Validation of break-apart and fusion MYC probes using a digital fluorescence in situ hybridization capture and imaging system

Review of In Situ Hybridization (ISH) Stain Images Using Computational Techniques

Recent advancements in medical imaging have greatly enhanced the application of computational techniques in digital pathology, particularly for the classification of breast cancer using in situ hybridization (ISH) imaging. HER2 amplification, a key prognostic marker in 20-25% of breast cancers, can be assessed through alterations in gene copy number or protein expression. However, challenges persist due to the heterogeneity of nuclear regions and complexities in cancer biomarker detection. This review examines semi-automated and fully automated computational methods for analyzing ISH images with a focus on HER2 gene amplification. Literature from 1997 to 2023 is analyzed, emphasizing silver-enhanced in situ hybridization (SISH) and its integration with image processing and machine learning techniques. Both conventional machine learning approaches and recent advances in deep learning are compared. The review reveals that automated ISH analysis in combination with bright-field microscopy provides a cost-effective and scalable solution for routine pathology. The integration of deep learning techniques shows promise in improving accuracy over conventional methods, although there are limitations related to data variability and computational demands. Automated ISH analysis can reduce manual labor and increase diagnostic accuracy. Future research should focus on refining these computational methods, particularly in handling the complex nature of HER2 status evaluation, and integrate best practices to further enhance clinical adoption of these techniques.

Optimized workflow for digitalized FISH analysis in pathology

BACKGROUND

Effective workflow management in a diagnostic pathology laboratory is critical to achieve rapid turnover while maintaining high quality. Fluorescence in situ hybridization analysis (FISH) is the preferred technique for detecting single chromosomal aberrations in diagnostic surgical pathology.

MATERIAL AND METHODS

FISH analysis applying a rapid hybridization protocol and using an automated whole-slide fluorescence scanning device (3DHISTECH, Sysmex, Switzerland) were implemented in our workflow. By analyzing 42 diagnostic cases, effects of two different scanning profiles on scanning time, and device memory usage were investigated. Manual signal counting (CaseViewer) and software based signal counting (FISHQuant) were compared.

RESULTS

The two scanning profiles, both including a Z-stack function, differed in their exposure time and digital gain. The "low profile" setting (LP) resulted in a significantly shorter scanning time and lower storage volume compared to the "high profile" (HP) setting, making the LP ideal for routine applications. Both signal counting methods (manual versus software based) provided similar cut-offs on a test-cohort of 13 samples.

CONCLUSION

Scanning FISH slides provides good picture quality, reduces the analysis time and allows easy picture archiving and facilitates remote diagnostics, allowing an effective workflow.

Antiproliferative and proapoptotic effects of Inula viscosa extract on Burkitt lymphoma cell line

Burkitt lymphoma is a very aggressive B-cell non-Hodgkin lymphoma. Although remarkable progress has been made in the therapeutic scenario for patients with Burkitt lymphoma, search and development of new effective anticancer agents to improve patient outcome and minimize toxicity has become an urgent issue. In this study, the antitumoral activity of Inula viscosa, a traditional herb obtained from plants collected on the Asinara Island, Italy, was evaluated in order to explore potential antineoplastic effects of its metabolites on Burkitt lymphoma. Raji human cell line was treated with increasing Inula viscosa extract concentration for cytotoxicity screening and subsequent establishment of cell cycle arrest and apoptosis. Moreover, gene expression profiles were performed to identify molecular mechanisms involved in the anticancer activities of this medical plant. The Inula viscosa extract exhibited powerful antiproliferative and cytotoxic activities on Raji cell line, showing a dose- and time-dependent decrease in cell viability, obtained by cell cycle arrest in the G2/M phase and an increase in cell apoptosis. The treatment with Inula viscosa caused downregulation of genes involved in cell cycle and proliferation (c-MYC, CCND1) and inhibition of cell apoptosis (BCL2, BCL2L1, BCL11A). The Inula viscosa extract causes strong anticancer effects on Burkitt lymphoma cell line. The molecular mechanisms underlying such antineoplastic activity are based on targeting and downregulation of genes involved in cell cycle and apoptosis. Our data suggest that Inula viscosa natural metabolites should be further exploited as potential antineoplastic agents against Burkitt lymphoma.

