Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease of unknown etiology characterized by distorted distal lung architecture, inflammation, and fibrosis. The molecular mechanisms involved in the pathophysiology of IPF are incompletely defined. Several lung cell types including alveolar epithelial cells, fibroblasts, monocyte-derived macrophages, and endothelial cells have been implicated in the development and progression of fibrosis. Regardless of the cell types involved, changes in gene expression, disrupted glycolysis, and mitochondrial oxidation, dysregulated protein folding, and altered phospholipid and sphingolipid metabolism result in activation of myofibroblast, deposition of extracellular matrix proteins, remodeling of lung architecture and fibrosis. Lipid mediators derived from phospholipids, sphingolipids, and polyunsaturated fatty acids play an important role in the pathogenesis of pulmonary fibrosis and have been described to exhibit pro- and anti-fibrotic effects in IPF and in preclinical animal models of lung fibrosis. This review describes the current understanding of the role and signaling pathways of prostanoids, lysophospholipids, and sphingolipids and their metabolizing enzymes in the development of lung fibrosis. Further, several of the lipid mediators and enzymes involved in their metabolism are therapeutic targets for drug development to treat IPF. Lipids are the principal constituents of cell membranes and play an essential role in several physiological and pathophysiological processes by mediating intracellular and extracellular cues. Phospholipids and sphingolipids, which are the structural components of the membranes, regulate cell shape, ion transport, intra- and inter-cellular communication and signaling. Many of the lipid-derived mediators are short-lived second messengers, and regulate cellular functions as migration, proliferation, apoptosis, redox balance, and cytoskeletal organization. Alteration or aberration in the generation of lipids mediators has been shown to regulate the physiology and pathophysiology of several disorders including, but not limited to, cancer, brain injury, cardiovascular diseases, kidney diseases, and pulmonary complications ,3,4,5,6.IPF is a progressive fibrotic disease of the lung of unknown etiology that occurs in older adults, diagnosed as usual interstitial pneumonia with a clinicopathologic criteria , whereinTGF-β is a critical cytokine that drives development of fibrosis. In mammals, three major isoforms of TGF-β have been identified, namely TGF-β1, -2, and -3 , and TGFAberrations in phospholipids and sphingolipids metabolism have been identified as potential contributors to the pathophysiology of IPF. A recent lipidomics study revealed that several lipids were found to be altered in plasma of IPF patients. Several glycerophospholipids that were screened in this study were found to be lowered in IPF patients. 30 out of the 159 glycerolipids were distinct between control and IPF patients . These aElovl6 was decreased in lungs of patients with IPF and lungs of bleomycin-treated mice  oscillations and prevented the activation of Akt and Ca2+/calmodulin-dependent protein kinase-II (CaMK-II) but did not prevent activation of Smad-2 or ERK. PGE2 also eliminated TGF-β-stimulated expression of collagen A1, and α-smooth muscle actin (α-SMA) . The -NH2 (amino) group on C2 is either free or linked to long-chain (C16–C18) or very long-chain (C20–C24) fatty acids with or without double bonds to generate ceramides. Ceramides can be further derivatized by the addition of a head group such as phosphorus, phosphocholine, glucose, galactose, or several sugar residues. Small amounts of sphingoid base containing a head group such as phosphorus, phosphocholine, or sugar units without the amide-linked fatty acid termed as “lyso sphingolipids” have been identified in biological fluids and tissues. As several excellent reviews describe the chemistry and biochemistry of sphingoid bases and sphingolipids [Sphingolipids are present across all eukaryotic cells and serve as structural and signaling lipids that regulate a variety of cellular functions under normal and pathological conditions. Advances in comprehensive lipid profiling techniques using LC-MS/MS and LC-ESI-MS/MS have identified close to 400 sphingolipidome in human plasma and tissues  that progolipids ,99,100, Sphingomyelin (SM), the most abundant sphingolipid in mammalian cells, is hydrolyzed by three major sphingomyelinases (SMases), namely acidic, alkaline, and neutral to generate ceramide and phosphocholine . CeramidSGPL1) to ethanolamine phosphate and Δ2-hexadecenal (∆2-HDE) [Sphingosine, derived from ceramide or dihydrosphingosine, obtained by biosynthesis from palmitoyl CoA and serine in the de novo pathway, is phosphorylated by sphingosine kinase (SPHK) 1 or 2 to generate S1P . S1P is (∆2-HDE) . In additrans-2-hexadecenoic acid followed by CoA addition to generate trans-∆2-hexadecenoyl CoA, which is reduced to palmitoyl CoA by Trans-2-enoyl-CoA reductase (TER) in mammalian cells [1–5 receptors on the plasma membrane of cells [In cells, ∆2-HDE is subsequently oxidized to an cells . The palan cells ; thus S1of cells . Ceramidof cells  and otheof cells , and to of cells ,113. Cerof cells . It is e2+-dependent neutral SMase; Mg2+-independent SMase; and alkaline SMase [SMPD1 the gene that encodes ASMase is subject to epigenetic regulation through methylation [Sphingomyelin, once considered to be an inert but essential membrane component, is now recognized as an important bioactive lipid and precursor for ceramide and sphingosylphosphocholine in mammalian cells . Sphingone SMase . Among tne SMase , and cysne SMase  are knowne SMase ,120. ASMne SMase . Althoughylation , which r56Fe radiation, the total lung ceramide levels were found to be elevated predominantly by the increase in palmitoyl fatty acid (C16:0)-containing ceramide molecular species [SMPD1, SMPD4, and DEGS1 mRNA expression that point to aberrant ceramide production, whereas reduced mRNA expression of ACER3 suggested dysregulated ceramide metabolism [In cells, ceramide could be generated by de novo biosynthesis, sphingomyelin degradation, synthesis from sphingosine and fatty acid, degradation of glucosyl- and galactosyl-ceramide and ceramide-1-phosphate ; however species . While ltabolism . However1–5 present on the plasma membrane of cells. S1P signals intracellularly, independent of S1P1–5, by binding to target proteins such as telomerase and HDACs [Traf2, but not Sphk1, disrupted TNF-α-mediated NF-kB and MAPK signaling causing skin inflammation [Sphk1 in mice or inhibition of SPHK1 by small molecule inhibitors conferred protection. Several excellent reviews have dealt with the role of S1P signaling in sepsis [S1P is the simplest bioactive sphingophospholipid that is present in circulating cells in the blood, biological fluids including plasma, BAL fluid, and in all the cell types in various organs. Cellular S1P levels are much lower (<0.5 µM) compared to plasma (0.5–1 µM) and tightly regulated by synthesis and degradation. About two-thirds of plasma S1P is bound to apolipoprotein M (apoM), which is a minor component of the High-density lipoprotein (HDL) particle ,131,132.nd HDACs , and modnd HDACs , and is nd HDACs . Additiond HDACs . Howeverammation . There iammation , BAL fluammation , and infammation ,146. Howammation , pulmonaammation , asthma ammation , experimammation , and IPFammation  circulatn sepsis , asthma n sepsis , and BPDn sepsis ; therefoThere is only one study that describes S1P levels in IPF. S1P levels were increased in BAL fluid and serum from IPF patients , which cSPHK1 or SPHK2 [Sphk1. Bleomycin upregulated the expression of SPHK1 in lungs compared to WT mice, and genetic deletion of Sphk1, but not Sphk2, attenuated bleomycin-induced mortality, lung injury and collagen deposition in the lungs. Further, administration of SPHK1 inhibitor, SKI-II to mice attenuated bleomycin-induced lung inflammation and collagen deposition in lungs confirming a role for SPHK1-mediated S1P in the development of PF [Sphk1 in fibroblasts and AECs, but not endothelial cells, protected mice from bleomycin-induced lung fibrosis [Increased S1P levels observed in plasma, BAL fluid, and lung tissues of IPF patients and in animal models of lung fibrosis could be attributed to modulation of its metabolism mediated by SPHKs, S1P lyase, and S1P phosphatases/lipid phosphate phosphatases. SPHK1, but not SPHK2, protein expression was increased in lung tissue lysates from IPF patients compared to control subjects, as well as in the murine model of bleomycin-induced lung inflammation and PF ,151. Micor SPHK2 . The caunt of PF . The devnt of PF ,157. Genfibrosis . Additiofibrosis . Furtherfibrosis . Thus, SDH-S1P levels, similar to S1P are increased in lung tissues of bleomycin-challenged mice  and plasSgpl1 or S1P lyase activity had an opposite effect on fibrogenesis. S1P lyase expression was upregulated in IPF lung tissues, primary lung fibroblasts isolated from patients with IPF and bleomycin-challenged mice. Knockdown of S1P lyase (+/−Sgpl1) in mice augmented bleomycin-induced PF, and patients with IPF had reduced Sgpl1 mRNA expression in PBMCs, exhibited higher severity of fibrosis and lower survival rate [S1P lyase irreversibly hydrolyzes S1P to ∆2-HDE and ethanolamine phosphate and thus regulates intracellular S1P levels ,136. S1Pval rate . Thus, t+/−Sgpl1 mouse lung and overexpression of hSGPL1 in HLFs clearly established a role for S1P in bleomycin-induced autophagy. Expression of beclin1, LC3, and the total number of autophagosomes in lung fibroblasts isolated from +/−Sgpl1 mice were significantly lower than in WT controls, and chloroquine treatment increased autophagosome numbers in lung fibroblasts isolated from WT mice compared with those from +/−Sgpl1 [hSGPL1 enhanced the expression of LC3 and beclin 1, and reversed TGF-β-induced decrease of LC3 expression and autophagosome formation [Autophagy, an intracellular catabolic process triggered to remove aggregated/misfolded protein(s) and damaged organelles, plays a role in IPF. Lung tissues from IPF patients demonstrated decreased autophagic activity as assessed by LC3, p62 protein expression and immunofluorescence, and numbers of autophagosomes . This inSgpl1+/− . Similarormation . Similarormation . Thus, iormation . Autophaormation . Thus, iormation .The first and rate-limiting enzyme in the de novo biosynthesis of sphingolipids is serine palmitoyltransferase (SPT), a pyridoxal phosphate-dependent enzyme, which condenses serine and palmitoyl CoA to generate 3-ketosphinganine (3-keto dihydrosphingosine) that is subsequently converted to ceramide and sphingomyelin  Figure . SPT is 1–5. Additionally, S1P generated in the nucleus signals within the nucleus independent of S1P1–5 and is involved in epigenetic regulation of pro-inflammatory genes activated by Pseudomonas aeruginosa in the lung epithelium [1–5 are coupled to Gi, Gα, Go, Gq, and G12/13 and this differential coupling dictates S1P signaling, in part, to various downstream effectors such as MAPKs, PI3K, Src, nMLCK, adenylate cyclase, phospholipase C (PLC), phospholipase D that result in a plethora of cellular responses [2,3 in PF; however, the role of S1P1, the predominant S1P receptor expressed in many mammalian cells, is unclear as complete deletion of S1p1 is embryonically lethal. However, some light has been shed on the S1P1 role in a vascular leak/lung fibrosis. In the bleomycin murine model, prolonged exposure of FTY720  and AUY954 (an S1P1 selective modulator) caused a pulmonary leak in mouse lungs while low doses of bleomycin did not induce lung fibrosis. However, administration of either FTY720 or AUY954 along with low doses of bleomycin exacerbated vascular leak that was accompanied by intra-alveolar coagulation and development of extensive lung fibrosis in mice [vβ6 expression in the lung and thrombin inhibition with dabigatran diminished αvβ6 expression and activation of the TGF-β canonical signaling [1 in lung endothelial cells [S)-phosphonate, that is non-hydrolyzable by lipid phosphate phosphatases, significantly inhibited bleomycin-induced alveolar-capillary leakage and inflammatory cell recruitment while FTY720 failed to confer protection against bleomycin-mediated lung inflammatory injury [S)-phosphonate is unclear, but it preserved expression of S1P1 on the cell surface while FTY720 allowed S1P1 internalization and recycling in endothelial cells.S1P signals intracellularly and extracellularly via five G-protein coupled receptors S1Pithelium . The S1Pesponses ,137. A g in mice . To unde in mice . The FTYignaling . Howeveral cells . In conty injury . The mec2 and S1P3 have been shown to be pro-inflammatory and profibrotic in the bleomycin model of lung fibrosis. Genetic deletion of S1pr2 or pharmacological inhibition of S1PR2 alleviated bleomycin-induced PF [S1pr2-deleted mice [S1pr2 in the development of bleomycin-induced lung fibrosis was demonstrated using S1pr2 KO mice and JTE-013 [S1pr3 attenuated bleomycin-induced lung inflammation and PF in mice without changing TGF-β levels, but by reducing connect tissue growth factor (CTGF) [S1PR2, or S1PR3, but not S1PR1, in HLFs attenuated Rho activity that is closely associated with fibrosis and differentiation of myofibroblasts [S1PR1 and S1PR3 could be therapeutic targets in PF. Interestingly, Fingolimod (FTY720) at 1.25 mg and 5.0 mg daily dose given to patients with relapsing multiple sclerosis showed a reduction in pulmonary function [S1Pduced PF . Bone mated mice . A simil JTE-013 , a pharm JTE-013 . Knockdor (CTGF) . S1PR1 ar (CTGF) . Depletiroblasts . Thus, bfunction  as obserSmad3-deficient mice showed alveolar destruction resembling emphysema but developed lung fibrosis in response to bleomycin [Sphk1 with siRNA or inhibition of SPHK1 activity with inhibitors decreased α-SMA and fibronectin expression upregulated by TGF-β [2 and S1P3, but not S1P1, with siRNA reduced TGF-β-induced α-SMA expression, and blocking SPHK1 had no effect on SMAD2/3 phosphorylation [Sphk1 deleted or SPHK1 inhibitor administered mice, demonstrating the interaction between the TGF-β and SPHK1/S1P signaling axis in vivo [2,3 signaling axis [SMAD3 siRNA [SMAD3 in regulating SGPL1 expression induced by TGF-β was verified by ChIP assay as well as hSGPL1 luciferase promoter activity in HLF [SPHK1 by SMAD3 or other transcriptional factors in response to TGF-β in normal and IPF lung fibroblasts needs to be further investigated. The TGF-β-mediated fibroblast differentiation to myofibroblast was attenuated by overexpression of SGPL1 in HLF and is attributed to the decrease in intracellular S1P level, increase in expression of LC3 and Beclin1, and autophagy [TGF-β is a critical cytokine that drives the development of IPF and PF in animal models. TGF-β promotes EMT in AECs ,190, fibleomycin . In addileomycin ,198. Intby TGF-β ,150,187.rylation . In the  in vivo ,150. Bot in vivo ,150, furing axis . TGF-β iD3 siRNA . The tray in HLF . The trautophagy . Thus, uThe pathophysiology of IPF is characterized by increased ROS production and an imbalance in redox status of the lung tissue ,201. The2, PLC, PLD, and lyso PLD or autotaxin (ATX) generate bioactive lipid molecules that play key roles in the development and progression of lung fibrosis [Phospholipids are essential components of all biological membranes and metabolic dysregulation of phospholipids have been shown to contribute to the pathogenesis of several pulmonary disorders including IPF and experimental PF. Lipidomics of IPF lungs or lungs of animal models have not been performed; however, phospholipid content in the BAL fluids was reduced in IPF lungs and mouse lungs of animal models. Aberrant phospholipid metabolism by phospholipid metabolizing enzymes such as PLAfibrosis . Further−/−Mfn1 and −/−Mfn2 mice challenged with bleomycin were found to have altered lipid metabolism of cholesterol, ceramides, phosphatidic acids, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, plasmalogen phosphatidylethanolamine, and decreased SP-B, SP-C gene expression [The lung surfactants, in addition to dipalmitoyl phosphatidylcholine, dipalmitoyl phosphatidylglycerol and phosphatidylinositol also include four surfactant proteins, SP-A, SP-B, SP-C and SP-D, which act as a defense mechanism against toxic pathogens or microbes trying to invade the lung. SP-A and SP-D serve as biomarkers of IPF, as seen by their ability to predict the survival rates in IPF patients. In the BAL fluid, the levels of phosphatidylglycerol were lower while the contents of phosphatidylinositol and sphingomyelin were elevated, and the dysregulated phospholipid levels correlated with the severity of the disease ,219,220.pression . Mfn1/2-1/PLA2 [N-acetyl-l-cysteine), antioxidants, and iron chelators suggesting the role of ROS, lipid peroxidation, and iron in the process. This study revealed a novel mechanism of the bleomycin-induced redox-sensitive activation of PLD that led to the generation of PA, which was cytotoxic to lung ECs, thus suggesting a possible bioactive lipid-signaling mechanism of microvascular disorders encountered in PF [Pld1−/−and Pld2−/− deficient mice were protected against bleomycin-induced lung inflammation and fibrosis, thereby establishing the role of PLD in fibrogenesis. Further, bleomycin stimulated mitochondrial superoxide production, mtDNA damage, and apoptosis, which was attenuated by the catalytically inactive mutants of PLD1 or PLD2, downregulation of PLD2 expression with siRNA or inhibition of PLD1 and PLD2 with specific small molecule inhibitors [PLD hydrolyzes phosphatidylcholine to phosphatidic acid (PA), and choline ,230,231.1/PLA2 ,235, res1/PLA2 ,237. PLD1/PLA2 ,239. PLDed in PF . A more hibitors , mTOR [2hibitors , and modhibitors . In addihibitors ; howeverDiacylglycerols are lipid intermediates generated de novo in cells for the biosynthesis of triglycerides (TGs) and phospholipids and a product of PLC and PLD pathways. DAGs are physiological and endogenous activators of protein kinase C (PKC) conventional  and novel  isoforms that are known regulators of pleiotropic downstream signaling cascades in cells. DAGs do not accumulate and are converted to PA by DAG kinase (DAGK) or TGs by acyltransferases. Of the ten isoforms of DAGK, DAGK-α has been shown to promote radiation-induced fibrosis . Radiati1/PLA2 while 1-acyl or 2-acyl lysophosphatidic acid (LPA) is formed from 1-acyl- or 2-acyl LPC by the action of lyso PLD or ATX [Lysophospholipids such as lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE) are generated from PC and PE, respectively by PLAD or ATX  , a major phospholipid of mitochondria, plays an important role in the structural organization, energy metabolism, and functioning of the mitochondria ,257. It hLYCAT in bleomycin-treated mouse lung restored the cardiolipin level and unsaturated to saturated fatty acid ratio and unsaturation index [Bleomycin challenge significantly decreased the cardiolipin level and mol% of C18:1 and C18:2 fatty acids in mouse lung compared to the control group. In contrast to C18:1 and C18:2, the mol% of C18:0 was higher in the lung of bleomycin-challenged mice. Bleomycin challenge shifted the unsaturated to saturated fatty acid ratio and unsaturation index were lower in bleomycin-challenged animals, indicating loss of unsaturated fatty acids, especially C18:1 and C18:2 fatty acids in the cardiolipin. Overexpression of on index .hLYCAT overexpression reduced several indices of lung fibrosis induced by bleomycin and radiation, whereas downregulation of native LYCAT expression by siRNA accentuated fibrogenesis in the preclinical bleomycin- and radiation mice models. In vitro, LYCAT overexpression attenuated bleomycin-induced cardiolipin remodeling, mitochondrial membrane potential, ROS generation, and apoptosis of AECs. Thus, modulating LYCAT expression could offer a novel approach to ameliorate the progression of lung fibrosis.LYCAT or Acyl-CoA cardiolipin acyltransferase (ALCAT1) is one of the key enzymes involved in remodeling the fatty acid composition of cardiolipin from saturated and monounsaturated to polyunsaturated (~60% linoleic acid) fatty acids in the mitochondria . DefectiLYCAT expressed in AECs of IPF lungs  and in iLPA is the simplest naturally occurring glycerophospholipid and consists of a glycerol backbone attached to a long-chain fatty acid of varying chain length and saturation/unsaturation and a free polar phosphate group. LPA is found in all cells and biological fluids including plasma, serum, and BAL, and its levels in biological fluids and tissues are elevated in several human pathologies including IPF and other forms of PF ,268,269.ENPP2 gene in