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Quantitative extracellular proteome analysis of fetal liver and adult bone marrow

ABSTRACT: We describe the proteomic composition of the extracellular environment of fetal and adult hematopoietic progenitors by data-independent acquisition mass spectrometry analysis.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Extracellular Region, Liver, Bone Marrow

SUBMITTER: Sudip Ghosh

LAB HEAD: Dr. Jenny Hansson

PROVIDER: PXD042251 | Pride | 2024-04-02

REPOSITORIES: Pride

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			Action	DRS
	20221207_BMEF_FLEF_directDIA.sne	Other
	211108_BMF_1_1_120min_Exploris_FAIMS_DIA_CV-45-60_23_4mz.raw	Raw
	211108_BMF_1_2_120min_Exploris_FAIMS_DIA_CV-45-60_23_4mz.raw	Raw
	211108_BMF_2_1_120min_Exploris_FAIMS_DIA_CV-45-60_23_4mz.raw	Raw
	211108_BMF_2_2_120min_Exploris_FAIMS_DIA_CV-45-60_23_4mz.raw	Raw

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1 - 5 of 18

Publications

A complex interplay of intra- and extracellular factors regulates the outcome of fetal- and adult-derived MLL-rearranged leukemia.

Jassinskaja Maria M Ghosh Sudip S Watral Joanna J Davoudi Mina M Claesson Stern Melina M Daher Ugarit U Eldeeb Mohamed M Zhang Qinyu Q Bryder David D Hansson Jenny J

Leukemia 20240330 5

Infant and adult MLL1/KMT2A-rearranged (MLLr) leukemia represents a disease with a dismal prognosis. Here, we present a functional and proteomic characterization of in utero-initiated and adult-onset MLLr leukemia. We reveal that fetal MLL::ENL-expressing lymphomyeloid multipotent progenitors (LMPPs) are intrinsically programmed towards a lymphoid fate but give rise to myeloid leukemia in vivo, highlighting a complex interplay of intra- and extracellular factors in determining disease subtype. W ...[more]

PMID: 38555405

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Quantitative secretome analysis of fetal and adult hematopoietic progenitors during leukemia initiation and its response to Fibulin and/or Fibronectin treatment.

Project description:We describe the proteomic composition of the secretome of fetal and adult hematopoietic progenitors during MLL-rearranged (MLLr) leukemia initiation as well as the pre-leukemic cells’ secretion response to the treatment with Fibulin (Fbln1) and/or Fibronectin (Fn1) using data-independent acquisition mass spectrometry analysis.

2024-04-02 | PXD049014 | Pride

Secretome and phosphoproteome analysis of THP-1 and KOPN-8 cells treated with Insulin-like growth factor 2.

Project description:We describe the secretome and phosphoproteome of human leukemia cell lines, THP-1 and KOPN-8, treated with Insulin-like growth factor 2 (IGF2) using data-independent acquisition mass spectrometry analysis.

2024-04-02 | PXD049016 | Pride

Unveiling the Proteome of the Fasting Heart: Insights into HIF-1 Pathway Regulation.

Project description:Fasting is a common dietary intervention known for its protective effects against metabolic and cardiovascular diseases. While its effects are mostly systemic, understanding tissue-specific changes in the heart is crucial for the identification of the mechanisms underlying fasting-induced cardioprotection. In this study, we performed a proteomic analysis to elucidate the proteome of the fasting heart. Our investigation identified a total of 4,652 proteins, with 127 exhibiting down-regulation and 118 showing up-regulation after fasting. Annotation analysis highlighted significant changes in processes such as lipid metabolism, the peroxisome pathway, and reactive oxygen species metabolism. Notably, the HIF-1 signaling pathway emerged as one of the focal points, with five affected proteins identified. Further experiments demonstrated down-regulation of HIF-1Î± at both transcript and protein levels. Intriguingly, while gene expression of Egln3 decreased, its protein product PHD3 remained unaffected by fasting. These findings underscore the regulation of the well-established cardioprotective HIF-1 signaling within the heart during 3-day fasting.

