An Endosomal NAADP-Sensitive Two-Pore Ca2+ Channel Regulates ER-Endosome Membrane Contact Sites to Control Growth Factor Signaling

The lysosomotrope GPN mobilises Ca2+ from acidic organelles

Lysosomes are acidic Ca²⁺ stores often mobilised in conjunction with endoplasmic reticulum (ER) Ca²⁺ stores. Glycyl-L-phenylalanine 2-naphthylamide (GPN) is a widely used lysosomotropic agent that evokes cytosolic Ca²⁺ signals in many cells. However, whether these signals are the result of a primary action on lysosomes is unclear in light of recent evidence showing that GPN mediates direct ER Ca²⁺ release through changes in cytosolic pH. Here, we show that GPN evoked rapid increases in cytosolic pH but slower Ca²⁺ signals. NH₄Cl evoked comparable changes in pH but failed to affect Ca²⁺. The V-type ATPase inhibitor, bafilomycin A1, increased lysosomal pH over a period of hours. Acute treatment modestly affected lysosomal pH and potentiated Ca²⁺ signals evoked by GPN. In contrast, chronic treatment led to more profound changes in luminal pH and selectively inhibited GPN action. GPN blocked Ca²⁺ responses evoked by the novel nicotinic acid adenine dinucleotide phosphate-like agonist, TPC2-A1-N. Therefore, GPN-evoked Ca²⁺ signals were better correlated with associated pH changes in the lysosome compared to the cytosol, and were coupled to lysosomal Ca²⁺ release. We conclude that Ca²⁺ signals evoked by GPN most likely derive from acidic organelles.

Summary: Methods of releasing calcium from lysosomes are limited but characterization of the effects of GPN in primary cultured human fibroblasts confirmed that it probably targets acidic organelles.

Lysosomal ion channels involved in cellular entry and uncoating of enveloped viruses: Implications for therapeutic strategies against SARS-CoV-2

Ion channels are necessary for correct lysosomal function including degradation of cargoes originating from endocytosis. Almost all enveloped viruses, including coronaviruses (CoVs), enter host cells via endocytosis, and do not escape endosomal compartments into the cytoplasm (via fusion with the endolysosomal membrane) unless the virus-encoded envelope proteins are cleaved by lysosomal proteases. With the ongoing outbreak of severe acute respiratory syndrome (SARS)-CoV-2, endolysosomal two-pore channels represent an exciting and emerging target for antiviral therapies. This review focuses on the latest knowledge of the effects of lysosomal ion channels on the cellular entry and uncoating of enveloped viruses, which may aid in development of novel therapies against emerging infectious diseases such as SARS-CoV-2.

Endoplasmic reticulum stress and unfolded protein response in cardiovascular diseases

Cardiovascular diseases (CVDs), such as ischaemic heart disease, cardiomyopathy, atherosclerosis, hypertension, stroke and heart failure, are among the leading causes of morbidity and mortality worldwide. Although specific CVDs and the associated cardiometabolic abnormalities have distinct pathophysiological and clinical manifestations, they often share common traits, including disruption of proteostasis resulting in accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER). ER proteostasis is governed by the unfolded protein response (UPR), a signalling pathway that adjusts the protein-folding capacity of the cell to sustain the cell's secretory function. When the adaptive UPR fails to preserve ER homeostasis, a maladaptive or terminal UPR is engaged, leading to the disruption of ER integrity and to apoptosis. ER stress functions as a double-edged sword, with long-term ER stress resulting in cellular defects causing disturbed cardiovascular function. In this Review, we discuss the distinct roles of the UPR and ER stress response as both causes and consequences of CVD. We also summarize the latest advances in our understanding of the importance of the UPR and ER stress in the pathogenesis of CVD and discuss potential therapeutic strategies aimed at restoring ER proteostasis in CVDs.

Axonal Organelles as Molecular Platforms for Axon Growth and Regeneration after Injury

Investigating the molecular mechanisms governing developmental axon growth has been a useful approach for identifying new strategies for boosting axon regeneration after injury, with the goal of treating debilitating conditions such as spinal cord injury and vision loss. The picture emerging is that various axonal organelles are important centers for organizing the molecular mechanisms and machinery required for growth cone development and axon extension, and these have recently been targeted to stimulate robust regeneration in the injured adult central nervous system (CNS). This review summarizes recent literature highlighting a central role for organelles such as recycling endosomes, the endoplasmic reticulum, mitochondria, lysosomes, autophagosomes and the proteasome in developmental axon growth, and describes how these organelles can be targeted to promote axon regeneration after injury to the adult CNS. This review also examines the connections between these organelles in developing and regenerating axons, and finally discusses the molecular mechanisms within the axon that are required for successful axon growth.

The SARS-Coronavirus Infection Cycle: A Survey of Viral Membrane Proteins, Their Functional Interactions and Pathogenesis

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a novel epidemic strain of Betacoronavirus that is responsible for the current viral pandemic, coronavirus disease 2019 (COVID-19), a global health crisis. Other epidemic Betacoronaviruses include the 2003 SARS-CoV-1 and the 2009 Middle East Respiratory Syndrome Coronavirus (MERS-CoV), the genomes of which, particularly that of SARS-CoV-1, are similar to that of the 2019 SARS-CoV-2. In this extensive review, we document the most recent information on Coronavirus proteins, with emphasis on the membrane proteins in the Coronaviridae family. We include information on their structures, functions, and participation in pathogenesis. While the shared proteins among the different coronaviruses may vary in structure and function, they all seem to be multifunctional, a common theme interconnecting these viruses. Many transmembrane proteins encoded within the SARS-CoV-2 genome play important roles in the infection cycle while others have functions yet to be understood. We compare the various structural and nonstructural proteins within the Coronaviridae family to elucidate potential overlaps and parallels in function, focusing primarily on the transmembrane proteins and their influences on host membrane arrangements, secretory pathways, cellular growth inhibition, cell death and immune responses during the viral replication cycle. We also offer bioinformatic analyses of potential viroporin activities of the membrane proteins and their sequence similarities to the Envelope (E) protein. In the last major part of the review, we discuss complement, stimulation of inflammation, and immune evasion/suppression that leads to CoV-derived severe disease and mortality. The overall pathogenesis and disease progression of CoVs is put into perspective by indicating several stages in the resulting infection process in which both host and antiviral therapies could be targeted to block the viral cycle. Lastly, we discuss the development of adaptive immunity against various structural proteins, indicating specific vulnerable regions in the proteins. We discuss current CoV vaccine development approaches with purified proteins, attenuated viruses and DNA vaccines.

