Persulfidation of ATG18a regulates autophagy under ER stress in Arabidopsis

Hydrogen sulfide (H₂S) is an endogenously generated gaseous signaling molecule, which recently has been implicated in autophagy regulation in both plants and mammals through persulfidation of specific targets. Persulfidation has been suggested as the molecular mechanism through which sulfide regulates autophagy in plant cells. ATG18a is a core autophagy component that is required for bulk autophagy and also for reticulophagy during endoplasmic reticulum (ER) stress. In this research, we revealed the role of sulfide in plant ER stress responses as a negative regulator of autophagy. We demonstrate that sulfide regulates ATG18a phospholipid-binding activity by reversible persulfidation at Cys103, and that this modification activates ATG18a binding capacity to specific phospholipids in a reversible manner. Our findings strongly suggest that persulfidation of ATG18a at C103 regulates autophagy under ER stress, and that the impairment of persulfidation affects both the number and size of autophagosomes.

Macroautophagy (hereafter referred to as autophagy, from the Greek meaning “self-eating”) is a major catabolic process in eukaryotic cells to degrade dysfunctional or unnecessary cellular components, either non-selectively or selectively (1, 2). It has conserved functions in development, cellular homeostasis, and stress responses from yeast to plants and mammals. In plants, autophagy is critically important in many aspects of plant life, including seedling establishment, development, stress resistance, metabolism, and reproduction (1). The autophagy mechanism involves the enclosure of a portion of the cytoplasm into a double membrane vesicle, named an autophagosome. The outer membrane of the autophagosome finally fuses with the vacuole (in yeast and plants) to release the inner autophagic body for hydrolytic degradation of the sequestered cargo. About 40 ATG (autophagy related) genes have been identified in Arabidopsis, which are required for autophagosome formation (3). Autophagy was initially characterized as a bulk degradation pathway induced by nutrient deprivation with a role in nutrient recycling to enable cell survival, but it also contributes to intracellular homeostasis by selectively degrading aggregated proteins, damaged mitochondria, ribosomes, toxic macromolecules, excess peroxisomes, and pathogens to prevent toxicity (4–6). In particular, although the endoplasmic reticulum (ER) is involved in autophagic processes as a source for membranes, it is also the target of a selective type of autophagy, termed reticulophagy or ER-phagy. In plants, this ER-phagy is induced in response to ER stress produced by tunicamycin (TM) or dithiothreitol (DTT) treatments (7) and upon starvation (8). Selective autophagy is mediated by the binding of adaptor proteins, which link a cargo targeted for degradation to the autophagosome machinery (9). These selective autophagy receptors share the feature of interacting with the autophagosome-localized protein ATG8 through an ATG8-interacting motif or a ubiquitin-interacting motif, leading to their recruitment into forming autophagosomes (10–12).An increasing number of targets for selective autophagy under different stress conditions have emerged in recent years, but the underlying mechanisms of regulation of their degradation are still so far unknown. The activation of bulk and selective autophagy must be tightly controlled by the cellular conditions. In that sense, ATG4 is the only ATG that has been shown to be redox regulated in animal, yeast, algae, and plant systems (13–18). Nevertheless, in the last decade, a growing number of targets involved in autophagy have been shown to be regulated by different posttranslational modifications (PTMs); for example, ATG4b and ATG1 are regulated by S‐nitrosylation and phosphorylation (19, 20). Therefore, the ability of the ATG proteins to interact with a number of autophagic regulators is modulated by different PTMs such as phosphorylation, glycosylation, ubiquitination, and S-nitrosylation (21).Protein persulfidation is another player in the redox regulation of certain proteins. It is the mechanism for sulfide-mediated signaling and is an oxidative posttranslational modification of cysteine residues caused by hydrogen sulfide (H₂S) in which thiolate (–SH) is transformed to a persulfide group (–SSH). Persulfidation of proteins can affect their function, localization inside the cells, stability, and resistance to oxidative stress (22–27). H₂S is an endogenously generated gaseous signaling molecule, which has been recently implicated in autophagy regulation both in plants and mammals (28–30).Analysis of the Arabidopsis des1 mutant, impaired in the cytosolic production of H₂S from cysteine, led to the conclusion that H₂S acts as an inhibitor of autophagy induced by nutrient deprivation (28). Interestingly, its action is independent of reactive oxygen species (ROS) and nitrogen starvation, and the mechanism of autophagy inhibition by H₂S has been proposed to be through persulfidation of specific targets (31). Recently, regulation of the proteolytic activity of ATG4 by persulfidation has been demonstrated in plants (16). Autophagy induced upon nitrogen starvation or osmotic stress was negatively regulated by sulfide, and the mechanism has been explained through persulfidation of C170 of this ATG4 protease, which inhibits proteolytic activity. Collectively, these results suggest that persulfidation may be the molecular mechanism through which sulfide regulates autophagy in plant cells. The susceptibility to persulfidation of the additional ATG-related proteins ATG18a, ATG3, ATG5, and ATG7 was revealed using a high throughput proteomic approach (32), although the role of this modification in these other ATG proteins has not yet been revealed. ATG18a is a core autophagy protein that binds to phosphoinositides (33, 34). It has a seven-bladed β-propeller structure formed by WD40 repeats that bind phosphatidylinositol 3-phosphate (PtdIns(3)P) or phosphatidylinositol (3, 5)-bisphosphate (PtdIns(3,5)P2). These two phosphoinositide-binding sites are located in blades five and six surrounding and sandwiching the conserved L/FRRG motif. ATG18a forms a complex with ATG2, which is involved in autophagosome biogenesis during phagophore expansion (34) and involved in the formation of preautophagosomal structures and lipid recruitment. ATG18a is essential for autophagy under several abiotic stresses, and RNA interference–ATG18a transgenic plants showed an autophagy-defective phenotype during nutrient stress and senescence (35, 36). atg18 mutants show defects in autophagosome formation and display an early senescence phenotype (34). In addition, the ER is a target of autophagy during ER stress in plants, and this ER stress–induced autophagy is dependent on the function of ATG18a (7). Thus, ATG18a is likely to be required for autophagosome formation in Arabidopsis for bulk autophagy and also for reticulophagy during ER stress (7).In this study, we aimed to clarify the role of sulfide in the regulation of autophagy under ER stress through persulfidation of ATG18a. We found that persulfidation affects ATG18a lipid-binding activity, which in turns regulates the number and size of autophagosomes produced upon ER stress.     

Primary cilia and the reciprocal activation of AKT and SMAD2/3 regulate stretch-induced autophagy in trabecular meshwork cells

Activation of autophagy is one of the responses elicited by high intraocular pressure (IOP) and mechanical stretch in trabecular meshwork (TM) cells. However, the mechanosensor and the molecular mechanisms by which autophagy is induced by mechanical stretch in these or other cell types is largely unknown. Here, we have investigated the mechanosensor and downstream signaling pathway that regulate cyclic mechanical stretch (CMS)-induced autophagy in TM cells. We report that primary cilia act as a mechanosensor for CMS-induced autophagy and identified a cross-regulatory talk between AKT1 and noncanonical SMAD2/3 signaling as critical components of primary cilia-mediated activation of autophagy by mechanical stretch. Furthermore, we demonstrated the physiological significance of our findings in ex vivo perfused eyes. Removal of primary cilia disrupted the homeostatic IOP compensatory response and prevented the increase in LC3-II protein levels in response to elevated pressure challenge, strongly supporting a role of primary cilia-mediated autophagy in regulating IOP homeostasis.

