bims-apauto Biomed News
on Apoptosis and autophagy
Issue of 2021‒02‒28
fourteen papers selected by
Su Hyun Lee
Seoul National University

  1. Nat Commun. 2021 Feb 26. 12(1): 1322
      The ubiquitin-proteasome system (UPS) and autophagy are two major quality control processes whose impairment is linked to a wide variety of diseases. The coordination between UPS and autophagy remains incompletely understood. Here, we show that ubiquitin ligase UBE3C and deubiquitinating enzyme TRABID reciprocally regulate K29/K48-branched ubiquitination of VPS34. We find that this ubiquitination enhances the binding of VPS34 to proteasomes for degradation, thereby suppressing autophagosome formation and maturation. Under ER and proteotoxic stresses, UBE3C recruitment to phagophores is compromised with a concomitant increase of its association with proteasomes. This switch attenuates the action of UBE3C on VPS34, thereby elevating autophagy activity to facilitate proteostasis, ER quality control and cell survival. Specifically in the liver, we show that TRABID-mediated VPS34 stabilization is critical for lipid metabolism and is downregulated during the pathogenesis of steatosis. This study identifies a ubiquitination type on VPS34 and elucidates its cellular fate and physiological functions in proteostasis and liver metabolism.
  2. Eur Rev Med Pharmacol Sci. 2021 Feb;pii: 24875. [Epub ahead of print]25(3): 1641-1649
      Autophagy is a main metabolic process in which eukaryotic cells use lysosomes to eliminate abnormal proteins and damaged organelles to maintain cell homeostasis. Studies have revealed that neurodegenerative diseases, tumor, hepatic diseases, etc. are related to abnormal autophagy processes in recent years. Recent studies have shown that TFEB is a major transcription regulator of autophagy-lysosomal pathway (ALP) transcriptional regulation, which positively regulates the expression of autophagy and lysosomal biogenesis-related genes, thereby promoting autophagosome formation, autophagosome-lysosome fusion, and degradation of autophagy substrates. It has also been found that TFEB promotes clearance of intracellular substrates through lysosomal exocytosis. Therefore, the study of biological functions and related regulatory mechanisms of TFEB will provide important clues and theoretical basis for further explaining its physiological pathogenesis and the treatment of related diseases.
  3. Front Oncol. 2020 ;10 619727
      Cancer progression involves a variety of pro-tumorigenic biological processes including cell proliferation, migration, invasion, and survival. A cellular pathway implicated in these pro-tumorigenic processes is autophagy, a catabolic route used for recycling of cytoplasmic components to generate macromolecular building blocks and energy, under stress conditions, to remove damaged cellular constituents to adapt to changing nutrient conditions and to maintain cellular homeostasis. During autophagy, cells form a double-membrane sequestering a compartment termed the phagophore, which matures into an autophagosome. Following fusion with the lysosome, the cargo is degraded inside the autolysosomes and the resulting macromolecules released back into the cytosol for reuse. Cancer cells use this recycling system during cancer progression, however the key autophagy players involved in this disease is unclear. Accumulative evidences show that autophagy receptors, crucial players for selective autophagy, are overexpressed during cancer progression, yet the mechanisms whereby pro-tumorigenic biological processes are modulated by these receptors remains unknown. In this review, we summarized the most important findings related with the pro-tumorigenic role of autophagy receptors p62/SQSTM1, NBR1, NDP52, and OPTN in cancer progression. In addition, we showed the most relevant cargos degraded by these receptors that have been shown to function as critical regulators of pro-tumorigenic processes. Finally, we discussed the role of autophagy receptors in the context of the cellular pathways implicated in this disease, such as growth factors signaling, oxidative stress response and apoptosis. In summary, we highlight that autophagy receptors should be considered important players of cancer progression, which could offer a niche for the development of novel diagnosis and cancer treatment strategies.
    Keywords:  aggressiveness; autophagy; autophagy receptors; cancer progression; metastasis
  4. Autophagy. 2021 Feb 22.
      In humans, TDRD7 (tudor domain containing 7) mutations lead to a syndrome combining congenital cataracts (CCs) and non-obstructive azoospermia (NOA), characterized by abnormal lens development and spermiogenesis. However, the molecular mechanism underlying TDRD7's functions in eye and testicular development are still largely unknown. Here, we show that the depletion of this gene in mice and humans resulted in the accumulation of autophagosomes and the disruption of macroautophagic/autophagic flux. The disrupted autophagic flux in tdrd7-deficient mouse embryonic fibroblasts (MEFs) was caused by a failure of autophagosome fusion with lysosomes. Furthermore, transcriptome analysis and biochemical assays showed that TDRD7 might directly bind to Tbc1d20 mRNAs and downregulate its expression, which is a key regulator of autophagosome maturation, resulting in the disruption of autophagosome maturation. In addition, we provide evidence to show that TDRD7-mediated autophagosome maturation maintains lens transparency by facilitating the removal of damaged proteins and organelles from lens fiber cells and the biogenesis of acrosome. Altogether, our results showed that TDRD7 plays an essential role in the maturation of autophagosomes and that tdrd7 deletion results in eye defects and testicular abnormalities in mice, implicating disrupted autophagy might be the mechanism that contributes to lens development and spermiogenesis defects in human.
