Robbins Basic Pathology 10th Edition PDF

Robbins BASIC PATHOLOGY Robbins BASIC PATHOLOGY TENTH EDITION Vinay Kumar, MBBS, MD, FRCPath Alice Hogge and Arthur A. Baer Distinguished Service Professor of Pathology Biological Sciences Division and The Pritzker Medical School University of Chicago Chicago, Illinois Abul K. Abbas, MBBS Distin...

Robbins BASIC PATHOLOGY Robbins BASIC PATHOLOGY TENTH EDITION Vinay Kumar, MBBS, MD, FRCPath Alice Hogge and Arthur A. Baer Distinguished Service Professor of Pathology Biological Sciences Division and The Pritzker Medical School University of Chicago Chicago, Illinois Abul K. Abbas, MBBS Distinguished Professor and Chair Department of Pathology University of California, San Francisco San Francisco, California Jon C. Aster, MD, PhD Professor of Pathology Brigham and Women’s Hospital and Harvard Medical School Boston, Massachusetts ARTIST James A. Perkins, MS, MFA 1600 John F. Kennedy Blvd. Philadelphia, Pennsylvania 19103-2899 ROBBINS BASIC PATHOLOGY, TENTH EDITION ISBN: 978-0-323-35317-5 International Edition: 978-0-323-48054-3 Copyright © 2018 by Elsevier Inc. All rights reserved. Previous editions copyrighted 2013, 2007, 2003, 1997, 1992, 1987, 1981, 1976, and 1971 No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the Publisher. Details on how to seek permission, further information about the Publisher’s permissions policies, and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency can be found at our website: www.elsevier.com/permissions. This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein). Notices Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary. Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein. In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility. With respect to any drug or pharmaceutical products identified, readers are advised to check the most current information provided (i) on procedures featured or (ii) by the manufacturer of each product to be administered, to verify the recommended dose or formula, the method and duration of administration, and contraindications. It is the responsibility of practitioners, relying on their own experience and knowledge of their patients, to make diagnoses, to determine dosages and the best treatment for each individual patient, and to take all appropriate safety precautions. To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein. Library of Congress Cataloging-in-Publication Data Names: Kumar, Vinay, 1944- editor. | Abbas, Abul K., editor. | Aster, Jon C., editor. | Perkins, James A., illustrator. Title: Robbins basic pathology / [edited by] Vinay Kumar, Abul K. Abbas, Jon C. Aster ; artist, James A. Perkins. Other titles: Basic pathology Description: Tenth edition. | Philadelphia, Pennsylvania : Elsevier, | Includes bibliographical references and index. Identifiers: LCCN 2017002902 | ISBN 9780323353175 (hardcover : alk. paper) Subjects: | MESH: Pathologic Processes Classification: LCC RB111 | NLM QZ 140 | DDC 616.07–dc23 LC record available at https://lccn.loc.gov/2017002902 Executive Content Strategist: James Merritt Director, Content Development: Rebecca Gruliow Publishing Services Manager: Julie Eddy Book Production Specialist: Clay S. Broeker Design Direction: Brian Salisbury Printed in Canada Last digit is the print number: 9 8 7 6 5 4 3 2 1 DEDICATION Dedicated to Our Grandchildren Kiera, Nikhil, and Kavi And Our Children Jonathan and Rehana Abbas Michael and Meghan Aster  Contributors Anthony Chang, MD Alexander J. Lazar, MD, PhD Professor Professor Department of Pathology Departments of Pathology, Genomic Medicine, and The University of Chicago Translational Molecular Pathology Chicago, Illinois The University of Texas MD Anderson Cancer Center Houston, Texas Lora Hedrick Ellenson, MD Professor and Chief of Gynecologic Pathology Susan C. Lester, MD, PhD Department of Pathology and Laboratory Medicine Assistant Professor and Chief of Breast Pathology Weill Cornell Medicine–New York Presbyterian Services Hospital Department of Pathology New York, New York Harvard Medical School Brigham and Women’s Hospital Jonathan I. Epstein, MD Boston, Massachusetts Professor Departments of Pathology, Urology, and Oncology Mark W. Lingen, DDS, PhD, FRCPath The Johns Hopkins Medical Institutions Professor Baltimore, Maryland Department of Pathology The University of Chicago Karen M. Frank, MD, PhD, D(ABMM) Chicago, Illinois Chief of Microbiology Service Department of Laboratory Medicine Tamara L. Lotan, MD Clinical Center Associate Professor of Pathology National Institutes of Health The Johns Hopkins Hospital Bethesda, Maryland Baltimore, Maryland Matthew P. Frosch, MD, PhD Anirban Maitra, MBBS Lawrence J. Henderson Associate Professor Professor Department of Pathology Pathology and Translational Molecular Pathology Massachusetts General Hospital and Harvard Medical University of Texas MD Anderson Cancer Center School Houston, Texas Boston, Massachusetts Alexander J. McAdam, MD, PhD Andrew Horvai, MD, PhD Associate Professor of Pathology Clinical Professor Department of Pathology Department of Pathology Harvard Medical School University of California, San Francisco Medical Director San Francisco, California Clinical Microbiology Laboratory Boston Children’s Hospital Aliya N. Husain, MBBS Boston, Massachusetts Professor Department of Pathology Richard N. Mitchell, MD, PhD The University of Chicago Lawrence J. Henderson Professor of Pathology Chicago, Illinois Member of the Harvard/MIT Health Sciences and Technology Faculty Zoltan G. Laszik, MD, PhD Department of Pathology Professor of Pathology Brigham and Women’s Hospital University of California, San Francisco Harvard Medical School San Francisco, California Boston, Massachusetts vi  Contributors vii Peter Pytel, MD Jerrold R. Turner, MD, PhD Professor Departments of Pathology and Medicine (GI) Department of Pathology Brigham and Women’s Hospital University of Chicago Harvard Medical School Chicago, Illinois Boston, Massachusetts Neil D. Theise, MD Professor Department of Pathology Icahn School of Medicine at Mount Sinai New York, New York  Clinical Consultants Harold J. Burstein, MD Joyce Liu, MD, MPH Dana-Farber Cancer Institute and Harvard Medical Dana-Farber Cancer Institute and Harvard Medical School School Boston, Massachusetts Boston, Massachusetts Diseases of the Breast Diseases of the Female Genital Tract Vanja Douglas, MD Graham McMahon, MD, MMSC University of California, San Francisco Brigham and Women’s Hospital and Harvard Medical San Francisco, California School Diseases of the Central Nervous System Boston, Massachusetts Diseases of the