less diversity in pathway mutational burden compared to non-users. Conclusions These results indicate NSAID use functions to limit overall mutations on which selection can act and supports a model in which specific mutant cell populations survive or expand better in the absence of NSAIDs. Electronic supplementary material The online version of this article (10.1186/s13073-018-0520-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Patricia C Galipeau
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA
| | - Kenji M Oman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA
| | - Thomas G Paulson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA
| | - Carissa A Sanchez
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA
| | - Qing Zhang
- Bioinformatics Shared Resource, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Jerry A Marty
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Mary K Kuhner
- Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle, WA, 98195-5065, USA
| | - Thomas L Vaughan
- Department of Epidemiology, University of Washington, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Brian J Reid
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA.,Department of Genome Sciences, University of Washington, Foege Building S-250, Box 355065, 3720 15th Ave NE, Seattle, WA, 98195-5065, USA.,Department of Medicine, University of Washington, Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, Seattle, WA, 98109-1024, USA
| | - Xiaohong Li
- Division of Human Biology, Fred Hutchinson Cancer Research Center, PO Box 19024, 1100 Fairview Ave N, Seattle, WA, 98109-1024, USA.
| |
Collapse
|
7
|
Watson NF, Buchwald D, Delrow JJ, Altemeier WA, Vitiello MV, Pack AI, Bamshad M, Noonan C, Gharib SA. Transcriptional Signatures of Sleep Duration Discordance in Monozygotic Twins. Sleep 2017; 40:2952682. [PMID: 28364472 DOI: 10.1093/sleep/zsw019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2017] [Indexed: 12/23/2022] Open
Abstract
Introduction Habitual short sleep duration is associated with adverse metabolic, cardiovascular, and inflammatory effects. Co-twin study methodologies account for familial (eg, genetics and shared environmental) confounding, allowing assessment of subtle environmental effects, such as the effect of habitual short sleep duration on gene expression. Therefore, we investigated gene expression in monozygotic twins discordant for actigraphically phenotyped habitual sleep duration. Methods Eleven healthy monozygotic twin pairs (82% female; mean age 42.7 years; SD = 18.1), selected based on subjective sleep duration discordance, were objectively phenotyped for habitual sleep duration with 2 weeks of wrist actigraphy. Peripheral blood leukocyte (PBL) RNA from fasting blood samples was obtained on the final day of actigraphic measurement and hybridized to Illumina humanHT-12 microarrays. Differential gene expression was determined between paired samples and mapped to functional categories using Gene Ontology. Finally, a more comprehensive gene set enrichment analysis was performed based on the entire PBL transcriptome. Results The mean 24-hour sleep duration of the total sample was 439.2 minutes (SD = 46.8 minutes; range 325.4-521.6 minutes). Mean within-pair sleep duration difference per 24 hours was 64.4 minutes (SD = 21.2; range 45.9-114.6 minutes). The twin cohort displayed distinctive pathway enrichment based on sleep duration differences. Habitual short sleep was associated with up-regulation of genes involved in transcription, ribosome, translation, and oxidative phosphorylation. Unexpectedly, genes down-regulated in short sleep twins were highly enriched in immuno-inflammatory pathways such as interleukin signaling and leukocyte activation, as well as developmental programs, coagulation cascade, and cell adhesion. Conclusions Objectively assessed habitual sleep duration in monozygotic twin pairs appears to be associated with distinct patterns of differential gene expression and pathway enrichment. By accounting for familial confounding and measuring real life sleep duration, our study shows the transcriptomic effects of habitual short sleep on dysregulated immune response and provides a potential link between sleep deprivation and adverse metabolic, cardiovascular, and inflammatory outcomes.
Collapse
Affiliation(s)
- N F Watson
- Department of Neurology, University of Washington, Seattle, WA.,UW Medicine Sleep Center, University of Washington, Seattle, WA.,Washington State Twin Registry, Seattle, WA.,Center for Research in the Management of Sleep Disorders, University of Washington, Seattle, WA
| | - D Buchwald
- Washington State Twin Registry, Seattle, WA.,Initiative for Research and Education to Advance Community Health, Elson S Floyd College of Medicine, Spokane, WA
| | - J J Delrow
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | - W A Altemeier
- Department of Medicine, University of Washington, Seattle, WA
| | - M V Vitiello
- Center for Research in the Management of Sleep Disorders, University of Washington, Seattle, WA.,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA
| | - A I Pack
- Division of Sleep Medicine/Department of Medicine and Center for Sleep and Circadian Neurobiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - M Bamshad
- Department of Pediatrics, University of Washington, Seattle, WA
| | - C Noonan
- Initiative for Research and Education to Advance Community Health, Elson S Floyd College of Medicine, Spokane, WA
| | - S A Gharib
- UW Medicine Sleep Center, University of Washington, Seattle, WA.,Department of Medicine, University of Washington, Seattle, WA
| |
Collapse
|
8
|
Harbison RA, Kubik M, Konnick E, Faden D, Xu C, Pritchard C, Rodriguez CP, Zhang Q, Delrow JJ, Chen C, Mendez E, Duvvuri U. Clonal repopulation dynamics in recurrent human papillomavirus-associated head and neck cancer. J Clin Oncol 2017. [DOI: 10.1200/jco.2017.35.15_suppl.e17517] [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: 11/20/2022] Open
Abstract
e17517 Background: Despite the better prognosis for human papillomavirus (HPV)-associated head and neck cancer (HNC) relative to HPV-negative HNC, 10 to 25% of HPV-associated cases recur within 3 years of completing therapy. We sought to investigate clonal repopulation dynamics in recurrent HPV-related oropharyngeal squamous cell carcinoma (OPSCC). Methods: Deep sequencing ( > 500X) using a CLIA-certified, targeted 262-gene multiplexed assay was performed on DNA extracted from 11 pairs of matched FFPE-preserved primary and subsequent recurrent p16-positive OPSCC samples including two pairs from the University of Washington and nine from the University of Pittsburgh. Results: 82% of patients were male with a median (IQR) age of 62 (15) years. Nine of eleven patients presented with advanced stage disease. Five were initially treated with surgery and concurrent chemoradiation, two with surgery, and four with concurrent chemoradiation. Median (IQR) time to recurrence was 10 (10.5) months. Four patients reported a history of tobacco use. The mean (SD) number of somatic nucleotide variants (SNVs) per tumor was 16.4 (12.2). 42% of SNVs occurred in the primary alone while 28% were unique to recurrences. 28% of SNVs were shared between primary-recurrent pairs. Three patients with distant or regional recurrences had different mutational profiles between the primary and recurrence suggesting repopulation by an early-appearing clone vs sampling error. One patient developed two local recurrences with conserved mutations in addition to de novo mutations in each subsequent recurrence suggesting repopulation by early and late evolving clones. Genes with a substantial functional impact that were frequently mutated in primary tumors include IDH2 and FBXW7. Recurrently mutated genes found in recurrent tumors include TET3, PIK3CA, STK11, and HDAC4. Conclusions: In thistargeted exome sequencing study of matched primary-recurrent OPSCC tumor pairs, we observed clonal repopulation with both transmitted and de novo mutations. Intriguingly, we noted a predilection for mutations involving genes regulating metabolism including IDH2 among primary tumors which has potential implications for precision medicine approaches.