    Keywords:  TBC1D20; TDRD7; acrosome biogenesis; autophagy; lens development; spermiogenesis
  5. Autophagy. 2021 Feb 25. 1-3
      Phase-separated droplets with liquid-like properties can be degraded by macroautophagy/autophagy, but the mechanism underlying this degradation is poorly understood. We have recently derived a physical model to investigate the interaction between autophagic membranes and such droplets, uncovering that intrinsic wetting interactions underlie droplet-membrane contacts. We found that the competition between droplet surface tension and the increasing tendency of growing membrane sheets to bend determines whether a droplet is completely engulfed or isolated in a piecemeal fashion, a process we term fluidophagy. Intriguingly, we found that another critical parameter of droplet-membrane interactions, the spontaneous curvature of the membrane, determines whether the droplet is degraded by autophagy or - counterintuitively - serves as a platform from which autophagic membranes expand into the cytosol. We also discovered that the interaction of membrane-associated LC3 with the LC3-interacting region (LIR) found in the autophagic cargo receptor protein SQSTM1/p62 and many other autophagy-related proteins influences the preferred bending directionality of forming autophagosomes in living cells. Our study provides a physical account of how droplet-membrane wetting underpins the structure and fate of forming autophagosomes.
    Keywords:  Autophagy; condensate; droplet; isolation membrane; membrane; p62; phase separation; piecemeal autophagy; wetting
  6. Autophagy. 2021 Feb 23. 1-15
      Alzheimer disease (AD) is the most prevalent neurodegenerative disorder leading to dementia in the elderly. Unfortunately, no cure for AD is available to date. Increasing evidence has proved the roles of misfolded protein aggregation due to impairment of the macroautophagy/autophagy-lysosomal pathway (ALP) in the pathogenesis of AD, and thus making TFEB (transcription factor EB), which orchestrates ALP, as a promising target for treating AD. As a complementary therapy, acupuncture or electroacupuncture (EA) has been commonly used for treating human diseases. Although the beneficial effects of acupuncture for AD have been primarily studied both pre-clinically and clinically, the real efficacy of acupuncture on AD remains inconclusive and the underlying mechanisms are largely unexplored. In this study, we demonstrated the cognitive-enhancing effect of three-needle EA (TNEA) in an animal model of AD with beta-amyloid (Aβ) pathology (5xFAD). TNEA reduced APP (amyloid beta (A4) precursor protein), C-terminal fragments (CTFs) of APP and Aβ load, and inhibited glial cell activation in the prefrontal cortex and hippocampus of 5xFAD. Mechanistically, TNEA activated TFEB via inhibiting the AKT-MAPK1-MTORC1 pathway, thus promoting ALP in the brains. Therefore, TNEA represents a promising acupuncture therapy for AD, via a novel mechanism involving TFEB activation.Abbreviations Aβ: β-amyloid; AD: Alzheimer disease; AIF1/IBA1: allograft inflammatory factor 1; AKT1: thymoma viral proto-oncogene 1; ALP: autophagy-lysosomal pathway; APP: amyloid beta (A4) precursor protein; BACE1: beta-site APP cleaving enzyme 1; CQ: chloroquine; CTFs: C-terminal fragments; CTSD: cathepsin D; EA: electroacupuncture; FC: fear conditioning; GFAP: glial fibrillary acidic protein; HI: hippocampus; LAMP1: lysosomal-associated membrane protein 1; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MAPK1/ERK2: mitogen-activated protein kinase 1; MAPT: microtubule-associated protein tau; MTORC1: mechanistic target of rapamycin kinase complex 1; MWM: Morris water maze; NFT: neurofibrillary tangles; PFC: prefrontal cortex; PSEN1: presenilin 1; SQSTM1/p62: sequestosome 1; TFEB: transcription factor EB; TNEA: three-needle electroacupuncture.
    Keywords:  Alzheimer disease; autophagy-lysosomal pathway; electroacupuncture; transcription factor EB
  7. Dev Cell. 2021 02 22. pii: S1534-5807(21)00113-1. [Epub ahead of print]56(4): 400-402
      Many pathogens are capable of disrupting autophagy within host cells. In this issue of Developmental Cell, Miao et al. discover that the SARS-CoV-2 protein ORF3a inhibits autophagosome-lysosome fusion by dysregulating the HOPS complex.
