Cell Movement in Health and Disease

Cell Movement in Health and Disease brings the several scientific domains related to the phenomena together, establishing a consistent foundation for researchers in this exciting field.

The content is presented in four main section. The first explores the foundations of Cell Movement, including overviews of cellular structure, signaling, physiology, motion-related proteins, and the interface with the cellular membrane. The second part covers the biological aspects of cellular movement, starting with chemical and mechanical sensing, describing the types of cell movement, mechanics at cell level, cell physiology, collective behavior, and the connections with the extracellular matrix. The following chapters provide an overview of the molecular machinery involved and cell-type specific movement. The third part of the book is dedicated to the translational aspects of cell movement, highlighting the key conditions associated with cell movement dysfunction, like cell invasion in cancer, wound healing, developmental issues, neurological dysfunctions, and immune response. The final part of the book covers key methods and modeling tools for cell movement research, including predictive mathematical models, in vitro and in vivo methods, biophysical and bioinformatics tools.

Cell Movement in Health and Disease is the ideal reference for scientists from different backgrounds converging to expand the understanding of this key cellular process. Cellular and molecular biologists will gain a better understanding of the physical principals operating at cellular level while biophysicist and biomedical engineers will benefit from the solid biology foundation provided by the book.

• Combines Biology, Physics and Modeling of cellular movement in one single source
• Updated with the current understanding of the field
• Includes key research methods for cell movement investigation
• Cover translational aspects of cellular movement

• Language: English
• Publisher: Academic Press
• Release date: Mar 30, 2022
• ISBN: 9780323901963

Book preview

Preface

With this book titled Cell Movement in Health and Disease, we provide a timely overview of different aspects of cell migration in different contexts. We decided to put together this new resource in order to address cell migration from different angles that have previously not been covered in similar textbooks. While looking for appropriate content of the book, we realized that the aspects of cell movement have not frequently been addressed in textbooks from a mechano-biological or translational viewpoint. Thus, we decided to follow our own expertise and include chapters on mechano-sensing, actin dynamics, and cell movement during cancer, inflammatory, and cardiovascular diseases. Other newly emerging concepts such as the migrasome and cell collective responses are also covered. Therefore, we hope that this book will provide sufficient insight into this exciting topic to be a useful resource of information for a broad readership including cell biologists, biochemists, biophysicists, biomedical engineers, as well as clinicians, and research physicians. Cell Movement in Health and Disease is supposed to serve as reference book for scientists from different backgrounds aiming to broaden their understanding of cell migration and as companion book for university courses and cell biology classes. The content is presented in four sections that cover (1) cellular basics of cell movement, including overviews of cellular structure, physiology, signaling, cytoskeleton, and motion-related proteins, (2) mechano-sensing, connections with the extracellular matrix, and the hydrodynamical aspects of cell movement, (3) translational aspects of cell movement, highlighting the key conditions causing aberrant cell movement, for example, during cancer metastasis or immune responses, and (4) novel key methods and modeling tools for cell migration research, including mathematical models, microfluidics tools, and state-of-the-art microscopy. By combining these key concepts related to cell movement, we hope to have established a valuable source of information for researchers interested in this exciting and multidisciplinary topic.

We welcome suggestions, comments, and corrections of inevitable mistakes that can appear in a book. Please contact us at [e-mail]; [e-mail]; or [e-mail].

Michael Schnoor, Lei-Miao Yin, and Sean X. Sun

I

Cell biological aspects of cell movement

Outline

Chapter 1. Cell structure and physiology

Chapter 2. Migrasome in cell movement: new horizon for cell signaling

Chapter 3. Cellular substructures, actin dynamics, and actin-binding proteins regulating cell migration

Chapter 4. Impact of cell—cell interactions on communication and collectiveness

Chapter 5. Cell migration

Chapter 1: Cell structure and physiology

Wanyu Zhao a , Weida Ren a , Dichun Huang, Yuan Sang, Lingbo Cao, and Junqi Huang ∗      Key Laboratory for Regenerative Medicine, Ministry of Education, College of Life Science and Technology, Jinan University, Guangzhou, China

Abstract

This chapter introduces the basic internal structures of a mammalian cell. The chapter also surveys the physiologies and a number of up-to-date advances of these elaborate intracellular structures. Comprehensive understanding of cell structure and physiology can undoubtedly promise new revelations for biomedical studies, in particular during current pandemic.

The term Cell stems from the Latin word Cella, which was coined by Robert Hooke (1665 AD) to describe grids on a section of cork, conceptually a close resemblance of a small room. This finding laid the groundwork for hundreds of years of research in cellulo.

The modern definition of Cell commonly referred to as the most basic structural and functional unit of a nonviral organism. A cell has its own boundaries, both externally and internally, separating the cell into different distinct yet functionally correlated discrete entities. Most of these highly ordered structures are spatially and temporally dynamic, which allow complex life activities to be self-reliance and self-regulated, consequently creating infinite possibilities for cells in constantly changing environments.

Keywords

Cell structure; Centrosome; Cytoskeleton; Endoplasmic reticulum; Golgi apparatus; Lysosome; Mitochondria; Nucleus; Physiology; Plasma membrane

Introduction

This chapter introduces the basic internal structures of a mammalian cell. The chapter also discusses the physiology and up-to-date advances of the elaborate intracellular substructures that form a cell. A comprehensive understanding of the cell structure and physiology is important to further our biomedical horizon of cellular functions in different contexts.

The term Cell stems from the Latin word Cella, which was first used by Robert Hooke (1665 AD) to describe grids on a section of cork, conceptually a close resemblance of a small room. This finding laid the groundwork for hundreds of years of research in cellulo.

The modern definition of Cell commonly refers to the most basic structural and functional unit of a nonviral organism. A cell has its own boundaries, both externally and internally, separating the cell into different distinct yet functionally correlated discrete entities. Most of these highly ordered structures are spatially and temporally dynamic, which allow complex life activities to be self-reliant and self-regulated, consequently creating infinite possibilities for cells in the constantly changing environments.

Cell structure and physiology

Cells assemble an assortment of intricate subcellular structures with distinct biochemical and biomechanical properties into a functional unit. It is now generally recognized that cells are made up of countless membrane-enclosed or membrane-free compartments within the cell border made up of the so-called plasma membrane. These internal structures are generally termed cellular organelles. The main organelles of a mammalian cell include: nucleus, mitochondria, endoplasmic reticulum (ER), Golgi apparatus, lysosome, and centrosome (Fig. 1.1). Although superficially isolated, the synergistic interactions between these organelles sustain cell homeostasis and self-reliance.

The plasma membrane together with these discrete organelles not only implement a plethora of physiological functions including the regulation of cell movement in health, but also engage in diseases as described in Section III of this book. In the following paragraphs, we explain the basic concepts of these bona fide structures and discuss advances in our understanding of organelle functions.

Plasma membrane

Each and every cell is encased in a giant bubble of membrane, known as the plasma membrane (also commonly referred to as the cell membrane). The plasma membrane isolates and maintains the cell's outmost boundary from the environment. Meanwhile, this cellular giant barrier also bridges extracellular cues and intracellular signaling pathways, enabling constant communications with the rapidly fluctuating environment. Therefore, the plasma membrane acts not only as a line of defense, but also as a customs inspector. It is indisputable that the wholeness and continuity of this pliable architecture sets the current criterion of cellular life or death.