The trabecular meshwork (TM) is a pressure-sensitive tissue located in the anterior segment of the eye and key regulator of intraocular pressure (IOP). Malfunction of this tissue results in improper drainage of aqueous humor outflow, leading to ocular hypertension, the major risk factor for developing glaucoma (1–3). The TM consists of an irregular lattice of collagen beams lined by TM endothelial-like cells, followed by a zone of loose connective tissue containing TM cells, through which aqueous humor must pass before leaving the eye. Changes in pressure gradients and fluid flow associated with eye movement, circadian rhythm, or the ocular pulse cause small and high variations in IOP, which are translated in continuous cycles of tissue deformation and relaxation. Cells in the TM are known to be able to sense these deformations as mechanical forces and respond to them by eliciting a variety of responses, including reorganization of actin cytoskeleton, changes in gene expression, secretion of cytokines, modulation of matrix metalloproteinases, and extracellular-matrix remodeling (reviewed in ref. 4). It is believed that these mechanoresponses are critical regulators of IOP homeostasis; however, the mechanosensors and the downstream mechanotransduction signaling in TM have still not been characterized.Our laboratory has identified the activation of macroautophagy (hereafter autophagy) as one of the responses elicited in TM cells following application of static or cyclic mechanical stretch (CMS) (5–7). Activation of autophagy was also observed quickly after pressure elevation in porcine perfused eyes (5), which prompted us to propose autophagy as a crucial physiological response to adapt to mechanical forces and maintain cellular homeostasis. The exact roles of autophagy in TM cells and tissue function are still under investigation. Most recently, we have shown the CMS-induced translocation of the autophagy marker LC3 (microtubule-associated protein 1 light chain 3) to the nuclear compartment, where it associates with the nucleolus and interacts with the ribophagy receptor NUFIP1 (nuclear FMR1 interacting protein 1), suggesting a potential role of CMS-induced autophagy in surveillance of the nucleolus activity (6). Furthermore, we have also recently provided direct evidence demonstrating autophagy as a regulator of TGF-β/SMAD-induced fibrogenesis in TM cells (8).Autophagy is a fundamental process for degradation or recycling of intracellular components, which is essential to maintain cellular homeostasis. Autophagy occurs constitutively at basal levels, but it is quickly activated upon several types of stress, such as nutrient depletion, pathogen infections, drug treatment, accumulation of aggregated proteins and damaged organelles, and mechanical stress (7, 9–11). The molecular mechanisms by which cells recognize stress and regulate autophagic activity are very complex and differ based on the stimuli. A variety of components, for example, receptor tyrosine kinases, second messengers (Ca²⁺ or cAMP [cyclic adenosine monophosphate]), protein kinases, and downstream autophagy-related (ATG) complexes, participate in the regulation of autophagy (10). Among them, the best characterized is MTOR (mechanistic target of rapamycin kinase), a negative regulator of autophagy (10, 12, 13). Although MTOR acts as a core sensor in autophagic regulation, numerous studies have shown the MTOR-independent autophagy activation upon different stresses (10). Indeed, our own study and that of King et al. showed that the induction of autophagy in response to mechanical stress occurs in an MTOR-independent manner (5, 14). The mechanosensor and the downstream signaling pathway responsible for the activation of autophagy in response to stretching have still not been identified.Primary cilium (PC) is a nonmotile cell-surface projection found almost ubiquitously in vertebrate cells, which acts as a cellular antenna that senses a wide variety of signals, including chemical and mechanical stimuli (15–19). PC plays a critical role in smell, sight, and mechanosensation. PC defects are associated with a number of human diseases termed ciliopathies. The most common feature in patients affected with ciliopathies include visual dysfunction (16). In particular, Lowe syndrome patients often develop ocular hypertension and glaucoma (20). Structurally, the PC consists of a microtubule-based core structure, called axoneme, and a basal body, which is a derivative of the centriole of centrosome from which axoneme is extended and surrounded by ciliary membrane (21). The ciliary membrane is a specialized domain extension of the plasma membrane enriched on signaling receptors and channels, including hedgehog (Hh) and Ca²⁺ pathways, which enables the PC to function as a signaling hub (16, 22, 23). Cargo trafficking into and out of the cilium is mediated by a specialized form of vesicle trafficking, named intraflagellar transport (IFT), that is composed of a multiprotein complex (16, 23).Recent studies have demonstrated the reciprocal relationship between PC and autophagy. Autophagy has been shown to both positively and negatively regulate ciliogenesis. Under nutrient-rich conditions, basal autophagy inhibits cilia growth by limiting trafficking of PC components to the basal body through direct degradation of IFT20 (24). In contrast, nutrient starvation triggers the autophagic degradation of oral-facial-digital syndrome 1 and promotes cilia growth (24, 25). Conversely, functional PC are required for activation of autophagy in response to starvation and fluid flow. In both cases, autophagy was initiated by the recruitment of ATG16L to the basal body, suggesting that this event is a hallmark for PC-induced autophagy. Intriguingly, the signaling pathway mediating PC-induced autophagy activation differed based on the stimuli. While Hh/smoothened (SMO) was reported to mediate activation of autophagy in response to starvation (24), the LKB1–AMPK–MTOR signaling pathway was found to regulate PC-induced autophagy and cell volume in kidney epithelial cells under shear stress (26, 27). Whether PC are also involved in the regulation of autophagy triggered by mechanical stretching has not yet been explored.The purpose of this study is to investigate a potential role of PC in stretch-induced autophagy in TM cells. Here, we report that PC acts as a mechanosensor for CMS-induced autophagy, and we identified AKT1 and SMAD2/3 as critical components of the signal mechanotransduction.     

Macrophage LC3-associated phagocytosis is an immune defense against Streptococcus pneumoniae that diminishes with host aging

Streptococcus pneumoniae is a leading cause of pneumonia and invasive disease, particularly, in the elderly. S. pneumoniae lung infection of aged mice is associated with high bacterial burdens and detrimental inflammatory responses. Macrophages can clear microorganisms and modulate inflammation through two distinct lysosomal trafficking pathways that involve 1A/1B-light chain 3 (LC3)-marked organelles, canonical autophagy, and LC3-associated phagocytosis (LAP). The S. pneumoniae pore-forming toxin pneumolysin (PLY) triggers an autophagic response in nonphagocytic cells, but the role of LAP in macrophage defense against S. pneumoniae or in age-related susceptibility to infection is unexplored. We found that infection of murine bone-marrow-derived macrophages (BMDMs) by PLY-producing S. pneumoniae triggered Atg5- and Atg7-dependent recruitment of LC3 to S. pneumoniae-containing vesicles. The association of LC3 with S. pneumoniae-containing phagosomes required components specific for LAP, such as Rubicon and the NADPH oxidase, but not factors, such as Ulk1, FIP200, or Atg14, required specifically for canonical autophagy. In addition, S. pneumoniae was sequestered within single-membrane compartments indicative of LAP. Importantly, compared to BMDMs from young (2-mo-old) mice, BMDMs from aged (20- to 22-mo-old) mice infected with S. pneumoniae were not only deficient in LAP and bacterial killing, but also produced higher levels of proinflammatory cytokines. Inhibition of LAP enhanced S. pneumoniae survival and cytokine responses in BMDMs from young but not aged mice. Thus, LAP is an important innate immune defense employed by BMDMs to control S. pneumoniae infection and concomitant inflammation, one that diminishes with age and may contribute to age-related susceptibility to this important pathogen.

Streptococcus pneumoniae (pneumococcus) commonly colonizes the nasopharynx asymptomatically but is also capable of infecting the lower respiratory tract to cause pneumonia and spreading to the bloodstream to cause septicemia and meningitis (1). Susceptibility to pneumonia and invasive disease caused by S. pneumoniae is remarkably higher in individuals aged 65 and over, leading to high rates of mortality and morbidity in the elderly population (1, 2). In countries, such as the United States and Japan, deaths due to pneumococcal pneumonia have been on the rise in parallel with the rapid growth in the elderly population (3, 4).A hallmark of pneumococcal pneumonia is a rapid and exuberant response by immune cells, such as neutrophils and macrophages. This innate immune response to S. pneumoniae lung infection is critical for pathogen clearance and the control of disease (5–7). Deficiencies in the number or function of innate phagocytic cells, such as neutropenia (8) or macrophage phagocytic receptor defects (9–12), lead to diminished pneumococcal clearance and increased risk of invasive pneumococcal disease in both mouse models and humans. Phagocytic activity in alveolar macrophages is important during early responses to subclinical infections (13–15), and during moderate S. pneumoniae lung infection, newly generated monocytes eggress from the bone marrow and migrate into the lungs, differentiating into monocyte-derived alveolar macrophages (16). In addition to directly eliminating the invading microbe, macrophages secrete key cytokines, such as tumor necrosis factor (TNF), interleukin-1β (IL-1β), and interleukin-6 (IL-6), that regulate effector cell functions and pulmonary inflammation (17–19).Although an innate immune response is critical for pathogen clearance, poorly controlled inflammation can lead to tissue damage and mortality (20, 21). For example, in murine models, neutrophilic infiltration can enhance pulmonary damage and disrupt epithelial barrier function, leading to bacteremia and mortality (22–25). Macrophages are critical not only in regulating the early inflammatory response, but are also crucial for curtailing inflammation during the resolution phase of infection to limit tissue damage and promote healing (26, 27).Elderly individuals have higher baseline and induced levels of inflammation, a phenomenon termed inflammaging (28), that contributes to many age-associated pathological conditions, including increased susceptibility to a variety of infectious diseases, such as S. pneumoniae infection (7, 28–30). S. pneumoniae-induced inflammation, characterized by increased levels of chemokines, proinflammatory cytokines, and decreased anti-inflammatory cytokines, such as IL-10, is enhanced in the elderly (29, 31) as well as in aged mice (32, 33) and correlates with ineffective immune responses. Age-related chronic exposure to TNF-α, for instance, dampens macrophage-mediated S. pneumoniae clearance during lung infection (34), and NLR family pyrin domain containing 3 inflammasome activation in macrophages diminishes upon aging in mice (35). However, the age-related changes in macrophage effector functions leading to diminished clearance of S. pneumoniae are incompletely understood.One important means of macrophage-mediated pathogen clearance is1A/1B-light chain-3 (LC3)-associated phagocytosis (LAP), a process by which cells target phagocytosed extracellular particles for efficient degradation (36–38). LAP combines the molecular machineries of phagocytosis and autophagy, resulting in the conjugation of the autophagic marker, the microtubule-associated protein LC3, to phosphatidylethanolamine on the phagosomal membrane, generating so-called “LAPosomes” that undergo facilitated fusion with lysosomes (38, 39). Canonical autophagy targets cytoplasmic components, such as damaged subcellular organelles and intracellular microbes for sequestration into double-membrane autophagic vesicles (40, 41). In contrast, LAPosomes retain the single-membrane nature of phagosomes, and their formation requires overlapping but nonidentical genes compared to canonical autophagy (42). In addition to enabling efficient degradation of phagocytosed bacteria, LAP also plays important immune regulatory roles, such as in curtailing proinflammatory cytokine production during the subsequent innate immune response (39, 43). Indeed, the LAP-mediated microbial defense and immunomodulatory functions work together to limit tissue damage and restore homeostasis (38).S. pneumoniae triggers canonical autophagy in epithelial cells and fibroblasts, and bacteria can be found in double-membrane vacuoles whose formation is dependent on autophagic machinery (44). Many bacterial pathogens that induce autophagy produce pore-forming toxins, which can damage endosomal membranes, thus, recruiting autophagic machinery to engulf injured organelles (45). Pneumococcus-induced autophagy is dependent on the cholesterol-dependent pore-forming toxin pneumolysin (PLY), which triggers the autophagic delivery of S. pneumoniae to lysosomes and results in bacterial killing (44, 46). Recently, a kinetic examination of S. pneumoniae-targeting autophagy in fibroblasts demonstrated that canonical autophagy was preceded by early and rapid PLY-dependent LAP (47). However, the requirements for this process were somewhat different from LAP in macrophages, and the pneumococcus-containing LAPosomes did not promote bacterial clearance but required subsequent transition to canonical autophagy to reduce bacterial numbers (46, 47).In the current study, we found that S. pneumoniae infection of murine bone-marrow-derived macrophages (BMDMs) induces LAP in a PLY-dependent manners and that age-related defects in BMDM LAP contributed to diminished bactericidal activity and enhanced proinflammatory cytokine production. Our results suggest that PLY-induced LAP promotes bacterial clearance, and age-associated dysregulation of this process may contribute to enhanced bacterial survival, poorly regulated inflammation, and increased susceptibility to invasive pneumococcal disease.     