Collapse
Affiliation(s)
- Richard A. Harbison
- Department of Otolaryngology: Head and Neck Surgery, University of Washington, Seattle, WA
| | - Mark Kubik
- University of Pittsburgh, Pittsburgh, PA
| | | | | | - Chang Xu
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | - Qing Zhang
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Chu Chen
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Eduardo Mendez
- Department of Otolaryngology: Head and Neck Surgery, University of Washington, Seattle, WA
| | | |
Collapse
|
9
|
Burwick N, Zhang MY, de la Puente P, Azab AK, Hyun TS, Ruiz-Gutierrez M, Sanchez-Bonilla M, Nakamura T, Delrow JJ, MacKay VL, Shimamura A. The eIF2-alpha kinase HRI is a novel therapeutic target in multiple myeloma. Leuk Res 2017; 55:23-32. [PMID: 28119225 DOI: 10.1016/j.leukres.2017.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 06/14/2016] [Revised: 11/14/2016] [Accepted: 01/04/2017] [Indexed: 12/16/2022]
Abstract
Dexamethasone (dex) induces apoptosis in multiple myeloma (MM) cells and is a frontline treatment for this disease. However resistance to dex remains a major challenge and novel treatment approaches are needed. We hypothesized that dex utilizes translational pathways to promote apoptosis in MM and that specific targeting of these pathways could overcome dex-resistance. Global unbiased profiling of mRNA translational profiles in MM cells treated with or without dex revealed that dex significantly repressed eIF2 signaling, an important pathway for regulating ternary complex formation and protein synthesis. We demonstrate that dex induces the phosphorylation of eIF2α resulting in the translational upregulation of ATF4, a known eIF2 regulated mRNA. Pharmacologic induction of eIF2α phosphorylation via activation of the heme-regulated eIF2α kinase (HRI) induced apoptosis in MM cell lines and in primary MM cells from patients with dex-resistant disease. In addition, co-culture with marrow stroma failed to protect MM cells from apoptosis induced by targeting the eIF2 pathway. Combination therapy with rapamycin, an mTOR inhibitor, and BTdCPU, an activator of HRI, demonstrated additive effects on apoptosis in dex-resistant cells. Thus, specific activation of the eIF2α kinase HRI is a novel therapeutic target in MM that can augment current treatment strategies.
Collapse
Affiliation(s)
- Nicholas Burwick
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA; Department of Medicine, University of Washington Medical Center, 1705 NE Pacific St., Seattle, WA, USA.
| | - Michael Y Zhang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA
| | - Pilar de la Puente
- Department of Radiation Oncology, Cancer Biology Division, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Abdel Kareem Azab
- Department of Radiation Oncology, Cancer Biology Division, Washington University in St. Louis School of Medicine, St. Louis, MO, USA
| | - Teresa S Hyun
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA; Department of Pathology, University of Washington Medical Center, 1705 NE Pacific St., Seattle, WA, USA
| | - Melisa Ruiz-Gutierrez
- Department of Pediatric Hematology/Oncology, Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA, USA; Department of Pediatrics, University of Washington, 1959 NE Pacific St., Seattle, WA, USA
| | - Marilyn Sanchez-Bonilla
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA
| | - Tomoka Nakamura
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA
| | - Jeffrey J Delrow
- Genomics Resource, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA
| | - Vivian L MacKay
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Akiko Shimamura
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, USA; Department of Pediatric Hematology/Oncology, Seattle Children's Hospital, 4800 Sand Point Way, Seattle, WA, USA; Department of Pediatrics, University of Washington, 1959 NE Pacific St., Seattle, WA, USA
| |
Collapse
|
10
|
Schietinger A, Philip M, Krisnawan VE, Chiu EY, Delrow JJ, Basom RS, Lauer P, Brockstedt DG, Knoblaugh SE, Hämmerling GJ, Schell TD, Garbi N, Greenberg PD. Tumor-Specific T Cell Dysfunction Is a Dynamic Antigen-Driven Differentiation Program Initiated Early during Tumorigenesis. Immunity 2016; 45:389-401. [PMID: 27521269 DOI: 10.1016/j.immuni.2016.07.011] [Citation(s) in RCA: 436] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 01/22/2016] [Accepted: 05/05/2016] [Indexed: 01/21/2023]
Abstract
CD8(+) T cells recognizing tumor-specific antigens are detected in cancer patients but are dysfunctional. Here we developed a tamoxifen-inducible liver cancer mouse model with a defined oncogenic driver antigen (SV40 large T-antigen) to follow the activation and differentiation of naive tumor-specific CD8(+) T (TST) cells after tumor initiation. Early during the pre-malignant phase of tumorigenesis, TST cells became dysfunctional, exhibiting phenotypic, functional, and transcriptional features similar to dysfunctional T cells isolated from late-stage human tumors. Thus, T cell dysfunction seen in advanced human cancers may already be established early during tumorigenesis. Although the TST cell dysfunctional state was initially therapeutically reversible, it ultimately evolved into a fixed state. Persistent antigen exposure rather than factors associated with the tumor microenvironment drove dysfunction. Moreover, the TST cell differentiation and dysfunction program exhibited features distinct from T cell exhaustion in chronic infections. Strategies to overcome this antigen-driven, cell-intrinsic dysfunction may be required to improve cancer immunotherapy.
Collapse
Affiliation(s)
- Andrea Schietinger
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Immunology, University of Washington, Seattle, WA 98109, USA; Program of Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Mary Philip
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Division of Hematology, University of Washington, Seattle, WA 98195, USA
| | - Varintra E Krisnawan
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Edison Y Chiu
- Department of Immunology, University of Washington, Seattle, WA 98109, USA
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ryan S Basom
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Peter Lauer
- Aduro BioTech, Inc., Berkeley, CA 94710, USA
| | | | - Sue E Knoblaugh
- Comparative Medicine Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Günter J Hämmerling
- Divisions of Cellular and Molecular Immunology, DKFZ, 69120 Heidelberg, Germany
| | - Todd D Schell
- Department of Microbiology & Immunology, Penn State Hershey College of Medicine, Hershey, PA 17033, USA
| | - Natalio Garbi
- Divisions of Cellular and Molecular Immunology, DKFZ, 69120 Heidelberg, Germany; Institutes of Molecular Medicine and Experimental Immunology, University of Bonn, 53127 Bonn, Germany
| | - Philip D Greenberg
- Department of Immunology, University of Washington, Seattle, WA 98109, USA; Program of Immunology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| |
Collapse
|
11
|
Bianchi-Frias D, Basom R, Delrow JJ, Coleman IM, Dakhova O, Qu X, Fang M, Franco OE, Ericson NG, Bielas JH, Hayward SW, True L, Morrissey C, Brown L, Bhowmick NA, Rowley D, Ittmann M, Nelson PS. Cells Comprising the Prostate Cancer Microenvironment Lack Recurrent Clonal Somatic Genomic Aberrations. Mol Cancer Res 2016; 14:374-84. [PMID: 26753621 DOI: 10.1158/1541-7786.mcr-15-0330] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 12/15/2015] [Indexed: 01/02/2023]
Abstract
UNLABELLED Prostate cancer-associated stroma (CAS) plays an active role in malignant transformation, tumor progression, and metastasis. Molecular analyses of CAS have demonstrated significant changes in gene expression; however, conflicting evidence exists on whether genomic alterations in benign cells comprising the tumor microenvironment (TME) underlie gene expression changes and oncogenic phenotypes. This study evaluates the nuclear and mitochondrial DNA integrity of prostate carcinoma cells, CAS, matched benign epithelium and benign epithelium-associated stroma by whole-genome copy-number analyses, targeted sequencing of TP53, and FISH. Array comparative genomic hybridization (aCGH) of CAS revealed a copy-neutral diploid genome with only rare and small somatic copy-number aberrations (SCNA). In contrast, several expected recurrent SCNAs were evident in the adjacent prostate carcinoma cells, including gains at 3q, 7p, and 8q, and losses at 8p and 10q. No somatic TP53 mutations were observed in CAS. Mitochondrial DNA (mtDNA) extracted from carcinoma cells and stroma identified 23 somatic mtDNA mutations in neoplastic epithelial cells, but only one mutation in stroma. Finally, genomic analyses identified no SCNAs, LOH, or copy-neutral LOH in cultured cancer-associated fibroblasts, which are known to promote prostate cancer progression in vivo IMPLICATIONS The gene expression changes observed in prostate cancer-adjacent stroma and the attendant contribution of the stroma to the development and progression of prostate cancer are not due to frequent or recurrent genomic alterations in the TME.