Figure 1.1  Schematic of cell structures. ① Plasma membrane, ② nucleus, ③ mitochondria, ④ endoplasmic reticulum, ⑤ Golgi apparatus, ⑥ lysosome, ⑦ centrosome, ⑧ filamentous actin, ⑨ microtubule, ⑩ intermediate filament, ⑪ peroxisome, and ⑫ filopodia.

Structure

To comprehend the plasma membrane structure, it is, first of all, to acquaint oneself with the fluid mosaic model (Fig. 1.2). The model emphasizes the thermodynamic mobility and heterogeneous propensity as a fundamental attribute of the semifluidic plasma membrane, albeit with a high degree of intrinsic flexibility and slightly further replenishment and refinements are proposed over the decades [1]. This model describes the main fabric of the plasma membrane as a mosaic reservoir of phospholipids, proteins, carbohydrates, etc. The intrinsic properties of these components and their interactivity define a multifaceted plasma membrane.

The plasma membrane is spontaneously a sheet of continuous membrane mainly composed of a phospholipid bilayer (consisting of two layers of lipid molecules), wrapped around all cell constituents [2]. Phospholipids are a group of specific lipids that contain a hydrophilic phosphate head and two hydrophobic side-by-side tails made up of fatty acids (ordinarily 16–18 carbons), typically interconnected by a glycerol molecule. The phosphate head is negatively charged, thus endowing the plasma membrane a water-attracting ability. Contrarily, the fatty acid tails are uncharged and are congenitally repelled by the aqueous environment. Due to the abovementioned intrinsic physiochemical properties of these phospholipids, two layers of phospholipids congregate together with the tail regions attracted to each other interiorly, forming the meticulous phospholipid bilayer. As the upmost basal membrane component, the phospholipid bilayer is composed of hundreds, if not thousands, of structurally diverse phospholipids. The aforementioned inborn characteristics of the phospholipid bilayer thus exclude most extracellular materials from the cell inner environment. Remarkably, peroxidation of the phospholipids is found to have contributed directly to a wide range of diseases, such as cancer, brain stroke, ischemic heart/kidney damages (see Section III of this book) [3].

Figure 1.2  Schematic of plasma membrane. ① Phospholipid, ② integral membrane protein, ③ peripheral membrane protein, ④ membrane channel, ⑤ carbohydrates, and ⑥ GlycoRNA.

The second major component of the plasma membrane is membrane protein. Numerous membrane proteins are neatly embedded into or anchored on the plasma membrane. Approximately 50% of the surface area of plasma membrane is occupied by membrane proteins. There are two main categories of these membrane proteins: the integral membrane protein and the peripheral membrane protein. Integral membrane proteins are proteins inserted into the phospholipid bilayer through their hydrophobic peptide sequences. These integral membrane proteins can be further subdivided according to different criteria. On this thin membrane of a cell, scores of integral membrane proteins penetrate the plasma membrane many times. Thereinto, in comparison to proteins partially drilling into the membrane, transmembrane proteins completely span the phospholipid bilayer. Correspondingly, peripheral membrane proteins are referred to proteins directly or indirectly attached to the inner or outer surface of the phospholipid bilayer. Peripheral membrane proteins typically form weak noncovalent or electrostatic bonds with the phospholipids or the integral membrane proteins within. Thus, the removal of these peripheral membrane proteins generally does not severely interfere with the integrity of the plasma membrane.

Alongside the phospholipid bilayer and the membrane proteins, carbohydrates are the third important constituents of the plasma membrane. Through glycosidic (covalent) bond, carbohydrate-attached lipids (glycolipids) and proteins (glycoproteins) are displayed on the exterior surface of the plasma membrane. These carbohydrates/oligosaccharides can differ in length and the glycan sequences. For glycolipids, the oligosaccharides are added onto the hydrophilic lipid head in the ER and the Golgi apparatus (both will be introduced in the later sections). For glycoproteins, the oligosaccharides are added onto the nitrogen atom of asparagine or arginine (N-linked glycosylation) or the hydroxyl oxygen of either serine or threonine residues (O-linked glycosylation) of the membrane proteins, as well in the ER or the Golgi apparatus. These covalently linked carbohydrates (glycoconjugates) are important for cell recognition, adhesion, cancer cell metastasis, programmed cell death regulation, kidney function, etc. Importantly, during virus or bacterial infection, these glycoconjugates frequently act as the first and major recognition and attaching sites [4]. The human receptor protein ACE2 of SARS-CoV-2 virus also has six sites of glycosylation [5].

Strikingly, a most recent study shows that RNA–glycan conjugates (glycoRNAs), a brand new type of glycoconjugates, also exist on the cell surface [6]. These glycoRNAs are able to bind the Siglec receptor, potentially playing a role in cell–cell recognition.

Selective permeability

This characteristic of the plasma membrane allows certain substances through but hinders the movement of others, is among the pivotal features of the plasma membrane. Selective permeability also creates different osmotic pressure between the cell interior and the outer environment. Largely due to the amphipathic characteristic of the phospholipid bilayer, inorganic or organic materials cross into or get out of the plasma membrane either by passive (non-energy-consuming) or active (energy-consuming) transport. Passive transport, either by simple diffusion or facilitated diffusion, refers to a phenomenon that molecules move along the concentration gradient from high to low without or with the help from certain transmembrane proteins. Being passive, both simple diffusion and facilitated diffusion do not require energy expenditure. Simple diffusion is the free and self-reliant movement of small molecules, such as certain lipids, oxygen and carbon dioxide gases, across the plasma membrane. Facilitated diffusion is the process wherein substances with bigger sizes and/or polarity diffuse across the plasma membrane in a manner depending on channels or carrier proteins. The uptake of glucose and certain amino acids are two examples of facilitated diffusion. Active transport, on the contrary, depicts processes that selected molecules are transported by special transmembrane proteins in a direction against their concentration gradients on the cost of consumption of adenosine triphosphate (ATP). Transmembrane proteins involved in the active transport are usually pumps. Moreover, active transport can be further divided into primary active transport and secondary active transport, depending on the direct or indirect involvement of ATP hydrolysis.

Plasma membrane damage and repair

Another profound feature of the plasma membrane is its ability to repair after modest damage, thereby maintaining cellular homeostasis. In a vast range of biological and pathological activities, the plasma membrane is inextricably and intermittently damaged. In particular, the plasma membrane undergoes constant damage and repair during cell movement. Typically, cells navigate by outstretching their anterior armlike pseudopods, while retracting their posterior parts simultaneously. This coordinated migration process thus exposes the plasma membrane under various mechanical and chemical stresses from the environment, consequently leading to breaching of the plasma membrane. Therefore, fine-tuned resealing of the plasma membrane is critical for maintaining cell homeostasis, preventing cell death and disease development. Proteins such as the ESCRT-III complexes, Annexin/S100A10, and SNARE proteins can facilitate plasma membrane repair. Indeed, boosting plasma membrane repair could be a potential therapeutic strategy for treating diseases attributed to poor membrane integrity (e.g., muscular dystrophies and spinal cord injury) [7]. In contrast, inadequate plasma membrane repair may dampen the survival of metastatic cancer cells [7].

