Key Autophagy Genes Research Articles

A calmodulin-like protein suppresses RNA silencing and promotes geminivirus infection by degrading SGS3 via the autophagy pathway in Nicotiana benthamiana.

A recently characterized calmodulin-like protein is an endogenous RNA silencing suppressor that suppresses sense-RNA induced post-transcriptional gene silencing (S-PTGS) and enhances virus infection, but the mechanism underlying calmodulin-like protein-mediated S-PTGS suppression is obscure. Here, we show that a calmodulin-like protein from Nicotiana benthamiana (NbCaM) interacts with Suppressor of Gene Silencing 3 (NbSGS3). Deletion analyses showed that domains essential for the interaction between NbSGS3 and NbCaM are also required for the subcellular localization of NbSGS3 and NbCaM suppressor activity. Overexpression of NbCaM reduced the number of NbSGS3-associated granules by degrading NbSGS3 protein accumulation in the cytoplasm. This NbCaM-mediated NbSGS3 degradation was sensitive to the autophagy inhibitors 3-methyladenine and E64d, and was compromised when key autophagy genes of the phosphatidylinositol 3-kinase (PI3K) complex were knocked down. Meanwhile, silencing of key autophagy genes within the PI3K complex inhibited geminivirus infection. Taken together these data suggest that NbCaM acts as a suppressor of RNA silencing by degrading NbSGS3 through the autophagy pathway.

The role of autophagy inhibition in the enhanced cytotoxicity of temozolomide on melanoma cell lines

Background. Despite advantages in treatment of metastatic melanoma it remains resistant to current therapy. Recent evidence indicates that tumor cells could overcome death through autophagy, a process that degrades cellular proteins and organelles to maintain cellular biosynthesis during nutrient deprivation or lack of energy. Objective: to investigate the involvement of autophagy inhibitors chloroquine (CQ) and LY-294.002 (LY) in temozolomide (TMZ) cytotoxicity in human melanoma cell lines. Materials and methods . The study was performed on patient-derived melanoma cell lines Mel Z, Mel IL and Mel MTP. The antiproliferative activity of combined TMZ and autophagy inhibitors treatment was determined by MTT assay and colony-forming assay. Cell cycle analysis, apoptosis activation and expression analysis of key autophagy markers under combined treatment was evaluated. Results . CQ and LY enhanced the cytotoxicity of TMZ and reduced colony formation in 3 melanoma cell lines, moreover both inhibitors increased cell population in G0 / G1 phase of cell cycle in Mel Z, Mel IL cell lines, but not in Mel MTP. CQ and LY synergistically activated apoptosis in all cell lines. The matrix RNA expression analysis of key autophagy genes showed autophagy involvement in enhanced cytotoxicity. Conclusions. Thus, autophagy inhibition on different stages of this process could overcome resistance to TMZ and be applicable as potent target in metastatic melanoma treatment.

Inhibition of the Autophagy Pathway Synergistically Potentiates the Cytotoxic Activity of Givinostat (ITF2357) on Human Glioblastoma Cancer Stem Cells.

Increasing evidence highlighted the role of cancer stem cells (CSCs) in the development of tumor resistance to therapy, particularly in glioblastoma (GBM). Therefore, the development of new therapies, specifically directed against GBM CSCs, constitutes an important research avenue. Considering the extended range of cancer-related pathways modulated by histone acetylation/deacetylation processes, we studied the anti-proliferative and pro-apoptotic efficacy of givinostat (GVS), a pan-histone deacetylase inhibitor, on cell cultures enriched in CSCs, isolated from nine human GBMs. We report that GVS induced a significant reduction of viability and self-renewal ability in all GBM CSC cultures; conversely, GVS exposure did not cause a significant cytotoxic activity toward differentiated GBM cells and normal mesenchymal human stem cells. Analyzing the cellular and molecular mechanisms involved, we demonstrated that GVS affected CSC viability through the activation of programmed cell death pathways. In particular, a marked stimulation of macroautophagy was observed after GVS treatment. To understand the functional link between GVS treatment and autophagy activation, different genetic and pharmacological interfering strategies were used. We show that the up-regulation of the autophagy process, obtained by deprivation of growth factors, induced a reduction of CSC sensitivity to GVS, while the pharmacological inhibition of the autophagy pathway and the silencing of the key autophagy gene ATG7, increased the cell death rate induced by GVS. Altogether these findings suggest that autophagy represents a pro-survival mechanism activated by GBM CSCs to counteract the efficacy of the anti-proliferative activity of GVS. In conclusion, we demonstrate that GVS is a novel pharmacological tool able to target GBM CSC viability and its efficacy can be enhanced by autophagy inhibitory strategies.

