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Sawyer JK, Kabiri Z, Montague RA, Allen SR, Stewart R, Paramore SV, Cohen E, Zaribafzadeh H, Counter CM, Fox DT. Exploiting codon usage identifies intensity-specific modifiers of Ras/MAPK signaling in vivo. PLoS Genet 2020; 16:e1009228. [PMID: 33296356 PMCID: PMC7752094 DOI: 10.1371/journal.pgen.1009228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/21/2020] [Accepted: 10/27/2020] [Indexed: 01/05/2023] Open
Abstract
Signal transduction pathways are intricately fine-tuned to accomplish diverse biological processes. An example is the conserved Ras/mitogen-activated-protein-kinase (MAPK) pathway, which exhibits context-dependent signaling output dynamics and regulation. Here, by altering codon usage as a novel platform to control signaling output, we screened the Drosophila genome for modifiers specific to either weak or strong Ras-driven eye phenotypes. Our screen enriched for regions of the genome not previously connected with Ras phenotypic modification. We mapped the underlying gene from one modifier to the ribosomal gene RpS21. In multiple contexts, we show that RpS21 preferentially influences weak Ras/MAPK signaling outputs. These data show that codon usage manipulation can identify new, output-specific signaling regulators, and identify RpS21 as an in vivo Ras/MAPK phenotypic regulator. Cellular communication is critical in controlling the growth of organs and must be carefully regulated to prevent disease. The Ras signaling pathway is frequently used for cellular communication of tissue growth regulation but can operate at different signaling strengths. Here, we used a novel strategy to identify genes that specifically tune weak or strong Ras signaling states. We find that the gene RpS21 preferentially tunes weak Ras signaling states.
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Affiliation(s)
- Jessica K. Sawyer
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Zahra Kabiri
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Ruth A. Montague
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Scott R. Allen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Rebeccah Stewart
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Sarah V. Paramore
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Erez Cohen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Hamed Zaribafzadeh
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Christopher M. Counter
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (CMC); (DTF)
| | - Donald T. Fox
- Department of Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, United States of America
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, United States of America
- * E-mail: (CMC); (DTF)
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2
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Arch JJ, Genung SR, Ferris MC, Kirk A, Slivjak ET, Fishbein JN, Schneider RL, Stanton AL. Presence and predictors of anxiety disorder onset following cancer diagnosis among anxious cancer survivors. Support Care Cancer 2020; 28:4425-4433. [PMID: 31925530 PMCID: PMC7347435 DOI: 10.1007/s00520-020-05297-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 01/03/2020] [Indexed: 01/10/2023]
Abstract
PURPOSE Despite cancer survivors' frequent endorsement of anxiety symptoms, assessing the full range of anxiety disorders (AD), their timing of onset relative to cancer diagnosis, co-morbidity with mood disorder, and predictors of post-cancer onset, is rare or absent to date. This study provides a step toward addressing these gaps. METHODS Cancer survivors at re-entry after primary treatment completion who screened positively for anxiety symptoms (N = 133) and sought care through an intervention trial completed standardized diagnostic interviews, dimensional assessment of disorder severity, and timing of disorder onset relative to cancer diagnosis. We evaluated sociodemographic and medical predictors of developing a first AD after cancer diagnosis. RESULTS Most ADs began after cancer diagnosis (58%); for 68% of affected patients, this represented their first AD episode. The most common was generalized anxiety disorder (GAD; 41%), where "cancer-focused GAD" was distinguished from "typical GAD"; the next most common were specific phobia (14%) and social anxiety disorder (13%). A minority (31%) of ADs were comorbid with major depression. Relative to having no AD, experiencing more lingering treatment side effects predicted developing a first AD after cancer diagnosis. Relative to having an AD that began before cancer diagnosis, reporting a higher cancer stage predicted developing a first AD after diagnosis. CONCLUSIONS Cancer survivors at re-entry seeking care for anxiety symptoms manifested a broad range of ADs which most commonly developed after cancer diagnosis and were prompted by the experience of cancer. Such disorders represent an unusually late-life, cancer-linked etiology that warrants further investigation and clinical attention.