Nucleus

As the defining feature of most eukaryotic cells, the nucleus is overwhelmingly central for life. Ever since the rise of the era of biomedical studies, the nucleus is the first intracellular organelle to be discovered and described [8]. Intriguingly, although there are countless macromolecules and higher-order subnuclear structures within the nucleus, the nucleus is never a heap of loose sand but rather behaves as the cell supreme command hub. It resembles the central processing unit of a computer, ensuring rapid information transfer, exchange, and execution. The nucleus also serves as a genetic bank, storing the hereditary material (deoxyribonucleic acid, DNA) of a cell. Proper functionality of a cell requires an intact cell nucleus. Significantly, as long as the nucleus is well preserved, life can be artificially resuscitated for the purpose of, for example, species preservation. The nuclear size, shape, and position enjoy a high degree of flexibility under different microenvironments. Being one of the largest and most conspicuous cell structures, the nucleus typically possesses a diameter of approximately 5–10μm and the shape of a nucleus is mostly spherical or oblong. Great quantities of physiologies and pathologies are associated with alterations to nuclear size, shape, and position. For example, during the cellular senescence process, nuclear size is often enlarged and the nuclear shape becomes irregular (forming blebs or even fragmentation) [9]. Moreover, during hematopoietic stem cell differentiation, certain cells of the immune system may develop partitioned or lobed nuclei [10]. It is suggested that these lobed nuclei can provide cells with proper plasticity to pass through tiny gaps in the endothelium [11]. Additionally, a recent advance showed that the nuclear size and/or shape can serve as a gauge of cell shape alteration and subsequently modulates cell movement plasticity [12]. Further, mispositioning of nuclei contributes to muscle disorders [13]. Importantly, the dynamic adjustment of the nuclear size, shape, and position also vigorously impact cell movement [14]. In most cases, the nuclear number in a nondividing cell is one. Some highly differentiated cells such as cardiomyocytes, osteoclasts, and hepatocytes may have multiple nuclei [15–17]. Multinucleation may serve as a hallmark for the maturation of these cells. Nonetheless, the detailed mechanism leading to such multinucleation may differ between cell types (through cell–cell fusion, or undergo karyokinesis but absence of cytokinesis). Remarkably, to execute specific physiological functions or under experimental conditions, cells can even be devoid of their nuclei (e.g., the erythrocytes, epidermal keratinocytes, lens fiber cells, and the crawling denucleated cells) [18–20]. Derived from erythroblasts, erythrocytes mature by ejecting the nuclei through enucleation, a process mediated by proteins such as the cytoskeleton (will be introduced in the later section). Intriguingly, experimentally denucleated cells can still maintain their biomechanical properties, therefore suitable for somatic cell nuclear transfer [21]. Anatomically, the nucleus can roughly be divided into four parts: nuclear envelope, chromatin, nucleoplasm, and nucleolus.

Nuclear envelope

The nucleus is sharply delimited by the nuclear envelope. The nuclear envelope is composed of two essentially continuous, parallel, and adjacent membranes (each is composed of a phospholipid bilayer). According to the spatial arrangement, these two membranes are often referred to as the outer nuclear membrane and the inner nuclear membrane. The outer nuclear membrane serves as the first line of barrier separating the nucleus from the cytoplasm, despite the fact that it is still physically connected to the ER (will be introduced in the later section). Contrastingly, the inner nuclear membrane is almost geographically isolated from the cytoplasm. However, rather than being an inert structure, the inner nuclear membrane is recently shown to be important for a considerable amount of lipid synthesis, thereafter mediating transcriptional regulation and nuclear lipid homeostasis [22]. Structurally, a regular gap (perinuclear space) of about 50nm exists between the inner and outer nuclear membranes. Strikingly, this gap can expand to the size of a few microns under certain pathological conditions [23]. The outer and inner nuclear membranes are intimately interconnected at the nuclear pore complex, where the cytoplasmic materials are selectively transported into the nucleoplasm. The nuclear pore complex is composed of about 1000 protein subunits (termed nucleoporins) [24] and this huge protein assembly accounts for more than 8% of the nuclear surface area. Other than the nuclear pore complex, the LINC (linker of nucleoskeleton and cytoskeleton) complex also spans and tethers the outer and inner nuclear membranes. The nuclear pore complex, the LINC complex, and the lamina contribute to the overall structural integrity of the nucleus. Finally, tightly underneath the inner nuclear membrane lies the nuclear lamina, which is a dense fibrillar meshwork composed predominantly of intermediate filaments (will be introduced in the later section) assembled from the lamin family roteins. Diseases associated with the dysfunctional nuclear envelope include, but are not limited to, Hutchinson–Gilford progeria syndrome, neurodegenerative diseases, Galloway–Mowat syndrome, etc. [25–27].

Chromatin

Among the innumerable important functions of the nucleus, before all else, it houses the genomic DNA of a cell. DNA is a macromolecule composed of two polynucleotide chains that wind together forming a double helix structure. In brief, DNA is the code of life. During interphase (cells spend about 90% of their time in this phase), the enormously compacted DNA together with the histone proteins form a complex termed chromatin. Within chromatin, nucleosome is the fundamental repeating unit and forms beads on a string structure revealed under electron microscopy. Chromatin thus represents a code lock, storing the precious genetic jewels of cells. Spatially, rather than randomly distributed within the nucleus, chromatin is segregated into territories/domains. Chromatin has preferentially three-dimensional nuclear zoning, either located peripherally or centrally. These megabase-sized topological domains are proved critical for regulating gene expression [28]. Commonly, chromatin exists in two forms: the heterochromatin and the euchromatin. Heterochromatic regions are generally highly condensed and transcriptionally repressive, preferentially localizing toward the nuclear periphery. In contrast, less condensed and transcriptionally active euchromatin regions frequently localize toward the nuclear interior. The detailed mechanism determining these hierarchical organizations remains inconclusive. Nonetheless, mounting evidence has implicated that chromatin is not static, but is instead dynamically fluctuating in the nucleus [29].

Nucleoplasm

The nucleoplasm, which is far from homogeneous, congenitally fills most of the nucleus volume. A myriad of proteins occupy the nucleoplasm. Substantial portions of these proteins form higher-ordered condensates known as nuclear bodies [30]. Currently, these micron-scaled nonmembranous structures can be categorized into more than 15 groups, namely, nucleolus (vide infra), Cajal bodies, PML bodies, nuclear speckles, paraspeckles, histone locus body, etc. As revealed meticulously by electron microscopy and superresolution microscopy, many of the nuclear bodies contain multilayers and process a grainy core, which often contains ribonucleoproteins. Some macromolecules within the nuclear bodies are believed to interact with each other through multivalent interactions, typically involving intrinsically disordered regions. The size, shape, and number of specific nuclear speckles vary under different situations or between cell lines. In general, nuclear bodies are involved in regulating chromosome structure, processing of pre-mRNAs, nuclear retention of RNAs, DNA damage repairs, and epigenetic gene regulation. Astoundingly, apart from proteins and ribonucleic acids, lipid droplets may also play important functions in the nucleoplasm, albeit in limited amounts [31].

