SRM Mass Spectrometry Assay for Androgen Receptor Quantification
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Solution Overview
Problem
Current cancer treatments, including traditional chemotherapeutic agents and targeted therapies, often fail to differentiate between rapidly dividing cancer cells and normal cells, leading to non-specific cell killing, and there is a need for more precise methods to determine the effectiveness of Androgen receptor (AR)-targeted therapeutic agents, which are only beneficial for patients with high AR protein expression in their cancer cells.
Innovation Solution
A quantitative proteomics-based assay using mass spectrometry, specifically a Selected Reaction Monitoring (SRM)/Multiple Reaction Monitoring (MRM) assay, measures the levels of AR protein in formalin-fixed tissues from cancer patients, employing specific peptides derived from the AR protein to provide accurate and precise quantification, enabling improved treatment decisions.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If traditional chemotherapeutic agents are used to kill rapidly dividing cells, then cancer cells are killed, but normal cells are also killed
Solution Approach 1:
The patent replaces traditional non-specific chemotherapeutic mechanisms with a highly specific mass spectrometry-based detection system. By using SRM/MRM to precisely measure AR protein levels, the system enables selection of patients who will respond to AR-targeted therapies, effectively replacing broad-spectrum cell killing with targeted molecular detection and response-based treatment selection.
2Reliability
If AR-targeted therapeutic agents are used, then treatment effectiveness is improved for patients with high AR expression, but it is difficult to determine which patients will benefit
Solution Approach 1:
The patent replaces difficult and imprecise AR protein detection methods with mass spectrometry-based SRM/MRM analysis. This substitution provides highly accurate and reliable quantification of AR protein levels in formalin-fixed tissues, enabling clinicians to confidently identify patients who will benefit from AR-targeted therapies.
Solution Approach 2:
The patent changes the detection parameter from qualitative or semi-quantitative AR assessment to precise quantitative measurement of AR protein levels. By measuring specific peptide ions (e.g., m/z 556.3→279.2, 556.3→245.1) through SRM/MRM, the system transforms AR detection into a reliable quantitative parameter that directly predicts treatment response.
3Measurement precision
If mass spectrometry assay is used to measure AR protein levels, then measurement precision is improved, but analysis time and complexity increase
Solution Approach 1:
The patent performs preliminary actions by using formalin-fixed paraffin-embedded (FFPE) tissues that have already been prepared and archived from routine pathology practice. These pre-fixed tissues can be directly analyzed by SRM/MRM without requiring fresh tissue processing, cell culture, or complex sample preparation, thereby significantly reducing analysis time while maintaining high measurement precision.
Solution Approach 2:
The patent makes the SRM/MRM assay universally applicable to routinely archived FFPE tissues, which are already present in pathology departments for diagnostic purposes. This multi-functional use of existing clinical samples eliminates the need for separate research-grade tissue processing, making the precise AR measurement accessible to routine clinical practice.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This method allows for precise measurement of AR protein levels in cancer tissues, aiding in cancer diagnosis and determining the most appropriate therapeutic agents for individual patients, thereby facilitating personalized medicine approaches.
Implementation Method 1
a quantitative proteomics-based assay that delivers a relevant measure of activation of the AR signal pathway
Implementation Method 2
The peptide sequence and fragmentation/transition ions are particularly useful in a mass spectrometry-based Selected Reaction Monitoring (SRM), which can also be referred to as a Multiple Reaction Monitoring (MRM) assay
Data Source
Figure 1A~1C
AI summary
The current disclosure provides for specific peptides, and derived ionization characteristics of the peptides, from the Androgen receptor protein (AR) that are particularly advantageous for quantifying the AR protein directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM) mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM) mass spectrometry. Such biological samples are chemically preserved and fixed wherein said biological sample is selected from tissues and cells treated with formaldehyde containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein sample is prepared from said biological sample using the Liquid Tissue reagents and protocol and the AR protein is quantitated in the Liquid Tissue sample by the method of SRM/MRM mass spectrometry by quantitating in the protein sample at least one or more of the peptides described. These peptides can be quantitated if they reside in a modified or an unmodified form. An example of a modified form of an AR peptide is phosphorylation of a tyrosine, threonine, serine, and/or other amino acid residues within the peptide sequence.