Changes in Prostate Gene Expression in Men Undergoing an Intensive Nutrition and Lifestyle Intervention

Total Page:16

File Type:pdf, Size:1020Kb

Changes in Prostate Gene Expression in Men Undergoing an Intensive Nutrition and Lifestyle Intervention Changes in prostate gene expression in men undergoing an intensive nutrition and lifestyle intervention Dean Ornish*†‡, Mark Jesus M. Magbanua§, Gerdi Weidner*, Vivian Weinberg¶, Colleen Kemp*, Christopher Green§, Michael D. Mattie§, Ruth Marlin*, Jeff Simkoʈ, Katsuto Shinohara§, Christopher M. Haqq§ and Peter R. Carroll§ §Department of Urology, The Helen Diller Family Comprehensive Cancer Center, and ʈDepartment of Pathology, University of California, 2340 Sutter Street, San Francisco, CA 94115; *Preventive Medicine Research Institute, 900 Bridgeway, Sausalito, CA 94965; †Department of Medicine, School of Medicine, University of California, 505 Parnassus Avenue, San Francisco, CA 94143; and ¶Biostatistics Core, The Helen Diller Family Comprehensive Cancer Center, University of California, 513 Parnassus Avenue, Box 0127, San Francisco, CA 94143 Communicated by J. Craig Venter, The J. Craig Venter Institute, Rockville, MD, April 2, 2008 (received for review February 13, 2008) Epidemiological and prospective studies indicate that comprehensive indolent low-risk prostate cancers, defined by strict clinical and lifestyle changes may modify the progression of prostate cancer. pathologic criteria designed to minimize the risk for metastatic However, the molecular mechanisms by which improvements in diet disease as a result of study participation (9). The 30 men who and lifestyle might affect the prostate microenvironment are poorly enrolled did not undergo surgery or radiation therapy to treat their understood. We conducted a pilot study to examine changes in low-risk tumors; rather, they underwent comprehensive lifestyle prostate gene expression in a unique population of men with low-risk changes (low-fat, whole-foods, plant-based nutrition; stress man- prostate cancer who declined immediate surgery, hormonal therapy, agement techniques; moderate exercise; and participation in a or radiation and participated in an intensive nutrition and lifestyle psychosocial group support). Participants donated serial prostate intervention while undergoing careful surveillance for tumor pro- needle biopsies at baseline and after 3 months of the lifestyle gression. Consistent with previous studies, significant improvements intervention, from which nanogram quantities of mRNA were in weight, abdominal obesity, blood pressure, and lipid profile were purified. At the time this clinical trial began, commercial expression observed (all P < 0.05), and surveillance of low-risk patients was safe. array platforms were not sensitive to nanogram RNA quantities. Gene expression profiles were obtained from 30 participants, pairing Therefore, a reproducible linear RNA amplification and printed RNA samples from control prostate needle biopsy taken before cDNA array platform was used, as in our previous studies of intervention to RNA from the same patient’s 3-month postinterven- melanoma (10), where subsequent studies have confirmed the tion biopsy. Quantitative real-time PCR was used to validate array validity of the gene expression findings (11, 12). Furthermore, observations for selected transcripts. Two-class paired analysis of quantitative real-time PCR (QRT-PCR) was used to provide initial global gene expression using significance analysis of microarrays confirmation of the study results, comparing in pairwise fashion detected 48 up-regulated and 453 down-regulated transcripts after