Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of DDR1-interacting proteins by IP-MS screening

ABSTRACT: To investigate and identify the potential DUBs that stabilize and interact with DDR1, we performed immunoprecipitation of endogenous DDR1 with anti-DDR1 antibody (specific IP) or anti-IgG antibody (negative control) in A549 cells followed by mass spectrometry analysis.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung

SUBMITTER: Wenbo Cheng

LAB HEAD: Yiying Xue

PROVIDER: PXD065332 | Pride | 2025-09-08

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	R24666-IP-DDR1.raw	Raw
	R24666-IP-IgG.raw	Raw
	UP000005640_9606_human.fasta	Fasta
	checksum.txt	Txt
	combined_modified_peptide.tsv	Tabular

Items per page:

1 - 5 of 6

Publications

Ubiquitin-specific protease 7-mediated stabilization of discoidin domain receptor 1 drives progression of TP53-Mutant cancers.

Xue Yiying Y Xiu Bing B Yang Muye M Zhang Yanwei Y Yang Changpeng C Zhang Lele L Yan Yilv Y Luo Xiu X Huang Yushan Y Mei Husheng H Li Guiming G Zhou Lixin L Chen Yisa Y Zhang Wenjun W Qian Changlin C Zhang Peng P Liu Juan J Liang Aibin A Zeng Yu Y Yang Jing J

The Journal of biological chemistry 20250724 9

Receptor tyrosine kinase DDR1 (Discoidin Domain Receptor 1) interacts with the extracellular matrix (ECM) to promote tumor cell proliferation through its intracellular kinase activity, while its extracellular non-enzymatic domain creates a physical barrier for immune evasion. Although DDR1 inhibitors and antibodies have been developed, targeting DDR1 kinase activity alone cannot fully block the biological effects mediated by its scaffold function. Therefore, developing DDR1 degraders presents a ...[more]

PMID: 40713963

Similar Datasets

Highly selective humanized DDR1 mAb reverses immune exclusion by disrupting collagen fiber alignment in breast cancer

Project description:Discoidin domain-containing receptor 1 (DDR1) plays an important role in cancer progression. However, the DDR1 function in tumors is still elusive. We recently reported that DDR1 promoted collagen fiber alignment and formation of a physical barrier, which causes immune exclusion from tumors. We also demonstrated that our DDR1 ECD-targeting mAbs can disrupt collagen fiber alignment and increase T Cell infiltration in tumors. In this study, we humanized a DDR1 ECD-targeting mAb and showed significant antitumor efficacy in an immunocompetent mouse model. We determined the binding epitope using gene mutagenesis, hydrogen-deuterium exchange mass spectrometry (HDX-MS), and X-ray crystallography. Mechanistically, we showed that the humanized mAb inhibited DDR1 phosphorylation and, more importantly, blocked DDR1 shedding and disrupted a physical barrier formed by collagen fiber alignment in tumors. This study not only paves a pathway for development of PRTH-101 as a cancer therapeutic, but also broaden our understanding of the roles of DDR1 in modulation of collagen alignments in tumor extracellular matrix and tumor immune microenvironment.

2023-06-19 | PXD042971 | Pride

DDR1 plays a distinctive role in mammary tumour growth

Project description:Purpose: The goals of this study are to compare mammary tumor transcriptome profiling with or without DDR1 in immunocompetent mice in an unbiased way. Methods: In vitro samples: DDR1 WT or KO in vitro cultured E0771 cells were sequenced. Rag1-/- samples: DDR1 WT or KO E0771 cells were injected in Rag1-/- mice, and tumors were harvested and sequenced. C57BL/6 samples: DDR1 WT or KO E0771 cells were firstly inoculated into Rag1-/- mice. When tumor volume reached approximately 200~300 mm3 (usually 20 days after inoculation), 60 mg of tumor organoid were transplanted to WT C57BL/6 mice. Tumor samples were collected on day 4 after transplantation for RNA-seq. Antibody treatment samples: DDR1 KO E0771 cells were reconstituted with human DDR1, then injected into C57BL/6 mice. Isotype control IgG or anti-hDDR1 ECD antibody treatment (10mg/kg intrutumural) started when tumor volume reached approximately 100 mm3. Tumor samples were collected on day 6 after treatment for RNA-seq. Results: Approximately 50 million sequence reads were obtained per sample and identified more than 20,000 transcript isoforms. Conclusions: The RNA-seq results represents the detailed analysis of DDR1 WT/KO mammary tumor transcriptomes in immunocompetent mice C57BL/6.