Nucleolus

The nucleolus is a prominent and largest nonmembrane-bound subcompartment of the nucleus, primarily formed by liquid–liquid phase separation [32]. It contains a highly dense chromatin region and a handful of associated proteins, which are arranged into a tripartite organization containing the fibrillar centers, the dense fibrillar components, and the granular compartment. The nucleolus assembles at specific regions of the genome containing rDNA. The number and size of the nucleolus vary remarkably under different cellular conditions. Moreover, the nucleolus has long been recognized as the critical site for the biogenesis of ribosomes, the key machinery responsible for messenger RNA translation. Most recently, multidisciplinary studies have suggested that the nucleolus is important for DNA-damage repair, protein quality control of nuclear proteins, cellular senescence, response to cellular stressors, cell cycle progression, maintenance of genome stability, etc. [33,34].

It is worth noting that how the nucleus evolved into a spatially enclosed region within a cell has been a topic of controversy. Through years of contention, prevailing theory holds that the nucleus could have arisen through a symbiotic partnership of an archaeal cell and a bacterium. Interestingly enough, the recent discovery that giant viruses could build nucleus-like and membrane-based viral factories in archaeal cells, provoking a rethinking that the eukaryotic nucleus could originate from host–virus interactions [35,36].

Mitochondria

Mitochondria, which indeed hold over 1000 proteins, are unambiguously vital and are broadly accepted to be the cell metabolite center and the energy-producing factory (powerhouse) [37]. Accordingly, mitochondria produce energy mainly from the breakdown of carbohydrates and fatty acids through the famous citric acid cycle (also known as tricarboxylic acid cycle or the Krebs cycle, elaborated elsewhere) [38]. Aerobic respiration of the multifaceted mitochondria helps produce a series of substances, including the synthesis of ATP, NADH, GTP, and phospholipids. Substantiated by DNA sequencing, this tubular organelle probably has originated from endocytosis of the symbiotic alphaproteobacterium some billion years ago and retains a great many vestiges of its bacterial ancestry [39]. Mitochondria are therefore considered semiautonomous. Notably, rather than forming peanut shape depicted in most schematics (due to easy abstraction and false impression from transmission electron microscopy sections), mitochondria most commonly form tubular networks. These reticular structures are highly dynamic, exemplified by constant mitochondrial fission and fusion. As a cell metabolic hub, mitochondria closely associates with apoptosis, ferroptosis, cellular senescence, production of reactive oxygen species (ROS), calcium regulation, etc.

Similar to the nucleus, the mitochondria are composed of outer and inner membranes (each is composed of a phospholipid bilayer), gapped by an intermembrane space. The porous outer mitochondrial membrane is permeable to most small molecules as it houses a large repertoire of pore-forming membrane proteins called porins. Larger molecules such as proteins are traversed through the outer mitochondrial membrane by translocases (e.g., the TOM complex). In contrast, the inner mitochondrial membrane is impermeable to a great many substances including ions and proteins. Nevertheless, mitochondrial matrix–localized proteins can be specifically imported across the inner mitochondrial membrane by translocases (e.g., TIM22 and TIM23 complexes). Inner mitochondrial membrane forms invaginations extensively. Thus, the inner mitochondrial membrane can be further divided into the inner boundary membrane and the cristae (the tubular or lamellar-like folds). The cristae largely increase the mitochondria inner surface area and hold the electron transport chain and linear arrays of synthases pivotal for ATP synthesis. The mitochondrial matrix refers to the viscous space encircled by the mitochondrial inner membrane. The matrix restricts a set of circular double-stranded DNA (mtDNA, ∼16.5kb in human cell) and proteins such as ribosomes and enzymes in this innermost mitochondrial compartment. In special cases, a cell may carry crowds of mitochondria that do not have exactly the same mtDNA sequences (known as heteroplasmy). The mtDNA is typically anchored to the inner mitochondrial membrane. In human cells, the mtDNA encodes 11 mRNAs, 2 rRNAs, and 22 tRNAs, which ultimately produce 13 proteins that are subunits of the ATP synthase, respiratory chain complexes I, III, and IV [40]. Absorbingly, a significant number of mitochondrial proteins are encoded by genes located in the nucleus. Most mitochondrial proteins (approximately 99%) are translated in the cytoplasm, whereupon they are subsequently transported into the mitochondria by specific mitochondrial targeting signal sequence. Both the mtDNA and the protein production machinery are overtly unique features amid other cellular structures.

As new discoveries continue to escalate, the role of mitochondria in various diseases is beginning to be elucidated. For example, inherited or acquired mutations in the mtDNA cause a range of detrimental diseases, such as Alpers' disease, Leber's hereditary optic neuropathy, renal oncocytomas, etc. Most recently, mitochondria mutations could be precisely targeted and specifically corrected in vitro through a CRISPR-free mitochondrial genome-editing technique [41]. Intriguingly, by using a mechanical plunger, cells are capable of taking up exogenous mitochondria [42].

Notably, mitochondria are also actively involved in cell motility [43]. During cancer cell migration, mitochondria can preferentially localize to the cell anterior, wherein energy is actively demanded. Moreover, mitochondria dynamics (unbalanced fission and fusion) are associated with cancer metastasis and T lymphocyte migration. Additionally, proteins (e.g., Bcl-2), metabolites, calcium, and ROS from mitochondria, each of which may play a role in the regulation of cancer cell migration.

Endoplasmic reticulum

The ER, as illustrated by its name, is a membranous lacework-like organelle that comprises distinct morphological domains such as tubules and flattened sacs (cisternae) [44]. ER, which accounted for a huge proportion of the cell endomembrane area, extends throughout the cell cytoplasm and hence is contiguous to almost all other organelles. Meanwhile, being the first organelle in the secretory pathway, ER constantly interwinds with a host of cell structures, such as the plasma membrane, the mitochondria, the Golgi apparatus, and the endolysosomal system. Certain ER proteins are shipped off to the Golgi apparatus (vide infra) by budding of vesicles. Moreover, ER is physically interlinked with the nuclear envelope, wherein the ER lumen connects the perinuclear space. Depending on whether ribosomes are studded on the membrane surface, ER can be classically grouped into two interconvertible types: rough ER and smooth ER. These two forms of ER frequently exist as interconnected or spatially separated entities. Intriguingly, ER is dynamically under rapid morphological remodeling, during which its protein and lipid compositions could vary substantially.

ER serves many roles. It is particularly important for the synthesis, folding, and transport of proteins (membrane proteins and a subpopulation of cytosolic proteins); the synthesis, storage, and transport of lipids; the storage and regulation of calcium; carbohydrate metabolism; cell detoxification; etc. [45]. The direct or indirect interactions between the ER and other cellular membrane system may bring to the fore a role in cancer, age-associated diseases, cardiovascular diseases, and so forth.

Protein synthesis and folding

About one-third of the total proteins are targeted to the ER during translation. However, the folding of protein is error-prone and the misfolded proteins are potentially hazardous. Therefore, the ER evolves a delicate surveillance system (namely the ER protein quality control system) for tackling this problem. Diverse chaperones and foldases within the ER ensure the correct conformation folding and subsequent modification of the ER proteins. Certain misfolded proteins could undergo several cycles of folding and refolding. Stubbornly misfolded proteins in the ER are tightly subject to the ER-associated degradation (ERAD) through proteasomes.

