Proteomics and Metabolomics

Teach Me in 10

Research by a team of neuroscientists from the University of Nevada, Las Vegas (UNVL) has shown that it is possible to identify the molecular mechanisms underlying a host of adverse symptoms associated with unique subtypes of neurodevelopmental disorders. This work could one day improve the lives of millions of people worldwide.
Intellectual disability (ID) is a common neurodevelopmental disorder that can arise from genetic mutations ranging from trisomy to single nucleotide polymorphism. Trisomy of the 21st chromosome (Down syndrome) is the most common underlying cause of ID, but mutations in a growing number of single genes have been identified as causative in ID, including NONO and ARHGEF9. 

In this episode of Teach Me in 10, UNLV neuroscientist Dr. Rochelle Hines joins us to discuss the team’s latest findings, which show that mutations in ARHGEF9  — the gene that codes for collybistin — lead to ID through impaired α2 subunit function.

Want to learn more? Rochelle suggests you check out the following resources:  

https://www.nature.com/articles/s41380-022-01468-z
https://www.nature.com/articles/s41467-018-05481-1

Neurodevelopmental Disorders With Rochelle Hines

Oncotarget

Oncotarget published this trending research paper on May 11, 2022 in Volume 13, entitled, "Proteomic analysis reveals dual requirement for Grb2 and PLCγ1 interactions for BCR-FGFR1-Driven 8p11 cell proliferation" by researchers from the Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA; Proteomics Facility, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA; UCSD Moores Cancer Center, University of California San Diego, La Jolla, CA.

DOI - https://doi.org/10.18632/oncotarget.28228

Correspondence to - Daniel J. Donoghue - ddonoghue@ucsd.edu

Abstract

Translocation of Fibroblast Growth Factor Receptors (FGFRs) often leads to aberrant cell proliferation and cancer. The BCR-FGFR1 fusion protein, created by chromosomal translocation t(8;22)(p11;q11), contains Breakpoint Cluster Region (BCR) joined to Fibroblast Growth Factor Receptor 1 (FGFR1). BCR-FGFR1 represents a significant driver of 8p11 myeloproliferative syndrome, or stem cell leukemia/lymphoma, which progresses to acute myeloid leukemia or T-cell lymphoblastic leukemia/lymphoma. Mutations were introduced at Y177F, the binding site for adapter protein Grb2 within BCR; and at Y766F, the binding site for the membrane associated enzyme PLCγ1 within FGFR1. We examined anchorage-independent cell growth, overall cell proliferation using hematopoietic cells, and activation of downstream signaling pathways. BCR-FGFR1-induced changes in protein phosphorylation, binding partners, and signaling pathways were dissected using quantitative proteomics to interrogate the protein interactome, the phosphoproteome, and the interactome of BCR-FGFR1. The effects on BCR-FGFR1-stimulated cell proliferation were examined using the PLCγ1 inhibitor U73122, and the irreversible FGFR inhibitor futibatinib (TAS-120), both of which demonstrated efficacy. An absolute requirement is demonstrated for the dual binding partners Grb2 and PLCγ1 in BCR-FGFR1-driven cell proliferation, and new proteins such as ECSIT, USP15, GPR89, GAB1, and PTPN11 are identified as key effectors for hematopoietic transformation by BCR-FGFR1.

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Keywords - oncogenic fusion protein, chromosomal translocation, protein interactome, phosphoproteome, stem cell leukemia/lymphoma

About Oncotarget

Oncotarget is a peer-reviewed, open access biomedical journal covering research on all aspects of oncology.

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Oncotarget is published by Impact Journals, LLC: https://www.ImpactJournals.com

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Trending With Impact: Grb2 and PLCγ1 Required in BCR-FGFR1-Driven SCLL

Next-generation sequencing (NGS) target enrichment methods provide solutions to focus on and sequence a small portion of the human genome. This saves sequencing and analysis costs for labs that study genetic diseases. These savings typically range from approximately 100 to 100,000 fold, depending on the application and the amount of the genome being targeted. Until now, there have been two primary target enrichment methods used in the field.
 Hybridization capture methods are considered high-performance solutions that tend to require cumbersome steps and an overnight hybridization incubation for optimal performance. On the other hand, amplicon technologies are considered fast and easy but generally do not have the same level of performance compared to capture technologies. Primer Extension Target Enrichment (PETE) is a newly developed technology that uses DNA polymerase extension reactions to provide a high-performance target enrichment solution that is easy to use and can be performed in a single day. 

In this Teach Me in 10, Brian Godwin, director of reagent and assay development at Roche sequencing, joins Lucy Lawrence to give us an overview of how each of the three target enrichment technologies work along. Godwin also shares a description of common target enrichment performance metrics.