each man’s postintervention to his own preintervention sample. the intervention. Pathway analysis identified significant modulation This article examines the relationship of comprehensive diet and of biological processes that have critical roles in tumorigenesis, lifestyle changes to gene expression in the prostate. including protein metabolism and modification, intracellular protein Results traffic, and protein phosphorylation (all P < 0.05). Intensive nutrition and lifestyle changes may modulate gene expression in the prostate. In the GEMINAL study, 273 men were screened, 96 declined to Understanding the prostate molecular response to comprehensive participate, 146 did not meet inclusion criteria, and 31 were lifestyle changes may strengthen efforts to develop effective preven- enrolled. The participants’ demographics included a mean age of tion and treatment. Larger clinical trials are warranted to confirm the 62.3 years (range 49–80) and a mean PSA level of 4.8 ng/ml (range results of this pilot study. 0.5–21.4) on the day of the initial biopsy. As expected from the trial eligibility criteria, all patients had a Gleason score of 6. Eighty-four exercise ͉ lifestyle changes ͉ prostate cancer ͉ SHOC2 ͉ stress management percent of the men identified their ethnicity as Caucasian, 9% Hispanic, 3% Asian, and 4% African-American. Two-thirds of the men were married, and 72% were currently employed. pidemiological evidence (1, 2) and migrant studies (3) indicate Trial eligibility required PSA Յ10 [or PSA Յ15 if the patient had Ethat the incidence of clinically significant prostate cancer is a history of benign prostatic hyperplasia (BPH)] at the time of much lower in parts of the world where people eat a predominantly screening. One outlier patient with a history of BPH and a prostate low-fat, plant-based diet. We (4, 5) and others (6) have shown volume of 90 cc, as assessed by transrectal ultrasound, had screening MEDICAL SCIENCES previously that diet and lifestyle interventions in men with early- stage prostate cancer decrease prostate-specific antigen (PSA) and decrease the rate of PSA increase. These studies provided some Author contributions: D.O. and M.J.M.M. contributed equally to this work; D.O., G.W., evidence that comprehensive lifestyle changes may have therapeu- R.M., C.M.H., and P.R.C. designed research; D.O., M.J.M.M., C.K., C.G., M.D.M., R.M., J.S., tic potential in early prostate cancers. However, although these K.S., C.M.H., and P.R.C. performed research; M.J.M.M., V.W., C.G., and C.M.H. analyzed interventions are associated with decreased circulating insulin-like data; and D.O., M.J.M.M., G.W., V.W., C.K., C.M.H., and P.R.C. wrote the paper. growth factor 1 (IGF1) (7), and although serum from men after Conflict of interest statement: Although none of the following is a true conflict of interest, in the spirit of full disclosure, D.O. writes general-interest books on preventive medicine, intervention has reduced the ability to stimulate prostate cell-line receives lecture honoraria, and consults with food companies to make more healthful growth in vitro (4), the actual molecular effects of these interven- foods. tions in prostate tissue have not been previously examined. Freely available online through the PNAS open access option. Many men with indolent prostate cancers detected by PSA Data deposition: The data reported in this paper have been deposited in the Gene screening will not exhibit disease progression during their lifetime; Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE10306). their treatment and associated side effects are unnecessary (8). We ‡To whom correspondence should