Comparative cytogenetics of microsatellite distribution in two tetra fishes Astyanax bimaculatus (Linnaeus, 1758) and Psalidodon scabripinnis (Jenyns, 1842).

Background: The main cytogenetic studies of the Characidae family comprise the genera Astyanax and Psalidodon involving the use of repetitive DNA probes. However, for the microsatellite classes, studies are still scarce and the function of these sequences in the genome of these individuals is still not understood. Thus, we aimed to analyze and compare the distribution of microsatellite sequences in the species Astyanax bimaculatus and Psalidodon scabripinnis. Methods: We collected biopsies from the fins of A. bimaculatus and P. scabripinnis to perform cell culture, followed by chromosome extraction, and mapped the distribution of 14 microsatellites by FISH in both species. Results and Discussion: The diploid number observed for both species was 2n = 50, with an acrocentric B microchromosome in A. bimaculatus and a metacentric B chromosome in P. scabripinnis. Regarding FISH, 11 probes hybridized in the karyotype of A. bimaculatus mainly in centromeric regions, and 13 probes hybridized in P. scabripinnis, mainly in telomeric regions, in addition to a large accumulation of microsatellite hybridization on its B chromosome. Conclusion: Comparative FISH mapping of 14 microsatellite motifs revealed different patterns of distribution both in autosomes and supernumerary chromosomes of A. bimaculatus and P. scabripinnis, suggesting independent evolutionary processes in each of these species, representing excellent data on chromosome rearrangements and cytotaxonomy.

Persons chronically exposed to low doses of ionizing radiation: A cytogenetic dosimetry study.

The dosimetry and control of exposure for individuals chronically exposed to ionizing radiation are important and complex issues. Assessment may be optimized by evaluating individual adaptation and radiosensitivity, but it is not possible for a single model to account for all relevant parameters. Our goal was to develop approaches for the calculation of doses for persons chronically exposed to ionizing radiation, taking their radiosensitivities into consideration. On the basis of ex vivo radiation of blood samples, dose-effect models were constructed for dose ranges 0.01-2.0 and 0.01-0.4 Gy, using different cytogenetic criteria. The frequencies of "dicentric chromosomes and rings" at low doses are too low to have predictive value. The different responses of subjects to radiation made it possible to categorize them according to their radiosensitivities and to generate separate dose-effect curves for radiosensitive, average, and radioresistant individuals, reducing the amount of error in retrospective dosimetry.

Feasibility, accuracy, and usability analysis of MapAML, a first-in-class app for integrated diagnosis in acute myeloid leukemia.

Performing a comprehensive diagnosis of acute myeloid leukemia (AML) is complex and involves the integration of clinical information, bone marrow morphology, immunophenotyping, cytogenetic, and molecular analysis, which can be challenging to the general hematologist. The aim of this study was to evaluate the usability and accuracy of MapAML, a smartphone app for integrated diagnosis in AML, created to aid the hematologist in its clinical practice. App performance was evaluated in dedicated sessions, in which 21 hematologists or fellows in hematology performed an integrated diagnosis of deidentified real-world clinical AML cases, first without and posteriorly with MapAML use. Diagnosis accuracy increased after MapAML utilization, with the average score going from 7.08 without app to 8.88 with app use (on a scale from 0 to 10), representing a significant accuracy improvement (p = .002). Usability evaluation was very favorable, with 81% of users considering the app very or extremely simple to use. There was also a significant increase in confidence to perform a complete and accurate diagnosis in AML after app use, with 61.9% of the participants willing to use the app in their clinical practice. In this study, MapAML increased accuracy with excellent usability for integrated diagnosis in AML.

Clinical Cytogenetics: Current Practices and Beyond.

BACKGROUND: Throughout history, the field of cytogenetics has witnessed significant changes due to the constant evolution of technologies used to assess chromosome number and structure. Similar to the evolution of single nucleotide variant detection from Sanger sequencing to next-generation sequencing, the identification of chromosome alterations has progressed from banding to fluorescence in situ hybridization (FISH) to chromosomal microarrays. More recently, emerging technologies such as optical genome mapping and genome sequencing have made noteworthy contributions to clinical laboratory testing in the field of cytogenetics. CONTENT: In this review, we journey through some of the most pivotal discoveries that have shaped the development of clinical cytogenetics testing. We also explore the current test offerings, their uses and limitations, and future directions in technology advancements. SUMMARY: Cytogenetics methods, including banding and targeted assessments like FISH, continue to hold crucial roles in cytogenetic testing. These methods offer a rapid turnaround time, especially for conditions with a known etiology involving recognized cytogenetic aberrations. Additionally, laboratories have the flexibility to now employ higher-throughput methodologies to enhance resolution for cases with greater complexity.