Antipsychotic drugs counteract autophagy and mitophagy in multiple sclerosis

Multiple sclerosis (MS) is a neuroinflammatory and neurodegenerative disease characterized by myelin damage followed by axonal and ultimately neuronal loss. The etiology and physiopathology of MS are still elusive, and no fully effective therapy is yet available. We investigated the role in MS of autophagy (physiologically, a controlled intracellular pathway regulating the degradation of cellular components) and of mitophagy (a specific form of autophagy that removes dysfunctional mitochondria). We found that the levels of autophagy and mitophagy markers are significantly increased in the biofluids of MS patients during the active phase of the disease, indicating activation of these processes. In keeping with this idea, in vitro and in vivo MS models (induced by proinflammatory cytokines, lysolecithin, and cuprizone) are associated with strongly impaired mitochondrial activity, inducing a lactic acid metabolism and prompting an increase in the autophagic flux and in mitophagy. Multiple structurally and mechanistically unrelated inhibitors of autophagy improved myelin production and normalized axonal myelination, and two such inhibitors, the widely used antipsychotic drugs haloperidol and clozapine, also significantly improved cuprizone-induced motor impairment. These data suggest that autophagy has a causal role in MS; its inhibition strongly attenuates behavioral signs in an experimental model of the disease. Therefore, haloperidol and clozapine may represent additional therapeutic tools against MS.

Multiple sclerosis (MS) is a neuroinflammatory disease, characterized by progressive neurological damage consisting in crumbling of the axonal myelin sheath in the central nervous system (CNS), followed by strong impairment in axonal conductance, axonal transection, and death of oligodendrocytes and neurons (1). MS onset is subacute or chronic, typically in a relapsing–remitting fashion, with phases of neuroinflammation corresponding to clinically evident disease followed by periods of oligodendrocyte proliferation, partial reconstitution of the myelin sheath, and corresponding clinical recovery. MS worsens over time, evolving into a progressive form, characterized by the disappearance of the relapsing–remitting phases and by permanent chronic lesions.Inflammation plays a central and fundamental role in MS (2). The initial phase of MS is characterized by signs of an autoimmune response including disruption of the blood–brain barrier, invasion of the CNS by immune cells, and presence of antibodies against myelin. These are believed to play a causative role in the onset of the disease. Immunological aggression is sustained by a macrophage- or microglia-driven secretion of proinflammatory cytokines, such as tumor necrosis factor alpha (TNF-α) (3, 4) or interleukin-1 beta (IL-1-β) (5, 6), which have been shown to promote neuronal, oligodendrocyte, and vascular damage in models of MS.Autophagy may also play a fundamental pathophysiological role in MS, but this has been only marginally explored thus far (1, 7). Autophagy represents a key intracellular function, which allows the cell to face periods of nutrient deprivation, meanwhile eliminating damaged and potentially harmful molecules, organelles, or invading microorganisms (8). These activities are grounded on the capacity of the cell to organize a double-membrane–lined autophagosome that, after engulfing the unwanted material, brings it to the lysosomal compartment, which in turn ensures degradation of proteins and recycling of nutrients.Many neurodegenerative diseases are characterized by pathological accumulation of misfolded or damaged proteins, suggesting an important role of autophagy in their pathophysiology (9, 10). In Alzheimer’s disease, for example, impairment of the autophagic flux due to reduced vesicle clearance has been associated to accumulation of an aggregated form of hyperphosphorylated tau protein and to extracellular amyloid-β (A-β) plaques (11). Similarly, in Parkinson’s disease, dysfunctional lysosomes and accumulation of autophagosomes are associated with intracellular inclusions of α-synuclein and other polyubiquitinated proteins.Several reports have demonstrated an increase in autophagic markers in human samples of MS patients (12). In particular, our and other groups have shown that autophagic and mitophagic markers are increased in serum and cerebrospinal fluid (CSF) of MS-affected individuals (13–15). However, the role of autophagy in MS remains still controversial. (16, 17).In this study, we investigated in detail the involvement of autophagy in MS. We used in vitro, ex vivo, and in vivo models to test the effect of proinflammatory cytokines, lysolecithin (LPC), and cuprizone (CPZ) on myelin production, axonal myelination, and motor performance. In particular, we investigated the occurrence of autophagy in the different models and examined the effect of autophagy inhibitors and of two antipsychotic drugs, clozapine and haloperidol, on autophagy and behavior, revealing a significant improvement in motor function in MS animals.The rationale for employing these antipsychotic drugs stems from neuroimaging and postmortem investigations on the brain of schizophrenia patients that revealed loss of white matter (18, 19) and down-regulation of genes involved in oligodendrocyte functioning and myelination (20, 21). Antipsychotic drugs, in particular haloperidol and clozapine, proved effective in improving cortical myelination as well as spatial working memory and locomotor activity in animal models (22–25). The molecular mechanism(s) underlying these effects are still obscure, but it has been recently suggested that these antipsychotic drugs may interfere with the autophagic process (26, 27). Our findings explore this mechanism of action of haloperidol and clozapine and disclose the opportunity of repurposing these drugs that are currently employed in other clinical settings for the treatment of MS.     

Selective autophagy of AKAP11 activates cAMP/PKA to fuel mitochondrial metabolism and tumor cell growth

Autophagy is a catabolic pathway that provides self-nourishment and maintenance of cellular homeostasis. Autophagy is a fundamental cell protection pathway through metabolic recycling of various intracellular cargos and supplying the breakdown products. Here, we report an autophagy function in governing cell protection during cellular response to energy crisis through cell metabolic rewiring. We observe a role of selective type of autophagy in direct activation of cyclic AMP protein kinase A (PKA) and rejuvenation of mitochondrial function. Mechanistically, autophagy selectively degrades the inhibitory subunit RI of PKA holoenzyme through A-kinase–anchoring protein (AKAP) 11. AKAP11 acts as an autophagy receptor that recruits RI to autophagosomes via LC3. Glucose starvation induces AKAP11-dependent degradation of RI, resulting in PKA activation that potentiates PKA-cAMP response element-binding signaling, mitochondria respiration, and ATP production in accordance with mitochondrial elongation. AKAP11 deficiency inhibits PKA activation and impairs cell survival upon glucose starvation. Our results thus expand the view of autophagy cytoprotection mechanism by demonstrating selective autophagy in RI degradation and PKA activation that fuels the mitochondrial metabolism and confers cell resistance to glucose deprivation implicated in tumor growth.

