Karin Rodland
A5077382678- Seismic Waves and Analysis
- Earthquake Detection and Analysis
- Methane Hydrates and Related Phenomena
- Ionosphere and magnetosphere dynamics
- Geophysics and Gravity Measurements
- Seismology and Earthquake Studies
- Advanced Proteomics Techniques and Applications
- Geophysical Methods and Applications
- Mass Spectrometry Techniques and Applications
- Astrophysics and Cosmic Phenomena
- Cytokine Signaling Pathways and Interactions
- Molecular Biology Techniques and Applications
- Cancer Genomics and Diagnostics
- Acute Myeloid Leukemia Research
- Ferroptosis and cancer prognosis
- Bioinformatics and Genomic Networks
- Protein Kinase Regulation and GTPase Signaling
- Multiple Myeloma Research and Treatments
- Advanced Biosensing Techniques and Applications
- RNA modifications and cancer
- Ubiquitin and proteasome pathways
- Protein Degradation and Inhibitors
- Metabolomics and Mass Spectrometry Studies
- Gene expression and cancer classification
- Cancer, Lipids, and Metabolism
Pacific Northwest National Laboratory
2016-2025
Oregon Health & Science University
2001-2025
Government of the United States of America
2023
Environmental Molecular Sciences Laboratory
2002-2021
Battelle
2003-2020
Fusion (United States)
2020
Fusion Academy
2020
Clinical Research Consortium
2020
Research Network (United States)
2018
Richland College
2017
ABSTRACT Human cytomegalovirus (HCMV), a member of the herpesvirus family, is large complex enveloped virus composed both viral and cellular gene products. While sequence HCMV genome has been known for over decade, full set proteins that compose virion are unknown. To approach this problem we have utilized gel-free two-dimensional capillary liquid chromatography-tandem mass spectrometry (MS/MS) Fourier transform ion cyclotron resonance MS to identify determine relative abundances in purified...
Glioblastoma (GBM) is the most aggressive nervous system cancer. Understanding its molecular pathogenesis crucial to improving diagnosis and treatment. Integrated analysis of genomic, proteomic, post-translational modification metabolomic data on 99 treatment-naive GBMs provides insights GBM biology. We identify key phosphorylation events (e.g., phosphorylated PTPN11 PLCG1) as potential switches mediating oncogenic pathway activation, well targets for EGFR-, TP53-, RB1-altered tumors. Immune...
The integration of mass spectrometry-based proteomics with next-generation DNA and RNA sequencing profiles tumors more comprehensively. Here this "proteogenomics" approach was applied to 122 treatment-naive primary breast cancers accrued preserve post-translational modifications, including protein phosphorylation acetylation. Proteogenomics challenged standard cancer diagnoses, provided detailed analysis the ERBB2 amplicon, defined tumor subsets that could benefit from immune checkpoint...
We undertook a comprehensive proteogenomic characterization of 95 prospectively collected endometrial carcinomas, comprising 83 endometrioid and 12 serous tumors. This analysis revealed possible new consequences perturbations to the p53 Wnt/β-catenin pathways, identified potential role for circRNAs in epithelial-mesenchymal transition, provided information about proteomic markers clinical genomic tumor subgroups, including relationships known druggable pathways. An extensive genome-wide...
Protein abundance and phosphorylation convey important information about pathway activity molecular pathophysiology in diseases including cancer, providing biological insight, informing drug diagnostic development, guiding therapeutic intervention. Analyzed tissues are usually collected without tight regulation or documentation of ischemic time. To evaluate the impact ischemia, we human ovarian tumor breast cancer xenograft tissue vascular interruption performed quantitative proteomics...
We report a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA and proteomics phosphoproteomics profiling, of 218 tumors across 7 histological types childhood brain cancer: low-grade glioma (n = 93), ependymoma (32), high-grade (25), medulloblastoma (22), ganglioglioma (18), craniopharyngioma (16), atypical teratoid rhabdoid tumor (12). Proteomics data identify common biological themes that span boundaries, suggesting treatments used for one type may be applied...
Sensitive detection of low-abundance proteins in complex biological samples has typically been achieved by immunoassays that use antibodies specific to target proteins; however, de novo development is associated with high costs, long lead times, and failure rates. To address these challenges, we developed an antibody-free strategy involves PRISM (high-pressure, high-resolution separations coupled intelligent selection multiplexing) for sensitive selected reaction monitoring (SRM)–based...