Interplay between cell cycle and autophagy induced by boswellic acid analog.

In this study, we investigated the role of autophagy induced by boswellic acid analog BA145 on cell cycle progression in pancreatic cancer cells. BA145 induced robust autophagy in pancreatic cancer cell line PANC-1 and exhibited cell proliferation inhibition by inducing cells to undergo G2/M arrest. Inhibition of G2/M progression was associated with decreased expression of cyclin A, cyclin B, cyclin E, cdc2, cdc25c and CDK-1. Pre-treatment of cells with autophagy inhibitors or silencing the expression of key autophagy genes abrogated BA145 induced G2/M arrest and downregulation of cell cycle regulatory proteins. It was further observed that BA145 induced autophagy by targeting mTOR kinase (IC50 1 μM), leading to reduced expression of p-mTOR, p-p70S6K (T389), p-4EBP (T37/46) and p-S6 (S240/244). Notably, inhibition of mTOR signalling by BA145 was followed by attendant activation of AKT and its membrane translocation. Inhibition of Akt through pharmacological inhibitors or siRNAs enhanced BA145 mediated autophagy, G2/M arrest and reduced expression of G2/M regulators. Further studies revealed that BA145 arbitrated inhibition of mTOR led to the activation of Akt through IGFR/PI3k/Akt feedback loop. Intervention in IGFR/PI3k/Akt loop further depreciated Akt phosphorylation and its membrane translocation that culminates in augmented autophagy with concomitant G2/M arrest and cell death.

Menopause-induced uterine epithelium atrophy results from arachidonic acid/prostaglandin E2 axis inhibition-mediated autophagic cell death.

Women experience menopause later in life. Menopause is characterized by dramatically decreased circulating estrogen level secondary to loss of ovarian function and atrophic state of genital organs. However, the molecular mechanisms for this process are not fully understood. In this study, we aimed to investigate the potential molecular mechanisms that underlie menopause-induced uterine endometrial atrophy. Our data showed that autophagy was activated in the uterine epithelial cells of both ovariectomized rats and peri-menopausal females. Endoplasmic reticulum (ER) stress occurred even prior to autophagy induction. Integrated bioinformatics analysis revealed that ER stress induced downstream decreased release of arachidonic acid (AA) and downregulation of AA/prostaglandin E2 (PGE2) axis, which led to Akt/mTOR signaling pathway inactivation. Consequently, autophagosomes were recruited and LC3-dependent autophagy was induced in uterine epithelial cells. Treatment with exogenous E2, PGE2, salubrinal or RNAi-mediated silencing of key autophagy genes could effectively counteract estrogen depletion-induced autophagy. Collectively, autophagy is a critical regulator of the uterine epithelium that accounts for endometrial atrophy after menopause.

Abstract 3528: Induction of cytoprotective autophagy and senescence in response to chemotherapy and ionizing-radiation as possible mechanisms of tumor dormancy

