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I think it is autophagy. Lysosomal degradation. Autophagocytosis.
Example of the brown pigment (lipofuscin) here:
I am not sure if autophagy is the right answer to the "pathogenic" mechanism of atrophy.
Is autophagy the pathogenic mechanism of atrophy? Or what pathogenic mechanism is involved if you see lipofuscin in the histologic slide?
Simple answer: Atrophy through autophagy.
LipofuscinLast updated June 02, 2021 Confocal image of a spinal motor neuron showing stained lipofuscin granules in blue and yellow. Micrograph showing a cluster of lipofuscin particles (arrow) in a nerve cell of the brain toluidine blue stain scale bar = 10 microns (0.01 millimeters)
Lipofuscin is the name given to fine yellow-brown pigment granules composed of lipid-containing residues of lysosomal digestion.   It is considered to be one of the aging or "wear-and-tear" pigments, found in the liver, kidney, heart muscle, retina, adrenals, nerve cells, and ganglion cells. 
Development of tissue-engineered membranes for the culture and transplantation of retinal pigment epithelial cells
15.3.2 Ageing retinal pigment epithelium
RPE cells undergo significant age-related changes with observed increase in β-galactosidase staining, telomere loss, mitochondrial deoxyribonucleic acid (DNA) damage, nuclear DNA damage, protein crosslinking and lipid hydroperoxidation, many of which are non-reversible in such post-mitotic cells ( de Jong, 2006 Handa, 2007 Zarbin, 2004 ). RPE in early AMD was observed to contain more melano- lipofuscin and melano-lysosomes than pure melanin and the number of lipofuscin granules increased. Melanosomes contained within the RPE are exposed to a variety of environmental and metabolic insults. There are suggestions that aged human melanosomes are highly phototoxic and can result in RPE dysfunction, while young melanosomes appear to confer photoprotection ( Rozanowski et al., 2008 ). Age-related changes in melanosomes, possibly the result of oxidative damage, include disorientation within the RPE, decline in number after the age of 40 years, increase in melanosome complexes with lysosomes and/or lipofuscin, loss of melanin resulting in fading of eye colour with age, and increases in shorter wavelength blue spectrum absorption.
Preferential accumulation of lipofuscin in ageing RPE within the macula is a heterogeneous mixture of non-degradable lipid peroxidation products. These products originate from conjugates formed by visual cycle retinoid in photoreceptor cells that accumulate in RPE cells due to the inability of the RPE cells to convert all all-trans-retinol into 11-cis-retinal. RPE lipofuscin is a potent generator of reactive oxygen species. It is hypothesized that such species, including reactive fragments from lipids and retinoids, contribute to the mechanisms of RPE lipofuscin pathogenesis ( Ng et al., 2008 ).
Lipofuscin autofluoresces a yellowish orange colour due to its composition being a heterogeneous mixture of cytotoxic fluorophore N-retinylidene-N-retinylethanolamine (A2E) and its photo-isomers A2E epoxides. There are suggestions of a possible link between A2E's role in interfering with normal lipid metabolism and a resultant delay in lipid degradation and accumulation, leading to increased RPE sensitivity to blue light. The above degenerative RPE changes ultimately lead to the formation of basal deposits, drusen, RPE cell apoptosis, followed by secondary damage to choriocapillaris and neurosensory retina, and resulting in ( de Jong, 2006 Handa, 2007 Zarbin, 2004 ).
What is the pathogenuc mechanism of brown pigment lipofuscin in muscle atrophy? - Biology
Guest Editor: Rajindar S. Sohal
This article is part of a series of reviews on “Oxidative Stress and Aging.” The full list of papers may be found on the homepage of the journal.
Ulf T. Brunk is currently Professor of Pathology at Linköping University, Linköping, Sweden (chairman of Department of Pathology II). He received his M.D. at Lund University, Lund, Sweden, and his Ph.D. at Uppsala University, Uppsala, Sweden. His main research areas are postmitotic aging, apoptosis, and atherosclerosis with a focus on intralysosomal iron-catalyzed oxidative reactions. He has formulated the “Lysosomal-Mitochondrial Axis Theory of Cellular Aging”.
Alexei Terman is currently Assistant Professor of Experimental Pathology at Linköping University, Linköping, Sweden. He received his M.D. from Kiev Medical Institute, Kiev, Ukraine, and his Ph.D. degree from Linköping University, Linköping, Sweden. His main research area is postmitotic aging with a focus on autophagocytotic degradation. He has formulated the “Garbage Catastrophe Theory of Aging”. For further information about research at the Department of Pathology in Linköping see: http://huweb.hu.liu.se/inst/inr/avdelning/patologi/.
Lipofuscin Composition and Distribution
LF is a fluorescent complex mixture composed of highly oxidized cross-linked macromolecules (proteins, lipids, and sugars) with multiple metabolic origins (Höhn et al., 2010 König et al., 2017 Rodolfo et al., 2018). The nature and structure of LF complexes seem to vary among tissues and show temporal heterogeneity in composition of oxidized proteins (30%), lipids (20%), metals cations (Fe 3+ , Fe 2+ , Cu 2+ , Zn 2+ , Al 3+ , Mn 2+ , Ca 2+ ) (2%), and sugar residues (Benavides et al., 2002 Double et al., 2008).
Because of its polymeric and highly cross-linked nature, LF cannot be degraded, nor cleared by exocytosis, thus being accumulated within the lysosomes and cell cytoplasm of long-lived post-mitotic and senescent animal cells. Opposite, proliferative cells efficiently dilute LF aggregates during cell division, showing low or no accumulation of the pigment (Brunk and Terman, 2002 Porta, 2002 Terman and Brunk, 2005 Rodgers et al., 2009 Firlag et al., 2013). For this reason, LF deposits are especially abundant in nerve cells, cardiac muscle cells, and skin.