Two-pore channels affect EGF receptor signaling by receptor trafficking and expression

Two-pore channels (TPCs) are key components for regulating Ca²⁺ current from endosomes and lysosomes to the cytosol. This locally restricted Ca²⁺ current forms the basis for fusion and fission events between endolysosomal membranes and thereby for intracellular trafficking processes. Here, we study the function of TPC1 and TPC2 for uptake, recycling, and degradation of epidermal growth factor receptor (EGFR) using a set of TPC knockout cells. RNA sequencing analysis revealed multiple changes in the expression levels of EGFR pathway-related genes in TPC1-deficient cells. We propose that a prolonged presence of activated EGFRs in endolysosomal signaling platforms, caused by genetic inactivation of TPCs, does not only affect EGFR signaling pathways but also increases de novo synthesis of EGFR. Increased basal phospho-c-Jun levels contribute to the high EGFR expression in TPC-deficient cells. Our data point to a role of TPCs not only as important regulators for the EGFR transportation network but also for EGFR-signaling and expression.

•

Two-pore channels differently affect intracellular trafficking of EGF receptors

•

Deletion of TPCs prolongs EGFR signaling in endolysosomal platforms

•

TPCs affect expression of EGFR downstream signaling components

•

JNK signaling contributes to increased EGFR expression in TPC-deficient cells

Targeting Endolysosomal Two-Pore Channels to Treat Cardiovascular Disorders in the Novel COronaVIrus Disease 2019

Emerging evidence hints in favor of a life-threatening link between severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and the cardiovascular system. SARS-CoV-2 may result in dramatic cardiovascular complications, whereas the severity of COronaVIrus Disease 2019 (COVID-19) and the incidence of fatalities tend to increase in patients with pre-existing cardiovascular complications. SARS-CoV-2 is internalized into the host cells by endocytosis and may then escape the endolysosomal system via endosomes. Two-pore channels drive endolysosomal trafficking through the release of endolysosomal Ca2+. Recent evidence suggested that the pharmacological inhibition of TPCs prevents Ebola virus and Middle East Respiratory Syndrome COronaVirus (MERS-CoV) entry into host cells. In this perspective, we briefly summarize the biophysical and pharmacological features of TPCs, illustrate their emerging role in the cardiovascular system, and finally present them as a reliable target to treat cardiovascular complications in COVID-19 patients.

The journey of Ca2+ through the cell - pulsing through the network of ER membrane contact sites

Calcium is the third most abundant metal on earth, and the fundaments of its homeostasis date back to pre-eukaryotic life forms. In higher organisms, Ca²⁺ serves as a cofactor for a wide array of (enzymatic) interactions in diverse cellular contexts and constitutes the most important signaling entity in excitable cells. To enable responsive behavior, cytosolic Ca²⁺ concentrations are kept low through sequestration into organellar stores, particularly the endoplasmic reticulum (ER), but also mitochondria and lysosomes. Specific triggers are then used to instigate a local release of Ca²⁺ on demand. Here, communication between organelles comes into play, which is accomplished through intimate yet dynamic contacts, termed membrane contact sites (MCSs). The field of MCS biology in relation to cellular Ca²⁺ homeostasis has exploded in recent years. Taking advantage of this new wealth of knowledge, in this Review, we invite the reader on a journey of Ca²⁺ flux through the ER and its associated MCSs. New mechanistic insights and technological advances inform the narrative on Ca²⁺ acquisition and mobilization at these sites of communication between organelles, and guide the discussion of their consequences for cellular physiology.

Two-pore channels as master regulators of membrane trafficking and endocytic well-being

Two-pore channels (TPCs) are a ubiquitous class of Ca2+- and Na+-permeable ion channels expressed within the endo-lysosomal system. They have emerged as central regulators of a wide array of physiological processes intimately linked to information processing. In this short review, we highlight how molecular and chemical strategies have uncovered multiple roles for TPCs in regulating various aspects of endo-lysosomal trafficking associated with disease. We summarise advances in the identification of new small molecules to pharmacologically target TPCs for medical benefit. Lastly, we discuss possible underpinning molecular mechanism(s) that translate TPC-mediated ionic fluxes to function.

Preventing a shock to the system. Two-pore channel 1 negatively regulates anaphylaxis

The mammalian two-pore channels TPC1 and TPC2 are patho-physiologically relevant endo-lysosomal cation channels regulated by the Ca²⁺ mobilising messenger NAADP and the phosphoinositide PI(3,5)P₂. Recent work by Arlt et al shows that genetic or chemical inhibition of TPC1 in mice promotes anaphylaxis in vivo through a mechanism involving enhanced endoplasmic reticulum Ca²⁺ release and secretion in mast cells.

TPC1 deficiency or blockade augments systemic anaphylaxis and mast cell activity

Mast cells and basophils are main drivers of allergic reactions and anaphylaxis, for which prevalence is rapidly increasing. Activation of these cells leads to a tightly controlled release of inflammatory mediators stored in secretory granules. The release of these granules is dependent on intracellular calcium (Ca2+) signals. Ca2+ release from endolysosomal compartments is mediated via intracellular cation channels, such as two-pore channel (TPC) proteins. Here, we uncover a mechanism for how TPC1 regulates Ca2+ homeostasis and exocytosis in mast cells in vivo and ex vivo. Notably, in vivo TPC1 deficiency in mice leads to enhanced passive systemic anaphylaxis, reflected by increased drop in body temperature, most likely due to accelerated histamine-induced vasodilation. Ex vivo, mast cell-mediated histamine release and degranulation was augmented upon TPC1 inhibition, although mast cell numbers and size were diminished. Our results indicate an essential role of TPC1 in endolysosomal Ca2+ uptake and filling of endoplasmic reticulum Ca2+ stores, thereby regulating exocytosis in mast cells. Thus, pharmacological modulation of TPC1 might blaze a trail to develop new drugs against mast cell-related diseases, including allergic hypersensitivity.