Endocrine System Hilary J. Goldberg, MD Brigham and Women’s Hospital, Harvard Medical Meyeon Park, MD School University of California, San Francisco Boston, Massachusetts San Francisco, California Diseases of the Lung Disease of the Kidney Ira Hanan, MD Anna E. Rutherford, MD, MPH University of Chicago Brigham and Women’s Hospital and Harvard Medical Chicago, Illinois School Diseases of the Gastrointestinal Tract Boston, Massachusetts Diseases of the Liver Cadence Kim, MD Urologic Associates Matthew J. Sorrentino, MD Philadelphia, Pennsylvania University of Chicago Diseases of the Male Genital System Chicago, Illinois Diseases of the Blood Vessels and Diseases of the Anne LaCase, MD Heart Dana Farber Cancer Institute and Harvard Medical School Boston, Massachusetts Diseases of Hematopoietic and Lymphoid Systems viii  Preface The tenth edition is an important milestone in the life of a text- as if it was written de novo and in many cases to remove book. This occasion is a propitious time to look back on parts of the text that had been present in the previous the origins of Basic Pathology, which are summed up best edition. It is our hope that these changes will unburden by quoting Stanley Robbins from the preface of the first the students and that the tenth edition will be seen as edition (1971): an up to date yet simple to comprehend book. “Of books as well as men, it may be observed that fat Third, because illustrations facilitate the understanding ones contain thin ones struggling to get out. In a sense, of difficult concepts such as control of the cell cycle and this book bears such a relationship to its more substantial the actions of cancer genes, the art has been significantly progenitor, Robbins Pathology. It arose from an appreciation revised and enhanced by adding depth so that the four- of the modern medical student’s dilemma. As the curricu- color figures are seen in three dimensions. lum has become restructured to place greater emphasis Finally, we have added a board of clinical consultants on clinical experience, time for reading is correspondingly to help us in keeping the clinical content accurate and curtailed.…In writing this book, rare and esoteric lesions up to date. are omitted without apology, and infrequent or trivial ones described only briefly. We felt it important, however, to As an additional “tool” to help students focus on the consider rather fully the major disease entities.” fundamentals, we have continued the use of Summary While the goals of “baby Robbins” remain true to the boxes designed to provide key “take home” messages. vision of Stanley Robbins, this edition has been revised on These have been retained at the risk of adding a few addi- the basis of a few additional principles. tional pages to the book because students have uniformly First, it is obvious that an understanding of disease told us that they find them useful. mechanisms is based more than ever on a strong foun- Although we have entered the genomic era, the time- dation of basic science. In keeping with this, we have honored tools of gross and microscopic analysis remain always woven the relevant basic cell and molecular useful, and morphologic changes are highlighted for ready biology into the sections on pathophysiology in various reference. The strong emphasis on clinicopathologic cor- chapters. In this edition we go one step further and intro- relations is maintained, and, wherever understood, the duce a new chapter titled “The Cell as a Unit of Health and impact of molecular pathology on the practice of medicine Disease” at the very beginning of the book. In this chapter is emphasized. We are pleased that all of this was accom- we have attempted to encapsulate aspects of cell and plished without a significant “bulge” in the waistline of molecular biology that we believe are helpful in prepar- the text. ing readers for discussions of specific diseases. It is, in We continue to firmly believe that clarity of writing and essence, a refresher course in cell biology. proper use of language enhance comprehension and facili- Second, as teachers, we are acutely aware that medical tate the learning process. Those familiar with the previous students feel overwhelmed by the rapid growth of infor- editions will notice significant reorganization of the text mation about the molecular basis of disease. We have in many chapters to improve the flow of information and therefore excluded those new “breakthroughs” in the make it more logical. We are now in the digital age, so the laboratory that have not yet reached the bedside. Thus, text will be available online. In addition, over 100 updated for example, the drugs developed for targeting cancer and revised cases developed by one of us (VK) will also be mutations that are still in clinical trials have not been available, linked to the electronic version of the text. We discussed except in those rare instances in which the hope that these interactive cases will enhance and reinforce evidence of efficacy is close to hand. Similarly, in geneti- learning of pathology through application to clinical cases. cally heterogeneous disorders, we have focused on the It is a privilege for us to edit this book, and we realize most common mutations without providing a catalog the considerable trust placed in us by students and teachers of all the genes and polymorphisms involved. Thus, of pathology. We remain acutely conscious of this respon- we have tried to balance discussions of advancement in sibility and hope that this edition will be worthy of and sciences with the needs of students in the early stages of possibly enhance the tradition of its forebears. their careers. This effort required us to read each chapter ix  Acknowledgments Any large endeavor of this type cannot be completed the past many editions. Upon his well-earned retirement, without the help of many individuals. We thank the con- he handed over the charge to Jim Merritt, who had previ- tributors of various chapters. Many are veterans of the older ously worked on the immunology texts authored by one sibling of this text, the so-called “Big Robbins,” and they of us (AKA). Jim is a consummate professional and took are listed in the table of contents. To each of them, a special over the “book” effortlessly. We are especially grateful to thanks. In addition, we are also very grateful to our clinical the entire production team, in particular Clay Broeker, consultants for their input. They are listed separately after Book Production Specialist, for tolerating our sometimes the contributor names. We are fortunate to continue our next