Disrupting the LC3 Interaction Region (LIR) Binding of Selective Autophagy Receptors Sensitizes AML Cell Lines to Cytarabine

Putyrski, Mateusz; Vakhrusheva, Olesya; Bonn, Florian; Guntur, Suchithra; Vorobyov, Andrew; Brandts, Christian; Đikić, Ivan; Ernst, Andreas

doi:10.3389/fcell.2020.00208

Cited by 21 publications

(22 citation statements)

References 53 publications

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“…230132 Escherichia coli OmiMAX ThermoFisher Cat. C854003 Recombinant DNA pETM33 EMBL pETM41 EMBL For detailed information on expression constructs see Dataset EV2 mCherry2‐C1 Addgene #54563 pEGFP‐C1 vector Clontech (Leuwen) Phagemid p8 Sidhu lab (Chen et al , 2015 ) Phagemid p3 Ernst lab (Putyrski et al , 2020 ) Antibodies M13 HRP‐conjugated M13 bacteriophage antibody Sino Biological Inc Cat: 11973‐MM05T‐H Oligonucleotides and sequence‐based reagents Oligonucleotides CustomArray Chemicals enzymes and other reagents Phusion polymerase High‐Fidelity polymerase Thermo Scientific Cat: F631XL ExoI Thermo Scientific Cat: EN0581 Nucleotide removal kit ...…”

Section: Methodsmentioning

confidence: 99%

Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome

Benz

Ali

Krystkowiak

et al. 2022

Molecular Systems Biology

138

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Specific protein–protein interactions are central to all processes that underlie cell physiology. Numerous studies have together identified hundreds of thousands of human protein–protein interactions. However, many interactions remain to be discovered, and low affinity, conditional, and cell type‐specific interactions are likely to be disproportionately underrepresented. Here, we describe an optimized proteomic peptide‐phage display library that tiles all disordered regions of the human proteome and allows the screening of ~ 1,000,000 overlapping peptides in a single binding assay. We define guidelines for processing, filtering, and ranking the results and provide PepTools, a toolkit to annotate the identified hits. We uncovered >2,000 interaction pairs for 35 known short linear motif (SLiM)‐binding domains and confirmed the quality of the produced data by complementary biophysical or cell‐based assays. Finally, we show how the amino acid resolution‐binding site information can be used to pinpoint functionally important disease mutations and phosphorylation events in intrinsically disordered regions of the proteome. The optimized human disorderome library paired with PepTools represents a powerful pipeline for unbiased proteome‐wide discovery of SLiM‐based interactions.

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Section: Methodsmentioning

confidence: 99%

Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome

Benz

Ali

Krystkowiak

et al. 2022

Molecular Systems Biology

138

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“…More and more studies have demonstrated autophagy could be a promising therapeutic target for overcoming drug resistance in AML [11][12][13][19][20] . As mention above, conventional chemotherapeutic agents including cytarabine and daunorubicin are able to induce autophagy as a survival mechanism to resist cytotoxic stress and counteract their therapeutic effects; inhibition of autophagy could synergize with these agents to overcome drug resistance, improve clinical outcomes in AML therapy [12,19,29] . Apart from chemotherapy, in targeting treatment, such as BET inhibitors [20] , histone methyltransferase inhibitors [30] , BCL2 inhibitors [31] , and FLT3 inhibitors reported in the present study, could also activate autophagy, serving as a cytoprotective adaptive mechanism against clone selective stress, to contribute to the drug resistance of AML stem cells; co-targeting autophagy could enhance the anti-leukemia effect of these inhibitors.…”

Section: Discussionmentioning

confidence: 99%

Autophagy Activation Induces Resistance to FLT3 Inhibitors in Acute Myeloid Leukemia with FLT3-ITD Mutation