Abstract Proliferative recovery in tumor cells subsequent to chemotherapy and/or radiation-induced prolonged growth arrest may prove to represent a state of autophagy and/or senescence. This may also be useful as an in vitro model of tumor dormancy. To explore this hypothesis, studies were performed in primary mouse mammary carcinoma cells (MMC) treated with Adriamycin (ADR) (0.25uM - 1uM) for 3 days (2h each) and ionizing radiation (IR) (6Gy). Promotion of autophagy was confirmed based on detection of autophagosomes based on acridine orange staining, the appearance of the autophagy marker, LC3.B, associated with autophagosome, degradation of p62/SQSTM1, a hallmark of autophagic flux (i.e. the completion of autophagy and degradation of autophagosome content). Autophagosome formation was observed 24h post ADR treatment and 72h post IR treatment. Furthermore, to understand the function of autophagy (cytoprotective, nonprotective or cytotoxic) autophagy was blocked either pharmacologically using chloroquine (CQ) or genetically by silencing of the key autophagy gene, ATG5. LC3.B appearance and p62/SQSTM1 degradation were more pronounced in wt (autophagy proficient) cells compared to ATG5 silenced cells, confirming that autophagy was inhibited by these pharmacological and genetic strategies. Furthermore, interference with autophagy sensitized the MMC cells to ADR and radiation. These observations indicated that ADR and IR induced autophagy was cytoprotective in the MMC cells. Unexpectedly, apoptosis (as measured by PI/ Annexin V assay) was not increased in response to either ADR alone or the combination of ADR and CQ, suggesting that sensitization was likely occurring through alternative pathways. An evaluation of select markers of senescence indicated enhanced expression of p21 as well as enhanced secretion of the autophagy/senescence associated marker, HMGB1, in response to Adriamycin and IR. Overall, these data suggest that both autophagy and senescence are induced in breast cancer cells by conventional therapies and could contribute to tumor dormancy. Inhibition of autophagy and/or senescence associated signaling pathways could lead to therapeutic strategies for interfering with proliferative recovery of tumor cells after standard modes of therapy. Studies are currently in progress to determine whether the senescence associated secretory phenotype (SASP) accompanies the induction of senescence. SASP has been associated with promotion of tumor growth and alternatively, with activation of an immune response to therapy. Citation Format: Theresa Thekkudan, Supriya Joshi, David Gewirtz. Induction of cytoprotective autophagy and senescence in response to chemotherapy and ionizing-radiation as possible mechanisms of tumor dormancy. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3528.

EPG5-related Vici syndrome: a paradigm of neurodevelopmental disorders with defective autophagy.

Vici syndrome is a progressive neurodevelopmental multisystem disorder due to recessive mutations in the key autophagy gene EPG5. We report genetic, clinical, neuroradiological, and neuropathological features of 50 children from 30 families, as well as the neuronal phenotype of EPG5 knock-down in Drosophila melanogaster. We identified 39 different EPG5 mutations, most of them truncating and predicted to result in reduced EPG5 protein. Most mutations were private, but three recurrent mutations (p.Met2242Cysfs*5, p.Arg417*, and p.Gln336Arg) indicated possible founder effects. Presentation was mainly neonatal, with marked hypotonia and feeding difficulties. In addition to the five principal features (callosal agenesis, cataracts, hypopigmentation, cardiomyopathy, and immune dysfunction), we identified three equally consistent features (profound developmental delay, progressive microcephaly, and failure to thrive). The manifestation of all eight of these features has a specificity of 97%, and a sensitivity of 89% for the presence of an EPG5 mutation and will allow informed decisions about genetic testing. Clinical progression was relentless and many children died in infancy. Survival analysis demonstrated a median survival time of 24 months (95% confidence interval 0-49 months), with only a 10th of patients surviving to 5 years of age. Survival outcomes were significantly better in patients with compound heterozygous mutations (P = 0.046), as well as in patients with the recurrent p.Gln336Arg mutation. Acquired microcephaly and regression of skills in long-term survivors suggests a neurodegenerative component superimposed on the principal neurodevelopmental defect. Two-thirds of patients had a severe seizure disorder, placing EPG5 within the rapidly expanding group of genes associated with early-onset epileptic encephalopathies. Consistent neuroradiological features comprised structural abnormalities, in particular callosal agenesis and pontine hypoplasia, delayed myelination and, less frequently, thalamic signal intensity changes evolving over time. Typical muscle biopsy features included fibre size variability, central/internal nuclei, abnormal glycogen storage, presence of autophagic vacuoles and secondary mitochondrial abnormalities. Nerve biopsy performed in one case revealed subtotal absence of myelinated axons. Post-mortem examinations in three patients confirmed neurodevelopmental and neurodegenerative features and multisystem involvement. Finally, downregulation of epg5 (CG14299) in Drosophila resulted in autophagic abnormalities and progressive neurodegeneration. We conclude that EPG5-related Vici syndrome defines a novel group of neurodevelopmental disorders that should be considered in patients with suggestive features in whom mitochondrial, glycogen, or lysosomal storage disorders have been excluded. Neurological progression over time indicates an intriguing link between neurodevelopment and neurodegeneration, also supported by neurodegenerative features in epg5-deficient Drosophila, and recent implication of other autophagy regulators in late-onset neurodegenerative disease.