Collapse
Affiliation(s)
- Daniella Bianchi-Frias
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ryan Basom
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ilsa M Coleman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Olga Dakhova
- Department of Pathology and Immunology, Baylor College of Medicine and Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Xiaoyu Qu
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Min Fang
- Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Omar E Franco
- Departments of Urologic Surgery and Cancer Biology, Vanderbilt University, Nashville, Tennessee
| | - Nolan G Ericson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jason H Bielas
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Simon W Hayward
- Departments of Urologic Surgery and Cancer Biology, Vanderbilt University, Nashville, Tennessee
| | - Lawrence True
- Department of Pathology, University of Washington, Seattle, Washington
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Lisha Brown
- Department of Urology, University of Washington, Seattle, Washington
| | - Neil A Bhowmick
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - David Rowley
- Department of Pathology and Immunology, Baylor College of Medicine and Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Michael Ittmann
- Department of Pathology and Immunology, Baylor College of Medicine and Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas, USA
| | - Peter S Nelson
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington. Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, Washington. Department of Pathology, University of Washington, Seattle, Washington. Department of Urology, University of Washington, Seattle, Washington. Department of Medicine, University of Washington, Seattle, Washington.
| |
Collapse
|
12
|
Kotini AG, Chang CJ, Boussaad I, Delrow JJ, Dolezal EK, Nagulapally AB, Perna F, Fishbein GA, Klimek VM, Hawkins RD, Huangfu D, Murry CE, Graubert T, Nimer SD, Papapetrou EP. Functional analysis of a chromosomal deletion associated with myelodysplastic syndromes using isogenic human induced pluripotent stem cells. Nat Biotechnol 2015; 33:646-55. [PMID: 25798938 PMCID: PMC4464949 DOI: 10.1038/nbt.3178] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 02/13/2015] [Indexed: 12/21/2022]
Abstract
Chromosomal deletions associated with human diseases, such as cancer are common, but synteny issues complicate modeling of these deletions in mice. We use cellular reprogramming and genome engineering to functionally dissect the loss of chromosome 7q [del(7q)], a somatic cytogenetic abnormality present in myelodysplastic syndromes (MDS). We derive del(7q)- and isogenic karyotypically normal induced pluripotent stem cells (iPSCs) from hematopoietic cells of MDS patients and show that the del(7q) iPSCs recapitulate disease-associated phenotypes, including impaired hematopoietic differentiation. These disease phenotypes are rescued by spontaneous dosage correction and can be reproduced in karyotypically normal cells by engineering hemizygosity of defined chr7q segments, in a 20 Mb region. We use a phenotype-rescue screen to identify candidate haploinsufficient genes that might mediate the del(7q)- hematopoietic defect. Our approach highlights the utility of human iPSCs both for functional mapping of disease-associated large-scale chromosomal deletions and for discovery of haploinsufficient genes.
Collapse
Affiliation(s)
- Andriana G Kotini
- 1] Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [3] The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chan-Jung Chang
- 1] Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [3] The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ibrahim Boussaad
- 1] Division of Hematology, Department of Medicine, University of Washington, Seattle, Washington, USA. [2] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - Jeffrey J Delrow
- Genomics Resource, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Emily K Dolezal
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Abhinav B Nagulapally
- 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Fabiana Perna
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - Gregory A Fishbein
- 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Virginia M Klimek
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - R David Hawkins
- 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Danwei Huangfu
- Developmental Biology Program, Sloan-Kettering Institute, New York, New York, USA
| | - Charles E Murry
- 1] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Pathology, University of Washington, Seattle, Washington, USA. [3] Center for Cardiovascular Biology, University of Washington, Seattle, Washington, USA. [4] Department of Bioengineering University of Washington, Seattle, Washington, USA. [5] Division of Cardiology, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Timothy Graubert
- MGH Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Stephen D Nimer
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Eirini P Papapetrou
- 1] Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [3] The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [4] Division of Hematology, Department of Medicine, University of Washington, Seattle, Washington, USA. [5] Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA. [6] Department of Pathology, University of Washington, Seattle, Washington, USA. [7] Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| |
Collapse
|
13
|
Zhang MY, Churpek JE, Keel SB, Walsh T, Lee MK, Loeb KR, Gulsuner S, Pritchard CC, Sanchez-Bonilla M, Delrow JJ, Basom RS, Forouhar M, Gyurkocza B, Schwartz BS, Neistadt B, Marquez R, Mariani CJ, Coats SA, Hofmann I, Lindsley RC, Williams DA, Abkowitz JL, Horwitz MS, King MC, Godley LA, Shimamura A. Germline ETV6 mutations in familial thrombocytopenia and hematologic malignancy. Nat Genet 2015; 47:180-5. [PMID: 25581430 PMCID: PMC4540357 DOI: 10.1038/ng.3177] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [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: 08/20/2014] [Accepted: 12/04/2014] [Indexed: 02/07/2023]
Abstract
We report germline missense mutations in ETV6 segregating with the dominant transmission of thrombocytopenia and hematologic malignancy in three unrelated kindreds, defining a new hereditary syndrome featuring thrombocytopenia with susceptibility to diverse hematologic neoplasms. Two variants, p.Arg369Gln and p.Arg399Cys, reside in the highly conserved ETS DNA-binding domain. The third variant, p.Pro214Leu, lies within the internal linker domain, which regulates DNA binding. These three amino acid sites correspond to hotspots for recurrent somatic mutation in malignancies. Functional studies show that the mutations abrogate DNA binding, alter subcellular localization, decrease transcriptional repression in a dominant-negative fashion and impair hematopoiesis. These familial genetic studies identify a central role for ETV6 in hematopoiesis and malignant transformation. The identification of germline predisposition to cytopenias and cancer informs the diagnosis and medical management of at-risk individuals.
Collapse
Affiliation(s)
- Michael Y Zhang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jane E Churpek
- 1] Section of Hematology/Oncology, Center for Clinical Cancer Genetics, University of Chicago, Chicago, Illinois, USA. [2] Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Siobán B Keel
- Department of Medicine, Division of Hematology, University of Washington, Seattle, Washington, USA
| | - Tom Walsh
- 1] Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA. [2] Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Ming K Lee
- 1] Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA. [2] Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Keith R Loeb
- 1] Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA. [2] Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Suleyman Gulsuner
- 1] Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA. [2] Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Marilyn Sanchez-Bonilla
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Jeffrey J Delrow
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Ryan S Basom
- Genomics and Bioinformatics Shared Resources, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Melissa Forouhar
- Pediatric Hematology Oncology, Madigan Army Medical Center, Tacoma, Washington, USA
| | - Boglarka Gyurkocza
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Bradford S Schwartz
- 1] Morgridge Institute for Research, University of Wisconsin, Madison, Wisconsin, USA. [2] Departments of Medicine and Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Barbara Neistadt
- 1] Section of Hematology/Oncology, Center for Clinical Cancer Genetics, University of Chicago, Chicago, Illinois, USA. [2] Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Rafael Marquez
- 1] Section of Hematology/Oncology, Center for Clinical Cancer Genetics, University of Chicago, Chicago, Illinois, USA. [2] Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Christopher J Mariani
- 1] Section of Hematology/Oncology, Center for Clinical Cancer Genetics, University of Chicago, Chicago, Illinois, USA. [2] Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Scott A Coats
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Inga Hofmann
- 1] Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School Boston, Massachusetts, USA. [2] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [3] Harvard Stem Cell Institute, Boston, Massachusetts, USA
| | - R Coleman Lindsley
- 1] Division of Hematology, Brigham and Women's Hospital, Boston, Massachusetts, USA. [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - David A Williams
- 1] Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School Boston, Massachusetts, USA. [2] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA. [3] Harvard Stem Cell Institute, Boston, Massachusetts, USA
| | - Janis L Abkowitz
- Department of Medicine, Division of Hematology, University of Washington, Seattle, Washington, USA
| | - Marshall S Horwitz
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Mary-Claire King
- 1] Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA. [2] Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Lucy A Godley
- 1] Section of Hematology/Oncology, Center for Clinical Cancer Genetics, University of Chicago, Chicago, Illinois, USA. [2] Comprehensive Cancer Center, University of Chicago, Chicago, Illinois, USA
| | - Akiko Shimamura
- 1] Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA. [2] Pediatric Hematology/Oncology, Seattle Children's Hospital, Seattle, Washington, USA. [3] Department of Pediatrics, University of Washington, Seattle, Washington, USA
| |
Collapse
|
14
|
Philip M, Funkhouser SA, Chiu EY, Phelps SR, Delrow JJ, Cox J, Fink PJ, Abkowitz JL. Heme exporter FLVCR is required for T cell development and peripheral survival. J Immunol 2015; 194:1677-85. [PMID: 25582857 DOI: 10.4049/jimmunol.1402172] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
All aerobic cells and organisms must synthesize heme from the amino acid glycine and the tricarboxylic acid cycle intermediate succinyl CoA for incorporation into hemoproteins, such as the cytochromes needed for oxidative phosphorylation. Most studies on heme regulation have been done in erythroid cells or hepatocytes; however, much less is known about heme metabolism in other cell types. The feline leukemia virus subgroup C receptor (FLVCR) is a 12-transmembrane domain surface protein that exports heme from cells, and it was shown to be required for erythroid development. In this article, we show that deletion of Flvcr in murine hematopoietic precursors caused a complete block in αβ T cell development at the CD4(+)CD8(+) double-positive stage, although other lymphoid lineages were not affected. Moreover, FLVCR was required for the proliferation and survival of peripheral CD4(+) and CD8(+) T cells. These studies identify a novel and unexpected role for FLVCR, a major facilitator superfamily metabolite transporter, in T cell development and suggest that heme metabolism is particularly important in the T lineage.
