Biology subjects

Itzhak, D. N.

Publications and source records attributed to Itzhak, D. N..

6 recordsLinked to original sources

bioRxiv2026

IRE1α undergoes a dynamic filament assembly cycle governed by unfolded proteins and BiP.

The endoplasmic reticulum is a major hub of protein synthesis, modification and trafficking that relies on the Unfolded Protein Response (UPR) to balance its folding capacity. IRE1, the most conserved of the UPR sensors, undergoes a change in oligomeric state upon activation that propagates the stress signal from the ER lumen to its cytoplasmic kinase/RNase domains. Here we show that opposing inputs from unfolded proteins and the ER chaperone machinery govern a dynamic cycle of IRE1 assembly. A bona fide unfolded ER client directly binds the IRE1 lumenal domain (LD) and promotes higher-order oligomerization. Model peptides further reveal that full assembly into LD filaments depends on ligand length, sequence, and the IRE1 oligomerization interfaces. The ER Hsp70, BiP, counterbalances this process through two distinct mechanisms: i) an ATP-independent interaction via the BiP nucleotide-binding domain buffers early IRE1 assembly by engaging its oligomerization interface, whereas ii) ATP-regulated BiP/ERDJ machinery actively dismantles assembled filaments. Together, our findings reconcile direct unfolded protein recognition with BiP-mediated regulation to establish LD oligomerization as a point of integration through which unfolded protein load and chaperone availability dynamically regulate IRE1 assembly state and signalling.

biochemistry↗

bioRxiv2025

Intrinsic Molecular Timers and a Biphasic Amplitude Limit Regulate the Integrated Stress Response

The Integrated Stress Response (ISR) is an evolutionarily conserved signaling network that remodels the translatome and transcriptome in response to multiple stresses, including nutrient deprivation, mitochondrial dysfunction, viral infection, and loss of protein homeostasis. Here, we present a comprehensive theoretical model of the ISR, calibrated to time-resolved proteomics data that captures how cells encode the magnitude and duration of stress signals to generate a homeostatic output. Our simulations and data converge on an ISR activation threshold defined by phosphorylated eIF2 levels, and sequential cascading delays in the accumulation of the ISR components ATF4, GADD34, CHOP, and DR5, suggesting hardwired molecular timers regulate ISR behaviors. Our combined experimental and computational analyses reveal limiting ATF4 levels, which can be suppressed when TC levels drop below a threshold that would allow its translation. While our model accurately predicts this initial saturation limit, its divergence from the data at high stress levels, correlated with minimal TC levels, identified a "translational cliff" that defines a finite ATF4-dependent ISR operational range. This work establishes a quantitative platform to probe ISR dynamics and generate novel, testable hypotheses.

systems biology↗

bioRxiv2023

Global organelle profiling reveals subcellular localization and remodeling at proteome scale

Defining the subcellular distribution of all human proteins and its remodeling across cellular states remains a central goal in cell biology. Here, we present a high-resolution strategy to map subcellular organization using organelle immuno-capture coupled to mass spectrometry. We apply this proteomics workflow to a cell-wide collection of membranous and membrane-less compartments. A graph-based representation of our data reveals the subcellular localization of over 7,600 proteins, defines spatial protein networks, and uncovers interconnections between cellular compartments. We demonstrate that our approach can be deployed to comprehensively profile proteome remodeling during cellular perturbation. By characterizing the cellular landscape following hCoV-OC43 viral infection, we discover that many proteins are regulated by changes in their spatial distribution rather than by changes in their total abundance. Our results establish that proteome-wide analysis of subcellular remodeling provides essential insights for the elucidation of cellular responses. Our dataset can be explored at organelles.czbiohub.org.

cell biology↗

bioRxiv2021

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

Elucidating the wiring diagram of the human cell is a central goal of the post-genomic era. We combined genome engineering, confocal live-cell imaging, mass spectrometry and data science to systematically map the localization and interactions of human proteins. Our approach provides a data-driven description of the molecular and spatial networks that organize the proteome. Unsupervised clustering of these networks delineates functional communities that facilitate biological discovery, and uncovers that RNA-binding proteins form a specific sub-group defined by unique interaction and localization properties. Furthermore, we discover that remarkably precise functional information can be derived from protein localization patterns, which often contain enough information to identify molecular interactions. Paired with a fully interactive website opencell.czbiohub.org, we provide a resource for the quantitative cartography of human cellular organization.

cell biology↗

bioRxiv2020

Small molecule enhancers of endosome-to-cytosol import augment anti-tumour immunity

Efficient cross-presentation of antigens by dendritic cells (DCs) is critical for initiation of anti-tumour immune responses. Yet, several steps of antigen intracellular traffic during cross-presentation are incompletely understood: in particular, the molecular mechanisms and the relative importance of antigen import from endocytic compartments into the cytosol. Here, we asked whether antigen import into the cytosol is rate-limiting for cross-presentation and anti-tumour immunity. By screening 700 FDA-approved drugs, we identified 37 import enhancers. We focused on prazosin and tamoxifen, and generated proteomic organellar maps of drug-treated DCs, covering the subcellular localisations of over 2000 proteins. By combining organellar mapping, quantitative proteomics, microscopy, and bioinformatics, we conclude that import enhancers undergo lysosomal trapping leading to membrane permeation and antigen release into the cytosol. Enhancing antigen import facilitates cross-presentation of both soluble and cell-associated antigens. Systemic administration of prazosin also led to reduced growth of MC38 tumours and to a synergistic effect with checkpoint immunotherapy in a melanoma model. Thus, inefficient antigen import into the cytosol limits antigen cross-presentation, restraining the potency of anti-tumour immune responses and efficacy of checkpoint blockers. HighlightsO_LIQuinazolamine derivatives are potent enhancers of antigen import into the cytosol C_LIO_LIAntigen import enhancement occurs as a consequence of lysosomal trapping C_LIO_LIAntigen import enhancers facilitate cross-presentation and synergise with PD-L1 C_LIO_LIProteomic organellar maps of cDC1s as a tool to detect biological effects of drugs C_LI O_FIG O_LINKSMALLFIG WIDTH=180 HEIGHT=200 SRC="FIGDIR/small/079491v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1d55245org.highwire.dtl.DTLVardef@c3d43org.highwire.dtl.DTLVardef@189fbc8org.highwire.dtl.DTLVardef@1f1280e_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2017

AP-4 vesicles unmasked by organellar proteomics to reveal their cargo and machinery

Adaptor protein 4 (AP-4) is an ancient membrane trafficking complex, whose function has largely remained elusive. In humans, AP-4 deficiency causes a severe neurological disorder of unknown aetiology. We apply unbiased proteomic methods, including Dynamic Organellar Maps, to find proteins whose subcellular localisation depends on AP-4. We identify three transmembrane cargo proteins, ATG9A, SERINC1 and SERINC3, and two AP-4 accessory proteins, RUSC1 and RUSC2. We demonstrate that AP-4 deficiency causes missorting of ATG9A in diverse cell types, including patient-derived cells, as well as dysregulation of autophagy. RUSC2 facilitates the transport of AP-4-derived, ATG9A-positive vesicles from the TGN to the cell periphery. These vesicles cluster in close association with autophagosomes, suggesting they are the \"ATG9A reservoir\" required for autophagosome biogenesis. Our study uncovers ATG9A trafficking as a ubiquitous function of the AP-4 pathway. Furthermore, it provides a potential molecular pathomechanism of AP-4 deficiency, through dysregulated spatial control of autophagy.

cell biology↗