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Wild-type versus Pdpy-7::GFP::TurboID control

ABSTRACT: DDA analysis of epidermally expressed GFP::TurboID in mixed-stage C. elegans versus wild-type (non-TurboID)

INSTRUMENT(S):

ORGANISM(S): Caenorhabditis Elegans

TISSUE(S): Whole Body

SUBMITTER: Dennis Province

LAB HEAD: David S. Fay

PROVIDER: PXD069753 | Pride | 2026-01-23

REPOSITORIES: Pride

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			Action	DRS
	FayDS_032124_01.mgf	Mgf
	FayDS_032124_01.mzid	Mzid
	FayDS_032124_01.raw	Raw
	FayDS_032124_02.mgf	Mgf
	FayDS_032124_02.mzid	Mzid

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1 - 5 of 15

Publications

Integrating endogenous TurboID and data-independent acquisition mass spectrometry for in vivo proximity labeling.

Fay David S DS Balasubramaniam Boopathi B Harrington Sean M SM Edeen Philip T PT

The EMBO journal 20251211 2

Proximity labeling has emerged as a powerful approach for identifying protein-protein interaction networks within living systems, particularly those involving weak or transient associations. Here, we present a comprehensive revised proximity labeling workflow, integrating TurboID labeling of endogenously expressed fusion proteins and data-independent acquisition (DIA) mass spectrometry (MS). We benchmark this pipeline with a study of five conserved Caenorhabditis elegans proteins-NEKL-2, NEKL-3, ...[more]

PMID: 41381733

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Proximity Labeling of NIMA Kinase Complex Components in C. elegans

Project description:Proximity labeling has emerged as a powerful approach for identifying protein–protein interactions within living systems, particularly those involving weak or transient associations. Here, we present a comprehensive proximity labeling study of five conserved Caenorhabditis elegans proteins—NEKL-2, NEKL-3, MLT-2, MLT-3, and MLT-4—that form two NEKL–MLT kinase–scaffold subcomplexes involved in membrane trafficking and actin regulation. Using endogenously expressed TurboID fusions and a data-independent acquisition (DIA) mass spectrometry (MS) pipeline, we profiled NEKL–MLT interactomes across 23 experiments, including several methodological variations, applying stringent controls and filtering strategies. By analyzing and comparing experimental outcomes, we develop a set of intuitive quantitative metrics to assess experimental outcomes and quality. We demonstrate that DIA-based workflows produce sensitive physiologically relevant findings, even in the presence of experimental noise and variability across biological replicates. Our approach is validated through the identification of known NEKL–MLT binding partners and conserved genetic suppressors of nekl–mlt mutant phenotypes. Gene ontology enrichment further supports the involvement of newly identified NEKL–MLT interactors in processes including membrane trafficking, cytoskeletal regulation, and cell adhesion. Additionally, several novel proximate interactors were functionally validated using genetic assays. Our findings underscore the utility of DIA-MS in proximity labeling applications and highlight the value of incorporating internal controls, quantitative metrics, and biological validation to enhance confidence in candidate interactors. Overall, this study provides a scalable, organismal-level strategy for probing endogenous protein networks and offers practical guidelines for proximity labeling in multicellular systems.

2026-01-23 | PXD069727 | Pride

The tongue squamous carcinoma cell line Cal27 primarily employs integrin α6β4-containing type II hemidesmosomes for adhesion which contribute to anticancer drug sensitivity

Project description:Integrins are heterodimeric cell surface glycoproteins used by cells to bind to the extracellular matrix (ECM) and regulate tumor cell proliferation, migration and survival. A causative relationship between integrin expression and resistance to anticancer drugs has been demonstrated in different tumors, including head and neck squamous cell carcinoma. Using a Cal27 tongue squamous cell carcinoma model, we have previously demonstrated that de novo expression of integrin αVβ3 confers resistance to several anticancer drugs (cisplatin, mitomycin C and doxorubicin) through a mechanism involving downregulation of active Src, increased cell migration and invasion. In the integrin αVβ3 expressing Cal27-derived cell clone 2B1, αVβ5 expression was also increased, but unrelated to drug resistance. To identify the integrin adhesion complex (IAC) components that contribute to the changes in Cal27 and 2B1 cell adhesion and anticancer drug resistance, we isolated IACs from both cell lines. Mass spectrometry (MS)-based proteomics analysis indicated that both cell lines preferentially use integrin α6β4, which is classically found in hemidesmosomes. The anticancer drug resistant cell clone 2B1 demonstrated an increased level of α6β4 accompanied with increased deposition of a laminin-332-containing ECM. Immunofluorescence and electron microscopy demonstrated the formation of type II hemidesmosomes by both cell types. Furthermore, suppression of α6β4 expression in both lines conferred resistance to anticancer drugs. Taken together, our results identify a key role for α6β4-containing type II hemidesmosomes in regulating anticancer drug sensitivity.