  8. Bioengineered. 2021 Dec;12(1): 697-707
      Growing evidences suggest that autophagy plays a momentous part in the tumorigenesis and development of hepatocellular carcinoma (HCC). However, there are not many researches to predict the prognosis of HCC using autophagy-related genes. Therefore, based on the clinical information and RNA-Seq data of The Cancer Genome Atlas data portal (TCGA), 13 autophagy‑related gene pairs were screened to build the autophagy‑related signature to predict the prognosis by least absolute shrinkage and selection operator (LASSO) regression analysis. Besides, the International Cancer Genome Consortium (ICGC) cohort was further applied to verify the autophagy‑related prognostic signature. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene set enrichment analysis (GSEA) were also used to predict the relevant function of the autophagy-related gene pairs signature. As shown in the results, the autophagy-related gene pairs were mainly involved in process utilizing autophagic mechanism, autophagy, macroautophagy and cellular response to oxidative stress. The immune cell levels in the high-risk and low-risk group were explored, which showed that the three immune cells were obviously increased in the high-risk group, while the five immune cells were obviously increased in the low-risk group. In conclusion, an autophagy‑related prognostic signature was established to predict the prognosis of HCC patients with great accuracy and we found that autophagy‑related prognostic signature was related to infiltrating immune cells.
    Keywords:  Autophagy-related gene pairs; hepatocellular carcinoma; immune; prognosis
  9. Curr Biol. 2021 Feb 17. pii: S0960-9822(21)00146-9. [Epub ahead of print]
      Mutations in WDR45 and WDR45B cause the human neurological diseases β-propeller protein-associated neurodegeneration (BPAN) and intellectual disability (ID), respectively. WDR45 and WDR45B, along with WIPI1 and WIPI2, belong to a WD40 repeat-containing phosphatidylinositol-3-phosphate (PI(3)P)-binding protein family. Their yeast homolog Atg18 forms a complex with Atg2 and is required for autophagosome formation in part by tethering isolation membranes (IMs) (autophagosome precursor) to the endoplasmic reticulum (ER) to supply lipid for IM expansion in the autophagy pathway. The exact functions of WDR45/45B are unclear. We show here that WDR45/45B are specifically required for neural autophagy. In Wdr45/45b-depleted cells, the size of autophagosomes is decreased, and this is rescued by overexpression of ATG2A, providing in vivo evidence for the lipid transfer activity of ATG2-WIPI complexes. WDR45/45B are dispensable for the closure of autophagosomes but essential for the progression of autophagosomes into autolysosomes. WDR45/45B interact with the tether protein EPG5 and target it to late endosomes/lysosomes to promote autophagosome maturation. In the absence of Wdr45/45b, formation of the fusion machinery, consisting of SNARE proteins and EPG5, is dampened. BPAN- and ID-related mutations of WDR45/45B fail to rescue the autophagy defects in Wdr45/45b-deficient cells, possibly due to their impaired binding to EPG5. Promoting autophagosome maturation by inhibiting O-GlcNAcylation increases SNARE complex formation and facilitates the fusion of autophagosomes with late endosomes/lysosomes in Wdr45/45b double knockout (DKO) cells. Thus, our results uncover a novel function of WDR45/45B in autophagosome-lysosome fusion and provide molecular insights into the development of WDR45/WDR45B mutation-associated diseases.
    Keywords:  BPAN; ID; WDR45; WDR45B; autophagy
  10. Autophagy. 2021 Feb 25.
      The mechanisms orchestrating recycling of lysosomes through autophagic lysosome reformation (ALR) is incompletely understood. Previous data show that genetic depletion of BLOC1S1/GCN5L1/BORCS1 increases autolysosome (AL) accumulation. We postulated that this phenotype may manifest due to perturbed ALR. We explored this in control and bloc1s1 liver-specific knockout (LKO) mouse hepatocytes, showing that in response to nutrient-deprivation LKO's fail to initiate ALR due to blunted lysosomal tubulation. As kinesin motor proteins and the intracellular cytoskeleton are requirements for tubular formation from ALs, we explored the interaction of BLOC1S1 with motor proteins and cytoskeletal factors. BLOC1S1 interacts with the ARL8B-KIF5B (GTPase and kinesin motor protein) complex to recruit KIF5B to ALs. Furthermore, BLOC1S1 interacts with the actin nucleation promoting factor WHAMM, which is an essential structural protein in the initiation of lysosomal tubulation (LT). Interestingly, the genetic reintroduction of BLOC1S1 rescues LT in LKO hepatocytes, but not when KIF5B is concurrently depleted. Finally, given the central role of MTORC1 signaling in ALR initiation, it was interesting that MTORC1 activity was increased despite the absence of LT in LKO hepatocytes. Concurrently, inhibition of MTORC1 abolished BLOC1S1 reconstitution-mediated rescue of LT in LKO hepatocytes. Taken together these data demonstrate that the functional interaction of BLOC1S1 with the kinesin binding complex and the actin cytoskeleton are a requirement for LT which, in parallel with MTORC1 signaling, initiate lysosome recycling via ALR.
