Homeostasis, a cell’s ability to maintain a constant internal environment, is essential to cell survival. It is predicated on achieving an equilibrium between the processes of production and degradation of cellular components. One major pathway for degradation is autophagy, an intracellular program involved in the disassembly and recycling of unnecessary or dysfunctional cellular components.
Autophagy (pronounced “aw-TAW-fuh-jee”), or “self-eating,” is a highly conserved adaptive response to stress. This ancient defense mechanism sequesters protein aggregates, pathogens, and damaged or dysfunctional organelles into vesicles – bubble-like structures inside the cell called autophagosomes – and then delivers them for destruction to release macromolecules such as proteins, fats, carbohydrates, and nucleic acids for energy and re-use. The primary goal of autophagy is to allow the cell to adapt to changing conditions and external stressors.
Autophagy differs from apoptosis, a type of cellular self-destruct mechanism that rids the body of damaged or aged cells. However, the two processes are governed by common signals and share common regulatory components, blurring the lines between their activities. In a simple analogy where autophagy is the first responder and apoptosis is the executioner, autophagy attempts to mitigate cellular damage, but if it is unsuccessful, apoptosis steps in to kill the cell.
The process of autophagy is activated by cellular stressors such as nutrient depletion, hypoxia, and the presence of toxins, and involves myriad genes, proteins, receptors, and signaling pathways. Although autophagy occurs at the cellular level, its activation at the whole-body level may improve metabolic fitness and extend lifespan. 
In general, autophagy is categorized as either non-selective or selective.
Non-selective autophagy can occur as part of the cell’s normal physiological functioning (referred to as basal autophagy) or in response to nutrient deprivation or other stressors as a means to maintain homeostasis. In this way, non-selective autophagy performs a general housekeeping role and maintains cellular quality control.
Selective autophagy, on the other hand, targets specific entities in the cell for destruction and removal and helps improve overall cellular function. This discriminatory form of autophagy relies on cues from damaged organelles, pathogens, or protein aggregates that demarcate them for destruction. It serves as a targeted cleansing program that removes slightly damaged or aging parts of the cell.
Several types of autophagy have been identified, and they differ from one another based on how and when they are triggered, the method of sequestration they employ, and the target of their destruction. Of special interest are two selective forms of autophagy: mitophagy and xenophagy.
Mitophagy involves the selective degradation of mitochondria. It helps ensure that the body’s cells are metabolically efficient, without excessive production of reactive oxygen species – a type of oxidative stress that naturally occurs during metabolism, the effects of which are enhanced by damaged mitochondria. Mitophagy ultimately serves as a trigger for mitochondrial biogenesis, the process by which new mitochondria are produced. Failures in mitophagy are associated with several chronic diseases, including cardiovascular disease, kidney disease, and Alzheimer’s disease.  
Xenophagy is a function of the innate immune system. It targets foreign pathogens (such as bacteria or viruses), regulates antigen presentation, and induces innate immune memory – a vital process wherein immune cells “remember” threats. Xenophagy may play a role in modulating cellular levels of non-microbial entities, as well, such as iron.
Three primary signals trigger autophagy, all of which involve nutrient sensing. Critical to each of these pathways is the decline in cellular levels of acetyl CoA, an end product of nutrient metabolism. Acetyl CoA alters the acetylation status of key proteins involved in autophagy (such as mTOR and AMP kinase), thereby serving as a common regulator for the many pathways that lead to its induction or inhibition.
When food is abundant, nutrient-sensing pathways signal the body to build new components and store excess nutrients. Food scarcity, however, and the accompanying reduction in acetyl CoA switch on homeostatic mechanisms – such as the mobilization of stored nutrients through autophagy. When mice or human volunteers experience starvation, autophagy can be observed on the whole-body level.
Acetyl CoA levels can also be modulated via nutrient deprivation or via calorie restriction mimetics, compounds that “trick” cells into inducing autophagy even in the setting of sufficient nutrient levels. Examples of calorie restriction mimetics include resveratrol, metformin, and rapamycin.