Getting intimate: Lysosomes and ER rendezvous to control autophagy

The endoplasmic reticulum (ER) is the source of lysosomal calcium. The finding that the protein TMBIM6 -a putative ER calcium channel and cell death regulator -promotes calcium transfer from the ER to lysosomes to induce autophagy uncovers a missing piece in the puzzle of inter-organelle communication.

TMEM16K is an interorganelle regulator of endosomal sorting

Communication between organelles is essential for their cellular homeostasis. Neurodegeneration reflects the declining ability of neurons to maintain cellular homeostasis over a lifetime, where the endolysosomal pathway plays a prominent role by regulating protein and lipid sorting and degradation. Here we report that TMEM16K, an endoplasmic reticulum lipid scramblase causative for spinocerebellar ataxia (SCAR10), is an interorganelle regulator of the endolysosomal pathway. We identify endosomal transport as a major functional cluster of TMEM16K in proximity biotinylation proteomics analyses. TMEM16K forms contact sites with endosomes, reconstituting split-GFP with the small GTPase RAB7. Our study further implicates TMEM16K lipid scrambling activity in endosomal sorting at these sites. Loss of TMEM16K function led to impaired endosomal retrograde transport and neuromuscular function, one of the symptoms of SCAR10. Thus, TMEM16K-containing ER-endosome contact sites represent clinically relevant platforms for regulating endosomal sorting.

NAADP-regulated two-pore channels drive phagocytosis through endo-lysosomal Ca2+ nanodomains, calcineurin and dynamin

Macrophages clear pathogens by phagocytosis and lysosomes that fuse with phagosomes are traditionally regarded as to a source of membranes and luminal degradative enzymes. Here, we reveal that endo-lysosomes act as platforms for a new phagocytic signalling pathway in which FcγR activation recruits the second messenger NAADP and thereby promotes the opening of Ca²⁺ -permeable two-pore channels (TPCs). Remarkably, phagocytosis is driven by these local endo-lysosomal Ca²⁺ nanodomains rather than global cytoplasmic or ER Ca²⁺ signals. Motile endolysosomes contact nascent phagosomes to promote phagocytosis, whereas endo-lysosome immobilization prevents it. We show that TPC-released Ca²⁺ rapidly activates calcineurin, which in turn dephosphorylates and activates the GTPase dynamin-2. Finally, we find that different endo-lysosomal Ca²⁺ channels play diverse roles, with TPCs providing a universal phagocytic signal for a wide range of particles and TRPML1 being only required for phagocytosis of large targets.

Ca2+ Signaling in Exocrine Cells

Calcium (Ca²⁺) and cyclic AMP (cAMP) signaling cross talk and synergize to stimulate the cardinal functions of exocrine cells, regulated exocytosis, and fluid and electrolyte secretion. This physiological process requires the organization of the two signaling pathways into complexes at defined cellular domains and close placement. Such domains are formed by membrane contact sites (MCS). This review discusses the basic properties of Ca²⁺ signaling in exocrine cells, the role of MCS in the organization of cell signaling and in cross talk and synergism between the Ca²⁺ and cAMP signaling pathways and, finally, the mechanism by which the Ca²⁺ and cAMP pathways synergize to stimulate epithelial fluid and electrolyte secretion.

Staying in touch with the endocytic network: The importance of contacts for cholesterol transport

Cholesterol homeostasis is critical for cell function and human health. Cholesterol is heterogeneously distributed among cellular membranes, with the redistribution of endocytosed dietary cholesterol playing a pivotal role in the regulation of cholesterol homeostasis. While gaps remain in our understanding of intracellular dietary cholesterol transport, a highly complex network of pathways is starting to emerge, often involving inter‐dependent vesicular and non‐vesicular transport mechanisms. The last decade has seen a surge in interest in non‐vesicular transport and inter‐organellar communication at membrane contact sites. By providing platforms for protein interactions, signalling events, lipid exchange and calcium flux, membrane contact sites (MCS) are now appreciated as controlling the fate of large amounts of lipid and play central roles in the regulation and co‐ordination of endocytic trafficking. Here, we review the role of MCS in multiple pathways for cholesterol export from the endocytic pathway and highlight the intriguing interplay between vesicular and non‐vesicular transport mechanisms and relationship with neurodegenerative disease.

The Role of Ca2+ Signaling in Aging and Neurodegeneration: Insights from Caenorhabditis elegans Models

Ca²⁺ is a ubiquitous second messenger that plays an essential role in physiological processes such as muscle contraction, neuronal secretion, and cell proliferation or differentiation. There is ample evidence that the dysregulation of Ca²⁺ signaling is one of the key events in the development of neurodegenerative processes, an idea called the "calcium hypothesis" of neurodegeneration. Caenorhabditis elegans (C. elegans) is a very good model for the study of aging and neurodegeneration. In fact, many of the signaling pathways involved in longevity were first discovered in this nematode, and many models of neurodegenerative diseases have also been developed therein, either through mutations in the worm genome or by expressing human proteins involved in neurodegeneration (β-amyloid, α-synuclein, polyglutamine, or others) in defined worm tissues. The worm is completely transparent throughout its whole life, which makes it possible to carry out Ca²⁺ dynamics studies in vivo at any time, by expressing Ca²⁺ fluorescent probes in defined worm tissues, and even in specific organelles such as mitochondria. This review will summarize the evidence obtained using this model organism to understand the role of Ca²⁺ signaling in aging and neurodegeneration.

Role of Two-Pore Channels in Embryonic Development and Cellular Differentiation

Since the identification of nicotinic acid adenine dinucleotide phosphate (NAADP) and its putative target, the two-pore channel (TPC), the NAADP/TPC/Ca2+ signaling pathway has been reported to play a role in a diverse range of functions in a variety of different cell types. TPCs have also been associated with a number of diseases, which arise when their activity is perturbed. In addition, TPCs have been shown to play key roles in various embryological processes and during the differentiation of a variety of cell types. Here, we review the role of NAADP/TPC/Ca2+ signaling during early embryonic development and cellular differentiation. We pay particular attention to the role of TPC2 in the development and maturation of early neuromuscular activity in zebrafish, and during the differentiation of isolated osteoclasts, endothelial cells, and keratinocytes. Our aim is to emphasize the conserved features of TPC-mediated Ca2+ signaling in a number of selected examples.