2021-09-07 | GSE139239 | GEO

DDR1 knockdown in BXPC3 cell line

Project description:Examination of effect of stable DDR1 knockdown by shRNA on transcriptional profile in BXPC3 cell line to understand role of DDR1 in tumorigenesis. Transcriptional profiles of parental BXPC3 cell line was compared to BXPC3 cells stably transfected with non-target shRNA or DDR1 shRNA, N=3 for each condition.

2014-05-01 | E-GEOD-39207 | biostudies-arrayexpress

DDR1 knockdown in BXPC3 cell line

Project description:Examination of effect of stable DDR1 knockdown by shRNA on transcriptional profile in BXPC3 cell line to understand role of DDR1 in tumorigenesis.

2014-05-01 | GSE39207 | GEO

SILAC phosphoproteome analysis upon transient Abl1/2 or DDR1 knockdown in human U-2 OS cells

Project description:Analysis of changes in the phosphoproteome upon transient siRNA-mediated knockdown of ABL1/ABL2 or DDR1 for 48 hours. CILAC phosphoproteome analysis was conducted after 48hrs using human U-2 OS cells.

2023-10-24 | PXD023146 | Pride

Collagenolysis dependent DDR1 signaling dictates pancreatic cancer outcome

Project description:Pancreatic ductal adenocarcinoma (PDAC) is a highly desmoplastic, aggressive cancer, frequently progressing and spreading by liver metastasis. Cancer-associated fibroblasts (CAF), extracellular matrix (ECM), and type I collagen (Col I) support or restrain PDAC progression and may impede blood supply and nutrient availability. The dichotomous role of the stroma in PDAC, and the mechanisms through which it influences patient survival and enables desmoplastic cancers to escape nutrient limitation remain poorly understood. Here we show that matrix metalloprotease (MMP)-cleaved or intact Col I (cCol I and iCol I, respectively) exert opposing effects on PDAC bioenergetics, macropinocytosis (MP), tumor growth and metastasis. While cCol I activates DDR1 (discoidin domain receptor-1)-NF-kB-p62-NRF2 signaling to promote PDAC growth, iCol I triggers DDR1 degradation and restrains PDAC growth. Patients whose tumors are iCol I enriched and DDR1 and NRF2 low have improved median survival compared to those with high cCol I, DDR1 and NRF2. Inhibition of DDR1-stimulated NF-kB or mitochondrial biogenesis blocked tumorigenesis in wildtype mice but not in mice expressing MMP-resistant Col I. The diverse effects of the tumor stroma on PDAC growth, metastasis, and patient survival are mediated through the Col I-DDR1-NF-kB-NRF2-mitochondrial biogenesis pathway, presenting new therapeutic opportunities.

2022-07-13 | GSE206218 | GEO

Ubiquitin specific peptidase 7 promotes TP53 mutant malignancy by deubiquitinating and stabilizing DDR1

Project description:Receptor tyrosine kinase DDR1 (Discoidin Domain Receptor 1) interacts with the extracellular matrix (ECM) to promote tumor cell proliferation through its intracellular kinase activity, while its extracellular non-enzymatic domain creates a physical barrier for immune evasion. Although DDR1 inhibitors and antibodies have been developed, targeting DDR1 kinase activity alone cannot fully block the biological effects mediated by its scaffold function. Therefore, developing DDR1 degraders presents a potentially more effective therapeutic strategy. Through screening a proprietary small-molecule ubiquitination library, we identified NSC632839, which significantly induces DDR1 protein degradation. Mechanistically, chemical proteomics and genetic studies demonstrated that NSC632839 functions by inhibiting USP7, which interacts with, stabilizes, and deubiquitinates DDR1, preventing its proteasomal degradation. Importantly, we observed that TP53 loss or mutation in tumor cells and clinical samples markedly upregulates DDR1 expression, thereby enhancing its interaction with USP7. Treatment with NSC632839 restores TP53 expression, resulting in a significant reduction in DDR1 levels. In various preclinical models, targeting USP7 with NSC632839 effectively eliminates tumor cells, offering a promising therapeutic strategy to overcome tumor relapse driven by TP53 mutations, both in vitro and in vivo. This study highlights the potential of DDR1 degradation via USP7 inhibition as a novel approach to treat TP53 mutation-enriched tumors.