Lipid biogenesis

The ER is also crucial for the synthesis, storage, and transport of the vast majority of lipids (e.g., glycerol phospholipids, cholesterol, and ceramide), therefore influencing the overall cell membrane homeostasis. Interestingly, lipid metabolism is subcompartmentalized as some phospholipid biosynthesizing enzymes are heterogeneous distributed within the ER. De novo synthesized phospholipids are sorted to their ultimate destinations through vesicular (e.g., COPII pathway) or nonvesicular mechanisms (e.g., via lipid transfer proteins at the membrane contact sites). Nonvesicular mechanisms could be more selective than the vesicular membrane transport axis. Curiously, most phospholipid synthesizing enzymes in the ER are under feedback inhibition, that is, their activities are regulated by the local lipid constitution of the very membranes to which these enzymes are localized.

ER stress response

ER stress, which depicts a status with an overwhelming accumulation of misfolded proteins in the ER, has been implicated in a plethora of cellular aberrations or physiological scenarios. Conditions such as extreme hypoxic stress, calcium deprivation, and impairing glycosylation can induce ER stress. ER stress response is a set of cellular events, commonly regulating ER chaperones and proteins in the degradation system, that are programmed to bias cell survival during cellular stress. ER stress response is involved in cancer, viral infections, cardiovascular diseases, Alzheimer's disease, etc. Moreover, proteins actively involved in the ER stress response have been linked with tumor cell migration/invasion [46].

Golgi

The Golgi apparatus (also called Golgi body/Golgi complex/Golgi), working as a post-office in the cell, lies at the heart for intracellular protein sorting, packing, routing, and recycling. As inferred in its name, the single-membrane-bound Golgi apparatus was first visualized in 1898 by Camillo Golgi. Morphologically, Golgi frequently locates in close vicinity to the perinuclear region and consists of 4–6 flattened tethered cisternae as well as associated vesicles. Unlike the interconnected cisternae of ER, the Golgi cisternae exist as individual disconnected sacs, however, laterally layered on top of each other. These Golgi cisternae are held together into close proximity by groups of Golgi stacking proteins, such as GM130 and p155 [47]. Most importantly, the Golgi apparatus is structurally and functionally polarized. Two faces exist in the Golgi apparatus, the cis face (the entry face, the convex side facing the ER/nucleus) and the trans face (the exit face, the concave side facing the cytoplasm). The subcellular positioning of the Golgi apparatus is highly dependent on microtubules and its associating motors (both will be introduced in the later section). Furthermore, Golgi dysfunction correlates with disorders such as cancer, neurodegenerative diseases, Smith-McCort dysplasia, etc.

Influxes of secretory proteins from the ER into the Golgi apparatus (ER–Golgi transport) take place at the ER cis face. Vesicles exit the former employer ER, largely in a COPII-dependent manner. Subsequently, these intra-Golgi proteins are directionally trafficked from the cis Golgi face/cisternae to the medial compartments, and eventually the trans Golgi face/cisternae. Two models are proposed to explain mechanisms of protein trafficking within the Golgi. The first is cisternal maturation model, depicting cargo transport that follows a Golgi cisternae traverse and maturation process. The second is the vesicular transport model, which argues that each Golgi cisterna is static and vesicles are moved from one stack to another via budding and fusion. Importantly, during these trafficking processes, proteins are posttranslationally modified (such as glycosylation, phosphorylation, palmitoylation, and sulfation). Similar to proteins, lipids synthesized from the ER are also further metabolized (such as addition of carbohydrates and transfer of the phosphorylcholine group) during their stay in the Golgi. Lastly, other than the Golgi-resident cargoes, other passenger macromolecules are then sorted into different vesicles through their signal peptides or associations with lipid subdomains. The end phase of the Golgi journey involves the budding off cargo-enclosed vesicles from the trans Golgi cisternae to diverse destined cellular structures (such as the plasma membrane and the lysosome) or the extracellular environment. In this protein sorting process at the trans Golgi cisternae, elaborate machineries are developed to ensure the accurate package of cargos [48]. In brief, cargo sensors (e.g., mannose-6-phosphate receptor, Cab45 protein, and lipid rafts) on the trans Golgi cisternae membrane are deputed to recognize different sorting cargo motifs. Conventionally, clathrin and its associated adaptors (such as AP-1, epsinR, and GGAs) are then recruited from the cytosol and promote the budding of membrane-enclosed cargoes. Disrupting Golgi, such as knockdown of the Golgi-localized proteins, can lead to aberrant cell migration behavior [49,50].

Lysosome

Lysosomes are specialized monolayer membrane-enclosed organelles that contain various abundant hydrolytic enzymes (such as proteases, lipases, and nucleases), lysosomal ion channels, and transporters [51]. Lysosome has classically been considered as the key ultimate compartment for macromolecule degeneration, damaged organelle clearance, cell membrane repairs, and catabolite recycling, thus important for cellular homeostasis. At present, it is widely appreciated that this dynamic multifunctional proteolytic organelle also serves as sensor and mediator for facilitating the cross-talk between diverse intracellular events, including but not limited to autophagy, inflammation, programmed cell death, etc. Typically, the shape of a lysosome is round or ovoid. Most lysosomes are between 0.2–0.8μm in diameter. The number of lysosomes per cell hinges on different cell types, which ranges from 50 to 1000. As a cellular intersection, lysosomes receive cargoes from both vesicles within the cell (by autophagy) and from the extracellular environment (by endocytosis or phagocytosis). It is distinctive that the acidity of the lysosome lumen engrossingly creates an optimal working environment for over 60 lysosomal hydrolases, most of which have acidic pH optima (between 4.5 and 5.5). This acidic characteristic has been attributed to the activity of vacuolar-type H+-ATPase (V-ATPase), which continuously pumps protons into lysosomes in an energy-dependent manner. Thus, it is understandable that alkalinity hinders lysosomal ability to degrade substrates. Additionally, live cell lysosomal pH fluctuations can be monitored by lysosomal targeting bis-chromophoric ratiometric fluorescent probes [52]. Lysosomes evolve dynamic membrane contact sites with other intracellular structures such as ER and mitochondria [53,54]. These direct interactions culminate in the regulation of lysosomal positioning, calcium release, cholesterol mobilization, etc. Neurons from patients with a subtype of Parkinson's disease show decreased lysosomal enzyme activity and prolonged mitochondria–lysosome interaction [55]. Consistent with its vital role in the cell, lysosomal dysfunction is deleterious for diseases such as lysosomal storage disorders, autoimmune disease, neurodegenerative disorders, etc. Lysosomal damage, such as lysosomal membrane permeabilization, engenders the dissolution of hazardous lysosomal enzymes, ultimately leading to a type of specific programmed cell death called lysosomal cell death. Lysosomal cell death can be induced by a number of stimuli, such as lysosomotropic compounds, ROS, and certain endogenous cell death effectors. Most recently, scientists reportedly demonstrate that β-coronaviruses, which include the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can hijack lysosomes for egress. During this process, lysosomes are deacidified and lysosomal degrading enzymes are inactivated [56]. Lastly, lysosomes also participate in the cell migration regulation, through processes such as autophagy and remodeling of the extracellular matrix [57].