2024-10-08 | PXD050458 | Pride

Derivation of rat induced pluripotent stem cells that share similarities with embryonic stem cells using a transposon system

Project description:Induced pluripotent stem (IPS) cells have attracted enormous attention due to their vast potential in regenerative medicine, pharmaceutical screening and basic research. The majority of prior established rat IPS cells were generated from somatic cells by retroviral and lentiviral transduction with expression of Oct4, Sox2, Klf4 and c-Myc and using chemical inhibitors of key differentiation pathways. A major difficulty in the application of this technology is the efficient delivery of reprogramming factors and the long-term maintenance of properties of stem cells. Here, we employed the PiggyBac (PB) transposon carrying four 2A peptide-linked reprogramming factors for generating rat IPS cells. These stable rat IPS cells are similar to embryonic stem (ES) cells in morphology, proliferation, teratoma formation, expression characteristic pluripotency markers, developmental potential, and germline transmission. Transcriptional profiling of the IPS cells revealed both pathways in common with ES cells from rat and unique signaling pathway to our cells, including Wnt, TGF and Notch. The cell lines and information obtained in this study will accelerate our understanding of the molecular regulation underlying germline pluripotency and pave the way for exploration of cell-based therapies using the rat. To compare the gene expression profiling between rat IPS cells and ES cells to show if the rat IPS cells had been reprogrammed into pluripotent status like rat ES cells at the gene expression level.

2012-02-16 | E-GEOD-35841 | biostudies-arrayexpress

Overactive mitochondrial DNA replication disrupts perinatal cardiac maturation

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Fusidic acid resistance through changes in the dynamics of EF-G

Project description:HDX-MS was used to study the binding of FusB to EF-G

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dcEF-regulated gene expression of human lung cancer cells

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2013-01-01 | E-GEOD-33845 | biostudies-arrayexpress

Multi-level proteomics reveals host-perturbation strategies of SARS-CoV-2 and SARS-CoV

Project description:The sudden global emergence of SARS-CoV-2 urgently requires an in-depth understanding of molecular functions of viral proteins and their interactions with the host proteome. Several omics studies have extended our knowledge of COVID-19 pathophysiology, including some focused on proteomic aspects1â€“3. To understand how SARS-CoV-2 and related coronaviruses manipulate the host we here characterized interactome, proteome and signaling processes in a systems-wide manner. This identified connections between the corresponding cellular events, revealed functional effects of the individual viral proteins and put these findings into the context of host signaling pathways. We investigated the closely related SARS-CoV-2 and SARS-CoV viruses as well as the influence of SARS-CoV-2 on transcriptome, proteome, ubiquitinome and phosphoproteome of a lung-derived human cell line. Projecting these data onto the global network of cellular interactions revealed relationships between the perturbations taking place upon SARS-CoV-2 infection at different layers and identified unique and common molecular mechanisms of SARS coronaviruses. The results highlight the functionality of individual proteins as well as vulnerability hotspots of SARS-CoV-2, which we targeted with clinically approved drugs. We exemplify this by identification of kinase inhibitors as well as MMPase inhibitors with significant antiviral effects against SARS-CoV-2.

2021-02-15 | PXD022282 | Pride

Quantitative cellular proteome analysis of Fetal- and Adult-Derived MLL-Rearranged Leukemia

Project description:Infant and adult MLL-rearranged (MLLr) leukemia represents a disease with few treatment options and a dismal prognosis. Here, we present an in-depth proteomic characterization of in utero-initiated and adult-onset MLLr leukemia in a mouse model of MLL-ENL-mediated leukemogenesis. We characterize early proteomic events of MLL-ENL-mediated transformation in fetal and adult progenitors.

2024-04-02 | PXD042249 | Pride

Proteomic analysis of pleomorphic dermal sarcoma

Project description:In this study, we aimed to unravel the molecular underpinnings of pleomorphic dermal sarcomas (PDS), rare skin tumors often seen in sun-exposed regions. Using mass spectrometry, we examined proteomic profiles of 20 samples of normal healthy skin tissue (SNT), 27 malignant melanomas (MM), 20 cutaneous squamous cell carcinomas (cSCC), and 24 PDS. Our analysis aimed to: I.) Determine the potential cell of origin for PDS by correlating protein abundance to tumor purity using both RNA- and DNA-sequencing data. II.) Investigate receptor/ligand (R/L) interactions and their related pathways, highlighting distinct signaling differences between cSCC, MM, and PDS. III.) Identify differential protein markers, such as MAP1B_HUMAN, that can distinguish between cSCC, MM, and PDS. IV.) Explore proteins linked to immunosuppression in PDS, with a focus on those related to the negative regulation of interferon-gamma signaling. Together, this comprehensive proteomic exploration provides valuable insights into PDS and potential therapeutic targets.

2024-06-16 | PXD046388 | Pride

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