Collapse
Affiliation(s)
- Mary Philip
- Division of Hematology, University of Washington, Seattle, WA 98195; Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | | | - Edison Y Chiu
- Division of Hematology, University of Washington, Seattle, WA 98195
| | - Susan R Phelps
- Division of Hematology, University of Washington, Seattle, WA 98195
| | - Jeffrey J Delrow
- Genomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | - James Cox
- University of Utah Metabolomics Core Facility, Salt Lake City, UT 84132; and
| | - Pamela J Fink
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Janis L Abkowitz
- Division of Hematology, University of Washington, Seattle, WA 98195;
| |
Collapse
|
15
|
Cai X, Dai Z, Reeves RS, Caballero-Benitez A, Duran KL, Delrow JJ, Porter PL, Spies T, Groh V. Autonomous stimulation of cancer cell plasticity by the human NKG2D lymphocyte receptor coexpressed with its ligands on cancer cells. PLoS One 2014; 9:e108942. [PMID: 25291178 PMCID: PMC4188595 DOI: 10.1371/journal.pone.0108942] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [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: 05/16/2014] [Accepted: 08/27/2014] [Indexed: 12/20/2022] Open
Abstract
The stimulatory NKG2D receptor on lymphocytes promotes tumor immune surveillance by targeting ligands selectively induced on cancer cells. Progressing tumors counteract by employing tactics to disable lymphocyte NKG2D. This negative dynamic is escalated as some human cancer cells co-opt expression of NKG2D, thereby complementing the presence of its ligands for autonomous stimulation of oncogenic signaling. Clinical association data imply relationships between cancer cell NKG2D and metastatic disease. Here we show that NKG2D promotes cancer cell plasticity by induction of phenotypic, molecular, and functional signatures diagnostic of the epithelial–mesenchymal transition, and of stem-like traits via induction of Sox9, a key transcriptional regulator of breast stem cell maintenance. These findings obtained with model breast tumor lines and xenotransplants were recapitulated by exvivo cancer cells from primary invasive breast carcinomas. Thus, NKG2D may have the capacity to drive high malignancy traits underlying metastatic disease.
Collapse
Affiliation(s)
- Xin Cai
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Zhenpeng Dai
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Rebecca S. Reeves
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Andrea Caballero-Benitez
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Kate L. Duran
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Jeffrey J. Delrow
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Peggy L. Porter
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Thomas Spies
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - Veronika Groh
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| |
Collapse
|
16
|
Iwata M, Sandstrom RS, Delrow JJ, Stamatoyannopoulos JA, Torok-Storb B. Functionally and phenotypically distinct subpopulations of marrow stromal cells are fibroblast in origin and induce different fates in peripheral blood monocytes. Stem Cells Dev 2013; 23:729-40. [PMID: 24131213 DOI: 10.1089/scd.2013.0300] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Marrow stromal cells constitute a heterogeneous population of cells, typically isolated after expansion in culture. In vivo, stromal cells often exist in close proximity or in direct contact with monocyte-derived macrophages, yet their interaction with monocytes is largely unexplored. In this report, isolated CD146(+) and CD146(-) stromal cells, as well as immortalized cell lines representative of each (designated HS27a and HS5, respectively), were shown by global DNase I hypersensitive site mapping and principal coordinate analysis to have a lineage association with marrow fibroblasts. Gene expression profiles generated for the CD146(+) and CD146(-) cell lines indicate significant differences in their respective transcriptomes, which translates into differences in secreted factors. Consequently, the conditioned media (CM) from these two populations induce different fates in peripheral blood monocytes. Monocytes incubated in CD146(+) CM acquire a tissue macrophage phenotype, whereas monocytes incubated in CM from CD146(-) cells express markers associated with pre-dendritic cells. Importantly, when CD14(+) monocytes are cultured in contact with the CD146(+) cells, the combined cell populations, assayed as a unit, show increased levels of transcripts associated with organismal development and hematopoietic regulation. In contrast, the gene expression profile from cocultures of monocytes and CD146(-) cells does not differ from that obtained when monocytes are cultured with CD146(-) CM. These in vitro results show that the CD146(+) marrow stromal cells together with monocytes increase the expression of genes relevant to hematopoietic regulation. In vivo relevance of these data is suggested by immunohistochemistry of marrow biopsies showing juxtaposed CD146(+) cells and CD68(+) cells associated with these upregulated proteins.
Collapse
Affiliation(s)
- Mineo Iwata
- 1 Fred Hutchinson Cancer Research Center , Seattle, Washington
| | | | | | | | | |
Collapse
|
17
|
Pattacini L, Murnane PM, Kahle EM, Bolton MJ, Delrow JJ, Lingappa JR, Katabira E, Donnell D, McElrath MJ, Baeten JM, Lund JM. Differential regulatory T cell activity in HIV type 1-exposed seronegative individuals. AIDS Res Hum Retroviruses 2013; 29:1321-9. [PMID: 23815575 DOI: 10.1089/aid.2013.0075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The potential role of conventional and regulatory T cells (Tregs) in protection from HIV-1 infection remains unclear. To address this question, we analyzed samples from 129 HIV-1-exposed seronegative individuals (HESN) from an HIV-1-serodiscordant couples cohort. To assess the presence of HIV-specific T cell responses and Treg function, we measured the proliferation of T cells in response to HIV-1 peptide pools in peripheral blood mononuclear cells (PBMCs) and PBMCs depleted of Tregs. We identified HIV-specific CD4(+) and CD8(+) T cell responses and, surprisingly, the overall CD4(+) and CD8(+) T cell response rate was not increased when Tregs were removed from cell preparations. Of the 20 individuals that had HIV-1-specific CD4(+) T cell responses, only eight had Tregs that could suppress this proliferation. When compared with individuals whose Tregs could suppress HIV-1-specific CD4(+) T cell proliferation, individuals with Tregs unable to suppress showed a trend toward increased T cell activation and Treg frequency and a significant increase in HIV-1-specific production of microphage inflammatory protein-1β (MIP-1β) by CD4(+) T cells, autocrine production of which has been shown to be protective in terms of HIV-1 infection of CD4(+) T cells.
