Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Top-down murine MMTV-PyMT proteoform landscape

ABSTRACT: We developed a top-down proteomic approach to characterize late-stage, primary tumor tissues harvested from MMTV-PyVT mice. This methodology allowed us to expand the coverage for high MW proteoforms using a murine model of breast cancer.

INSTRUMENT(S):

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Mammary Ductal Carcinoma Cell

DISEASE(S): Breast Cancer

SUBMITTER: Suzanne Ponik

LAB HEAD: Ying Ge

PROVIDER: PXD059164 | Pride | 2026-03-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	HEPES_Set1_unfractionated.d.zip	Other
	ProteoformIDS_toppicoutputs_SECProteformLandscapeTumor.xlsx	Xlsx

Items per page:

1 - 2 of 2

Publications

Deciphering Proteoform Landscape of Mammary Carcinoma by Top-Down Proteomics.

Knott Samantha J SJ Tucholski Trisha T Josyer Harini H Inman David D Friedl Andreas A Zhu Yanlong Y Ge Ying Y Ponik Suzanne M SM

Journal of proteome research 20250212 3

Defining the proteoform landscape of breast cancer can provide unique insights into the signaling pathways driving disease progression. While bottom-up proteomics has been utilized to profile breast cancer, it lacks the ability to capture intact proteoforms that may underpin the disease. Top-down proteomics is ideally suited to characterize intact proteoforms; however, most top-down proteomics studies have been limited to low molecular weight (MW) proteins (<50 kDa). Herein, we employed a two-di ...[more]

PMID: 39936522

Similar Datasets

Functionally Integrated Top-down Proteomics for Standardized Assessment of Human Induced Pluripotent Stem Cell-derived Engineered Cardiac Tissues

Project description:3-dimensional (3D) human induced pluripotent stem cell-derived engineered cardiac tissues (hiPSC-ECTs) have emerged as a promising alternative to 2-dimensional hiPSC-cardiomyocyte monolayer systems because hiPSC-ECTs are a closer representation of endogenous cardiac tissues and more faithfully reflect the relevant cardiac pathophysiology. The ability to perform functional and molecular assessments using the same hiPSC-ECT construct would allow for more reliable correlation between observed functional performance and underlying molecular events, and thus is critically needed. Herein, for the first time, we have established an integrated method that permits sequential assessment of functional properties and top-down proteomics from the same single hiPSC-ECT construct. We quantitatively determined the differences in isometric twitch force and the sarcomeric proteoforms between two groups of hiPSC-ECTs that differed in the duration of time of 3D-ECT culture. Importantly, by using this integrated method we discovered a new and strong correlation between the measured contractile parameters and the phosphorylation levels of alpha-tropomyosin between the two groups of hiPSC-ECTs. The integration of functional assessments together with molecular characterization by top-down proteomics in the same hiPSC-ECT construct enables a holistic analysis of hiPSC-ECTs to accelerate their applications in disease modeling, cardiotoxicity, and drug discovery.

2021-01-07 | PXD022814 | Pride

Expression data from MMTV-PyMT Induced Tumors

Project description:Loss of E2F transcription factos alters metastatic capacity of MMTV-PyMT tumors. We used microarrays to futher characterize the effects of E2F loss on mammary tumorigenesis in MMTV-PyMT mice.

2018-02-22 | GSE104397 | GEO

Mechanisms associated with systemic effects of cancer

Project description:Cancer is considered as a disease of a specific organ, but its effects are felt throughout the body. The systemic effects of cancer can lead to weakness in muscles and heart, which hastens cancer-associated death. miR-486 is a myogenic microRNA and its reduced expression in skeletal muscle is observed in muscular dystrophy. Muscle-specific transgenic expression of miR-486 using muscle creatine kinase promoter (MCK-miR-486) partially rescues skeletal muscle defects in muscular dystrophy animal models. We had previously demonstrated reduced circulating and skeletal muscle levels of miR-486 in several cancer types and lower miR-486 levels correlated with skeletal muscle defects and functional limitations in mammary tumor models. Therefore, skeletal muscle defects induced by cancer could resemble defects observed in various dystrophies, which could be reversed through skeletal muscle expression of miR-486. We performed functional limitations studies and biochemical analysis of skeletal muscles of MMTV-Neu transgenic mice that mimic HER2+ breast cancer and MMTV-PyMT transgenic mice that mimic luminal subtype B breast cancer and these mice crossed to MCK-miR-486 transgenic mice. miR-486 significantly prevented tumor-induced reduction in muscle contraction force, grip strength, and rotarod performance in MMTV-Neu, but not in MMTV-PyMT mice. In MMTV-Neu model, miR-486 reversed several of the cancer-induced changes in skeletal muscle including loss of p53, phospho-AKT, and phospho-laminin alpha 2 (LAMA2) and gain of phosphorylation of the pre-mRNA processing factor hnRNPA0 and the splicing factor SRSF10. LAMA2 is a part of the dystrophin-associated glycoprotein complex, and its loss-of-function mutation is associated with congenital muscular dystrophy. Thus, similar to muscular dystrophy, miR-486 has the potential to reverse skeletal muscle defects and cancer burden in select cancer types.