Centrosome

Centrosome, which contains two orthogonally oriented centrioles embedded in a dense mass of centroplasm (known as pericentriolar material), acts as the microtubule-organizing center (MTOC) in mammalian cells [58]. The term centrosome was coined by Theodor Boveri in 1887, who introduced centrosome as the dynamic center and the true division organ of the cell. As said, currently it is well known that centrosomes are essential for microtubule (will be introduced in the later section) polymerization and organization. The centrosome comprises over 100 different proteins. Centrioles are cylindrical concentric microtubule-based structures. Each centriole comprises nine microtubule triplets without central microtubule (known as 9×4+0 formula) and a set of interconnecting protein structures organized around a central hub [59]. During metaphase, the centrosomes help assemble the radical bipolar spindles (microtubule-based machine) responsible for chromosome segregation. Microtubules in the centrioles, which are not affected by microtubule depolymerizing drugs or low temperature, are more stabilized than interphase cytosolic microtubules or mitotic spindles. As the master MTOC, centrosome is involved in diverse cellular processes, including but not limited to cell cycle progression, cell polarity, cilium or flagellum assembly, embryogenesis, cytokinetic abscission, etc. Furthermore, centrosome abnormalities participate in several human diseases, such as brain disorders and ciliopathies.

Centrioles disengage and duplicate themselves during S phase per cell cycle, producing two polarized centrioles of different ages [60]. The older mother centriole is inherited from the previous cell cycle whereas the younger daughter centriole is formed de novo. The newly assembled centriole usually forms in association with the mother centriole. However, it can also form without preexisting centriole. Structurally, the mother centriole is equipped with distal and subdistal appendages, while the daughter centriole is typically devoid of appendages. Moreover, the proximal ends of the mother and daughter centrioles are linked through a bundle of thin fibers made up of β-catenin, C-NAP1, and rootletin. Microtubule-nucleating centers locate near or on the centriole, predominately the mother one. The number of centrosomes per cell matters. Importantly, cells with supernumerary centrosomes are often seen in cancer cells. This abnormal number of centrosomes could lead to the formation of multipolar spindles, thereby increasing the likelihood of chromosome segregation failure and aneuploidy, eventually resulting in genomic instability. Moreover, centrosome is required for directional cell migration by defining the rear of cells [61,62].

Other cellular structures

In addition to the aforementioned well-known intracellular structures, there are other cell structures that also have unique architectures and impacts on cells, exemplified by the cytoskeleton (including filamentous actin, microtubule, and intermediate filament), peroxisome, vacuoles, etc. Besides, it is worth mentioning that there are countless protein complex structures within the cell territory and the list is steadily increasing. For instance, recent advantages showed that reticular adhesions, formed by Integrin αvβ5 in the absence of both Talin and F-actin, are a newfound class of cell-matrix adhesions mediating cell attachment during mitosis [63]. Another example is the discovery of circular extrachromosomal DNA in cancer cells, which is almost never found in normal cells [64]. In the next section, we will introduce the peroxisomes and the cytoskeleton.

Peroxisome

Peroxisomes are small versatile organelles ubiquitously distributed in the cytoplasm [65]. Historically, the origin of the definition of peroxisome came from its ability to produce hydrogen peroxide. Nevertheless, peroxisomes also contain catalases that can neutralize hydrogen peroxide toxicity. Apart from its intricate function in hydrogen peroxide metabolism, peroxisomes are involved in the synthesis of a subset of lipids (such as ether phospholipids and plasmalogens) and the degradation of fatty acids. To participate in various metabolic reactions, peroxisomes contain more than 50 different enzymes, all of which imported from the cytosol. These enzymes are involved in the breaking down of fatty acids and hydrogen peroxide metabolism. Bound by a single membrane, peroxisomes do not possess genetic material but can self-replicate by growth and fission that is similar to mitochondria. Peroxisomes can also undergo de novo biogenesis from the ER and the mitochondria [66]. To adapt to a changing environment, the number, size, morphology, and protein composition of the peroxisomes are strictly regulated. Most peroxisomes are relatively static (undergo slow, short-range displacements). Only around 10% of peroxisomes exhibit fast directed trajectories over time in a microtubule-dependent manner. A fair amount of evidence has conferred a role for peroxisomes in stem cell differentiation, ferroptosis (a type of programmed cell death), intestinal epithelial repair, and cell migration [67–69].

Figure 1.3  Schematic of actin, microtubule, and intermediate filament.

Cytoskeleton

The cytoskeleton (cyto denotes cell, therefore figuratively, means the skeleton of the cell) is an evolutionarily highly conserved proteinaceous filament system of a cell. It includes actin, microtubules, and intermediate filaments, along with their binding and regulatory proteins. Despite the connotation of being a cell framework, the highly ordered cytoskeleton exists in dynamic equilibrium. The best-known functions of the cytoskeleton are to support cell mechanics, cell division, cell locomotion, organelle movements, signal transduction, etc. It is now clear that these polymeric structures also influence gene transcription, protein translation, nucleus expansion, DNA damage repair, chromatin regulation, glycolysis, etc. Moreover, although long considered individualists, it is becoming increasingly apparent that the three cytoskeleton structures, to a great extent, cross talk with one another. Intriguingly, targeting the cytoskeleton offers a valuable strategy in cancer chemotherapy. A number of cytoskeleton-related inhibitors have been used to promote the demise of cancer cells, such as the actin filament–targeted compound chondramide and TR100, the microtubule inhibitor colchicine and indibulin, the intermediate filament–targeted compound withaferin A, and arylquin 1. It has been illuminated that cytoskeleton is essential for the infection of viruses, including the coronavirus family members [70].

Since the actin cytoskeleton will be introduced in Chapter 3, here we will focus on a brief induction to the microtubules and intermediate filaments system (Fig. 1.3).

Microtubules are relatively rigid assemblages important for cell shape, cell motility, and cell division. These polymeric microtubules are made up of tubulin oligomers including α, β, and γ forms, each could contain several conformations or isotypes. Being the largest structure of the three types of cytoskeletal fibers, microtubules hardly form bifurcations but extend throughout the cell cytoplasm and are capable of rapidly growing or shrinking by polymerization or depolymerization. Microscopically, microtubules are hollow tubes (an annulus of 25nm outer diameter and 12.5nm inner diameter). The body of these tubes is composed of head-to-tail arranged α- and β-tubulin heterodimers. In mammalian cells, α- and β-tubulin bind each other in rotation and line up laterally, thereby forming 13 polarized linear protofilaments. Consequently, the terminus ended with β-tubulin is called the plus end, and that with α-tubulin is the minus end. The plus end extends toward the plasma membrane, whereas the minus end often anchored near the MTOC or toward the cell interior. To sustain the growth of microtubules, new tubulin dimers are predominantly added onto the plus end rather than the minus end. The polarity of the microtubules is essential in determining the direction of cargo movement. Microtubules are constantly assembled and dismantled through cycles of GTP hydrolysis. The stochastic or controlled consumption of GTP causes rounds of growth and catastrophe of microtubules, a phenomenon known as dynamic instability. Toward the sublevel, the α-tubulin subunit is composed of 450 amino acids and the β-tubulin subunit consists of 455 amino acids, both of which have a molecular weight of about 55kDa. The stability and function of microtubules can be modulated through posttranslational modification of the tubulin subunits, such as acetylation, polyglycylation, and polyglutamylation. Strikingly, recent work showed that the microtubule lumen could be filled by extended segments of filamentous actin under certain induction conditions [71].

