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Harvesting secreted proteins from cell lines after 24 hours hypoxia

ABSTRACT: Cancers are often associated with hypoxia and metabolic reprogramming, resulting in enhanced tumor progression. Here, we aimed to study breast cancer hypoxia responses, focusing on secreted proteins from low-grade (luminal-like) and high-grade (basal-like) cell lines before and after hypoxia.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Breast Cancer

SUBMITTER: Kenneth Finne

LAB HEAD: Lars A. Akslen

PROVIDER: PXD040532 | Pride | 2023-06-23

REPOSITORIES: Pride

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Hypoxia inducible factors positively regulate hepatitis B virus replication by activating the basal core promoter

Project description:Background and Aims: Chronic HBV infection is a major cause of liver disease and cancer. Virus-host interactions and the pathogenesis of virus-induced liver disease are only partially understood. Hypoxia has been shown to play a major role in disease biology and carcinogenesis and HBV replicates a naturally hypoxic organ. In this study we aimed to investigate the role of liver hypoxia for HBV infection. Methods: Using cell culture, animal models and human tissues we investigated the impact of hyproxia on the HBV life cycle. Results: Establishing liver cell-based model systems that mimic hepatic oxygen, we uncover a major role of hypoxia in regulating HBV transcription. Hypoxia-inducible factors (HIFs) perturb HBV replication and expression in cell-based and animal models. Conservation of hypoxia responsive elements in the viral basal core promoter uncover an essential role for HIFs in regulating the hepadnaviridae family of hepatotropic viruses. Conclusions: Identifying a role for this conserved oxygen sensors in regulating HBV replication provides a new understanding of virus-host interactions and liver disease biology, improve state-of-the-art HBV model systems and unravels new opportunities for therapeutic targeting of chronic hepatitis B.

2023-07-20 | PXD020086 | Pride

Transcriptomics Analyses of soybean leaves and roots sample during water-deficit

Project description:Microarray experiments were performed on the roots and leaves samples seperately using custom based Nimblgen platform (12plex). This is a time-course study. The plants were grown in controlled growth chamber condiditons ambiient to soybean growth and development using a hydrophonics system. The tissues were harvested after 30days of growth in six time points- 0min, 30mins, 1hour, 2hours, 3hours and 5hours of dehydration. We used a hydrophonics system for the trancriptomics analysis of the soybean(William -82) root and leaves samples to study the reponse during water- deficit or drought. Plants were grown in controlled growth chamber conditions and harvested after 30days in six time-points. The plants were transferred to empty pots without touching to nullify any possibility of wounding and harvested subsequently. For 0mins, plants were taken out of the well-watered conditions and transfered to empty boxes and immediately harvested for both tisses and hence called 0-min dehydrated tissue. Similarly other time-points were processed (for instance, 2hrs of dehydration, plants were dehydrated for 2hours after being taken out from well-waterted pots and then harvested). Tissues for three biological replicates and three plants per biological replicates were collected for each time-point (n=9). RNA was islolated from both tissues using RNeasy Kit from Qiagen and quality was accessed with Nano-drop as well as with Agilent-Bioanalyzer using RNA-600 kit. 20ug of sample was processed at Micro Array Facility.

2015-04-26 | E-GEOD-49537 | biostudies-arrayexpress

A Composite DNA Element that Functions as a Maintainer Required for Epigenetic Inheritance of Heterochromatin

Project description:Epigenetic inheritance of heterochromatin requires DNA sequence-independent propagation mechanisms, coupling to RNAi, or input from DNA sequence, but how DNA contributes to inheritance is not understood. Here, we identify a DNA element (termed “maintainer”) that is sufficient for epigenetic inheritance of preexisting histone H3 lysine 9 methylation (H3K9me) and heterochromatin in Schizosaccharomyces pombe, but cannot establish de novo gene silencing in wild-type cells. This maintainer is a composite DNA element with binding sites for the Atf1/Pcr1 and Deb1 transcription factors and the Origin Recognition Complex (ORC), located within a 130-base pair region, and can be converted to a silencer in cells with lower rates of H3K9me turnover, suggesting that it participates in recruiting the H3K9 methyltransferase Clr4/Suv39h. These results suggest that, in the absence of RNAi, histone H3K9me is only heritable when it can collaborate with maintainer-associated DNA-binding proteins that help recruit the enzyme responsible for its epigenetic deposition.

2022-10-14 | PXD027214 | Pride

Integrative analysis of KRAS wildtype metastatic pancreatic ductal adenocarcinoma reveals mutation and expression-based similarities to cholangiocarcinoma

Project description:Oncogenic KRAS mutations are absent in approximately 10% of patients with metastatic pancreatic ductal adenocarcinoma (mPDAC) and may represent a subgroup of mPDAC with therapeutic options beyond standard-of-care cytotoxic chemotherapy. While distinct gene fusions have been implicated in KRAS wildtype mPDAC, information regarding other types of mutations remain limited, and gene expression patterns associated with KRAS wildtype mPDAC have not been reported. Here, we leverage sequencing data from the PanGen trial to perform comprehensive characterization of the molecular landscape of KRAS wildtype mPDAC and reveal increased frequency of chr1q amplification encompassing transcription factors PROX1 and NR5A2. By leveraging data from colorectal adenocarcinoma and cholangiocarcinoma samples, we highlight novel similarities between cholangiocarcinoma and KRAS wildtype mPDAC involving both mutation and expression-based signatures and validate these findings using an independent dataset. These data further establish KRAS wildtype mPDAC as a unique molecular entity, with therapeutic opportunities extending beyond gene fusion events.

