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Article ; Online: Direct quantification of autophagic flux by a single molecule-based probe.

Geng, Jiefei / Klionsky, Daniel J

2017 Volume 13, Issue 4, Page(s) 639–641

Abstract: Macroautophagy/autophagy remains a rapidly advancing research topic, and there continues to be a need for constantly evolving methodology to investigate this pathway at each individual step. Accordingly, new assays to measure autophagic flux in a robust ... ...

Abstract	Macroautophagy/autophagy remains a rapidly advancing research topic, and there continues to be a need for constantly evolving methodology to investigate this pathway at each individual step. Accordingly, new assays to measure autophagic flux in a robust and reliable manner are essential to understand the mechanism and physiological roles of autophagy. Kaizuka et al. recently reported a new fluorescence probe, GFP-LC3-RFP-LC3ΔG to directly demonstrate autophagic flux without being combined with lysosomal inhibitors (see the Kaizuka et al. punctum in this issue of the journal). When expressed in cells, the probe is cleaved into a degradable/quenchable part, GFP-LC3, and stable/cytosolic part, RFP-LC3ΔG. The latter serves as an internal control and a decrease of the GFP:RFP ratio indicates the occurrence of autophagy. Since the key index of this probe is the degradation of GFP-LC3, it can be used to measure the cumulative effect of basal autophagy. The assay is applicable to high-throughput drug discovery as well as in vivo analysis.
Language	English
Publishing date	2017-04-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.1080/15548627.2017.1280646
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Article ; Online: An immune-based tool platform for in vivo cell clearance.

Zhang, Jieqiong / Tsukui, Tatsuya / Wu, Xiumin / Brito, Alyssa / Trumble, John Maxwell / Caraballo, Juan C / Allen, Greg M / Zavala-Solorio, José / Zhang, Chunlian / Paw, Jonathan / Lim, Wendell A / Geng, Jiefei / Kutskova, Yuliya / Freund, Adam / Kolumam, Ganesh / Sheppard, Dean / Cohen, Robert L

Life science alliance

2023 Volume 6, Issue 8

Abstract: Immunological targeting of pathological cells has been successful in oncology and is expanding to other pathobiological contexts. Here, we present a flexible platform that allows labeling cells of interest with the surface-expressed model antigen ... ...

Abstract	Immunological targeting of pathological cells has been successful in oncology and is expanding to other pathobiological contexts. Here, we present a flexible platform that allows labeling cells of interest with the surface-expressed model antigen ovalbumin (OVA), which can be eliminated via either antigen-specific T cells or newly developed OVA antibodies. We demonstrate that hepatocytes can be effectively targeted by either modality. In contrast, pro-fibrotic fibroblasts associated with pulmonary fibrosis are only eliminated by T cells in initial experiments, which reduced collagen deposition in a fibrosis model. This new experimental platform will facilitate development of immune-based approaches to clear potential pathological cell types in vivo.
MeSH term(s)	Humans ; Antibodies ; Fibroblasts ; Hepatocytes ; Kinetics ; Pulmonary Fibrosis
Chemical Substances	Antibodies
Language	English
Publishing date	2023-06-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2575-1077
ISSN (online)	2575-1077
DOI	10.26508/lsa.202201869
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Article ; Online: The Golgi as a potential membrane source for autophagy.

Geng, Jiefei / Klionsky, Daniel J

Autophagy

2010 Volume 6, Issue 7, Page(s) 950–951

Abstract: In macroautophagy (hereafter autophagy), a morphological hallmark is the formation of double-membrane vesicles called autophagosomes that sequester and deliver cytoplasmic components to the lysosome/vacuole for degradation. This process begins with an ... ...