Molecular Mechanisms of Calcium Signaling During Phagocytosis

Calcium (Ca²⁺) is a ubiquitous second messenger involved in the regulation of numerous cellular functions including vesicular trafficking, cytoskeletal rearrangements and gene transcription. Both global as well as localized Ca²⁺ signals occur during phagocytosis, although their functional impact on the phagocytic process has been debated. After nearly 40 years of research, a consensus may now be reached that although not strictly required, Ca²⁺ signals render phagocytic ingestion and phagosome maturation more efficient, and their manipulation make an attractive avenue for therapeutic interventions. In the last decade many efforts have been made to identify the channels and regulators involved in generating and shaping phagocytic Ca²⁺ signals. While molecules involved in store-operated calcium entry (SOCE) of the STIM and ORAI family have taken center stage, members of the canonical, melastatin, mucolipin and vanilloid transient receptor potential (TRP), as well as purinergic P2X receptor families are now recognized to play significant roles. In this chapter, we review the recent literature on research that has linked specific Ca²⁺-permeable channels and regulators to phagocytic function. We highlight the fact that lipid mediators are emerging as important regulators of channel gating and that phagosomal ionic homeostasis and Ca²⁺ release also play essential parts. We predict that improved methodologies for measuring these factors will be critical for future advances in dissecting the intricate biology of this fascinating immune process.

Does lysosomal rupture evoke Ca2+ release? A question of pores and stores

Lysosomotropic agents have been used to permeabilize lysosomes and thereby implicate these organelles in diverse cellular processes. Since lysosomes are Ca²⁺ stores, this rupturing action, particularly that induced by GPN, has also been used to rapidly release Ca²⁺ from lysosomes. However, a recent study has questioned the mechanism of action of GPN and concluded that, acutely, it does not permeabilize lysosomes but releases Ca²⁺ directly from the ER instead. We therefore appraise these provocative findings in the context of the existing literature. We suggest that further work is required to unequivocally rule out lysosomes as contributors to GPN-evoked Ca²⁺ signals.

IP3 Receptors Preferentially Associate with ER-Lysosome Contact Sites and Selectively Deliver Ca2+ to Lysosomes

Inositol 1,4,5-trisphosphate (IP₃) receptors (IP₃Rs) allow extracellular stimuli to redistribute Ca²⁺ from the ER to cytosol or other organelles. We show, using small interfering RNA (siRNA) and vacuolar H⁺-ATPase (V-ATPase) inhibitors, that lysosomes sequester Ca²⁺ released by all IP₃R subtypes, but not Ca²⁺ entering cells through store-operated Ca²⁺ entry (SOCE). A low-affinity Ca²⁺ sensor targeted to lysosomal membranes reports large, local increases in cytosolic [Ca²⁺] during IP₃-evoked Ca²⁺ release, but not during SOCE. Most lysosomes associate with endoplasmic reticulum (ER) and dwell at regions populated by IP₃R clusters, but IP₃Rs do not assemble ER-lysosome contacts. Increasing lysosomal pH does not immediately prevent Ca²⁺ uptake, but it causes lysosomes to slowly redistribute and enlarge, reduces their association with IP₃Rs, and disrupts Ca²⁺ exchange with ER. In a "piston-like" fashion, ER concentrates cytosolic Ca²⁺ and delivers it, through large-conductance IP₃Rs, to a low-affinity lysosomal uptake system. The involvement of IP₃Rs allows extracellular stimuli to regulate Ca²⁺ exchange between the ER and lysosomes.

NAADP Receptors

Of the established Ca²⁺-mobilizing messengers, NAADP is arguably the most tantalizing. It is the most potent, often efficacious at low nanomolar concentrations, and its receptors undergo dramatic desensitization. Recent studies have identified a new class of calcium-release channel, the two-pore channels (TPCs), as the likely targets for NAADP regulation, even though the effect may be indirect. These channels localized at endolysosomes, where they mediate local Ca²⁺ release, and have highlighted a new role of acidic organelles as targets for messenger-evoked Ca²⁺ mobilization. Three distinct roles of TPCs have been identified. The first is to effect local Ca²⁺ release that may play a role in endolysosomal function including vesicular fusion and trafficking. The second is to trigger global calcium release by recruiting Ca²⁺-induced Ca²⁺-release (CICR) channels at lysosomal-endoplasmic reticulum (ER) junctions. The third is to regulate plasma membrane excitability by the targeting of Ca²⁺ release from appropriately positioned subplasma membrane stores to regulate plasma membrane Ca²⁺-activated channels. In this review, I discuss the role of nicotinic acid adenine nucleotide diphosphate (NAADP)-mediated Ca²⁺ release from endolysosomal stores as a widespread trigger for intracellular calcium signaling mechanisms, and how studies of TPCs are beginning to enhance our understanding of the central role of lysosomes in Ca²⁺ signaling.

ER morphology and endo-lysosomal crosstalk: Functions and disease implications

The endoplasmic reticulum (ER) is a continuous endomembrane system comprising the nuclear envelope, ribosome-studded sheets, dense peripheral matrices, and an extensive polygonal network of interconnected tubules. In addition to performing numerous critical cellular functions, the ER makes extensive contacts with other organelles, including endosomes and lysosomes. The molecular and functional characterization of these contacts has advanced significantly over the past several years. These contacts participate in key functions such as cholesterol transfer, endosome tubule fission, and Ca²⁺ exchange. Disruption of key proteins at these sites can result in often severe diseases, particularly those affecting the nervous system.

Pyridine Nucleotide Metabolites and Calcium Release from Intracellular Stores

Ca²⁺ signals are probably the most common intracellular signaling cellular events, controlling an extensive range of responses in virtually all cells. Many cellular stimuli, often acting at cell surface receptors, evoke Ca²⁺ signals by mobilizing Ca²⁺ from intracellular stores. Inositol trisphosphate (IP₃) was the first messenger shown to link events at the plasma membrane to release Ca²⁺ from the endoplasmic reticulum (ER), through the activation of IP₃-gated Ca²⁺ release channels (IP₃ receptors). Subsequently, two additional Ca²⁺ mobilizing messengers were discovered, cADPR and NAADP. Both are metabolites of pyridine nucleotides, and may be produced by the same class of enzymes, ADP-ribosyl cyclases, such as CD38. Whilst cADPR mobilizes Ca²⁺ from the ER by activation of ryanodine receptors (RyRs), NAADP releases Ca²⁺ from acidic stores by a mechanism involving the activation of two pore channels (TPCs). In addition, other pyridine nucleotides have emerged as intracellular messengers. ADP-ribose and 2'-deoxy-ADPR both activate TRPM2 channels which are expressed at the plasma membrane and in lysosomes.