One important milestone in the microtubule field is the discovery of the motor protein kinesin and dynein, which drive the processive movement of various intracellular cargos along the microtubules. Powered by ATP, most kinesins move toward the plus end of microtubules (with a few exceptions), whereas the dynein family members move in the opposite direction. The direction of cargo movement is determined via a tug-of-war mechanism. Kinesin typically functions as a dimer (either homodimer or heterodimer) and moves along the same single microtubule protofilament from one end to the other. The movement of this kinesis dimer is highly dependent on their motor domains. The motor domain of a kinesis harbors two important functions: microtubule binding and ATP hydrolysis. Different kinesins can engage on the same vesicle simultaneously. The movement of kinesin is highly processive. These remarkable motors may take about a hundred or more steps before they dissociate with the microtubules. Intriguingly, some kinesins can switch microtubule tracks at microtubule intersections, albeit with a preference to remain on the same microtubule track. These switches endow kinesins with the ability to navigate the whole microtubule networks, enriching the sites where cargoes can be delivered. Dynein is the largest cytoskeletal motor protein. Remarkably different from the kinesin family proteins, a single dynein takes responsibility in the cytoplasm. Nevertheless, dynein does not work as a lone wolf. It forms a complex with a bunch of other proteins such as dynactin and BICD2. Cargoes of the dynein machinery comprise ribonucleoproteins, organelles (e.g., mitochondria, ER, Golgi, and lysosome), RNAs, viruses, etc. Apart from translocating cargoes on the microtubules, dynein can also attach on the cell cortex, contributing to the modulation of microtubule dynamics [72].

Microtubules are essential for cell motility [73]. The polarity and asymmetric organization of microtubules allow directional delivery of essential components (membrane, proteins, mRNAs, mitochondria, etc.) toward the leading edge of a migrating cell. Additionally, microtubule dynamics are also tightly coupled with the turnover of focal adhesions, which are crucial for cell migration. Moreover, controlled assembly and disassembly of the microtubule network act as force generators that are of the essence for dynamic formation of cell protrusions and retractions. Pharmacological depolymerization of microtubules can change cells from persistent to oscillatory migration [74]. Thus, abnormalities in microtubule regulation can lead to deviant cell motility or invasiveness.

Intermediate filaments (IFs) are elaborate apolar filaments found in the cytoplasm and the nucleus. IFs are about 10nm in cross section, which is between the diameters of the actin filaments and microtubules. Unlike actin and the microtubules, intermediate filament proteins are generic terms of diverse filaments composing of a wide variety of structurally related, yet different proteins (about 70 genes encoding the intermediate filament proteins). Hitherto, six different types of intermediate filaments have been reported. These filaments are composed of vimentin, lamins, keratin, acidic and basic keratins, glial fibrillary acidic protein, desmin, peripherin, nestin, etc. All these intermediate proteins possess a tripartite structure. The central α-helix core region (about 310 AAs, the primary dimerization region) is a characteristic element common to all IF-forming proteins, while the amino- and carboxyl- termini vary extensively. IFs may act as tension sensors by unfolding themselves [75]. IF monomers first form dimers (∼45nm in length, either homodimer or heterodimer), which then laterally assembled into tetramers (∼60nm). Once formed, these tetramers then self-bundle into unit length filaments (∼60nm), which eventually shape the intermediate filaments. Unlike the actin filament and microtubule counterparts, intermediate filaments are relatively stable and lack NTPase activity, albeit more extensible. However, it is easy to misconstrue that the intermediate filaments are completely static. It should be noted that most intermediate filaments are under assembly and degradation readily. Furthermore, intermediate filaments are subjected to posttranslational modifications such as phosphorylation, sumoylation, acetylation, and ubiquitylation [76]. Functionally, intermediated filaments play important roles in cell mechanical integrity regulation, cell adhesion, cell signal transduction, organelle positioning, etc. These intermediate filaments also play a role in promoting collective directed cell migration by modulating the distribution of forces generated by the actomyosin network [66].

IFs also act as powerful modulators for cell migratory properties [77,78]. For example, perturbation of vimentin or keratin impairs directional cell migration. Nestin, a type VI intermediate filament, is considered a biomarker of the invasive phenotype of glioblastoma. Furthermore, intermediate filaments go through major rearrangements during cell migration, forming a polarized network that coordinates nucleus rigidity, cell contractility, and focal contacts [79].

Summary

The cell being the most basic unit of eukaryotic lives, its proper functioning depends on the concerted action of every single internal structure. This chapter provides an elementary introduction to the main structures and physiologies of a cell. It also illustrates some cutting-edge findings of each structure. The main constituents and functions of these cell structures are summarized in Table 1.1.

Utilizing imaging methodologies and biochemistry techniques, cell research has rapidly flourished over the centuries. It is now evident that the inner milieu of a cell is compartmentalized. These intracellular structures include plasma membrane, nucleus, mitochondria, ER, Golgi, lysosome, centrosome, cytoskeleton, peroxisome, etc. It is imperative that these intracellular structures maintain their borderlines and own unique characteristics, yet interplay reciprocally as a symphony orchestra.

Soaking in the century of biology, we are now step by step closer to a comprehensive understanding of these intricate cell structures. Nevertheless, one must recognize that new cellular substructures may still be waiting for discovery, exemplified by the latest substantiated migrasome structure and the plasma membrane–localized GlycoRNAs [6,80,81]. Thus, it is hoped that, with the latest technical progress such as artificial intelligence, superresolution imaging, high-throughput screening, and synthetic biology, new insights into cell structure and physiology can be attained.

Collectively, one could imagine that the discovery of the cell secrets may have no end. Given that now is a time of unprecedented opportunity for biomedical studies, there is still much to learn about these elegant structures.

Table 1.1

Glossary

Carbohydrates    A class of molecules made up of carbon, oxygen, and hydrogen atoms. On the plasma membrane, carbohydrates are linked to proteins (glycoproteins), lipids (glycolipids), or RNA (glycoRNA).

Cell    The most basic structural and functional unit of a nonviral organism.

Centrosome    A membraneless assembly that serves as the main microtubule-organizing center.

Cytoskeleton    An evolutionarily highly conserved proteinaceous filament system of a cell. The cytoskeleton contains microfilaments (actin), microtubules, and intermediate filaments.

Endoplasmic reticulum    A continuous membrane-bound organelle (made of sacs and tubules) important for protein synthesis, protein folding, lipid biogenesis, stress response, etc.

Fluid mosaic model    A comprehensive model explains the architecture of biological membranes.

GlycoRNA    RNA–glycan conjugates.

Golgi apparatus    A membrane-bound organelle that is responsible for processing, warehousing, sorting, and shipping diverse proteins and lipids.

Lysosome    A membrane-enclosed organelle that contains various digestive enzymes.

Mitochondria    A double membrane–bound organelle which is key for energy production and metabolism of a cell.

Nucleus    A specialized double membrane–bound organelle found in eukaryotic cells. The nucleus contains genetic DNA that determines cell structure and function.

Organelle    Specialized membrane-enclosed or membrane-free structures within a cell.

Peroxisome    A membrane-enclosed organelle that contains oxidative enzymes such as catalases.

Phospholipid bilayer    A sheet of continuous membrane composed of two layers of lipid molecules.

Plasma membrane    The cell's outmost boundary composed of a giant bubble of membrane.

Plasma membrane proteins    Proteins embedded into or attached on the plasma membrane.