to “impossible” demands and for putting up with our collaboration with Jim Perkins, whose illustrations bring idiosyncrasies during the periods of extreme exhaustion abstract ideas to life and clarify difficult concepts, and we that afflict all authors who undertake what seems like an welcome members of our clinical advisory board who read endless task. We are thankful to the entire Elsevier team various chapters for accuracy and appropriateness of the for sharing our passion for excellence, including Karen clinical content; they are listed on a separate page. Our Giacomucci, Brian Salisbury, Tim Santner, Kristine McK- assistants, Trinh Nu and Thelma Wright from Chicago, ercher, and Melissa Darling. We also thank numerous stu- Ana Narvaez from San Francisco, and Muriel Goutas from dents and teachers scattered across the globe for raising Boston, deserve thanks for coordinating the tasks. questions about the clarity of content and serving as the Many colleagues have enhanced the text by providing ultimate “copyeditors.” Their efforts reassured us that the helpful critiques in their areas of interest. These include Dr. book is read seriously by them. Rick Aster, who provided “late-breaking news” in the area Ventures such as this exact a heavy toll from the fami- of climate change science. Many others offered critiques of lies of the authors. We thank them for their tolerance of various chapters; they include Drs. Jerry Turner, Jeremy our absences, both physical and emotional. We are blessed Segal, Nicole Cipriani, and Alex Gallan at the University and strengthened by their unconditional support and love of Chicago. Alex Gallan single handedly reviewed and and by their sharing with us the belief that our efforts are updated over 100 clinical cases available online. Others worthwhile and useful. We are especially grateful to our have provided us with photographic gems from their per- wives Raminder Kumar, Ann Abbas, and Erin Malone, sonal collections; they are individually acknowledged in who continue to provide steadfast support. the credits for their contribution(s). For any unintended And finally, we the editors salute each other; our part- omissions, we offer our apologies. nership thrives because of a shared vision of excellence Many at Elsevier deserve recognition for their roles in in teaching despite differences in opinions and individual the production of this book. This text was fortunate to be in styles. the hands of Rebecca Gruliow (Director, Content Develop- ment), who has been our partner for several editions. Others VK deserving of our thanks are Bill Schmitt, Executive Content AKA Strategist, who has been our friend and cheerleader for JCA x http://ebooksmedicine.net  Online Resources for Instructors and Students Resources for Instructors statins, targeted therapy for breast cancer, vitamin D, aspirin and NSAIDs, treatment of Marfan syndrome, and The following resources for instructors are available for more. These exemplify how the understanding of molecu- use when teaching via Evolve. Contact your local sales lar pathogenesis has led to the development of therapy. representative for more information, or go directly to the Evolve website to request access: https://evolve.elsevier. Videos com. Note: It may take 1-3 days for account access setup and Students can access 30 videos online at StudentConsult. verification upon initial account setup. com. The videos cover acute appendicitis, adenomyosis, arteriosclerosis, Barrett’s esophagus, basal cell carcinoma, Image Collection breast cancer, chronic obstructive pyelonephritis, CML, To assist in the classroom, we have made the images avail- cystic fibrosis with bronchiectatsis, diabetic glomeruloscle- able for instructors for teaching purposes. The images are rosis, ectopic pregnancy, eczematous dermatitis, familial provided in JPEG, PowerPoint, and PDF versions with adenomatous polyposis syndrome, giardiasis, hemochro- labels on/off and may be downloaded for use in lecture matosis, Hirschsprung’s disease, ischemic cardiomy- presentations. opathy, massive hepatocellular necrosis, mature cystic teratoma, metastatic squamous cell carcinoma, mucinous Test Bank colorectal adenocarcinoma, multiple sclerosis, necrotizing Instructors can access a complete test bank of over 250 vasculitis, osteoarthritis, pancreatic cancer, renal cell carci- multiple-choice questions for use in teaching. noma, sarcoidosis, seminoma, tuberculosis, and ulcerative colitis. Resources for Students Clinical Cases The following resources are available at StudentConsult. Students can study over 100 clinical cases available com to students with purchase of Robbins Basic Pathology online on Studentconsult.com. The clinical cases are (10th edition). designed to enhance clinical pathologic correlations and pathophysiology. Textbook Online The complete textbook is available online at Student- Self-Assessment Questions Consult.com. The online version is fully searchable and Students can test and score themselves with interactive provides all figures from the print book, with enhanced multiple-choice questions linked to chapters online at functionality for many, including clickable enlargements StudentConsult.com. and slideshow views of multiple-part images. Targeted Therapy Boxes Students have access online at StudentConsult.com to 14 targeted therapy boxes on clinical therapy topics, including xi http://ebooksmedicine.net  See Targeted Therapy available online at studentconsult.com C H A P T E R The Cell as a Unit of Health and Disease 1 CHAPTER OUTLINE The Genome 1 Waste Disposal: Lysosomes and Extracellular Matrix 21 Noncoding DNA 1 Proteasomes 13 Components of the Extracellular Histone Organization 3 Cellular Metabolism and Mitochondrial Matrix 22 Micro-RNA and Long Noncoding RNA 4 Function 13 Maintaining Cell Populations 24 Cellular Housekeeping 6 Cellular Activation 16 Proliferation and the Cell Cycle 24 Plasma Membrane: Protection and Nutrient Cell Signaling 16 Stem Cells 25 Acquisition 8 Signal Transduction Pathways 16 Concluding Remarks 28 Cytoskeleton 11 Modular Signaling Proteins, Hubs, and Cell-Cell Interactions 12 Nodes 18 Biosynthetic Machinery: Endoplasmic Reticulum Transcription Factors 19 and Golgi Apparatus 12 Growth Factors and Receptors 19 Pathology literally translates to the study of suffering (Greek the genome. The potential for these new powerful tools pathos = suffering, logos = study); as applied to modern to expand our understanding of pathogenesis and drive medicine, it is the study of disease. Virchow was certainly therapeutic innovation excites and inspires scientists and