Optimizing Run Control Performance in Tissue-Based Biomarker Testing: Experience of an Industry-Based CAP/CLIA Laboratory

Introduction/Objective

Introduction: In contrast to traditional labs, our CAP/CLIA Lab performs patient sample testing only for pharma-sponsored clinical trials. Very limited patient material is received, usually in the form of unstained slides rather than wet tissues. Strict run control (RC) quality measures are therefore essential to avoid repeat testing, exhaustion of patient material and/or delay of patient enrollment decisions. We describe methods to optimize RC staining performance and consistency.

Methods/Case Report

Methods: The RC failure rate was evaluated retrospectively and prospectively from January 2018 through March 2021. Specific failure modes were evaluated, including: 1) instrument-related (catastrophic mechanical failure, slide derailment, low temperature error), 2) stain-related (lighter or darker staining vs. reference), 3) tissue-related (tissue loss/fall-off). RC failures were also tracked by instrument and by individual biomarker.

Results (if a Case Study enter NA)

Results: 33,189 patient samples (84,130 slides) were tested from January 2018 through March 2021. Concurrently, 14,794 RC slides were tested across more than 115 biomarkers, including immunohistochemistry, multiplex immunofluorescence, and in situ hybridization assays. The RC failure rates by year were: 2018: 3.2 % (116 RCs), 2019: 3.8% (156 RCs), 2020: 1.9% (100 RCs), and 2021 (through March) 1.3% (21 RCs). The decrease in RC failure rate was a direct result of process changes addressing each of the failure modes, including, but not limited to: 1) improvement in slide storage conditions, 2) more selective RC tissue selection, and 3) more consistent interaction with on-site instrument support.

Conclusion

Process improvements addressing pre-analytic and analytic RC failure modes have resulted in a year-over-year decrease in RC failures. Consequently, our first-pass rates for immunohistochemical, immunofluorescence multiplex, and in-situ hybridization testing of patient samples have increased. Close monitoring of RC failure rates and near-real-time troubleshooting of individual RC failures are important components of successful operation in our unique laboratory setting, where patient material for testing is limited.

A myosin I isoform in the nucleus

A nuclear isoform of myosin I beta that contains a unique 16-amino acid amino-terminal extension has been identified. An affinity-purified antibody to the 16-amino acid peptide demonstrated nuclear staining. Confocal and electron microscopy revealed that nuclear myosin I beta colocalized with RNA polymerase II in an alpha-amanitin- and actinomycin D-sensitive manner. The antibody coimmunoprecipitated RNA polymerase II and blocked in vitro RNA synthesis. This isoform of myosin I beta appears to be in a complex with RNA polymerase II and may affect transcription.

Regulation of cytoskeletal mechanics and cell growth by myosin light chain phosphorylation

The role of myosin light chain phosphorylation in regulating the mechanical properties of the cytoskeleton was studied in NIH/3T3 fibroblasts expressing a truncated, constitutively active form of smooth muscle myosin light chain kinase (tMK). Cytoskeletal stiffness determined by quantifying the force required to indent the apical surface of adherent cells showed that stiffness was increased twofold in tMK cells compared with control cells expressing the empty plasmid (Neo cells). Cytoskeletal stiffness quantified using magnetic twisting cytometry showed an approximately 1.5-fold increase in stiffness in tMK cells compared with Neo cells. Electronic volume measurements on cells in suspension revealed that tMK cells had a smaller volume and are more resistant to osmotic swelling than Neo cells. tMK cells also have smaller nuclei, and activation of mitogen-activated protein kinase (MAP kinase) and translocation of MAP kinase to the nucleus are slower in tMK cells than in control cells. In tMK cells, there is also less bromodeoxyuridine incorporation, and the doubling time is increased. These data demonstrate that increased myosin light chain phosphorylation correlates with increased cytoskeletal stiffness and suggest that changing the mechanical characteristics of the cytoskeleton alters the intracellular signaling pathways that regulate cell growth and division.

Evidence for the presence of myosin I in the nucleus

We produced and affinity-purified polyclonal antibodies to adrenal myosin I. These antibodies recognize adrenal myosin I by Western blot analysis (116 kDa) and inhibit the actin-activated ATPase activity of purified adrenal myosin I. They also recognize a 120-kDa protein in extracts prepared from many different cell lines. Fluorescence microscopy demonstrated the presence of immunoreactive material in the perinuclear region, the leading edges, and the nuclei of 3T3 cells. Fluorescence microscopy also demonstrated nuclear staining in mouse oocytes at the germinal vesicle stage and in the pronuclei during fertilization. Confocal and immunoelectron microscopy confirmed the intranuclear localization. Electron microscopy also demonstrated staining of structures in nucleoli that are thought to be associated with rDNA transcription. Western blot analyses revealed the presence of the 120-kDa protein in extracts prepared from nuclei that are apparently free of cytosolic contamination. The same nuclear protein binds 125I-calmodulin and is photoaffinity labeled with [alpha-32P]ATP. The 120-kDa protein was partially purified from twice washed nuclei using ammonium sulfate fractionation and gel filtration chromatography. Column fractions containing 120-kDa protein as revealed by Western blot analysis also contain K+-EDTA ATPase activity. The 120-kDa protein was also shown to bind actin in the absence, but not the presence, of ATP. Since K+-EDTA ATPase activity, actin, and ATP binding are defining features of the members of the myosin superfamily of proteins, we propose that the 120-kDa protein is a previously undescribed myosin I isoform that is an intranuclear actin-based molecular motor.