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Autophagic turnover of NBR1 restricts metastatic colonization during mammary tumor progression

ABSTRACT: Autophagic turnover of NBR1 restricts metastatic colonization during mammary tumor progression

PROVIDER: PRJNA510992 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8360420_1.fastq.gz	Fastqsanger.gz
	SRR8360420_2.fastq.gz	Fastqsanger.gz
	SRR8360421_1.fastq.gz	Fastqsanger.gz
	SRR8360421_2.fastq.gz	Fastqsanger.gz
	SRR8360422_1.fastq.gz	Fastqsanger.gz

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Autophagic turnover of NBR1 restricts metastatic colonization during mammary tumor progression

Project description:Autophagy is implicated in promoting the metastatic potential of tumor cells. Utilizing a mouse model of mammary cancer to temporally delete essential autophagy regulators, ATG12 or ATG5, in tumor cells during distinct stages of carcinoma progression, we determine a stage-specific role for autophagy in suppressing metastatic colonization. In stark contrast to the tumor-promoting role of autophagy in primary mammary tumors, autophagy restricts colonization of disseminated tumor cells (DTCs) and prevents the acquisition of basal epithelial characteristics, effects that are dependent on turnover of the autophagy-specific substrate, Neighbor to BRCA1 (NBR1). Analysis of human breast cancer samples corroborates the importance of NBR1 in overall survival and metastasis, highlighting NBR1 as a potential therapeutic target in preventing DTCs from developing into overt, clinical disease.

2020-02-19 | GSE124209 | GEO

INTEGRATED MULTI-OMICS ANALYSES OF MAIZE REVEAL ROLES FOR AUTOPHAGIC RECYCLING IN PROTEOME REMODELING AND LIPID TURNOVER

Project description:The turnover of cytoplasmic material via autophagic encapsulation and delivery to vacuoles is essential for recycling cellular constituents, especially under nutrient-limiting conditions. To determine how cells/tissues rely on autophagy, we applied in-depth multi-omic analyses to study maize (Zea mays) autophagy mutants grown under nitrogen-replete and starvation conditions. Surprisingly, broad alterations in the leaf metabolome were evident in plants missing the core autophagy component ATG12 even without stress, particularly affecting products of lipid turnover and secondary metabolites, which were underpinned by substantial changes in the transcriptome and/or proteome. Cross-comparison of mRNA and protein abundances allowed for the identification of organelles, protein complexes, and individual proteins targeted for selective autophagic clearance, and revealed several processes controlled by this catabolism. Collectively, we describe a facile proteomic strategy to survey autophagic substrates, and show that autophagy has a greater than expected influence in sculpting plant proteomes and membranes both before and during nitrogen stress.

2018-10-08 | PXD009627 | Pride

Autophagic Degradation of NBR1 Restricts Metastatic Outgrowth during Mammary Tumor Progression.

Project description: Not available

| S-EPMC7108946 | biostudies-literature

A multi-subunit capture complex facilitates degradation of ER stalled MHC-I in pancreatic cancer

Project description:Pancreatic ductal adenocarcinoma (PDAC) evades immune surveillance partly through autophagic capture and lysosomal degradation of major histocompatibility complex class I (MHC-I). However, the basis for this susceptibility remains unclear. Using synchronized ER exit assays, we show that PDAC cells retain MHC-I in the endoplasmic reticulum and inefficiently traffic it to the plasma membrane. An autophagic capture complex composed of the ER-phagy receptor TEX264 and the cargo receptor NBR1 mediates targeting of MHC-I for lysosomal degradation. Suppression of either receptor restores MHC-I levels and increases surface presentation. Binding of MHC-I to the capture complex is linked to antigen presentation efficiency as inhibition of antigen loading enhances MHC-I binding to the TEX264–NBR1 complex, whereas expression of high-affinity ER-targeted peptides reduces binding and promotes surface localization. A genome-wide CRISPRi screen identified the ER-resident E3 ligase NFXL1 as a mediator of MHC-I ubiquitylation and autophagic capture. Elevated NFXL1 correlates with reduced MHC-I expression and poor patient prognosis, highlighting a targetable pathway regulating PDAC immunogenicity.