Macroautophagy (henceforth autophagy) is a catabolic process that degrades various cellular cargos through lysosomes. The autophagy process includes the formation and trafficking of autophagosomes, which sequester the cellular cargos destined for the clearance. Autophagy is activated in response to nutrient deprivation or cellular injuries and serves as a recycling mechanism that maintains cellular homeostasis through degradation of cytoplasmic components. Autophagy provides cell self-nourishment and supports cellular metabolism by supplying breakdown products (1, 2); therefore, autophagy is a fundamental cell protection mechanism. Whether autophagy has a direct function beyond recycling of the breakdown molecules to maintain metabolic homeostasis and cell survival, however, is poorly understood. In certain cancer types, autophagy plays an important role in sustaining the aggressive growth of the tumor cells by enhancing cell metabolism. Although our group and others have previously shown an inhibitory function of Beclin 1–mediated autophagy in tumorigenesis (3, 4), the current view is that tumors, once established, rely heavily on autophagy to survive due to high metabolic demand. One potential mechanism is that the metabolic products generated by autophagy provide tumor cells with metabolic rewiring that enables them to survive even under nutrient-poor conditions (5, 6). However, it remains unclear whether autophagy plays a role beyond the production of metabolic fuel sources to maintain metabolic plasticity and tumor cell growth.Available evidence has demonstrated the selectivity of autophagy in the digestion of certain cellular cargoes mediated by autophagy adaptors/receptors. Characterization of the autophagy adaptors has shed light on the versatile physiological function of autophagy in the maintenance of the homeostasis for large molecules and cellular organelles (7, 8). These adaptors recognize and recruit selective cargos to autophagy machinery for degradation through direct interaction with yeast autophagy gene Atg8 homologs of mammalian LC3/GABARAP/Gate16 proteins. While a few autophagy receptors have been reported, it is clear that many more are yet to be identified (7, 8).The best-known signaling pathways that control the metabolic stress-induced autophagy are mediated by mTOR and AMPK kinases, both of which are the master regulators for cellular metabolism (9, 10). Cyclic adenosine monophosphate (cAMP)-dependent protein kinase (PKA) is also a key kinase of cell metabolism that governs diverse cellular pathways, including cellular glucose metabolism and bioenergetic processes (11–13). Surprisingly, whether and how cAMP/PKA regulates autophagy or vice versa is poorly understood in mammals (14–16). cAMP/PKA signaling has emerged over recent years as a key regulator for mitochondrial functions, highlighting the mechanism of cAMP/PKA in cellular metabolism control (17, 18). Despite an established role for PKA in the regulation of mitochondrial metabolism, whether autophagy and PKA converge to regulate metabolic reprogramming and cell survival remains unknown.The PKA holoenzyme consists of two regulatory subunits (R) and two catalytic subunits (C). The R subunits are inhibitory of catalytic kinase activity; upon binding to cAMP, the R subunit dissociates from C subunit, resulting in activation of PKA (19). Furthermore, the specific cellular functions of PKA are controlled by a number of A-kinase–anchoring proteins (AKAPs). The AKAPs bind the R subunits and restrict the PKA holoenzyme to various intracellular compartments, providing spatiotemporal regulation of PKA activity (20). However, the functions of many AKAPs are poorly characterized.Here, we report a role of autophagy that controls cellular metabolism beyond the production of metabolic sources—it activates cAMP/PKA kinase activity by selective degradation of the inhibitory subunit of R1α through autophagy receptor AKAP11 in response to glucose starvation. AKAP11-mediated cAMP/PKA activation leads to elevation of mitochondrial metabolism and cell protection. Our study reveals a previously unrecognized function of autophagy in metabolic rewiring of cells that promote cell survival under energy crisis. Our study thus suggests that selective autophagy induced RI degradation and PKA activation may contribute to the resistance of tumor cells to metabolic stress.     

Electrochromic shift supports the membrane destabilization model of Tat-mediated transport and shows ion leakage during Sec transport

The mechanism and pore architecture of the Tat complex during transport of folded substrates remain a mystery, partly due to rapid dissociation after translocation. In contrast, the proteinaceous SecY pore is a persistent structure that needs only to undergo conformational shifts between “closed” and “opened” states when translocating unfolded substrate chains. Where the proteinaceous pore model describes the SecY pore well, the toroidal pore model better accounts for the high-energy barrier that must be overcome when transporting a folded substrate through the hydrophobic bilayer in Tat transport. Membrane conductance behavior can, in principle, be used to distinguish between toroidal and proteinaceous pores, as illustrated in the examination of many antimicrobial peptides as well as mitochondrial Bax and Bid. Here, we measure the electrochromic shift (ECS) decay as a proxy for conductance in isolated thylakoids, both during protein transport and with constitutively assembled translocons. We find that membranes with the constitutively assembled Tat complex and those undergoing Tat transport display conductance characteristics similar to those of resting membranes. Membranes undergoing Sec transport and those with the substrate-engaged SecY pore result in significantly more rapid electric field decay. The responsiveness of the ECS signal in membranes with active SecY recalls the steep relationship between applied voltage and conductance in a proteinaceous pore, while the nonaccelerated electric field decay with both Tat transport and the constitutive Tat complex under the same electric field is consistent with the behavior of a toroidal pore.

The twin arginine translocation pathway is uniquely able to transport fully folded substrates in an ATP-independent manner, relying instead on an electrochemical gradient (i.e., the proton motive force, or pmf) across the transporting membrane. It is crucial to the transport of substrates requiring various cofactors and hetero-oligomeric complexes in prokaryotes and of substrates vital to photosynthetic machinery in thylakoids (1). In plant mitochondria, the Rieske Fe/S protein required for the biogenesis of complex III is transported by the Tat pathway (2–6). It is implicated in both the virulence and antibiotic resistance of various infectious bacteria (7–12) and has been studied for its potential in biotechnology applications (13–15). The uniqueness of Tat functionality and its appearance across the kingdoms of life make it a valuable research target for crop modification, biotechnology, and pathogenesis. Unfortunately, much of the knowledge about its mechanism has been hard won, and the pore structure remains a mystery, likely due to the transient nature of the active complex.The active Tat complex in thylakoids consists of three core subunits, Tha4, Hcf106, and cpTatC, which are homologous to the bacterial TatA, TatB, and TatC, respectively (1, 16). An N-terminal signal peptide with a twin-arginine motif inserts into the cis-side leaflet at the TatBC receptor complex (17–19). Subsequent oligomerization of TatA subunits (20–22) at the TatBC receptor complex results in rings of varying sizes (22, 23), but it is unclear whether these structures represent transport pores. Of particular note is the short TatA transmembrane helix (TMH). Composed of only 16 residues, the solid-state NMR solution suggests that the TMH must tilt and draw a portion of the cis-side amphipathic helix (APH) into the membrane in order to cross the bilayer (24), establishing a resting state of hydrophobic mismatch. During transport, a conformational shift increasing the angle between the TMH and APH results in exacerbated hydrophobic mismatch, as the APH is moved radially away from the center and the TMH is pulled up toward the cis-side in the active state (25, 26). For both native and foreign substrates, the Tat-targeted signal peptide and the pmf are sufficient to cause assembly of the active translocon and achieve transport (27–31). After the translocation event, the complex dissociates into TatA and TatBC components (1, 15, 16) with the exception of some residual TatA bound to the receptor complex in a nonactive state and a spectrum of smaller TatA oligomers (32).Within the thylakoid membrane, it is useful to compare the Tat complex with the general secretory translocon (Sec) because they both function in the same membrane environment (1, 33). Sec translocation first requires recruitment of the substrate to the soluble SecA ATPase to form the substrate–SecA complex, which is then recruited to the SecY pore (1). In the inactive state, the proteinaceous SecY pore prevents ion leakage through a combination of a trans-side plug domain and an internal array of hydrophobic residues (34). Following substrate–SecA docking, a conformational shift in SecY allows substrate movement through the open pore in an ATP-dependent process driven by SecA (35). In the mammalian homolog Sec61, leakage of NAD⁺ ions is recorded during ribosome-bound nascent chain transport in a fluorescence quenching study, suggesting the pore can reach 4 to 6 nm in diameter (36). However, X-ray structures of substrate-fused SecA complexed with SecY (35), conductance studies in ribosome-bound substrates engaged with SecY (37), and SecY plug deletion mutants (38) in Escherichia coli have estimated the open SecY pore diameter to range from 7.3 to 8.8 Å, almost 10-fold lower. This small diameter likely contributes to the restriction of ion movement during Sec transport (39).While the Sec machinery only transports unfolded substrates (40), the Tat pore accommodates substrates ranging from a single unfolded chain in an engineered system (13) to a folded substrate with an average diameter of 70 Å (41). This extended size range raises an interesting question about the pore architecture. In the Sec translocon, X-ray crystallography of the SecY channel in Methanocaldococcus jannaschii (42) and Thermotoga maritima (43) reveals that the SecY pore channel excludes lipids in both the resting state and when engaged with its SecA partner. Further structural work on the E. coli substrate-engaged SecA–SecY complex shows that the SecY channel excludes lipids during transport as well (35). No such structural information about the Tat pore exists, but functional data suggest that TatA plays an important role in the pore (20, 44, 45) and cryogenic electron microscopy structures of TatA oligomers reveal rings of an internal diameter ranging from 30 to 70 Å (23). During transport of the 17-kDa subunit of the oxygen-evolving complex (OE23), the Tat pathway exhibits very low ion leakage (46), estimated to be less than 1 pS. This is despite the exchange of 80,000 protons per substrate (47). Extensive mapping of subunit–subunit and subunit–substrate contacts has revealed no putative plug domain (20, 48–51) that could be compared to that in the SecY protein.Pore architecture can be characterized by membrane conductance behavior. Conductance measured through proteinaceous pores representing the barrel-stave model has a very steep dependence on the voltage applied, whereas conductance in toroidal pores requires a larger voltage to be detected and increases more slowly in response to increasing voltage (52–54). Performing similar experiments on the Tat and Sec translocons would require functional reconstitution of both complexes into an in vitro setting. However, decay of the electrochromic shift (ECS) signal can be used as a measure of ion conductance (46). A transient absorption peak at ∼515 nm arising from carotenoid pigments in response to the native electric field generated by charge separation in the photosynthetic reaction centers (55) can be measured by delivering a single-saturating flash. The decay rate of such a signal is a direct measurement of how quickly the electric field is dissipated by ion movement across the membrane.In the experiments reported herein, ECS signal decay rates revealing the conductance states of resting isolated membranes and those engaged in ongoing transport and in the presence of a constitutively assembled and/or substrate-engaged translocon are used to probe the pore architecture in the Tat and Sec complexes. Increased conductance across the thylakoid membrane is indicated by a more rapidly decaying ECS signal. We find that conductance in thylakoid membranes during Sec-mediated transport and substrate-engaged SecY is consistently higher than that during Tat-mediated transport and with the constitutively assembled Tat complex, respectively, despite the much larger Tat pore required to transport a fully folded substrate. This points to a difference not only in mechanism but in pore architecture between the two. Conductance behavior of membranes undergoing Sec-mediated transport is consistent with that of a proteinaceous pore, while the resistance demonstrated by membranes undergoing Tat-mediated transport is more reminiscent of toroidal pores.     