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Affiliation(s)
- Joanna J Arch
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, 80309-0345, USA.
- Division of Cancer Prevention and Control, University of Colorado Cancer Center, Aurora, CO, 80045, USA.
| | - Sarah R Genung
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, 80309-0345, USA
| | - Michelle C Ferris
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, 80309-0345, USA
| | - Alex Kirk
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, 80309-0345, USA
| | - Elizabeth T Slivjak
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, 80309-0345, USA
| | - Joel N Fishbein
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, 80309-0345, USA
| | - Rebecca L Schneider
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, 80309-0345, USA
| | - Annette L Stanton
- Department of Psychology, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, 90095, USA
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Abstract
Epigenetic age acceleration-the difference between an individual's DNA methylation age and chronological age-is associated with many diseases including cancer. This study aims to evaluate epigenetic age acceleration as a prognostic biomarker for gliomas. DNA methylation data of gliomas patients (516 low-grade and intermediate-grade gliomas and 140 glioblastoma) were obtained from The Cancer Genome Atlas (TCGA) and patient epigenetic ages were computed using Horvath's age prediction model. We used multivariate linear regression to assess the association of epigenetic age acceleration with tumor molecular subtypes, including Codel, Classic-like, G-CIMP-high, G-CIMP-low, Mesenchymal-like and PA-like. Compared with Codel subtype, epigenetic ages in other molecular subtypes show deceleration after controlling age and race. Age deceleration for Classic-like, G-CIMP-high, G-CIMP-low, Mesenchymal-like and PA-like were 15.42 years (CI: 7.98-22.86, p = 5.38E-05), 25.00 years (CI: 20.79-29.22, p = 4.06E-28), 28.56 years (CI: 14.37-42.74, p = 8.75E-05), 45.34 years (CI: 38.80-51.88, p = 2.15E-36), and 53.58 years (CI: 44.90-62.26, p = 4.81E-30), respectively. Then, Cox proportional hazards regression was used to assess the association of epigenetic age acceleration with patient overall survival. Our results show epigenetic age acceleration is positively associated with patient overall survival (per 10-year age acceleration, HR = 0.89; 95%CI: 0.82-0.97; p = 9.04E-03) in multivariate analysis. When stratified by molecular subtypes, epigenetic age acceleration remains positively associated with patient survival after adjusting age and tumor grade. In conclusion, epigenetic age acceleration is significantly associated with molecular subtypes and patient overall survival in gliomas, indication that epigenetic age acceleration has potential as a quantitative prognostic biomarker for gliomas.
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Affiliation(s)
- Chunlei Zheng
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
| | - Nathan A. Berger
- Center for Science, Health, and Society, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States of America
| | - Li Li
- Department of Family Medicine, School of Medicine, University of Virginia, Charlottesville, VA, United States of America
| | - Rong Xu
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States of America
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Ramesh N, Sei E, Tsai PC, Bai S, Zhao Y, Troncoso P, Corn PG, Logothetis C, Zurita AJ, Navin NE. Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing. Genome Biol 2020; 21:162. [PMID: 32631448 PMCID: PMC7336456 DOI: 10.1186/s13059-020-02045-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/13/2020] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Investigating genome evolution in response to therapy is difficult in human tissue samples. To address this challenge, we develop an unbiased whole-genome plasma DNA sequencing approach that concurrently measures genomic copy number and exome mutations from archival cryostored plasma samples. This approach is applied to study longitudinal blood plasma samples from prostate cancer patients, where longitudinal tissue biopsies from the bone and other metastatic sites have been challenging to collect. RESULTS A molecular characterization of archival plasma DNA from 233 patients and genomic profiling of 101 patients identifies clinical correlations of aneuploid plasma DNA profiles with poor survival, increased plasma DNA concentrations, and lower plasma DNA size distributions. Deep-exome sequencing and genomic copy number profiling are performed on 23 patients, including 9 patients with matched metastatic tissues and 12 patients with serial plasma samples. These data show a high concordance in genomic alterations between the plasma DNA and metastatic tissue samples, suggesting the plasma DNA is highly representative of the tissue alterations. Longitudinal sequencing of 12 patients with 2-5 serial plasma samples reveals clonal dynamics and genome evolution in response to hormonal and chemotherapy. By performing an integrated evolutionary analysis, minor subclones are identified in 9 patients that expanded in response to therapy and harbored mutations associated with resistance. CONCLUSIONS This study provides an unbiased evolutionary approach to non-invasively delineate clonal dynamics and identify clones with mutations associated with resistance in prostate cancer.