2026-07-22 | GSE325129 | GEO

Quantitative mapping of autophagic cargo during nutrient stress reveals YIPF3 - YIPF4 as membrane receptors for Golgiphagy_part2_neurons

Project description:During nutrient stress, macroautophagy is employed to degrade cellular macromolecules, thereby providing biosynthetic building blocks while simultaneously remodeling the proteome. While the machinery responsible for initiation of macroautophagy is well characterized, our understanding of the extent to which individual proteins, protein complexes and organelles are selected for autophagic degradation, and the underlying targeting mechanisms is limited. Here, we use orthogonal proteomic strategies to provide a global molecular inventory of autophagic cargo during nutrient stress in mammalian cell lines. Through prioritization of autophagic cargo, we identify a heterodimeric pair of membrane-embedded proteins, YIPF3 and YIPF4, as receptors for Golgiphagy. During nutrient stress, YIPF4 is mobilized into ATG8-positive vesicles that traffic to lysosomes as measured via Golgiphagy flux reporters in a process that requires the VPS34 and ULK1-FIP200 arms of the autophagy system. Cells lacking YIPF3 or YIPF4 are selectively defective in elimination of Golgi membrane proteins during nutrient stress. By merging absolute protein abundance with autophagic turnover, we create a global protein census describing how autophagic degradation maps onto protein abundance and subcellular localization. Our results, available via an interactive web tool, reveal that autophagic turnover prioritizes membrane-bound organelles (principally Golgi and ER) for proteome remodeling during nutrient stress.

2023-09-13 | PXD043923 | Pride

Quantitative mapping of autophagic cargo during nutrient stress reveals YIPF3 - YIPF4 as membrane receptors for Golgiphagy

2023-09-06 | PXD038358 | Pride

INTEGRATED MULTI-OMICS ANALYSES OF MAIZE REVEAL ROLES FOR AUTOPHAGIC DURING FIXED CARBON STARVATION

Project description:The turnover of cytoplasmic material via autophagic encapsulation and delivery to vacuoles is essential for recycling cellular constituents, especially under nutrient-limiting conditions. To determine how cells/tissues rely on autophagy, we applied in-depth multi-omic analyses to study maize (Zea mays) autophagy mutants grown after fixed carbon starvation. Surprisingly, broad alterations in the leaf metabolome were evident in plants missing the core autophagy component ATG12 even without stress, particularly affecting products of lipid turnover and secondary metabolites, which were underpinned by substantial changes in the transcriptome and/or proteome. Cross-comparison of mRNA and protein abundances allowed for the identification of organelles, protein complexes, and individual proteins targeted for selective autophagic clearance, and revealed several processes controlled by this catabolism. Fixed carbon starvation induced the proteins involved in alternative respiration together with the upregulation of various alternative catabolic processes. Collectively, we describe a facile proteomic strategy to survey autophagic substrates, and show that autophagy has a greater than expected influence in sculpting plant proteomes and membranes both before and during nitrogen stress.

2020-07-15 | PXD017077 | Pride

The autophagy receptor NBR1 directs the clearance of photodamaged chloroplasts

Project description:The ubiquitin-binding NBR1 autophagy receptor plays a prominent role in recognizing ubiquitylated protein aggregates for vacuolar degradation during macroautophagy. Here, we show that upon exposing Arabidopsis plants to intense light, NBR1 associates with photodamaged chloroplasts independently of ATG7, a core component of the canonical autophagy machinery. NBR1 coats both the surface and interior of chloroplasts which is then followed by direct engulfment of the organelle into the central vacuole via a microautophagy-type process. The relocalization of NBR1 into chloroplasts does not require the chloroplast translocon complexes embedded in the envelope but is instead greatly enhanced by removing the self-oligomerization mPB1 domain of NBR1. The delivery of NBR1-decorated chloroplasts into vacuoles depends on the ubiquitin-binding UBA2 domain of NBR1 but is independent of the E3 ligases SP1 and PUB4, known to direct the ubiquitylation of chloroplast surface proteins. Compared to wild type plants, nbr1 mutants have altered levels of a subset of chloroplast proteins and display abnormal chloroplast density and sizes upon high light exposure. We postulate that, as photodamaged chloroplasts lose envelope integrity, cytosolic ligases reach the chloroplast interior to ubiquitylate thylakoid and stroma proteins which are then recognize by NBR1 for autophagic clearance. This study uncovers a new function of NBR1 in the degradation of damaged chloroplasts by microautophagy.

2023-01-16 | PXD039183 | Pride

Cellular context restricts IDR plasticity to a single essential effector interface for m6A-dependent mRNA turnover [Chan_RNA-seq_experiment 2]

Project description:Cellular context restricts IDR plasticity to a single essential effector interface for m6A-dependent mRNA turnover [Chan_RNA-seq_experiment 2]

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Cellular context restricts IDR plasticity to a single essential effector interface for m6A-dependent mRNA turnover [Chan_RNA-seq_experiment 1]

Project description:Cellular context restricts IDR plasticity to a single essential effector interface for m6A-dependent mRNA turnover [Chan_RNA-seq_experiment 1]

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