Conditional destabilization of the TPLATE complex impairs endocytic internalization

In plants, endocytosis is essential for many developmental and physiological processes, including regulation of growth and development, hormone perception, nutrient uptake, and defense against pathogens. Our toolbox to modulate this process is, however, rather limited. Here, we report a conditional tool to impair endocytosis. We generated a partially functional TPLATE allele by substituting the most conserved domain of the TPLATE subunit of the endocytic TPLATE complex (TPC). This substitution destabilizes TPC and dampens the efficiency of endocytosis. Short-term heat treatment increases TPC destabilization and reversibly delocalizes TPLATE from the plasma membrane to aggregates in the cytoplasm. This blocks FM uptake and causes accumulation of various known endocytic cargoes at the plasma membrane. Short-term heat treatment therefore transforms the partially functional TPLATE allele into an effective conditional tool to impair endocytosis. Next to their role in endocytosis, several TPC subunits are also implicated in actin-regulated autophagosomal degradation. Inactivating TPC via the WDX mutation, however, does not impair autophagy, thus enabling specific and reversible modulation of endocytosis in planta.

Endocytosis is an evolutionarily conserved eukaryotic pathway by which extracellular material and plasma membrane (PM) components are internalized via vesicles (1, 2). Clathrin-mediated endocytosis (CME), relying on the scaffolding protein clathrin, is the most prominent and the most studied endocytic pathway (3–5). As clathrin does not interact directly with the PM, nor does it recognize cargoes, adaptor proteins are required to act as essential links between the clathrin coat and the PM (6). In plant cells, material selected for CME is recognized by two adaptor complexes, the adaptor complex 2 (AP-2) and the TPLATE complex (TPC) (7–9). In contrast to TPC, single subunit mutants of AP-2 are viable (7, 8, 10–13) and AP-2 recruitment and dynamics appear to rely on TPC function (8, 14).TPC represents an ancestral adaptor complex, which is however absent in present-day metazoans and yeasts. It was experimentally identified as an octameric complex in Arabidopsis and as a hexametric complex in Dictyostelium (8, 15). Plants, however, are the only eukaryotic supergroup identified so far where TPC is essential for life (8, 15), as knockout or severe knockdown of single subunits of TPC in Arabidopsis leads to pollen or seedling lethality, respectively (8, 13). Two TPC subunits, AtEH1/Pan1 and AtEH2/Pan1, were not associated with the other TPC core components when the complex was forced into the cytoplasm by truncating the TML subunit and did not copurify with the other TSET components in Dictyostelium. This indicates that they may be auxiliary components to the core TPC (8, 15). These AtEH/Pan1 proteins were recently identified as important players in actin-regulated autophagy in plants. AtEH/Pan1 proteins recruit several components of the endocytic machinery to the autophagosomes, and are degraded together with them under stress conditions (16). However, whether this pathway serves to degrade specific cargoes or to regulate the endocytic machinery itself (17), and whether the whole TPC is required for this degradation pathway, remains unclear.Genetic and chemical tools to manipulate endocytosis have been extensively investigated via interfering with the functions of endocytic players, such as clathrin (18–22), adaptor proteins (7, 10–12, 14, 23–25), and dynamin-related proteins (26–30). The chemical inhibitors originally used to affect CME in plants have recently been described to possess undesirable side effects (31) or to affect proteins that are not only specific for endocytosis: for example, clathrin itself, as it is also involved in TGN trafficking (19, 22). The same is true for several genetic tools currently available to affect CME in plants (18, 21, 22, 30). Manipulation of TPC, functioning exclusively at the PM, represents a very good candidate to affect CME more specifically. So far however, there are no chemical tools to target TPC functions or dominant-negative mutants available. Inducible silencing works, but causes seedling lethality and takes several days to become effective (8). The only tools to manipulate TPC function in viable plants consist of knock-down mutants with very mild reduction of expression and consequently similar mild effects on CME (8, 14, 16, 32).     

Autophagy is required for proper cysteine homeostasis in pancreatic cancer through regulation of SLC7A11

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest forms of cancer and is highly refractory to current therapies. We had previously shown that PDAC can utilize its high levels of basal autophagy to support its metabolism and maintain tumor growth. Consistent with the importance of autophagy in PDAC, autophagy inhibition significantly enhances response of PDAC patients to chemotherapy in two randomized clinical trials. However, the specific metabolite(s) that autophagy provides to support PDAC growth is not yet known. In this study, we demonstrate that under nutrient-replete conditions, loss of autophagy in PDAC leads to a relatively restricted impairment of amino acid pools, with cysteine levels showing a significant drop. Additionally, we made the striking discovery that autophagy is critical for the proper membrane localization of the cystine transporter SLC7A11. Mechanistically, autophagy impairment results in the loss of SLC7A11 on the plasma membrane and increases its localization at the lysosome in an mTORC2-dependent manner. Our results demonstrate a critical link between autophagy and cysteine metabolism and provide mechanistic insights into how targeting autophagy can cause metabolic dysregulation in PDAC.

Despite progress in cancer therapy, the prognosis for pancreatic ductal adenocarcinoma (PDAC) remains extremely poor with a 5-y survival rate of just 9% and it is predicted to become the second leading cause of cancer death in the United States by 2030 (1–3). The PDAC tumor microenvironment is highly desmoplastic and is composed of heterogeneous cell types, as well as an exuberant extracellular matrix. Together, this leads to poor perfusion and extreme hypoxia, creating a nutrient-limited environment with impaired drug penetration (4, 5). Another hallmark of PDAC is elevated basal autophagy which plays multiple protumorigenic roles, including promoting immune evasion and supporting its metabolic demand in this austere microenvironment (6–10). Therefore, clinical strategies have been employed to inhibit autophagy in PDAC patients using lysosomal inhibitors such as chloroquine or hydroxychloroquine (11, 12).While autophagy can support diverse metabolic processes through the degradation of various cargo, how it supports PDAC metabolism has not been fully elucidated. In the present study, we found that autophagy has a selective role in sustaining cysteine (Cys) pools in PDAC. One of the major mechanisms of Cys homeostasis is through the import of cystine (the oxidized dimer of cysteine) through system x_c⁻, a cystine/glutamate antiporter composed of SLC7A11 (xCT) and SLC3A2 (13). Recently, it was shown that both Cys and SLC7A11 are critical for PDAC growth (14). Here, we report that under low Cys conditions, SLC7A11 utilizes autophagy machinery to allow localization at the plasma membrane. Moreover, we demonstrate that loss of autophagy increases phosphorylation of SLC7A11 by mTORC2, and it remains primarily localized at the lysosome where its cystine import function is impaired. In summary, we identify a mechanism of Cys homeostasis in PDAC where the function of SLC7A11 is coordinately sustained by autophagic machinery and mTORC2 activity based on intracellular Cys levels.     

Circular swimming motility and disordered hyperuniform state in an algae system

Active matter comprises individually driven units that convert locally stored energy into mechanical motion. Interactions between driven units lead to a variety of nonequilibrium collective phenomena in active matter. One of such phenomena is anomalously large density fluctuations, which have been observed in both experiments and theories. Here we show that, on the contrary, density fluctuations in active matter can also be greatly suppressed. Our experiments are carried out with marine algae (Effrenium voratum), which swim in circles at the air–liquid interfaces with two different eukaryotic flagella. Cell swimming generates fluid flow that leads to effective repulsions between cells in the far field. The long-range nature of such repulsive interactions suppresses density fluctuations and generates disordered hyperuniform states under a wide range of density conditions. Emergence of hyperuniformity and associated scaling exponent are quantitatively reproduced in a numerical model whose main ingredients are effective hydrodynamic interactions and uncorrelated random cell motion. Our results demonstrate the existence of disordered hyperuniform states in active matter and suggest the possibility of using hydrodynamic flow for self-assembly in active matter.

Active matter exists over a wide range of spatial and temporal scales (1–6) from animal groups (7, 8) to robot swarms (9–11), to cell colonies and tissues (12–16), to cytoskeletal extracts (17–20), to man-made microswimmers (21–25). Constituent particles in active matter systems are driven out of thermal equilibrium at the individual level; they interact to develop a wealth of intriguing collective phenomena, including clustering (13, 22, 24), flocking (11, 26), swarming (12, 13), spontaneous flow (14, 20), and giant density fluctuations (10, 11). Many of these observed phenomena have been successfully described by particle-based or continuum models (1–6), which highlight the important roles of both individual motility and interparticle interactions in determining system dynamics.Current active matter research focuses primarily on linearly swimming particles which have a symmetric body and self-propel along one of the symmetry axes. However, a perfect alignment between the propulsion direction and body axis is rarely found in reality. Deviation from such a perfect alignment leads to a persistent curvature in the microswimmer trajectories; examples of such circle microswimmers include anisotropic artificial micromotors (27, 28), self-propelled nematic droplets (29, 30), magnetotactic bacteria and Janus particles in rotating external fields (31, 32), Janus particle in viscoelastic medium (33), and sperm and bacteria near interfaces (34, 35). Chiral motility of circle microswimmers, as predicted by theoretical and numerical investigations, can lead to a range of interesting collective phenomena in circular microswimmers, including vortex structures (36, 37), localization in traps (38), enhanced flocking (39), and hyperuniform states (40). However, experimental verifications of these predictions are limited (32, 35), a situation mainly due to the scarcity of suitable experimental systems.Here we address this challenge by investigating marine algae Effrenium voratum (41, 42). At air–liquid interfaces, E. voratum cells swim in circles via two eukaryotic flagella: a transverse flagellum encircling the cellular anteroposterior axis and a longitudinal one running posteriorly. Over a wide range of densities, circling E. voratum cells self-organize into disordered hyperuniform states with suppressed density fluctuations at large length scales. Hyperuniformity (43, 44) has been considered as a new form of material order which leads to novel functionalities (45–49); it has been observed in many systems, including avian photoreceptor patterns (50), amorphous ices (51), amorphous silica (52), ultracold atoms (53), soft matter systems (54–61), and stochastic models (62–64). Our work demonstrates the existence of hyperuniformity in active matter and shows that hydrodynamic interactions can be used to construct hyperuniform states.     