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Affiliation(s)
- Naveen Ramesh
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX USA
| | - Emi Sei
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Pei Ching Tsai
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Shanshan Bai
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Yuehui Zhao
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Patricia Troncoso
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Paul G. Corn
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Christopher Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Amado J. Zurita
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Nicholas E. Navin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX USA
- David H. Koch Center for Applied Research of Genitourinary Cancers, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
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Lee HJ, Hou Y, Chen Y, Dailey ZZ, Riddihough A, Jang HS, Wang T, Johnson SL. Regenerating zebrafish fin epigenome is characterized by stable lineage-specific DNA methylation and dynamic chromatin accessibility. Genome Biol 2020; 21:52. [PMID: 32106888 PMCID: PMC7047409 DOI: 10.1186/s13059-020-1948-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 08/20/2019] [Accepted: 01/28/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Zebrafish can faithfully regenerate injured fins through the formation of a blastema, a mass of proliferative cells that can grow and develop into the lost body part. After amputation, various cell types contribute to blastema formation, where each cell type retains fate restriction and exclusively contributes to regeneration of its own lineage. Epigenetic changes that are associated with lineage restriction during regeneration remain underexplored. RESULTS We produce epigenome maps, including DNA methylation and chromatin accessibility, as well as transcriptomes, of osteoblasts and other cells in uninjured and regenerating fins. This effort reveals regeneration as a process of highly dynamic and orchestrated transcriptomic and chromatin accessibility changes, coupled with stably maintained lineage-specific DNA methylation. The epigenetic signatures also reveal many novel regeneration-specific enhancers, which are experimentally validated. Regulatory networks important for regeneration are constructed through integrative analysis of the epigenome map, and a knockout of a predicted upstream regulator disrupts normal regeneration, validating our prediction. CONCLUSION Our study shows that lineage-specific DNA methylation signatures are stably maintained during regeneration, and regeneration enhancers are preset as hypomethylated before injury. In contrast, chromatin accessibility is dynamically changed during regeneration. Many enhancers driving regeneration gene expression as well as upstream regulators of regeneration are identified and validated through integrative epigenome analysis.
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Affiliation(s)
- Hyung Joo Lee
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
| | - Yiran Hou
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yujie Chen
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Zea Z Dailey
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Aiyana Riddihough
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hyo Sik Jang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA.
| | - Stephen L Johnson
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, 63110, USA
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Stampouloglou E, Cheng N, Federico A, Slaby E, Monti S, Szeto GL, Varelas X. Yap suppresses T-cell function and infiltration in the tumor microenvironment. PLoS Biol 2020; 18:e3000591. [PMID: 31929526 PMCID: PMC6980695 DOI: 10.1371/journal.pbio.3000591] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 01/24/2020] [Accepted: 12/18/2019] [Indexed: 12/11/2022] Open
Abstract
A major challenge for cancer immunotherapy is sustaining T-cell activation and recruitment in immunosuppressive solid tumors. Here, we report that the levels of the Hippo pathway effector Yes-associated protein (Yap) are sharply induced upon the activation of cluster of differentiation 4 (CD4)-positive and cluster of differentiation 8 (CD8)-positive T cells and that Yap functions as an immunosuppressive factor and inhibitor of effector differentiation. Loss of Yap in T cells results in enhanced T-cell activation, differentiation, and function, which translates in vivo to an improved ability for T cells to infiltrate and repress tumors. Gene expression analyses of tumor-infiltrating T cells following Yap deletion implicates Yap as a mediator of global T-cell responses in the tumor microenvironment and as a negative regulator of T-cell tumor infiltration and patient survival in diverse human cancers. Collectively, our results indicate that Yap plays critical roles in T-cell biology and suggest that Yap inhibition improves T-cell responses in cancer.