mammalian cells [1 or PLA2 and lecithin cholesterol acyltransferase (LCAT) enzyme. LCAT is a transacylase that transfers fatty acid from sn-2 position of PC to cholesterol to generate LPC and cholesteryl ester that is predominantly C81:1 (oleic acid) [At least two major pathways have been identified for LPA production in biological systems. The first pathway is mediated by autotaxin (ATX) or lysophospholipase D that utilizes extracellular LPC as a substrate to generate LPA and the majority of plasma LPA is produced via this mechanism ,269,271.an cells ,274. It an cells . It was an cells  and usesan cells ,271. LPCan cells ,277,278.ic acid) . ATX canic acid) ,267,271.1 or PLA2 can hydrolyze PA to 1-acyl or 2-acyl-sn-glycero-3-phosphate within the cell [1-PLA2/PA pathways may vary based on the fatty acid composition of the substrate. The third minor pathway of intracellular LPA production involves phosphorylation of 1-acyl- or 2-acyl-monoglycerol by acylglycerol kinase (AGK) [AGK, independent of its kinase activity, dysregulates mitochondrial protein import leading to Sengers syndrome [The second pathway of intracellular LPA generation in cells involves phospholipase A1/A2 mediated hydrolysis of PA derived from either the de novo biosynthesis or PLD1/PLD2 signaling axis that uses PC, PS, and PE as substrates. While it will be difficult to distinguish between the two pools of PA generated inside the cell, specific PLAthe cell ,235. These (AGK) ,280. AGKsyndrome . The rol1–6. The six receptors are widely distributed with overlapping specificities and different affinity for LPA [i, G12/13, Gq/11, and Gs that initiate numerous signaling cascades within the cell. Several studies have identified stimulation of MAPKs, PI3K, Rho, Rac, and phospholipase activation by LPA through differential coupling to various Gα proteins. Of the six LPARs, LPA6 has sequence homology with P2Y receptor and higher affinity to 2-acyl LPA than 1-acyl LPA [The numerous physiological and pathophysiological responses of LPA are mediated through six 7-transmembrane G-protein coupled receptors (GPCRs) collectively termed as LPA for LPA . The LPAacyl LPA . These rThe transcriptional factor, PPARγ regulates a wide range of physiological and pathophysiological activities including energy metabolism, inflammation, atherogenesis, and fibrosis ,285. LPAElevated LPA levels were found in BAL fluids of IPF patients and the bleomycin murine model ,291. TheENPP2 was identified as a candidate gene regulating lung formation, development, and remodeling by genome-wide linkage analysis coupled with expression profiling [ENPP2 in mouse (−/−ENPP2) was embryonically lethal [+/−ENPP2) in mouse had no major phenotypic effect in lungs. Overexpression of ENPP2 in bronchial epithelium or liver resulted in a 2-fold increase of ATX expression in plasma without any phenotype suggesting ATX/LPA signaling axis per se has no consequence on lung morphology and function [ENPP2 in bronchial epithelial cells and macrophages reduced ATX levels in BAL fluid and disease severity confirming a pathophysiological role for ATX in lung fibrosis [rofiling . Based oy lethal ,298,299;function . ATX is function ,301. Thefibrosis . A numbefibrosis , PF-8380fibrosis , BBT-877fibrosis , and GLPfibrosis  have beefibrosis , indicat1–3 has been identified to be involved in the development of PF. Fibroblasts isolated from IPF lungs had elevated expression of LPA1, and inhibition of LPA1 reduced fibroblast responses to chemotactic activity [Lpar1 deficient mice that were exposed to bleomycin, and LPA signaling through LPA1 induced apoptosis of normal bronchial epithelial cells [1 promoted resistance of lung fibroblasts to apoptosis. An antagonist of LPA1, BMS-986020, was found to lessen the extent of the decline in the forced vital capacity of lungs in IPF patients [1 antagonist AM966 attenuated bleomycin-induced vascular leakage, lung injury, inflammation and fibrosis [1 promotes apoptotic and profibrotic responses in lung epithelial cells and fibroblasts, respectively. Other LPA1 antagonists such as AM152, SAR100842 and ONO-7300243 have been shown to be beneficial in vivo against bleomycin mediated lung inflammation and fibrosis and in vitro on epithelial cell apoptosis and fibroblast migration and differentiation; however, none have advanced to or beyond clinical trials. Similar to LPA1, deficiency of Lpar2 in mice conferred protection from bleomycin-induced lung inflammatory injury and PF in mice [+ apoptotic alveolar and bronchial epithelial cells was observed in the lung tissues of bleomycin-challenged Lpar2 mice compared to the WT mice. Further, LPA-induced expression of TGF-β and differentiation of HLFs was reduced in lung fibroblasts deficient of Lpar2. LPA was found to signal through Lpar2 to regulate the ERK1/2, SMAD3, AKT, and p38 MAPK pathways, but not SMAD2 and JNK pathways during PF [3–6 in IPF and experimental lung fibrosis is yet to be established.LPA signaling via LPAactivity . The numal cells . In contpatients  while anfibrosis . Thus, L in mice . Reduceduring PF  , hydroperoxyl (●OOH) radicals, and ROS to generate lipid peroxidation end products, mildly oxidized and truncated oxidized phospholipids [N-acetylcysteine, and the iron chelator, deferoxamine attenuated the bleomycin-mediated oxidative stress and lung injury [+/−Gpx4) mice showed enhanced bleomycin-induced lung fibrosis and TGF-β-mediated myofibroblast differentiation in vitro [Membrane lipids are rich in polyunsaturated fatty acids, which are susceptible to oxidation and peroxidation by hydroxyl  increased foam cell formation and exacerbated lung fibrosis in mice from bleomycin challenge [sn-glycero-3-phosphocholine (POVPC), an Ox-PC, to +/+Pai-1 increased hydroxyproline in the lung and reduced serum SP-D levels in contrast to −/−Pai-1 mice treated with POVPC [There is compelling evidence for monocyte-derived macrophages and not residential lung macrophages to be involved in the development of PF in experimental murine models . Accumulrophages ,320,321.hallenge ,322. Anoth POVPC ,324. TheMUC5B and Sftpc gene confer a predisposition to the development of IPF. In the last three decades, several target genes and proteins have been identified as key players in the pathophysiology healing and lung repair that result in lung fibrosis. With the advancement in mass spectrometry and lipidomics, mediators derived from fatty acids, glycerolipids, phospholipids, and sphingolipids have been identified in lung tissues and biological fluids of IPF patients and experimental models of fibrosis. These bioactive lipid mediators exhibit pro- or anti-fibrotic effects in vivo and in vitro. PLA2 catalyzed hydrolysis of a phospholipid such as PC enriched in arachidonic acid generates free AA that is subsequently converted by COX2/PG synthase to prostanoids such as PGD2, PGE2, PGF2α, and by 5-LO to LTs. While PGD2 and PGF2α and LTs have pro-fibrotic properties, PGE2 exhibits anti-fibrotic effects in the experimental bleomycin model of PF and TGF-β-induced fibroblast activation. The SPHK1/S1P/S1PR, PLD2/PA, and ATX/LPA/LPAR signaling axes have been identified as significant contributors to fibrosis in IPF patients and bleomycin/radiation models of PF. Blocking SPHK1 with SKI-II attenuated lung inflammation and development of lung fibrosis 3 weeks post-bleomycin challenge indicating a long-term beneficial effect of this SPHK1 inhibitor. However, PF543 is yet to be evaluated for its efficacy in clinical trials. As S1P signals via S1PRs, and deletion of S1PR2 or S1PR3 ameliorated bleomycin-induced PF, use of specific receptor antagonists for S1PR2 or S1PR3 might be beneficial, which needs further investigation.IPF is a heterogeneous interstitial lung disease caused by abnormal host-defense, activation of immune and non-immune cells, and dysfunctional wound, male gender, cigarette-smoking, and mutations in 1 with antagonists such as BMS-976278, AM152, SAR100842, and ONO-7300243 conferred protection against bleomycin-mediated lung inflammation and fibrosis in vivo and in vitro on epithelial cell apoptosis and fibroblast migration and differentiation; BMS-976278 has shown promise in clinical trials. Another promising target is LYCAT, a cardiolipin remodeling enzyme, which is upregulated in the lungs of IPF patients and bleomycin treated animals. LYCAT overexpression in mouse lung reduced bleomycin-induced PF and activation of LYCAT activity or enhances its expression in lung epithelial cells and fibroblasts might be a novel approach to reduce PF in pre-clinical models before advancing to human studies. Other potential targets for drug development for IPF include cysLTs and its receptors. Montelukast, a cysLT type I receptor antagonist, approved by the FDA for the management of asthma. Although Montelukast showed some beneficial effects against IPF, and its potential as a therapeutic agent for lung fibrosis is inconclusive and require more trials. Another class of mediators known as lipoxins, resolvins, protectins, and maresins, which are derived from polyunsaturated fatty acids may modulate the resolution of inflammation and fibrosis. Resolvin D1 is one lipid mediator that is derived from eicosapentaenoic acid and docosahexaenoic acid attenuates lung inflammation and interstitial fibrosis as well as inhibits TGF-β-induced EMT suggesting it as a potential therapeutic agent against IPF. Thus, understanding the mechanisms of generation, and signaling pathways of lipid mediators generated in PF provides an opportunity to develop therapies to attenuate the development of lung fibrosis and facilitate the process resolution of fibrotic injury.There has been tremendous advancement in developing ATX inhibitor(s) as a potential therapy in IPF . The ATX