Automated Deep Learning-Based Diagnosis and Molecular Characterization of Acute Myeloid Leukemia Using Flow Cytometry.

The current flow cytometric analysis of blood and bone marrow samples for diagnosis of acute myeloid leukemia (AML) relies heavily on manual intervention in the processing and analysis steps, introducing significant subjectivity into resulting diagnoses and necessitating highly trained personnel. Furthermore, concurrent molecular characterization via cytogenetics and targeted sequencing can take multiple days, delaying patient diagnosis and treatment. Attention-based multi-instance learning models (ABMILMs) are deep learning models that make accurate predictions and generate interpretable insights regarding the classification of a sample from individual events/cells; nonetheless, these models have yet to be applied to flow cytometry data. In this study, we developed a computational pipeline using ABMILMs for the automated diagnosis of AML cases based exclusively on flow cytometric data. Analysis of 1820 flow cytometry samples shows that this pipeline provides accurate diagnoses of acute leukemia (area under the receiver operating characteristic curve [AUROC] 0.961) and accurately differentiates AML vs B- and T-lymphoblastic leukemia (AUROC 0.965). Models for prediction of 9 cytogenetic aberrancies and 32 pathogenic variants in AML provide accurate predictions, particularly for t(15;17)(PML::RARA) [AUROC 0.929], t(8;21)(RUNX1::RUNX1T1) (AUROC 0.814), and NPM1 variants (AUROC 0.807). Finally, we demonstrate how these models generate interpretable insights into which individual flow cytometric events and markers deliver optimal diagnostic utility, providing hematopathologists with a data visualization tool for improved data interpretation, as well as novel biological associations between flow cytometric marker expression and cytogenetic/molecular variants in AML. Our study is the first to illustrate the feasibility of using deep learning-based analysis of flow cytometric data for automated AML diagnosis and molecular characterization.

ChatGPT as an aid for pathological diagnosis of cancer.

Diagnostic workup of cancer patients is highly reliant on the science of pathology using cytopathology, histopathology, and other ancillary techniques like immunohistochemistry and molecular cytogenetics. Data processing and learning by means of artificial intelligence (AI) has become a spearhead for the advancement of medicine, with pathology and laboratory medicine being no exceptions. ChatGPT, an artificial intelligence (AI)-based chatbot, that was recently launched by OpenAI, is currently a talk of the town, and its role in cancer diagnosis is also being explored meticulously. Pathology workflow by integration of digital slides, implementation of advanced algorithms, and computer-aided diagnostic techniques extend the frontiers of the pathologist's view beyond a microscopic slide and enables effective integration, assimilation, and utilization of knowledge that is beyond human limits and boundaries. Despite of it's numerous advantages in the pathological diagnosis of cancer, it comes with several challenges like integration of digital slides with input language parameters, problems of bias, and legal issues which have to be addressed and worked up soon so that we as a pathologists diagnosing malignancies are on the same band wagon and don't miss the train.

The incidence of translocation t(11;14) among patients with multiple myeloma in a single clinic.

OBJECTIVES: Data regarding bone marrow (BM) sampling and cytogenetic testing rates for identification of translocation (11q13;14q32) and their changes over time in a multiple myeloma (MM) population are limited. We analyzed these metrics at a clinic specializing in the treatment of MM. METHODS: A total of 760 BM aspirate samples from 351 patients were collected between August 2004 and October 2021. We analyzed BM sampling statistics, cytogenetic testing frequency, and the incidence rates for the t(11;14) translocation in a single clinic specializing in the treatment of MM. RESULTS: We report that most (54.4%) patients had only 1 aspirate collected; the main reason (64.6%) for BM collection was to confirm disease progression. Less than half (47.5%) of BM samples collected for evaluation of MM disease had cytogenetic testing, but the rates have markedly increased in recent years. Our data demonstrated an incidence rate of 19.3% for t(11;14). CONCLUSIONS: This report suggests that some patients may need to retest for this genetic aberration due to the possibility of false negatives and the potential benefit of identifying the t(11;14) marker for patients who may be candidates for a highly effective targeted therapy consisting of the BCL-2 inhibitor venetoclax.

Physiological mechanism of action and partial separation of herbicide-active compounds from the Diaporthe sp. extract on Amaranthus tricolor L.