Introducing Primer Extension Target Enrichment for NGS With Brian Godwin

Aging (Aging-US)

Aging (Aging-US) published this trending research paper in Volume 14, Issue 7, entitled, “The tobacco phosphatidylethanolamine-binding protein NtFT4 increases the lifespan of Drosophila melanogaster by interacting with the proteostasis network” by researchers from the Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Münster, Germany; Institute of Plant Biology and Biotechnology, University of Münster, Münster, Germany; Institute of Neuro- and Behavioral Biology, University of Münster, Münster, Germany; TRM Ltd, Scarborough, United Kingdom.

DOI - https://doi.org/10.18632/aging.204005

Corresponding author - Philip Känel - philip.kaenel@ime.fraunhofer.de

Abstract
Proteostasis reflects the well-balanced synthesis, trafficking and degradation of cellular proteins. This is a fundamental aspect of the dynamic cellular proteome, which integrates multiple signaling pathways, but it becomes increasingly error-prone during aging. Phosphatidylethanolamine-binding proteins (PEBPs) are highly conserved regulators of signaling networks and could therefore affect aging-related processes. To test this hypothesis, we expressed PEPBs in a heterologous context to determine their ectopic activity. We found that heterologous expression of the tobacco (Nicotiana tabacum) PEBP NtFT4 in Drosophila melanogaster significantly increased the lifespan of adult flies and reduced age-related locomotor decline. Similarly, overexpression of the Drosophila ortholog CG7054 increased longevity, whereas its suppression by RNA interference had the opposite effect. In tobacco, NtFT4 acts as a floral regulator by integrating environmental and intrinsic stimuli to promote the transition to reproductive growth. In Drosophila, NtFT4 engaged distinct targets related to proteostasis, such as HSP26. In older flies, it also prolonged Hsp26 gene expression, which promotes longevity by maintaining protein integrity. In NtFT4-transgenic flies, we identified deregulated genes encoding proteases that may contribute to proteome stability at equilibrium. Our results demonstrate that the expression of NtFT4 influences multiple aspects of the proteome maintenance system via both physical interactions and transcriptional regulation, potentially explaining the aging-related phenotypes we observed.

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Keywords - aging, proteostasis, heat shock proteins, chaperone, locomotor activity

About Aging-US

Launched in 2009, Aging-US publishes papers of general interest and biological significance in all fields of aging research and age-related diseases, including cancer—and now, with a special focus on COVID-19 vulnerability as an age-dependent syndrome. Topics in Aging-US go beyond traditional gerontology, including, but not limited to, cellular and molecular biology, human age-related diseases, pathology in model organisms, signal transduction pathways (e.g., p53, sirtuins, and PI-3K/AKT/mTOR, among others), and approaches to modulating these signaling pathways.

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Trending With Impact: Tobacco Gene Increases Lifespan in Fruit Flies

Creative Proteomics videos

Proteomics studies play an increasing role in the field of biology. The use of mass spectrometry (MS) in combination with a range of separation methods is the main principal methodology for proteomics. The two principal approaches to identifying and characterizing proteins using MS are the “bottom-up”, which analyze peptides by proteolytic digestion, and “top-down”, which analyze intact proteins.  https://www.creative-proteomics.com/resource/top-down-proteomics-vs-bottom-up-proteomics.htm

Bottom-up Proteomics and Top-down Proteomics at Creative Proteomics

SILAC-based quantitative proteomics (SILAQ) is an innovative technology used in high throughput quantitative analysis of large protein complexes, protein-protein and protein-small molecule interactions. https://www.creative-proteomics.com/Services/SILAC-based-proteomics-analysis.htm

SILAQ

Creative Proteomics has established a highly sensitive HPLC-MS/MS pipeline that can analyze N- and O-methylation in both eukaryotic and prokaryotic organisms. In addition, we have optimized our protocol, to enable more fast and sensitive site mapping service for methylation analysis.

https://www.creative-proteomics.com/services/Methylation.htm

Protein Methylation Analysis

Glycans are defined as the compounds that consist of a large number of monosaccharides linked glycosidically. Glycans have diverse biological functions and it can be classified into two broad categories. One is the structural and modulatory properties of glycans and the other is the specific recognition of glycans by other molecules, most commonly, glycan-binding proteins (GBPs). The GBPs can be divided into two types, intrinsic GBPs and extrinsic GBPs. The intrinsic GBPs recognize glycans from the same organism and mediate cell-cell interactions or recognize extracellular molecules. The extrinsic GBPs which contain pathogenic microbial adhesins, agglutinins, or toxins, recognize glycans from different organisms and some also mediate symbiotic relationships.

Brief Introduction of Glycan Microarrays

Custom Videos from Technology Networks

Watch this video from Sartorius to learn more about the iQue Forecyt® Software: EC50/IC50 curves and iQue® Human NK Cell Killing Kits.

Proteomics and Metabolomics

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