correct in asserting that disease originates at the cellular the lay public alike. level, but we now realize that cellular disturbances arise from alterations in molecules (genes, proteins, and others) Noncoding DNA that influence the survival and behavior of cells. Thus, the foundation of modern pathology is understanding the cel- The human genome contains about 3.2 billion DNA base lular and molecular abnormalities that give rise to diseases. pairs. Yet, within the genome there are only roughly 20,000 It is helpful to consider these abnormalities in the context protein-encoding genes, comprising just 1.5% of the of normal cellular structure and function, which is the genome. The proteins encoded by these genes are the fun- theme of this introductory chapter. damental constituents of cells, functioning as enzymes, It is unrealistic (and even undesirable) to condense the structural elements, and signaling molecules. Although vast and fascinating field of cell biology into a single 20,000 underestimates the actual number of proteins chapter. Consequently, rather than attempting a compre- encoded (many genes produce multiple RNA transcripts hensive review, the goal here is to survey basic principles that encode distinct protein isoforms), it is nevertheless and highlight recent advances that are relevant to the startling that worms composed of fewer than 1000 cells— mechanisms of disease that are emphasized throughout the and with genomes 30-fold smaller—are also assembled rest of the book. from roughly 20,000 protein-encoding genes. Perhaps even more unsettling is that many of these proteins are recogniz- able homologs of molecules expressed in humans. What THE GENOME then separates humans from worms? The answer is not completely known, but evidence sup- The sequencing of the human genome at the beginning of ports the assertion that the difference lies in the 98.5% of the 21st century represented a landmark achievement of the human genome that does not encode proteins. The biomedical science. Since then, the rapidly dropping cost function of such long stretches of DNA (which has been of sequencing and the computational capacity to analyze called the “dark matter” of the genome) was mysterious for vast amounts of data promise to revolutionize our under- many years. However, it is now clear that more than 85% of standing of health and disease. At the same time, the the human genome is ultimately transcribed, with almost emerging information has also revealed a breathtaking 80% being devoted to the regulation of gene expression. It level of complexity far beyond the linear sequencing of follows that whereas proteins provide the building blocks 1 http://ebooksmedicine.net 2 CHAPTER 1 The Cell as a Unit of Health and Disease Heterochromatin Nucleolus Heterochromatin Euchromatin Euchromatin Nucleus (dense, inactive) (disperse, active) Nucleosome DNA Transcription Promoter Exon Exon Enhancer Exon Pre- Cell mRNA Intron Intron Splicing Intron p arm q arm mRNA Telomeres 5’ UTR 3’ UTR Open-reading frame Centromere Translation Chromosome Protein Fig. 1.1 The organization of nuclear DNA. At the light microscopic level, the nuclear genetic material is organized into dispersed, transcriptionally active euchromatin or densely packed, transcriptionally inactive heterochromatin; chromatin can also be mechanically connected with the nuclear membrane, and nuclear membrane perturbation can thus influence transcription. Chromosomes (as shown) can only be visualized by light microscopy during cell division. During mitosis, they are organized into paired chromatids connected at centromeres; the centromeres act as the locus for the formation of a kinetochore protein complex that regulates chromosome segregation at metaphase. The telomeres are repetitive nucleotide sequences that cap the termini of chromatids and permit repeated chromosomal replication without loss of DNA at the chromosome ends. The chromatids are organized into short “P” (“petite”) and long “Q” (“next letter in the alphabet”) arms. The characteristic banding pattern of chromatids has been attributed to relative GC content (less GC content in bands relative to interbands), with genes tending to localize to interband regions. Individual chromatin fibers are composed of a string of nucleosomes— DNA wound around octameric histone cores—with the nucleosomes connected via DNA linkers. Promoters are noncoding regions of DNA that initiate gene transcription; they are on the same strand and upstream of their associated gene. Enhancers are regulatory elements that can modulate gene expression across distances of 100 kB or more by looping back onto promoters and recruiting additional factors that are needed to drive the expression of pre-mRNA species. The intronic sequences are subsequently spliced out of the pre-mRNA to produce the definitive message that includes exons that are translated into protein and 3′- and 5′-untranslated regions (UTR) that may have regulatory functions. In addition to the enhancer, promoter, and UTR sequences, noncoding elements are found throughout the genome; these include short repeats, regulatory factor binding regions, noncoding regulatory RNAs, and transposons. and machinery required for assembling cells, tissues, and regulation may prove to be more important in disease cau- organisms, it is the noncoding regions of the genome that sation than structural changes in specific proteins. Another provide the critical “architectural planning.” surprise that emerged from genome sequencing is that any The major classes of functional non–protein-coding DNA two humans are typically >99.5% DNA-identical (and are sequences found in the human genome include (Fig. 1.1): 99% sequence-identical with chimpanzees)! Thus, individ- Promoter and enhancer regions that bind protein tran- ual variation, including differential susceptibility to dis- scription factors eases and environmental exposures, is encoded in 200 inactive heterochromatin and (2) histochemically dis- nucleotides in length. persed and transcriptionally active euchromatin. Because Micro-RNAs (miRNAs) are relatively short RNAs (22 only euchromatin permits gene expression and thereby nucleotides on average) that function primarily to dictates cellular identity and activity, there are a host of modulate the translation of target mRNAs into their mechanisms that tightly regulate the state of chromatin corresponding proteins. Posttranscriptional silencing (described below). of gene expression by miRNA is a fundamental and DNA methylation. High levels of DNA methylation in evolutionarily conserved mechanism of gene