LF fluorescence shows a large heterogeneity in the emission spectra, which reveals differences in its chemical composition, as a result of its ripening in specific metabolic pathways (Schwartsburd, 1995). In general, the LF fluorescence emission presents a very wide spectra ranging from 400 to 700 nm, with a maximum around of 578 nm for excitation at 364 nm (Warburton et al., 2007). Due to its elevated levels within brain tissue, LF fluorescence interferes with different analytical techniques such as immunoconfocal microscopy. Thus, different experimental protocols have been used to block LF autofluorescence in tissue samples, such as Sudan Black, copper sulfate or picric acid treatments. However, these methods do not allow the study of LF concurrently with neurodegeneration markers, thus impeding the analysis of LF contribution to pathology.
Additionally, as LF plays a clear role in cellular senescence, and increasing interest is focused on the study of its potential pathophysiological role, several methods have been developed to quantify LF in brain tissue. Based on its high lipid content, classical methods of isolation and quantitation of LF employed organic solvent extraction or density gradient ultracentrifugation protocols (Siakotos, 1974 Taubold et al., 1975 Ottis et al., 2012). However, due to its fluorescent properties, most recent methods for LF detection and quantification are based on the use of fluorescence microscopy (Moore et al., 1995 Jung et al., 2010 Zheng et al., 2010 Jensen et al., 2016). Provided that LF presents a very broad fluorescence spectrum, fluorescence images of tissue preparations can be acquired over a broad range of wavelengths. Depending on the need to colocalized LF autofluorescence with other cellular structures, non-overlapping anti-antibodies or probes should be selected (Jung et al., 2010). For example, DNA probes emitting in the far-red range can be combined with the detection of LF in both green and red channels (Zheng et al., 2010). Recently, we have developed a method based on channel filtering of confocal microscopy to identify and discriminate LF autofluorescence signals from the specific ones, such as amyloid plaques in the AD brain (see Figure 1) (Kun et al., 2018).
Figure 1. Confocal fluorescence microscopy analysis of AD brain tissue. The characteristic perinuclear lipofuscin deposits can be clearly identified in brain tissue by autofluorescent emission at 510 nm (A, green) and at 570 nm (B, red), with excitation at 488 nm and 561 nm, respectively. Additionally, amyloid beta plaques (C, white) were immunostained by the specific monoclonal antibody 4G8 (Covance) followed by an anti-antibody conjugated to a fluorophore excitable to 633 nm and emitting light from 670 to 700 nm (Invitrogen GAM-A-21052). DNA in nuclear domains was identified by DAPI probe (D, blue). In the merged image (E), lipofuscin aggregates (pink-orange) appears widely distributed throughout the tissue with incidental colocalization within the amyloid beta plaques. Images represent a single confocal plane of cryosections of prefrontal cortex from an AD patient treated with 70% formic acid for 10 s. The yellow arrows indicate LF aggregates that are located within senile plaques. Adapted with permission from chapter 31 𠇌haracterization of Amyloid-β Plaques and Autofluorescent Lipofuscin Aggregates in Alzheimer's Disease Brain: A Confocal Microscopy Approach” in Amyloid Proteins. Methods and Protocols, Volume 1179 in Methods Molecular Biology Series (ISBN: 978-1-4939-7815-1) Series Ed.: Walker, John M. Humana Press-Springer.
Week 1: General pathology, cell damage, cell death
- Physical & chemical responses in blood vessels.
- Interaction of many types of specialised cells.
- may or may not cause gross or microscopic lesions.
1. Atrophy: reduction in size
2. Hypertrophy: increased size
- increase in number of cells or organ which leads to increase in size.
- Architectural or cellular disorder
- found in cytoplasm of old animal's cells.
- affected tissue will look green-brown grossly
- collecting histologic or other diagnostic samples
- Preparing and staining blood and tissue smears.
- Setting up running diagnostic tests or working in diagnostic laboratories.
- Filling in the submission forms including the history.
- analysis of body fluids = cytology and chemistry
1. Gross examination of findings = important medical record
- When these compounds escape, they enter circulation and are often detectable in blood.
- Necrosis: uncontrolled cell death caused by injury in living animal. (cell leakage)
- deeper lesions where the epithelium is missing (ulcerations)
- burn may show initially as white mark (coagulation necrosis & dehydration of epithelial cells)
2. Karyorrhexis = nuclear membrane dissolves and chromatin break up into small pieces.
- liquefied and architecture is destroyed
--> myeloperoxidase in neutrophils.
- often seen in granulomas as the major cell type of inflammatory cells are macrophages.
--> tissue is pasty white and granular
--> no normal architecture
- commonly with pancreatitis denaturing peritoneal fat around the fat pancreas. And trauma to subcutaneous fat.
- Saponification: enzymes denature the fat and turn it into a firm waxy soap-like substance.
- commonly noted on extremities like limbs, hooves, tails, ear tips.
--> dry gangrene: green, dehydrated and withered and may slough off.
--> Gas gangrene: bacteria producing gas cause emphysema (short breath) in the tissue which has a crackly crepitant feel.
--> Moist gangrene: bacteria proliferate in the area of necrosis causing moist putrefaction which is foul smelling.
--> Wet gangrene: bacteria proliferate and reaction of the adjacent living tissue causes swelling and oozing of fluid.
- scarring = replacement of tissue with fibrous connective tissue. occurs in non-healing tissue or those lacking stroma.
- Erosion, ulceration, sloughing = the necrotic tissue is shed from body leaving a defect
- deletion of autoreactive T cells in thymic development to prevent autoimmune disease.
It appears to be the product of the oxidation of unsaturated fatty acids and may be symptomatic of membrane damage, or damage to mitochondria and lysosomes. Aside from a large lipid content, lipofuscin is known to contain sugars and metals, including mercury, aluminum, iron, copper and zinc. 