2025-09-03 | GSE301195 | GEO

CH6824025, potent and selective DDR1 inhibitor, reduces kidney fibrosis in UUO mice

Project description:Discoidin domain receptor 1 (DDR1) is a collagen receptor with tyrosine kinase activity, and its expression is enhanced in various disease conditions. Although previous research suggests that DDR1 contributes to renal disease progression, DDR1 inhibitors for renal fibrosis have yet to be developed. In this study, we used unilateral ureteral obstruction (UUO) mice to investigate whether CH6824025, a strong and selective DDR1 phosphorylation inhibitor, can improve renal fibrosis. Furthermore, to analyze its action in detail, we performed 10x Visium spatial transcriptomics (ST) analysis on the kidney. Orally administered CH6824025 suppressed the phosphorylation of DDR1 in renal tissue, and the amount of hydroxyproline, the Sirius red-positive area, and the mRNA expression of fibrosis and inflammation-related genes in the kidney were significantly decreased. 10x Visium ST analysis suggested that DDR1 is mainly expressed in distal nephrons under normal conditions, but that its expression appears to increase in the injured proximal tubules in UUO mice. Comparing mRNA expression in DDR1 positive spots in the vehicle and the CH6824025 administration group, oxidative phosphorylation and mitochondrial dysfunction were improved, and pathways involved in fibrosis inhibited in the CH6824025 administration group. Downstream analysis suggested that mRNA expression changes in the CH6824025 administration group contribute to the inhibition of cell movement. Taken together, our findings suggest that CH6824025 inhibited the migration of inflammatory cells to the injury site in UUO mice, reduced inflammation, and brought about the maintenance of cell homeostasis and inhibition of fibrosis. DDR1 inhibitors are expected to be a promising treatment for renal fibrosis.

2024-12-31 | GSE273978 | GEO

DDR1 regulates RUNX1-CBFβ to control breast stem cell differentiation

Project description:Understanding epithelial stem cell differentiation and morphogenesis during breast tissue development is essential, as disruption in these processes underlie breast cancer formation. Recent work has shown that epithelial stem and progenitor cells use the collagen receptor Discoidin Domain Receptor 1 (DDR1) for differentiation into both basal and luminal cell lineages, which together are necessary for complex ductal-lobular morphogenesis. Here, we used a next-generation single cell derived organoid model that generates miniaturized breast tissue, to study how single stem cells can give rise to multiple cell types and compound tissue structures. We show that DDR1inhibition traps cells in a bipotent state, blocking alveolar morphogenesis and luminal cell expansion necessary for complex epithelium formation. Disrupting RUNX1 function produced nearly identical phenotypes, underscoring its critical role downstream of DDR1. Mechanistically, DDR1 affects the interaction and expression of RUNX1 and its cofactor CBFβ, thereby regulating its activity. Mutational analyses in breast cancer patients reveal frequent alterations in the DDR1-RUNX1 signaling axis, particularly co-occurring mutations. Together, these findings uncover DDR1-RUNX1 as a central signaling pathway driving breast epithelial differentiation, whose dysregulation may contribute fundamentally to breast cancer pathogenesis.

2025-06-09 | GSE298818 | GEO

Comparative transcriptome of proliferative cells, dormant cells and awaken cells throught a DDR1 depletion

Project description:The goal of this study is to compare the trancriptome of proliferative THEP3 cells to their dormant counterpart DHEP3 and an awaken version through DDR1 receptor depletion (shRNA control verus shRNA DDR1) to identify target genes involved in the dormancy state and the awakening process from where metatsiss will arise.

2021-10-20 | GSE182890 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data