regula- gene regulatory elements typically result in chroma- tion present in all eukaryotes (plants and animals). tin condensation and transcriptional silencing. Like Even bacteria have a primitive version of the same histone modifications (see later), DNA methylation is general machinery that they use to protect themselves tightly regulated by methyltransferases, demethylating against foreign DNA (e.g., from phages and viruses). enzymes, and methylated-DNA-binding proteins. The human genome contains almost 6000 miRNA genes, Histone modifying factors. Nucleosomes are highly only 3.5-fold less than the number of protein-coding dynamic structures regulated by an array of nuclear genes. Moreover, individual miRNAs appear to regu- proteins and post-translational modifications: late multiple protein-coding genes, allowing each Chromatin remodeling complexes can reposition nucleo- miRNA to coregulate entire programs of gene expres- somes on DNA, exposing (or obscuring) gene regula- sion. Transcription of miRNA genes produces a primary tory elements such as promoters. transcript (pri-miRNA) that is processed into progres- “Chromatin writer” complexes carry out more than sively smaller segments, including trimming by the 70 different covalent histone modifications generi- enzyme Dicer. This generates mature single-stranded cally denoted as marks. These include methylation, miRNAs of 21 to 30 nucleotides that associate with a acetylation, and phosphorylation of specific histone multiprotein aggregate called RNA-induced silencing amino acid residues: Histone methylation of lysines complex (RISC; Fig. 1.3). Subsequent base pairing and arginines is accomplished by specific writer between the miRNA strand and its target mRNA directs enzymes; methylation of histone lysine residues the RISC to either induce mRNA cleavage or to repress can lead to transcriptional activation or repression, its translation. In this way, the target mRNA is posttran- depending on which histone residue is “marked.” scriptionally silenced. Histone acetylation of lysine residues (occurring through histone acetyl transferases) tends to open Taking advantage of the same pathway, small interfering up chromatin and increase transcription; histone RNAs (siRNAs) are short RNA sequences that can be intro- deacetylases (HDAC) reverse this process, leading duced into cells. These serve as substrates for Dicer and to chromatin condensation. Histone phosphorylation interact with the RISC complex in a manner analogous to of serine residues can variably open or condense endogenous miRNAs. Synthetic siRNAs that can target chromatin, to increase or decrease transcription, specific mRNA species are therefore powerful laboratory respectively. tools to study gene function (so-called knockdown technol- Histone marks are reversible through the activity of ogy); they also are promising as therapeutic agents to “chromatin erasers.” Other proteins function as “chro- silence pathogenic genes, e.g., oncogenes involved in neo- matin readers,” binding histones that bear particular plastic transformation. marks and thereby regulating gene expression. Long noncoding RNA (lncRNA). The human genome also contains a very large number of lncRNAs—at least The mechanisms involved in the cell-specific epigenetic 30,000, with the total number potentially exceeding regulation of genomic organization and gene expression coding mRNAs by 10- to 20-fold. lncRNAs modulate are undeniably complex. Despite the intricacies, learning gene expression in many ways (Fig. 1.4); for example, to manipulate these processes will likely bear significant they can bind to regions of chromatin, restricting RNA therapeutic benefits because many diseases are associated polymerase access to coding genes within the region. with inherited or acquired epigenetic alterations, and The best-known example of a repressive function dysregulation of the “epigenome” has a central role in the involves XIST, which is transcribed from the X chromo- genesis of benign and malignant neoplasms (Chapter 6). some and plays an essential role in physiologic X chro- Moreover—unlike genetic changes—epigenetic alterations mosome inactivation. XIST itself escapes X inactivation, (e.g., histone acetylation and DNA methylation) are readily but forms a repressive “cloak” on the X chromosome reversible and are therefore amenable to intervention; from which it is transcribed, resulting in gene silencing. indeed, HDAC inhibitors and DNA methylation inhibitors Conversely, it has been appreciated that many enhanc- are already being used in the treatment of various forms ers are sites of lncRNA synthesis, with the lncRNAs of cancer. expanding transcription from gene promoters through http://ebooksmedicine.net  The Genome 5 A. Gene activation Ribonucleoprotein miRNA gene transcription complex lncRNA Gene activation pri-miRNA Decoy lncRNA Target gene B. Gene suppression pre-miRNA Gene suppression Export protein pre-miRNA C. Promote chromatin modification Dicer Methylation, acetylation Target mRNA miRNA D. Assembly of protein complexes Act on chromatin structure Unwinding of miRNA duplex RISC Multi-subunit complex complex Fig. 1.4 Roles of long noncoding RNAs (lncRNAs). (A) Long noncoding RNAs (lncRNAs) can facilitate transcription factor binding and thus promote Imperfect Perfect gene activation. (B) Conversely, lncRNAs can preemptively bind transcription match match factors and thus prevent gene transcription. (C) Histone and DNA modifica- Target tion by acetylases or methylases (or deacetylases and demethylases) may be mRNA directed by the binding of lncRNAs. (D) In other instances lncRNAs may act Translational mRNA as scaffolding to stabilize secondary or tertiary structures and/or multisub- repression cleavage unit complexes that influence general chromatin architecture or gene activity. (Adapted from Wang KC, Chang HY: Molecular mechanisms of long noncoding RNAs, Mol Cell 43:904, 2011.) a variety of mechanisms (Fig. 1.4). Ongoing studies are exploring the role of lncRNAs in diseases like athero- Ribosome sclerosis and cancer. GENE SILENCING Gene Editing Exciting new developments that permit exquisitely specific Fig. 1.3 Generation of microRNAs (miRNA) and their mode of action in genome editing stand to usher in an era of molecular revo- regulating gene function. miRNA genes are transcribed to produce a primary lution. These advances come from a wholly unexpected miRNA (pri-miRNA), which is processed within the nucleus to form pre- source: the discovery of clustered regularly interspaced miRNA composed of a single RNA strand with secondary hairpin loop short