    Keywords:  Autophagic lysosome reformation; GCN5L1; MTORC1; autophagy; hepatocyte; lysosomal tubulation; lysosome
  11. Autophagy. 2021 Feb 25. 1-3
      Neurons are long-lived cells that communicate via release of neurotransmitter at specialized contacts termed synapses. The maintenance of neuronal health and the regulation of synaptic function requires the efficient removal of damaged or dispensable proteins and organelles from synapses. How macroautophagy/autophagy contributes to neuronal and synaptic protein turnover, and what its main physiological substrates are in healthy neurons is largely unknown. We have now shown that loss of neuronal autophagy facilitates presynaptic neurotransmission by controlling the axonal endoplasmic reticulum and, thereby, axonal and synaptic calcium homeostasis.
    Keywords:  Autophagy; SV protein; calcium; endoplasmic reticulum; er-phagy; neurotransmission; reticulophagy; ryanodine receptor; synapse
  12. Carcinogenesis. 2021 Feb 24. pii: bgab016. [Epub ahead of print]
      The incidence of malignant melanoma, a neoplasm of melanocytic cells, is increasing rapidly. The lymph nodes are often the first site of metastasis and can herald systemic dissemination, which is almost uniformly fatal. RLIP, a multi-specific ATP-dependent transporter that is over-expressed in several types of cancers, plays a central role in cancer cell resistance to radiation and chemotherapy. RLIP appears to be necessary for cancer cell survival because both in-vitro cell culture and in-vivo animal tumor studies show that the depletion or inhibition of RLIP causes selective toxicity to malignant cells. RLIP depletion/inhibition triggers apoptosis in cancer cells by inducing the accumulation of endogenously formed glutathione-conjugates. In our in-vivo studies, we administered RLIP antibodies or antisense oligonucleotides to mice bearing subcutaneous xenografts of SKMEL2 and SKMEL5 melanoma cells and demonstrated that both treatments caused significant xenograft regression with no apparent toxic effects. Anti-RLIP antibodies and antisense, which respectively inhibit RLIP-mediated transport and deplete RLIP expression, showed similar tumor regressing activities, indicating that the inhibition of RLIP transport activity at the cell surface is sufficient to achieve anti-tumor activity. Furthermore, RLIP antisense treatment reduced levels of RLIP, pSTAT3, pJAK2, pSrc, Mcl-1, and Bcl2, as well as CDK4 and cyclin B1, and increased levels of Bax and pAMPK. These studies indicate that RLIP serves as a key effector in the survival of melanoma cells and is a valid target for cancer therapy. Overall, compounds that inhibit, deplete, or downregulate RLIP will function as wide-spectrum agents to treat melanoma, independent of common signaling pathway mutations.
    Keywords:  AMPK; JAK2/STAT3; Melanoma; RLIP; tumor xenografts
  13. Biosci Biotechnol Biochem. 2021 Feb 24. 85(3): 621-625
      Puerarin can protect chondrocytes, whereby ameliorating osteoarthritis. Puerarin also promotes autophagy. Autophagy maintains chondrocyte homeostasis. The role of autophagy in puerarin-protected chondrocytes is unknown. Puerarin promoted chondrocyte autophagy. Puerarin-protected chondrocytes were reversed by autophagy inhibitors and Beclin1 inhibitor. 3-MA or Beclin1 inhibitor in vivo reversed puerarin-ameliorated cartilage damage of osteoarthritis mice. Thus, puerarin can protect chondrocytes through Beclin1-dependent autophagy activation.