Collapse
Affiliation(s)
- Laura Pattacini
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Pamela M. Murnane
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Erin M. Kahle
- Department of Global Health, University of Washington, Seattle, Washington
- Infectious Disease Institute, Makerere University, Kampala, Uganda
| | - Michael J. Bolton
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jeffrey J. Delrow
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jairam R. Lingappa
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Medicine, University of Washington, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Elly Katabira
- Infectious Disease Institute, Makerere University, Kampala, Uganda
| | - Deborah Donnell
- Department of Global Health, University of Washington, Seattle, Washington
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Global Health, University of Washington, Seattle, Washington
| | - Jared M. Baeten
- Department of Global Health, University of Washington, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
- Department of Medicine, University of Washington, Seattle, Washington
| | - Jennifer M. Lund
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Global Health, University of Washington, Seattle, Washington
| |
Collapse
|
18
|
Rincon-Arano H, Halow J, Delrow JJ, Parkhurst SM, Groudine M. UpSET recruits HDAC complexes and restricts chromatin accessibility and acetylation at promoter regions. Cell 2012. [PMID: 23177352 DOI: 10.1016/j.cell.2012.11.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Developmental gene expression results from the orchestrated interplay between genetic and epigenetic mechanisms. Here, we describe upSET, a transcriptional regulator encoding a SET domain-containing protein recruited to active and inducible genes in Drosophila. However, unlike other Drosophila SET proteins associated with gene transcription, UpSET is part of an Rpd3/Sin3-containing complex that restricts chromatin accessibility and histone acetylation to promoter regions. In the absence of UpSET, active chromatin marks and chromatin accessibility increase and spread to genic and flanking regions due to destabilization of the histone deacetylase complex. Consistent with this, transcriptional noise increases, as manifest by activation of repetitive elements and off-target genes. Interestingly, upSET mutant flies are female sterile due to upregulation of key components of Notch signaling during oogenesis. Thus UpSET defines a class of metazoan transcriptional regulators required to fine tune transcription by preventing the spread of active chromatin.
Collapse
Affiliation(s)
- Hector Rincon-Arano
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | | | | |
Collapse
|
19
|
Schietinger A, Delrow JJ, Basom RS, Blattman JN, Greenberg PD. Rescued tolerant CD8 T cells are preprogrammed to reestablish the tolerant state. Science 2012; 335:723-7. [PMID: 22267581 DOI: 10.1126/science.1214277] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tolerant self-antigen-specific CD8 T cells fail to proliferate in response to antigen, thereby preventing autoimmune disease. By using an in vivo mouse model, we show that tolerant T cells proliferate and become functional under lymphopenic conditions, even in a tolerogenic environment. However, T cell rescue is only transient, with tolerance reimposed upon lymphorepletion even in the absence of tolerogen (self-antigen), challenging the prevailing paradigm that continuous antigen exposure is critical to maintain tolerance. Genome-wide messenger RNA and microRNA profiling revealed that tolerant T cells have a tolerance-specific gene profile that can be temporarily overridden under lymphopenic conditions but is inevitably reimposed, which suggests epigenetic regulation. These insights into the regulatory mechanisms that maintain or break self-tolerance may lead to new strategies for the treatment of cancer and autoimmunity.
Collapse
Affiliation(s)
- Andrea Schietinger
- Department of Immunology, University of Washington (UW), Seattle, WA 98195, USA
| | | | | | | | | |
Collapse
|
20
|
Abed M, Barry KC, Kenyagin D, Koltun B, Phippen TM, Delrow JJ, Parkhurst SM, Orian A. Degringolade, a SUMO-targeted ubiquitin ligase, inhibits Hairy/Groucho-mediated repression. EMBO J 2011; 30:1289-301. [PMID: 21343912 PMCID: PMC3094120 DOI: 10.1038/emboj.2011.42] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 01/26/2011] [Indexed: 11/09/2022] Open
Abstract
Transcriptional cofactors are essential for proper embryonic development. One such cofactor in Drosophila, Degringolade (Dgrn), encodes a RING finger/E3 ubiquitin ligase. Dgrn and its mammalian ortholog RNF4 are SUMO-targeted ubiquitin ligases (STUbLs). STUbLs bind to SUMOylated proteins via their SUMO interaction motif (SIM) domains and facilitate substrate ubiquitylation. In this study, we show that Dgrn is a negative regulator of the repressor Hairy and its corepressor Groucho (Gro/transducin-like enhancer (TLE)) during embryonic segmentation and neurogenesis, as dgrn heterozygosity suppresses Hairy mutant phenotypes and embryonic lethality. Mechanistically Dgrn functions as a molecular selector: it targets Hairy for SUMO-independent ubiquitylation that inhibits the recruitment of its corepressor Gro, without affecting the recruitment of its other cofactors or the stability of Hairy. Concomitantly, Dgrn specifically targets SUMOylated Gro for sequestration and antagonizes Gro functions in vivo. Our findings suggest that by targeting SUMOylated Gro, Dgrn serves as a molecular switch that regulates cofactor recruitment and function during development. As Gro/TLE proteins are conserved universal corepressors, this may be a general paradigm used to regulate the Gro/TLE corepressors in other developmental processes.
Collapse
Affiliation(s)
- Mona Abed
- Cancer and Vascular Biology Research Center, Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Brewood GP, Delrow JJ, Schurr JM. Calf-Thymus Topoisomerase I Equilibrates Metastable Secondary Structure Subsequent to Relaxation of Superhelical Stress. Biochemistry 2010; 49:3367-80. [DOI: 10.1021/bi9017126] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Greg P. Brewood
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700
| | - Jeffrey J. Delrow
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700
| | - J. Michael Schurr
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700
| |
Collapse
|
22
|
Holcomb IN, Grove DI, Kinnunen M, Friedman CL, Gallaher IS, Morgan TM, Sather CL, Delrow JJ, Nelson PS, Lange PH, Ellis WJ, True LD, Young JM, Hsu L, Trask BJ, Vessella RL. Genomic alterations indicate tumor origin and varied metastatic potential of disseminated cells from prostate cancer patients. Cancer Res 2008; 68:5599-608. [PMID: 18632612 DOI: 10.1158/0008-5472.can-08-0812] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Disseminated epithelial cells can be isolated from the bone marrow of a far greater fraction of prostate-cancer patients than the fraction of patients who progress to metastatic disease. To provide a better understanding of these cells, we have characterized their genomic alterations. We first present an array comparative genomic hybridization method capable of detecting genomic changes in the small number of disseminated cells (10-20) that can typically be obtained from bone marrow aspirates of prostate-cancer patients. We show multiple regions of copy-number change, including alterations common in prostate cancer, such as 8p loss, 8q gain, and gain encompassing the androgen-receptor gene on Xq, in the disseminated cell pools from 11 metastatic patients. We found fewer and less striking genomic alterations in the 48 pools of disseminated cells from patients with organ-confined disease. However, we identify changes shared by these samples with their corresponding primary tumors and prostate-cancer alterations reported in the literature, evidence that these cells, like those in advanced disease, are disseminated tumor cells (DTC). We also show that DTCs from patients with advanced and localized disease share several abnormalities, including losses containing cell-adhesion genes and alterations reported to associate with progressive disease. These shared alterations might confer the capability to disseminate or establish secondary disease. Overall, the spectrum of genomic deviations is evidence for metastatic capacity in advanced-disease DTCs and for variation in that capacity in DTCs from localized disease. Our analysis lays the foundation for elucidation of the relationship between DTC genomic alterations and progressive prostate cancer.