Neuromodulator release in neurons requires two functionally redundant calcium sensors

Neuropeptides and neurotrophic factors secreted from dense core vesicles (DCVs) control many brain functions, but the calcium sensors that trigger their secretion remain unknown. Here, we show that in mouse hippocampal neurons, DCV fusion is strongly and equally reduced in synaptotagmin-1 (Syt1)- or Syt7-deficient neurons, but combined Syt1/Syt7 deficiency did not reduce fusion further. Cross-rescue, expression of Syt1 in Syt7-deficient neurons, or vice versa, completely restored fusion. Hence, both sensors are rate limiting, operating in a single pathway. Overexpression of either sensor in wild-type neurons confirmed this and increased fusion. Syt1 traveled with DCVs and was present on fusing DCVs, but Syt7 supported fusion largely from other locations. Finally, the duration of single DCV fusion events was reduced in Syt1-deficient but not Syt7-deficient neurons. In conclusion, two functionally redundant calcium sensors drive neuromodulator secretion in an expression-dependent manner. In addition, Syt1 has a unique role in regulating fusion pore duration.

To date, over 100 genes encoding neuropeptides and neurotrophic factors, together referred to as neuromodulators, are identified, and most neurons express neuromodulators and neuromodulator receptors (1). Neuromodulators travel through neurons in dense core vesicles (DCVs) and, upon secretion, regulate neuronal excitability, synaptic plasticity, and neurite outgrowth (2–4). Dysregulation of DCV secretion is linked to many brain disorders (5–7). However, the molecular mechanisms that regulate neuromodulator secretion remain largely elusive.Neuromodulator secretion, like neurotransmitter secretion from synaptic vesicles (SVs), is tightly controlled by Ca²⁺. The Ca²⁺ sensors that regulate secretion have been described for other secretory pathways but not for DCV exocytosis in neurons. Synaptotagmin (Syt) and Doc2a/b are good candidate sensors due to their interaction with SNARE complexes, phospholipids, and Ca²⁺ (8–11). The Syt family consists of 17 paralogs (12, 13). Eight show Ca²⁺-dependent lipid binding: Syt1 to 3, Syt5 to 7, and Syt9 and 10 (14, 15). Syt1 mediates synchronous SV fusion (8), consistent with its low Ca²⁺-dependent lipid affinity (15, 16) and fast Ca²⁺/membrane dissociation kinetics (16, 17). Syt1 is also required for the fast fusion in chromaffin cells (18) and fast striatal dopamine release (19). Synaptotagmin-7 (Syt7), in contrast, drives asynchronous SV fusion (20), in line with its a higher Ca²⁺ affinity (15) and slower dissociation kinetics (16). Syt7 is also a major calcium sensor for neuroendocrine secretion (21) and secretion in pancreatic cells (22–24). Other sensors include Syt4, which negatively regulates brain-derived neurothropic factor (25) and oxytocin release (26), in line with its Ca²⁺ independency. Syt9 regulates hormone secretion in the anterior pituitary (27) and, together with Syt1, secretion from PC12 cells (28, 29). Syt10 controls growth factor secretion (30). However, Syt9 and Syt10 expression is highly restricted in the brain (31–33). Hence, the calcium sensors for neuronal DCV fusion remain largely elusive. Because DCVs are generally not located close to Ca²⁺ channels (34), we hypothesized that DCV fusion is triggered by high-affinity Ca²⁺ sensors. Because of their important roles in vesicle secretion, their Ca²⁺ binding ability, and their high expression levels in the brain (20, 31, 35–38), we addressed the roles of Doc2a/b, Syt1, and Syt7 in neuronal DCV fusion.In this study, we used primary Doc2a/b-, Syt1-, and Syt7-null (knockout, KO) neurons expressing DCV fusion reporters (34, 39–41) with single-vesicle resolution. We show that both Syt1 and Syt7, but not Doc2a/b, are required for ∼60 to 90% of DCV fusion events. Deficiency of both Syt1 and Syt7 did not produce an additive effect, suggesting they function in the same pathway. Syt1 overexpression (Syt1-OE) rescued DCV fusion in Syt7-null neurons, and vice versa, indicating that the two proteins compensate for each other in DCV secretion. Moreover, overexpression of Syt1 or Syt7 in wild-type (WT) neurons increased DCV fusion, suggesting they are both rate limiting for DCV secretion. We conclude that DCV fusion requires two calcium sensors, Syt1 and Syt7, that act in a single/serial pathway and that both sensors regulate fusion in a rate-limiting and dose-dependent manner.     

INAUGURAL ARTICLE by a Recently Elected Academy Member:The effect of parathyroid hormone on osteogenesis is mediated partly by osteolectin

We previously described a new osteogenic growth factor, osteolectin/Clec11a, which is required for the maintenance of skeletal bone mass during adulthood. Osteolectin binds to Integrin α11 (Itga11), promoting Wnt pathway activation and osteogenic differentiation by leptin receptor⁺ (LepR⁺) stromal cells in the bone marrow. Parathyroid hormone (PTH) and sclerostin inhibitor (SOSTi) are bone anabolic agents that are administered to patients with osteoporosis. Here we tested whether osteolectin mediates the effects of PTH or SOSTi on bone formation. We discovered that PTH promoted Osteolectin expression by bone marrow stromal cells within hours of administration and that PTH treatment increased serum osteolectin levels in mice and humans. Osteolectin deficiency in mice attenuated Wnt pathway activation by PTH in bone marrow stromal cells and reduced the osteogenic response to PTH in vitro and in vivo. In contrast, SOSTi did not affect serum osteolectin levels and osteolectin was not required for SOSTi-induced bone formation. Combined administration of osteolectin and PTH, but not osteolectin and SOSTi, additively increased bone volume. PTH thus promotes osteolectin expression and osteolectin mediates part of the effect of PTH on bone formation.

The maintenance and repair of the skeleton require the generation of new bone cells throughout adult life. Osteoblasts are relatively short-lived cells that are constantly regenerated, partly by skeletal stem cells within the bone marrow (1). The main source of new osteoblasts in adult bone marrow is leptin receptor-expressing (LepR⁺) stromal cells (2–4). These cells include the multipotent skeletal stem cells that give rise to the fibroblast colony-forming cells (CFU-Fs) in the bone marrow (2), as well as restricted osteogenic progenitors (5) and adipocyte progenitors (6–8). LepR⁺ cells are a major source of osteoblasts for fracture repair (2) and growth factors for hematopoietic stem cell maintenance (9–11).One growth factor synthesized by LepR⁺ cells, as well as osteoblasts and osteocytes, is osteolectin/Clec11a, a secreted glycoprotein of the C-type lectin domain superfamily (5, 12, 13). Osteolectin is an osteogenic factor that promotes the maintenance of the adult skeleton by promoting the differentiation of LepR⁺ cells into osteoblasts. Osteolectin acts by binding to integrin α11β1, which is selectively expressed by LepR⁺ cells and osteoblasts, activating the Wnt pathway (12). Deficiency for either Osteolectin or Itga11 (the gene that encodes integrin α11) reduces osteogenesis during adulthood and causes early-onset osteoporosis in mice (12, 13). Recombinant osteolectin promotes osteogenic differentiation by bone marrow stromal cells in culture and daily injection of mice with osteolectin systemically promotes bone formation.Osteoporosis is a progressive condition characterized by reduced bone mass and increased fracture risk (14). Several factors contribute to osteoporosis development, including aging, estrogen insufficiency, mechanical unloading, and prolonged glucocorticoid use (14). Existing therapies include antiresorptive agents that slow bone loss, such as bisphosphonates (15, 16) and estrogens (17), and anabolic agents that increase bone formation, such as parathyroid hormone (PTH) (18), PTH-related protein (19), and sclerostin inhibitor (SOSTi) (20). While these therapies increase bone mass and reduce fracture risk, they are not a cure.PTH promotes both anabolic and catabolic bone remodeling (21–24). PTH is synthesized by the parathyroid gland and regulates serum calcium levels, partly by regulating bone formation and bone resorption (23–25). PTH1R is a PTH receptor (26, 27) that is strongly expressed by LepR⁺ bone marrow stromal cells (8, 28–30). Recombinant human PTH (Teriparatide; amino acids 1 to 34) and synthetic PTH-related protein (Abaloparatide) are approved by the US Food and Drug Administration (FDA) for the treatment of osteoporosis (19, 31). Daily (intermittent) administration of PTH increases bone mass by promoting the differentiation of osteoblast progenitors, inhibiting osteoblast and osteocyte apoptosis, and reducing sclerostin levels (32–35). PTH promotes osteoblast differentiation by activating Wnt and BMP signaling in bone marrow stromal cells (28, 36, 37), although the mechanisms by which it regulates Wnt pathway activation are complex and uncertain (38).Sclerostin is a secreted glycoprotein that inhibits Wnt pathway activation by binding to LRP5/6, a widely expressed Wnt receptor (7, 8), reducing bone formation (39, 40). Sclerostin is secreted by osteocytes (8, 41), negatively regulating bone formation by inhibiting the differentiation of osteoblasts (41, 42). SOSTi (Romosozumab) is a humanized monoclonal antibody that binds sclerostin, preventing binding to LRP5/6 and increasing Wnt pathway activation and bone formation (43). It is FDA-approved for the treatment of osteoporosis (20, 44) and has activity in rodents in addition to humans (45, 46).The discovery that osteolectin is a bone-forming growth factor raises the question of whether it mediates the effects of PTH or SOSTi on osteogenesis.     