MiR-409-3p sensitizes colon cancer cells to oxaliplatin by inhibiting Beclin-1-mediated autophagy.

The chemoresistance of colon cancer cells limits the efficacy of chemotherapy. miR-409-3p has been shown to be downregulated in various types of cancer. In the present study, we examined the role of miR-409-3p in colon cancer as well as the effects of miR‑409-3p on the sensitivity of colon cancer cells to oxaliplatin. The expression of miR-409 was significantly downregulated in the human colon cancer cell lines compared with the normal colon epithelial cells. Importantly, the miR-409-3p expression levels were lower in human colon cancer patient samples than in normal colon tissues. Moreover, we observed a negative correlation between the miR‑409-3p levels and resistance to oxaliplatin: the oxaliplatin-resistant colon cancer cells exhibited significantly downregulated miR‑409-3p levels, but higher autophagic activity than the oxaliplatin-sensitive cells. Using bioinformatics analysis, we predicted that miR‑409-3p miRNA binds to the key autophagy gene encoding Beclin-1. Our findings indicated that the overexpression of miR‑409-3p inhibited Beclin-1 expression and autophagic activity by binding to the 3'-untranslated region of Beclin-1 mRNA. In addition, the overexpression of miR‑409-3p enhanced the chemosensitivity of the oxaliplatin-sensitive and oxaliplatin-resistant colon cancer cells. The restoration of Beclin-1 abrogated these effects of miR‑409-3p. In a xenograft model using nude mice, we examined the effects of miR‑409-3p on tumor growth during chemotherapy. miR‑409-3p overexpression sensitized the tumor to chemotherapy, while inhibiting chemotherapy-induced autophagy in a manner dependent on Beclin-1. The findings of our study suggest that miR-409-3p is capable of enhancing the chemosensitivity of colon cancer cells by inhibiting Beclin-1-mediated autophagy.

Congenital disorders of autophagy: an emerging novel class of inborn errors of neuro-metabolism.

Single gene disorders of the autophagy pathway are an emerging, novel and diverse group of multisystem diseases in children. Clinically, these disorders prominently affect the central nervous system at various stages of development, leading to brain malformations, developmental delay, intellectual disability, epilepsy, movement disorders, and neurodegeneration, among others. Frequent early and severe involvement of the central nervous system puts the paediatric neurologist, neurogeneticist, and neurometabolic specialist at the forefront of recognizing and treating these rare conditions. On a molecular level, mutations in key autophagy genes map to different stages of this highly conserved pathway and thus lead to impairment in isolation membrane (or phagophore) and autophagosome formation, maturation, or autophagosome-lysosome fusion. Here we discuss 'congenital disorders of autophagy' as an emerging subclass of inborn errors of metabolism by using the examples of six recently identified monogenic diseases: EPG5-related Vici syndrome, beta-propeller protein-associated neurodegeneration due to mutations in WDR45, SNX14-associated autosomal-recessive cerebellar ataxia and intellectual disability syndrome, and three forms of hereditary spastic paraplegia, SPG11, SPG15 and SPG49 caused by SPG11, ZFYVE26 and TECPR2 mutations, respectively. We also highlight associations between defective autophagy and other inborn errors of metabolism such as lysosomal storage diseases and neurodevelopmental diseases associated with the mTOR pathway, which may be included in the wider spectrum of autophagy-related diseases from a pathobiological point of view. By exploring these emerging themes in disease pathogenesis and underlying pathophysiological mechanisms, we discuss how congenital disorders of autophagy inform our understanding of the importance of this fascinating cellular pathway for central nervous system biology and disease. Finally, we review the concept of modulating autophagy as a therapeutic target and argue that congenital disorders of autophagy provide a unique genetic perspective on the possibilities and challenges of pathway-specific drug development.

Thyroid Hormone Stimulation of Autophagy Is Essential for Mitochondrial Biogenesis and Activity in Skeletal Muscle.