Roles for the Endoplasmic Reticulum in Regulation of Neuronal Calcium Homeostasis

By influencing Ca²⁺ homeostasis in spatially and architecturally distinct neuronal compartments, the endoplasmic reticulum (ER) illustrates the notion that form and function are intimately related. The contribution of ER to neuronal Ca²⁺ homeostasis is attributed to the organelle being the largest reservoir of intracellular Ca²⁺ and having a high density of Ca²⁺ channels and transporters. As such, ER Ca²⁺ has incontrovertible roles in the regulation of axodendritic growth and morphology, synaptic vesicle release, and neural activity dependent gene expression, synaptic plasticity, and mitochondrial bioenergetics. Not surprisingly, many neurological diseases arise from ER Ca²⁺ dyshomeostasis, either directly due to alterations in ER resident proteins, or indirectly via processes that are coupled to the regulators of ER Ca²⁺ dynamics. In this review, we describe the mechanisms involved in the establishment of ER Ca²⁺ homeostasis in neurons. We elaborate upon how changes in the spatiotemporal dynamics of Ca²⁺ exchange between the ER and other organelles sculpt neuronal function and provide examples that demonstrate the involvement of ER Ca²⁺ dyshomeostasis in a range of neurological and neurodegenerative diseases.

Calcium Dyshomeostasis and Lysosomal Ca2+ Dysfunction in Amyotrophic Lateral Sclerosis

Recent findings in the understanding of amyotrophic lateral sclerosis (ALS) revealed that alteration in calcium (Ca²⁺) homeostasis may largely contribute to motor neuron demise. A large part of these alterations is due to dysfunctional Ca²⁺-storing organelles, including the endoplasmic reticulum (ER) and mitochondria. Very recently, lysosomal Ca²⁺ dysfunction has emerged as an important pathological change leading to neuronal loss in ALS. Remarkably, the Ca²⁺-storing organelles are interacting with each other at specialized domains controlling mitochondrial dynamics, ER/lysosomal function, and autophagy. This occurs as a result of interaction between specific ionic channels and Ca²⁺-dependent proteins located in each structure. Therefore, the dysregulation of these ionic mechanisms could be considered as a key element in the neurodegenerative process. This review will focus on the possible role of lysosomal Ca²⁺ dysfunction in the pathogenesis of several neurodegenerative diseases, including ALS and shed light on the possibility that specific lysosomal Ca²⁺ channels might represent new promising targets for preventing or at least delaying neurodegeneration in ALS.

Calcium Mobilization in Endothelial Cell Functions

Endothelial cells (ECs) constitute the innermost layer that lines all blood vessels from the larger arteries and veins to the smallest capillaries, including the lymphatic vessels. Despite the histological classification of endothelium of a simple epithelium and its homogeneous morphological appearance throughout the vascular system, ECs, instead, are extremely heterogeneous both structurally and functionally. The different arrangement of cell junctions between ECs and the local organization of the basal membrane generate different type of endothelium with different permeability features and functions. Continuous, fenestrated and discontinuous endothelia are distributed based on the specific function carried out by the organs. It is thought that a large number ECs functions and their responses to extracellular cues depend on changes in intracellular concentrations of calcium ion ([Ca²⁺]_i). The extremely complex calcium machinery includes plasma membrane bound channels as well as intracellular receptors distributed in distinct cytosolic compartments that act jointly to maintain a physiological [Ca²⁺]_i, which is crucial for triggering many cellular mechanisms. Here, we first survey the overall notions related to intracellular Ca²⁺ mobilization and later highlight the involvement of this second messenger in crucial ECs functions with the aim at stimulating further investigation that link Ca²⁺ mobilization to ECs in health and disease.

Functions of aryl hydrocarbon receptor (AHR) and CD38 in NAD metabolism and nonalcoholic steatohepatitis (NASH)

Aryl hydrocarbon receptor (AHR), identified in studies of dioxin toxicity, has been characterized as ligand-activated transcription factor involved in diverse functions including microbial defense, cell proliferation, immunity and NAD metabolism. AHR targets of the latter function are PARPs/ARTs and CD38 that are regulating glucose and lipid metabolism via NAD-dependent sirtuins. Deregulation of these pathways may facilitate obesity and age-dependent pathologies. The present commentary is focused on AHR and CD38 signaling in liver. CD38 is functioning as ectoNADase and Ca²⁺ mobilizing enzyme in endoplasmic reticulum and endolysosomal membranes. Deregulation of TCDD-activated AHR and CD38 may facilitate hepatic steatosis and inflammation. However, these proteins are also involved in protection against inflammation and CD38-mediated age-related decreased NAD levels that may be responsible for neurodegeneration. Further knowledge about the complexity of these pathways is needed to avoid pathologies. Therapeutic modulation of AHR and CD38 remains a challenging task.

Involvement of organelles and inter-organellar signaling in the pathogenesis of HIV-1 associated neurocognitive disorder and Alzheimer's disease

Endolysosomes, mitochondria, peroxisomes, endoplasmic reticulum, and plasma membranes are now known to physically and functionally interact with each other. Such findings of inter-organellar signaling and communication has led to a resurgent interest in cell biology and an increased appreciation for the physiological actions and pathological consequences of the dynamic physical and chemical communications occurring between intracellular organelles. Others and we have shown that HIV-1 proteins implicated in the pathogenesis of neuroHIV and that Alzheimer's disease both affects the structure and function of intracellular organelles. Intracellular organelles are highly mobile, and their intracellular distribution almost certainly affects their ability to interact with other organelles and to regulate such important physiological functions as endolysosome acidification, cell motility, and nutrient homeostasis. Indeed, compounds that acidify endolysosomes cause endolysosomes to exhibit a mainly perinuclear pattern while compounds that de-acidify endolysosomes cause these organelles to exhibit a larger profile as well as movement towards plasma membranes. Endolysosome pH might be an early event in the pathogenesis of neuroHIV and Alzheimer's disease and in terms of organellar biology endolysosome changes might be upstream of HIV-1 protein-induced changes to other organelles. Thus, inter-organellar signaling mechanisms might be involved in the pathogenesis of neuroHIV and other neurological disorders, and a better understanding of inter-organellar signaling might lead to improved therapeutic strategies.

