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Journal articles on the topic 'Proximal interactomics'

Author: Grafiati

Published: 15 June 2024

Last updated: 31 July 2025

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1

Sofianatos, Yorgos, Étienne Coyaud, and Caroline Demeret. "Towards a three-dimensional mapping of virus-host proximal protein interactions." Project Repository Journal 13, no. 1 (2022): 14–17. http://dx.doi.org/10.54050/prj1318790.

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Towards a three-dimensional mapping of virus-host proximal protein interactions The SARS-CoV-2 proximal interactome project sets out to build a comprehensive, three-dimensional map of protein virus-host protein interactions inside living human cells. It aims to shed light on unknown mechanisms of infection. It is made possible by a combination of advanced interactomics techniques coupled with algorithms for the 3D visualisation of networks.

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2

Harris, C. Jake, Marion Scheibe, Somsakul Pop Wongpalee, et al. "A DNA methylation reader complex that enhances gene transcription." Science 362, no. 6419 (2018): 1182–86. http://dx.doi.org/10.1126/science.aar7854.

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DNA methylation generally functions as a repressive transcriptional signal, but it is also known to activate gene expression. In either case, the downstream factors remain largely unknown. By using comparative interactomics, we isolated proteins in Arabidopsis thaliana that associate with methylated DNA. Two SU(VAR)3-9 homologs, the transcriptional antisilencing factor SUVH1, and SUVH3, were among the methyl reader candidates. SUVH1 and SUVH3 bound methylated DNA in vitro, were associated with euchromatic methylation in vivo, and formed a complex with two DNAJ domain-containing homologs, DNAJ1

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Haider, Nasir A., Joanna Kelly, Duncan Smith, and Claus Jorgensen. "Abstract A099: Utilising interactomics to uncover oncogenic KRAS signalling networks in the context of the tumor microenvironment." Cancer Research 84, no. 2_Supplement (2024): A099. http://dx.doi.org/10.1158/1538-7445.panca2023-a099.

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Abstract Extensive genetic analyses of Pancreatic Ductal Adenocarcinoma (PDAC) tumors have identified the GTPase KRAS as a major driver of tumorigenesis, with over 90% of tumors possessing oncogenic KRAS mutations, primarily at the mutational hotspot G12. KRAS G12 mutants are constitutively active, and promote cancer growth by hyperdriving multiple downstream effector pathways via direct physical interactions with proteins such as PI3K and RAF. Despite KRASG12Mut being a promising drug target, direct targeting of KRASG12Mut or downstream pathways has shown limited success, with the emergence o

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Chua, Xien Yu, Timothy Aballo, William Elnemer, Melanie Tran, and Arthur Salomon. "Quantitative Interactomics of Lck-TurboID in Living Human T Cells Unveils T Cell Receptor Stimulation-Induced Proximal Lck Interactors." Journal of Proteome Research 20, no. 1 (2020): 715–26. http://dx.doi.org/10.1021/acs.jproteome.0c00616.

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5

Scandore, Cody, Kendall Johnson, Chris May, et al. "Abstract 4244: Application of a membrane interactomics (MInt) platform for novel surface target discovery." Cancer Research 85, no. 8_Supplement_1 (2025): 4244. https://doi.org/10.1158/1538-7445.am2025-4244.

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Abstract Despite advances in cancer therapeutics, there remains a critical need to identify new protein targets and targeting approaches for drug development, particularly those with improved efficacy and safety profiles. To address these challenges, InduPro leverages a high-resolution proximity proteomics technology that uses photocatalyst-generated reactive probes to label cell surface protein microenvironments (1, 2). Combining this technology with quantitative mass spectrometry, we achieve high-throughput characterization of the plasma membrane protein interactome at an unprecedented detai

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Malone, Clare F., Anna de Regt, Chris May, et al. "Abstract 4255: Membrane interactomics (MInt) platform identifies EGFR and CDCP1 as effective co-targets for bispecific antibody drug conjugate IDP-001." Cancer Research 85, no. 8_Supplement_1 (2025): 4255. https://doi.org/10.1158/1538-7445.am2025-4255.