be addressed. E-mail: [email protected]. report here the results of the Gene Expression Modulation by This article contains supporting information online at www.pnas.org/cgi/content/full/ Intervention with Nutrition and Lifestyle (GEMINAL) study, a 0803080105/DCSupplemental. prospective single-arm pilot clinical intervention study in men with © 2008 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0803080105 PNAS ͉ June 17, 2008 ͉ vol. 105 ͉ no. 24 ͉ 8369–8374 Downloaded by guest on September 30, 2021 Table 1. Cardiovascular risk factors and psychological functioning at baseline and 3 months 95% CI of change Baseline, 3 months, Mean change, Variable Mean Ϯ SD Mean Ϯ SD 3-month baseline Lower Upper P* Cardiovascular risk factors BMI 26.5 Ϯ 3.6 23.9 Ϯ 3.0 Ϫ2.6 Ϫ3.0 Ϫ2.2 Ͻ0.001 Systolic blood pressure, mmHg 129.5 Ϯ 15.1 120.3 Ϯ 12.6 Ϫ9.2 Ϫ13.8 Ϫ4.6 Ͻ0.001 Diastolic blood pressure, mmHg 68.2 Ϯ 10.7 62.8 Ϯ 10.3 Ϫ5.4 Ϫ8.4 Ϫ2.3 Ͻ0.002 LDL, mg/dl 121.7 Ϯ 28.2 87.6 Ϯ 25.1 Ϫ34.2 Ϫ41.6 Ϫ26.8 Ͻ0.001 HDL, mg/dl 48.5 Ϯ 12.7 40.2 Ϯ 12.1 Ϫ8.3 Ϫ11.5 Ϫ5.2 Ͻ0.001 Total cholesterol, mg/dl 191.7 Ϯ 33.1 146.5 Ϯ 31.6 Ϫ45.2 Ϫ54.4 Ϫ36.0 Ͻ0.001 LDL/HDL ratio 2.7 Ϯ 1.0 2.3 Ϯ 0.8 Ϫ0.4 Ϫ0.6 Ϫ0.1 Ͻ0.002 Triglycerides, mg/dl 107.0 Ϯ 72.1 93.6 Ϯ 46.3 Ϫ13.4 Ϫ32.3 5.5 0.158 C-reactive protein (ln) 0.12 Ϯ 1.1 Ϫ0.14 Ϯ 1.3 Ϫ0.26 Ϫ0.64 0.12 0.168 Psychological functioning SF-36 Mental component summary 49.7 Ϯ 11.8 56.2 Ϯ 5.5 6.5 2.6 10.3 Ͻ0.003 Physical component summary 54.7 Ϯ 4.9 55.4 Ϯ 5.5 0.8 Ϫ1.5 3.0 0.485 Impact of Event Scale Intrusive thoughts 6.2 Ϯ 5.6 3.7 Ϯ 4.8 Ϫ2.5 Ϫ4.2 Ϫ0.8 Ͻ0.01 Avoidance 10.1 Ϯ 6.8 7.1 Ϯ 5.8 Ϫ3.0 Ϫ5.9 Ϫ0.1 Ͻ0.05 *Paired-samples t test, two-tailed. PSAs of 11.6–12.1 ng/ml, meeting eligibility criteria, but had a PSA score for physical health (Ͼ55.7) and near the lowest-quartile cutoff of 21.4 ng/ml on the day of initial biopsy. After the 3-month score for mental health (Ͻ49.9) (24). The psychological distress intervention, this patient’s PSA decreased to 13.9 ng/ml, and his reported in this sample was comparable with the level of distress prostate volume decreased to 75 cc. All other participants had reported by other men diagnosed with prostate cancer (mean screening and initial biopsy-day PSA values of Ͻ10 ng/ml.
Recommended publications
  • C8cc08685k1.Pdf
    Electronic Supplementary Material (ESI) for ChemComm. This journal is © The Royal Society of Chemistry 2018 Supporting Information Minimalist Linkers Suitable for Irreversible Inhibitors in Simultaneous Proteome Profiling, Live-Cell Imaging and Drug Screening Cuiping Guo,Yu Chang, Xin Wang, Chengqian Zhang, Piliang Hao*, Ke Ding and Zhengqiu Li* School of Pharmacy, Jinan University, Guangzhou, China 510632 *Corresponding author ([email protected]) 1. General Information All chemicals were purchased from commercial vendors and used without further purification, unless indicated otherwise. All reactions requiring anhydrous conditions were carried out under argon or nitrogen atmosphere using oven-dried glassware. AR-grade solvents were used for all reactions. Reaction progress was monitored by TLC on pre-coated silica plates (Merck 60 F254 nm, 0.25 µm) and spots were visualized by UV, iodine or other suitable stains. Flash column chromatography was carried out using silica gel (Qingdao Ocean). All NMR spectra (1H-NMR, 13C-NMR) were recorded on Bruker 300 MHz/400 MHz NMR spectrometers. Chemical shifts were reported in parts per million (ppm) referenced with respect to appropriate internal standards or residual solvent peaks (CDCl3 = 7.26 ppm, DMSO-d6 = 2.50 ppm). The following abbreviations were used in reporting spectra, br s (broad singlet), s (singlet), d (doublet), t (triplet), q (quartet), m (multiplet), dd (doublet of doublets). Mass spectra were obtained on Agilent LC-ESI-MS system. All analytical HPLC were carried out on Agilent system. Water with 0.1% TFA and acetonitrile with 0.1% TFA were used as eluents and the flow rate was 0.5 mL/min.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2012/0070450 A1 Ishikawa Et Al