Collapse
Affiliation(s)
- Ilona N Holcomb
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Orian A, Delrow JJ, Rosales Nieves AE, Abed M, Metzger D, Paroush Z, Eisenman RN, Parkhurst SM. A Myc-Groucho complex integrates EGF and Notch signaling to regulate neural development. Proc Natl Acad Sci U S A 2007; 104:15771-6. [PMID: 17898168 PMCID: PMC2000393 DOI: 10.1073/pnas.0707418104] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [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] [Indexed: 01/02/2023] Open
Abstract
Integration of patterning cues via transcriptional networks to coordinate gene expression is critical during morphogenesis and misregulated in cancer. Using DNA adenine methyltransferase (Dam)ID chromatin profiling, we identified a protein-protein interaction between the Drosophila Myc oncogene and the Groucho corepressor that regulates a subset of direct dMyc targets. Most of these shared targets affect fate or mitosis particularly during neurogenesis, suggesting the dMyc-Groucho complex may coordinate fate acquisition with mitotic capacity during development. We find an antagonistic relationship between dMyc and Groucho that mimics the antagonistic interactions found for EGF and Notch signaling: dMyc is required to specify neuronal fate and enhance neuroblast mitosis, whereas Groucho is required to maintain epithelial fate and inhibit mitosis. Our results suggest that the dMyc-Groucho complex defines a previously undescribed mechanism of Myc function and may serve as the transcriptional unit that integrates EGF and Notch inputs to regulate early neuronal development.
Collapse
Affiliation(s)
- Amir Orian
- Division of Basic Sciences
- Rappaport Faculty of Medicine and Research Institute, Technion–Israel Institute of Technology, Haifa 31096, Israel; and
- To whom correspondence may be addressed. E-mail: , , or
| | - Jeffrey J. Delrow
- Genomic Resource, Fred Hutchinson Cancer Research Center, Seattle, WA 98109
| | | | - Mona Abed
- Rappaport Faculty of Medicine and Research Institute, Technion–Israel Institute of Technology, Haifa 31096, Israel; and
| | | | - Ze'ev Paroush
- Department of Biochemistry, Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Robert N. Eisenman
- Division of Basic Sciences
- To whom correspondence may be addressed. E-mail: , , or
| | - Susan M. Parkhurst
- Division of Basic Sciences
- To whom correspondence may be addressed. E-mail: , , or
| |
Collapse
|
24
|
Loch CM, Ramirez AB, Liu Y, Sather CL, Delrow JJ, Scholler N, Garvik BM, Urban ND, McIntosh MW, Lampe PD. Use of high density antibody arrays to validate and discover cancer serum biomarkers. Mol Oncol 2007; 1:313-20. [PMID: 19383305 DOI: 10.1016/j.molonc.2007.08.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 08/22/2007] [Accepted: 08/23/2007] [Indexed: 11/16/2022] Open
Abstract
Perhaps the greatest barrier to translation of serum biomarker discoveries is the inability to evaluate putative biomarkers in high throughput validation studies. Here we report on the development, production, and implementation of a high-density antibody microarray used to evaluate large numbers of candidate ovarian cancer serum biomarkers. The platform was shown to be useful for evaluation of individual antibodies for comparative analysis, such as with disease classification, and biomarker validation and discovery. We demonstrate its performance by showing that known tumor markers behave as expected. We also identify several promising biomarkers from a candidate list and generate hypotheses to support new discovery studies.
Collapse
Affiliation(s)
- Christian M Loch
- Molecular Diagnostics Program, Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Abstract
Array-based comparative genomic hybridization (array-CGH) provides a high-throughput, high-resolution method to measure relative changes in DNA copy number simultaneously at thousands of genomic loci. Typically, these measurements are reported and displayed linearly on chromosome maps, and gains and losses are detected as deviations from normal diploid cells. We propose that one may consider denoising the data to uncover the true copy number changes before drawing inferences on the patterns of aberrations in the samples. Nonparametric techniques are particularly suitable for data denoising as they do not impose a parametric model in finding structures in the data. In this paper, we employ wavelets to denoise the data as wavelets have sound theoretical properties and a fast computational algorithm, and are particularly well suited for handling the abrupt changes seen in array-CGH data. A simulation study shows that denoising data prior to testing can achieve greater power in detecting the aberrant spot than using the raw data without denoising. Finally, we illustrate the method on two array-CGH data sets.
Collapse
Affiliation(s)
- Li Hsu
- Biostatistics Program, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, M2-B500, Seattle, WA 98109, USA.
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Loo LWM, Grove DI, Williams EM, Neal CL, Cousens LA, Schubert EL, Holcomb IN, Massa HF, Glogovac J, Li CI, Malone KE, Daling JR, Delrow JJ, Trask BJ, Hsu L, Porter PL. Array Comparative Genomic Hybridization Analysis of Genomic Alterations in Breast Cancer Subtypes. Cancer Res 2004; 64:8541-9. [PMID: 15574760 DOI: 10.1158/0008-5472.can-04-1992] [Citation(s) in RCA: 176] [Impact Index Per Article: 8.8] [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] [Indexed: 11/16/2022]
Abstract
In this study, we performed high-resolution array comparative genomic hybridization with an array of 4153 bacterial artificial chromosome clones to assess copy number changes in 44 archival breast cancers. The tumors were flow sorted to exclude non-tumor DNA and increase our ability to detect gene copy number changes. In these tumors, losses were more frequent than gains, and gains in 1q and loss in 16q were the most frequent alterations. We compared gene copy number changes in the tumors based on histologic subtype and estrogen receptor (ER) status, i.e., ER-negative infiltrating ductal carcinoma, ER-positive infiltrating ductal carcinoma, and ER-positive infiltrating lobular carcinoma. We observed a consistent association between loss in regions of 5q and ER-negative infiltrating ductal carcinoma, as well as more frequent loss in 4p16, 8p23, 8p21, 10q25, and 17p11.2 in ER-negative infiltrating ductal carcinoma compared with ER-positive infiltrating ductal carcinoma (adjusted P values < or = 0.05). We also observed high-level amplifications in ER-negative infiltrating ductal carcinoma in regions of 8q24 and 17q12 encompassing the c-myc and c-erbB-2 genes and apparent homozygous deletions in 3p21, 5q33, 8p23, 8p21, 9q34, 16q24, and 19q13. ER-positive infiltrating ductal carcinoma showed a higher frequency of gain in 16p13 and loss in 16q21 than ER-negative infiltrating ductal carcinoma. Correlation analysis highlighted regions of change commonly seen together in ER-negative infiltrating ductal carcinoma. ER-positive infiltrating lobular carcinoma differed from ER-positive infiltrating ductal carcinoma in the frequency of gain in 1q and loss in 11q and showed high-level amplifications in 1q32, 8p23, 11q13, and 11q14. These results indicate that array comparative genomic hybridization can identify significant differences in the genomic alterations between subtypes of breast cancer.