Thyroid hormone (TH) and autophagy share similar functions in regulating skeletal muscle growth, regeneration, and differentiation. Although TH recently has been shown to increase autophagy in liver, the regulation and role of autophagy by this hormone in skeletal muscle is not known. Here, using both in vitro and in vivo models, we demonstrated that TH induces autophagy in a dose- and time-dependent manner in skeletal muscle. TH induction of autophagy involved reactive oxygen species (ROS) stimulation of 5'adenosine monophosphate-activated protein kinase (AMPK)-Mammalian target of rapamycin (mTOR)-Unc-51-like kinase 1 (Ulk1) signaling. TH also increased mRNA and protein expression of key autophagy genes, microtubule-associated protein light chain 3 (LC3), Sequestosome 1 (p62), and Ulk1, as well as genes that modulated autophagy and Forkhead box O (FOXO) 1/3a. TH increased mitochondrial protein synthesis and number as well as basal mitochondrial O2 consumption, ATP turnover, and maximal respiratory capacity. Surprisingly, mitochondrial activity and biogenesis were blunted when autophagy was blocked in muscle cells by Autophagy-related gene (Atg)5 short hairpin RNA (shRNA). Induction of ROS and 5'adenosine monophosphate-activated protein kinase (AMPK) by TH played a significant role in the up-regulation of Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A), the key regulator of mitochondrial synthesis. In summary, our findings showed that TH-mediated autophagy was essential for stimulation of mitochondrial biogenesis and activity in skeletal muscle. Moreover, autophagy and mitochondrial biogenesis were coupled in skeletal muscle via TH induction of mitochondrial activity and ROS generation.

Distinct roles for the p53-like transcription factor XprG and autophagy genes in the response to starvation

Autophagy and autolysis are two cannibalistic pathways which allow filamentous fungi to obtain nutrients once environmental nutrient sources are exhausted. In Aspergillus nidulans, the effects of mutations in two key autophagy genes, atgA, the ATG1 ortholog, and atgH, the ATG8 ortholog, were compared with mutations in xprG, which encodes a transcriptional activator that plays a key role in autolysis. The anti-fungal drug rapamycin induces autophagy in a range of organisms. Mutations in atgA and atgH did not alter sensitivity to rapamycin, which inhibits growth and asexual spore production (conidiation), indicating that autophagy is not required for rapamycin sensitivity in A. nidulans. In contrast, inhibition of conidiation by rapamcyin was partially suppressed by the xprG1 gain-of-function mutation, indicating that XprG acts in the pathway(s) affected by rapamycin. It was anticipated that the absence of an intact autophagy pathway would accelerate the response to starvation. However, extracellular and intracellular protease production in response to carbon or nitrogen starvation was not increased in the atgAΔ and atgHΔ mutants, and the onset of autolysis was not accelerated. Compared to wild-type strains and the xprGΔ and xprG1 mutants, conidiation of the autophagy mutants was reduced in carbon- or nitrogen-limiting conditions but not during growth on nutrient-sufficient medium. Nuclear localization of the global nitrogen regulator AreA in response to nitrogen starvation was blocked in the xprG2 loss-of-function mutant, but not in the atgHΔ mutant. Conversely, the atgAΔ mutation but not the xprGΔ mutation prevented vacuolar accumulation of GFP-AtgH, a hallmark of autophagy. These results indicate that in A. nidulans there is little interaction between autophagy and autolysis and the two pathways are activated in parallel during starvation.

Autophagy limits proliferation and glycolytic metabolism in acute myeloid leukemia.

Decreased autophagy contributes to malignancies; however, it is unclear how autophagy has an impact on tumor growth. Acute myeloid leukemia (AML) is an ideal model to address this as (i) patient samples are easily accessible, (ii) the hematopoietic stem and progenitor cells (HSPC) where transformation occurs is well characterized and (iii) loss of the key autophagy gene Atg7 in HSPCs leads to a lethal pre-leukemic phenotype in mice. Here we demonstrate that loss of Atg5 results in an identical HSPC phenotype as loss of Atg7, confirming a general role for autophagy in HSPC regulation. Compared with more committed/mature hematopoietic cells, healthy human and mouse HSPCs displayed enhanced basal autophagic flux, limiting mitochondrial damage and reactive oxygen species in this long-lived population. Taken together, with our previous findings these data are compatible with autophagy-limiting leukemic transformation. In line with this, autophagy gene losses are found within chromosomal regions that are commonly deleted in human AML. Moreover, human AML blasts showed reduced expression of autophagy genes and displayed decreased autophagic flux with accumulation of unhealthy mitochondria, indicating that deficient autophagy may be beneficial to human AML. Crucially, heterozygous loss of autophagy in an MLL–ENL model of AML led to increased proliferation in vitro, a glycolytic shift and more aggressive leukemias in vivo. With autophagy gene losses also identified in multiple other malignancies, these findings point to low autophagy, providing a general advantage for tumor growth.

