Biology subjects

Ulke-Lemee, A.

Publications and source records attributed to Ulke-Lemee, A..

2 recordsLinked to original sources

bioRxiv2026

LAMPrEY: a Python-based automated quality control tool for large-scale proteomics datasets

Over the past years, proteomics has moved increasingly towards the analysis of large cohorts of biological specimens. This has been made possible by significant improvements in mass spectrometry technology, chromatographic separation methods, and improved data acquisition strategies. These technological advances now routinely enable experiments that yield vast datasets that substantially outstrip the capacity of existing proteomics data analysis approaches. Processing such large datasets requires purpose-built, quality control tools designed to organize and analyze the data while recording all processing parameters for reproducibility. To address this need, we developed an open-source, Python-based software platform, Large-scale Automated Multi-level Proteomics Evaluation by Python (LAMPrEY), a comprehensive quality-control pipeline for quantitative proteomics analyses of large cohorts of samples. LAMPrEY features GUI-based file submission, automated processing with MaxQuant and RawTools, an interactive analytics dashboard, and an application programming interface (API) for programmatic usage that collectively enable rapid, reproducible analysis and interpretation of proteomics data. We demonstrate the longitudinal monitoring and analytical capabilities of LAMPrEY using TMT11 quantitative proteomics data generated from 910 Enterococcus faecium isolates collected from bloodstream infection patients. LAMPrEY is an open-source software that can be accessed at www.lewisresearchgroup.org/software.

bioinformatics↗

bioRxiv2020

Heat Shock Protein 27 Immune Complex Upregulates LDLR Expression Thereby Reducing Plasma Cholesterol and Atherogenesis

Elevated Heat Shock Protein 27 levels predict relative freedom from cardiovascular events. In ApoE-/- mice HSP27 over-expression or twice daily subcutaneous injections reduce blood and plaque cholesterol levels, inflammation and atherogenesis. While natural antibodies to HSP27 are present in human blood their role is unknown. Here, we show that blood levels of both HSP27 and anti-HSP27 IgG antibodies are elevated in healthy controls compared to patients with cardiovascular disease. ApoE-/- mice vaccinated with recombinant HSP25 (murine ortholog) develop elevated anti-HSP25 IgG antibodies and reduced levels of cholesterol, inflammation and atherosclerosis. The effects on cholesterol metabolism were divergent: increased hepatic LDLR expression and reduced plasma PCSK9 levels. In vitro, a polyclonal anti-HSP27 IgG antibody combined with rHSP27 to upregulate hepatocyte LDLR expression via an NF-kB-dependent pathway that is independent of SREBP2 expression and intracellular cholesterol levels. HSP27 immunotherapy represents a novel means of lowering not only cholesterol but also PCSK9.Competing Interest StatementEOB and YXC are inventors on US patents 8343915B2 and 8343916B2 and EOB, CS and YXC are inventors on US patent application PCT/CA2016/051018, all pertaining to HSP27 diagnostics / therapeutics. EOB is the Scientific Co-Founder of Pemi31 Therapeutics Inc., a startup company that controls the aforementioned intellectual property. EOB, CS and YXC have equity interests in Pemi31 Therapeutics Inc.View Full Text

pathology↗