Collapse
MESH Headings
- Adult
- Aged
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Lobular/genetics
- Carcinoma, Lobular/metabolism
- Carcinoma, Lobular/pathology
- DNA, Neoplasm/analysis
- DNA, Neoplasm/genetics
- Female
- Flow Cytometry
- Gene Dosage
- Humans
- Middle Aged
- Nucleic Acid Hybridization
- Receptors, Estrogen/biosynthesis
- Reproducibility of Results
Collapse
Affiliation(s)
- Lenora W M Loo
- Division of Human Biology, Division of Public Health Sciences, and Genomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Bianchi-Frias D, Orian A, Delrow JJ, Vazquez J, Rosales-Nieves AE, Parkhurst SM. Hairy transcriptional repression targets and cofactor recruitment in Drosophila. PLoS Biol 2004; 2:E178. [PMID: 15252443 PMCID: PMC449821 DOI: 10.1371/journal.pbio.0020178] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.1] [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: 10/13/2003] [Accepted: 04/14/2004] [Indexed: 12/01/2022] Open
Abstract
Members of the widely conserved Hairy/Enhancer of split family of basic Helix-Loop-Helix repressors are essential for proper Drosophila and vertebrate development and are misregulated in many cancers. While a major step forward in understanding the molecular mechanism(s) surrounding Hairy-mediated repression was made with the identification of Groucho, Drosophila C-terminal binding protein (dCtBP), and Drosophila silent information regulator 2 (dSir2) as Hairy transcriptional cofactors, the identity of Hairy target genes and the rules governing cofactor recruitment are relatively unknown. We have used the chromatin profiling method DamID to perform a global and systematic search for direct transcriptional targets for Drosophila Hairy and the genomic recruitment sites for three of its cofactors: Groucho, dCtBP, and dSir2. Each of the proteins was tethered to Escherichia coli DNA adenine methyltransferase, permitting methylation proximal to in vivo binding sites in both Drosophila Kc cells and early embryos. This approach identified 40 novel genomic targets for Hairy in Kc cells, as well as 155 loci recruiting Groucho, 107 loci recruiting dSir2, and wide genomic binding of dCtBP to 496 loci. We also adapted DamID profiling such that we could use tightly gated collections of embryos (2-6 h) and found 20 Hairy targets related to early embryogenesis. As expected of direct targets, all of the putative Hairy target genes tested show Hairy-dependent expression and have conserved consensus C-box-containing sequences that are directly bound by Hairy in vitro. The distribution of Hairy targets in both the Kc cell and embryo DamID experiments corresponds to Hairy binding sites in vivo on polytene chromosomes. Similarly, the distributions of loci recruiting each of Hairy's cofactors are detected as cofactor binding sites in vivo on polytene chromosomes. We have identified 59 putative transcriptional targets of Hairy. In addition to finding putative targets for Hairy in segmentation, we find groups of targets suggesting roles for Hairy in cell cycle, cell growth, and morphogenesis, processes that must be coordinately regulated with pattern formation. Examining the recruitment of Hairy's three characterized cofactors to their putative target genes revealed that cofactor recruitment is context-dependent. While Groucho is frequently considered to be the primary Hairy cofactor, we find here that it is associated with only a minority of Hairy targets. The majority of Hairy targets are associated with the presence of a combination of dCtBP and dSir2. Thus, the DamID chromatin profiling technique provides a systematic means of identifying transcriptional target genes and of obtaining a global view of cofactor recruitment requirements during development.
Collapse
Affiliation(s)
- Daniella Bianchi-Frias
- 1Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattle, Washington, United States of America
| | - Amir Orian
- 1Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattle, Washington, United States of America
| | - Jeffrey J Delrow
- 2Genomics Resource, Fred Hutchinson Cancer Research CenterSeattle, Washington, United States of America
| | - Julio Vazquez
- 3Scientific Imaging, Fred Hutchinson Cancer Research CenterSeattle, WashingtonUnited States of America
| | - Alicia E Rosales-Nieves
- 1Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattle, Washington, United States of America
| | - Susan M Parkhurst
- 1Division of Basic Sciences, Fred Hutchinson Cancer Research CenterSeattle, Washington, United States of America
| |
Collapse
|
28
|
Abstract
Most microarray scanning software for glass spotted arrays provides estimates for the intensity for the "foreground" and "background" of two channels for every spot. The common approach in further analyzing such data is to first subtract the background from the foreground for each channel and to use the ratio of these two results as the estimate of the expression level. The resulting ratios are, after possible averaging over replicates, the usual inputs for further data analysis, such as clustering. If, with this background correction procedure, the foreground intensity was smaller than the background intensity for a channel, that spot (on that array) yields no usable data. In this paper it is argued that this preprocessing leads to estimates of the expression that have a much larger variance than needed when the expression levels are low.
Collapse
Affiliation(s)
- Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, MP 1002, Seattle, WA 98109-1024, USA.
| | | | | | | |
Collapse
|
29
|
Fujimoto BS, Clendenning JB, Delrow JJ, Heath PJ, Schurr M. Fluorescence and Photobleaching Studies of Methylene Blue Binding to DNA. ACTA ACUST UNITED AC 2002. [DOI: 10.1021/j100077a033] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
30
|
Abstract
The question of long-range allosteric transitions of DNA secondary structure and their possible involvement in transcriptional activation is discussed in the light of new results. A variety of recent evidence strongly supports a fluctuating long-range description of DNA secondary structure. Balanced equilibria between two or more different secondary structures, and the occurrence of very large domain sizes, have been documented in several instances. Long-range allosteric effects stemming from changes in sequence or secondary structure over a small region of the DNA have been observed to extend over distances up to hundreds of base pairs in some cases. The discovery that coherent bending strain beyond a threshold level in small (N < or = 250 base pairs (bp)] circular DNAs significantly alters the DNA secondary structure has important implications, especially for transcriptional activators that either bend the DNA directly or are involved in the formation of DNA loops of sufficiently small size (N < or = 250 bp). Whether the RNA polymerase is activated primarily via protein: protein contacts, as is widely believed, or instead via a bend-induced allosteric transition of the DNA in such a small loop, is now an open question. Binding of the transcriptional activator Sp1 to linear DNA induces a remarkably long-range change in its secondary structure, and catabolite activator protein binding to a supercoiled DNA behaves similarly, though possibly for different reasons. Compelling evidence for a bend-induced long-range structural transmission effect of the transcriptional activator integration host factor on RNA polymerase activity was recently reported. These results may augur a new paradigm in which allosteric transitions of duplex DNA, as well as of the proteins, are involved in the regulation of transcription.
Collapse
Affiliation(s)
- J M Schurr
- Department of Chemistry, University of Washington, Seattle 98195-1700, USA
| | | | | | | |
Collapse
|
31
|
Abstract
Changes in the average secondary structures of three different linear DNAs over the premelting region from 5 to 60 degrees C were investigated by measuring their CD spectra and also their torsion elastic constants (<alpha>) by time-resolved fluorescence polarization anisotropy. For one of these DNAs, the Haell fragment of pBR322, the apparent diffusion coefficients [Dapp(k)] at small and large scattering vectors (k) were also measured by dynamic light scattering. With increasing temperature, all three DNAs exhibited typical premelting changes in their CD spectra, and these were accompanied by 1.4- to 1.7-fold decreases in <alpha>. Also for the 1876 base pair fragment, Dapp(k) at large scattering vectors, which is sensitive to the dynamic bending rigidity, decreased by 17%, even though there was no change at small scattering vectors, where Dapp(k) = D0 is the translational diffusion coefficient of the center-of-mass. These observations demonstrate conclusively that the premelting CD changes of these DNAs are associated with a significant change in average secondary structure and mechanical properties, though not in persistence length. In the presence of 0.5 M tetramethylammonium chloride (TMA-Cl) the premelting change in CD is largely suppressed, and the corresponding changes in <alpha> and Dapp(k) at large scattering vectors are substantially diminished. These observations suggest that TMA-Cl, which binds preferentially to A.T-rich regions and stabilizes those regions (relative to G.C-rich regions) against melting, effectively stabilizes the prevailing low-temperature secondary structure sufficiently that the DNA is effectively trapped in that state over the temperature range observed.
Collapse
Affiliation(s)
- J J Delrow
- Department of Chemistry, University of Washington, Seattle 98195-1700, USA
| | | | | | | |
Collapse
|
32
|
Abstract
Monte Carlo simulations using temperature-invariant torsional and bending rigidities fail to predict the rather steep decline of the experimental supercoiling free energy with increasing temperature, and consequently fail to predict the correct sign and magnitude of the supercoiling entropy. To illustrate this problem, values of the twist energy parameter (E(T)), which governs the supercoiling free energy, were simulated using temperature-invariant torsion and bending potentials and compared to experimental data on pBR322 over a range of temperatures. The slope, -dE(T)/dT, of the simulated values is also compared to the slope derived from previous calorimetric data. The possibility that the discrepancies arise from some hitherto undetected temperature dependence of the torsional rigidity was investigated. The torsion elastic constant of an 1876-bp restriction fragment of pBR322 was measured by time-resolved fluorescence polarization anisotropy of intercalated ethidium over the range 278-323 K, and found to decline substantially over that interval. Simulations of a 4349-bp model DNA were performed using these measured temperature-dependent torsional rigidities. The slope, -dE(T)/dT, of the simulated data agrees satisfactorily with the slope derived from previous calorimetric measurements, but still lies substantially below that of Duguet's data. Models that involve an equilibrium between different secondary structure states with different intrinsic twists and torsion constants provide the most likely explanation for the variation of the torsion constant with T and other pertinent observations.