Abstract	In macroautophagy (hereafter autophagy), a morphological hallmark is the formation of double-membrane vesicles called autophagosomes that sequester and deliver cytoplasmic components to the lysosome/vacuole for degradation. This process begins with an initial sequestering compartment, the phagophore, which expands into the mature autophagosome. A tremendous amount of work has been carried out to elucidate the mechanism of how the autophagosome is formed. However, an important missing piece in this puzzle is where the membrane comes from. Independent lines of evidence have shown that preexisting organelles may continuously supply lipids to support autophagosome formation. In our analysis, we identified several components of the late stage secretory pathway that may redirect Golgi-derived membrane to autophagosome formation in response to starvation conditions.
MeSH term(s)	Autophagy/physiology ; Cell Membrane/metabolism ; Cell Membrane/ultrastructure ; Golgi Apparatus/metabolism ; Golgi Apparatus/ultrastructure ; Intracellular Membranes/metabolism ; Intracellular Membranes/ultrastructure ; Protein Transport ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Secretory Pathway/physiology
Chemical Substances	Saccharomyces cerevisiae Proteins
Language	English
Publishing date	2010-10-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.4161/auto.6.7.13009
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Article ; Online: Synergistic effect of a novel autophagy inhibitor and Quizartinib enhances cancer cell death.

Ouchida, Amanda Tomie / Li, Yingbo / Geng, Jiefei / Najafov, Ayaz / Ofengeim, Dimitry / Sun, Xiaoxiao / Yu, Qiang / Yuan, Junying

Cell death & disease

2018 Volume 9, Issue 2, Page(s) 138

Abstract: Drug combinations have been increasingly applied in chemotherapy as a strategy to enhance the efficacy of anti-cancer treatment. The appropriate drug combinations may achieve synergistic effects beyond monotherapies alone. AC220 (Quizartinib), an FLT3 ... ...

Abstract	Drug combinations have been increasingly applied in chemotherapy as a strategy to enhance the efficacy of anti-cancer treatment. The appropriate drug combinations may achieve synergistic effects beyond monotherapies alone. AC220 (Quizartinib), an FLT3 receptor tyrosine kinase inhibitor, developed for the treatment of AML, has been tested in phase II human clinical trials. However, AC220 as a monotherapy is not efficacious enough. In this study, we performed a small-molecule screening of 12 640 compounds in order to find a compound that increase the AC220 efficacy in chemotherapy. We identified that TAK-165, a HER2 inhibitor, even when used at low nanomolar doses in combination with AC220, was able to induce cell death in different cancer cells, but not in non-cancer cell lines. We showed that TAK-165 and AC220 act synergistically to downregulate key signaling pathways and potently induce cancer cell death. Furthermore, we demonstrated that TAK-165 inhibited autophagy in a HER2-independent manner. Finally, we showed that the combination of TAK-165 and AC220 induced cell death in cancer cells through the activation of chaperone-mediated autophagy. Overall, these findings support the strategy for using AC220 and an autophagy inhibitor such as TAK-165 in a combinatorial treatment to enhance the efficacy of cancer therapies.
MeSH term(s)	Apoptosis/drug effects ; Autophagy/drug effects ; Benzothiazoles/pharmacology ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Drug Synergism ; Humans ; Neoplasms/pathology ; Oxazoles/chemistry ; Oxazoles/pharmacology ; Phenylurea Compounds/pharmacology ; Receptor, ErbB-2/metabolism ; Signal Transduction/drug effects ; Triazoles/chemistry ; Triazoles/pharmacology
Chemical Substances	Benzothiazoles ; Oxazoles ; Phenylurea Compounds ; TAK-165 ; Triazoles ; quizartinib (7LA4O6Q0D3) ; ERBB2 protein, human (EC 2.7.10.1) ; Receptor, ErbB-2 (EC 2.7.10.1)
Language	English
Publishing date	2018-01-26
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2541626-1
ISSN	2041-4889 ; 2041-4889
ISSN (online)	2041-4889
ISSN	2041-4889
DOI	10.1038/s41419-017-0170-9
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Article ; Online: Investigation of Aspergillus flavus in animal virulence.

Lan, Huahui / Wu, Lianghuan / Sun, Ruilin / Yang, Kunlong / Liu, Yinghang / Wu, Jiefei / Geng, Longpo / Huang, Chuanzhong / Wang, Shihua

Toxicon : official journal of the International Society on Toxinology

2018 Volume 145, Page(s) 40–47

Abstract: Aspergillus flavus is a common fungal pathogen of plants, animals and humans. Recently, many genes of A. flavus have been reported involving in regulation of pathogenesis in crops, but whether these genes are involved in animal virulence is still unknown. ...