Previous studies showed that monoclonal immunoglobulins G (IgGs) of “monoclonal gammopathy of undetermined significance” (MGUS) and myeloma were hyposialylated, thus presumably pro-inflammatory, and for about half of patients, the target of the monoclonal IgG was either a virus—Epstein–Barr virus (EBV), other herpes viruses, hepatitis C virus (HCV)—or a glucolipid, lysoglucosylceramide (LGL1), suggesting antigen-driven disease in these patients. In the present study, we show that monoclonal IgAs share these characteristics. We collected 35 sera of patients with a monoclonal IgA , and we were able to purify 25 of the 35 monoclonal IgAs . Monoclonal IgAs from MGUS and myeloma patients were significantly less sialylated than IgAs from healthy volunteers. When purified monoclonal IgAs were tested against infectious pathogens and LGL1, five myeloma patients had a monoclonal IgA that specifically recognized viral proteins: the core protein of HCV in one case, EBV nuclear antigen 1 (EBNA-1) in four cases (21.1% of IgA myeloma). Monoclonal IgAs from three myeloma patients reacted against LGL1. In summary, monoclonal IgAs are hyposialylated and as described for IgG myeloma, significant subsets  of patients with IgA myeloma may have viral or self (LGL1) antigen-driven disease. Myeloma is preceded by an asymptomatic stage termed monoclonal gammopathy of undetermined significance (MGUS) –4. In MGThe causes of MGUS have long remained unknown, although it is established that chronic infection may lead to the emergence of oligoclonal and eventually, monoclonal plasma cells and the subsequent production of a so-called “monoclonal Ig.” In addition, it is thought that certain genetic backgrounds, ethnicity, lipid disorders, and obesity may increase the risk of developing myeloma. Consistent with these observations, the study of Ig genes in malignant plasma cells had revealed restricted heavy-chain variable-region use and highly hypermutated Ig heavy- and light-chain genes, which supports antigen-mediated selection of the malignant clone , 9. Recevia chronic antigen-driven stimulation of the B-cell receptor (BCR) that has identical heavy and light chain specificity to the secreted IgG. Interestingly, monoclonal IgGs may contribute to the inflammation associated with MGUS and myeloma, since they have a very low level of sialylation of the Fc fragment, a characteristic typically associated with a pro-inflammatory action . Among those, 6 MGUS and 22 myeloma were diagnosed at the University Hospitals (CHUs) in Tours and Bordeaux (France) over the 2010–2016 period. Samples of blood serum from seven additional patients with IgA myeloma from international cohorts of relapsed myeloma were provided by Novartis .g (4°C), and serum aliquots were frozen. Measurement of Ig concentration, separation of monoclonal IgAs from other Igs, and verification of purity were performed as described previously  were coated overnight at 4°C with 50 μl of goat anti-human IgA antibody  diluted 1:500 in 25 mM borate buffer pH 9. After washing with PBS-Tween 0.05%, wells were saturated for 2 h at 37°C with 0.25% B-grade bovine gelatin  diluted in 0.1% PBS-Tween; 50 μl of monoclonal IgA (400 ng/ml) was then added . After washing, 50 μl of biotinylated mouse anti-human IgA1 or IgA2 antibody  was added . After washing, 50 μl of streptavidin-HRP  was added . After washing, 50 μl of 3,3′,5,5′-tetramethylbenzidine (TMB) was added. The reaction was stopped with 50 μl of sulfuric acid (0.5 M). Optical density was read at 450 nm using a Spark 10 M multimode microplate reader .Helicobacter pylori (H. pylori), Toxoplasma gondii (T. gondii), and Borrelia burgdorferi (B. burgdorferi) . Fluorescence signals were detected with the Odyssey infrared imaging system scanner at 21-μm resolution  and quantified using the GenePix® Pro 4 Microarray Acquisition and Analysis Software  , HSV-2, cytomegalovirus (CMV), varicella zoster virus (VZV), HCV, dorferi) –15, 21. CA, USA) –15, 21. negative , 21.Nitrocellulose membranes  were spotted with recombinant EBNA-1 protein, relevant and irrelevant EBV peptides, or HCV core protein, then dried . SaturatFor LGL1-specific immunoblotting, polyvinylidene fluoride (PVDF) membranes were incubated for 90 min in 100 μg/ml of LGL1 in 0.1 M sodium bicarbonate, rinsed 3 times in PBS and 0.1% Tween 20 detergent, then blocked for 2 h with 5% bovine serum albumin (BSA) . SamplesSambucus nigra agglutinin (SNA) diluted 1:750  for 90 min and then 50 μl of streptavidin HRP diluted 1:1,000  for 1 h, at 37°C. Then, 50 μl of TMB, the chromogenic substrate for HRP  was added, and the reaction was stopped by 50 μl of 0.5 M sulfuric acid, after 3 min for IgA detection, and after 5 min for sialic acid detection. Optical densities (OD) were measured using a Spark 10 M multimode microplate reader  at 450 nm. The percentage of sialylation was calculated as follows: [SNA OD signal/IgA OD signal]/[ng IgA in SNA well/ng IgA in IgA well] × 100. In all experiments, internal controls were used to assess reproducibility.An enzyme linked lectin assay (ELLA) was developed to analyze IgA sialylation, and an enzyme linked immuno-sorbent assay (ELISA) was used for the detection of total IgAs, as previously described . Ninety-U-test or a Kruskal–Wallis test followed by Dunn's post-hoc test was performed. The tests used are indicated in the legends of figures and tables. A value of p < 0.05 was considered statistically significant.Data analysis was performed by GraphPad Prism 6.01 software. Patient parameters were expressed as medians and ranges, or/and means ± standard error of the mean (SEM). The Chi-2 test was used. For continuous variables, a Mann–Whitney The study was promoted by the CHU of Nantes, France (# RC12 0085) with the approval of the local and national ethical committee . Written informed consents were obtained from patients and healthy donors, by the blood bank (Etablissement Français du Sang (EFS), Nantes, France). A convention was signed between CRCINA and EFS Pays de La Loire.In this retrospective study, 35 patients with a monoclonal IgA were recruited . Annotated clinical data were available for 26 patients ; the biological and clinical characteristics of patients are shown in T. gondii of MGUS, and myeloma patients were comparable to those of our previous studies and to those observed in the general population. The rates of positive IgG serology differed for HSV-2 (high frequency of positivity in the IgA cohort) and VZV (likely underestimated by the MIAA) , and HSV-2   using the MIAA, which tests for reactivity to lysates and/or antigens representing nine infectious pathogens , 15, 21.he MIAA) , 15, 21.he MIAA) –35. The ct test) . They weMonoclonal IgAs were separated individually from other Igs from blood serum, then incubated on the MIAA. In general, monoclonal IgAs were more difficult to purify than monoclonal IgGs because of their migration in agarose in the beta–gamma zone . AltogetPurified monoclonal IgAs from MGUS and myeloma patients were analyzed with the LGL1 assay adapted from Nair et al. . As showWe compared the clinical characteristics of the four myeloma patients with EBNA-1-specific monoclonal IgA [“EBNA-1(+)” patients] with those of the 17 myeloma patients with a monoclonal IgA that was non-reactive for pathogens of the MIAA assay [“MIAA(–)” patients] . Compare***p < 0.0001, Mann–Whitney U-test)   12, 21), 21***p  U-test) . In addi U-test) , Table 4This is the first analysis of the antigenic origins of IgA myeloma. In this small cohort, no antigenic target was identified for the monoclonal IgAs from MGUS patients, but for patients with IgA myeloma, two viruses  were candidate targets for the monoclonal IgA of 5/19 patients (26.3%). In addition, the monoclonal IgA of 3/19 myeloma patients (15.8%) reacted with LGL1, a glucolipidic auto-antigen. These results imply that chronic stimulation by viral antigens or auto-antigen LGL1 may underlie the initiation of ~40% of IgA myeloma, as reported for MGUS and myeloma with a monoclonal IgG , 12.H. pylori, T. gondii, B. burgdorferi, and higher for VZV. Thus, this cohort of patients with IgA myeloma maintained IgG- and/or IgA-mediated protection against EBV, CMV, HSV-1, HSV-2, and VZV.In this study, myeloma patients with a monoclonal IgA were typically older and had stage III disease, consistent with IgA myeloma being more severe than IgG myeloma –28. AnalTwo viral proteins, EBV EBNA-1 and HCV core, were specifically recognized by monoclonal IgAs from certain myeloma patients; these proteins are also the targets of monoclonal IgGs in both MGUS and myeloma –15. BecaAltogether, our findings suggest that for a significant fraction (>30%) of patients with IgA or IgG myeloma, the initial cause of disease may be chronic antigen stimulation due to a viral infection (particularly by EBV or HCV) or autoimmunity against LGL1 –14. ThesStreptococcus pneumoniae for instance) . Several auto-antigens have been associated with CLL, notably cytoskeleton components , cardiolipin, proline-rich acidic protein-1 (PRAP-1), dUTPase, and auto-antigens at the surface of apoptotic cells and bacteria (nstance) –51. Evidnstance) –54. Reganstance) . The varnstance) –58. Thusnstance) , 52–54. nstance) –14. Of nnstance) . KnowingIgA glycosylation was also analyzed. Monoclonal IgAs differed from IgAs from healthy donors by their low level of sialylation, a characteristic observed for monoclonal IgGs and associated with a pro-inflammatory action of the Ig Fc fragment upon binding to FcγR, notably in monocytes and macrophages . HoweverIn aging populations, the incidence of MGUS and the subsequent risk of myeloma and other MGUS-associated diseases increase , 61. TheIn conclusion, EBV EBNA-1, the HCV core protein, and LGL1, a glucolipid, were identified as candidate antigenic targets of the purified monoclonal Igs of patients with IgA myeloma. An abnormal immune response to these viruses or to LGL1 may therefore be part of the pathogenesis of IgA myeloma, as reported for IgG myeloma. Detecting patients who present with LGL1- or virus-associated MGUS or myeloma is important since it is possible to add antigen target reduction to classic treatments.The datasets generated for this study are available on request to the corresponding author.The studies involving human participants were reviewed and approved by Local ethics committee, CHU Nantes. The patients/participants provided their written informed consent to participate in this study.SH, AB, EB-C, and JH designed the research, analyzed the data, and wrote the manuscript. AB, CS, NM, SA-M, MF, EB-C, and JH performed the experiments and edited the manuscript. AT, EP, PL, and FM contributed patient samples and data. All approved the version to be submitted for publication and agreed to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the article are appropriately investigated and resolved.The authors declare that this study received funding from Janssen (USA). Janssen had no role in study design, data collection and analysis, or preparation of the manuscript.