    US 20120070450A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2012/0070450 A1 Ishikawa et al. (43) Pub. Date: Mar. 22, 2012 (54) LEUKEMA STEM CELLMARKERS Publication Classification (51) Int. Cl. A 6LX 39/395 (2006.01) (75) Inventors: Fumihiko Ishikawa, Kanagawa CI2O I/68 (2006.01) (JP): Osamu Ohara, Kanagawa GOIN 2L/64 (2006.01) (JP); Yoriko Saito, Kanagawa (JP); A6IP35/02 (2006.01) Hiroshi Kitamura, Kanagawa (JP); C40B 30/04 (2006.01) Atsushi Hijikata, Kanagawa (JP); A63L/7088 (2006.01) Hidetoshi Ozawa, Kanagawa (JP); C07K 6/8 (2006.01) Leonard D. Shultz, Bar Harbor, C7H 2L/00 (2006.01) A6II 35/12 (2006.01) ME (US) CI2N 5/078 (2010.01) (52) U.S. Cl. .................. 424/173.1; 424/178.1; 424/93.7: (73) Assignee: RIKEN, Wako-shi (JP) 435/6.14; 435/723; 435/375; 506/9: 514/44 A: 530/389.6; 530/391.7:536/24.5 (57) ABSTRACT (21) Appl. No.: 13/258,993 The invention provides a test method for predicting the initial onset or a recurrence of acute myeloid leukemia (AML) com PCT Fled: prising (1) measuring the expression level of human leukemic (22) Mar. 24, 2010 stem cell (LSC) marker genes in a biological sample collected from a Subject for a transcription product or translation prod uct of the gene as an analyte and (2) comparing the expression (86) PCT NO.: PCT/UP2010/0551.31 level with a reference value; an LSC-targeting therapeutic agent for AML capable of Suppressing the expression of a S371 (c)(1), gene selected from among LSC marker genes or a Substance (2), (4) Date: Dec.
    [Show full text]
  • The Mitochondrial Kinase PINK1 in Diabetic Kidney Disease
    International Journal of Molecular Sciences Review The Mitochondrial Kinase PINK1 in Diabetic Kidney Disease Chunling Huang * , Ji Bian , Qinghua Cao, Xin-Ming Chen and Carol A. Pollock * Kolling Institute, Sydney Medical School, Royal North Shore Hospital, University of Sydney, St. Leonards, NSW 2065, Australia; [email protected] (J.B.); [email protected] (Q.C.); [email protected] (X.-M.C.) * Correspondence: [email protected] (C.H.); [email protected] (C.A.P.); Tel.: +61-2-9926-4784 (C.H.); +61-2-9926-4652 (C.A.P.) Abstract: Mitochondria are critical organelles that play a key role in cellular metabolism, survival, and homeostasis. Mitochondrial dysfunction has been implicated in the pathogenesis of diabetic kidney disease. The function of mitochondria is critically regulated by several mitochondrial protein kinases, including the phosphatase and tensin homolog (PTEN)-induced kinase 1 (PINK1). The focus of PINK1 research has been centered on neuronal diseases. Recent studies have revealed a close link between PINK1 and many other diseases including kidney diseases. This review will provide a concise summary of PINK1 and its regulation of mitochondrial function in health and disease. The physiological role of PINK1 in the major cells involved in diabetic kidney disease including proximal tubular cells and podocytes will also be summarized. Collectively, these studies suggested that targeting PINK1 may offer a promising alternative for the treatment of diabetic kidney disease. Keywords: PINK1; diabetic kidney disease; mitochondria; mitochondria quality control; mitophagy Citation: Huang, C.; Bian, J.; Cao, Q.; 1. Introduction Chen, X.-M.; Pollock, C.A.