The accumulation of lipofuscin-like material may be the result of an imbalance between formation and disposal mechanisms: Such accumulation can be induced in rats by administering a protease inhibitor (leupeptin) after a period of three months, the levels of the lipofuscin-like material return to normal, indicating the action of a significant disposal mechanism.  However, this result is controversial, as it is questionable if the leupeptin-induced material is true lipofuscin.   There exists evidence that "true lipofuscin" is not degradable in vitro    whether this holds in vivo over longer time periods is not clear.
Although the etiology and pathogenesis of sporadic PD have yet to be established, several predisposing factors and pathogenic pathways have been implicated. Among the latter are oxidative stress associated with mitochondrial dysfunction, 95-98 proteolytic stress due to dysfunction of the ubiquitin-proteasome system (UPS), 99,100 and local inflammation. 101-103 These are not exclusive mechanisms in fact, they can be mutually reinforcing. 104 Moreover, each of the three pathways may lead to activation of the intracellular machinery of programmed cell death (PCD), suspected of being a final common mechanism of the neuron loss in PD. 104
The suspected causal factors in PD include environmental toxins, particularly enhancers of oxidative stress, 105-107 and nuclear genetic defects. Evidence of mitochondrial dysfunction in PD ensured that defective mitochondrial genes linked to PD would be sought assiduously in PD patients, yet to date there is still no compelling evidence for such a link. 108,109 On the other hand, studies of families in which the inheritance of PD follows mendelian patterns have already identified five genes in which mutations arc associated with typical PD phenotypes (Table II) 110,111 .
Three of the PD-related genes - PARK1, PARK2, andPARK5 - code for proteins found in LBs. 110,112 Two of these - parkin (the product of PARK2) and UCH-L1 (the product, of PARK5) - are enzymatic components of the UPS for intracellular protein clearance. 99 The third is α-synuclein, the product, of PARK1 and a presynaptic protein that, in the fibrillar form, constitutes roughly 40% of a typical LB. 113 A fourth gene, PARK7, codes for DJ-1, a protein linked to oxidative stress defenses and possible chaperone functions that could help to limit, misfolding of other proteins and thereby reduce proteolytic stress. 114 The fifth PD gene, NR4A2 (also known by its product's name, NURR1), 115-117 encodes a protein that regulates transcription of the TH gene and whose postmitotic expression is critical to the specification and development of midbrain DA neurons. 118-121 Defects in this gene could lead to striatal DA depletion and the characteristic motor impairments of PD, but of course such mutations by themselves would not account for the neurodegenerative process in PD, which invariably extends well beyond the midbrain and affects numerous types of nondopaminergic cell groups (Table I).
|Gene||Locus||Inheritance||Onset||LB pathology||Product||Properties||Functional role||Found in LBs|
|PARK2||6q25-27||AR||Early||No||Parkin||E3 ubiquitin ligase||Preproteolytic||Yes|
|PARK5||4p14||AD||Late||Unknown||UCH-L1||Ubiquitin C-terminal||Ubiquitin removal||Yes|
|hydroxylase L1||for recycling|
|for DAT and TH||neurogenesis|
The burgeoning linkage data related to these and other loci have reignited interest in the possibility of identifying potential susceptibility genes 122-124 that might, interact with environmental factors in polygenic fashion to produce the range phenotypes observed in nonfamilial PD. Recent, evidence suggests that some PARK5 mutations may increase susceptibility to development of late-onset PD, 125 while others may actually decrease susceptibility 126 Thus far, however, it does not appear that single gene mutations figure prominently in sporadic PD. 127-130 Moreover, twin studies have repeatedly indicated that heritability factors among patients with late-onset PD are minimal to nonexistent. 131,132
The search for environmental factors that might initiate or enhance the neurodegenerative process in PD intensified following the discovery of MPTP-induced parkinsonism. As oxidative stress had been clearly implicated in the pathogenesis of MPTP-induced parkinsonism, 14,133 it was natural to focus to some extent, on environmental oxidants and inhibitors of mitochondrial respiration. Tetrahydroisoquinoline (TIQ) and β-carboline (β-C) derivatives, which are structurally related to MPTP and occur naturally in many foods, produce nigrostriatal damage in experimental animals and have been detected in brain and cerebrospinal fluid (CSF) in PD patients. 106,134 As with MPTP's conversion to MPP + , there is metabolic activation of TIQ and β-C derivatives by conversion to quinolinium and β-carbolinium species, respectively, which are DAT substrates and appear to be toxic to mitochondria. 106-134
Pesticides have also been suggested as possible causal or contributing factors in some cases of sporadic PD. 105 Both paraquat, and rotcnone arc potent inhibitors of mitochondrial complex I, and both are potentially neurotoxic. 135,136 While neuronal toxicity of paraquat is generally lacking in specificity, rotenone has been shown to produce an excellent model of PD in rodents when administered chronically in low doses. 137 Chronic infusions of rotenone produce selective degeneration of nigrostriatal DA neurons and formation of α-synuclein-positive LB-like structures, accompanied by signs of parkinsonism. 138,139 Although epidemiological studies have often suggested a linkage between exposure to pesticides and development of PD, 140,141 the interpretability of such findings has generally been limited by uncertainties concerning the chemical identity, route, intensity, and duration of exposures. 106,134
Signs of oxidative stress are abundant in the substantia nigra of patients with PD. 95 Mitochondrial complex I activity is depressed. 142 Levels of intrinsic antioxidants, such as glutathione, are reduced, 143 while oxidized products of proteins, lipids, and DNA increase significantly. 144-147 Increasing levels of oxidative stress can eventually lead to apoptosis through the intrinsic (or “mitochondrial”) PCD pathway due to cytoplasmic release of cytochrome c, which is proapoptotic, from dysfunctional mitochondria. 104
Pathogenic factors peculiar to DA neurons