TP53, which is mutated with high frequency in more cancers than any other tumor suppressor gene. Beyond the loss of wild-type p53 functions, mutations in the TP53 gene often lead to the expression of full-length proteins with new malignant properties. Among the defined oncogenic functions of mutant p53 is its effect on cell metabolism and autophagy. Due to the importance of autophagy as a stress adaptive response, it is frequently dysfunctional in human cancers. However, the role of p53 is enigmatic in autophagy regulation. While the complex action of the wild-type p53 on autophagy has extensively been described in literature, in this review, we focus on the conceivable role of distinct mutant p53 proteins in regulating different autophagic pathways and further discuss the available evidence suggesting a possible autophagy stimulatory role of mutant p53. Moreover, we describe the involvement of different autophagic pathways in targeting and degrading mutant p53 proteins, exploring the potential strategies of targeting mutant p53 in cancer by autophagy.One of the most notoriously altered genes in human cancer is the tumor-suppressor  Yet, nohe cells . This pror types . Accordi diverse . TherefoTP53 mutations, is widely recognized and beyond the scope of this review. Instead, the central focus will be on what we currently know about the conceivable roles of distinct mutant p53 proteins in regulating different autophagic pathways. Further, given that alterations in autophagy activity might vary in different types and stages of tumors, we will elaborate on the emerging rationale that the functional effects of distinct mutant p53 proteins on autophagy may also differ. Given that autophagy is tightly connected to dynamic changes in metabolism, we discuss the concept that in certain conditions cancer cells with mutant p53 may favor instead of counteract autophagy. Furthermore, it is well known today that autophagic pathways are reported to mediate the stability of mutant p53 proteins. In the following parts, we will describe the involvement of different autophagic pathways in controlling the cellular level and degradation of mutant p53 proteins as well as the potential therapeutic strategies for targeting mutant p53 in cancer by various autophagic pathways.For the purpose of this review, we will focus on describing and discussing the considerable distinct effects of mutant p53 proteins may exert on autophagy, although other mutant p53 activities may affect different aspects of tumor biology. Autophagy is a fundamental catabolic process by which eukaryotic cells digest macromolecules and damaged organelles in the lysosomes. A well-defined positive regulatory role of wild-type p53 on autophagy with resulting counteracting autophagy inhibitory effect caused by Autophagy is a highly conserved homeostatic recycling process, where it functions to mediate the degradation of cellular macromolecules, damaged organelles or internalized pathogens in the lysosomes , 33. Undvia the activity of hydrolases in autolysosomes   .ATG5, ATG7, and BECN1 where impaired autophagy accelerates tumorigenesis in animals  (PTEN), d) promoting the expression of the MA core machinery  (DRAM1 (damage-regulated autophagy modulator 1) and splice variants that effects several stages of autophagy (HIF-1 (hypoxia inducible factor 1), g) inducing regulators (Isg20L1 and HSF1 (heat shock transcription factor 1) that in turn transactivates autophagy related genes (ATG7) (TGM2 (transglutaminase 2) which promotes autophagic flux by enhancing autophagic protein degradation and autolysosome clearance  stimulating the nutrient energy sensor AMPK (AMP-activated protein kinase)  , 70, b) , REDD1) , 72, c) 2, ATG7) , 74, e) utophagy , f) upres (ATG7) , h) indulearance , i) intelearance , and dirlearance , 80]. ThmiR-34a and miRs-34a/34c-5p that targets ATG9A and ATG4B, respectively)  inhibition of the AMP-dependent kinase and thereby activating mTOR , b) inductively) , 84, d) ctively) , 86, andctively) , and f) ctively) .PRKN (Parkin), a key effector of this selective autophagy, involved in degradation of impaired mitochondria  , but not the wild-type, have been shown to interact with AMPKα through the DNA-binding domain, where mutant p53 disrupt the interaction of AMPKα-LKB1. This causes inhibited AMPKα phosphorylation and suppressed AMPK activity. In addition, a role of p53R273H was demonstrated to control the mevalonate pathway (MVP) through the transcriptional modulation of SREBP1, a downstream target of AMPK  , most likely due to the lack of a C-terminal p53 nuclear export signal, whereas the cellular localization of the mutant p53G245C differs with the confluency of the cell culture. Nonetheless, based on its effect on the AMPK-mTOR axis, the cancer related expression of p53R248W,C176S,R273H,R175H, R175H mutants are shown to display a gained function of affecting metabolism, thereby inhibit autophagy irrespectively of tissue of origin or prevalence to a subcellular localization  , most of, ATG12) Figure 1, ATG12) . mTOR fu, ATG12) . AMPK, o, ATG12) , 103. Thy stress . Now, se of AMPK . Further2 (PKM2) , a key elization .de novo serine synthesis, urea cycle and oxidative phosphorylation  , 127. Thβ signaling and by regulating the expression of various pro-EMT-Transcription factors  were upregulated in cancer cells. Apart from stimulating the expression of endosomal proteins, both the wild-type and p53R273H mutants are indicated to effect proteins involved in the secretory pathway, protein secretion via extracellular vesicles (EV) and exosomes of endosomal origin  induce stabilization of mutant p53, while, the overexpression of Ulk1 or Beclin-1 results in mutant p53 degradation  the cruciferous-vegetable-derived phenethyl isothiocyanate (PEITC), which render the p53R175H,R273H, R248Q mutants by degradation following reactivation of the mutants, e) heat shock protein 90 (HSP90) inhibitors such as 17-allylamino-17-demethoxygeldanamycin (17-AAG) or ganetespib  show difference in SAHA sensitivity. This strongly suggests that, cell type and -contexts need to be considered for SAHA-mediated cytotoxicity in cancer cells. Further, the Zn(II)-curcumin and capsaicin by acting on protein folding is able to reactivate wild-type p53 that induces its target gene DRAM to promote autophagy, while gambogic acid is shown to induce mutant p53 protein degradation through proteasome ubiquitination by carboxy terminus of Hsc70 interacting protein (CHIP). CHIP, on the other hand, known to display chaperone and E3 ligase activity, is involved in stabilizing and degrading both wild‐type and mutant p53 proteins, where the degradation of mutant p53 by CHIP was shown to be via autophagy through K63‐linked polyubiquitination. Under both normal and hypoxic conditions CHIP was shown to selectively degrade aggregation‐prone mutants p53R110L, p53R110P and p53R175H, without significant effects on the level of nonaggregating mutant p53R248W and p53R273H utophagy , c) inhinetespib , and f)  mutants , 164–167 mutants , that rep53R273H . Moreovetability , 170. Fotability . Howevervia CMA was uncovered  that are consistent with an Hsc70 recognition motif  , 47. Thuin vitro and in vivo  was able to induce the degradation of p53R248Q through MA , the Ragnar Söderberg Foundation and the Swedish Cancer Society (Cancerfonden). Special thanks to Dr. Zhang for the graphic design of figures.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Infectious and genetic factors are invoked, respectively in isolated biliary atresia (BA), or syndromic BA, with major extrahepatic anomalies. However, isolated BA is also associated with minor extrahepatic gut and cardiovascular anomalies and multiple susceptibility genes, suggesting common origins.We investigated novel susceptibility genes with genome-wide association, targeted sequencing and tissue staining in BA requiring liver transplantation, independent of BA subtype. Candidate gene effects on morphogenesis, developmental pathways, and ciliogenesis, which regulates left-right patterning were investigated with zebrafish knockdown and mouse knockout models, mouse airway cell cultures, and liver transcriptome analysis.MAN1A2) were significantly associated with BA and with other polymorphisms known to affect MAN1A2 expression but were not differentially enriched in either BA subtype. In zebrafish embryos, man1a2 knockdown caused poor biliary network formation, ciliary dysgenesis in Kupffer’s vesicle, cardiac and liver heterotaxy, and dysregulated egfra and other developmental genes. Suboptimal man1a2 knockdown synergized with suboptimal EGFR signaling or suboptimal knockdown of the EGFR pathway gene, adenosine-ribosylation-factor-6, which had minimal effects individually, to reproduce biliary defects but not heterotaxy. In cultured mouse airway epithelium, Man1a2 knockdown arrested ciliary development and motility. Man1a2–/– mice, which experience respiratory failure, also demonstrated portal and bile ductular inflammation. Human BA liver and Man1a2–/– liver exhibited reduced Man1a2 expression and dysregulated ciliary genes, known to cause multisystem human laterality defects.Single nucleotide polymorphisms in Mannosidase-1-α-2 (MAN1A2. man1a2 regulates laterality, in addition to hepatobiliary morphogenesis, by regulating ciliogenesis in zebrafish and mice, providing a novel developmental basis for multisystem defects in BA.BA requiring transplantation associates with sequence variants in  The hetelopment . AdditioMAN1A2 as a susceptibility gene, which explains the multisystem involvement in BA. Our experimental approach combines GWAS in children with LTx for BA, zebrafish and mouse models, and liver transcriptome analysis in human BA and animal models.Here, we evaluate susceptibility to end-stage liver disease, which requires LTx in children with BA, independent of BA subtype. This restricts our GWAS to a cohort with homogeneous end-stage liver disease, without the heterogeneity introduced by including children without LTx, and in whom the liver disease has likely arrested at various stages. We identify MAN1A2, identified potentially causal SNPs in LD with BA-associated SNPs. RT-qPCR and immunohistochemistry characterized expression of the MAN1A2 gene and protein in affected BA liver. The effect of MAN1A2 on biliary morphogenesis, left-right patterning, and ciliogenesis was evaluated with knockdown in zebrafish and mouse airway epithelial cell cultures, respectively  and Quad Infinium 660k (Illumina) at the Center for Applied Genomics at the Children’s Hospital of Philadelphia. Replicated candidate SNPs were assayed with TaqMan SNP Genotyping Assays in the third batch of 32 BA cases. Genotyping calls with Taqman assays were identical to those called with SNP arrays in a subset of 19 randomly selected cases from the first two batches.p = 0.00005), and low minor allele frequency (MAF < 0.01) as described in p < 0.005), and which retained this level of significance in the replication cohort.A final list of 507540 and 522193 SNPs in both SNP array versions of HumHap Infinium 550K and Quad Infinium 660k were identified, respectively, after excluding missing genotype data (>0.10), Hardy-Weinberg equilibrium (HWE) test (P = 0.005) in the discovery cohort with 24 of these SNPs also remaining significant in the replication cohort (MAN1A2 gene demonstrated significantly higher MAF in the discovery cohort (p = 7.18E-05) and replication cohort (p = 9.73E-04) and in the 89 combined BA cases (p = 1.72E-08). The two top-ranked intronic SNPs rs12131109 and rs7531715 in LD (r2 > 0.8) in the MAN1A2 gene demonstrated significantly higher MAF in the discovery cohort , replication cohort  and in 89 combined BA cases   vs. p = 6.97E-10 (n = 121 vs. 2060), respectively, for rs753175. However, the odds ratio estimate remains approximately the same and SNPs achieved genome-wide significance after adjusting for False Discovery Rate using Benjamini Y method (FDR_BY)  . Genome-ctively) , 3. In t(FDR_BY) .p = 0.859, NS, test of proportions).Interestingly, our BA cohort of 121 children included 98 with biliary involvement only and 23 children with extrahepatic abdominal and cardiovascular anomalies . The MAFMAN1A2 gene inclusive of the 20 kb upstream and downstream sequences identified 498 SNP variants. Genotyping calls for rs7531715 and rs12131109 with NGS were identical to those determined with SNP arrays (n = 38) and Taqman assay (n = 2) for 40 of 43 BA cases (r2≥ 0.8) with the two BA-associated SNPs are negatively correlated with MAN1A2 expression at p ≤ 1.2067E-09 in Caucasian populations (MAN1A2 expression (p = 3.42e-19) in the liver  at least to 96 hpf  line that expresses GFP in BECs  line to visualize Kupffer’s vesicle cells , Hedgehog , and the TGF-β  signaling pathways. In previous zebrafish studies, biliary dysgenesis was induced with aberrant signaling of either the EGFR or Hedgehog pathway . Compared to single-injected larvae, co-injected larvae demonstrated greatly reduced PED6 accumulation in the gallbladder . This treatment impaired proper biliary network formation, as accessed by PED6   . Arl13b man1a2 morphant zebrafish liver, we asked whether developmental and cilia pathways, and genes associated with aberrant laterality in humans were also dysregulated in the whole transcriptome of Man1a2–/– liver and lung and human BA liver  proteins. Sequence variants in genes for CPLANE proteins induce ciliopathies in mice and humans.Conducted in an exploratory cohort of 137 Caucasian children with BA, all of whom received LTx at our center, GWAS and biological interrogation of the MAN1A2 and BA is applicable to Caucasians but not East Asians, in whom the SNP locus is monomorphic. Further, although the associated SNPs do not affect MAN1A2 expression in public databases, both are in LD (r2 > 0.8) with several others identified by targeted sequencing of subject samples, which are known MAN1A2 eQTLs (MAN1A2 gene expression (p = 3.42E-19) in previous human liver studies   . This tr= 0.006) . These fh larvae , 3A. Theman1a2 knockdown, i.e., regulating left-right patterning in addition to biliary morphogenesis is independent of its effect on developmental pathways such as EGF  can be found below: The studies involving human participants were reviewed and approved by the Institutional Review Board, University of Pittsburgh. Written informed consent to participate in this study was provided by the participants’ legal guardian/next of kin. The animal study was reviewed and approved by Animal Care and Use Committee, University of Pittsburgh.–/– mouse experiments. JF, KP, GG, MA, and NM conducted, described Man1a2–/– mouse studies. AB, CA, CT, and LF recruited subjects, coordinated study, prepared genomic material. AD, RHS, VM, HH, SS, KS, DK, CL, and WC interpreted findings for respective human therapeutic areas, edited manuscript. SS supervised the bioinformatics and systems biology analysis. DS designed, described, supervised zebrafish experiments. RS designed, supervised the entire project and wrote the manuscript. All authors contributed to the article and approved the submitted version.JS and MN conducted, described zebrafish, and human genomic studies, respectively, AB, SD, and BH conducted, supervised targeted NGS. JG, JM, DL, QS, QY, and BH designed, implemented, cross-checked genotyping, and sequencing analyses. LS and SR analyzed immunohistochemistry. MS, NK, and CL designed, conducted, described mouse airway cell culture, and Dnah11The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Hand grip strength (HS) measures muscular strength and associates with multiple health outcomes and mortality. Studies of epigenetic and transcriptomic markers could help elucidate the biology behind HS; markers for which monozygotic (MZ) twins are excellent study populations. We performed integrated enrichment analyses (IEA) of an epigenome-wide association analysis (EWAS) and a transcriptome-wide association analysis (TWAS) of HS in blood samples of 452 MZ twins (56-80 years of age). Unsupervised IEA were conducted by the KeyPathwayMiner algorithm, while supervised IEA were performed by the KEGG and Reactome databases. No individual CpG site or probe passed correction for multiple testing. Investigating the overlap in genes with p-values<0.01, 0.005 or 0.001 in the EWAS and TWAS, revealed 67, 21 and 2 unique genes, respectively. The latter 2 were TESK2 and VWA1. By the supervised approach, the 67-gene overlap identified three pathways related to “antigen processing and presentation”, driven by HLA-A, HLA-B, TAP2 and PSME2. With the unsupervised approach the 21-gene and 67-gene overlaps revealed networks containing 7 and 19 genes, respectively. Exception nodes  were CREBBP and CSNK2A2 for the former, and APP and HSP90AB1 for the latter. The remaining IEA revealed no gene sets or networks. Several of these genes have previously been linked to HS relevant traits, e.g. arthritis , smooth muscle and cardiovascular function  and sarcopenia (HSP90AB1). Hence, this study reports genes and pathways previously reported for physical functioning, yet also novel candidates for further verification.


In addition, RAGE may undergo ligand-driven multimodal dimerization or oligomerization mediated through self-association of some of its subunits. We conclude our review by proposing possible future lines of study that could result in control of cancer progression through RAGE inhibition.Interactions of the receptor for advanced glycation end product (RAGE) and its ligands in the context of their role in diabetes mellitus, inflammation, and carcinogenesis have been extensively investigated. This review focuses on the role of RAGE-ligands and anti-RAGE drugs capable of controlling cancer progression. Different studies have demonstrated interaction of RAGE with a diverse range of acidic (negatively charged) ligands such as advanced glycation end products (AGEs), high-mobility group box1 (HMGB1), and S100s, and their importance to cancer progression. Some RAGE-ligands displayed effects on anti- and pro-apoptotic proteins through upregulation of the phosphatidylinositide 3-kinase (PI3K)/protein kinase B (Akt)/mammalian target of rapamycin (mTOR), mitogen-activated protein kinases (MAPKs), matrix metalloproteinases (MMPs), vascular endothelial growth factor (VEGF), and nuclear factor kappa B (NF- Structupagation ,10. As apagation ,12,13,14Apoptosis is a programmed cell death, which plays a significant role in tumor invasiveness and metastasis. Any defects in apoptosis play a pivotal role in initiation and progression of carcinogenesis . Hence, In this review, we will discuss the new studies concerning ligands and inhibitors of RAGE and their roles in cancer progression. We recommend some future studies that could help to delineate the mechanism by which RAGE-ligands could induce cancer progression. We also provide a guide for targeted inhibition of RAGE by its ligands, which may serve as novel targets to improve current cancer therapies. κB, and extracellular signal-regulated kinase (ERK) pathways [AGEs are formed through a nonenzymatic process also known as Maillard reaction. This reaction is initiated between the free amino group of a protein and a carbonyl group from a reducing sugar to produce AGEs  followedpathways ,21. AGEspathways ,25,26,27The AGEs studies presented in Janus kinase (JAK)/signal transducer and activator of transcription (STAT) signaling plays an important role in a variety of diseases, including cancer . JAK/STAIt was also established that after binding to RAGE, AGEs upregulated some MAPK pathways and related MAPK family members such as ERK, specificity protein 1 (Sp1), matrix metalloproteinase 2 (MMP2), MMP9, and p38 ,35,36,37Nuclear factor (erythroid-derived 2)-like 2 (Nrf-2): Keap1 complex could lead to cancer cell proliferation and metastasis through regulation of p53 apoptotic pathway ,40. ActiκB [κB, VEGF, and mouse double minute 2 homolog (MDM2). These three molecules protected the cancer cells from apoptosis. Overexpressed NF-κB resulted in increased cancer cells’ proliferation and protected them from apoptosis. Upregulation of NF-κB abrogated the activities of the caspases with cancer proliferation [A number of different studies demonstrated that induction of AGEs led to upregulation of phosphatidylinositide 3-kinase (PI3K) ,33, protκB ,42,43,44κB ,24 and dκB  in varioferation . Moreoveferation . FinallyHigh-mobility group box1 (HMGB1) is a crucial factor in the development and progression of breast, colon, gastrointestinal, and liver cancers ,47,48,49Beclin-1 has been associated with cancer cell autophagy. However, Rohatgi and Shaw have determined that Beclin-1 induced tumor progression by regulation of growth factor receptor signaling in an autophagy-independent manner . Beclin-Numerous studies have recognized the upregulation of the ERK/MAPK pathway by HMGB1 in colon carcinoma ,55, renaMicroRNAs (miRNAs or miR) are small noncoding RNAs that participate in the regulation of diverse cell functions . The abnMMPs are a group of proteolytic enzymes that degrade multiple extracellular matrix components to promote tumor invasion, angiogenesis and metastasis, and therefore they represent ideal pharmacologic targets for cancer therapy . HMGB1 pκB expression in human pancreatic (BxPC-3) [κB upregulated Snail, which subsequently upregulated N-cadherin [HMGB1 upregulated NF-(BxPC-3) , hepatoc(BxPC-3) ,72, fibr(BxPC-3) ,75, non-(BxPC-3) , HCC [77(BxPC-3) . Overexpcadherin  and vimecadherin . N-cadhecadherin  and phoscadherin ,66.HMGB1 upregulated PI3K/Akt, which subsequently regulated various cellular proteins that induced cell proliferation and decreased apoptosis of cancer cells ,81,82. OS100 proteins are involved in many aspects of regulation of proliferation, differentiation, apoptosis, and inflammation . CancersAngiogenesis is defined as the formation of new blood vessels from preexisting vessels and has been characterized as an essential process for cancer cell proliferation and viability because it supplies the cancer cells with nutrients and oxygen . NotablyS100s members upregulated MAPK family members either ERK, Cdc42/p38, or SAPK/ JNK pathways that led to the progression of colorectal , thyroid (human specimens), nasopharyngeal (human specimens), breast (human specimens), and prostate (LNCaP and PC-3) cancers ,108,109.Molecular-based assessments of breast cancers have revealed expression of S100s, including S100A2, S100A4, and S100A7, with different expression levels during breast tumorigenesis and progression . Nasser κB that induced progression of different types of cancer including pancreatic, melanoma, breast, prostate, colon, neuroblastoma, and esophageal [κB/Snail and led to cancer metastasis. Thus, to understand the effects of cancer progression due to induction of the S100s family members through the NF-κB pathway, it is essential to study their effects on the inhibitors of apoptosis members (IAPs), B-cell lymphoma (Bcl-2), and Snail.Activation of RAGE by S100A4, S100A7, S100A8, S100A9, S100A14, S100B, and S100P was associated with upregulation of NF-ophageal ,114,115.ophageal ,116 