Speaker: Stefani Thomas, University of Minnesota
Topic: Beyond the BRCA genes: A proteome-centric view of high-grade serous ovarian cancer
Date: Monday, April 19th, 2021
Time: 2:00 PM Presentation
Location: Webinar – see emails on April 9 and 15 for invite link. Join the mailing list
Abstract: The mutational status of a solid tumor can predict the therapeutic efficacy of a specific drug in a molecularly defined subset of patients. Poly (ADP-ribose) polymerase inhibitors (PARPi) have emerged as a novel class of drugs to treat advanced ovarian cancer with mutations in BRCA1/2 genes. Unfortunately, there is considerable inter-patient heterogeneity in BRCA1/2–based determinations of PARPi treatment sensitivity. Determining proteome-level mechanisms of PARPi sensitivity could enhance our ability to select the ovarian cancer patient population that would benefit the most from PARPi therapy, consequently improving survival and overall treatment response. Our laboratory is applying mass spectrometry-based proteomics to identify protein signatures of PARPi sensitivity. This presentation will provide an overview of the experimental models and analytical approaches that we are utilizing toward a long-term goal of identifying prognostic protein biomarkers of PARPi sensitivity in patients with high-grade serous ovarian cancer.
3rd Annual North American Mass Spectrometry Summer School
June 29 – July 1, 2021 Virtual
Join us for our third annual mass spectrometry summer school. We are proud to have assembled over a dozen world leading experts in mass spectrometry for this three-day course. Our goal is to provide our students, both from academia and industry, an engaging and inspiring program covering the latest in the application of mass spectrometry to omic analyses. Tutorial lectures range from mass analyzers to the basics of data analysis. Also planned are several workshops – aimed at both scientific and professional development. This program is made possible by generous funding from the National Science Foundation (Integrated Organismal Systems, Plant Genome Research Program, Grant No. 2010789) and the National Institutes of Health National Center for Quantitative Biology of Complex Systems (P41 GM108538). As such, there is no cost to participate.
Registration closes on May 15, 2021: https://www.ncqbcs.com/resources/training/summer-school
Scott McLuckey | Purdue University
Rachel Loo | University of California-Los Angeles
Joshua Coon | University of Wisconsin-Madison
Shawnna Buttery | STAR Protocols, Cell Press
Jesper Velgaard Olsen | University of Copenhagen
Lingjun Li | University of Wisconsin-Madison
Jürgen Cox | Max Planck Institute of Biochemistry
Edward Huttlin | Harvard University
Susan Olesik | Ohio State University
Evgenia Shishkova | University of Wisconsin-Madison
Jessica Prenni | Colorado State University
Vicki Wysocki | Ohio State University
John Bowden | University of Florida
Telling your science story
Speaker: Michael Marty, University of Arizona
Topic: Using native mass spectrometry and nanodiscs to study assembly of membrane protein and antimicrobial peptide complexes
Date: Monday, March 15th, 2021
Time: 1:00 PM Presentation
Location: Webinar – see emails on March 4 and 11 for invite link. Join the mailing list
Abstract: Native mass spectrometry (MS) has emerged as a powerful technique for studying the oligomeric state and interactions of membrane proteins. However, native MS can be challenging for smaller and more fragile membrane protein and transmembrane peptide complexes. To address this challenge, we have used native MS to study small viral membrane protein complexes in both detergent micelles and lipid nanodiscs. Using charge reduction reagents for stabilization and advanced data analysis techniques to unravel complex spectra, we discovered that viroporin complexes can be highly sensitive to their environment, showing different oligomeric states in different lipids/detergents, with different pH conditions, and with addition of antiviral drugs. Unexpected oligomeric states have been observed that do not match existing structural models, highlighting previously unseen behavior of these complexes. We have also studied assembly of antimicrobial peptide complexes in lipid nanodiscs. Antimicrobial peptides are also highly sensitive to the lipid environment, showing unique assembly pathways that are controlled by the thickness of the lipid bilayer. Ultimately, we expect these applications of native MS will reveal new insights into the biology of infectious disease and provide new directions for antiviral and antibacterial drug discovery.
Speaker: Allen Everett, Johns Hopkins University
Topic: Proteomics Discovery of Circulating Pulmonary Hypertension Biomarkers: IGF binding proteins are associated with disease severity
Date: Monday, February 15th, 2021
Time: 1:00 PM Presentation
Location: Webinar – see emails on Feb. 4 and 11 for invite link. Join the mailing list
Background: Pulmonary arterial hypertension is a progressive and fatal disease characterized by sustained elevations of pulmonary artery pressure. We lack circulating, diagnostic and prognostic markers to improve outcomes and develop new therapies.
Methods and Results: We performed proteomics discovery using high resolution mass spectrometry to identify new circulating biomarkers of pulmonary arterial hypertension. Plasma samples from patients with idiopathic pulmonary arterial hypertension (N=9, age 35.2 ± 11.2 years, 89% female) and normal controls (N=9, age 34.8 ± 10.6 years, 100% female) were processed by liquid chromatography/tandem mass spectrometry. A total of 826 (0.047 False Discovery Rate) idiopathic pulmonary arterial hypertension and 461 (0.087 False Discovery Rate) control proteins were identified. By Volcano plot, 153 proteins showed > 2 fold change, P<0.05. Carbonic anhydrase 2 (CA2) and Insulin like growth factor binding protein (IGFBP2) were top molecules by spectral counts. When all IGF axis molecules were examined, spectral counts for IGF1, IGF2, IGFBP1, IGFBP4, and IGFBP7 were also different between PAH and control. ELISA verification (N=41 PAH and N=39 controls) demonstrated that IGF1 and 2 were decreased and IGFBP1, 2, 4, 5, 7 and CA2 were increased in PAH. In association with disease severity, IGFBP2, 4 and 7 were associated with decreased 6MWD and IGFBP1, 2, 5 associated with PVR. IGFBP2, 4, and 7 were associated with survival (Kaplan Meier). CA2 was not associated with clinical severity.
Conclusions: We identified candidate plasma proteins that can distinguish PAH from control and verified CA2 and multiple members of the IGF axis associated with PAH and PAH severity. Suggesting that the IGF axis may play an important role in PAH pathogenesis and may be an important diagnostic for PAH, response to therapy and play a role in the pathogenesis of PAH.
Speaker: Shao-En Ong, University of Washington
Topic: Kinome analyses for pharmacoproteomics
Date: Tuesday, January 19th, 2021
Time: 2:00 PM Presentation
Location: Webinar – see emails on Jan. 8 and 15 for invite link. Join the mailing list
Abstract: With few targeted therapies for genetic alterations in cancer, pharmacogenomics has been used to link genetic features with drug response. Because proteomics allows sensitive and direct measurements of cellular signaling pathways, we developed a novel pharmacoproteomics platform to identify kinase pathways correlating with drug response by combining kinobead-based activity profiling of 346 kinases and high-throughput screening of 299 kinase inhibitors in 17 hepatocellular carcinoma (HCC) cell lines. We identified novel kinases involved in drug resistance, that upon small molecule inhibition or genetic knockdown, rewired cellular signaling and restored chemosensitivity. We applied kinobead-MS in clinical HCC samples to identify signatures of drug sensitivity common to cell lines and patient tumors. Our broadly applicable approach identifies kinome features responsible for the activity of individual drugs and provides a resource for biomarker discovery and target deconvolution.