One-fits-all pretreatment protocol facilitating Fluorescence In Situ Hybridization on formalin-fixed paraffin-embedded, fresh frozen and cytological slides

Background

The Fluorescence In Situ Hybridization (FISH) technique is a very useful tool for diagnostic and prognostic purposes in molecular pathology. However, clinical testing on patient tissue is challenging due to variables of tissue processing that can influence the quality of the results. This emphasizes the necessity of a standardized FISH protocol with a high hybridization efficiency. We present a pretreatment protocol that is easy, reproducible, cost-effective, and facilitates FISH on all types of patient material simultaneously with good quality results.

During validation, FISH analysis was performed simultaneously on formalin-fixed paraffin-embedded, fresh frozen and cytological patient material in combination with commercial probes using our optimized one-fits-all pretreatment protocol. An optimally processed sample is characterized by strong specific signals, intact nuclear membranes, non-disturbing autofluorescence and a homogeneous DAPI staining.

Results

In our retrospective cohort of 3881 patient samples, overall 93% of the FISH samples displayed good quality results leading to a patient diagnosis. All FISH were assessed on quality aspects such as adequacy and consistency of signal strength (brightness), lack of background and / or cross-hybridization signals, and additionally the presence of appropriate control signals were evaluated to assure probe accuracy. In our analysis 38 different FISH probes from 3 commercial manufacturers were used (Cytocell, Vysis and ZytoLight). The majority of the patients in this cohort displayed good signal quality and barely non-specific background fluorescence on all tissue types independent of which commercial probe was used.

Conclusion

The optimized one-fits-all FISH method is robust, reliable and reproducible to deliver an accurate result for patient diagnostics in a lean workflow and cost-effective manner. This protocol can be used for widespread application in cancer and non-cancer diagnostics and research.

Molecular Fingerprinting of Anatomically and Temporally Distinct B-Cell Lymphoma Samples by Next-Generation Sequencing to Establish Clonal Relatedness

CONTEXT.—

B-cell lymphomas exhibit balanced translocations that involve immunoglobulin loci and result from aberrant V(D)J recombination, class switch recombination, or somatic hypermutation. Although most of the breakpoints in the immunoglobulin loci occur in defined regions, those in the partner genes vary; therefore, it is unlikely that 2 independent clones would share identical breakpoints in both partners. Establishing whether a new lesion in a patient with history of lymphoma represents recurrence or a new process can be relevant. Polymerase chain reaction (PCR)-based clonality assays used in this setting rely only on evaluating the length of a given rearrangement. In contrast, next-generation sequencing (NGS) provides the exact translocation breakpoint at single-base resolution.

OBJECTIVE.—

To determine if translocation breakpoint coordinates can serve as a molecular fingerprint unique to a distinct clonal population.

DESIGN.—

Thirty-eight follicular lymphoma/diffuse large B-cell lymphoma samples collected from different anatomic sites and/or at different time points from 18 patients were analyzed by NGS. For comparison, PCR-based B-cell clonality and fluorescence in situ hybridization studies were performed on a subset of cases.

RESULTS.—

IGH-BCL2 rearrangements were detected in all samples. The breakpoint coordinates on derivative chromosome(s) were identical in all samples from a given patient, but distinct between samples derived from different patients. Additionally, 5 patients carried a second rearrangement also with conserved breakpoint coordinates in the follow-up sample(s).

CONCLUSIONS.—

Breakpoint coordinates in the immunoglobulin and partner genes can be used to establish clonal relatedness of anatomically/temporally distinct lesions. Additionally, an NGS-based approach has the potential to detect secondary translocations that may have prognostic and therapeutic significance.