palindromic repeats (CRISPRs) and Cas (or CRISPR- structures that form stretches of double-stranded RNA. After this pre- miRNA is exported out of the nucleus via specific transporter proteins, the associated genes). These are linked genetic elements that cytoplasmic enzyme Dicer trims the pre-miRNA to generate mature double- endow prokaryotes with a form of acquired immunity to stranded miRNAs of 21 to 30 nucleotides.The miRNA subsequently unwinds, phages and plasmids. Bacteria use this system to sample and the resulting single strands are incorporated into the multiprotein RISC. the DNA of infecting agents, incorporating it into the host Base pairing between the single-stranded miRNA and its target mRNA genome as CRISPRs. CRISPRs are transcribed and pro- directs RISC to either cleave the mRNA target or to repress its translation. cessed into an RNA sequence that binds and directs the In either case, the target mRNA gene is silenced posttranscriptionally. nuclease Cas9 to a sequences (e.g., a phage), leading to its cleavage and the destruction of the phage. Gene editing repurposes this process by using artificial guide RNAs (gRNAs) that bind Cas9 and are complementary to a DNA http://ebooksmedicine.net 6 CHAPTER 1 The Cell as a Unit of Health and Disease sequence of interest. Once directed to the target sequence of the system (and the excitement about its genetic engi- by the gRNA, Cas9 induces double-strand DNA breaks. neering potential) comes from its impressive flexibility and Repair of the resulting highly specific cleavage sites specificity, which is substantially better than other previ- can lead to somewhat random disruptive mutations in the ous editing systems. Applications include inserting specific targeted sequences (through nonhomologous end joining mutations into the genomes of cells to model cancers and [NHEJ]), or the precise introduction of new sequences of other diseases, and rapidly generating transgenic animals interest (by homologous recombination). Both the gRNAs from edited embryonic stem cells. On the flip side, it now is and the Cas9 enzyme can be delivered to cells with a single feasible to selectively “correct” mutations that cause hered- easy-to-build plasmid (Fig. 1.5). However, the real beauty itable disease, or—perhaps more worrisome—to just elimi- nate less “desirable” traits. Predictably, the technology has inspired a vigorous debate regarding its application. Homologous gRNA sequence CELLULAR HOUSEKEEPING The viability and normal activity of cells depend on a Cas9 protein gRNA variety of fundamental housekeeping functions that all dif- ferentiated cells must perform. Many normal housekeeping functions are compart- mentalized within membrane-bound intracellular organ- elles (Fig. 1.6). By isolating certain cellular functions within distinct compartments, potentially injurious degradative enzymes or reactive metabolites can be concentrated Cleavage or stored at high concentrations in specific organelles Double-stranded without risking damage to other cellular constituents. DNA Moreover, compartmentalization allows for the creation Target genomic of unique intracellular environments (e.g., low pH or high sequence calcium) that are optimal for certain enzymes or metabolic pathways. New proteins destined for the plasma membrane or Double-stranded DNA break secretion are synthesized in the rough endoplasmic reticulum (RER) and physically assembled in the Golgi apparatus; pro- teins intended for the cytosol are synthesized on free ribo- somes. Smooth endoplasmic reticulum (SER) may be abundant in certain cell types such as gonads and liver where it serves as the site of steroid hormone and lipoprotein syn- NHEJ thesis, as well as the modification of hydrophobic com- pounds such as drugs into water-soluble molecules for HDR export. Cells catabolize the wide variety of molecules that they endocytose, as well as their own repertoire of proteins and organelles—all of which are constantly being degraded Insertion/ Donor DNA and renewed. Breakdown of these constituents takes deletion place at three different sites, ultimately serving different DNA with random mutation DNA with specific mutation functions. Proteasomes are “disposal” complexes that degrade Fig. 1.5 Gene editing with clustered regularly interspersed short palin- dromic repeats (CRISPRs)/Cas9. In bacteria, DNA sequences consisting of denatured or otherwise “tagged” cytosolic proteins and CRISPRs are transcribed into guide RNAs (gRNAs) with a constant region release short peptides. In some cases the peptides so and a variable sequence of about 20 bases. The constant regions of gRNAs generated are presented in the context of class I major bind to Cas9, permitting the variable regions to form heteroduplexes with histocompatibility molecules to help drive the adaptive homologous host cell DNA sequences. The Cas9 nuclease then cleaves the immune response (Chapter 5). In other cases, protea- bound DNA, producing a double-stranded DNA break. To perform gene somal degradation of regulatory proteins or transcrip- editing, gRNAs are designed with variable regions that are homologous to a target DNA sequence of interest. Coexpression of the gRNA and Cas9 in tion factors can trigger or shut down cellular signaling cells leads to efficient cleavage of the target sequence. In the absence of pathways. homologous DNA, the broken DNA is repaired by non­homologous end Lysosomes are intracellular organelles that contain joining (NHEJ), an error-prone method that often introduces disruptive enzymes that digest a wide range of macromolecules, insertions or deletions (indels). By contrast, in the presence of a homologous including proteins, polysaccharides, lipids, and nucleic “donor” DNA spanning the region targeted by CRISPR/Cas9, cells instead acids. They are the organelle in which phagocytosed may use homologous DNA recombination (HDR) to repair the DNA break. HDR is less efficient than NHEJ, but has the capacity to introduce precise microbes and damaged or unwanted cellular organelles changes in DNA sequence. Potential applications of CRISPR/Cas9 coupled are degraded and eliminated. with HDR include the repair of inherited genetic defects and the creation Peroxisomes are specialized cell organelles that contain of pathogenic mutations. catalase, peroxidase and other oxidative enzymes. They http://ebooksmedicine.net  Cellular Housekeeping 7 Relative volumes of intracellular organelles (hepatocyte) Compartment % total volume number/cell role in the cell Cytosol 54% 1 metabolism, transport, protein translation Mitochondria 22% 1700 energy generation, apoptosis