    Keywords:  Beclin1; Puerarin; autophagy; chondrocyte; osteoarthritis
  14. Autophagy. 2021 Feb 08. 1-382
    Daniel J Klionsky, Amal Kamal Abdel-Aziz, Sara Abdelfatah, Mahmoud Abdellatif, Asghar Abdoli, Steffen Abel, Hagai Abeliovich, Marie H Abildgaard, Yakubu Princely Abudu, Abraham Acevedo-Arozena, Iannis E Adamopoulos, Khosrow Adeli, Timon E Adolph, Annagrazia Adornetto, Elma Aflaki, Galila Agam, Anupam Agarwal, Bharat B Aggarwal, Maria Agnello, Patrizia Agostinis, Javed N Agrewala, Alexander Agrotis, Patricia V Aguilar, S Tariq Ahmad, Zubair M Ahmed, Ulises Ahumada-Castro, Sonja Aits, Shu Aizawa, Yunus Akkoc, Tonia Akoumianaki, Hafize Aysin Akpinar, Ahmed M Al-Abd, Lina Al-Akra, Abeer Al-Gharaibeh, Moulay A Alaoui-Jamali, Simon Alberti, Elísabet Alcocer-Gómez, Cristiano Alessandri, Muhammad Ali, M Abdul Alim Al-Bari, Saeb Aliwaini, Javad Alizadeh, Eugènia Almacellas, Alexandru Almasan, Alicia Alonso, Guillermo D Alonso, Nihal Altan-Bonnet, Dario C Altieri, Élida M C Álvarez, Sara Alves, Cristine Alves da Costa, Mazen M Alzaharna, Marialaura Amadio, Consuelo Amantini, Cristina Amaral, Susanna Ambrosio, Amal O Amer, Veena Ammanathan, Zhenyi An, Stig U Andersen, Shaida A Andrabi, Magaiver Andrade-Silva, Allen M Andres, Sabrina Angelini, David Ann, Uche C Anozie, Mohammad Y Ansari, Pedro Antas, Adam Antebi, Zuriñe Antón, Tahira Anwar, Lionel Apetoh, Nadezda Apostolova, Toshiyuki Araki, Yasuhiro Araki, Kohei Arasaki, Wagner L Araújo, Jun Araya, Catherine Arden, Maria-Angeles Arévalo, Sandro Arguelles, Esperanza Arias, Jyothi Arikkath, Hirokazu Arimoto, Aileen R Ariosa, Darius Armstrong-James, Laetitia Arnauné-Pelloquin, Angeles Aroca, Daniela S Arroyo, Ivica Arsov, Rubén Artero, Dalia Maria Lucia Asaro, Michael Aschner, Milad Ashrafizadeh, Osnat Ashur-Fabian, Atanas G Atanasov, Alicia K Au, Patrick Auberger, Holger W Auner, Laure Aurelian, Riccardo Autelli, Laura Avagliano, Yenniffer Ávalos, Sanja Aveic, Célia Alexandra Aveleira, Tamar Avin-Wittenberg, Yucel Aydin, Scott Ayton, Srinivas Ayyadevara, Maria Azzopardi, Misuzu Baba, Jonathan M Backer, Steven K Backues, Dong-Hun Bae, Ok-Nam Bae, Soo Han Bae, Eric H Baehrecke, Ahruem Baek, Seung-Hoon Baek, Sung Hee Baek, Giacinto Bagetta, Agnieszka Bagniewska-Zadworna, Hua Bai, Jie Bai, Xiyuan Bai, Yidong Bai, Nandadulal Bairagi, Shounak Baksi, Teresa Balbi, Cosima T Baldari, Walter Balduini, Andrea Ballabio, Maria Ballester, Salma Balazadeh, Rena Balzan, Rina Bandopadhyay, Sreeparna Banerjee, Sulagna Banerjee, Ágnes Bánréti, Yan Bao, Mauricio S Baptista, Alessandra Baracca, Cristiana Barbati, Ariadna Bargiela, Daniela Barilà, Peter G Barlow, Sami J Barmada, Esther Barreiro, George E Barreto, Jiri Bartek, Bonnie Bartel, Alberto Bartolome, Gaurav R Barve, Suresh H Basagoudanavar, Diane C Bassham, Robert C Bast, Alakananda Basu, Henri Batoko, Isabella Batten, Etienne E Baulieu, Bradley L Baumgarner, Jagadeesh Bayry, Rupert Beale, Isabelle Beau, Florian Beaumatin, Luiz R G Bechara, George R Beck, Michael F Beers, Jakob Begun, Christian Behrends, Georg M N Behrens, Roberto Bei, Eloy Bejarano, Shai Bel, Christian Behl, Amine Belaid, Naïma Belgareh-Touzé, Cristina Bellarosa, Francesca Belleudi, Melissa Belló Pérez, Raquel Bello-Morales, Jackeline Soares de Oliveira Beltran, Sebastián Beltran, Doris Mangiaracina Benbrook, Mykolas Bendorius, Bruno A Benitez, Irene Benito-Cuesta, Julien Bensalem, Martin W Berchtold, Sabina Berezowska, Daniele