    [Show full text]
  • The C9orf72-Interacting Protein Smcr8 Is a Negative Regulator of Autoimmunity and Lysosomal Exocytosis
    Downloaded from genesdev.cshlp.org on October 5, 2021 - Published by Cold Spring Harbor Laboratory Press The C9orf72-interacting protein Smcr8 is a negative regulator of autoimmunity and lysosomal exocytosis Yingying Zhang,1,2,3 Aaron Burberry,1,2,3 Jin-Yuan Wang,1,2,3 Jackson Sandoe,1,2,3 Sulagna Ghosh,1,2,3 Namrata D. Udeshi,4 Tanya Svinkina,4 Daniel A. Mordes,1,2,3,5 Joanie Mok,1,2,3 Maura Charlton,1,2,3 Quan-Zhen Li,6,7 Steven A. Carr,4 and Kevin Eggan1,2,3 1Department of Stem Cell and Regenerative Biology, 2Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA; 3Stanley Center for Psychiatric Research, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA; 4Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA; 5Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA; 6Department of Immunology, 7Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA While a mutation in C9ORF72 is the most common genetic contributor to amyotrophic lateral sclerosis (ALS), much remains to be learned concerning the function of the protein normally encoded at this locus. To elaborate further on functions for C9ORF72, we used quantitative mass spectrometry-based proteomics to identify interacting proteins in motor neurons and found that its long isoform complexes with and stabilizes SMCR8, which further enables interaction with WDR41. To study the organismal and cellular functions for this tripartite complex, we generated Smcr8 loss-of-function mutant mice and found that they developed phenotypes also observed in C9orf72 loss-of- function animals, including autoimmunity.
    [Show full text]
  • Exosomes from Nischarin-Expressing Cells Reduce Breast Cancer Cell Motility and Tumor Growth
    Author Manuscript Published OnlineFirst on January 11, 2019; DOI: 10.1158/0008-5472.CAN-18-0842 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Exosomes from Nischarin-Expressing Cells Reduce Breast Cancer Cell Motility and tumor growth Mazvita Maziveyi1,7, Shengli Dong1, Somesh Baranwal2, Ali Mehrnezhad3, Rajamani Rathinam4, Thomas M. Huckaba5, Donald E. Mercante6, Kidong Park3, Suresh K. Alahari1 1Department of Biochemistry and Molecular Biology, LSUHSC School of Medicine, New Orleans, LA, USA 2Center of Biochemistry and Microbial Science, Central University of Punjab, Bathinda-151001, India 3Department of Electrical Engineering and Computer Engineering, Louisiana State University, Baton Rouge, LA, USA 4Wayne State University, Detroit, MI, USA 5Department of Biology, Xavier University of Louisiana, New Orleans, LA, USA 6School of Public Health, LSUHSC School of Medicine, New Orleans, LA, USA 7Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, Texas *Corresponding author; Suresh K. Alahari, PhD; Fred G. Brazda Professor of Biochemistry, LSUHSC School of Medicine, New Orleans, LA 70112, USA; Tel: 504-568-4734 [email protected] Running Title: Nischarin regulates exosome production Conflicts of Interest No potential conflicts of interest were disclosed. Downloaded from cancerres.aacrjournals.org on September 29, 2021. © 2019 American Association for Cancer Research. Author Manuscript Published OnlineFirst on January 11, 2019; DOI: 10.1158/0008-5472.CAN-18-0842 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Abstract: Exosomes are small extracellular microvesicles that are secreted by cells when intracellular multivesicular bodies (MVB) fuse with the plasma membrane.