Factors peculiar to midbrain DA neurons may enhance the risk of oxidative damage in SNc, though they clearly are not essential to the neurodegenerative process, as it affects most other vulnerable cell groups. Cytosolic DA can increase oxidative stress within nigral neurons by several routes. Spontaneous autooxidation of DA produces reactive DA-quinone species and the superoxide anion (O2·), as well as hydrogen peroxide (H2O2). 148 When not sequestered in synaptic vesicles, DA can form complexes with cysteine that, inhibit mitochondrial complex I. 149 Glutamatergic activation of N-methyl-D-aspartate (NMDA) receptors on SNc neurons results in Ca 2+ influx that may activate nitric oxide (NO) synthase (NOS), 149 thereby increasing the availability of NO that could in turn combine with the superoxide anion to produce peroxynitrite (ONOO·), which can cause nitrative damage to proteins, lipids, and DNA. 96,150,151
In PD, there is progressive accumulation of intracellular iron in SNc neurons and microglia. 152-154 Why this occurs is uncertain, 153,155 but the excess nigral iron is likely to enhance local oxidative stress. Ordinarily, accumulation of tissue iron is accompanied by concomitant increases in local ferritin levels, which serve to moderate the risk of local redox toxicity that would otherwise be associated with the increased iron. However, in PD, the expected increase in local ferritin does not occur. 155,156 Iron is chemically inactive when bound to ferritin as Fe 3+ , whereas unbound iron in the ferrous state (Fe 2+ ) can combine with H2O2 in the Fenton reaction to produce the reactive hydroxyl radical (OH·). 152 This and other reactive oxygen species (ROS) are also generated in the course of DA metabolism and turnover. 148 Activities of TH and monoamine oxidase generate H2O2. In the presence of ferrous iron, the superoxide anion and H2O2 - two weakly reactive free radical species - can combine in the Haber- Weiss reaction to produce the more reactive OH· radical this is believed to be the dominant, pathway for biological production of the OH· radical. 155
Neuromelanin (NM) may play a role in nigral, and possibly LC, degeneration, but whether that role is toxic or protective remains uncertain. In humans and nonhuman primates, both the DA-producing neurons of SNc and the NA-producing neurons of LC are darkly pigmented due to perikaryal accumulation of NM within double-membrancd organelles known as NM granules. 152,157 NM. is produced by spontaneous autooxidation of cytosolic DA and NA in SNc and LC neurons, respectively. 152 The selective vulnerability of SNc and LC neurons in both PD and MPTP-induced parkinsonism prompted early suggestions that NM might contribute to the neurodegenerative process. Recent studies suggest NM may have the opposite effect, at least, early in the disease. For example, it was noted that the nigral DA neurons most susceptible to early loss in PD - those in the ventral tier of the SNc - typically contain lower amounts of NM than do their less vulnerable counterparts in the dorsal tier. 16 Biochemical studies have shown that as NM is synthesized and accumulates intracellularly during the life of an SNc neuron, it appears to be capable of binding and inactivating redox-active metal ions (in particular Fe 2+ ), intrinsically generated quinones and ROS, 152,158 and environmental toxins such as paraquat. 157
While SNc iron levels are still relatively low early in the course of PD, NM contains a preponderance of highaffinity iron -binding sites that, could oxidize redox-active Fe 2+ and chelate the inactive Fe 3+ that results, thereby reducing the potential for oxidative stress. 157 Later, as PD progresses and cytosolic Fe 2+ concentrations rise due to continued accumulation of intracellular iron, NM's high affinity iron-binding sites could become saturated, leaving only the low-affinity sites to bind redox-active Fe 2+ , which they do without oxidizing it to the inactive ferric form. 152 NM-bound Fe 2+ would then remain free to catalyze production of OH· radicals via the Fenton reaction. 134,152,157
A second mechanism implicated in PD pathogenesis is proteolytic stress resulting from dysfunction of the UPS of nonlysosomal protein degradation. 99 The UPS is an essential pathway for degradation and clearance of misfolded or otherwise damaged intracellular proteins. Several converging lines of evidence suggest that protein aggregation related to proteolytic stress could be an important aggravating or contributing factor in the neurodegeneration of PD.
LBs, the sine qua nons of PD, are proteinaceous inclusions, of which the principal component is fibrillar a-synuclein. 159,160 The normal role of α-synuclein as a presynaptic protein is unknown, but it may be involved in synaptic maintenance or plasticity. 161,162 Approximately half of the α-synuclein within a presynaptic terminal remains unfolded, as a cytosolic protein capable of binding to synaptic vesicles the remainder is concentrated near synaptic vesicles where it binds to plasma membranes in a predominantly α-helical form. 148 These and other properties have led to suggestions that α-synuclein plays a role in the maintenance and recycling of synaptic vesicles. 162 As concentrations of cytosolic α-synuclein rise, it may itself begin to have adverse effects. It may increase demands on the UPS for protein degradation and clearance, thus enhancing proteolytic stress. 163 In its native form, α-synuclein may bind to and thus sequester an important antiapoptotic protein, 14-3-3, thereby compromising a potential safeguard against activation of the machinery of PCD. 148 In high concentrations, unfolded α-synuclein forms β-pleated sheets known as protofibrils, which may be cytotoxic. 164 Protofibrils may increase the permeability of synaptic vesicles, causing leakage of DA into the cytoplasm which increases oxidative stress. 164,165 By a seeding process, protofibrils can form nontoxic fibrils of α-synuclein, which are the main constituents of LBs. 166
LBs also contain lesser amounts of several UPS-related proteins. These include the following: (i) ubiquitin, the peptide with which damaged proteins are tagged in preparation for degradation by the 26S proteasome (ii) fragments of the 26S proteasome (iii) the E3 ubiquitin ligase parkin, which assists in preproteolytic ubiquination and (iv) ubiquitin C-terminal hydroxylase L1 (UCH-L1), which removes ubiquitin for recycling following proteasomal degradation. 111,148 This evidence for a role of proteolytic stress in the pathogenesis of sporadic PD is reinforced by the fact that mutations in the genes coding for a-synuclein, parkin, and UCH-L1 are associated with some forms of familial PD. 111,167
Oxidative stress can exacerbate proteolytic stress by increasing the amounts of oxidized and nitrated proteins that must be cleared by the UPS. DA-quinones produced by spontaneous autooxidation of DA can form covalent bonds with α-synuclein, also contributing to proteolytic stress. 148,168 DA-quinone bonding might also interfere with α-synuclein's putative role in maintenance and recycling of synaptic vesicles, 148,149 which could in turn result in increased levels of unsequestered cytosolic DA thereby enhancing oxidative stress.