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MESH Headings
- Adaptor Proteins, Signal Transducing/antagonists & inhibitors
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/physiology
- Animals
- Cell Cycle Proteins/antagonists & inhibitors
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/physiology
- Cell Proliferation/genetics
- Cells, Cultured
- Chemotaxis, Leukocyte/genetics
- Down-Regulation/genetics
- Down-Regulation/immunology
- Immunotherapy, Adoptive
- Melanoma, Experimental/immunology
- Melanoma, Experimental/pathology
- Melanoma, Experimental/therapy
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Skin Neoplasms/immunology
- Skin Neoplasms/pathology
- Skin Neoplasms/therapy
- T-Lymphocytes/physiology
- Tumor Microenvironment/genetics
- Tumor Microenvironment/immunology
- YAP-Signaling Proteins
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Affiliation(s)
- Eleni Stampouloglou
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Nan Cheng
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Anthony Federico
- Division of Computational Biology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Emily Slaby
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
| | - Stefano Monti
- Division of Computational Biology, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Gregory L. Szeto
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland, United States of America
- Translational Center for Age-Related Disease and Disparities, University of Maryland Baltimore County, Baltimore, Maryland, United States of America
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, United States of America
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Abstract
The activity of the commensal microbiota significantly impacts human health and has been linked to the development of many diseases, including cancer. Gnotobiotic animal models have shown that the microbiota has many effects on host physiology, including on the development and regulation of immune responses. More recently, evidence has indicated that the microbiota can more specifically influence the outcome of cancer immunotherapy. Therapeutic interventions to optimize microbiota composition to improve immunotherapy outcomes have shown promise in mouse studies. Ongoing endeavors are translating these pre-clinical findings to early stage clinical testing. In this review we summarize 1) basic methodologies and considerations for studies of host-microbiota interactions; 2) experimental evidence towards a causal link between gut microbiota composition and immunotherapeutic efficacy; 3) possible mechanisms governing the microbiota-mediated impact on immunotherapy efficacy. Moving forward, there is need for a deeper understanding of the underlying biological mechanisms that link specific bacterial strains to host immunity. Integrating microbiome effects with other tumor and host factors regulating immunotherapy responsiveness versus resistance could facilitate optimization of therapeutic outcomes.
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Affiliation(s)
- Jessica Fessler
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Vyara Matson
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Thomas F Gajewski
- Department of Pathology, The University of Chicago, Chicago, IL, USA.
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago, 5841 S. Maryland Ave., MC2115, Chicago, IL, 60637, USA.
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Marusak HA, Iadipaolo AS, Harper FW, Elrahal F, Taub JW, Goldberg E, Rabinak CA. Neurodevelopmental consequences of pediatric cancer and its treatment: applying an early adversity framework to understanding cognitive, behavioral, and emotional outcomes. Neuropsychol Rev 2018; 28:123-175. [PMID: 29270773 PMCID: PMC6639713 DOI: 10.1007/s11065-017-9365-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 11/08/2017] [Indexed: 01/29/2023]
Abstract
Today, children are surviving pediatric cancer at unprecedented rates, making it one of modern medicine's true success stories. However, we are increasingly becoming aware of several deleterious effects of cancer and the subsequent "cure" that extend beyond physical sequelae. Indeed, survivors of childhood cancer commonly report cognitive, emotional, and psychological difficulties, including attentional difficulties, anxiety, and posttraumatic stress symptoms (PTSS). Cognitive late- and long-term effects have been largely attributed to neurotoxic effects of cancer treatments (e.g., chemotherapy, cranial irradiation, surgery) on brain development. The role of childhood adversity in pediatric cancer - namely, the presence of a life-threatening disease and endurance of invasive medical procedures - has been largely ignored in the existing neuroscientific literature, despite compelling research by our group and others showing that exposure to more commonly studied adverse childhood experiences (i.e., domestic and community violence, physical, sexual, and emotional abuse) strongly imprints on neural development. While these adverse childhood experiences are different in many ways from the experience of childhood cancer (e.g., context, nature, source), they do share a common element of exposure to threat (i.e., threat to life or physical integrity). Therefore, we argue that the double hit of early threat and cancer treatments likely alters neural development, and ultimately, cognitive, behavioral, and emotional outcomes. In this paper, we (1) review the existing neuroimaging research on child, adolescent, and adult survivors of childhood cancer, (2) summarize gaps in our current understanding, (3) propose a novel neurobiological framework that characterizes childhood cancer as a type of childhood adversity, particularly a form of early threat, focusing on development of the hippocampus and the salience and emotion network (SEN), and (4) outline future directions for research.