Abstract 996: Retinoic acids activate autophagy in breast cancer cells through the FOXO3A-RARA pathway and blocking autophagy enhances retinoic acid-mediated cell death

Abstract A series of pre-clinical studies showed promising anti-cancer effects of retinoic acids (RA) in breast cancer models. However, clinical studies were mostly disappointing possibly also due to the trial design and emerging resistances. One way to confer resistance to a given treatment is activation of protective autophagy. Autophagy is a cellular recycling mechanism that is characterized by the formation of double-membraned autophagosomes. Autophagosomes engulf bulk cytoplasm or selected contents thereof and transfer them to lysosomes for degradation. Activation of autophagy upon anti-cancer treatment may allow prolonged survival of the tumor cells. We therefore asked if autophagy is activated by all-trans retinoic acid (ATRA), a pan-retinoic acid receptor (RAR) agonist, in mammary tumor cells and if autophagy might protect the cells from the pro-apoptotic effects of ATRA. We found that ATRA induces autophagic flux in ATRA-sensitive SKBR3 but not in -resistant MD-MBA- 453 human breast cancer cells as seen by increased LC3B-II protein abundance and turnover of long-lived proteins. Moreover, using RA receptor alpha (RARA), RARB and RARG agonists as well as RARA knockdown breast cancer cells we demonstrated that activation of autophagy by RA depends on RARA expression. RA-treatment also caused induction of the transcription factor FOXO3A, a known transcriptional target of RARA. Since the expression of several autophagy genes namely the ATG8 family members, Beclin-1 and PI3KC3 are controlled by FOXO3A, we tested if FOXO3A might link ATRA-mediated signaling to autophagy activation. Indeed, depleting FOXO3A in SKBR3 cells resulted in significantly decreased autophagic activity and autophagy gene expression upon RA treatment. Importantly, blocking autophagy by knocking down the key autophagy genes ATG5 or ATG7 in breast cancer cells resulted in significantly increased apoptosis under ATRA treatment. Of note, inhibition of autophagy also attenuated cyto-differentiation similarly to the phenotype seen in RARA knockdown breast cancer cells. In summary, our data demonstrate for the first time that retinoic acids induce autophagy in breast cancer cells via the FOXO3A-RARA axis. Furthermore, inhibition of autophagy results in enhanced ATRA-mediated apoptosis representing a potential new treatment strategy for a selected group of breast cancer patients. Citation Format: Anna M. Schlaefli, Enrico Garattini, Mario P. Tschan. Retinoic acids activate autophagy in breast cancer cells through the FOXO3A-RARA pathway and blocking autophagy enhances retinoic acid-mediated cell death. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 996. doi:10.1158/1538-7445.AM2015-996

Rare Variants of ATG5 Are Likely to Be Associated With Chinese Patients With Systemic Lupus Erythematosus.

Recently, common variants within or near ATG5, which is a key autophagy gene required for the formation of autophagosomes, have been identified as a candidate gene of systemic lupus erythematosus (SLE) by several genome-wide association studies. Moreover, elevated ATG5 expression was observed in SLE as well as other autoimmune diseases. However, no significant associations between variants within ATG5 and SLE were identified in several Chinese populations. The present study was conducted to further check the genetic role of ATG5 by associating both common and rare variants of ATG5 in Chinese patients with lupus nephritis (LN), a major phenotype with poor prognosis in SLE.To detect the association of common variants of ATG5 with LN, 7 tagging single nucleotide polymorphisms (SNPs) designed in immunochip and 4 SNPs reported to be associated with SLE were genotyped in 500 LN patients and 500 healthy controls. Furthermore, direct sequencing of exons and their flanking regions in 90 LN patients, 30 SLE patients, and 60 healthy controls were performed. Functional genomic annotation was performed by using public databases.None of the 11 tagging SNPs was observed to be associated with LN. By sequencing, 13 variants were identified, including 5 common SNPs, 7 not previously described, and 1 reported as rare variants (<1%) in the Single Nucleotide Polymorphism Database or the 1000 Genome project. None of the 5 common SNPs showed significant association between patients and controls, whereas increased frequencies of rare or novel variants were observed in patients compared with healthy controls, with 6/90 in LN patients, 2/30 in SLE patients, and 1/163 in healthy controls. Although these rare variants were observed to be located in the flanking regions of exons instead of missense mutations, patients carrying them tended to have severe clinical phenotype, and in silicon analysis suggested their regulatory effects.Increased frequencies of rare variants of ATG5 were identified in patients with LN and SLE compared with healthy controls, highlighting a likely important role of rare ATG5 variants in Chinese SLE patients.