Abstract	Aspergillus flavus is a common fungal pathogen of plants, animals and humans. Recently, many genes of A. flavus have been reported involving in regulation of pathogenesis in crops, but whether these genes are involved in animal virulence is still unknown. Here, we used a previous easy-to-use infection model for A. flavus based on mouse model by intravenous inoculation of A. flavus conidia. The outcome of infections in mice model showed that A. flavus NRRL3357 and laboratory strain CA14 PTS were both in dose dependent manner and highly reproducible. The progress of disease could be monitored by mice survival and histology analysis. Fungal burden analysis indicated it was gradually decreased within 7 days after infection. Moreover, aspergillosis caused by A. flavus significantly up-regulated gene expression levels of immune response mediators, including INF-γ, TNF-α, Dectin-1 and TLR2. Furthermore, the defined deletion A. flavus strains that previously displayed virulence in crop infection were also determined in this mouse model, and the results showed comparable degrees of infection in mice. Our results suggested that intravenous inoculation of conidia could be a suitable model for testing different A. flavus mutants in animal virulence. We hope to use this model to determine distinct A. flavus strains virulence in animals and study novel therapeutic methods to help control fungus diseases in the future.
MeSH term(s)	Administration, Intravenous ; Animals ; Aspergillosis/microbiology ; Aspergillosis/pathology ; Aspergillus flavus/genetics ; Aspergillus flavus/growth & development ; Aspergillus flavus/pathogenicity ; Disease Models, Animal ; Female ; Gene Expression ; Lung/microbiology ; Lung/pathology ; Mice, Inbred ICR ; Virulence
Language	English
Publishing date	2018-03-02
Publishing country	England
Document type	Journal Article
ZDB-ID	204479-1
ISSN	1879-3150 ; 0041-0101
ISSN (online)	1879-3150
ISSN	0041-0101
DOI	10.1016/j.toxicon.2018.02.043
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Article ; Online: Determining Atg protein stoichiometry at the phagophore assembly site by fluorescence microscopy.

Geng, Jiefei / Klionsky, Daniel J

Autophagy

2009 Volume 6, Issue 1, Page(s) 144–147

Abstract: In eukaryotic cells, autophagy is a lysosomal/ vacuolar degradative pathway necessary for the turnover of different macromolecules. Autophagy is under precise regulation, not only qualitatively but also quantitatively, and excess or reduced levels of ... ...

Abstract	In eukaryotic cells, autophagy is a lysosomal/ vacuolar degradative pathway necessary for the turnover of different macromolecules. Autophagy is under precise regulation, not only qualitatively but also quantitatively, and excess or reduced levels of autophagy may lead to various human diseases. In yeast, genetic screens led to the identification of more than 30 autophagy-related (ATG) genes, and most of the gene products reside at the phagophore assembly site (PAS). However, our attempt to understand the quantitative properties of autophagy is usually hampered, because traditional methods of analysis cannot provide stoichiometric information. We have recently used a fluorescence microscopy-based method to study the stoichiometry of Atg proteins at the PAS, trying to explain the mechanism of how the vesicle formation process is precisely regulated. This article describes a practical guide on this method. Its application and further analysis will improve our understanding of the quantitative properties of autophagy.
MeSH term(s)	Adaptor Proteins, Signal Transducing/analysis ; Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Autophagy/physiology ; Cells, Cultured ; Clinical Laboratory Techniques ; Humans ; Microscopy, Fluorescence/methods ; Phagosomes/chemistry ; Phagosomes/metabolism ; Protein Binding ; Protein Multimerization ; Small Ubiquitin-Related Modifier Proteins/analysis ; Small Ubiquitin-Related Modifier Proteins/metabolism ; Vesicular Transport Proteins/analysis ; Vesicular Transport Proteins/metabolism ; Yeasts
Chemical Substances	Adaptor Proteins, Signal Transducing ; Small Ubiquitin-Related Modifier Proteins ; Vesicular Transport Proteins
Language	English
Publishing date	2009-11-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.4161/auto.6.1.10249
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Article: Investigation of Aspergillus flavus in animal virulence