thatBecause of stimulation of RAGE by the S100B in melanoma, lung, breast, colorectal, and ovarian cancers ,119,120 The PI3K/Akt/mTOR pathway exists as one of the most attractive targets to block cancer progression . This paDiverse studies have demonstrated constitutive activation of STAT3 in a wide variety of human tumors including hematological malignancies and solid tumors inducing cell proliferation, angiogenesis, invasion, and metastasis . This caRAGE signaling blocking in cell and animal models has shown that targeting RAGE affects the development and metastasis of cancer . As discCancer is often mixed with neuropathic pain. For this reason, frequently in patients with cancer-related neuropathic pain opioids such as anticonvulsants  and antidepressants (e.g. duloxetine and tricyclics) are used . DuloxetκB activation. Moreover, ethyl pyruvate reduced HMGB1 serum levels in mice and inhibited the growth of malignant mesothelioma xenografts. Therefore, ethyl pyruvate is an effective drug for malignant mesothelioma. In another in vitro study, ethyl pyruvate attenuated the non-small cell lung cancer cell lines growth, invasion, and migration and induced apoptosis via the downregulation of HMGB1-RAGE axis and the NF-κB/STAT3 pathway [Ethyl pyruvate, the ethyl ester of pyruvic acid), has been shown to be an effective HMGB1-inhibitor in inflammation-related diseases and several cancers ,146. Pel pathway  as illusPhellinus linteus and it has several biological activities such as antioxidant [κB pathway activation through antioxidant activities [Natural plant products can be important for developing drug products. Hispidin is a polyphenol compound derived from ioxidant  and antiioxidant . Hispidiioxidant . In addiioxidant . Rat phetivities . Both thκB activation through RAGE using an NF-κB-dependent luciferase reporter assay and the HT1080 cell line. LMWH significantly inhibited the migration, invasion, tumor formation, and lung metastasis of HT1080RAGE cells, but not of HT1080mock or HT1080dnRAGE cells [The low-molecular-weight heparins (LMWHs) are an old class of anti-thrombotic drugs and tend to be the preferred anticoagulant in many indices that are important for modern hematology and oncology with patients who are at elevated risk of both hemorrhage and venous thromboembolism . LMWH atGE cells  , caspase-9, and caspase-3.▪Studies of the effect of RAGE-ligands’ pathway signaling on extrinsic pathway components such as tumor necrosis factor receptor-associated death domain (TRADD), Fas-associated death domain (FADD), caspase-8, and caspase-10.▪Studies of the effect of RAGE-ligands’ pathway signaling on Bcl-2 family, either the pro-apoptotic  or anti-apoptotic (Bcl-Xl and Bcl-2). ▪Studies of the effect of RAGE-ligands’ pathway signaling on molecules that induce cell survival and metastasis including E-cadherin, hypoxia-inducible factor 1-alpha (HIF-1α), PTEN, and MDM2.▪Studies of the effect of RAGE-ligands’ pathway signaling on cyclin-dependent kinases  and regulatory cyclin subunits .▪Studies of the effect of RAGE-ligands’ pathway signaling on molecules that facilitate cell survival and metastasis such as β-catenin, epidermal growth factor receptor (EGFR), VEGF, and vimentin.▪Discovery of new drugs that downregulate RAGE and its ligands to control cancer progression.▪The role of RAGE-ligands in cancer senescence and senotherapies.From the studies reviewed here, it can be concluded that RAGE-ligand complexes induce upregulation of an array of anti-apoptotic proteins and downregulate pro-apoptotic proteins to promote cancer cell progression, as illustrated in


While numerous studies implicate Ca2+ mishandling in AD, the cellular basis for loss of cognitive function remains under investigation. The process of synaptic degradation and degeneration in AD is slow, and constitutes a series of maladaptive processes each contributing to a further destabilization of the Ca2+ homeostatic machinery. Ca2+ homeostasis involves precise maintenance of cytosolic Ca2+ levels, despite extracellular influx via multiple synaptic Ca2+ channels, and intracellular release via organelles such as the endoplasmic reticulum (ER) via ryanodine receptor (RyRs) and IP3R, lysosomes via transient receptor potential mucolipin channel (TRPML) and two pore channel (TPC), and mitochondria via the permeability transition pore (PTP). Furthermore, functioning of these organelles relies upon regulated inter-organelle Ca2+ handling, with aberrant signaling resulting in synaptic dysfunction, protein mishandling, oxidative stress and defective bioenergetics, among other consequences consistent with AD. With few effective treatments currently available to mitigate AD, the past few years have seen a significant increase in the study of synaptic and cellular mechanisms as drivers of AD, including Ca2+ dyshomeostasis. Here, we detail some key findings and discuss implications for future AD treatments.Ca AD, as a progressive neurodegenerative disease, is characterized by Camopathy”  and synamopathy” ,4, and wmopathy” , and maye models ,7,8,9. Ceostasis ,11, botht models ,14,15,162+ entry points in the neuronal architecture, expressing both pre- and postsynaptic Ca2+ channels/receptors, including presynaptic RyRs, N/P/Q voltage gated Ca2+ channels (VGCCs), α7 nicotinic acetylcholine receptors (α7 nAChRs), and postsynaptic L-type VGCCs, RyRs and NMDA receptors (NMDARs). NMDARs in particular are one of the most well characterized postsynaptic glutamate receptors, with a high Ca2+ permeability and an established role in hippocampal synaptic plasticity [2+, but postsynaptic depolarization results in removal of Mg2+ block, and receptor disinhibition. Repeated NMDAR activation enhances postsynaptic Ca2+ entry, an effect which is facilitated by RyRs through Ca2+-induced-Ca2+ release (CICR), thus driving increased postsynaptic AMPA receptor (AMPAR) expression and subsequent synaptic long-term potentiation (LTP). This dual role of the NMDAR as coincidence detector and postsynaptic Ca2+ entry channel makes it uniquely positioned to mediate synaptic potentiation resulting from concurrent pre- and postsynaptic activation, thus forming a mechanistic basis for Hebbian plasticity and associative learning.Synapses are unique Caasticity . At hype2+ channel antagonists could serve as a useful pointer for a role for those Ca2+ channels in the pathophysiology of AD, with the failure of large scale clinical trials for L-type VGCC antagonists in particular, contrasting with the positive effects of memantine [2+ release within spines [Paradoxically, NMDARS, as well as playing a role in synaptic plasticity, may also play a role in synaptic loss  and cellemantine . AD is cemantine ,23, inclemantine , and simemantine ,27,28,29n spines ,31, and n spines , resultin spines ,34,35. In spines ,37,38. Sn spines .2+ hyperactivity in vivo, in presymptomatic AD mice, an effect which is blocked by AMPA receptor and NMDAR antagonists, suggesting that this hyperactivity is synaptically driven [2+ hyperactivity occurred mainly in the vicinity of insoluble dense core plaques, these plaques are also surrounded by soluble Aβ [2+ signaling in AD mice [2+ hyperactivity observed in an AD mouse model was inhibited by the sarcoplasmic endoplasmic Ca2+-ATPase (SERCA) pump inhibitor cyclopiazonic acid, indicating that this Ca2+ hyperactivity is driven by activation of presynaptic Ca2+ stores [2+ activated SK2 channels is increased in a 3xTg AD mouse model [+ current (IA) [2+ in hippocampal neurons [3 receptor activation [2+ hyperexcitability observed in vivo in AD mice.Hippocampal and cortical neurites in close proximity to amyloid plaques demonstrate Cay driven ,7. Altholuble Aβ ,41, whicluble Aβ . Further AD mice , raising+ stores . In cont+ stores ,44,45. Ise model , leadingent (IA) , thus fu neurons , possibltivation , effectstivation , isoflurWhile the last two decades have seen a large increase in the number of studies using AD mouse models, a more recent development has been in the use of human induced neurons (HiNs), which are neurons derived from tissue samples taken from patients, to study synaptic transmission ,52,53. I2+ and affect neurotransmitter release [2+ channels could serve as a therapeutic target for AD.More recently, proteomics has emerged as a method that allows for high throughput analysis of protein expression in small tissue samples , includi release ,67, and  release ,69, sugg2+ permeable homomeric α7nAChR isoform [2+ influx [nAChRs are essential for normal cognitive function ,71, and  isoform ,73. α7nA isoform , and als isoform ,76, and  isoform , and pos isoform ,79, with+ influx ,81,82,83+ influx ,81,84 an+ influx .2+ influx, both in oocytes and presynaptic terminals in hippocampus [2+ influx, an effect which was blocked by an α7nAChR antagonist [Aβ binds with high affinity to α7nAChRs ,87, resupocampus ,94. Low pocampus  and picopocampus . In addipocampus ,98 and cpocampus . Cells ttagonist . Galantatagonist .2+ effects in AD. In addition to α7nAChR mediated Ca2+ influx, activation of α7nAChRs triggers CICR via ryanodine sensitive Ca2+ stores [2+ overload via already increased RyR function [Although a role for α7nAChRs in the etiology of AD has not been established, many animal studies have demonstrated cognitive enhancing effects of compounds targeting α7nAChRs , includi+ stores , includi+ stores , which a+ stores . As RyR function , possiblAs of now, there are only two FDA-approved classes of drugs used in the symptomatic treatment of AD: the noncompetitive NMDA antagonist memantine, and the acetylcholinesterase inhibitors, donepezil, galantamine and rivastigmine, with both classes of drugs having a synaptic site of action. Although both memantine and donepezil have been shown to be moderately effective in the treatment of AD symptoms, there is an urgent need for disease-modifying approaches, which currently requires the identification of novel compounds and receptor targets at the pre- or postsynaptic level. While a number of studies have identified promising small molecules targeting NMDARs ,51, α7nA2+ levels are tightly regulated and maintained at low nM concentrations, despite a much higher extracellular Ca2+ concentration, and similarly elevated Ca2+ levels within intracellular organelles such as the ER. The ER is located throughout the cell, including pre- and postsynaptically, at synaptic terminals and dendritic spines respectively. RyRs, as well as having a role in gating ER Ca2+, are sensitive to changes in cytosolic Ca2+ through the process of CICR, with increases in postsynaptic Ca2+ resulting in RyR activation and release of ER Ca2+ into the cytosol. CICR has the effect of amplifying postsynaptic Ca2+ generated from influx via Ca2+ permeable receptors/ion channels such as NMDA receptors (NMDAR) and voltage gated Ca2+ channels (VGCCs), and RyR mediated CICR is upregulated in neurons in 3xTg AD mice [2+ allows for a large rapid increase in cytosolic Ca2+, this increased Ca2+ is usually rapidly removed from the cytosol, against a concentration gradient, by Ca2+ ATPases including the SERCA pump, which is also located on the ER membrane. The ER membrane also expresses IP3 receptors, although these are not thought to be synaptically expressed [Cytosolic Ca AD mice . Althougxpressed .2+ regulation. Although PS1 is a part of the γ-secretase complex which cleaves amyloid precursor protein (APP), it is also expressed on the ER membrane where it regulates RyR and IP3R channel properties [2+ leak channel [2+ regulation, and RyR dysfunction is implicated in the Ca2+ dysregulation