2022-02-16 | PXD028810 | Pride

Circulating extracellular vesicle protein biomarker associated with early cancer lesions for early detection of high-grade serous ovarian cancer

Project description:Small extracellular vesicles (sEVs), lipid-bilayer delimited particles (50-200 nm) released by cells, are considered a new class of liquid biopsy biomarkers for stealth cancers, e.g., HGSOC. HGSOC originates from the fallopian tube (FT) and progresses from p53 signatures to a precursor lesion called serous tubal intraepithelial carcinoma (STIC). We hypothesize that sEVs play a role in ovarian pathogenesis, carry cargo reflective of the site of origin, and are biomarkers for early detection. To advance this idea, we established a case-control study cohort of archival plasma samples from 30 HGSOC patients (10 early-stage and 20 late-stage) and 40 healthy controls. sEVs were isolated using size exclusion chromatography, and proteomic profiles were established using mass spectrometry (LC-MS/MS). 1,078 EV proteins (exo-proteins) were identified across all samples, with 52 upregulated exo-proteins in early-stage HGSOC, and 59 upregulated exo-proteins in late-stage HGSOC (logFC>1, p<0.05). Upregulated exo-proteins were prioritized based on FT origin and tissue expression in STIC lesions. Seven candidate exo-proteins were validated by immunohistochemistry in FT with STIC lesions and HGSOC tissues and by western blot in FT/HGSOC cell-derived EVs. In summary, our EV proteomics using early-stage HGSOC clinical samples uncovered exo-biomarkers for early detection; potentially while still confined to the FT.

2026-01-08 | PXD067228 | Pride

Parenchymal and Dyshorric Fibrillar Amyloid Pathology in the rTg-D Rat Model of Cerebral Amyloid Angiopathy Type-2

Project description:Whole brain tissue proteomics from rat models of cerebral small vessel disease and Alzheimer's disease, including the rTg-DI model of Cerebral Amyloid Angiopathy (CAA) Type-1, the rTg-D model of CAA Type-2 with both hemizygous and homozygous animals, and the TgSD-AD model of Alzheimer's Disease.

2025-11-17 | PXD061304 | Pride

HDAC3 mediates retinal endothelial cell metabolic reprogramming and angiogenesis

Project description:Quantitative data-independent acquisition (DIA) analysis of effects of RGFP treatment in bovine retinal epithelial cells subjected to oxygen/glucose deprivation and reperfusion; 4 experimental groups (Normoxia_DMSO; Normoxia_RGFP; OGDR_DMSO; OGDR_RGFP) with 5 replicates of each.

2025-10-06 | PXD065925 | Pride

Exploring Proteomic Differences in PBMCs for Sex-Specific Insights into Alzheimer’s Disease

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2026-01-14 | PXD070232 | Pride

Defining the Ovarian Cancer Precancerous Landscape through Modeling Fallopian Tube Epithelium Reprogramming Driven by Extracellular Vesicles

Project description:Serous tubal intraepithelial carcinomas (STIC lesions) in the human fallopian tube epithelium (hFTE) are theorized to give rise to high grade serous ovarian cancers (HGSOC). Small extracellular vesicles (sEVs) are known to mediate key signaling in both normal and cancerous tissues, but few ex vivo systems exist for studying sEV impact on hFTE tissue. Here, we present a microfluidic tissue culture platform with combined spatial transcriptomic and proteomic readouts that allows us to profile dual responses in tissue exposed to sEV “messages”—capturing both short-term transcriptomic shifts in the tissue and long-term changes in protein cargo of secreted EVs (the “reply”). Using spatial transcriptomics, we show that the short-term 1-day exposure to ovarian cancer-derived sEVs alters expression of 61 transcripts in secretory cells, the progenitor of HGSOC, notably upregulating immune-related mRNA, including CXCL family chemokines, VCAM1, and pro-inflammatory mediators (NFKB1, IL1B, IFNA7/17). Additionally, we observed the long-term 14-day exposure to sEVs alters the expression of 7 transcripts and 25 EV cargo proteins of fallopian tube derived EVs (“secondary release EVs”) following stimulus from cancer EVs. Together, tissue transcriptomics and tissue-derived EV proteomics indicate that ovarian cancer derived sEVs rewire target cell signaling to modify the tubal immune landscape. This study provides insights into the early molecular changes associated with the pathogenesis of ovarian cancer in its tissue of origin, providing a platform to study EV-tissue interactions and identify how sEVs drive cell signaling reprogramming in hFTE.

2025-07-15 | PXD066017 | Pride

293FT Cell Endogenous FANCA Protein-Protein Interactions

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2019-07-25 | PXD010570 | Pride

The melanoma cell line MDA-MB-435 adhesome in long-term culture and its comparison to the adhesome upon integrin αV knockdown

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Anoxygenic Photosynthesis and Dark Carbon Metabolism in the Purple Sulfur Bacterium “Thiodictyon syntrophicum“ nov. strain Cad16T

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2019-03-29 | PXD010641 | Pride

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