Genetic Screening Test to Detect Translocations in Acute Leukemias by Use of Targeted Locus Amplification

BACKGROUND

Over 500 translocations have been identified in acute leukemia. To detect them, most diagnostic laboratories use karyotyping, fluorescent in situ hybridization, and reverse transcription PCR. Targeted locus amplification (TLA), a technique using next-generation sequencing, now allows detection of the translocation partner of a specific gene, regardless of its chromosomal origin. We present a TLA multiplex assay as a potential first-tier screening test for detecting translocations in leukemia diagnostics.

METHODS

The panel includes 17 genes involved in many translocations present in acute leukemias. Procedures were optimized by using a training set of cell line dilutions and 17 leukemia patient bone marrow samples and validated by using a test set of cell line dilutions and a further 19 patient bone marrow samples. Per gene, we determined if its region was involved in a translocation and, if so, the translocation partner. To balance sensitivity and specificity, we introduced a gray zone showing indeterminate translocation calls needing confirmation. We benchmarked our method against results from the 3 standard diagnostic tests.

RESULTS

In patient samples passing QC, we achieved a concordance with benchmarking tests of 81% in the training set and 100% in the test set, after confirmation of 4 and nullification of 3 gray zone calls (in total). In cell line dilutions, we detected translocations in 10% aberrant cells at several genetic loci.

CONCLUSIONS

Multiplex TLA shows promising results as an acute leukemia screening test. It can detect cryptic and other translocations in selected genes. Further optimization may make this assay suitable for diagnostic use.

c-Myc regulates the CDK1/cyclin B1 dependent‑G2/M cell cycle progression by histone H4 acetylation in Raji cells

Overexpression of c-Myc is involved in the tumorigenesis of B-lineage acute lymphoblastic leukemia (B‑ALL), but the mechanism is not well understood. In the present study, a c‑Myc‑knockdown model (Raji‑KD) was established using Raji cells, and it was indicated that c‑Myc regulates the expression of genes associated with cell cycle progression in G2/M‑phase, cyclin D kinase (CDK)1 and cyclin B1, by modulating 60 kDa Tat‑interactive protein (TIP60)/males absent on the first (MOF)‑mediated histone H4 acetylation (AcH4), which was then completely restored by re‑introduction of the c‑Myc gene into the Raji‑KD cells. The expression of CDK1 and cyclin B1 was markedly suppressed in Raji‑KD cells, resulting in G2/M arrest. In comparison to Raji cells, the proliferation of Raji‑KD cells was significantly reduced, and it was recovered via re‑introduction of the c‑Myc gene. In the tumorigenesis assays, the loss of c‑Myc expression significantly suppressed Raji cell‑derived lymphoblastic tumor formation. Although c‑Myc also promotes Raji cell apoptosis via the caspase‑3‑associated pathway, CDK1/cyclin B1‑dependent‑G2/M cell cycle progression remains the major driving force of c‑Myc‑controlled tumorigenesis. The present results suggested that c‑Myc regulates cyclin B1‑ and CDK1‑dependent G2/M cell cycle progression by TIP60/MOF-mediated AcH4 in Raji cells.

The role of informatics in patient-centered care and personalized medicine

The practice of cytopathology has dramatically changed due to advances in genomics and information technology. Cytology laboratories have accordingly become increasingly dependent on pathology informatics support to meet the emerging demands of precision medicine. Pathology informatics deals with information technology in the laboratory, and the impact of this technology on workflow processes and staff who interact with these tools. This article covers the critical role that laboratory information systems, electronic medical records, and digital imaging plays in patient-centered personalized medicine. The value of integrated diagnostic reports, clinical decision support, and the use of whole-slide imaging to better evaluate cytology samples destined for molecular testing is discussed. Image analysis that offers more precise and quantitative measurements in cytology is addressed, as well as the role of bioinformatics tools to cope with Big Data from next-generation sequencing. This article also highlights the barriers to the widespread adoption of these disruptive technologies due to regulatory obstacles, limited commercial solutions, poor interoperability, and lack of standardization. Cancer Cytopathol 2017;125(6 suppl):494-501. © 2017 American Cancer Society.