observed in AD [2+ responses are increased in the soma and dendritic spines of hippocampal and cortical pyramidal neurons of AD mice expressing PS1 mutations (2+ dyshomeostasis observed in an AD mouse model [2+ release [2+ responses to high frequency stimulation (HFS) are increased in hippocampal and cortical neurons from several AD mouse models [2+ signaling is the restoration of reduced presynaptic vesicle stores observed in AD mice back to normal levels upon treatment with Ryanodex [Mutations in the presenilin 1 (PS1) gene are linked to familial AD, an early onset form of the disease, and these mutations have specific functional implications for Caoperties ,123,124, channel ,126. Mututations  [9,30,12se model . Human-i release , and RyR release ,130. Pose models ,9,131, e2+ signaling may also have implications for synaptic plasticity and LTP, which are impaired in AD mice [2+ and is accompanied by an increased release probability of glutamate. This form of short term plasticity is necessary for the synaptic tagging processes involved in LTP [2+ signaling in the impaired short and long-term synaptic plasticity observed in AD mice [2+ effects of RyR activation, due to decreased RyR expression [In addition to effects on basal synaptic transmission, changes in RyR-Ca AD mice ,45. Highd in LTP , howeverd in LTP . Chronic AD mice . Presenipression  and selepression . Thus, i2+ is maintained in part due to the actions of Ca2+-ATPases, which rapidly remove Ca2+ from the cell cytosol, against a concentration gradient. One of the major cellular Ca2+-ATPases is the SERCA pump, located on the ER membrane. SERCA function is facilitated by presenilin, and knockdown of the genes for presenilin 1 and presenilin 2 results in elevated cytosolic Ca2+, due to decreased SERCA mediated clearance of cytosolic Ca2+ [2+ channels on the ER membrane, results in increased Aβ [2+ response to SERCA inhibition by thapsigargin, indicating increased SERCA function [2+ hyperactivity observed in cortical neurons of AD mice in vivo [2+ sensors and Orai Ca2+ channels facilitate ER Ca2+ filling through the process of store-operated-Ca2+ entry (SOCE), a process which is deficient in PS1 mutant expressing neurons [2+ release is elevated in AD neurons , pyruvate dehydrogenase complex (PDHC), α-ketoglutarate dehydrogenase complex (KGDHC), malate dehydrogenase (MDH), and increasing ROS production while decreasing ATP production [2+ overload, contributed to mitochondrial dysfunction and impaired energy metabolism in AD.The main function of the mitochondria is the production of ATP. Unavoidably, the by-products of electron transport in aerobic respiration are reactive oxygen species (ROS), due to electron leaks at complex I and III. Caoduction . Redox poduction . Additiooduction . This su2+ transfer and cellular homeostasis. Mitochondrial Ca2+ uptake controls the rate of energy production, regulates intracellular Ca2+ signaling, and mediates cell death. Ca2+ transfer between these organelles is facilitated via the mitochondrial-associated membrane proteins (MAM). Numerous molecular proteins have been identified to support this physical interaction. Of interest, the glucose-regulated protein 75 (GRP75) is linked to IP3R and facilitates Ca2+ into the mitochondrial intermembrane space. From there, voltage-dependent anion-selective channel protein 1 (VDAC1) on the outer mitochondrial membrane, and the mitochondrial Ca2+ uniporter (MCU) on the inner mitochondrial membrane, transfer the Ca2+ to the mitochondrial matrix to stimulate the mitochondrial dehydrogenase and increase ETC activity and ATP synthesis. [2+ uptake. In AD, many genes involved in mitochondrial Ca2+ transport are altered [2+ influx, such as MCU, are downregulated whereas genes encoding mitochondrial Ca2+ efflux, such as NCLX, are upregulated, suggesting a compensatory mechanism to avoid excessive Ca2+ uptake. Additionally, studies report that, soluble Aβ aggregations increase cytosolic Ca2+, leading to mitochondrial Ca2+ overload via MCU. Excessive Ca2+ taken up by mitochondria leads to caspase activation and neuronal cell death [The dynamic function of the mitochondria requires crosstalk between other major organelles, such as the ER . Mitochonthesis. ,162,163. altered ,165,166.ll death .2+, VDAC1 supports transport of superoxide anions [3R and RyRs have been shown to be redox-sensitive, ROS and Ca2+ may play a regulatory role in ER-mitochondria communication. During AD- associated Ca2+ overload, mitochondrial Ca2+ influx elevates oxidative stress and increases ROS production. In AD, accumulated ROS has profound effects on cellular functions by oxidizing several proteins, such as the redox-sensitive RyR and IP3R channels. Thus, Ca2+ induced ROS increase and ROS-mediated Ca2+ increase creates a self-amplifying loop that furthers neurotoxicity and cellular dyshomeostasis, and neuronal death [PSEN1/2 may alter mitochondrial Ca2+ transport. Additionally, increased contact sites between ER and mitochondria, via MAM proteins in AD result in elevation in ER-mitochondrial Ca2+ signaling and increased mitochondrial superoxide production [In addition to Cae anions  and sincal death ,171,172.oduction ,177,178.2+ is released from the mitochondria through the Na+/Ca2+ exchanger (NCLX) and the permeability transition pore [2+ released; where the low conductance state amplifies Ca2+ waves and the high conductance state releases a surge of Ca2+ and apoptotic signals such as cytochrome C [2+ concentration, Ca2+ released from the mitochondria signals for apoptosis and increases AD pathology [Caion pore . The twochrome C ,181. Theathology . Howeverathology ,183. Addathology . Mitochoathology ,186,187.1 for fission and Mfn1, Mfn2, and OPA1 for fusion [2+ signaling led to increased DLP1 activation, resulting in excessive mitochondrial translocation and fission [2+ handling and increased oxidative stress disrupts mitochondrial function, advancing AD pathology. Disrupted DLP1 and Mfn2 function is also responsible for reduced mitochondrial distribution. In AD, mitochondria are less abundant in neuronal processes of susceptible pyramidal neurons [Mitochondrial morphology and distribution are also crucial for neuronal homeostasis and synaptic function. Mitochondria undergo fusion and fission in the cytoplasm, which is a process to maintain a healthy pool of mitochondria with proper distribution. These mechanisms are controlled by DLPr fusion . In AD,  fission ,190. Rec fission ,192. Exc neurons ,194. Inc neurons ,196.2+ signaling and colocalization of the two organelles. Intracellular Ca2+ signaling relieves the inhibitory mammalian target of rapamycin (mTOR) block, thus activating mitophagy and initiating autophagosome biogenesis  [2+ signaling, as seen in AD, may disrupt degradation of damaged organelle via inactivation of lysosomal proteolysis and increase accumulation of cellular debris [Damaged mitochondria are cleared through mitophagy, the selective degradation of mitochondria by autophagy following organelle damage or extreme cellular stress . Mitopha and 11) ,201,202.r debris ,204,205.2+ stores are responsible for regulating autophagy—a catabolic pathway utilizing the enzymatic activity of lysosomes to degrade and recycle large, bulky cellular debris, aggregated proteins, and damaged organelles. There are three types of autophagy: macroautophagy, microautophagy, and chaperone-mediated autophagy, however for simplicity, this review will focus on macroautophagy and be referred to as “autophagy”. More detailed descriptions of the aforementioned can be found in these reviews [2+ signaling hinders clearance of pathological protein deposits.Lysosomal Ca reviews ,206. Aut reviews ,208, theTranscriptomic profiles from the collective ongoing studies known as Rush Memory and Aging Project (ROSMAP), reveal clusters of genes that are associated with pathological protein handling. Specifically, higher expression of SORL1 and ABCA7 transcripts are associated with tau tangle pathology, while elevated BIN1 transcripts are associated with beta amyloid in AD brains . PLXNB1 + pump (vATPase) driving the influx of H+ into the lysosome [+ exchangers with AD suggest that proton leak pathways may regulate pathological Aβ generation and contribute to disease etiology [2+ signaling, as seen in AD, can hinder lysosomal acidification and impair proteolytic enzymes in lysosomes, further AD proteinopathy and impair lysososmal trafficking, resulting in neuritic dystrophy.The key, critical feature of lysosomes is the acidic lumen (pH ~4.5) necessary for protein degradation and autophagosome digestion. The acidic pH is maintained by an active vacuolar-ATPase Hlysosome ,212,213.etiology . In the etiology . Mutatioetiology ,216. Theetiology . Additioetiology ,219,220.+ channels (lysoNaV). The Na+ efflux potentiates the influx of protons by the vATPase to restore lysosomal acidity. However, lysoNaV are also Ca2+ permeable, therefore aberrant Ca2+ increase and changes in the Ca2+ concentration gradient, as seen in early pathology of AD, can hinder lysosomal acidity by reducing the driving force of H+ influx to restore lysosomal function [Additionally, an increase in the lysosomal pH disrupts the homeostatic mechanisms to maintain the lysosomal membrane potential. The alkaline lumen depolarizes the lysosomal membrane via activation of lysosomal voltage-activated Nafunction ,221,222.2+ efflux channels, lysosomal transient receptor potential Ca2+ channel mucolipin subfamily member (TRPML1) and two-pore channel (TPC) [2+ efflux through TRPML1, activates a calcineurin-dependent pathway that, via TFEB, enhances the transcription of genes involved in autophagy and lysosomal expression, such as LC3-II, ATG9B, UVRAG, WIPI, SQSTM1, MAPLC3B, GLA, GNS, HEXA, MCOLN1, TMEM55B, and ATP6V1H [This shift to a more alkaline lysosomal lumen causes hyperactivity of the lysosomal Cael (TPC) ,224,225 el (TPC) ,227,228) ATP6V1H ,230,231.2+ release is also responsible for fusion of autophagosomes to lysosomes. In a manner similar to neuronal vesicular fusion, lysosomal Ca2+ efflux channels such as, P/Q type VGCC, facilitate fusion between lysosomal tethering proteins, such as synaptogamin 7, SNAP29, and SNARE VAMP 7/8, to autophagosomal tethering proteins such as syntaxin 17 and possible SNARE proteins [2+ concentration, as in AD, can influence fusion of autophagosomes to malfunctioned lysosome, resulting in accumulation of cargo vesicles with maladaptive proteins, furthering neurotoxicity.This lysosomal-mediated Caproteins ,234,235.2+ stores are also involved in maintaining synaptic transmission. When mGluR1 is activated, NAADP-evoked lysosomal Ca2+ release from lysosomal Ca2+ channels, presumably through TPC, is amplified into Ca2+ waves via RyR activation [2+ entry through GluN receptors and facilitates the induction of LTP [2+ release facilitates fusion to the plasma membrane and release of cathepsin B. Cathepsin B then regulates structural plasticity and dendritic spine formation [Recent studies have shown that lysosomal functions go beyond their primary role as the degradative compartment within a neuron. Lysosomal Cativation . This sin of LTP . When VGormation ,239, howormation .2+ amplification suppresses autophagic flux [2+ signaling, as seen in neurodegenerative diseases, can alter this trigger zone and therefore disrupt autophagic clearance and synaptic plasticity.The systemic destruction of collective organelles leads to the neuron’s demise. The close proximity of the ER to the lysosome can enhance AD pathology  and PS mgic flux  and indugic flux ,238,239