Rough ER 9% 1* synthesis of membrane and secreted proteins Smooth ER, Golgi 6% 1* protein modification, sorting, catabolism Nucleus 6% 1 cell regulation, proliferation, DNA transcription Endosomes 1% 200 intracellular transport and export, ingestion of extracellular substances Lysosomes 1% 300 cellular catabolism Peroxisomes 1% 400 very long-chain fatty acid metabolism Rough Free endoplasmic ribosomes reticulum Nucleolus Golgi Nucleus apparatus Lysosome Mitochondrion Endosome Smooth Cytoskeleton endoplasmic Plasma reticulum membrane Peroxisome Centrioles Microtubules Fig. 1.6 Basic subcellular constituents of cells. The table presents the number of various organelles within a typical hepatocyte, as well as their volume within the cell. The figure shows geographic relationships but is not intended to be accurate to scale. *Rough and smooth ER form a single compartment; the Golgi apparatus is organized as a set of discrete stacked cisternae interconnected by transport vesicles. (Adapted from Weibel ER, Stäubli W, Gnägi HR, et al: Correlated morphometric and biochemical studies on the liver cell. I. Morphometric model, stereologic methods, and normal morphometric data for rat liver, J Cell Biol 42:68, 1969.) play a specialized role in the breakdown of very long Most of the adenosine triphosphate (ATP) that powers chain fatty acids, generating hydrogen peroxide in the cells is made through oxidative phosphorylation in the process. mitochondria. However, mitochondria also serve as an important source of metabolic intermediates that are The contents and position of cellular organelles also needed for anabolic metabolism. They also are sites of syn- are subject to regulation. Endosomal vesicles shuttle inter- thesis of certain macromolecules (e.g., heme), and contain nalized material to the appropriate intracellular sites or important sensors of cell damage that can initiate and regu- direct newly synthesized materials to the cell surface or late the process of apoptotic cell death. targeted organelle. Movement of both organelles and pro- Cell growth and maintenance require a constant supply teins within the cell and of the cell in its environment is of both energy and the building blocks that are needed orchestrated by the cytoskeleton. These structural proteins for synthesis of macromolecules. In growing and dividing also regulate cellular shape and intracellular organiza- cells, all of these organelles have to be replicated (organel- tion, requisites for maintaining cell polarity. This is par- lar biogenesis) and correctly apportioned in daughter cells ticularly critical in epithelia, in which the top of the cell following mitosis. Moreover, because the macromolecules (apical) and the bottom and side of the cell (basolateral) are and organelles have finite life spans (mitochondria, e.g., often exposed to different environments and have distinct last only about 10 days), mechanisms also must exist functions. that allow for the recognition and degradation of “worn http://ebooksmedicine.net 8 CHAPTER 1 The Cell as a Unit of Health and Disease out” cellular components. The final catabolism occurs in cells undergoing apoptosis (programmed cell death), it lysosomes. becomes an “eat me” signal for phagocytes. In the With this as a primer, we now move on to discuss cel- special case of platelets, it serves as a cofactor in the lular components and their function in greater detail. clotting of blood. Glycolipids and sphingomyelin are preferentially expressed Plasma Membrane: Protection and on the extracellular face; glycolipids (and particularly Nutrient Acquisition gangliosides, with complex sugar linkages and terminal sialic acids that confer negative charges) are important Plasma membranes (and all other organellar membranes) in cell–cell and cell–matrix interactions, including inflam- are more than just static lipid sheaths. Rather, they are matory cell recruitment and sperm–egg interactions. fluid bilayers of amphipathic phospholipids with hydro- philic head groups that face the aqueous environment and Certain membrane components associate laterally with hydrophobic lipid tails that interact with each other to each other in the bilayer, leading to distinct domains called form a barrier to passive diffusion of large or charged lipid rafts. Because inserted membrane proteins have differ- molecules (Fig. 1.7A). The bilayer is composed of a hetero- ent intrinsic solubilities in various lipid domains, they tend geneous collection of different phospholipids, which are to accumulate in certain regions of the membrane (e.g., distributed asymmetrically—for example, certain mem- rafts) and to become depleted from others. Such nonran- brane lipids preferentially associate with extracellular or dom distributions of lipids and membrane proteins impact cytosolic faces. Asymmetric partitioning of phospholipids cell–cell and cell–matrix interactions, as well as intracel- is important in several cellular processes: lular signaling and the generation of specialized membrane Phosphatidylinositol on the inner membrane leaflet can be regions involved in secretory or endocytic pathways. phosphorylated, serving as an electrostatic scaffold for The plasma membrane is liberally studded with a intracellular proteins; alternatively, polyphosphoinosit- variety of proteins and glycoproteins involved in (1) ion ides can be hydrolyzed by phospholipase C to generate and metabolite transport, (2) fluid-phase and receptor- intracellular second signals such as diacylglycerol and mediated uptake of macromolecules, and (3) cell–ligand, inositol trisphosphate. cell–matrix, and cell–cell interactions. Proteins interact Phosphatidylserine is normally restricted to the inner with the lipid bilayer by one of four general arrangements face where it confers a negative charge and is involved (Fig. 1.7B): in electrostatic interactions with proteins; however, Most proteins are transmembrane (integral) proteins, when it flips to the extracellular face, which happens in having one or more relatively hydrophobic α-helical Extracellular Glycosylphosphatidylinositol Outside protein (GPI) linked protein Glycolipids Phosphatidyl- Sphingo- Lipid choline myelin raft P (outer mostly) (outer mostly) P Phosphatidyl- Phosphatidyl- Phosphatidyl- Cholesterol ethanolamine serine inositol (both faces) (inner mostly) (inner mostly) (both faces) Transmembrane proteins Cytosolic Cytoplasm protein Lipid-linked protein A B Fig. 1.7 Plasma membrane organization and asymmetry. (A) The plasma membrane is a bilayer of phospholipids, cholesterol, and associated proteins. The phospholipid distribution