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Affiliation(s)
- Hilary A Marusak
- Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Ave., Suite 2190, Detroit, MI, 48202, USA.
| | - Allesandra S Iadipaolo
- Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Ave., Suite 2190, Detroit, MI, 48202, USA
| | - Felicity W Harper
- Population Studies and Disparities Research Program, Karmanos Cancer Institute, Detroit, MI, USA
- Department of Oncology, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Farrah Elrahal
- Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Ave., Suite 2190, Detroit, MI, 48202, USA
| | - Jeffrey W Taub
- Department of Pediatrics, School of Medicine, Wayne State University, Detroit, MI, USA
- Children's Hospital of Michigan, Detroit, MI, USA
| | - Elimelech Goldberg
- Department of Pediatrics, School of Medicine, Wayne State University, Detroit, MI, USA
- Kids Kicking Cancer, Southfield, MI, USA
| | - Christine A Rabinak
- Department of Pharmacy Practice, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, 259 Mack Ave., Suite 2190, Detroit, MI, 48202, USA
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, USA
- Department of Psychiatry and Behavioral Neurosciences, School of Medicine, Wayne State University, Detroit, MI, USA
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Hui D, Mori M, Meng YC, Watanabe SM, Caraceni A, Strasser F, Saarto T, Cherny N, Glare P, Kaasa S, Bruera E. Automatic referral to standardize palliative care access: an international Delphi survey. Support Care Cancer 2018; 26:175-180. [PMID: 28726065 PMCID: PMC5705294 DOI: 10.1007/s00520-017-3830-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [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: 03/17/2017] [Accepted: 07/10/2017] [Indexed: 12/25/2022]
Abstract
PURPOSE Palliative care referral is primarily based on clinician judgment, contributing to highly variable access. Standardized criteria to trigger automatic referral have been proposed, but it remains unclear how best to apply them in practice. We conducted a Delphi study of international experts to identify a consensus for the use of standardized criteria to trigger automatic referral. METHODS Sixty international experts stated their level of agreement for 14 statements regarding the use of clinician-based referral and automatic referral over two Delphi rounds. A consensus was defined as an agreement of ≥70% a priori. RESULTS The response rate was 59/60 (98%) for the first round and 56/60 (93%) for the second round. Twenty-six (43%), 19 (32%), and 11 (18%) respondents were from North America, Asia/Australia, and Europe, respectively. The panel reached consensus that outpatient palliative care referral should be based on both automatic referral and clinician-based referral (agreement = 86%). Only 18% felt that referral should be clinician-based alone, and only 7% agreed that referral should be based on automatic referral only. There was consensus that automatic referral criteria may increase the number of referrals (agreement = 98%), facilitate earlier palliative care access, and help administrators to set benchmarks for quality improvement (agreement = 86%). CONCLUSIONS Our panelists favored the combination of automatic referral to augment clinician-based referral. This integrated referral framework may inform policy and program development.