Chemokine CCL5 promotes robust optic nerve regeneration and mediates many of the effects of CNTF gene therapy

Ciliary neurotrophic factor (CNTF) is a leading therapeutic candidate for several ocular diseases and induces optic nerve regeneration in animal models. Paradoxically, however, although CNTF gene therapy promotes extensive regeneration, recombinant CNTF (rCNTF) has little effect. Because intraocular viral vectors induce inflammation, and because CNTF is an immune modulator, we investigated whether CNTF gene therapy acts indirectly through other immune mediators. The beneficial effects of CNTF gene therapy remained unchanged after deleting CNTF receptor alpha (CNTFRα) in retinal ganglion cells (RGCs), the projection neurons of the retina, but were diminished by depleting neutrophils or by genetically suppressing monocyte infiltration. CNTF gene therapy increased expression of C-C motif chemokine ligand 5 (CCL5) in immune cells and retinal glia, and recombinant CCL5 induced extensive axon regeneration. Conversely, CRISPR-mediated knockdown of the cognate receptor (CCR5) in RGCs or treating wild-type mice with a CCR5 antagonist repressed the effects of CNTF gene therapy. Thus, CCL5 is a previously unrecognized, potent activator of optic nerve regeneration and mediates many of the effects of CNTF gene therapy.

Like most pathways in the mature central nervous system (CNS), the optic nerve cannot regenerate once damaged due in part to cell-extrinsic suppressors of axon growth (1, 2) and the low intrinsic growth capacity of adult retinal ganglion cells (RGCs), the projection neurons of the eye (3–5). Consequently, traumatic or ischemic optic nerve injury or degenerative diseases such as glaucoma lead to irreversible visual losses. Experimentally, some degree of regeneration can be induced by intraocular inflammation or growth factors expressed by inflammatory cells (6–10), altering the cell-intrinsic growth potential of RGCs (3–5), enhancing physiological activity (11, 12), chelating free zinc (13, 14), and other manipulations (15–19). However, the extent of regeneration achieved to date remains modest, underlining the need for more effective therapies.Ciliary neurotrophic factor (CNTF) is a leading therapeutic candidate for glaucoma and other ocular diseases (20–23). Activation of the downstream signal transduction cascade requires CNTF to bind to CNTF receptor-α (CNTFRα) (24), which leads to recruitment of glycoprotein 130 (gp130) and leukemia inhibitory factor receptor-β (LIFRβ) to form a tripartite receptor complex (25). CNTFRα anchors to the plasma membrane through a glycosylphosphatidylinositol linkage (26) and can be released and become soluble through phospholipase C-mediated cleavage (27). CNTF has been reported to activate STAT3 phosphorylation in retinal neurons, including RGCs, and to promote survival, but it is unknown whether these effects are mediated by direct action of CNTF on RGCs via CNTFRα (28). Our previous studies showed that CNTF promotes axon outgrowth from neonate RGCs in culture (29) but fails to do so in cultured mature RGCs (8) or in vivo (6). Although some studies report that recombinant CNTF (rCNTF) can promote optic nerve regeneration (20, 30, 31), others find little or no effect unless SOCS3 (suppressor of cytokine signaling-3), an inhibitor of the Jak-STAT pathway, is deleted in RGCs (5, 6, 32). In contrast, multiple studies show that adeno-associated virus (AAV)-mediated expression of CNTF in RGCs induces strong regeneration (33–40). The basis for the discrepant effects of rCNTF and CNTF gene therapy is unknown but is of considerable interest in view of the many promising clinical and preclinical outcomes obtained with CNTF to date.Because intravitreal virus injections induce inflammation (41), we investigated the possibility that CNTF, a known immune modulator (42–44), might act by elevating expression of other immune-derived factors. We report here that the beneficial effects of CNTF gene therapy in fact require immune system activation and elevation of C-C motif chemokine ligand 5 (CCL5). Depletion of neutrophils, global knockout (KO) or RGC-selective deletion of the CCL5 receptor CCR5, or a CCR5 antagonist all suppress the effects of CNTF gene therapy, whereas recombinant CCL5 (rCCL5) promotes axon regeneration and increases RGC survival. These studies point to CCL5 as a potent monotherapy for optic nerve regeneration and to the possibility that other applications of CNTF and other forms of gene therapy might similarly act indirectly through other factors.     

Improved bounds on entropy production in living systems

Living systems maintain or increase local order by working against the second law of thermodynamics. Thermodynamic consistency is restored as they consume free energy, thereby increasing the net entropy of their environment. Recently introduced estimators for the entropy production rate have provided major insights into the efficiency of important cellular processes. In experiments, however, many degrees of freedom typically remain hidden to the observer, and, in these cases, existing methods are not optimal. Here, by reformulating the problem within an optimization framework, we are able to infer improved bounds on the rate of entropy production from partial measurements of biological systems. Our approach yields provably optimal estimates given certain measurable transition statistics. In contrast to prevailing methods, the improved estimator reveals nonzero entropy production rates even when nonequilibrium processes appear time symmetric and therefore may pretend to obey detailed balance. We demonstrate the broad applicability of this framework by providing improved bounds on the energy consumption rates in a diverse range of biological systems including bacterial flagella motors, growing microtubules, and calcium oscillations within human embryonic kidney cells.

Thermodynamic laws place fundamental limits on the efficiency and fitness of living systems (1, 2). To maintain cellular order and perform essential biological functions such as sensing (3–6), signaling (7), replication (8, 9) or locomotion (10), organisms consume energy and dissipate heat. In doing so, they increase the entropy of their environment (2), in agreement with the second law of thermodynamics (11). Obtaining reliable estimates for the energy consumption and entropy production in living matter holds the key to understanding the physical boundaries (12–14) that constrain the range of theoretically and practically possible biological processes (3). Recent experimental (6, 15, 16) and theoretical (17–20) advances in the imaging and modeling of cellular and subcellular dynamics have provided groundbreaking insights into the thermodynamic efficiency of molecular motors (14, 21), biochemical signaling (16, 22, 23) and reaction (24) networks, and replication (9) and adaption (25) phenomena. Despite such major progress, however, it is also known that the currently available entropy production estimators (26, 27) can fail under experimentally relevant conditions, especially when only a small set of observables is experimentally accessible or nonequilibrium transport currents (28–30) vanish.To help overcome these limitations, we introduce here a generic optimization framework that can produce significantly improved bounds on the entropy production in living systems. We will prove that these bounds are optimal given certain measurable statistics. From a practical perspective, our method requires observations of only a few coarse-grained state variables of an otherwise hidden Markovian network. We demonstrate the practical usefulness by determining improved entropy production bounds for bacterial flagella motors (10, 31), growing microtubules (32, 33), and calcium oscillations (7, 34) in human embryonic kidney cells.Generally, entropy production rates can be estimated from the time series of stochastic observables (35). Thermal equilibrium systems obey the principle of detailed balance, which means that every forward trajectory is as likely to be observed as its time reversed counterpart, neutralizing the arrow of time (36). By contrast, living organisms operate far from equilibrium, which means that the balance between forward and reversed trajectories is broken and net fluxes may arise (1, 37–39). When all microscopic details of a nonequilibrium system are known, one can measure the rate of entropy production by comparing the likelihoods of forward and reversed trajectories in sufficiently large data samples (35, 36). However, in most if not all biophysical experiments, many degrees of freedom remain hidden to the observer, demanding methods (28, 40, 41) that do not require complete knowledge of the system. A powerful alternative is provided by thermodynamic uncertainty relations (TURs), which use the mean and variance of steady-state currents to bound entropy production rates (18, 19, 26, 42–48). Although highly useful when currents can be measured (44–47), or when the system can be externally manipulated (40, 49), these methods give, by construction, trivial zero bounds for current-free nonequilibrium systems, such as driven one-dimensional (1D) nonperiodic oscillators. In the absence of currents, potential asymmetries in the forward and reverse trajectories can still be exploited to bound the entropy production rate (29, 30, 50), but to our knowledge no existing method is capable of producing nonzero bounds when forward and reverse trajectories are statistically identical. Moreover, even though previous bounds can become tight in some cases (51), optimal entropy production estimators for nonequilibrium systems are in general unknown.To obtain bounds that are provably optimal under reasonable conditions on the available data, we reformulate the problem here within an optimization framework. Formally, we consider any steady-state Markovian dynamics for which only coarse-grained variables are observable, where these observables may appear non-Markovian. We then search over all possible underlying Markovian systems to identify the one which minimizes the entropy production rate while obeying the observed statistics. More specifically, our algorithmic implementation leverages information about successive transitions, allowing us to discover nonzero bounds on entropy production even when the coarse-grained statistics appear time symmetric. We demonstrate this for both synthetic test data and experimental data (52) for flagella motors. Subsequently, we consider the entropy production of microtubules (33), which slowly grow before rapidly shrinking in steady state, to show how refined coarse graining in space and time leads to improved bounds. The final application to calcium oscillations in human embryonic kidney cells (34) illustrates how external stimulation with drugs can increase entropy production.     