Mechanism of Liver Injury Caused by Autophagy Deficiency

Autophagy is a vital intracellular degradation process which is required for many physiological &amp; pathological processes. Deficiency of autophagy in the liver causes severe injury characterized by increased liver function enzymes in serum &amp; hepatocyte hyperplasia &amp; degeneration. Mice lacking one of the key autophagy genes, such as Atg7, could also be subjected to a high mortality due to liver failure. However it is not clear how autophagy deficiency causes liver injury. The goal of this study is thus to investigate the potential mechanism of injury. A careful examination of the liver histology of the Atg7‐deficient mice indicates that there was inflammation, cell death, &amp; significant ductular reaction. We hypothesized that there was a notable level of cholestasis, which can cause cholestatic hepatitis &amp; thus liver injury. Indeed, further blood chemistry analysis indicated a raised level of total bile acids, cholesterol, &amp; alkaline phosphatase. This exciting new finding suggests a molecular linker from autophagy to cholestasis regulation. Previously it has been reported that anti‐oxidative stress master gene, Nrf2, is involved in autophagy deficiency‐induced liver injury. Indeed, deletion of Nrf2 in Atg7 or Atg5‐deficient mice reversed the liver condition &amp; corrected the injury phenotype, indicating that Nrf2 participates in the pathological changes caused by autophagy deficiency. Remarkably, co‐deletion of Nrf2 in Atg7‐deficient mice also significantly tamed the cholestatic features. These observations support the notion that Nrf2 over‐activation is the key factor in the development of cholestasis, which then cause hepatocyte apoptosis &amp; liver injury.Autophagy deficiency can cause cholestasis, which could be responsible for the liver injury seen in the autophagy‐deficient mice.

Lazarillo-related Lipocalins confer long-term protection against type I Spinocerebellar Ataxia degeneration contributing to optimize selective autophagy.

BackgroundA diverse set of neurodegenerative disorders are caused by abnormal extensions of polyglutamine (poly-Q) stretches in various, functionally unrelated proteins. A common feature of these diseases is altered proteostasis. Autophagy induction is part of the endogenous response to poly-Q protein expression. However, if autophagy is not resolved properly, clearance of toxic proteins or aggregates cannot occur effectively. Likewise, excessive autophagy induction can cause autophagic stress and neurodegeneration. The Lipocalins ApoD, Glial Lazarillo (GLaz) and Neural Lazarillo (NLaz) are neuroprotectors upon oxidative stress or aging. In this work we test whether these Lipocalins also protect against poly-Q-triggered deterioration of protein quality control systems.ResultsUsing a Drosophila retinal degeneration model of Type-1 Spinocerebellar Ataxia (SCA1) combined with genetic manipulation of NLaz and GLaz expression, we demonstrate that both Lipocalins protect against SCA1 neurodegeneration. They are part of the endogenous transcriptional response to SCA1, and their effect is non-additive, suggesting participation in a similar mechanism. GLaz beneficial effects persist throughout aging, and appears when expressed by degenerating neurons or by retinal support and glial cells. GLaz gain-of-function reduces cell death and the extent of ubiquitinated proteins accumulation, and decreases the expression of Atg8a/LC3, p62 mRNA and protein levels, and GstS1 induction. Over-expression of GLaz is able to reduce p62 and ubiquitinated proteins levels when rapamycin-dependent and SCA1-dependent inductions of autophagy are combined. In the absence of neurodegeneration, GLaz loss-of-function increases Atg8a/LC3 mRNA and p62 protein levels without altering p62 mRNA levels. Knocking-down autophagy, by interfering with Atg8a or p62 expression or by expressing dominant-negative Atg1/ULK1 or Atg4a transgenes, rescues SCA1-dependent neurodegeneration in a similar extent to the protective effect of GLaz. Further GLaz-dependent improvement is concealed.ConclusionsThis work shows for the first time that a Lipocalin rescues neurons from pathogenic SCA1 degeneration by optimizing clearance of aggregation-prone proteins. GLaz modulates key autophagy genes and lipid-peroxide clearance responsive genes. Down-regulation of selective autophagy causes similar and non-additive rescuing effects. These data suggest that SCA1 neurodegeneration concurs with autophagic stress, and places Lazarillo-related Lipocalins as valuable players in the endogenous protection against the two major contributors to aging and neurodegeneration: ROS-dependent damage and proteostasis deterioration.Electronic supplementary materialThe online version of this article (doi:10.1186/s13024-015-0009-8) contains supplementary material, which is available to authorized users.