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EGFR is a biologically validated target which is overexpressed and activated in many human cancers and associated with poor prognosis. However, most current EGFR targeting therapies encompassing multiple modalities have shown limited therapeutic efficacy, frequently due to on-target toxicity in non-malignant tissues where EGFR is expressed. To improve selectivity via co-localization targeting over co-expression alone, we utilized InduPro’s proprietary MInt platform across multiple cancer cell systems to identify CDCP1 as a tumor associated proximity antigen to EGFR on tumor cells. Like EGFR, C

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Ibarz, Antoni, Ignasi Sanahuja, Waldo G. Nuez-Ortín, Laura Martínez-Rubio, and Laura Fernández-Alacid. "Physiological Benefits of Dietary Lysophospholipid Supplementation in a Marine Fish Model: Deep Analyses of Modes of Action." Animals 13, no. 8 (2023): 1381. http://dx.doi.org/10.3390/ani13081381.

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Given the hydrophilic structure of lysophospholipids (LPLs), their dietary inclusion translates into a better emulsifying capacity of the dietary components. The present study aimed to understand the mechanisms underlying the growth-promoting effect of LPL supplementation by undertaking deep analyses of the proximal intestine and liver interactomes. The Atlantic salmon (Salmo salar) was selected as the main aquaculture species model. The animals were divided into two groups: one was fed a control diet (C-diet) and the other a feed (LPL-diet) supplemented with an LPL-based digestive enhancer (0

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Kumar, Mukesh, Kanchan Singh, Jayant Joshi, et al. "Mechanistic insights into Alpha-Synuclein binding to P2RX7: A molecular dynamic and docking study." PLOS One 20, no. 5 (2025): e0319098. https://doi.org/10.1371/journal.pone.0319098.

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Alpha-synucleinopathies, characterized by extracellular alpha-synuclein (αSyn or SNCA) accumulation and aggregation, have been linked to neurological disorders including Parkinson’s disease and multiple system atrophy. P2RX7 is a non-selective cationic transmembrane purinergic receptor activated by elevated levels of extracellular ATP, which typically occurs during inflammatory conditions. Activation of P2RX7 by αSyn is implicated in neuronal degeneration, potentially causing pore dilation and increased inflammation. By integrating the data curation, molecular docking, and molecular dynamics (

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9

Osagie, Oloruntoba I., Jordann Smakk, Deborah E. Citrin, and Travis H. Stracker. "Abstract 4802: Identification of critical hypoxia induced factors in castrate resistant prostate cancer." Cancer Research 83, no. 7_Supplement (2023): 4802. http://dx.doi.org/10.1158/1538-7445.am2023-4802.

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Abstract Background: Prostate cancer (PCa) is the second most diagnosed cancer in men and the second cause of cancer-related death amongst men worldwide. PCa is a heterogeneous disease, and the outcome is worse for patients when the disease progresses from localized PCa to a castrate-resistant disease. Androgen receptor (AR) signaling is crucial for PCa development and has been a major therapeutic target for decades. Despite the success made with hormone therapy to block AR signaling, castration resistant disease can arise through mutations and amplifications of the androgen receptor (AR) and

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10

Cutler, Jevon, Rahia Tahir, Jingnan Han, et al. "Differential Signaling through p190 and p210 Forms of BCR-ABL Fusion Proteins Revealed By Proteomic Analysis." Blood 126, no. 23 (2015): 3651. http://dx.doi.org/10.1182/blood.v126.23.3651.3651.