Mining of Ebola virus entry inhibitors identifies approved drugs as two-pore channel pore blockers

Two-pore channels (TPCs) are Ca2+-permeable ion channels localised to the endo-lysosomal system where they regulate trafficking of various cargoes including viruses. As a result, TPCs are emerging as important drug targets. However, their pharmacology is ill-defined. There are no approved drugs to target them. And their mechanism of ligand activation is largely unknown. Here, we identify a number of FDA-approved drugs as TPC pore blockers. Using a model of the pore of human TPC2 based on recent structures of mammalian TPCs, we virtually screened a database of ~1500 approved drugs. Because TPCs have recently emerged as novel host factors for Ebola virus entry, we reasoned that Ebola virus entry inhibitors may exert their effects through inhibition of TPCs. Cross-referencing hits from the TPC virtual screen with two recent high throughput anti-Ebola screens yielded approved drugs targeting dopamine and estrogen receptors as common hits. These compounds inhibited endogenous NAADP-evoked Ca2+ release from sea urchin egg homogenates, NAADP-mediated channel activity of TPC2 re-routed to the plasma membrane, and PI(3,5)P2-mediated channel activity of TPC2 expressed in enlarged lysosomes. Mechanistically, single channel analyses showed that the drugs reduced mean open time consistent with a direct action on the pore. Functionally, drug potency in blocking TPC2 activity correlated with inhibition of Ebola virus-like particle entry. Our results expand TPC pharmacology through the identification of approved drugs as novel blockers, support a role for TPCs in Ebola virus entry, and provide insight into the mechanisms underlying channel regulation. This article is part of a Special Issue entitled: ECS Meeting edited by Claus Heizmann, Joachim Krebs and Jacques Haiech.

Faraway, so close! Functions of Endoplasmic reticulum-Endosome contacts

Eukaryotic cells are partitioned into functionally distinct organelles. Long considered as independent units in the cytosol, organelles are actually in constant and direct interaction with each other, mostly through the establishment of physical connections named membrane contact sites. Membrane contact sites constitute specific active regions involved in organelle dynamics, inter-organelle exchanges and communications. The endoplasmic reticulum (ER), which spreads throughout the cytosol, forms an extensive network that has many connections with the other organelles of the cell. Ample connections between the ER and endocytic organelles are observed in many cell types, highlighting their prominent physiological roles. Even though morphologically similar - a contact is a contact -, the identity of ER-Endosome contacts is defined by their specific molecular composition, which in turn determines the function of the contact. Here, we review the molecular mechanisms of ER-Endosome contact site formation and their associated cellular functions. This article is part of a Special Issue entitled Endoplasmic reticulum platforms for lipid dynamics edited by Shamshad Cockcroft and Christopher Stefan.

Coming together to define membrane contact sites

Close proximities between organelles have been described for decades. However, only recently a specific field dealing with organelle communication at membrane contact sites has gained wide acceptance, attracting scientists from multiple areas of cell biology. The diversity of approaches warrants a unified vocabulary for the field. Such definitions would facilitate laying the foundations of this field, streamlining communication and resolving semantic controversies. This opinion, written by a panel of experts in the field, aims to provide this burgeoning area with guidelines for the experimental definition and analysis of contact sites. It also includes suggestions on how to operationally and tractably measure and analyze them with the hope of ultimately facilitating knowledge production and dissemination within and outside the field of contact-site research.

Lysosomal Ion Channels as Decoders of Cellular Signals

Lysosomes, the degradation center of the cell, are filled with acidic hydrolases. Lysosomes generate nutrient-sensitive signals to regulate the import of H+, hydrolases, and endocytic and autophagic cargos, as well as the export of their degradation products (catabolites). In response to environmental and cellular signals, lysosomes change their positioning, number, morphology, size, composition, and activity within minutes to hours to meet the changing cellular needs. Ion channels in the lysosome are essential transducers that mediate signal-initiated Ca2+/Fe2+/Zn2+ release and H+/Na+/K+-dependent changes of membrane potential across the perimeter membrane. Dysregulation of lysosomal ion flux impairs lysosome movement, membrane trafficking, nutrient sensing, membrane repair, organelle membrane contact, and lysosome biogenesis and adaptation. Hence, activation and inhibition of lysosomal channels by synthetic modulators may tune lysosome function to maintain cellular health and promote cellular clearance in lysosome storage disorders.

Remodeling of secretory lysosomes during education tunes functional potential in NK cells

Inhibitory signaling during natural killer (NK) cell education translates into increased responsiveness to activation; however, the intracellular mechanism for functional tuning by inhibitory receptors remains unclear. Secretory lysosomes are part of the acidic lysosomal compartment that mediates intracellular signalling in several cell types. Here we show that educated NK cells expressing self-MHC specific inhibitory killer cell immunoglobulin-like receptors (KIR) accumulate granzyme B in dense-core secretory lysosomes that converge close to the centrosome. This discrete morphological phenotype is independent of transcriptional programs that regulate effector function, metabolism and lysosomal biogenesis. Meanwhile, interference of signaling from acidic Ca²⁺ stores in primary NK cells reduces target-specific Ca²⁺-flux, degranulation and cytokine production. Furthermore, inhibition of PI(3,5)P₂ synthesis, or genetic silencing of the PI(3,5)P₂-regulated lysosomal Ca²⁺-channel TRPML1, leads to increased granzyme B and enhanced functional potential, thereby mimicking the educated state. These results indicate an intrinsic role for lysosomal remodeling in NK cell education.

Endolysosomal Ca2+ Signalling and Cancer Hallmarks: Two-Pore Channels on the Move, TRPML1 Lags Behind!