2022-05-19 | PXD028554 | Pride

Optimization of Higher-Energy Collisional Dissociation Fragmentation Energies for Intact Protein-level Tandem Mass Tag Labeling

Project description:Isobaric chemical tag labeling (e.g., iTRAQ and TMT) is a commonly used approach in quantitative proteomics research. Typically, peptides are covalently labeled with isobaric chemical tags, and quantification is enabled through detection of low-mass reporter ions generated after MS2 fragmentation. Recently, we have introduced and optimized a platform for intact protein-level TMT labeling that demonstrated >90% labeling efficiency in complex sample with top-down proteomics. Higher-energy collisional dissociation (HCD) is a commonly utilized fragmentation method for peptide-level isobaric chemical tag labeling because it produces accurate reporter ion intensities and avoids the loss of low mass ions. HCD energies have been optimized for peptide-level isobaric chemical tag labeling; however, fragmentation energies have not been systematically evaluated for TMT-labeled intact proteins for both protein identification and quantitation. In this study, we report a systematic evaluation of normalized HCD fragmentation energies on TMT-labeled HeLa lysate with top-down proteomics. Our results suggested that reporter ions often require higher collisional energy for higher ion intensities while most of intact proteins fragment when normalized HCD energies are between 30% and 50%. We further demonstrated that a stepped HCD fragmentation scheme with energies between 30 and 50% resulted in the optimized quantitation and identification for TMT-labeled intact HeLa protein lysate by providing average reporter ion intensity as > 3.60 E4 and average PrSM as > 1000 PrSM counts with high confidence.

2023-01-17 | PXD037491 | Pride

Effect of Spot14 Loss on Gene Expression Profile of MMTV-PyMT Mouse Tumors

Project description:The objective of this study was to determine the effect of Thyroid Hormone Responsive Protein Spot14 (Spot14) loss on the gene expression profiles of tumors from MMTV-Polyomavirus middle-T antigen (PyMT) mice. MMTV-PyMT/S14-heterozygous mice were crossed with S14-heterozygous mice and 1 cm tumors from MMTV-PyMT control (wild-type S14) or MMTV-PyMT/S14-null offspring were profiled using Affymetrix gene arrays. Tumor latency was not different between groups; however, tumors lacking S14 grew significantly slower than control tumors. Loss of S14 also decreased the levels of de novo synthesized fatty acids in mammary tumors. In additional studies, performed on MMTV-Neu mice, we found that S14 overexpression was associated with increased tumor cell proliferation and elevated levels of tumor fatty acids. Gene expression profiling revealed that S14 loss and overexpression in mouse mammary tumors altered pathways associated with proliferation and metabolism. This study provides important information about the role of S14 in mammary tumorigenesis and tumor metabolism. Microarray analysis was performed on 4 mammary tumors from MMTV-PyMT mice and 4 tumors from MMTV-PyMT/S14-null mice.

2014-09-01 | E-GEOD-55886 | biostudies-arrayexpress

Expression data of MMTV-PyMT mice mammary tumor with or without JAM-A

Project description:Junction Adhesion Molecule-A (JAM-A) is present on leukocytes and platelets where it promotes cell adhesion and motility. We are interested in an interaction between JAM-A and tumor progression/metastases. To address this point, we mated JAM-A-/- mice and mouse mammary tumor model MMTV-PyMT mice which, which express polyoma middle T antigen under the control of mouse mammary tumor virus. MMTV-PyMT mice show 100% penetration of mammary tumor and highly metastases to lung. MMTV-PyMT mice without JAM-A show less primary tumor progression, therefore JAM-A enhance primary tumor progression. Then we are addressing the molecular mechanism of this phenomenon by in vivo. Furthermore, we would like to examine JAM-A deficient MMTV tumor signature. Each 3 MMTV-PyMT JAm-A+/+ (JamA+) and 3 MMTV JAM-A-/- (JamA-) mammary tumor were resected at early stages of tumor development for RNA extraction and hybridization on Affymetrix microarrays.

2010-10-01 | E-GEOD-22555 | biostudies-arrayexpress

Effect of Spot14 Loss on Gene Expression Profile of MMTV-PyMT Mouse Tumors

2014-09-01 | GSE55886 | GEO

RANK-Fc treatment in MMTV-PyMT late carcinoma

Project description:Transcriptional profile of MMTV-PyMT late carcinomas after adjuvant or neoadjuvant treatment with RANK-Fc (receptor activator of NF-kB) cells isolated from one single MMTV-PyMT carcinoma were orthotopically injected in syngeneic WT mice, which were randomized 1:1 for neoadjuvant RANK-Fc or mock treatment (passage 1) for 4 weeks. Cells isolated from both treatment arms were pooled and injected into the fat pad of FvB recipients (passage 2) in limiting dilutions (mimicking occult disease) and again randomized 1:1 for additional RANK-Fc (adjuvant) or mock treatment

2016-12-19 | GSE66085 | GEO

Expression data of MMTV-PyMT mice mammary tumor with or without JAM-A

2010-10-01 | GSE22555 | GEO

Single-cell RNA profiling of mammary gland tumours in MMTV-PyMT mouse model of breast cancer.

Project description:Here, we use single cell sequencing to delineate the heterogeneity of tumours from the genetically engineered MMTV-PyMT mouse model of breast cancer (MMTV-PyMT::K14Cre::Rosa-tdTomato mice).

2024-05-08 | GSE159478 | GEO