Collapse
Affiliation(s)
- J J Delrow
- Department of Chemistry, University of Washington, Seattle 98195-1700, USA
| | | | | |
Collapse
|
33
|
Abstract
A 1000 base pair (bp) model supercoiled DNA is simulated using spherical screened Coulomb interactions between subunits on one hand and equivalent hard-cylinder interactions on the other. The amplitudes, or effective charges, of the spherical screened Coulomb electrostatic potentials are chosen so that the electrostatic potential surrounding the middle of a linear array of 2001 subunits (31.8 A diameter) closely matches the solution of the nonlinear Poisson-Boltzmann equation for a cylinder with 12 A radius and the full linear charge density of DNA at all distances beyond the 24 A hard-core diameter. This superposition of spherical screened Coulomb potentials is practically identical to the particular solution of the cylindrical linearized Poisson-Boltzmann equation that matches the solution of the nonlinear Poisson-Boltzmann equation at large distances. The interaction energy between subunits is reckoned from the effective charges according to the standard DLVO expression. The equivalent hard-cylinder diameter is chosen following Stigter's protocol for matching second virial coefficients, but for the full linear charge density of DNA. The electrostatic persistence length of the model with screened Coulomb interactions is extremely sensitive to the (arbitrarily) chosen subunit length at the higher salt concentrations. The persistence length of the hard-cylinder model is adjusted to match that of the screened Coulomb model for each ionic condition. Simulations for a superhelix density sigma = -0.05 using a spherical screened Coulomb interaction plus a 24 A hard-cylinder core (SCPHC) potential indicate that the radius of gyration of this 1000 bp DNA actually undergoes a slight increase as the NaCl concentration is raised from 0.01 to 1.0M. Thus, merely softening the potential from hard-cylinder to screened Coulomb form does not produce a large decrease in radius of gyration with increasing NaCl concentration for DNAs of this size. Radii of gyration, static structure factors, and diffusion coefficients obtained using the equivalent hard-cylinder (EHC) potential agree well with those obtained using the SCPHC potential in 1.0M NaCl, but in 0.1M NaCl the agreement is not as good, and in 0.01M NaCl the agreement is definitely unsatisfactory. These conclusions differ in significant respects from those obtained in previous studies.
Collapse
Affiliation(s)
- J J Delrow
- Department of Chemistry, University of Washington, Seattle 98195-1700, USA
| | | | | |
Collapse
|
34
|
Gebe JA, Delrow JJ, Heath PJ, Fujimoto BS, Stewart DW, Schurr JM. Effects of Na+ and Mg2+ on the structures of supercoiled DNAs: comparison of simulations with experiments. J Mol Biol 1996; 262:105-28. [PMID: 8831783 DOI: 10.1006/jmbi.1996.0502] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.1] [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] [Indexed: 02/02/2023]
Abstract
Recent cryo-electron microscopy (cryo-EM) results suggest that sufficient NaCl concentration (> or approximately 0.1 M) and superhelix density (> or approximately-0.05) cause circular DNAs to adopt highly extended, tightly interwound configurations, in which the strands are laterally contiguous along almost their entire length. Millimolar levels of MgCl2 reportedly act synergistically with NaCl to produce similar conformations. However, Monte Carlo simulations with purely repulsive interduplex forces failed to reproduce such structures. In the present work, solution measurements of particular physical properties were performed both to characterize the effects of Na+ and Mg2+ on DNA structure and to provide quantitative tests of Monte Carlo simulations of circular DNAs. Supercoiled p30 delta DNAs in 10 mM Tris plus 0, 0.122, and 0.1 M NaCl, and 0.1 M NaCl plus 4 mM Mg2+ were examined by static and dynamic light scattering (LS and DLS), time-resolved fluorescence polarization anisotropy (FPA) of intercalated ethidium, and circular dichroism (CD) spectroscopy. Upon addition of 0.122 M NaCl, the radius of gyration (Rg) decreased substantially, which indicates that p30 delta adopts a more compact structure. This contradicts the cryo-EM studies, where molecular extension and Rg both increase upon adding 0.1 M NaCl. In 0.1 M NaCl, the torsion constant measured by FPA is practically invariant to superhelix density, and the plateau diffusion coefficient at large scattering vector (Dplat) is likewise nearly the same at both relaxed and native superhelix densities. Such invariance is difficult to reconcile with any transition from relaxed circles to tightly interwound structures with laterally contiguous strands. Metropolis Monte Carlo simulations were performed to generate canonically distributed sets of structures, from which average Do values and scattered intensity ratios, [symbol: see text]I (zero) [symbol: see text]/[symbol: see text] l(k) [symbol: see text], were calculated. Agreement between simulations and experiments in regard to [symbol: see text] I(O) [symbol: see text] /[symbol: see text] I(k) [symbol: see text], D(zero) and the supercoiling free energy, delta Gsc (delta l), is remarkably good for the most extensively studied p30 delta samples. The simulated structures exhibit no sign of very tight interwinding with extensive lateral contacts, but instead exhibit most probable superhelix diameters of 85 to 90 A. When 4 mM Mg2+ was added to native supercoiled p30 delta in 0.1 M NaCl, Rg decreased, D(zero) increased, and the longest internal relaxation rate (1/tau 2(zero)) increased, all of which indicate a further overall contraction of the molecular envelope. The torsion constant exhibited a slight increase that is hardly statistically significant. In this case, agreement between the simulations and experiments was only semi-quantitative for most samples investigated, although the predicted contraction was exhibited by all five samples of p30 delta and one of pBR322 DNA. The simulated structures in 0.1 M NaCl plus 4 mM Mg2+ again showed no sign of extensive lateral contacts. A plausible explanation is proposed for the highly extended, tightly interwound structures seen in cryo-EM, and explicitly tested by Monte Carlo simulations of a 1000 bp circular DNA at +25 and -50 degrees C. Structures identical to those seen in cryo-EM are in fact the equilibrium structures in the simulations at -50 degrees C, and the estimated time for equilibration (2.3 x 10(-6) second) is much smaller than the estimated time for vitrification (1 x 10(-4) second).
Collapse
Affiliation(s)
- J A Gebe
- Department of Chemistry, University of Washington Seattle 98195-1700, USA
| | | | | | | | | | | |
Collapse
|
35
|
Paulson JR, Mesner PW, Delrow JJ, Mahmoud NN, Ciesielski WA. Rapid analysis of mitotic histone H1 phosphorylation by cationic disc electrophoresis at neutral pH in minigels. Anal Biochem 1992; 203:227-34. [PMID: 1384384 DOI: 10.1016/0003-2697(92)90307-s] [Citation(s) in RCA: 8] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A new method is described for analysis of histone H1 and other basic proteins by cationic disc electrophoresis in polyacrylamide gels at neutral pH. The multiphasic buffer (disc) system uses Na+ as leading ion, L-histidine as trailing ion, and Hepes as buffering counterion. These "Hepes/histidine gels" have three advantages over conventional acid-urea gels for studies of H1 phosphorylation and dephosphorylation: speed, convenience, and the need for only small amounts of cells or chromatin. Core histones and their acetylated forms can also be separated in gels containing 0.4% Triton X-100. The difference in electrophoretic mobility between mitotic (superphosphorylated) and interphase H1 from HeLa cells is approximately twice as great at neutral pH as at pH 4.5, making it possible to separate these two H1 forms rapidly and easily in Hepes/histidine "minigels" only 5-cm long. Total histones can be rapidly prepared by simply neutralizing 0.2 N HCl extracts, and the entire analysis, from harvesting cells to destaining gels, can be carried out in 1 day. The stacking effect of the disc system produces sharp bands and high resolution even with relatively dilute samples.
Collapse
Affiliation(s)
- J R Paulson
- Department of Chemistry, University of Wisconsin Oshkosh, 54901
| | | | | | | | | |
Collapse
|