The acidic vesicles of the endolysosomal (EL) system are emerging as an intracellular Ca²⁺ store implicated in the regulation of multiple cellular functions. The EL Ca²⁺ store releases Ca²⁺ through a variety of Ca²⁺-permeable channels, including Transient Receptor Potential (TRP) Mucolipin 1-3 (TRPML1-3) and two-pore channels 1-2 (TPC1-2), whereas EL Ca²⁺ refilling is sustained by the proton gradient across the EL membrane and/or by the endoplasmic reticulum (ER). EL Ca²⁺ signals may be either spatially restricted to control vesicle trafficking, autophagy and membrane repair or may be amplified into a global Ca²⁺ signal through the Ca²⁺-dependent recruitment of ER-embedded channels. Emerging evidence suggested that nicotinic acid adenine dinucleotide phosphate (NAADP)-gated TPCs sustain multiple cancer hallmarks, such as migration, invasiveness and angiogenesis. Herein, we first survey the EL Ca²⁺ refilling and release mechanisms and then focus on the oncogenic role of EL Ca²⁺ signaling. While the evidence in favor of TRPML1 involvement in neoplastic transformation is yet to be clearly provided, TPCs are emerging as an alternative target for anticancer therapies.

5-Azido-8-ethynyl-NAADP: A bifunctional, clickable photoaffinity probe for the identification of NAADP receptors

Nicotinic acid adenine dinucleotide phosphate is an evolutionarily conserved second messenger, which mobilizes Ca²⁺ from acidic stores. The molecular identity of the NAADP receptor has yet to be defined. In pursuit of isolating and identifying NAADP-binding proteins, we synthesized and characterized a bifunctional probe that incorporates both a photoactivatable crosslinking azido moiety at the 5-position of the nicotinic ring and a 'clickable' ethynyl moiety to the 8-adenosyl position in NAADP. Microinjection of this 5N₃-8-ethynyl-NAADP into cultured U2OS cells induced robust Ca²⁺ responses. Higher concentrations of 5N₃-8-ethynyl were required to elicit Ca²⁺ release or displace ³²P-NAADP in radioligand binding experiments in sea urchin egg homogenates. In human cell extracts, incubation of ³²P-5N₃-8-ethynyl-NAADP followed by UV irradiation resulted in selective labeling of 23 kDa and 35 kDa proteins and photolabeling of these proteins was prevented when incubated in the presence of unlabeled NAADP. Compared to the monofunctional ³²P-5N₃-NAADP, the clickable ³²P-5N₃-8-ethynyl-NAADP demonstrated less labeling of the 23 kDa and 35 kDa proteins (~3-fold) but provided an opportunity for further enrichment through the 'clickable' ethynyl moiety. No proteins were specifically labeled by ³²P-5N₃-8-ethynyl-NAADP in sea urchin egg homogenate. These experiments demonstrate that 5N₃-8-ethynyl-NAADP is biologically active and selectively labels putative NAADP-binding proteins in mammalian systems, evidencing a 'bifunctional' probe with utility for isolating NAADP-binding proteins.

Trafficking of Adhesion and Growth Factor Receptors and Their Effector Kinases

Cell adhesion to macromolecules in the microenvironment is essential for the development and maintenance of tissues, and its dysregulation can lead to a range of disease states, including inflammation, fibrosis, and cancer. The biomechanical and biochemical mechanisms that mediate cell adhesion rely on signaling by a range of effector proteins, including kinases and associated scaffolding proteins. The intracellular trafficking of these must be tightly controlled in space and time to enable effective cell adhesion and microenvironmental sensing and to integrate cell adhesion with, and compartmentalize it from, other cellular processes, such as gene transcription, protein degradation, and cell division. Delivery of adhesion receptors and signaling proteins from the plasma membrane to unanticipated subcellular locales is revealing novel biological functions. Here, we review the expected and unexpected trafficking, and sites of activity, of adhesion and growth factor receptors and intracellular kinase partners as we begin to appreciate the complexity and diversity of their spatial regulation.

Lysosomal storage diseases

Lysosomal storage diseases (LSDs) are a group of over 70 diseases that are characterized by lysosomal dysfunction, most of which are inherited as autosomal recessive traits. These disorders are individually rare but collectively affect 1 in 5,000 live births. LSDs typically present in infancy and childhood, although adult-onset forms also occur. Most LSDs have a progressive neurodegenerative clinical course, although symptoms in other organ systems are frequent. LSD-associated genes encode different lysosomal proteins, including lysosomal enzymes and lysosomal membrane proteins. The lysosome is the key cellular hub for macromolecule catabolism, recycling and signalling, and defects that impair any of these functions cause the accumulation of undigested or partially digested macromolecules in lysosomes (that is, 'storage') or impair the transport of molecules, which can result in cellular damage. Consequently, the cellular pathogenesis of these diseases is complex and is currently incompletely understood. Several LSDs can be treated with approved, disease-specific therapies that are mostly based on enzyme replacement. However, small-molecule therapies, including substrate reduction and chaperone therapies, have also been developed and are approved for some LSDs, whereas gene therapy and genome editing are at advanced preclinical stages and, for a few disorders, have already progressed to the clinic.

Mitochondrial junctions with cellular organelles: Ca2+ signalling perspective

Cellular organelles form multiple junctional complexes with one another and the emerging research area dealing with such structures and their functions is undergoing explosive growth. A new research journal named “Contact” has been recently established to facilitate the development of this research field. The current consensus is to define an organellar junction by the maximal distance between the participating organelles; and the gap of 30 nm or less is considered appropriate for classifying such structures as junctions or membrane contact sites. Ideally, the organellar junction should have a functional significance, i.e. facilitate transfer of calcium, sterols, phospholipids, iron and possibly other substances between the organelles (Carrasco and Meyer in Annu Rev Biochem 80:973–1000, 2011; Csordas et al. in Trends Cell Biol 28:523–540, 2018; Phillips and Voeltz in Nat Rev Mol Cell Biol 17:69–82, 2016; Prinz in J Cell Biol 205:759–769, 2014). It is also important to note that the junction is not just a result of a random organelle collision but have active and specific formation, stabilisation and disassembly mechanisms. The nature of these mechanisms and their role in physiology/pathophysiology are the main focus of an emerging research field. In this review, we will briefly describe junctional complexes formed by cellular organelles and then focus on the junctional complexes that are formed by mitochondria with other organelles and the role of these complexes in regulating Ca²⁺ signalling.

