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Select item 104741561.

The transcription factor NRF1 (NFE2L1) activates aggrephagy by inducing p62 and GABARAPL1 after proteasome inhibition to maintain proteostasis

Atsushi Hatanaka, Sota Nakada, Gen Matsumoto, Katsuya Satoh, Iori Aketa, Akira Watanabe, Tomoaki Hirakawa, Tadayuki Tsujita, Tsuyoshi Waku, Akira Kobayashi

Sci Rep. 2023; 13: 14405. Published online 2023 Sep 1. doi: 10.1038/s41598-023-41492-9

PMCID:: PMC10474156

Abstract Article PDF–2.8M

Select item 103875642.

METTL3 promotes hyperoxia-induced pyroptosis in neonatal bronchopulmonary dysplasia by inhibiting ATG8-mediated autophagy

Lili Xu, Zhan Shi, Zhaojun Pan, Rong Wu

Clinics (Sao Paulo) 2023 Jan-Dec; 78: 100253. Published online 2023 Jul 19. doi: 10.1016/j.clinsp.2023.100253

PMCID:: PMC10387564

Abstract Article PDF–3.9M

Select item 103338843.

Large‐scale phosphomimetic screening identifies phospho‐modulated motif‐based protein interactions

Johanna Kliche, Dimitriya Hristoforova Garvanska, Leandro Simonetti, Dilip Badgujar, Doreen Dobritzsch, Jakob Nilsson, Norman E Davey, Ylva Ivarsson

Mol Syst Biol. 2023 Jul; 19(7): e11164. Published online 2023 May 23. doi: 10.15252/msb.202211164

PMCID:: PMC10333884

Abstract Article PDF–5.0M

Select item 102473664.

Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum

Alexis González, Adriana Covarrubias-Pinto, Ramachandra M. Bhaskara, Marius Glogger, Santosh K. Kuncha, Audrey Xavier, Eric Seemann, Mohit Misra, Marina E. Hoffmann, Bastian Bräuning, Ashwin Balakrishnan, Britta Qualmann, Volker Dötsch, Brenda A. Schulman, Michael M. Kessels, Christian A. Hübner, Mike Heilemann, Gerhard Hummer, Ivan Dikić

Nature. 2023; 618(7964): 394–401. Published online 2023 May 24. doi: 10.1038/s41586-023-06089-2

PMCID:: PMC10247366

Abstract Article PDF–24M

Select item 100752255.

ATG8-dependent LMX1B-autophagy crosstalk shapes human midbrain dopaminergic neuronal resilience

Natalia Jiménez-Moreno, Madhu Kollareddy, Petros Stathakos, Joanna J. Moss, Zuriñe Antón, Deborah K. Shoemark, Richard B. Sessions, Ralph Witzgall, Maeve Caldwell, Jon D. Lane

J Cell Biol. 2023 May 1; 222(5): e201910133. Published online 2023 Apr 4. doi: 10.1083/jcb.201910133

PMCID:: PMC10075225

Abstract Article PDF–8.5M

Select item 100729066.

Multiplexed kinase interactome profiling quantifies cellular network activity and plasticity

Martin Golkowski, Andrea Lius, Tanmay Sapre, Ho-Tak Lau, Taylor Moreno, Dustin J. Maly, Shao-En Ong

Mol Cell. Author manuscript; available in PMC 2023 Apr 4.

Published in final edited form as: Mol Cell. 2023 Mar 2; 83(5): 803–818.e8. Published online 2023 Feb 2. doi: 10.1016/j.molcel.2023.01.015

PMCID:: PMC10072906

Abstract Article PDF–4.2M

Select item 100339377.

Assessment of community efforts to advance network-based prediction of protein–protein interactions

Xu-Wen Wang, Lorenzo Madeddu, Kerstin Spirohn, Leonardo Martini, Adriano Fazzone, Luca Becchetti, Thomas P. Wytock, István A. Kovács, Olivér M. Balogh, Bettina Benczik, Mátyás Pétervári, Bence Ágg, Péter Ferdinandy, Loan Vulliard, Jörg Menche, Stefania Colonnese, Manuela Petti, Gaetano Scarano, Francesca Cuomo, Tong Hao, Florent Laval, Luc Willems, Jean-Claude Twizere, Marc Vidal, Michael A. Calderwood, Enrico Petrillo, Albert-László Barabási, Edwin K. Silverman, Joseph Loscalzo, Paola Velardi, Yang-Yu Liu

Nat Commun. 2023; 14: 1582. Published online 2023 Mar 22. doi: 10.1038/s41467-023-37079-7

PMCID:: PMC10033937

Abstract Article PDF–1.5M

Select item 97979888.