Local inflammation is readily apparent at sites of neuron loss in both PD and MPTP-induced parkinsonism. 103,169,170 Most, of the inflammatory cells at these sites are activated microglia, although lesser numbers of reactive astrocytes are seen as well. 103,170,171 While the astrocytes are suspected of playing an overall protective role in PD by such mechanisms as sequestration and metabolization of DA, glutathione-mediated scavenging of ROS and production of glial-derived neurotrophic factor (GDNF), the microglia, are believed instead to facilitate the neurodegenerative process in PD. 149,155,172 Microglial accumulation and activation occurs in sites where neurons eventually die and arc lost, such as SNc. NM. is known to be proinflammatory when released to the extracellular environment, as occurs of course when NM-laden nigral neurons eventually succumb to the neurodegenerative process. 149,155,172 Microglial infiltration in regions of neuron loss could therefore represent merely a secondary response to the presence of dead and dying neurons. 149,155 Yet experimental studies in toxin-induced animal models suggest that such inflammation also plays a causal role in the neurodegenerative process inasmuch as they show that, death of SNc neurons can be averted by treatment with anti-inflammatory agents. 103
Activated microglia appear to be the main source of increased levels of inducible NOS (iNOS) in parkinsonian nigra. 104 Induction of iNOS is associated with sustained increases in local NO production. 173 NO can diffuse readily across cell membranes to enter nearby SNc neurons, where it could combine with locally produced superoxide anion to produce peroxynitrite, exacerbating nitration-induced damage to intracellular lipids, proteins, and DNA in nigral neurons. 151,174
Activated microglia also produce cytokines capable of amplifying the local inflammatory response by activating still more microglia, in the vicinity. 175 Several of these, including tumor necrosis factor α (TNF-α), have been identified in nigral tissue of PD patients. 175,176 By binding to TNF receptor 1 on the surface of nearby SNc neurons, 176 microglial-derived TNF-α could activate the TNF receptor family th domain” and thereby trigger the extrinsic (or th receptor”) PCD pathway leading from initiator caspase 8 to the executioner caspases and cell death. 104 Postmortem nigral tissue in PD patients is characterized by elevated caspasc activities 177 and other indicators of PCD. 178-181
Implications of pathogenesis for neuroprotective therapy
Current, understanding of the pathogenesis of PD implies that appropriate neuroprotective therapies aimed at reducing oxidative or proteolytic stress, blocking the putative toxic effects of microglial activation, or promoting neuronal growth and repair, should be effective in preventing, slowing, or reversing both the underlying neurodegenerative process and the natural progression of the disease. Such therapies could include antioxidants, anti-inflammatory agents, neuronal growth factor infusions, and neural “transplant” procedures, as well as potential gene therapies and pharmacological interventions targeting enhancement of intracellular protein clearance or suppression of PCD pathways. To date, these approaches have had little success in achieving the intended outcomes. We still have no proven neuroprotective or restorative therapies that prevent, slow, or reverse the neurodegeneration or progression of PD, despite concerted efforts to develop such measures over the past two decades. 182,183 It remains uncertain, therefore, whether any of the pathogenic mechanisms proposed to date has a primary role in disease initiation, although it does seem likely that all, when present, could contribute to disease progression. This suggests that current models of the pathogenesis of PD remain incomplete. Such is the case especially for those predisposing factors that may be selective for nigral DA neurons. The roles of iron and NM, and the toxic effects of DA metabolism in SNc neurons, do not explain the similar pathology in other cell groups such as dorsal glossopharyngeus-vagus complex or the intermediolateral column of spinal cord.
Various experimental strategies - including pharmacological and gene-based therapies aimed at reducing oxidative or proteolytic stress or inflammation or reversing defective neurogenesis - do protect against genetic or toxin-induced parkinsonism in certain animal models. 184 Such protection, however, often requires that the therapy has been in place at or before the time of toxic exposure or expression of toxic alleles. This may account in part for the lack of effective neuroprotective strategics in human PD, as these can only be tested in subjects if they already have the disease. 182,185 Nonetheless, until we are able to intervene directly in the neurodegenerative process by blocking one or more of the implicated pathogenic pathways, the causative role of these mechanisms in human disease will remain uncertain.
Cell Injury, Aging, and Death
Disease and injury are increasingly being understood as cellular and genetic phenomena. Although pathophysiologic processes are often presented in terms of systemic effects and manifestations, ultimately it is the cells that make up the systems that are affected. Even complex multisystem disorders such as cancer ultimately are the result of alterations in cell function. As the mysterious mechanisms of diseases are understood on the cellular and molecular levels, more specific methods of diagnosis, treatment, and prevention can be developed. This chapter presents the general characteristics of cellular injury, adaptation, aging, and death that underlie the discussions of systemic pathophysiologic processes presented in later chapters of this text.
