Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new biomarkers have been successfully translated into clinical use, due in part to inadequate ...protein assay technologies to support large-scale testing of hundreds of candidate biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues. Although the feasibility of using targeted, multiple reaction monitoring mass spectrometry (MRM-MS) for quantitative analyses of FFPE tissues has been demonstrated, protocols have not been systematically optimized for robust quantification across a large number of analytes, nor has the performance of peptide immuno-MRM been evaluated. To address this gap, we used a test battery approach coupled to MRM-MS with the addition of stable isotope-labeled standard peptides (targeting 512 analytes) to quantitatively evaluate the performance of three extraction protocols in combination with three trypsin digestion protocols (i.e., nine processes). A process based on RapiGest buffer extraction and urea-based digestion was identified to enable similar quantitation results from FFPE and frozen tissues. Using the optimized protocols for MRM-based analysis of FFPE tissues, median precision was 11.4% (across 249 analytes). There was excellent correlation between measurements made on matched FFPE and frozen tissues, both for direct MRM analysis (R 2 = 0.94) and immuno-MRM (R 2 = 0.89). The optimized process enables highly reproducible, multiplex, standardizable, quantitative MRM in archival tissue specimens.
Abstract
Background
Conventional HER2-targeting therapies improve outcomes for patients with HER2-positive breast cancer (BC), defined as tumors showing HER2 protein overexpression by ...immunohistochemistry and/or ERBB2 gene amplification determined by in situ hybridization (ISH). Emerging HER2-targeting compounds show benefit in some patients with neither HER2 protein overexpression nor ERBB2 gene amplification, creating a need for new assays to select HER2-low tumors for treatment with these compounds. We evaluated the analytical performance of a targeted mass spectrometry-based assay for quantifying HER2 protein in formalin-fixed paraffin-embedded (FFPE) and frozen BC biopsies.
Methods
We used immunoaffinity-enrichment coupled to multiple reaction monitoring-mass spectrometry (immuno-MRM-MS) to quantify HER2 protein (as peptide GLQSLPTHDPSPLQR) in 96 frozen and 119 FFPE BC biopsies. We characterized linearity, lower limit of quantification (LLOQ), and intra- and inter-day variation of the assay in frozen and FFPE tissue matrices. We determined concordance between HER2 immuno-MRM-MS and predicate immunohistochemistry and ISH assays and examined the benefit of multiplexing the assay to include proteins expressed in tumor subcompartments (e.g., stroma, adipose, lymphocytes, epithelium) to account for tissue heterogeneity.
Results
HER2 immuno-MRM-MS assay linearity was ≥103, assay coefficient of variation was 7.8% (FFPE) and 5.9% (frozen) for spiked-in analyte, and 7.7% (FFPE) and 7.9% (frozen) for endogenous measurements. Immuno-MRM-MS-based HER2 measurements strongly correlated with predicate assay HER2 determinations, and concordance was improved by normalizing to glyceraldehyde-3-phosphate dehydrogenase. HER2 was quantified above the LLOQ in all tumors.
Conclusions
Immuno-MRM-MS can be used to quantify HER2 in FFPE and frozen BC biopsies, even at low HER2 expression levels.
Knowledge of the stability of analytes in clinical specimens is a prerequisite for proper transport and preservation of samples to avoid laboratory errors. The new version of ISO 15189:2022 and the ...European directive 2017/746 increase the requirements on this topic for manufacturers and laboratories. Within the project to generate a stability database of European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Working Group Preanalytical Phase (WG-PRE), the need to standardise and improve the quality of published stability studies has been detected, being a manifest deficit the absence of international guidelines for the performance of stability studies on clinical specimens.
These recommendations have been developed and summarised by consensus of the WG-PRE and are intended primarily to improve the quality of sample stability claims included in information for users provided by assay supplier companies, according to the requirements of the new European regulations and standards for accreditation.
This document provides general recommendations for the performance of stability studies, oriented to the estimation of instability equations in the usual working conditions, allowing flexible adaptation of the maximum permissible error specifications to obtain stability limits adapted to the intended use.
We present this recommendation based on the opinions of the EFLM WG-PRE group for the standardisation and improvement of stability studies, with the intention to improve the quality of the studies and the transferability of their results to laboratories.