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Affiliation(s)
- David Hui
- Department of Palliative Care, Rehabilitation and Integrative Medicine, Unit 1414, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA.
| | - Masanori Mori
- Palliative Care Team, Seirei Mikatahara General Hospital, Hamamatsu, Shizuoka, Japan
| | - Yee-Choon Meng
- Department of Palliative Care, Rehabilitation and Integrative Medicine, Unit 1414, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
- Department of Palliative Care, Tan Tock Seng Hospital, Singapore, Singapore
| | - Sharon M Watanabe
- Division of Palliative Care Medicine, Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Augusto Caraceni
- Palliative Care, Pain Therapy and Rehabilitation, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Florian Strasser
- Oncological Palliative Medicine, Hematology-Oncology, Cantonal Hospital, St. Gallen, Switzerland
| | - Tiina Saarto
- Department of Palliative Care, University of Helsinki and Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | - Nathan Cherny
- Cancer Pain and Palliative Medicine Service, Department of Medical Oncology, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Paul Glare
- Pain and Palliative Care Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stein Kaasa
- European Palliative Care Research Centre, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Oncology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Eduardo Bruera
- Department of Palliative Care, Rehabilitation and Integrative Medicine, Unit 1414, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX, 77030, USA
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Gao G, Pierce BL, Olopade OI, Im HK, Huo D. Trans-ethnic predicted expression genome-wide association analysis identifies a gene for estrogen receptor-negative breast cancer. PLoS Genet 2017; 13:e1006727. [PMID: 28957356 PMCID: PMC5619687 DOI: 10.1371/journal.pgen.1006727] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 12/02/2016] [Accepted: 03/30/2017] [Indexed: 01/22/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 90 susceptibility loci for breast cancer, but the underlying biology of those associations needs to be further elucidated. More genetic factors for breast cancer are yet to be identified but sample size constraints preclude the identification of individual genetic variants with weak effects using traditional GWAS methods. To address this challenge, we utilized a gene-level expression-based method, implemented in the MetaXcan software, to predict gene expression levels for 11,536 genes using expression quantitative trait loci and examine the genetically-predicted expression of specific genes for association with overall breast cancer risk and estrogen receptor (ER)-negative breast cancer risk. Using GWAS datasets from a Challenge launched by National Cancer Institute, we identified TP53INP2 (tumor protein p53-inducible nuclear protein 2) at 20q11.22 to be significantly associated with ER-negative breast cancer (Z = -5.013, p = 5.35×10−7, Bonferroni threshold = 4.33×10−6). The association was consistent across four GWAS datasets, representing European, African and Asian ancestry populations. There are 6 single nucleotide polymorphisms (SNPs) included in the prediction of TP53INP2 expression and five of them were associated with estrogen-receptor negative breast cancer, although none of the SNP-level associations reached genome-wide significance. We conducted a replication study using a dataset outside of the Challenge, and found the association between TP53INP2 and ER-negative breast cancer was significant (p = 5.07x10-3). Expression of HP (16q22.2) showed a suggestive association with ER-negative breast cancer in the discovery phase (Z = 4.30, p = 1.70x10-5) although the association was not significant after Bonferroni adjustment. Of the 249 genes that are 250 kb within known breast cancer susceptibility loci identified from previous GWAS, 20 genes (8.0%) were statistically significant associated with ER-negative breast cancer (p<0.05), compared to 582 (5.2%) of 11,287 genes that are not close to previous GWAS loci. This study demonstrated that expression-based gene mapping is a promising approach for identifying cancer susceptibility genes. Although individual genetic variant-based genome-wide association studies have greatly increased our understanding of the genetic susceptibility to breast cancer, the genetic variants identified to date account for a relatively small proportion of the heritability. Shifting the focus of analysis from individual genetic variants to genes or gene sets could lead to the identification of novel genes involved in breast cancer risk. Here, we take advantage of a recently developed gene-level expression-based association method MetaXcan to examine the association of genetically-predicted expression levels for 11,536 genes across the human genome with breast cancer risk. The MetaXcan method uses external information on the effects of genetic variants on gene expression. We show that the TP53INP2 gene on human chromosome 20 is significantly associated with estrogen-receptor negative breast cancer (P = 5.35×10−7, Bonferroni threshold = 4.33×10−6). The association is consistent across analyses of four datasets, representing European, African and Asian ancestry populations. As a downstream gene of p53, TP53INP2 may affect breast cancer risk through p53 signaling pathway. Furthermore, TP53INP2, also known as DOR (Diabetes And Obesity-Regulated Gene), has been linked to obesity and diabetes, suggesting a novel biological pathway for the known association between obesity and breast cancer risk.