Acknowledgments

We would like to thank Ms. Ziqi Wang for her specialties in helping with the schematic and Dr. Huabin Wang for proofreading the manuscript. Funding derived from the Program for Guangdong Introducing Innovative and Entrepreneurial Teams, grant number 2017ZT07S347; the Guangzhou Basic and Applied Basic Research Foundation, grant number 202102020509; the National Natural Science Foundation of China, grant number 31701174.

References

1. Bernardino de la Serna J, et al. There is no simple model of the plasma membrane organization.  Front Cell Dev Biol . 2016;4:106.

2. Harayama T, Riezman H. Understanding the diversity of membrane lipid composition.  Nat Rev Mol Cell Biol . 2018;19(5):281–296.

3. Jiang X, Stockwell B.R, Conrad M. Ferroptosis: mechanisms, biology and role in disease.  Nat Rev Mol Cell Biol . 2021;22(4):266–282.

4. Reily C, et al. Glycosylation in health and disease.  Nat Rev Nephrol . 2019;15(6):346–366.

5. Zhao P, et al. Virus-receptor interactions of glycosylated SARS-CoV-2 spike and human ACE2 receptor.  Cell Host Microbe . 2020;28(4):586–601 e6.

6. Flynn R.A, et al. Small RNAs are modified with N-glycans and displayed on the surface of living cells.  Cell . 2021;184:3109–3124.

7. Dias C, Nylandsted J. Plasma membrane integrity in health and disease: significance and therapeutic potential.  Cell Discov . 2021;7(1):4.

8. Pederson T. The nucleus introduced.  Cold Spring Harb Perspect Biol . 2011;3(5).

9. Pathak R.U, Soujanya M, Mishra R.K. Deterioration of nuclear morphology and architecture: a hallmark of senescence and aging.  Ageing Res Rev . 2021;67:101264.

10. Tigner A, Ibrahim S.A, Murray I. Histology, white blood cell. In:  StatPearls . Treasure Island, FL: StatPearls Publishing LLC; 2021.

11. Skinner B.M, Johnson E.E. Nuclear morphologies: their diversity and functional relevance.  Chromosoma . 2017;126(2):195–212.

12. Lomakin A.J, et al. The nucleus acts as a ruler tailoring cell responses to spatial constraints.  Science . 2020;370(6514).

13. Folker E.S, Baylies M.K. Nuclear positioning in muscle development and disease.  Front Physiol . 2013;4:363.

14. Calero-Cuenca F.J, Janota C.S, Gomes E.R. Dealing with the nucleus during cell migration.  Curr Opin Cell Biol . 2018;50:35–41.

15. Landim-Vieira M, et al. Cardiomyocyte nuclearity and ploidy: when is double trouble?  J Muscle Res Cell Motil . 2020;41(4):329–340.

16. Kodama J, Kaito T. Osteoclast multinucleation: review of current literature.  Int J Mol Sci . 2020;21(16).

17. Donne R, et al. Polyploidy in liver development, homeostasis and disease.  Nat Rev Gastroenterol Hepatol . 2020;17(7):391–405.

18. Nowak R.B, et al. Tropomodulin 1 controls erythroblast enucleation via regulation of F-actin in the enucleosome.  Blood . 2017;130(9):1144–1155.

19. Wang W.L, et al. Lens fiber cell differentiation and denucleation are disrupted through expression of the N-terminal nuclear receptor box of NCOA6 and result in p53-dependent and p53-independent apoptosis.  Mol Biol Cell . 2010;21(14):2453–2468.

20. Efremov Y.M, et al. Nanomechanical properties of enucleated cells: contribution of the nucleus to the passive cell mechanics.  J Nanobiotechnol . 2020;18(1):134.

21. Wang X, et al. Epigenetic reprogramming during somatic cell nuclear transfer: recent progress and future directions.  Front Genet . 2020;11:205.

22. Merta H, Bahmanyar S. The inner nuclear membrane takes on lipid metabolism.  Dev Cell . 2018;47(4):397–399.

23. Roos A, et al. Myopathy in Marinesco-Sjögren syndrome links endoplasmic reticulum chaperone dysfunction to nuclear envelope pathology.  Acta Neuropathol . 2014;127(5):761–777.

24. Lin D.H, Hoelz A. The structure of the nuclear pore complex (an update).  Annu Rev Biochem . 2019;88:725–783.

25. Worman H.J, Ostlund C, Wang Y. Diseases of the nuclear envelope.  Cold Spring Harb Perspect Biol . 2010;2(2):a000760.

26. Hachiya N, et al. Nuclear envelope and nuclear pore complexes in neurodegenerative diseases-new perspectives for therapeutic interventions.  Mol Neurobiol . 2021;58(3):983–995.

27. Guglielmi V, Sakuma S, D'Angelo M.A. Nuclear pore complexes in development and tissue homeostasis.  Development . 2020;147(23).

28. Fritz A.J, et al. Chromosome territories and the global regulation of the genome.  Genes Chromosomes Cancer . 2019;58(7):407–426.

29. Ashwin S.S, et al. Organization of fast and slow chromatin revealed by single-nucleosome dynamics.  Proc Natl Acad Sci U S A . 2019;116(40):19939–19944.

30. Sabari B.R, Dall'Agnese A, Young R.A. Biomolecular condensates in the nucleus.  Trends Biochem Sci . 2020;45(11):961–977.

31. Sołtysik K, et al. Nuclear lipid droplets derive from a lipoprotein precursor and regulate phosphatidylcholine synthesis.  Nat Commun . 2019;10(1):473.

32. Lafontaine D.L.J, et al. The nucleolus as a multiphase liquid condensate.  Nat Rev Mol Cell Biol . 2021;22(3):165–182. .

33. Frottin F, et al. The nucleolus functions as a phase-separated protein quality control compartment.  Science . 2019;365(6451):342–347.

34. Lindström M.S, et al. Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis.  Oncogene . 2018;37(18):2351–2366.

35. Chaikeeratisak V, et al. Assembly of a nucleus-like structure during viral replication in bacteria.  Science . 2017;355(6321):194–197.

36. Bell P.J.L. Evidence supporting a viral origin of the eukaryotic nucleus.  Virus Res . 2020;289:198168.

37. Pfanner N, Warscheid B, Wiedemann N. Mitochondrial proteins: from biogenesis to functional networks.  Nat Rev Mol Cell Biol . 2019;20(5):267–284.

38. Alabduladhem T.O, Bordoni B. Physiology, Krebs cycle. In:  StatPearls . Treasure Island, FL: StatPearls Publishing LLC; 2021.

39. Roger A.J, Muñoz-Gómez S.A, Kamikawa R. The origin and diversification of mitochondria.  Curr Biol . 2017;27(21):R1177–R1192.

40. Gustafsson C.M, Falkenberg M, Larsson N.G. Maintenance and expression of mammalian mitochondrial DNA.  Annu Rev Biochem . 2016;85:133–160.

41. Mok B.Y, et al. A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing.  Nature . 2020;583(7817):631–637.

42. Patananan A.N, et al. Pressure-driven mitochondrial transfer pipeline generates mammalian cells of desired genetic combinations and fates.  Cell Rep . 2020;33(13):108562.

43. Denisenko T.V, Gorbunova A.S, Zhivotovsky B. Mitochondrial involvement in migration, invasion and metastasis.  Front Cell Dev Biol . 2019;7:355.

44. Schwarz D.S, Blower M.D. The endoplasmic reticulum: structure, function and response to cellular signaling.  Cell Mol Life Sci