Thirteen fungi that produce compounds with herbicidal activities were isolated, identified, and extracted under the assumption that the mechanism of action occurs during seed exposure to the extract. The extracts from all the fungal strains considerably decreased the growth parameters of Amaranthus tricolor L. The EC010 strain extracts showed the greatest effect. Through ITS region gene sequencing methods, the isolated EC010 was identified as a genus of Diaporthe. The results showed a significant (p < 0.05) inhibitory effect of 91.25% on germination and a decrease in shoot and root length by 91.28% and 95.30%, respectively. The mycelium of Diaporthe sp. was extracted using sequential extraction techniques for the partial separation of the herbicidal fraction. According to the bioassay activities, the EtOAc fraction showed the highest inhibitory activity. The osmotic stress of the A. tricolor seeds was studied. Although the extract increased the accumulation of proline and soluble protein, the treated seeds showed lower imbibition. While the activity of α-amylase was dramatically decreased after treatment. A cytogenetic assay in the treated Allium cepa L. root revealed a decrease in the mitotic index, an altered mitotic phase index, and a promotion of mitotic abnormalities. Accordingly, the Diaporthe sp. may serve as a potential herbicidal compound resource.

Complementary Tumor Diagnosis by Single Cell-Based Cytogenetics Using Multi-marker Fluorescence In Situ Hybridization (mFISH).

Multi-color (or multi-marker) fluorescence in situ hybridization (mFISH) is a well-established, valuable, complementary tool for prenatal and pathological (tumor) diagnosis. A variety of chromosomal abnormalities, such as partial or total chromosomal gains, losses, inversions, or translocations, which are considered to cause genetic syndromes, can relatively easily be detected on a cell-by-cell basis. Individual cells either in suspension (e.g., in the form of a cytological specimen derived from body fluids) or within a tissue (e.g., a solid tumor specimen or biopsy) can be quantitatively evaluated with respect to the chromosomal hybridization markers of interest (e.g., a gene or centromeric region) and with due consideration of cellular heterogeneity. FISH is helpful or even essential for the (sub-)classification, stratification, and unambiguous diagnosis of a number of malignant diseases and contributes to treatment decision in many cases. Here, the diagnostic power and limitations of typical FISH and mFISH approaches (except chromosome painting and RNA hybridization) are discussed, with special emphasis on tumor and single-cell diagnostics. Well-established and novel FISH protocols, the latter addressed to accelerate and flexibilize the preparation and hybridization of formalin-fixed and paraffin-embedded tissues, are provided. Moreover, guidelines and molecular aspects important for data interpretation are discussed. Finally, sophisticated multiplexed approaches and those that analyze very rare single-cell events, which are not yet implemented in diagnostic procedures, will be touched upon. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: (m)FISH applied to formaldehyde-fixed paraffin-embedded tissues Basic Protocol 2: (m)FISH applied to cytological specimens.

Postirradiation temperature influences DSB repair and dicentric chromosome formation-potential impact for dicentric chromosome analysis in interlaboratory comparisons.

The objective was to investigate the influence of different pre-storage temperatures in the dicentric chromosome analysis (DCA) protocol (22°C vs. 37°C) by using γ-H2AX + 53BP1 foci as a marker for deoxyribonucleic acid (DNA) double-strand break (DSB) damage induction and repair and the formation of dicentric chromosomes as a result of mis-repair. Repair of γ-H2AX + 53BP1 DSB foci was absent in samples that were incubated for 2 h at 22°C after exposure of 0.5 and 1.2 Gy. When 0.5- and 1.2-Gy-exposed samples were incubated at 37°C for 2 h, there was an average decline of 31 and 52% of DSB foci, respectively. This indicated that DNA repair occurred. There was a 27% decrease in dicentric chromosome yield at 1.2 Gy and a 15% decrease at 3.5 Gy after post-irradiation incubation for 2 h at 37°C relative to the observed dicentric frequencies at 22°C. Recommended to re-phase: our data suggested that there were more open DSBs after a 2-h incubation at 22°C, which contributed to more mis-repair and dicentric formation from the start of culture. Our findings are corroborated by publications showing that lesion interaction based on enzymatic activity is suppressed below 21°C. As such temperature variations can be a source of variation in DCA during interlaboratory comparison studies, we propose to establish a common guide for the standardisation of pre-culture conditions in cytogenetic dosimetry proficiency testing.

A standardized and automated CBMN assay for biological dosimetry: the CytoRADx™ system.

Major nuclear accidents can result in many casualties, and it is important to assess the absorbed radiation dose to support treatment decisions. Biological dosimetry (BD) allows retrospective determination of dose using biological markers. To achieve consistent cytogenetic assay results across labs, the current practice requires each lab to generate periodic, unique calibration curves using in vitro dose-effect experiments. Here, we present CytoRADx™, a standardized biodosimetry system that integrates automated dose calculation in a high-throughput platform without the need for lab-specific calibration curves. CytoRADx consists of an improved, standardized Cytokinesis Block Micronucleus assay combined with automated analysis utilizing an established slide scanning device. We tested CytoRADx for accuracy and reproducibility across different instruments, sites, days and operators. Our results demonstrate that CytoRADx eliminates the time-consuming, lab-specific calibration curves, allowing multiple laboratories to obtain consistent results and to distribute the testing burden in the event of a large-scale accident.

