The utility of FISH analysis in the diagnosis of BCOR-rearranged sarcomas

BACKGROUND

A BCL6 corepressor (BCOR) gene alteration is a genetic signature of rare subsets of sarcomas. The identification of this alteration has recently contributed to the definition of new entities in the current WHO (2020) classification of soft tissue and bone tumours. We retrospectively examined cases of BCOR-rearranged sarcoma (BRS) to assess the reliability of the BCOR FISH analysis using an IVD (in vitro diagnostic) probe.

METHODS

We investigated and compared the molecular diagnostic strategies and features by collecting 17 data from patients with a BCOR gene rearrangement detected using quantitative-Reverse Transcription-Polymerase Chain Reaction (qRTPCR), Next-Generation Sequencing (NGS) and Fluorescence in situ hybridization (FISH).

RESULTS

We describe fourteen BCOR::CCNB3 sarcomas, one spindle cell sarcoma with a novel BCOR::MAML1 fusion, one spindle cell sarcoma with a novel BCOR::AHR fusion, and one ossifying fibromyxoid tumour with a BCOR::ZC3H7B fusion. FISH analysis of all, except one, BCOR::CCNB3 sarcoma, showed a FISH break-apart pattern with mild signal separation. The MAML1::BCOR sarcoma showed large-space split signals, while in the two patients with AHR::BCOR and ZC3H7B::BCOR fusions, no BCOR rearrangement was observed using FISH.

CONCLUSIONS

Our study indicates that BCOR FISH analysis using an IVD probe, may be useful to detect the presence of a BCOR rearrangement, including both translocations and inversions; however, negative results, in some cases, can occur.

Acetylcholinesterase-induced fluorescence turn-off of an oligothiophene-grafted quartz surface sensitive to myristoylcholine

Immobilized oligothiophene chains that are able to assemble/disassemble upon interaction with a cationic surfactant to detect acetylcholinesterase activity by altering their photoluminescence.

Influence of chain end groups on the matrix-assisted laser desorption/ionization spectra of polymer blends

The positive ion matrix-assisted laser desorption/ionization (MALDI) spectrum of an equimolar blend of Nylon 6 (Ny6) and hydroxyl-terminated polybutyleneterephthalate (PBT) shows a surprisingly strong imbalance between the two components. Since the average molar masses and the polydispersions of the two polymers are comparable, it follows that the efficiency of MALDI is quite different for the two components of the blend. This finding prompted us to a more detailed study, and to synthesize Ny6 and PBT samples terminated with different end groups, in order to analyze their blends by MALDI. The negative ion MALDI spectra of the mixtures investigated show that PBT samples do not yield signals, so that only Ny6 peaks appear in these spectra. By comparing positive and negative ion MALDI spectra of mixtures of Ny6 terminated with various end groups, it was found that the peak intensity depends on the nature of the end groups. The results reported in the present study may help to clarify some fundamental aspects of the mechanisms of ion formation, when MALDI mass spectrometry is applied to macromolecules. End group ionization efficiency appears to be the most important parameter in determining the relative intensity of peaks in the MALDI spectra of the polymer blends investigated. End-group-dependent ionization is the key to the rationalization of the relative peak intensities in MALDI spectra of polymer mixtures.

Analysis of poly(bisphenol A carbonate) by size exclusion chromatography/matrix-assisted laser desorption/ionization. 2. self-association due to phenol end groups

We report here a case of apparent failure of the size exclusion chromatography/matrix-assisted laser desorption/ionization (SEC/MALDI) method to provide polymer fractions with narrow molar mass distribution, showing that intermolecular chain association is responsible for this phenomenon. Poly(bisphenol A carbonate) (PC) chains terminated with hydroxyl groups undergo self-association by hydrogen bonding, providing macromolecular aggregates with higher hydrodynamic volume. These aggregates are eluted through SEC columns at the same volume as higher molar mass chains, which remain non-associated. Thus, self-association affects negatively the SEC fractionation experiments, and even the sharpest SEC fractions contain a heterogeneous mixture of PC chains of different size. When the off-line SEC/MALDI procedure is applied, the SEC fraction is diluted in the matrix which, being a dissociating medium (carboxylic acid) for hydrogen-bonded aggregates, suppresses the chains' self-association. Therefore, the MALDI spectra of these PC fractions indicate a polydisperse character, with irregular bimodal distributions of peaks. As a consequence, in the presence of chain association, the SEC/MALDI method for the calculation of molar masses of polymers cannot be directly applied. In the present case we have found that, under opportune experimental conditions, self-association in polycarbonates can be avoided, so that nearly monodisperse SEC fractions can be obtained and the SEC/MALDI method can be applied. Our results also show that MALDI is a very sensitive technique for the detection of association of polymers in dilute solutions. Copyright 1999 John Wiley & Sons, Ltd.

Analysis of poly(bisphenol A carbonate) by size exclusion chromatography/matrix-assisted laser desorption/ionization. 1. End group and molar mass determination

The determination of molar mass (MM) data for polydisperse polymers by SEC/MALDI involves the fractionation of samples through analytical size exclusion chromatography (SEC). Selected SEC fractions are then analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and the mass spectra of these nearly monodisperse samples allow the determination of the average molar masses. The SEC/MALDI procedure has now been applied to two polycarbonate samples, PC1 and PC2. The results show that the MALDI spectra of the SEC fractions allow not only the detection of linear and cyclic oligomers contained in these samples, but also the simultaneous determination of their average molar masses. Two slightly differing SEC calibration plots were obtained, due to the smaller hydrodynamic volume of the polycarbonate cyclic chains with respect to the linear ones. In agreement with theory, the ratio (M(cycle)/M(linear))(Ve) at a fixed elution volume was found to be 1.22, independent of the molar mass values. Copyright 1999 John Wiley & Sons, Ltd.