    [Show full text]
  • A Minimum-Labeling Approach for Reconstructing Protein Networks Across Multiple Conditions
    A Minimum-Labeling Approach for Reconstructing Protein Networks across Multiple Conditions Arnon Mazza1, Irit Gat-Viks2, Hesso Farhan3, and Roded Sharan1 1 Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel. Email: [email protected]. 2 Dept. of Cell Research and Immunology, Tel Aviv University, Tel Aviv 69978, Israel. 3 Biotechnology Institute Thurgau, University of Konstanz, Unterseestrasse 47, CH-8280 Kreuzlingen, Switzerland. Abstract. The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to fa- cilitate the interpretation and representation of these data. A fundamen- tal challenge in this domain is the reconstruction of a protein-protein sub- network that underlies a process of interest from a genome-wide screen of associated genes. Despite intense work in this area, current algorith- mic approaches are largely limited to analyzing a single screen and are, thus, unable to account for information on condition-specific genes, or reveal the dynamics (over time or condition) of the process in question. Here we propose a novel formulation for network reconstruction from multiple-condition data and devise an efficient integer program solution for it. We apply our algorithm to analyze the response to influenza in- fection in humans over time as well as to analyze a pair of ER export related screens in humans. By comparing to an extant, single-condition tool we demonstrate the power of our new approach in integrating data from multiple conditions in a compact and coherent manner, capturing the dynamics of the underlying processes. 1 Introduction With the increasing availability of high-throughput data, network biol- arXiv:1307.7803v1 [q-bio.QM] 30 Jul 2013 ogy has become the method of choice for filtering, interpreting and rep- resenting these data.
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • The Schizophrenia Risk Gene Product Mir-137 Alters Presynaptic Plasticity
    The schizophrenia risk gene product miR-137 alters presynaptic plasticity The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Siegert, S., J. Seo, E. J. Kwon, A. Rudenko, S. Cho, W. Wang, Z. Flood, et al. 2015. “The schizophrenia risk gene product miR-137 alters presynaptic plasticity.” Nature neuroscience 18 (7): 1008-1016. doi:10.1038/nn.4023. http://dx.doi.org/10.1038/nn.4023. Published Version doi:10.1038/nn.4023 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:24983896 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA HHS Public Access Author manuscript Author Manuscript Author ManuscriptNat Neurosci Author Manuscript. Author manuscript; Author Manuscript available in PMC 2016 January 01. Published in final edited form as: Nat Neurosci. 2015 July ; 18(7): 1008–1016. doi:10.1038/nn.4023. The schizophrenia risk gene product miR-137 alters presynaptic plasticity Sandra Siegert1,2, Jinsoo Seo1,2,*, Ester J. Kwon1,2,*, Andrii Rudenko1,2,*, Sukhee Cho1,2, Wenyuan Wang1,2, Zachary Flood1,2, Anthony J. Martorell1,2, Maria Ericsson4, Alison E. Mungenast1,2, and Li-Huei Tsai1,2,3,5 1Picower Institute for Learning and Memory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA 2Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA 3Broad Institute of MIT and Harvard, Cambridge, MA, USA 4Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA Abstract Non-coding variants in the human MIR137 gene locus increase schizophrenia risk at a genome- wide significance level.
    [Show full text]
  • Divergence of Human and Mouse Brain Transcriptome Highlights Alzheimer Disease Pathways
    Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways Jeremy A. Millera,b, Steve Horvathc,d, and Daniel H. Geschwindb,c,1 aInterdepartmental Program for Neuroscience, Departments of cHuman Genetics and dBiostatistics, and bProgram in Neurogenetics and Neurobehavioral Genetics, Department of Neurology and Semel Institute, University of California, Los Angeles, CA 90095-1769 Edited by Joseph S. Takahashi, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, and approved June 1, 2010 (received for review December 10, 2009) Because mouse models play a crucial role in biomedical research works by merging data from many microarray studies, and then related to the human nervous system, understanding the similari- applying weighted gene coexpression network analysis (WGCNA) ties and differences between mouse and human brain is of (4–7). WGCNA elucidates the higher-order relationships between fundamental importance. Studies comparing transcription in hu- genes based on their coexpression relationships, delineating modules man and mouse have come to varied conclusions, in part because of of biologically related genes and permitting a robust view of their relatively small sample sizes or underpowered methodologies. transcriptome organization (3, 5, 8, 9). Within groups of highly coexpressed genes (“modules”) that comprise the core functional To better characterize gene expression differences between mouse fi and human, we took a systems-biology approach by using weighted units of the transcriptional network, WGCNA also identi es gene coexpression network analysis on more than 1,000 micro- the most highly connected, or most central genes within each module, referred to as “hubs.” We find that both gene expression arrays from brain.