Sex and dose rate effects in automated cytogenetics.

Testing and validation of biodosimetry assays is routinely performed using conventional dose rate irradiation platforms, at a dose rate of approximately 1 Gy/min. In contrast, the exposures from an improvised nuclear device will be delivered over a large range of dose rates with a prompt irradiation component, delivered in less than 1 µs, and a protracted component delivered over hours and days. We present preliminary data from a large demographic study we have undertaken for investigation of age, sex and dose rate effects on dicentric and micronucleus yields. Our data demonstrate reduced dicentric and micronucleus yields at very high dose rates. Additionally, we have seen small differences between males and females, with males having slightly fewer micronuclei and slightly more dicentrics than females, at high doses.

SETD2 safeguards the genome against isochromosome formation.

Isochromosomes are mirror-imaged chromosomes with simultaneous duplication and deletion of genetic material which may contain two centromeres to create isodicentric chromosomes. Although isochromosomes commonly occur in cancer and developmental disorders and promote genome instability, mechanisms that prevent isochromosomes are not well understood. We show here that the tumor suppressor and methyltransferase SETD2 is essential to prevent these errors. Using cellular and cytogenetic approaches, we demonstrate that loss of SETD2 or its epigenetic mark, histone H3 lysine 36 trimethylation (H3K36me3), results in the formation of isochromosomes as well as isodicentric and acentric chromosomes. These defects arise during DNA replication and are likely due to faulty homologous recombination by RAD52. These data provide a mechanism for isochromosome generation and demonstrate that SETD2 and H3K36me3 are essential to prevent the formation of this common mutable chromatin structure known to initiate a cascade of genomic instability in cancer.

Clinical and cytogenetic characteristics of primary and secondary plasma cell leukemia under the new IMWG definition criteria: a retrospective study.

BACKGROUND: Plasma cell leukemia (PCL) is a rare and aggressive plasma cell disorder, exhibiting a more unfavorable prognosis than multiple myeloma. PCL is classified into pPCL and sPCL. Recently, the IMWG has recommended new PCL definition criteria, which require the presence of ≥5% circulating plasma cells in peripheral blood smears. Due to its low incidence, research on pPCL and sPCL is limited. METHODS: We conducted a retrospective study and analyzed clinical and cytogenetic data of pPCL and sPCL patients. Overall survival (OS) and progression-free survival (PFS) were assessed by the Kaplan-Meier method, and survival distributions were compared using the log-rank test. RESULTS: This is a small cohort comprising 23 pPCL and 9 sPCL patients. Notably, sPCL patients showed a higher incidence of extramedullary infiltration and a higher percentage of bone marrow plasma cells (p = 0.015 and 0.025, respectively). Although no significant difference was found between the two groups in OS and PFS, a trend emerged suggesting a superior survival outcome for pPCL patients, with a higher cumulative 1-year PFS rate (38.3% vs. 13.3%) and a lower early mortality rate (mortality rate at 3 months: 15% vs. 33%). We also suggested that pPCL patients carrying t(11;14) may have a longer median survival time than individuals with other cytogenetic abnormalities, but this was not confirmed due to the small sample size. CONCLUSION: Our study revealed clinical and cytogenetic features of pPCL and sPCL patients according to the new diagnostic criteria. The findings suggested a generally better prognosis for pPCL than sPCL and the likelihood of t(11;14) translocation acting as a favorable prognostic factor in pPCL. It is important to note that our study had a limited sample size, which may lead to bias. We hope well-designed studies can be conducted to provide more results.

InpactorDB: A Plant LTR Retrotransposon Reference Library.

LTR retrotransposons (LTR-RT) are major components of plant genomes. These transposable elements participate in the structure and evolution of genes and genomes through their mobility and their copy number amplification. For example, they are commonly used as evolutionary markers in genetic, genomic, and cytogenetic approaches. However, the plant research community is faced with the near absence of free availability of full-length, curated, and lineage-level classified LTR retrotransposon reference sequences. In this chapter, we will introduce InpactorDB, an LTR retrotransposon sequence database of 181 plant species representing 98 plant families for a total of 67,241 non-redundant elements. We will introduce how to use newly sequenced genomes to identify and classify LTR-RTs in a similar way with a standardized procedure using the Inpactor tool. InpactorDB is freely available at https://inpactordb.github.io .