For many years, basic and clinical researchers have taken advantage of the analytical sensitivity specificity afforded by mass spectrometry in measurement proteins. Clinical laboratories are now beginning to deploy these work flows as well. assays that use proteolysis generate peptides for protein quantification characterization, synthetic stable isotope-labeled internal standard central importance. No general recommendations currently available surrounding spectrometric assays.The Proteomic...
Mass spectrometry (MS)-based proteomics has great potential for overcoming the limitations of antibody-based immunoassays antibody-independent, comprehensive, and quantitative proteomic analysis single cells. Indeed, recent advances in nanoscale sample preparation have enabled effective processing In particular, concept using boosting/carrier channels isobaric labeling to increase sensitivity MS detection also been increasingly used small-sized samples including However, full such approaches...
Clear cell renal carcinomas (ccRCCs) represent ∼75% of RCC cases and account for most RCC-associated deaths. Inter- intratumoral heterogeneity (ITH) results in varying prognosis treatment outcomes. To obtain the comprehensive profile ccRCC, we perform integrative histopathologic, proteogenomic, metabolomic analyses on 305 ccRCC tumor segments 166 paired adjacent normal tissues from 213 cases. Combining histologic molecular profiles reveals ITH 90% ccRCCs, with 50% demonstrating immune...
Post-translational modifications (PTMs) play key roles in regulating cell signaling and physiology both normal cancer cells. Advances mass spectrometry enable high-throughput, accurate, sensitive measurement of PTM levels to better understand their role, prevalence, crosstalk. Here, we analyze the largest collection proteogenomics data from 1,110 patients with profiles across 11 types (10 National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium [CPTAC]). Our study reveals...
Changes in the concentration of extracellular calcium can affect balance between proliferation and differentiation several cell types, including keratinocytes, breast epithelial cells, fibroblasts. This report demonstrates that elevation stimulates proliferation-associated signaling pathways rat fibroblasts implicates calcium-sensing receptors (CaR) as mediators this response. Rat-1 express CaR mRNA protein respond to known agonists with increased IP3 production release intracellular...
INTRODUCTION: The advent of high throughput technologies capable comprehensive analysis genes, transcripts, proteins and other significant biological molecules has provided an unprecedented opportunity for the identification molecular markers disease processes. However, it simultaneously complicated problem extracting meaningful signatures processes from these complex datasets. process biomarker discovery characterization provides opportunities more sophisticated approaches to integrating...
Abstract Endothelin is a potent vasoconstrictive peptide recently isolated by Yanagisawa, M., Kurihara, H., Kimura, S., Tamobe, Y., Kobayashi, Mitsui, Yazaki, Goto, K., and Masaki, T. (1988) Nature 332, 411-415). In order to understand the mechanism of action endothelin in various cell types we have examined effects on second messenger levels Rat-1 fibroblasts A10 smooth muscle cells. stimulated 15-fold increase accumulation inositol trisphosphate cells, with half-maximal stimulation...
Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality their gene products despite well-known limitations this "guilt-by-association" (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome data can outperform transcriptome for coexpression based function prediction has not been systematically investigated. Here, we address question by...
Various genetic mutations associated with cancer are known to alter cell signaling, but it is not clear whether they dysregulate signaling pathways by altering the abundance of pathway proteins. Using a combination RNA sequencing and ultrasensitive targeted proteomics, we defined primary components-16 core proteins 10 feedback regulators-of epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) in normal human mammary epithelial cells then quantified their absolute...
Protein modification by O-linked β-N-acetylglucosamine (O-GlcNAc) is emerging as an important factor in the pathogenesis of sporadic Alzheimer's disease (AD); however, detailed molecular characterization this protein post-translational at proteome level has been highly challenging, owing to its low stoichiometry and labile nature. Herein, we report most comprehensive, quantitative proteomics analysis for O-GlcNAcylation postmortem human brain tissues with without AD use isobaric tandem mass...
Many gene products exhibit great structural heterogeneity because of an array modifications. These modifications are not directly encoded in the genomic template but often affect functionality proteins. Protein glycosylation plays a vital role proper protein functions. However, analysis glycoproteins has been challenging compared with other modifications, such as phosphorylation. Here, we perform integrated proteomic and glycoproteomic 83 prospectively collected high-grade serous ovarian...