    [Show full text]
  • Breast Cancer Tumor Suppressors: a Special Emphasis on Novel Protein Nischarin Mazvita Maziveyi and Suresh K
    Published OnlineFirst September 21, 2015; DOI: 10.1158/0008-5472.CAN-15-1395 Cancer Review Research Breast Cancer Tumor Suppressors: A Special Emphasis on Novel Protein Nischarin Mazvita Maziveyi and Suresh K. Alahari Abstract Tumor suppressor genes regulate cell growth and prevent vast number of cellular processes, including neuronal protection spontaneous proliferation that could lead to aberrant tissue and hypotension. The NISCH promoter experiences hypermethy- function. Deletions and mutations of these genes typically lead lation in several cancers, whereas some highly aggressive breast to progression through the cell-cycle checkpoints, as well as cancer cells exhibit genomic loss of the NISCH locus. Further- increased cell migration. Studies of these proteins are important more, we discuss data illustrating a novel role of Nischarin as as they may provide potential treatments for breast cancers. In this a tumor suppressor in breast cancer. Analysis of this new para- review, we discuss a comprehensive overview on Nischarin, a digm may shed light on various clinical questions. Finally, the novel protein discovered by our laboratory. Nischarin, or imida- therapeutic potential of Nischarin is discussed. Cancer Res; 75(20); zoline receptor antisera-selected protein, is a protein involved in a 4252–9. Ó2015 AACR. Introduction (6, 7). It also interacts with LIM kinase (LIMK) in order to prevent cytoskeletal reorganization (8). Typically, scaffold proteins such Breast cancer initiation and progression involve several genetic as Nischarin are characterized as caretaker genes because their events that can activate oncogenes and/or abrogate the function of effects on tumor growth are indirect. tumor suppressor genes. Tumor suppressor genes are commonly lost or deleted in cancers, facilitating the initiation and progres- sion of cancer through several biological events, including cell Discovery of Nischarin proliferation, cell death, cell migration, and cell invasion.
    [Show full text]
  • Associated 16P11.2 Deletion in Drosophila Melanogaster
    ARTICLE DOI: 10.1038/s41467-018-04882-6 OPEN Pervasive genetic interactions modulate neurodevelopmental defects of the autism- associated 16p11.2 deletion in Drosophila melanogaster Janani Iyer1, Mayanglambam Dhruba Singh1, Matthew Jensen1,2, Payal Patel 1, Lucilla Pizzo1, Emily Huber1, Haley Koerselman3, Alexis T. Weiner 1, Paola Lepanto4, Komal Vadodaria1, Alexis Kubina1, Qingyu Wang 1,2, Abigail Talbert1, Sneha Yennawar1, Jose Badano 4, J. Robert Manak3,5, Melissa M. Rolls1, Arjun Krishnan6,7 & 1234567890():,; Santhosh Girirajan 1,2,8 As opposed to syndromic CNVs caused by single genes, extensive phenotypic heterogeneity in variably-expressive CNVs complicates disease gene discovery and functional evaluation. Here, we propose a complex interaction model for pathogenicity of the autism-associated 16p11.2 deletion, where CNV genes interact with each other in conserved pathways to modulate expression of the phenotype. Using multiple quantitative methods in Drosophila RNAi lines, we identify a range of neurodevelopmental phenotypes for knockdown of indi- vidual 16p11.2 homologs in different tissues. We test 565 pairwise knockdowns in the developing eye, and identify 24 interactions between pairs of 16p11.2 homologs and 46 interactions between 16p11.2 homologs and neurodevelopmental genes that suppress or enhance cell proliferation phenotypes compared to one-hit knockdowns. These interac- tions within cell proliferation pathways are also enriched in a human brain-specific network, providing translational relevance in humans. Our study indicates a role for pervasive genetic interactions within CNVs towards cellular and developmental phenotypes. 1 Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA. 2 Bioinformatics and Genomics Program, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
    [Show full text]
  • Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
    Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement.
    [Show full text]