Lan, Huahui / Lianghuan Wu / Ruilin Sun / Kunlong Yang / Yinghang Liu / Jiefei Wu / Longpo Geng / Chuanzhong Huang / Shihua Wang

Toxicon. 2018 Apr., v. 145

2018

Abstract	Aspergillus flavus is a common fungal pathogen of plants, animals and humans. Recently, many genes of A. flavus have been reported involving in regulation of pathogenesis in crops, but whether these genes are involved in animal virulence is still unknown. Here, we used a previous easy-to-use infection model for A. flavus based on mouse model by intravenous inoculation of A. flavus conidia. The outcome of infections in mice model showed that A. flavus NRRL3357 and laboratory strain CA14 PTS were both in dose dependent manner and highly reproducible. The progress of disease could be monitored by mice survival and histology analysis. Fungal burden analysis indicated it was gradually decreased within 7 days after infection. Moreover, aspergillosis caused by A. flavus significantly up-regulated gene expression levels of immune response mediators, including INF-γ, TNF-α, Dectin-1 and TLR2. Furthermore, the defined deletion A. flavus strains that previously displayed virulence in crop infection were also determined in this mouse model, and the results showed comparable degrees of infection in mice. Our results suggested that intravenous inoculation of conidia could be a suitable model for testing different A. flavus mutants in animal virulence. We hope to use this model to determine distinct A. flavus strains virulence in animals and study novel therapeutic methods to help control fungus diseases in the future.
Keywords	Aspergillus flavus ; Toll-like receptor 2 ; animal models ; animal pathogenic fungi ; aspergillosis ; conidia ; crops ; disease control ; dose response ; gene expression ; gene expression regulation ; genes ; histology ; immune response ; interferon-gamma ; intravenous injection ; mice ; mutants ; pathogenesis ; plant pathogenic fungi ; tumor necrosis factor-alpha ; virulence
Language	English
Dates of publication	2018-04
Size	p. 40-47.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	204479-1
ISSN	1879-3150 ; 0041-0101
ISSN (online)	1879-3150
ISSN	0041-0101
DOI	10.1016/j.toxicon.2018.02.043
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The Atg8 and Atg12 ubiquitin-like conjugation systems in macroautophagy. 'Protein modifications: beyond the usual suspects' review series.

Geng, Jiefei / Klionsky, Daniel J

EMBO reports

2008 Volume 9, Issue 9, Page(s) 859–864

Abstract: As a lysosomal/vacuolar degradative pathway that is conserved in eukaryotic organisms, autophagy mediates the turnover of long-lived proteins and excess or aberrant organelles. The main characteristic of autophagy is the formation of a double-membrane ... ...

Abstract	As a lysosomal/vacuolar degradative pathway that is conserved in eukaryotic organisms, autophagy mediates the turnover of long-lived proteins and excess or aberrant organelles. The main characteristic of autophagy is the formation of a double-membrane vesicle, the autophagosome, which envelops part of the cytoplasm and delivers it to the lysosome/vacuole for breakdown and eventual recycling of the degradation products. Among the approximately 30 autophagy-related (Atg) genes identified so far, there are two ubiquitin-like proteins, Atg12 and Atg8. Analogous to ubiquitination, Atg12 is conjugated to Atg5 by Atg7--an E1-like protein--and Atg10--an E2-like protein. Similarly, Atg7 and Atg3 are the respective E1-like and E2-like proteins that mediate the conjugation of Atg8 to phosphatidylethanolamine. Both Atg12-Atg5 and Atg8 localize to the developing autophagosome. The Atg12-Atg5 conjugate facilitates the lipidation of Atg8 and directs its correct subcellular localization. Atg8-phosphatidylethanolamine is probably a scaffold protein that supports membrane expansion and the amount present correlates with the size of autophagosomes.
MeSH term(s)	Animals ; Autophagy/physiology ; Humans ; Models, Biological ; Models, Molecular ; Protein Isoforms/chemistry ; Protein Isoforms/metabolism ; Protein Isoforms/physiology ; Protein Processing, Post-Translational ; Protein Structure, Secondary ; Ubiquitin/chemistry ; Ubiquitin/metabolism ; Ubiquitin/physiology
Chemical Substances	Protein Isoforms ; Ubiquitin
Language	English
Publishing date	2008-08-14
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2020896-0
ISSN	1469-3178 ; 1469-221X
ISSN (online)	1469-3178
ISSN	1469-221X
DOI	10.1038/embor.2008.163
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Zs.A 5433: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Quantitative regulation of vesicle formation in yeast nonspecific autophagy.