TBK1 posphorylation activates LIR-dependent degradation of the inflammation repressor TNIP1

Jianwen Zhou, Nikoline Lander Rasmussen, Hallvard Lauritz Olsvik, Vyacheslav Akimov, Zehan Hu, Gry Evjen, Stéphanie Kaeser-Pebernard, Devanarayanan Siva Sankar, Carole Roubaty, Pauline Verlhac, Nicole van de Beek, Fulvio Reggiori, Yakubu Princely Abudu, Blagoy Blagoev, Trond Lamark, Terje Johansen, Jörn Dengjel

J Cell Biol. 2023 Feb 6; 222(2): e202108144. Published online 2022 Dec 27. doi: 10.1083/jcb.202108144

PMCID:: PMC9797988

Abstract Article PDF–6.9M

Select item 95808919.

Loss of GABARAPL1 confers ferroptosis resistance to cancer stem‐like cells in hepatocellular carcinoma

Xiaojing Du, Zhuoran Qi, Jinzhi Xu, Mengzhou Guo, Xingxing Zhang, Zhijie Yu, Xin Cao, Jinglin Xia

Mol Oncol. 2022 Oct; 16(20): 3703–3719. Published online 2022 Sep 5. doi: 10.1002/1878-0261.13305

PMCID:: PMC9580891

Abstract Article PDF–3.3M

Select item 945097910.

HYPK coordinates degradation of polyneddylated proteins by autophagy

Debasish Kumar Ghosh, Akash Ranjan

Autophagy. 2022; 18(8): 1763–1784. Published online 2021 Nov 26. doi: 10.1080/15548627.2021.1997053

PMCID:: PMC9450979

Abstract Article PDF–6.3M

Select item 927928511.

Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery

Pierre C. Havugimana, Raghuveera Kumar Goel, Sadhna Phanse, Ahmed Youssef, Dzmitry Padhorny, Sergei Kotelnikov, Dima Kozakov, Andrew Emili

Nat Commun. 2022; 13: 4043. Published online 2022 Jul 13. doi: 10.1038/s41467-022-31809-z

PMCID:: PMC9279285

Abstract Article PDF–2.5M

Select item 911973612.

OpenCell: proteome-scale endogenous tagging enables the cartography of human cellular organization

Nathan H. Cho, Keith C. Cheveralls, Andreas-David Brunner, Kibeom Kim, André C. Michaelis, Preethi Raghavan, Hirofumi Kobayashi, Laura Savy, Jason Y. Li, Hera Canaj, James Y.S. Kim, Edna M. Stewart, Christian Gnann, Frank McCarthy, Joana P. Cabrera, Rachel M. Brunetti, Bryant B. Chhun, Greg Dingle, Marco Y. Hein, Bo Huang, Shalin B. Mehta, Jonathan S. Weissman, Rafael Gómez-Sjöberg, Daniel N. Itzhak, Loic A. Royer, Matthias Mann, Manuel D. Leonetti

Science. Author manuscript; available in PMC 2022 Sep 11.

Published in final edited form as: Science. 2022 Mar 11; 375(6585): eabi6983. Published online 2022 Mar 11. doi: 10.1126/science.abi6983

PMCID:: PMC9119736

Abstract Article PDF–3.3M

Select item 876207813.

An ALS-associated variant of the autophagy receptor SQSTM1/p62 reprograms binding selectivity toward the autophagy-related hATG8 proteins

Andrew Brennan, Robert Layfield, Jed Long, Huw E.L. Williams, Neil J. Oldham, Daniel Scott, Mark S. Searle

J Biol Chem. 2022 Feb; 298(2): 101514. Published online 2021 Dec 18. doi: 10.1016/j.jbc.2021.101514

PMCID:: PMC8762078

Abstract Article PDF–2.4M

Select item 816503014.

Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome

Edward L. Huttlin, Raphael J. Bruckner, Jose Navarrete-Perea, Joe R. Cannon, Kurt Baltier, Fana Gebreab, Melanie P. Gygi, Alexandra Thornock, Gabriela Zarraga, Stanley Tam, John Szpyt, Brandon M. Gassaway, Alexandra Panov, Hannah Parzen, Sipei Fu, Arvene Golbazi, Eila Maenpaa, Keegan Stricker, Sanjukta Guha Thakurta, Tian Zhang, Ramin Rad, Joshua Pan, David P. Nusinow, Joao A. Paulo, Devin K. Schweppe, Laura Pontano Vaites, J. Wade Harper, Steven P. Gygi

Cell. Author manuscript; available in PMC 2022 May 27.

Published in final edited form as: Cell. 2021 May 27; 184(11): 3022–3040.e28. Published online 2021 May 6. doi: 10.1016/j.cell.2021.04.011

PMCID:: PMC8165030

Abstract Article PDF–2.2M

Select item 812213815.

Non-canonical autophagy drives alternative ATG8 conjugation to phosphatidylserine

Joanne Durgan, Alf H. Lystad, Katherine Sloan, Sven R. Carlsson, Michael I. Wilson, Elena Marcassa, Rachel Ulferts, Judith Webster, Andrea F. Lopez-Clavijo, Michael J. Wakelam, Rupert Beale, Anne Simonsen, David Oxley, Oliver Florey

Mol Cell. 2021 May 6; 81(9): 2031–2040.e8. doi: 10.1016/j.molcel.2021.03.020

PMCID:: PMC8122138

Abstract Article

Select item 779568416.

Lack of GABARAP-Type Proteins Is Accompanied by Altered Golgi Morphology and Surfaceome Composition

Julia L. Sanwald, Jochen Dobner, Indra M. Simons, Gereon Poschmann, Kai Stühler, Alina Üffing, Silke Hoffmann, Dieter Willbold

Int J Mol Sci. 2021 Jan; 22(1): 85. Published online 2020 Dec 23. doi: 10.3390/ijms22010085

PMCID:: PMC7795684

Abstract Article PDF–2.8M

Select item 775156317.

Mass spectrometry proteomics reveals a function for mammalian CALCOCO1 in MTOR-regulated selective autophagy

Jonathan A. Stefely, Yu Zhang, Elyse C. Freiberger, Nicholas W. Kwiecien, Hala Elnakat Thomas, Alexander M. Davis, Nathaniel D. Lowry, Catherine E. Vincent, Evgenia Shishkova, Nicholas A. Clark, Mario Medvedovic, Joshua J. Coon, David J. Pagliarini, Carol A. Mercer

Autophagy. 2020; 16(12): 2219–2237. Published online 2020 Feb 2. doi: 10.1080/15548627.2020.1719746

PMCID:: PMC7751563

Abstract Article PDF–6.2M

Select item 738231318.

MAP4K Interactome Reveals STRN4 as a Key STRIPAK Complex Component in Hippo Pathway Regulation

Gayoung Seo, Han Han, Rebecca Elizabeth Vargas, Bing Yang, Xu Li, Wenqi Wang

Cell Rep. Author manuscript; available in PMC 2020 Jul 25.

Published in final edited form as: Cell Rep. 2020 Jul 7; 32(1): 107860. doi: 10.1016/j.celrep.2020.107860

PMCID:: PMC7382313

Abstract Article PDF–2.6M

Select item 733540219.

Autophagic Network Analysis of the Dual Effect of Sevoflurane on Neurons Associated with GABARAPL1 and 2

Guolin Lu, Dongdong Rao, Min Zhou, Liangpu Xu, Longxin Zhang, Sujing Zhang, Yuping Wang

Biomed Res Int. 2020; 2020: 1587214. Published online 2020 Jun 26. doi: 10.1155/2020/1587214

PMCID:: PMC7335402

Abstract Article PDF–2.9M

Select item 732206720.

RIG-I regulates myeloid differentiation by promoting TRIM25-mediated ISGylation

Song-Fang Wu, Li Xia, Xiao-Dong Shi, Yu-Jun Dai, Wei-Na Zhang, Jun-Mei Zhao, Wu Zhang, Xiang-Qin Weng, Jing Lu, Huang-Ying Le, Sheng-ce Tao, Jiang Zhu, Zhu Chen, Yue-Ying Wang, Saijuan Chen

Proc Natl Acad Sci U S A. 2020 Jun 23; 117(25): 14395–14404. Published online 2020 Jun 8. doi: 10.1073/pnas.1918596117

PMCID:: PMC7322067

Abstract Article PDF–2.7M

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