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Abstract Chromosomal translocations involving chromosome 9q34 and 22q11 generate the BCR-ABL1 fusion gene. The location of the translocation within the BCR gene dictates which exons are excluded or included in the resulting fusion with the ABL1 gene. The most common translocations produce three main protein products with molecular weights of 190, 210, and 230 kD. Interestingly, the p190 and p210 BCR-ABL1 forms are associated with different clinical characteristics. Specifically, BCR-ABL1+ acute lymphoblastic leukemia (ALL) cases typically harbor the p190 form, whereas chronic myelogenous leuke

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11

Tanco, Sebastian, Veronique Jonckheere, Arun Kumar Tharkeshwar, et al. "Proximal partners of the organellar N-terminal acetyltransferase NAA60: insights into Golgi structure and transmembrane protein topology." Open Biology 15, no. 2 (2025). https://doi.org/10.1098/rsob.240225.

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Biotin identification (BioID) is an interactomics approach that utilizes proximity labelling to map the local interactome or proxeome of proteins within a cell. This study applies BioID to investigate proteins proximal to NAA60 (N-alpha-acetyltransferase 60), an N-terminal acetyltransferase (NAT) of pathological significance in human disease, characterized by its unique Golgi localization. NAA60 is known to N-terminally acetylate transmembrane proteins that present their N-terminus on the cytosolic face of the membrane, and its involvement in maintaining Golgi structure has previously been est

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12

Ruminski, Kilian, Javier Celis-Gutierrez, Nicolas Jarmuzynski, et al. "Mapping the SLP76 interactome in T cells lacking each of the GRB2-family adaptors reveals molecular plasticity of the TCR signaling pathway." Frontiers in Immunology 14 (March 15, 2023). http://dx.doi.org/10.3389/fimmu.2023.1139123.

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The propagation and diversification of signals downstream of the T cell receptor (TCR) involve several adaptor proteins that control the assembly of multimolecular signaling complexes (signalosomes). The global characterization of changes in protein-protein interactions (PPI) following genetic perturbations is critical to understand the resulting phenotypes. Here, by combining genome editing techniques in T cells and interactomics studies based on affinity purification coupled to mass spectrometry (AP-MS) analysis, we determined and quantified the molecular reorganization of the SLP76 interact

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Kulyyassov, Arman, Gulsamal Zhubanova, Erlan Ramanculov, and Vasily Ogryzko. "Proximity Utilizing Biotinylation of Nuclear Proteins in vivo." Central Asian Journal of Global Health 3 (June 15, 2015). http://dx.doi.org/10.5195/cajgh.2014.165.

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Introduction. The human genome consists of roughly 30,000 genes coding for over 500,000 different proteins, of which more than 10,000 proteins can be produced by the cell at any given time (the cellular “proteome”). It has been estimated that over 80% of proteins do not operate alone, but in complexes. These protein-protein interactions (PPI) are regulated by several mechanisms. For example, post-translational modifications (methylation, acetylation, phosphorylation, or ubiquitination) or metal-binding can lead to conformational changes that alter the affinity and kinetic parameters of the int

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14

Vukić, Dragana, Anna Cherian, Salla Keskitalo, et al. "Distinct interactomes of ADAR1 nuclear and cytoplasmic protein isoforms and their responses to interferon induction." Nucleic Acids Research, November 30, 2024. https://doi.org/10.1093/nar/gkae1106.

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Abstract The RNA editing enzyme adenosine deaminase acting on RNA 1 (ADAR1) is essential for correct functioning of innate immune responses. The ADAR1p110 isoform is mainly nuclear and ADAR1p150, which is interferon (IFN) inducible, is predominately cytoplasmic. Using three different methods – co-immunoprecipitation (co-IP) of endogenous ADAR1, Strep-tag co-IP and BioID with individual ADAR1 isoforms – a comprehensive interactome was generated during both homeostasis and the IFN response. Both known and novel interactors as well as editing regulators were identified. Nuclear proteins were dete

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15

Al Mismar, Rasha, Payman Samavarchi-Tehrani, Brendon Seale, Vesal Kasmaeifar, Claire E. Martin, and Anne-Claude Gingras. "Extracellular proximal interaction profiling by cell surface–targeted TurboID reveals LDLR as a partner of liganded EGFR." Science Signaling 17, no. 861 (2024). http://dx.doi.org/10.1126/scisignal.adl6164.