Bergamaschi, Matteo Bergami, Andreas Bergmann, Laura Berliocchi, Clarisse Berlioz-Torrent, Amélie Bernard, Lionel Berthoux, Cagri G Besirli, Sebastien Besteiro, Virginie M Betin, Rudi Beyaert, Jelena S Bezbradica, Kiran Bhaskar, Ingrid Bhatia-Kissova, Resham Bhattacharya, Sujoy Bhattacharya, Shalmoli Bhattacharyya, Md Shenuarin Bhuiyan, Sujit Kumar Bhutia, Lanrong Bi, Xiaolin Bi, Trevor J Biden, Krikor Bijian, Viktor A Billes, Nadine Binart, Claudia Bincoletto, Asa B Birgisdottir, Geir Bjorkoy, Gonzalo Blanco, Ana Blas-Garcia, Janusz Blasiak, Robert Blomgran, Klas Blomgren, Janice S Blum, Emilio Boada-Romero, Mirta Boban, Kathleen Boesze-Battaglia, Philippe Boeuf, Barry Boland, Pascale Bomont, Paolo Bonaldo, Srinivasa Reddy Bonam, Laura Bonfili, Juan S Bonifacino, Brian A Boone, Martin D Bootman, Matteo Bordi, Christoph Borner, Beat C Bornhauser, Gautam Borthakur, Jürgen Bosch, Santanu Bose, Luis M Botana, Juan Botas, Chantal M Boulanger, Michael E Boulton, Mathieu Bourdenx, Benjamin Bourgeois, Nollaig M Bourke, Guilhem Bousquet, Patricia Boya, Peter V Bozhkov, Luiz H M Bozi, Tolga O Bozkurt, Doug E Brackney, Christian H Brandts, Ralf J Braun, Gerhard H Braus, Roberto Bravo-Sagua, José M Bravo-San Pedro, Patrick Brest, Marie-Agnès Bringer, Alfredo Briones-Herrera, V Courtney Broaddus, Peter Brodersen, Jeffrey L Brodsky, Steven L Brody, Paola G Bronson, Jeff M Bronstein, Carolyn N Brown, Rhoderick E Brown, Patricia C Brum, John H Brumell, Nicola Brunetti-Pierri, Daniele Bruno, Robert J Bryson-Richardson, Cecilia Bucci, Carmen Buchrieser, Marta Bueno, Laura Elisa Buitrago-Molina, Simone Buraschi, Shilpa Buch, J Ross Buchan, Erin M Buckingham, Hikmet Budak, Mauricio Budini, Geert Bultynck, Florin Burada, Joseph R Burgoyne, M Isabel Burón, Victor Bustos, Sabrina Büttner, Elena Butturini, Aaron Byrd, Isabel Cabas, Sandra Cabrera-Benitez, Ken Cadwell, Jingjing Cai, Lu Cai, Qian Cai, Montserrat Cairó, Jose A Calbet, Guy A Caldwell, Kim A Caldwell, Jarrod A Call, Riccardo Calvani, Ana C Calvo, Miguel Calvo-Rubio Barrera, Niels Os Camara, Jacques H Camonis, Nadine Camougrand, Michelangelo Campanella, Edward M Campbell, François-Xavier Campbell-Valois, Silvia Campello, Ilaria Campesi, Juliane C Campos, Olivier Camuzard, Jorge Cancino, Danilo Candido de Almeida, Laura Canesi, Isabella Caniggia, Barbara Canonico, Carles Cantí, Bin Cao, Michele Caraglia, Beatriz Caramés, Evie H Carchman, Elena Cardenal-Muñoz, Cesar Cardenas, Luis Cardenas, Sandra M Cardoso, Jennifer S Carew, Georges F Carle, Gillian Carleton, Silvia Carloni, Didac Carmona-Gutierrez, Leticia A Carneiro, Oliana Carnevali, Julian M Carosi, Serena Carra, Alice Carrier, Lucie Carrier, Bernadette Carroll, A Brent Carter, Andreia Neves Carvalho, Magali Casanova, Caty Casas, Josefina Casas, Chiara Cassioli, Eliseo F Castillo, Karen Castillo, Sonia Castillo-Lluva, Francesca Castoldi, Marco Castori, Ariel F Castro, Margarida Castro-Caldas, Javier Castro-Hernandez, Susana Castro-Obregon, Sergio D Catz, Claudia Cavadas, Federica Cavaliere, Gabriella Cavallini, Maria Cavinato, Maria L Cayuela, Paula Cebollada Rica, Valentina Cecarini, Francesco Cecconi, Marzanna Cechowska-Pasko, Simone Cenci, Victòria Ceperuelo-Mallafré, João J Cerqueira, Janete M Cerutti, Davide Cervia, Vildan Bozok Cetintas, Silvia Cetrullo, Han-Jung Chae, Andrei S Chagin, Chee-Yin Chai, Gopal Chakrabarti, Oishee Chakrabarti, Tapas Chakraborty, Trinad Chakraborty, Mounia