Lysosome trafficking and signaling in health and neurodegenerative diseases

Lysosomes, single-membrane organelles defined by a uniquely strong acidic lumenal pH and high content of acid hydrolases, are the shared degradative compartments of the endocytic and autophagic pathways. These pathways, and especially lysosomes, are points of particular vulnerability in many neurodegenerative diseases. Beyond the role of lysosomes in substrate degradation, new findings have ascribed to lysosomes the leading role in sensing and responding to cellular nutrients, growth factors and cellular stress. This review aims to integrate recent concepts of basic lysosome biology and pathobiology as a basis for understanding neurodegenerative disease pathogenesis. Here, we discuss the newly recognized signaling functions of lysosomes and specific aspects of lysosome biology in neurons while re-visiting the classical defining criteria for lysosomes and the importance of preserving strict definitions. Our discussion emphasizes dynein-mediated axonal transport of maturing degradative organelles, with further consideration of their roles in synaptic function. We finally examine how distinctive underlying disturbances of lysosomes in various neurodegenerative diseases result in unique patterns of auto/endolysosomal mistrafficking. The rapidly emerging understanding of lysosomal trafficking and disruptions in lysosome signaling is providing valuable clues to new targets for disease-modifying therapies.

Two-pore channels and disease

Two-pore channels (TPCs) are Ca²⁺-permeable endo-lysosomal ion channels subject to multi-modal regulation. They mediate their physiological effects through releasing Ca²⁺ from acidic organelles in response to cues such as the second messenger, NAADP. Here, we review emerging evidence linking TPCs to disease. We discuss how perturbing both local and global Ca²⁺ changes mediated by TPCs through chemical and/or molecular manipulations can induce or reverse disease phenotypes. We cover evidence from models of Parkinson's disease, non-alcoholic fatty liver disease, Ebola infection, cancer, cardiac dysfunction and diabetes. A need for more drugs targeting TPCs is identified.

Integration of nicotinic acid adenine dinucleotide phosphate (NAADP)-dependent calcium signalling

Nicotinic acid adenine dinucleotide phosphate (NAADP) is currently the most potent endogenous Ca²⁺ mobilizing second messenger. Upon specific extracellular stimulation, rapid production of NAADP has been observed in different cell types from sea urchin eggs to mammalian cells. More than 20 years after the discovery of NAADP, there is still controversy surrounding its metabolism and target receptors/ion channels and organelles. This article briefly reviews recent developments in the NAADP field. Besides the metabolism of NAADP, this review focuses on assumed organelles and putative targets, e.g. ion channels, with special emphasis on ryanodine receptor type 1 (RyR1) and two-pore channels (TPCs). The role of NAADP as a Ca²⁺ trigger is also discussed and the importance of NAADP in the formation of initial Ca²⁺ microdomains is highlighted.

Ryanodine Receptors in Autophagy: Implications for Neurodegenerative Diseases?

Intracellular Ca²⁺ signaling is important in the regulation of several cellular processes including autophagy. The endoplasmic reticulum (ER) is the main and largest intracellular Ca²⁺ store. At the ER two protein families of Ca²⁺ release channels, inositol 1,4,5-trisphosphate receptors (IP₃Rs) and ryanodine receptors (RyRs), are expressed. Several studies have reported roles in the regulation of autophagy for the ubiquitously expressed IP₃R. For instance, IP₃R-mediated Ca²⁺ release supresses basal autophagic flux by promoting mitochondrial metabolism, while also promoting the rapid initial increase in autophagic flux in response to nutrient starvation. Insights into the contribution of RyRs in autophagy have been lagging significantly compared to the advances made for IP₃Rs. This is rather surprising considering that RyRs are predominantly expressed in long-lived cells with specialized metabolic needs, such as neurons and muscle cells, in which autophagy plays important roles. In this review article, recent studies revealing roles for RyRs in the regulation of autophagy will be discussed. Several RyR-interacting proteins that have been established to modulate both RyR function and autophagy will also be highlighted. Finally, the involvement of RyRs in neurodegenerative diseases will be addressed. Inhibition of RyR channels has not only been shown to be beneficial for treating several of these diseases but also regulates autophagy.

Reticulon 3-dependent ER-PM contact sites control EGFR nonclathrin endocytosis

The integration of endocytic routes is critical to regulate receptor signaling. A nonclathrin endocytic (NCE) pathway of the epidermal growth factor receptor (EGFR) is activated at high ligand concentrations and targets receptors to degradation, attenuating signaling. Here we performed an unbiased molecular characterization of EGFR-NCE. We identified NCE-specific regulators, including the endoplasmic reticulum (ER)-resident protein reticulon 3 (RTN3) and a specific cargo, CD147. RTN3 was critical for EGFR/CD147-NCE, promoting the creation of plasma membrane (PM)-ER contact sites that were required for the formation and/or maturation of NCE invaginations. Ca²⁺ release at these sites, triggered by inositol 1,4,5-trisphosphate (IP₃)-dependent activation of ER Ca²⁺ channels, was needed for the completion of EGFR internalization. Thus, we identified a mechanism of EGFR endocytosis that relies on ER-PM contact sites and local Ca²⁺ signaling.

Ins and outs of Ca2+ transport by acidic organelles and cell migration

Much contemporary evidence underscores the pathophysiological importance of Ca²⁺ handling by acidic organelles such as lysosomes. Whereas our knowledge of how Ca²⁺ is released from these acidic Ca²⁺ stores (the ‘outs’) is advancing, we know relatively little about how Ca²⁺ uptake is effected (the ‘ins’). Here I highlight new work identifying animal Ca²⁺/H⁺ (CAX) exchangers that localize to acidic organelles, mediate Ca²⁺ uptake and regulate cell migration in vivo. Continued molecular definition of the acidic Ca²⁺ store toolkit provides new insight into Ca²⁺-dependent function.

EGFR Trafficking in Physiology and Cancer

Signaling from the epidermal growth factor receptor (EGFR) elicits multiple biological responses, including cell proliferation, migration, and survival. Receptor endocytosis and trafficking are critical physiological processes that control the strength, duration, diversification, and spatial restriction of EGFR signaling through multiple mechanisms, which we review in this chapter. These mechanisms include: (i) regulation of receptor density and activation at the cell surface; (ii) concentration of receptors into distinct nascent endocytic structures; (iii) commitment of the receptor to different endocytic routes; (iv) endosomal sorting and postendocytic trafficking of the receptor through distinct pathways, and (v) recycling to restricted regions of the cell surface. We also highlight how communication between organelles controls EGFR activity along the endocytic route. Finally, we illustrate how abnormal trafficking of EGFR oncogenic mutants, as well as alterations of the endocytic machinery, contributes to aberrant EGFR signaling in cancer.