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Plasma membrane proteins play pivotal roles in receiving and transducing signals from other cells and from the environment and are vital for cellular functionality. Enzyme-based, proximity-dependent approaches, such as biotin identification (BioID), combined with mass spectrometry have begun to illuminate the landscape of proximal protein interactions within intracellular compartments. To extend the potential of these approaches to study the extracellular environment, we developed extracellular TurboID (ecTurboID), a method designed to profile the interactions between proteins on the surfaces

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16

Chastney, Megan R., Craig Lawless, Jonathan D. Humphries, et al. "Topological features of integrin adhesion complexes revealed by multiplexed proximity biotinylation." Journal of Cell Biology 219, no. 8 (2020). http://dx.doi.org/10.1083/jcb.202003038.

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Integrin adhesion complexes (IACs) bridge the extracellular matrix to the actin cytoskeleton and transduce signals in response to both chemical and mechanical cues. The composition, interactions, stoichiometry, and topological organization of proteins within IACs are not fully understood. To address this gap, we used multiplexed proximity biotinylation (BioID) to generate an in situ, proximity-dependent adhesome in mouse pancreatic fibroblasts. Integration of the interactomes of 16 IAC-associated baits revealed a network of 147 proteins with 361 proximity interactions. Candidates with underapp

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17

Pavinato, Lisa, Marina Villamor-Payà, Maria Sanchiz-Calvo, et al. "Functional analysis of TLK2 variants and their proximal interactomes implicates impaired kinase activity and chromatin maintenance defects in their pathogenesis." Journal of Medical Genetics, December 15, 2020, jmedgenet—2020–107281. http://dx.doi.org/10.1136/jmedgenet-2020-107281.

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IntroductionThe Tousled-like kinases 1 and 2 (TLK1 and TLK2) are involved in many fundamental processes, including DNA replication, cell cycle checkpoint recovery and chromatin remodelling. Mutations in TLK2 were recently associated with ‘Mental Retardation Autosomal Dominant 57’ (MRD57, MIM# 618050), a neurodevelopmental disorder characterised by a highly variable phenotype, including mild-to-moderate intellectual disability, behavioural abnormalities, facial dysmorphisms, microcephaly, epilepsy and skeletal anomalies.MethodsWe re-evaluate whole exome sequencing and array-CGH data from a larg

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18

Szczesniak, Laura M., Caden G. Bonzerato, and Richard J. H. Wojcikiewicz. "Identification of the Bok Interactome Using Proximity Labeling." Frontiers in Cell and Developmental Biology 9 (May 31, 2021). http://dx.doi.org/10.3389/fcell.2021.689951.

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The function of the Bcl-2 family member Bok is currently enigmatic, with various disparate roles reported, including mediation of apoptosis, regulation of mitochondrial morphology, binding to inositol 1,4,5-trisphosphate receptors, and regulation of uridine metabolism. To better define the roles of Bok, we examined its interactome using TurboID-mediated proximity labeling in HeLa cells, in which Bok knock-out leads to mitochondrial fragmentation and Bok overexpression leads to apoptosis. Labeling with TurboID-Bok revealed that Bok was proximal to a wide array of proteins, particularly those in

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19

Oakley, James V., Benito F. Buksh, David F. Fernández, et al. "Radius measurement via super-resolution microscopy enables the development of a variable radii proximity labeling platform." Proceedings of the National Academy of Sciences 119, no. 32 (2022). http://dx.doi.org/10.1073/pnas.2203027119.

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The elucidation of protein interaction networks is critical to understanding fundamental biology as well as developing new therapeutics. Proximity labeling platforms (PLPs) are state-of-the-art technologies that enable the discovery and delineation of biomolecular networks through the identification of protein-protein interactions. These platforms work via catalytic generation of reactive probes at a biological region of interest; these probes then diffuse through solution and covalently “tag” proximal biomolecules. The physical distance that the probes diffuse determines the effective labelin

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