Chami, Georgios Chamilos, David W Chan, Edmond Y W Chan, Edward D Chan, H Y Edwin Chan, Helen H Chan, Hung Chan, Matthew T V Chan, Yau Sang Chan, Partha K Chandra, Chih-Peng Chang, Chunmei Chang, Hao-Chun Chang, Kai Chang, Jie Chao, Tracey Chapman, Nicolas Charlet-Berguerand, Samrat Chatterjee, Shail K Chaube, Anu Chaudhary, Santosh Chauhan, Edward Chaum, Frédéric Checler, Michael E Cheetham, Chang-Shi Chen, Guang-Chao Chen, Jian-Fu Chen, Liam L Chen, Leilei Chen, Lin Chen, Mingliang Chen, Mu-Kuan Chen, Ning Chen, Quan Chen, Ruey-Hwa Chen, Shi Chen, Wei Chen, Weiqiang Chen, Xin-Ming Chen, Xiong-Wen Chen, Xu Chen, Yan Chen, Ye-Guang Chen, Yingyu Chen, Yongqiang Chen, Yu-Jen Chen, Yue-Qin Chen, Zhefan Stephen Chen, Zhi Chen, Zhi-Hua Chen, Zhijian J Chen, Zhixiang Chen, Hanhua Cheng, Jun Cheng, Shi-Yuan Cheng, Wei Cheng, Xiaodong Cheng, Xiu-Tang Cheng, Yiyun Cheng, Zhiyong Cheng, Zhong Chen, Heesun Cheong, Jit Kong Cheong, Boris V Chernyak, Sara Cherry, Chi Fai Randy Cheung, Chun Hei Antonio Cheung, King-Ho Cheung, Eric Chevet, Richard J Chi, Alan Kwok Shing Chiang, Ferdinando Chiaradonna, Roberto Chiarelli, Mario Chiariello, Nathalia Chica, Susanna Chiocca, Mario Chiong, Shih-Hwa Chiou, Abhilash I Chiramel, Valerio Chiurchiù, Dong-Hyung Cho, Seong-Kyu Choe, Augustine M K Choi, Mary E Choi, Kamalika Roy Choudhury, Norman S Chow, Charleen T Chu, Jason P Chua, John Jia En Chua, Hyewon Chung, Kin Pan Chung, Seockhoon Chung, So-Hyang Chung, Yuen-Li Chung, Valentina Cianfanelli, Iwona A Ciechomska, Mariana Cifuentes, Laura Cinque, Sebahattin Cirak, Mara Cirone, Michael J Clague, Robert Clarke, Emilio Clementi, Eliana M Coccia, Patrice Codogno, Ehud Cohen, Mickael M Cohen, Tania Colasanti, Fiorella Colasuonno, Robert A Colbert, Anna Colell, Miodrag Čolić, Nuria S Coll, Mark O Collins, María I Colombo, Daniel A Colón-Ramos, Lydie Combaret, Sergio Comincini, Márcia R Cominetti, Antonella Consiglio, Andrea Conte, Fabrizio Conti, Viorica Raluca Contu, Mark R Cookson, Kevin M Coombs, Isabelle Coppens, Maria Tiziana Corasaniti, Dale P Corkery, Nils Cordes, Katia Cortese, Maria do Carmo Costa, Sarah Costantino, Paola Costelli, Ana Coto-Montes, Peter J Crack, Jose L Crespo, Alfredo Criollo, Valeria Crippa, Riccardo Cristofani, Tamas Csizmadia, Antonio Cuadrado, Bing Cui, Jun Cui, Yixian Cui, Yong Cui, Emmanuel Culetto, Andrea C Cumino, Andrey V Cybulsky, Mark J Czaja, Stanislaw J Czuczwar, Stefania D'Adamo, Marcello D'Amelio, Daniela D'Arcangelo, Andrew C D'Lugos, Gabriella D'Orazi, James A da Silva, Hormos Salimi Dafsari, Ruben K Dagda, Yasin Dagdas, Maria Daglia, Xiaoxia Dai, Yun Dai, Yuyuan Dai, Jessica Dal Col, Paul Dalhaimer, Luisa Dalla Valle, Tobias Dallenga, Guillaume Dalmasso, Markus Damme, Ilaria Dando, Nico P Dantuma, April L Darling, Hiranmoy Das, Srinivasan Dasarathy, Santosh K Dasari, Srikanta Dash, Oliver Daumke, Adrian N Dauphinee, Jeffrey S Davies, Valeria A Dávila, Roger J Davis, Tanja Davis, Sharadha Dayalan Naidu, Francesca De Amicis, Karolien De Bosscher, Francesca De Felice, Lucia De Franceschi, Chiara De Leonibus, Mayara G de Mattos Barbosa, Guido R Y De Meyer, Angelo De Milito, Cosimo De Nunzio, Clara De Palma, Mauro De Santi, Claudio De Virgilio, 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Oku, Sara Oliván, Jorge M A Oliveira, Michael Ollmann, James A Olzmann, Shakib Omari, M Bishr Omary, Gizem Önal, Martin Ondrej, Sang-Bing Ong, Sang-Ging Ong, Anna Onnis, Juan A