Cells are confronted by many challenges to their integrity and survival and have efficient mechanisms for coping with an altered cellular environment. Cells respond to environmental changes or injury in three general ways: (1) when the change is mild or short-lived, the cell may withstand the assault and completely return to normal. This is called a reversible cell injury. (2) The cell may adapt to a persistent but sublethal injury by changing its structure or function. Generally, adaptation also is reversible. (3) Cell death may occur if the injury is too severe or prolonged. Cell death is irreversible and may occur by two different processes termed necrosis and apoptosis. Necrosis is cell death caused by external injury, whereas apoptosis is triggered by intracellular signaling cascades that result in cell suicide. Necrosis is considered to be a pathologic process associated with significant tissue damage, whereas apoptosis may be a normal physiologic process in some instances and pathologic in others.
Reversible Cell Injury
Regardless of the cause, reversible injuries and the early stages of irreversible injuries often result in cellular swelling and the accumulation of excess substances within the cell. These changes reflect the cell’s inability to perform normal metabolic functions owing to insufficient cellular energy in the form of adenosine triphosphate (ATP) or dysfunction of associated metabolic enzymes. Once the acute stress or injury has been removed, by definition of a reversible injury, the cell returns to its preinjury state.
Cellular swelling attributable to accumulation of water, or hydropic swelling, is the first manifestation of most forms of reversible cell injury. 1 Hydropic swelling results from malfunction of the sodium-potassium (Na + -K + ) pumps that normally maintain ionic equilibrium of the cell. Failure of the Na + -K + pump results in accumulation of sodium ions within the cell, creating an osmotic gradient for water entry. Because Na + -K + pump function is dependent on the presence of cellular ATP, any injury that results in insufficient energy production also will result in hydropic swelling (Figure 4-1). Hydropic swelling is characterized by a large, pale cytoplasm, dilated endoplasmic reticulum, and swollen mitochondria. With severe hydropic swelling, the endoplasmic reticulum may rupture and form large water-filled vacuoles. Generalized swelling in the cells of a particular organ will cause the organ to increase in size and weight. Organ enlargement is indicated by the suffix -megaly (e.g., splenomegaly denotes an enlarged spleen, hepatomegaly denotes an enlarged liver).
Excess accumulations of substances in cells may result in cellular injury because the substances are toxic or provoke an immune response, or merely because they occupy space needed for cellular functions. In some cases, accumulations do not in themselves appear to be injurious but rather are indicators of cell injury. Intracellular accumulations may be categorized as (1) excessive amounts of normal intracellular substances such as fat, (2) accumulation of abnormal substances produced by the cell because of faulty metabolism or synthesis, and (3) accumulation of pigments and particles that the cell is unable to degrade (Figure 4-2).
Normal intracellular substances that tend to accumulate in injured cells include lipids, carbohydrates, glycogen, and proteins. Faulty metabolism of these substances within the cell results in excessive intracellular storage. In some cases, the enzymes required for breaking down a particular substance are absent or abnormal as a result of a genetic defect. In other cases, altered metabolism may be due to excessive intake, toxins, or other disease processes.
A common site of intracellular lipid accumulation is the liver, where many fats are normally stored, metabolized, and synthesized. Fatty liver is often associated with excessive intake of alcohol. 2 Mechanisms whereby alcohol causes fatty liver remain unclear, but it is thought to result from direct toxic effects as well as the preferential metabolism of alcohol instead of lipid (see Chapter 38 for a discussion of fatty liver). Lipids may also contribute to atherosclerotic diseases and accumulate in blood vessels, kidney, heart, and other organs. Fat-filled cells tend to compress cellular components to one side and cause the tissue to appear yellowish and greasy (Figure 4-3). In several genetic disorders, the enzymes needed to metabolize lipids are impaired these include Tay-Sachs disease and Gaucher disease, in which lipids accumulate in neurologic tissue.
Glycosaminoglycans (mucopolysaccharides) are large carbohydrate complexes that normally compose the extracellular matrix of connective tissues. Connective tissue cells secrete most of the glycosaminoglycan into the extracellular space, but a small portion remains inside the cell and is normally degraded by lysosomal enzymes. The mucopolysaccharidoses are a group of genetic diseases in which the enzymatic degradation of these molecules is impaired and they collect within the cell. Mental disabilities and connective tissue disorders are common findings.
Like other disorders of accumulation, excessive glycogen storage can be the result of inborn errors of metabolism, but a common cause is diabetes mellitus. 1 Diabetes mellitus is associated with impaired cellular uptake of glucose, which results in high serum and urine glucose levels. Cells of the renal tubules reabsorb the excess filtered glucose and store it intracellularly as glycogen. The renal tubule cells also are a common site for abnormal accumulations of proteins. Normally, very little protein escapes the bloodstream into the urine. However, with certain disorders, renal glomerular capillaries become leaky and allow proteins to pass through them. Renal tubule cells recapture some of the escaped proteins through endocytosis, resulting in abnormal accumulation.
Cellular stress may lead to accumulation and aggregation of denatured proteins. The abnormally folded intracellular proteins may cause serious cell dysfunction and death if they are allowed to persist in the cell. A family of stress proteins (also called chaperone or heat-shock proteins) is responsible for binding and refolding aberrant proteins back into their correct three-dimensional forms (Figure 4-4). If the chaperones are unsuccessful in correcting the defect, the abnormal proteins form complexes with another protein called ubiquitin . Ubiquitin targets the abnormal proteins to enter a proteosome complex, where they are digested into fragments that are less injurious to cells (see Figure 4-4). In some cases, the accumulated substances are not metabolized by normal intracellular enzymes. In diabetes, for instance, high serum glucose levels result in excessive glucose uptake by neuronal cells because they do not require insulin for glucose uptake. 3 (Diabetes mellitus is discussed in Chapter 41.)