Genetically encoded fluorescent indicators require fluorescent protein moieties to report biological events as fluorescent signals. In the case of indicators that use a change in protein conformation ...to alter the degree of fluorescence resonance energy transfer (FRET) between two fluorophores, ideal fluorescent protein components should have no intrinsic environmental sensitivity, so that their FRET level indicates only the concentration of the analyte of interest. In the case of single fluorescent protein indicators, in which a protein conformational change can be directly tranduced into a fluorescence intensity change, an ideal fluorescent protein component should be maximally environmentally sensitive, but to just one analyte, to minimize interference and cross talk. In this dissertation, I report what I learned about the biochemical and structural properties of fluorescent proteins, and how I used that knowledge to design fluorescent indicators. The first chapter is a biochemical and structural classification of an environmentally insensitive Yellow Fluorescent Protein useful in the construction of indicators. The second chapter is a report of a new, very environmentally sensitive class of fluorescent proteins that form the basis of a new type of fluorescent indicator. The third chapter outlines the design, testing, and analysis of a new type of calcium indicator based on the protozoan protein spasmin. The fourth and fifth chapters describe the biochemical, structural and chemical classification of the Discosoma red fluorescent protein, DsRed, and efforts made to improve DsRed's utility as a component of fluorescent indicators.
Background Patients with pulmonary atresia or critical pulmonary stenosis with intact ventricular septum (PA/IVS) and biventricular circulation may require pulmonary valve replacement (PVR). Right ...ventricular (RV) remodeling after PVR is well described in tetralogy of Fallot (TOF); we sought to investigate RV changes in PA/IVS using cardiac magnetic resonance imaging. Methods and Results A retrospective cohort of patients with PA/IVS who underwent PVR at Boston Children's Hospital from 1995 to 2021 with cardiac magnetic resonance imaging before and after PVR was matched 1:3 with patients with TOF by age at PVR. Median regression modeling was performed with post-PVR indexed RV end-diastolic volume as the primary outcome. A total of 20 patients with PA/IVS (cases) were matched with 60 patients with TOF (controls), with median age at PVR of 14 years. Pre-PVR indexed RV end-diastolic volume was similar between groups; cases had higher RV ejection fraction (51.4% versus 48.6%;
=0.03). Pre-PVR RV free wall and left ventricular (LV) longitudinal strain were similar, although LV midcavity circumferential strain was decreased in cases (-15.6 versus -17.1;
=0.001). At a median of 2 years after PVR, indexed RV end-diastolic volume was similarly reduced; cases continued to have higher RV ejection fraction (52.3% versus 46.9%;
=0.007) with less reduction in RV mass (Δ4.5 versus 9.6 g/m
;
=0.004). Post-PVR, RV and LV longitudinal strain remained unchanged, and LV circumferential strain was similar, although lower in cases. Conclusions Compared with patients with TOF, patients with PA/IVS demonstrate similar RV remodeling after PVR, with lower reduction in RV mass and comparatively higher RV ejection fraction. Although no differences were detected in peak systolic RV or LV strain values, further investigation of diastolic parameters is needed.
Abstract only
Background:
Patients with pulmonary atresia with intact ventricular septum (PA/IVS) and critical pulmonary stenosis (CPS) managed to a biventricular circulation may eventually require ...pulmonary valve replacement (PVR) for pulmonary regurgitation (PR). Right ventricular (RV) remodeling after PVR has been well described in tetralogy of Fallot (TOF); we sought to investigate RV volumetric and functional changes in PA/IVS using CMR.
Methods:
A retrospective cohort of PA/IVS and CPS patients who underwent PVR at Boston Children’s Hospital from 1995-2021 with CMR before and after PVR was matched 1:3 with TOF patients by age at PVR. Patients with initial intervention >2 weeks of age or 1.5 ventricle circulation were excluded. Median regression modeling accounting for matching was performed with reduction in indexed right ventricular end diastolic volume (RVEDVi) post PVR as the primary outcome, adjusting for covariates including tricuspid regurgitation (TR) and PVR valve size.
Results:
Twenty PA/IVS or CPS patients (cases) were matched with 60 TOF (controls), with median age at PVR 14 years; at median follow-up 8 years post PVR, 95% were NYHA Class I. Pre-PVR RVEDVi was similar between groups (165 vs 167 ml/m
2
, p=0.7), although cases had higher RV EF (51.4 vs 48.6%, p=0.03), TR fraction (23 vs 9%, p=0.008), and a trend toward lower RV mass; PR fraction, LV volumes and EF were similar. Pre-PVR RV free wall and LV longitudinal strain were similar, although LV circumferential strain was worse in cases (-15.6 vs -17.1, p=0.01). At median 2 years after PVR, RVEDVi was similarly reduced from 166 to 118 ml/m
2
(p=0.73), although cases had higher RV EF (52.3% vs 46.9%, p=0.007) with less reduction in indexed RV mass (Δ4.5 vs 9.6 g/m
2
, p=0.02); LV volumes and EF were similar. Post PVR, RV and LV longitudinal strain remained unchanged both within and between groups; LV circumferential strain was similar post PVR and remained lower in cases vs controls.
Conclusion:
Patients with PA/IVS after PVR demonstrate similar RV remodeling to TOF patients, with lesser reduction in RV mass and comparatively better post RV EF. CMR strain imaging found no significant pre-post differences in RV or LV systolic parameters. Further investigation is needed to evaluate for changes in diastolic parameters.
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