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Affiliation(s)
- Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, United States of America
| | - Brandon L. Pierce
- Department of Public Health Sciences, University of Chicago, Chicago, United States of America
- Department of Human Genetics, University of Chicago, Chicago, United States of America
| | - Olufunmilayo I. Olopade
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, United States of America
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, United States of America
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, United States of America
- * E-mail:
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Lazaris C, Kelly S, Ntziachristos P, Aifantis I, Tsirigos A. HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking. BMC Genomics 2017; 18:22. [PMID: 28056762 PMCID: PMC5217551 DOI: 10.1186/s12864-016-3387-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [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: 10/06/2016] [Accepted: 12/07/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Chromatin conformation capture techniques have evolved rapidly over the last few years and have provided new insights into genome organization at an unprecedented resolution. Analysis of Hi-C data is complex and computationally intensive involving multiple tasks and requiring robust quality assessment. This has led to the development of several tools and methods for processing Hi-C data. However, most of the existing tools do not cover all aspects of the analysis and only offer few quality assessment options. Additionally, availability of a multitude of tools makes scientists wonder how these tools and associated parameters can be optimally used, and how potential discrepancies can be interpreted and resolved. Most importantly, investigators need to be ensured that slight changes in parameters and/or methods do not affect the conclusions of their studies. RESULTS To address these issues (compare, explore and reproduce), we introduce HiC-bench, a configurable computational platform for comprehensive and reproducible analysis of Hi-C sequencing data. HiC-bench performs all common Hi-C analysis tasks, such as alignment, filtering, contact matrix generation and normalization, identification of topological domains, scoring and annotation of specific interactions using both published tools and our own. We have also embedded various tasks that perform quality assessment and visualization. HiC-bench is implemented as a data flow platform with an emphasis on analysis reproducibility. Additionally, the user can readily perform parameter exploration and comparison of different tools in a combinatorial manner that takes into account all desired parameter settings in each pipeline task. This unique feature facilitates the design and execution of complex benchmark studies that may involve combinations of multiple tool/parameter choices in each step of the analysis. To demonstrate the usefulness of our platform, we performed a comprehensive benchmark of existing and new TAD callers exploring different matrix correction methods, parameter settings and sequencing depths. Users can extend our pipeline by adding more tools as they become available. CONCLUSIONS HiC-bench consists an easy-to-use and extensible platform for comprehensive analysis of Hi-C datasets. We expect that it will facilitate current analyses and help scientists formulate and test new hypotheses in the field of three-dimensional genome organization.