Finally, a variety of pigments and inorganic particles may be present in cells. Some pigment accumulations are normal, such as the accumulation of melanin in tanned skin, whereas others signify pathophysiologic processes. Pigments may be produced by the body (endogenous) or may be introduced from outside sources (exogenous). In addition to melanin, the iron-containing substances hemosiderin and bilirubin are endogenous pigments that, when present in excessive amounts, indicate disease processes. Hemosiderin and bilirubin are derived from hemoglobin. Excessive amounts may indicate abnormal breakdown of hemoglobin-containing red blood cells (RBCs), prolonged administration of iron, and the presence of hepatobiliary disorders. Inorganic particles that may accumulate include calcium, tar, and mineral dusts such as coal, silica, iron, lead, and silver. Mineral dusts generally are inhaled and accumulate in lung tissue (Figure 4-5). Inhaled dusts cause chronic inflammatory reactions in the lung, which generally result in destruction of pulmonary alveoli and capillaries and the formation of scar tissue. Over many years, the lung may become stiff and difficult to expand because of extensive scarring (see Chapter 23).
Deposits of calcium salts occur in conditions of altered calcium intake, excretion, or metabolism. Impaired renal excretion of phosphate may result in the formation of calcium phosphate salts that are deposited in the tissues of the eye, heart, and blood vessels. Calcification of the heart valves may cause obstruction to blood flow through the heart or interfere with valve closing. Calcification of blood vessels may result in narrowing of vessels and insufficient blood flow to distal tissues. Dead and dying tissues often become calcified (filled with calcium salts) and appear as dense areas on x-ray films. For example, lung damage resulting from tuberculosis often is apparent as calcified areas, called tubercles.
With the exception of inorganic particles, the intracellular accumulations generally are reversible if the causative factors are removed.
The cellular response to persistent, sublethal stress reflects the cell’s efforts to adapt. Cellular stress may be due to an increased functional demand or a reversible cellular injury. Although the term adaptation implies a change for the better, in some instances an adaptive change may not be beneficial. The common adaptive responses are atrophy (decreased cell size), hypertrophy (increased cell size), hyperplasia (increased cell number), metaplasia (conversion of one cell type to another), and dysplasia (disorderly growth) (Figure 4-6). Each of these changes is potentially reversible when the cellular stress is relieved.
Atrophy occurs when cells shrink and reduce their differentiated functions in response to a variety of normal and injurious factors. The general causes of atrophy may be summarized as (1) disuse, (2) denervation, (3) ischemia, (4) nutrient starvation, (5) interruption of endocrine signals, (6) and persistent cell injury. Apparently, atrophy represents an effort by the cell to minimize its energy and nutrient consumption by decreasing the number of intracellular organelles and other structures.
A common form of atrophy is the result of a reduction in functional demand, sometimes called disuse atrophy. For example, immobilization by bed rest or casting of an extremity results in shrinkage of skeletal muscle cells. On resumption of activity, the tissue resumes its normal size. Denervation of skeletal muscle results in a similar decrease in muscle size caused by loss of nervous stimulation. Inadequate blood supply to a tissue is known as ischemia. If the blood supply is totally interrupted, the cells will die, but chronic sublethal ischemia usually results in cell atrophy. The heart, brain, kidneys, and lower leg are common sites of ischemia. Atrophic changes in the lower leg attributable to ischemia include thin skin, muscle wasting, and hair loss. Atrophy also is a consequence of chronic nutrient starvation, whether the result of poor intake, absorption, or distribution to the tissues. Many glandular tissues throughout the body depend on growth-stimulating (trophic) signals to maintain size and function. For example, the adrenal cortex, thyroid, and gonads are maintained by trophic hormones from the pituitary gland and will atrophy in their absence. Atrophy that results from persistent cell injury is most commonly related to chronic inflammation and infection.
The biochemical pathways that result in cellular atrophy are imperfectly known however, two pathways for protein degradation have been implicated. The first is the previously mentioned ubiquitin-proteosome system, which degrades targeted proteins into small fragments (see Figure 4-4). The second involves the lysosomes that may fuse with intracellular structures leading to hydrolytic degradation of the components. Certain substances apparently are resistant to degradation and remain in the lysosomal vesicles of atrophied cells. For example, lipofuscin is an age-related pigment that accumulates in residual vesicles in atrophied cells, giving them a yellow-brown appearance.
Hypertrophy is an increase in cell mass accompanied by an augmented functional capacity. Cells hypertrophy in response to increased physiologic or pathophysiologic demands. Cellular enlargement results primarily from a net increase in cellular protein content. 4 Like the other adaptive responses, hypertrophy subsides when the increased demand is removed however, the cell may not entirely return to normal because of persistent changes in connective tissue structures. Organ enlargement may be a result of both an increase in cell size (hypertrophy) and an increase in cell number (hyperplasia). For example, an increase in skeletal muscle mass and strength in response to repeated exercise is primarily the result of hypertrophy of individual muscle cells, although some increase in cell number is also possible because muscle stem cells (satellite cells) are able to divide. Physiologic hypertrophy occurs in response to a variety of trophic hormones in sex organs—the breast and uterus, for example. Certain pathophysiologic conditions may place undue stress on some tissues, causing them to hypertrophy. Liver enlargement in response to bodily toxins and cardiac muscle enlargement in response to high blood pressure (Figure 4-7) represent hyperplastic and hypertrophic adaptations to pathologic conditions. Hypertrophic adaptation is particularly important for cells, such as differentiated muscle cells, that are unable to undergo mitotic division.