2022-10-15 | PXD036632 | Pride

iTRAQ-based quantitative proteomic analysis of membrane and nuclear fractions of glioma (WHO grade II, III and IV) tissues to map on Chromosome 12 and identification of mass spectrometry evidence for 'missing proteins'

Project description:Glioma tumors arise from normal glial cells (astrocytes). Gliomas are morphologically and clinically classified into four malignancy grades as Grade I, II, III and IV. Grade I and II comprise low grade gliomas that grow slowly, are well differentiated and have a better prognosis and survival compared to grades III and IV. In contrast, grade III-IV lack endothelial proliferation and are highly vascular with a tendency to infiltrate and have areas of extensive necrosis and hypoxia. In the present study, we used iTRAQ (isobaric tags for relative and absolute quantitation) - based quantitative proteomic approach followed by liquid chromatography and high resolution tandem mass spectrometry (LC-MS/MS) to identify differential membrane and nuclear proteins mapping to Chromosome 12 from three different grades of astrocytoma tumors (WHO Grade II, III and IV) compared to control.

2019-06-04 | PXD000848 | Pride

iTRAQ-based quantitative proteomic analysis of nuclear fractions of glioma (WHO grade II, III and IV) tissues to identify altered transcriptional regulatory proteins

Project description:Glioma tumors arise from normal glial cells (astrocytes). Gliomas are morphologically and clinically classified into four malignancy grades as Grade I, II, III and IV. Grade I and II comprise low grade gliomas that grow slowly, are well differentiated and have a better prognosis and survival compared to grades III and IV. In contrast, grade III-IV lack endothelial proliferation and are highly vascular with a tendency to infiltrate and have areas of extensive necrosis and hypoxia. In the present study, we used iTRAQ (isobaric tags for relative and absolute quantitation) - based quantitative proteomic approach followed by online liquid chromatography and high resolution tandem mass spectrometry (LC-MS/MS) to identify differential nuclear proteins enriched with transcriptional regulatory function from three different grades of astrocytoma tumors (WHO Grade II, III and IV) compared to control.

2019-08-06 | PXD014111 | Pride

Structural characterization of the reaction center-light harvesting 1-PufXY complex from Rhodobacter sphaeroides

Project description:Photosynthesis in purple bacteria, represented by Rhodobacter sphaeroides as a long-established model organism, utilizes a protein-cofactor complex to capture solar energy. This complex is embedded in specialized spherical membrane structures and comprises a central reaction center (RC) encircled by a ring of light harvesting 1 (LH1) polypeptides. The energy derived from light absorption drives the reduction of ubiquinone, entering from the membrane, to generate ubiquinol. The photosynthetic cycle is therefore dependent on the exchange of ubiquinone and ubiquinol to and from the RC. This exchange requires an additional protein (PufX) which prevents complete closure of the LH1 ring, leaving a channel which connects the RC with the membrane. The structure of the RC-LH1-PufX complex is under investigation by cryo-EM, revealing the presence of a previously undiscovered protein (PufY) that is also involved in channel formation. Proteomic analysis has verified the identities of the expected protein components of this complex, additionally confirming the presence of the newly-discovered PufY polypeptide mapped into the cryo-EM structure.

2022-02-15 | PXD028048 | Pride

LC-MS/MS of the reaction center-light harvesting 1 complex from Gemmatimonas phototrophica

Project description:Gemmatimonas phototrophica is the only phototrophic member of the recently discovered bacterial phylum Gemmatimonadetes. It was isolated from a freshwater lake in the Gobi desert and first described in 2014. So far, Gemmatimonas phototrophica is the only bacterium to have received a complete set of photosynthesis-related genes by horizontal gene transfer from an ancient phototrophic species from the phylum Proteobacteria. This organism illustrates the possibility for engineering phototrophic capability in a non-phototrophic organism and is therefore of great interest to the field of synthetic biology. The structure of the photosynthetic reaction center-light harvesting 1 complex is under investigation by cryo-EM. Proteomic analysis verified the identities of the expected protein components of this complex and, additionally revealed polypeptides that were previously undiscovered and could be mapped to the cryo-EM images.

2022-04-04 | PXD024609 | Pride

Hypoxia-induced proteomic remodeling of human mammary cancer associated fibroblast

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2019-02-15 | PXD006535 | Pride

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2013-07-15 | E-GEOD-42102 | biostudies-arrayexpress

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