Orellana, Sara Orellana-Muñoz, Maria Del Mar Ortega-Villaizan, Xilma R Ortiz-Gonzalez, Elena Ortona, Heinz D Osiewacz, Abdel-Hamid K Osman, Rosario Osta, Marisa S Otegui, Kinya Otsu, Christiane Ott, Luisa Ottobrini, Jing-Hsiung James Ou, Tiago F Outeiro, Inger Oynebraten, Melek Ozturk, Gilles Pagès, Susanta Pahari, Marta Pajares, Utpal B Pajvani, Rituraj Pal, Simona Paladino, Nicolas Pallet, Michela Palmieri, Giuseppe Palmisano, Camilla Palumbo, Francesco Pampaloni, Lifeng Pan, Qingjun Pan, Wenliang Pan, Xin Pan, Ganna Panasyuk, Rahul Pandey, Udai B Pandey, Vrajesh Pandya, Francesco Paneni, Shirley Y Pang, Elisa Panzarini, Daniela L Papademetrio, Elena Papaleo, Daniel Papinski, Diana Papp, Eun Chan Park, Hwan Tae Park, Ji-Man Park, Jong-In Park, Joon Tae Park, Junsoo Park, Sang Chul Park, Sang-Youel Park, 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Andrew Thorburn, Lipi Thukral, Thomas Thum, Michael Thumm, Ling Tian, Ales Tichy, Andreas Till, Vincent Timmerman, Vladimir I Titorenko, Sokol V Todi, Krassimira Todorova, Janne M Toivonen, Luana Tomaipitinca, Dhanendra Tomar, Cristina Tomas-Zapico, Sergej Tomić, Benjamin Chun-Kit Tong, Chao Tong, Xin Tong, Sharon A Tooze, Maria L Torgersen, Satoru Torii, Liliana Torres-López, Alicia Torriglia, Christina G Towers, Roberto Towns, Shinya Toyokuni, Vladimir Trajkovic, Donatella Tramontano, Quynh-Giao Tran, Leonardo H Travassos, Charles B Trelford, Shirley Tremel, Ioannis P Trougakos, Betty P Tsao, Mario P Tschan, Hung-Fat Tse, Tak Fu Tse, Hitoshi Tsugawa, Andrey S Tsvetkov, David A Tumbarello, Yasin Tumtas, María J Tuñón, Sandra Turcotte, Boris Turk, Vito Turk, Bradley J Turner, Richard I Tuxworth, Jessica K Tyler, Elena V Tyutereva, Yasuo Uchiyama, Aslihan Ugun-Klusek, Holm H Uhlig, Marzena Ułamek-Kozioł, Ilya V Ulasov, Midori Umekawa, Christian Ungermann, Rei Unno, Sylvie Urbe, Elisabet 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Zhang, Menghuan Zhang, Peng Zhang, Sheng Zhang, Wei Zhang, Xiangnan Zhang, Xiao-Wei Zhang, Xiaolei Zhang, Xiaoyan Zhang, Xin Zhang, Xinxin Zhang, Xu Dong Zhang, Yang Zhang, Yanjin Zhang, Yi Zhang, Ying-Dong Zhang, Yingmei Zhang, Yuan-Yuan Zhang, Yuchen Zhang, Zhe Zhang, Zhengguang Zhang, Zhibing Zhang, Zhihai Zhang, Zhiyong Zhang, Zili Zhang, Haobin Zhao, Lei Zhao, Shuang Zhao, Tongbiao Zhao, Xiao-Fan Zhao, Ying Zhao, Yongchao Zhao, Yongliang Zhao, Yuting Zhao, Guoping Zheng, Kai Zheng, Ling Zheng, Shizhong Zheng, Xi-Long Zheng, Yi Zheng, Zu-Guo Zheng, Boris Zhivotovsky, Qing Zhong, Ao Zhou, Ben Zhou, Cefan Zhou, Gang Zhou, Hao Zhou, Hong Zhou, Hongbo Zhou, Jie Zhou, Jing Zhou, Jing Zhou, Jiyong Zhou, Kailiang Zhou, Rongjia Zhou, Xu-Jie Zhou, Yanshuang Zhou, Yinghong Zhou, Yubin Zhou, Zheng-Yu Zhou, Zhou Zhou, Binglin Zhu, Changlian Zhu, Guo-Qing Zhu, Haining Zhu, Hongxin Zhu, Hua Zhu, Wei-Guo Zhu, Yanping Zhu, Yushan Zhu, Haixia Zhuang, Xiaohong Zhuang, Katarzyna Zientara-Rytter, Christine M Zimmermann, Elena Ziviani, Teresa Zoladek, Wei-Xing Zong, Dmitry B Zorov, Antonio Zorzano, Weiping Zou, Zhen Zou, Zhengzhi Zou, Steven Zuryn, Werner Zwerschke, Beate Brand-Saberi, X Charlie Dong, Chandra Shekar Kenchappa, Zuguo Li, Yong Lin, Shigeru Oshima, Yueguang Rong, Judith C Sluimer, Christina L Stallings, Chun-Kit Tong.
      In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.
    Keywords:  Autophagosome; LC3; cancer; flux; lysosome; macroautophagy; neurodegeneration; phagophore; stress; vacuole