Exercise is widely recognized for its many health benefits, including lifespan expansion and protection against cardiovascular diseases, diabetes, cancer, and neurodegenerative diseases. Exercise induces autophagy in the brain and several organs involved in metabolism in mice, including the liver, pancreas, adipose tissue, and muscles, which may explain how exercise benefits the whole body. Endurance training, in particular, induces autophagy in mice, mediating the deleterious effects of diabetes and obesity.
In addition to its role as a manager of quality control and homeostasis, autophagy serves as a trigger for immunosurveillance, the process by which immune cells seek out and identify foreign pathogens such as bacteria, viruses, and precancerous or cancerous cells in the body.
Immunosurveillance activates when autophagy facilitates the release of ATP from dying cells, which attracts the attention of myeloid cells, a critical arm of the body’s immune system largely responsible for innate defense against an array of pathogens. The released ATP activates a special class of cellular proteins known as purinergic receptors, which in turn switch on various elements of the immune system, including the inflammasome, a key player in the body’s inflammatory response. Immunosurveillance is critical in suppressing tumor development and subsequent growth. Its activation is a predictor of long-term success from chemotherapeutic treatments and may help to explain the complex relationship between autophagy and cancer.
A growing body of evidence suggests that autophagy may contribute to longevity and healthspan. Caloric restriction, a potent inducer of autophagy, extends lifespan in many organisms, but it also reduces the risk of many age-related chronic diseases, such as diabetes, cardiovascular disease, cancer, and brain atrophy – likely attributable to the beneficial effects of autophagy. 
Failures in autophagy have been implicated in the pathogenesis of cancer, autoimmune disease, infectious disease, and neurodegenerative disease. A common factor among all of these conditions is inflammation. Autophagy promotes the production of proinflammatory mediators, which can lead to inappropriate immune activation and subsequent disease states.
Whereas autophagy promotes suppression during tumor initiation, it provides critical protection during tumor progression. In early-stage cancer, the initial suppression of autophagy may help prevent attracting undue attention from the immune system but may facilitate ongoing transformation. In later stage cancer, autophagy may help cancer cells survive within the hostile tumor microenvironment. Metabolic stress is relatively well tolerated in cancer cell lines because of their capacity to activate the autophagic response.
Although autophagy is generally considered a beneficial process, it can have deleterious effects in autoimmune diseases. In rheumatoid arthritis, upregulation of TNF-alpha, a proinflammatory cell-signaling protein, induces autophagy, promoting the differentiation of osteoclasts, a type of bone cell that breaks down mineralized tissue in the joint, destroying the joint architecture. Similarly, dysregulation of autophagy signaling has been implicated in lupus and Crohn’s disease.
Some pathogens have developed strategies to successfully evade autophagy. For example, M. tuberculosis, the bacterium responsible for tuberculosis, commandeers autophagic mechanisms by hiding inside the autophagosome, impairing the processes that break down the pathogen. The bacterium can also interfere with one of the steps involved in xenophagy, ultimately impairing the body’s immune response. Similarly, human immunodeficiency virus, or HIV, reduces cellular levels of key proteins involved in xenophagy induction.
Failures in mitophagy are strongly implicated in Parkinson's disease, a neurodegenerative disorder characterized by mitochondrial dysfunction and energy deficits in dopaminergic neurons in the brain. A growing body of evidence suggests that mitophagy is compromised in Parkinson's disease and promotes the accumulation of dysfunctional mitochondria. Impaired mitophagy likely contributes to the aggregation of misfolded proteins, which in turn impairs mitochondrial homeostasis.
Autophagy is a complex process that influences many aspects of health and disease. It plays crucial roles in maintaining cellular homeostasis by participating in cell metabolism and survival and host defense. Failures in autophagy are associated with a wide array of chronic conditions, such as cancer, autoimmune disease, neurodegenerative disease, and aging. Modulation of autophagy may represent a promising therapeutic approach for extending human lifespan and healthspan.