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Affiliation(s)
- Charalampos Lazaris
- Department of Pathology, NYU School of Medicine, New York, NY 10016 USA
- Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016 USA
| | - Stephen Kelly
- Applied Bioinformatics Laboratories, Office of Science & Research, NYU School of Medicine, New York, NY 10016 USA
- Genome Technology Center, Office of Science & Research, NYU School of Medicine, New York, NY 10016 USA
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611 USA
| | - Iannis Aifantis
- Department of Pathology, NYU School of Medicine, New York, NY 10016 USA
- Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016 USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, NY 10016 USA
- Laura and Isaac Perlmutter Cancer Center and Helen L. and Martin S. Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016 USA
- Applied Bioinformatics Laboratories, Office of Science & Research, NYU School of Medicine, New York, NY 10016 USA
- Genome Technology Center, Office of Science & Research, NYU School of Medicine, New York, NY 10016 USA
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Kota V, Sommer G, Durette C, Thibault P, van Niekerk EA, Twiss JL, Heise T. SUMO-Modification of the La Protein Facilitates Binding to mRNA In Vitro and in Cells. PLoS One 2016; 11:e0156365. [PMID: 27224031 PMCID: PMC4880191 DOI: 10.1371/journal.pone.0156365] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 04/11/2016] [Accepted: 05/12/2016] [Indexed: 02/05/2023] Open
Abstract
The RNA-binding protein La is involved in several aspects of RNA metabolism including the translational regulation of mRNAs and processing of pre-tRNAs. Besides its well-described phosphorylation by Casein kinase 2, the La protein is also posttranslationally modified by the Small Ubiquitin-like MOdifier (SUMO), but the functional outcome of this modification has not been defined. The objective of this study was to test whether sumoylation changes the RNA-binding activity of La. Therefore, we established an in vitro sumoylation assay for recombinant human La and analyzed its RNA-binding activity by electrophoretic mobility shift assays. We identified two novel SUMO-acceptor sites within the La protein located between the RNA recognition motif 1 and 2 and we demonstrate for the first time that sumoylation facilitates the RNA-binding of La to small RNA oligonucleotides representing the oligopyrimidine tract (TOP) elements from the 5' untranslated regions (UTR) of mRNAs encoding ribosomal protein L22 and L37 and to a longer RNA element from the 5' UTR of cyclin D1 (CCND1) mRNA in vitro. Furthermore, we show by RNA immunoprecipitation experiments that a La mutant deficient in sumoylation has impaired RNA-binding activity in cells. These data suggest that modulating the RNA-binding activity of La by sumoylation has important consequences on its functionality.
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Affiliation(s)
- Venkatesh Kota
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, Charleston, South Carolina, United States of America
| | - Gunhild Sommer
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, Charleston, South Carolina, United States of America
| | - Chantal Durette
- Institute of Research in Immunology and Cancer University de Montreal, Station Centre-ville, Montreal, Canada
| | - Pierre Thibault
- Institute of Research in Immunology and Cancer University de Montreal, Station Centre-ville, Montreal, Canada
| | - Erna A. van Niekerk
- Department of Neurosciences-0626, University of California, San Diego, La Jolla, California, United States of America
| | - Jeffery L. Twiss
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Tilman Heise
- Medical University of South Carolina, Department of Biochemistry & Molecular Biology, Charleston, South Carolina, United States of America
- * E-mail:
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Abstract
Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE insertions can result in single-gene disease in an individual. In humans, the non-LTR retrotransposon Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous TE. In addition to mobilizing its own RNA to new genomic locations via a "copy-and-paste" mechanism, LINE-1 is able to retrotranspose other RNAs including Alu, SVA, and occasionally cellular RNAs. To date in humans, 124 LINE-1-mediated insertions which result in genetic diseases have been reported. Disease causing LINE-1 insertions have provided a wealth of insight and the foundation for valuable tools to study these genomic parasites. In this review, we provide an overview of LINE-1 biology followed by highlights from new reports of LINE-1-mediated genetic disease in humans.
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Affiliation(s)
- Dustin C. Hancks
- />Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Haig H. Kazazian
- />McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins School of Medicine, Baltimore, MD USA
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Abstract
Lysine methylation is a common posttranslational modification (PTM) of histones that is important for the epigenetic regulation of transcription and chromatin in eukaryotes. Increasing evidence demonstrates that in addition to histones, lysine methylation also occurs on various non-histone proteins, especially transcription- and chromatin-regulating proteins. In this review, we will briefly describe the histone lysine methyltransferases (KMTs) that have a broad spectrum of non-histone substrates. We will use p53 and nuclear receptors, especially estrogen receptor alpha, as examples to discuss the dynamic nature of non-histone protein lysine methylation, the writers, erasers, and readers of these modifications, and the crosstalk between lysine methylation and other PTMs in regulating the functions of the modified proteins. Understanding the roles of lysine methylation in normal cells and during development will shed light on the complex biology of diseases associated with the dysregulation of lysine methylation on both histones and non-histone proteins.
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Affiliation(s)
- Xi Zhang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yaling Huang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- The Genes and Development and the Epigenetics and Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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