ARG5 rs2245214 C/G Polymorphism Frequency in a Romanian Population.

Purpose. The aim of this study was to assess the frequency of a key autophagy gene ATG5 rs2245214 C/G polymorphism in a Romanian volunteer cohort, as there are no data regarding an Eastern European population. Material/Methods. DNA was extracted from peripheral blood of 105 Romanian unrelated volunteers. The ATG5 rs2245214 C/G polymorphism was genotyped by Real-Time PCR using allelic discrimination TaqMan assay. RealTime PCR was performed on a ViiA™ 7 Real Time PCR System. Hardy–Weinberg equilibrium of allele frequencies at individual loci was assessed using the Chi-squared test. Results. The genotype frequencies in controls were distributed in accordance with Hardy–Weinberg equilibrium (χ² = 1.07; p = 0.3). We found CC genotype in 53 subjects (50.48 %), CG genotype in 40 (38.10 %) and GG genotype in 12 subjects (11.42 %).The G risk allele was found in 52 individuals, and the frequency of the minor G allele was 0.3. Conclusion. This is the first report on a Romanian population regarding the frequency of the ATG5 gene rs2245214 polymorphism. Our results are slightly different to the distribution pattern from other Caucasian populations and larger studies including various ethnic groups are required.

Dangerous Membranes: Viruses That Subvert Autophagosomes

Dangerous Membranes: Viruses That Subvert Autophagosomes

Autophagy is essential for effector CD8(+) T cell survival and memory formation.

The importance of autophagy in memory CD8 T cell differentiation in vivo is not well defined. We show here that autophagy is dynamically regulated in virus-specific CD8 T cells during acute lymphocytic choriomeningitis virus infection. Autophagy decreased in activated proliferating T cells, and was then upregulated at the peak of the effector T cell response. Consistent with this model, deletion of the key autophagy genes Atg7 or Atg5 in virus-specific CD8 T cells had minimal effect on generating effector cells but greatly enhanced their death during the contraction phase resulting in compromised memory formation. These findings provide insight into when autophagy is needed during effector and memory T cell differentiation in vivo and also warrant a re-examination of our current concepts about the relationship between T cell activation and autophagy.

Starvation-response may not involve Atg1-dependent autophagy induction in non-unikont parasites.

Autophagy, the lysosome-mediated self-degradation process, is implicated in survival during starvation in yeast, Dictyostelium and animals. In these eukaryotic taxa (collectively called Unikonts), autophagy is induced primarily through the Atg1/ULK1 complex in response to nutrient depletion. Autophagy has also been well-studied in non-unikont parasites, such as Trypanosoma and Plasmodium, and found important in their life-cycle transitions. However, how autophagy is induced in non-unikonts remains largely unrevealed. Using a bioinformatics approach, we examined the presence of Atg1 and of its complex in the genomes of 40 non-unikonts. We found that these genomes do not encode typical Atg1 proteins: BLAST and HMMER queries matched only with the kinase domain of Atg1, while other segments responsible for regulation and protein-binding were missing. Non-unikonts also lacked other components of the Atg1-inducing complex. Orthologs of an alternative autophagy inducer, Atg6 were found only in the half of the species, indicating that the other half may possess other inducing mechanisms. As key autophagy genes have differential expression patterns during life-cycle, we raise the possibility that autophagy in these protists is induced mainly at the post-transcriptional level. Understanding Atg1-independent autophagy induction mechanisms in these parasites may lead to novel pharmacological interventions, not affecting human Atg1-dependent autophagy.