Adipose tissue is a critical regulator of osteoarthritis

Osteoarthritis (OA), the leading cause of pain and disability worldwide, disproportionally affects individuals with obesity. The mechanisms by which obesity leads to the onset and progression of OA are unclear due to the complex interactions among the metabolic, biomechanical, and inflammatory factors that accompany increased adiposity. We used a murine preclinical model of lipodystrophy (LD) to examine the direct contribution of adipose tissue to OA. Knee joints of LD mice were protected from spontaneous or posttraumatic OA, on either a chow or high-fat diet, despite similar body weight and the presence of systemic inflammation. These findings indicate that adipose tissue itself plays a critical role in the pathophysiology of OA. Susceptibility to posttraumatic OA was reintroduced into LD mice using implantation of a small adipose tissue depot derived from wild-type animals or mouse embryonic fibroblasts that undergo spontaneous adipogenesis, implicating paracrine signaling from fat, rather than body weight, as a mediator of joint degeneration.

Osteoarthritis (OA) is the leading cause of pain and disability worldwide and is associated with increased all-cause mortality and cardiovascular disease (1, 2). OA is strongly associated with obesity, suggesting that either increased biomechanical joint loading or systemic inflammation and metabolic dysfunction related to obesity are responsible for joint degeneration (1, 2). However, increasing evidence is mounting that changes in biomechanical loading due to increased body mass do not account for the severity of obesity-induced knee OA (1–9). These observations suggest that other factors related to the presence of adipose tissue and adipose tissue-derived cytokines—termed adipokines—play critical roles in this process and other musculoskeletal conditions (1, 2, 6, 7, 10). As there are presently no disease-modifying OA drugs available, direct evidence linking adipose tissue and cartilage health could provide important mechanistic insight into the natural history of OA and obesity and therefore guide the development and translation of novel OA therapeutic strategies designed to preserve joint health.The exact contribution of the adipokine-signaling network in OA has been difficult to determine due to the complex interactions among metabolic, biomechanical, and inflammatory factors related to obesity (11). To date, the link between increased adipose tissue mass and OA pathogenesis has largely been correlative (6, 7, 12), and, as such, the direct effect of adipose tissue and the adipokines it releases has been difficult to separate from other factors such as dietary composition or excess body mass in the context of obesity, which is most commonly caused by excessive nutrition (2, 6, 7). In particular, leptin, a proinflammatory adipokine and satiety hormone secreted proportionally to adipose tissue mass is most consistently increased in obesity-induced OA (1), and leptin knockout mice are protected from OA (6, 7). However, it remains to be determined whether leptin directly contributes to OA pathogenesis, independent of its effect on metabolism (and weight). Additional adipokines that have been implicated in the onset and progression of OA include adiponectin, resistin, visfatin, chimerin, and inflammatory cytokines such as interleukin-1 (IL-1), IL-6, and tumor necrosis factor-α (TNF-α) (13). The infrapatellar fat pad represents a local source of adipokines within the knee joint, but several studies indicate strong correlations with visceral adipose tissue, outside of the joint organ system, with OA severity (14). Furthermore, adipokine receptors are found on almost all cells within the joint and, therefore, could directly contribute to OA pathogenesis through synovitis, cartilage damage, and bone remodeling (13). The role of other adipokines (15) in OA pathogenesis remains to be determined, as it has been difficult to separate and directly test the role of adipokines from other biomechanical, inflammatory, and metabolic factors that contribute to OA pathogenesis.To directly investigate the mechanisms by which adipose tissue affects OA, we used a transgenic mouse with lipodystrophy (LD) that completely lacks adipose tissue and, therefore, adipokine signaling. The LD model system affords the unique opportunity to directly examine the effects of adipose tissue and its secretory factors on musculoskeletal pathology without the confounding effect of diet (16, 17). While LD mice completely lack adipose tissue depots, they demonstrate similar body mass to wild-type (WT) controls on a chow diet (12, 16–19). These characteristics provide a unique model that can be used to eliminate the factor of loading due to body mass on joint damage and, thus, to directly test the effects of fat and factors secreted by fat on musculoskeletal tissues. Of particular interest, LD mice also exhibit several characteristics that have been associated with OA, including sclerotic bone (11, 20), metabolic derangement (3, 5, 7–9, 21, 22), and muscle weakness (2). Despite these OA-predisposing features, LD mice are protected from OA and implantation of adipose tissue back into LD mice restores susceptibility to OA—demonstrating a direct relationship between adipose tissue and cartilage health, independent of the effect of obesity on mechanical joint loading.     

Evolution and global charge conservation for polarization singularities emerging from non-Hermitian degeneracies

Core concepts in singular optics, especially the polarization singularities, have rapidly penetrated the surging fields of topological and non-Hermitian photonics. For open photonic structures with non-Hermitian degeneracies in particular, polarization singularities would inevitably encounter another sweeping concept of Berry phase. Several investigations have discussed, in an inexplicit way, connections between both concepts, hinting at that nonzero topological charges for far-field polarizations on a loop are inextricably linked to its nontrivial Berry phase when degeneracies are enclosed. In this work, we reexamine the seminal photonic crystal slab that supports the fundamental two-level non-Hermitian degeneracies. Regardless of the invariance of nontrivial Berry phase (concerning near-field Bloch modes defined on the momentum torus) for different loops enclosing both degeneracies, we demonstrate that the associated far polarization fields (defined on the momentum sphere) exhibit topologically inequivalent patterns that are characterized by variant topological charges, including even the trivial scenario of zero charge. Moreover, the charge carried by the Fermi arc actually is not well defined, which could be different on opposite bands. It is further revealed that for both bands, the seemingly complex evolutions of polarizations are bounded by the global charge conservation, with extra points of circular polarizations playing indispensable roles. This indicates that although not directly associated with any local charges, the invariant Berry phase is directly linked to the globally conserved charge, physical principles underlying which have all been further clarified by a two-level Hamiltonian with an extra chirality term. Our work can potentially trigger extra explorations beyond photonics connecting Berry phase and singularities.

Pioneered by Pancharatnam, Berry, Nye, and others (1–10), Berry phase and singularities have become embedded languages all across different branches of photonics. Optical Berry phase is largely manifested through either polarization evolving Pancharatnam–Berry phase or the spin-redirection Bortolotti–Rytov–Vladimirskii–Berry phase (2, 4, 5, 11–15); while optical singularities are widely observed as singularities of intensity (caustics) (6), phase (vortices) (7), or polarization (8–10). As singularities for complex vectorial waves, polarization singularities are skeletons of electromagnetic waves and are vitally important for understanding various interference effects underlying many applications (16–20).There is a superficial similarity between the aforementioned two concepts: Both the topological charge of polarization field [Hopf index of line field (21, 22)] and Berry phase are defined on a closed circuit. Despite this, it is quite unfortunate that almost no definite connections have been established between them in optics. This is fully understandable: Berry phase is defined on the Pancharatnam connection (parallel transport) that decides the phase contrast between neighboring states on the loop (3, 4); while the polarization charge reflects accumulated orientation rotations of polarization ellipses, which has no direct relevance to the overall phase of each state. This explains why in pioneering works where both concepts were present (23–27), their interplay was rarely elaborated on.Spurred by studies into bound states in the continuum, polarization singularities have gained enormous renewed interest in open periodic photonic structures, manifested in different morphologies with both fundamental and higher-order half-integer charges (28–50). Simultaneously, the significance of Berry phase has been further reinforced in surging fields of topological and non-Hermitian photonics (1, 23, 26, 51–56). In open periodic structures involving band degeneracies, Berry phase and polarization singularity would inevitably meet, which sparks the influential work on non-Hermitian degeneracy (36) and several other following studies (40, 43, 45) discussing both concepts simultaneously. Although not claimed explicitly, those works hint that nontrivial Berry phase produces nonzero polarization charges.Aiming to bridge Berry phase and polarization singularity, we reexamine the seminal photonic crystal slab (PCS) that supports elementary two-level non-Hermitian degeneracies. It is revealed that with an invariant nontrivial π Berry phase, the corresponding polarization fields on different isofrequency contours enclosing both non-Hermitian degenerate points (or equivalently exceptional points [EPs]) (26) exhibit diverse patterns characterized by different polarization charges, even including the trivial zero charge. It is further revealed that the charge carried by the Fermi arc is actually not well defined, which could be different on opposite bands. We also discover that such complexity of field evolutions is constrained by global charge conservation for both bands, with extra points of circular polarizations (C points) playing pivotal roles. This reveals the explicit connection between globally conserved charge and the invariant Berry phase, underlying which the physical mechanisms have been further clarified by a two-level Hamiltonian with an extra chirality term (25). We show that such an unexpected connection is generically manifest in various structures, despite the fact that Berry phase and polarization charge actually characterize different entities of near-field Bloch modes and their projected far polarization fields, respectively: Bloch modes are defined on the momentum torus and can be folded into the irreducible Brillouin zone; while polarization fields are defined on the momentum sphere, due to the involvement of out-of-plane wave vectors along which there is no periodicity. Our study can spur further investigations in other subjects beyond photonics to explore conceptual interconnectedness, where both the concepts of Berry phase and singularities are present.