within the membrane is asymmetric; phosphatidylcholine and sphingomyelin are overrepresented in the outer leaflet, and phosphatidyl- serine (negative charge) and phosphatidylethanolamine are predominantly found on the inner leaflet; glycolipids occur only on the outer face where they contribute to the extracellular glycocalyx. Non-random partitioning of certain membrane components such as cholesterol creates membrane domains known as lipid rafts. (B) Membrane-associated proteins may traverse the membrane (singly or multiply) via α-helical hydrophobic amino acid sequences; depending on the sequence and hydrophobicity of these domain, such proteins may be enriched or excluded from lipid rafts and other membrane domain. Proteins on the cytosolic face may associate with membranes through posttranslational modifications, for example, farnesylation or addition of palmitic acid. Proteins on the extracytoplasmic face may associate with the membrane via glycosyl phosphatidyl inositol linkages. Besides protein–protein interactions within the mem- brane, membrane proteins can also associate with extracellular and/or intracytoplasmic proteins to generate large, relatively stable complexes (e.g., the focal adhesion complex). Transmembrane proteins can translate mechanical forces (e.g., from the cytoskeleton or ECM) as well as chemical signals across the mem- brane. It is worth remembering that a similar organization of lipids and associated proteins also occurs within the various organellar membranes. http://ebooksmedicine.net  Cellular Housekeeping 9 segments that traverse the lipid bilayer. Integral mem- low-molecular-weight species (ions and small molecules brane proteins typically contain positively charged up to approximately 1000 daltons), channel proteins and amino acids in their cytoplasmic domains that anchor carrier proteins may be used (although this discussion the proteins to the negatively charged head groups of focuses on plasma membranes, it should be noted that membrane phospholipids. similar pores and channels are needed for transport across Proteins may be synthesized in the cytosol and post- organellar membranes). Each transported molecule (e.g., translationally attached to prenyl groups (e.g., farnesyl, ion, sugar, nucleotide) requires a transporter that is typi- related to cholesterol) or fatty acids (e.g., palmitic or cally highly specific (e.g., glucose but not galactose): myristic acid) that insert into the cytosolic side of the Channel proteins create hydrophilic pores that, when plasma membrane. open, permit rapid movement of solutes (usually Attachment to membranes can occur through glyco- restricted by size and charge; Fig. 1.8). sylphosphatidylinositol (GPI) anchors on the extracel- Carrier proteins bind their specific solute and undergo a lular face of the membrane. series of conformational changes to transfer the ligand Extracellular proteins can noncovalently associate with across the membrane; their transport is relatively slow. transmembrane proteins, which serve to anchor them to the cell. In many cases, a concentration and/or electrical gradi- ent between the inside and outside of the cell drives solute Many plasma membrane proteins function together as movement via passive transport (virtually all plasma mem- larger complexes; these may assemble under the control branes have an electrical potential difference across them, of chaperone molecules in the RER or by lateral diffusion with the inside negative relative to the outside). In other in the plasma membrane. The latter mechanism is charac- cases, active transport of certain solutes against a concentra- teristic of many protein receptors (e.g., cytokine receptors) tion gradient is accomplished by carrier molecules (not that dimerize or trimerize in the presence of ligand to form channels) using energy released by ATP hydrolysis or a functional signaling units. Although lipid bilayers are fluid coupled ion gradient. Transporter ATPases include the in the two-dimensional plane of the membrane, membrane notorious multidrug resistance (MDR) protein, which pumps components can nevertheless be constrained to discrete polar compounds (e.g., chemotherapeutic drugs) out of domains. This can occur by localization to lipid rafts (dis- cells and may render cancer cells resistant to treatment. cussed earlier), or through intercellular protein–protein Because membranes are freely permeable to water, it interactions (e.g., at tight junctions) that establish discrete moves into and out of cells by osmosis, depending on rela- boundaries; indeed, this strategy is used to maintain cell tive solute concentrations. Thus, extracellular salt in excess polarity (e.g., top/apical versus bottom/basolateral) in epi- of that in the cytosol (hypertonicity) causes a net movement thelial layers. Alternatively, unique domains can be formed of water out of cells, whereas hypotonicity causes a net through the interaction of membrane proteins with cyto- movement of water into cells. The cytosol is rich in charged skeletal molecules or an extracellular matrix (ECM). metabolites and protein species, which attract a large The extracellular face of the plasma membrane is dif- number of counterions that tend to increase the intracel- fusely studded with carbohydrates, not only as complex lular osmolarity. As a consequence, to prevent overhydra- oligosaccharides on glycoproteins and glycolipids, but also tion cells must constantly pump out small inorganic ions as polysaccharide chains attached to integral membrane (e.g., Na+)—typically through the activity of membrane proteoglycans. This glycocalyx functions as a chemical and ion-exchanging ATPases. Loss of the ability to generate mechanical barrier, and is also involved in cell–cell and energy (e.g., in a cell injured by toxins or ischemia) there- cell–matrix interactions. fore results in osmotic swelling and eventual rupture of cells. Similar transport mechanisms also regulate intracel- Passive Membrane Diffusion lular and intraorganellar pH; most cytosolic enzymes Small, nonpolar molecules such as O2 and CO2 readily dis- prefer to work at pH 7.4, whereas lysosomal enzymes func- solve in lipid bilayers and therefore rapidly diffuse across tion best at pH 5 or less. them, as do hydrophobic molecules (e.g., steroid-based molecules such as estradiol or vitamin D). Similarly, small Receptor-Mediated and polar molecules (0.5 g/24 hours, or red cell casts Neurologic disorder Seizures, psychosis, myelitis, or neuropathy, in the absence of offending drugs or other known causes Hemolytic anemia Hemolytic anemia Leukopenia or Leukopenia—