Geng, Jiefei / Klionsky, Daniel J

Autophagy

2008 Volume 4, Issue 7, Page(s) 955–957

Abstract: In eukaryotic cells, autophagy is a degradative pathway necessary for the turnover of bulk cytoplasm. In yeast, this pathway also mediates the specific transport of a vacuolar hydrolase zymogen, precursor aminopeptidase (prApe1), from the cytoplasm to ... ...

Abstract	In eukaryotic cells, autophagy is a degradative pathway necessary for the turnover of bulk cytoplasm. In yeast, this pathway also mediates the specific transport of a vacuolar hydrolase zymogen, precursor aminopeptidase (prApe1), from the cytoplasm to the vacuole. Autophagy is under precise regulation, not only qualitatively but also quantitatively, especially in the steps involved in the vesicle formation process. We have recently used a fluorescence microscopy-based method to study the stoichiometry of autophagy-related (Atg) proteins during different conditions. This analysis shows that increased expression of Atg11 in the cytoplasm to vacuole targeting (Cvt) pathway increases the amount of this protein localized at the phagophore assembly site (PAS). In turn, under nutrient-rich conditions, the increased level of Atg11 causes the recruitment of higher than normal levels of Atg8 and Atg9 to the PAS, resulting in the formation of more Cvt vesicles, whereas the vesicle size is not affected. Combined with results from previous studies in starvation conditions, in this addendum we discuss the possible role of Atg8 and Atg9 in quantitatively regulating the vesicle formation process.
MeSH term(s)	Autophagy ; Autophagy-Related Protein 8 Family ; Autophagy-Related Proteins ; Cytoplasm/metabolism ; Cytoplasm/physiology ; Membrane Proteins/metabolism ; Microtubule-Associated Proteins/metabolism ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae/physiology ; Saccharomyces cerevisiae Proteins/metabolism ; Vacuoles/metabolism ; Vacuoles/physiology ; Vesicular Transport Proteins/metabolism
Chemical Substances	ATG8 protein, S cerevisiae ; ATG9 protein, S cerevisiae ; Atg11 protein, S cerevisiae ; Autophagy-Related Protein 8 Family ; Autophagy-Related Proteins ; Membrane Proteins ; Microtubule-Associated Proteins ; Saccharomyces cerevisiae Proteins ; Vesicular Transport Proteins
Language	English
Publishing date	2008-10-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2454135-7
ISSN	1554-8635 ; 1554-8627
ISSN (online)	1554-8635
ISSN	1554-8627
DOI	10.4161/auto.6791
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Article ; Online: Regulation of RIPK1 activation by TAK1-mediated phosphorylation dictates apoptosis and necroptosis

Jiefei Geng / Yasushi Ito / Linyu Shi / Palak Amin / Jiachen Chu / Amanda Tomie Ouchida / Adnan Kasim Mookhtiar / Heng Zhao / Daichao Xu / Bing Shan / Ayaz Najafov / Guangping Gao / Shizuo Akira / Junying Yuan

Nature Communications, Vol 8, Iss 1, Pp 1-

2017 Volume 12

Abstract: TNFα can promote three distinct mechanisms of cell death: necroptosis, RIPK1-independent and dependent apoptosis. Here the authors show that TNFα-induced phosphorylation of RIPK1 in the intermediate domain by TAK1 plays a key role in regulating this ... ...

Abstract	TNFα can promote three distinct mechanisms of cell death: necroptosis, RIPK1-independent and dependent apoptosis. Here the authors show that TNFα-induced phosphorylation of RIPK1 in the intermediate domain by TAK1 plays a key role in regulating this decision.
Keywords	Science ; Q
Language	English
Publishing date	2017-08-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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