Xu¹,

Yin²,

Yang³

et al. 2021

Preprint

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Background: Autophagy plays a critical role in drug resistance in acute myeloid leukemia (AML), including the subtype with FLT3-ITD mutation. Yet how autophagy is activated and mediates resistance to FLT3 inhibitors in FLT3-ITD-positive AML remains unsure. Methods: We detected the alteration of autophagy in FLT3-ITD-positive leukemic cells after versus before acquired resistance to FLT3 inhibitors; tested the stimulative effect of acquired D835Y mutation and bone marrow micro-environment (BME) on autophagy; explored the mechanism of autophagy mediating FLT3 inhibitor resistance. Results: Sorafenib-resistant cells markedly overexpressed autophagy in comparison with sorafenib-sensitive cells or the cells before sorafenib treatment. Both acquired D835Y mutation and BME activated cytoprotective autophagy to induce FLT3 inhibitor resistance. Autophagy activation decreased the suppression efficacy of FLT3 inhibitors on FLT3 downstream signaling and then weakened their anti-leukemia effect. Inhibition of autophagy with CQ significantly enhanced the suppressive effect of FLT3 inhibitor on FLT3 downstream signaling, in the end overcame FLT3 inhibitor resistance. Conclusions: Autophagy might be stimulated by acquired mutation or BME, and bypass activate FLT3 downstream signaling to mediate FLT3 inhibitor resistance in FLT3-ITD-positive AML. Targeting autophagy could be a promising strategy to overcome resistance.

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“…18 Lebih menarik lagi, sebuah penelitian terkini dari Putyrski dan koleganya yang diterbitkan tahun 2020 menyatakan bahwa LC3 memiliki area interaksi (dinamakan sebagai LC3 interaction region atau LIR), yang berisi kantung ikatan yaitu hydrophobic binding pocket 1 atau HP1, yang terdiri dari residu asam amino Trp, Phe, atau Tyr, serta HP2 dengan residu Leu, Val, atau Ile. 19…”

Section: Rigid Body Docking Dengan Menggunakan Korelasi Fft (Fast Fourier Transform)unclassified

INTERAKSI MOLEKULAR DARI RICIN-A DENGAN Beclin-1, LC3, DAN p62 PADA PROSES AUTOFAGI

Herawati

Lesmana

Levita

et al. 2022

JFB

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Autofagi merupakan proses adaptasi yang dilakukan sebagai pertahanan dalam respon seluler, seperti kekurangan nutrisi atau stress metabolik lain. Mekanisme autofagi diregulasi oleh protein yang dinamakan Autophagy-Related Genes (ATG). Autofagi juga telah banyak dikaitkan dengan berbagai penyakit pada manusia, misalnya kanker atau penyakit degeneratif lainnya. Ricin merupakan protein toksik yang berasal dari biji jarak Ricinus communis L. dan banyak dieksplorasi untuk aktivitas antikanker melalui jalur pensinyalan caspase (apoptosis), namun belum ada penelitian pada jalur autofagi. Penelitian ini dilakukan untuk menelaah mode ikatan yang terjadi antara ricin-A dan protein-protein yang berperan pada setiap tahap proses autofagi (Beclin-1, LC3 atau Light Chain 3, dan p62/Sequistrosome1). Metode yang digunakan adalah simulasi penambatan protein-protein menggunakan server online ClusPro (https://cluspro.org). Hasil penelitian menunjukkan bahwa ricin-A dapat berinteraksi dengan Beclin-1. LC3, dan p62 melalui pembentukan ikatan hidrogen dengan afinitas baik. Dapat disimpulkan bahwa ricin-A berperan penting dalam proses autofagi dan dapat dikembangkan menjadi fitofarmaka terapi kanker.

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Disrupting the LC3 Interaction Region (LIR) Binding of Selective Autophagy Receptors Sensitizes AML Cell Lines to Cytarabine

Cited by 21 publications

References 53 publications

Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome

Proteome‐scale mapping of binding sites in the unstructured regions of the human proteome

Autophagy Activation Induces Resistance to FLT3 Inhibitors in Acute Myeloid Leukemia with FLT3-ITD Mutation

INTERAKSI MOLEKULAR DARI RICIN-A DENGAN Beclin-1, LC3, DAN p62 PADA PROSES AUTOFAGI

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