Cells that are capable of mitotic division generally increase their functional capacity by increasing the number of cells (hyperplasia) as well as by hypertrophy. Hyperplasia usually results from increased physiologic demands or hormonal stimulation. Persistent cell injury also may lead to hyperplasia. Examples of demand-induced hyperplasia include an increase in RBC number in response to high altitude and liver enlargement in response to drug detoxification. Trophic hormones induce hyperplasia in their target tissues. Estrogen, for example, leads to an increase in the number of endometrial and uterine stromal cells. Dysregulation of hormones or growth factors can result in pathologic hyperplasia, such as that which occurs in thyroid or prostate enlargement.
Chronic irritation of epithelial cells often results in hyperplasia. Calluses and corns, for example, result from chronic frictional injury to the skin. The epithelium of the bladder commonly becomes hyperplastic in response to the chronic inflammation of cystitis.
Metaplasia is the replacement of one differentiated cell type with another. This most often occurs as an adaptation to persistent injury, with the replacement cell type better able to tolerate the injurious stimulation. 1 Metaplasia is fully reversible when the injurious stimulus is removed. Metaplasia often involves the replacement of glandular epithelium with squamous epithelium. Chronic irritation of the bronchial mucosa by cigarette smoke, for example, leads to the conversion of ciliated columnar epithelium to stratified squamous epithelium. Metaplastic cells generally remain well differentiated and of the same tissue type, although cancerous transformations can occur. Some cancers of the lung, cervix, stomach, and bladder appear to derive from areas of metaplastic epithelium.
Dysplasia refers to the disorganized appearance of cells because of abnormal variations in size, shape, and arrangement. Dysplasia occurs most frequently in hyperplastic squamous epithelium, but it may also be seen in the mucosa of the intestine. Dysplasia probably represents an adaptive effort gone astray. Dysplastic cells have significant potential to transform into cancerous cells and are usually regarded as pre neoplastic lesions. (See Chapter 7 for a discussion of cancer.) Dysplasia that is severe and involves the entire thickness of the epithelium is called carcinoma in situ. Mild forms of dysplasia may be reversible if the inciting cause is removed.
Irreversible Cell Injury
Pathologic cellular death occurs when an injury is too severe or prolonged to allow cellular adaptation or repair. Two different processes may contribute to cell death in response to injury: necrosis and apoptosis. Necrosis usually occurs as a consequence of ischemia or toxic injury and is characterized by cell rupture, spilling of contents into the extracellular fluid, and inflammation. Apoptosis (from a Greek word meaning falling off, as in leaves from a tree) occurs in response to injury that does not directly kill the cell but triggers intracellular cascades that activate a cellular suicide response. Apoptotic cells generally do not rupture and are ingested by neighboring cells with minimal disruption of the tissue and without inflammation. Apoptosis is not always a pathologic process and occurs as a necessity of development and tissue remodeling.
Necrotic cells demonstrate typical morphologic changes, including a shrunken (pyknotic) nucleus that is subsequently degraded (karyolysis), a swollen cell volume, dispersed ribosomes, and disrupted plasma and organelle membranes (Figure 4-8). The disruption of the permeability barrier of the plasma membrane appears to be a critical event in the death of the cell. 5
Localized injury or death of tissue is generally reflected in the entire system as the body attempts to remove dead cells and works to compensate for loss of tissue function. Several manifestations indicate that the system is responding to cellular injury and death. A general inflammatory response is often present, with general malaise, fever, increased heart rate, increased white blood cell (WBC) count, and loss of appetite. With the death of necrotic cells, intracellular contents are released and often find their way into the bloodstream. The presence of specific cellular enzymes in the blood is used as an indicator of the location and extent of cellular death. For example, an elevated serum amylase level indicates pancreatic damage, and an elevated creatine kinase (MB isoenzyme) or cardiac troponin level indicates myocardial damage. The location of pain caused by tissue destruction may also aid in the diagnosis of cellular death.
Four different types of tissue necrosis have been described: coagulative, liquefactive, fat, and caseous (Figure 4-9). They differ primarily in the type of tissue affected. Coagulative necrosis is the most common. Manifestations of coagulative necrosis are the same, regardless of the cause of cell death. In general, the steps leading to coagulative necrosis may be summarized as follows: (1) ischemic cellular injury, leading to (2) loss of the plasma membrane’s ability to maintain electrochemical gradients, which results in (3) an influx of calcium ions and mitochondrial dysfunction, and (4) degradation of plasma membranes and nuclear structures (Figure 4-10). The area of coagulative necrosis is composed of denatured proteins and is relatively solid. The coagulated area is then slowly dissolved by proteolytic enzymes and the general tissue architecture is preserved for a relatively long time (weeks). This is in contrast to liquefactive necrosis.
FIGURE 4-9 The four primary types of tissue necrosis. A, Coagulative B, liquefactive C, fat D, caseous. ( A, From Crowley L: Introduction to human disease, ed 4, Sudbury, MA, 1996, Jones and Bartlett, www.jbpub.com. Reprinted with permission. B-D, From Kumar V et al: Robbins and Cotran pathologic basis of disease, ed 8, Philadelphia, 2010, Saunders, pp 16-17.)
Lipofuscin quantification is used for age determination in various crustaceans such as lobsters and spiny lobsters.   Since these animals lack bony parts, they cannot be aged in the same way as bony fish, in which annual increments in the ear-bones or otoliths are commonly used. Age determination of fish and shellfish is a fundamental step in generating basic biological data such as growth curves, and is needed for many stock assessment methods. Several studies have indicated that quantifying the amount of lipofuscin present in the eye-stalks of various crustaceans can give an index of their age. This method has not yet been widely applied in fisheries management mainly due to problems in relating lipofuscin levels in wild-caught animals with accumulation curves derived from aquarium-reared animals.