Search Results (168)

Amaranthus L. includes valuable and promising crops of multi-purpose use, having high morphological diversity and complicated taxonomy. Their karyotypes and genomic relationships remain insufficiently studied. For the first time, a comparative repeatome analysis of Amaranthus tricolor L., Amaranthus cruentus L., and Amaranthus hypochondriacus L. was performed based on the high-throughput sequencing data obtained via bioinformatic analyses using the RepeatExplorer2/TAREAN/DANTE_LTR pipelines. Interspecific variations in the abundance of Ty1 Copia and Ty3 Gypsy retroelements, DNA transposons, and ribosomal and satellite DNA (satDNA) were detected. Based on fluorescence in situ hybridization (FISH), chromosome mapping of 45S rDNA, 5S rDNA, and satDNAs AmC9 and AmC70, and unique karyograms of A. tricolor, A. cruentus, Amaranthus paniculatus L., and A. hypochondriacus were constructed. The analysis of the interspecies genome diversity/similarity in DNA repeat contents, sequences of the identified satDNAs, and chromosome distribution patterns of the studied molecular markers indicated that these species might also share a common evolutionary ancestor. However, the genomes of A. cruentus, A. paniculatus, and A. hypochondriacus were more similar compared to A. tricolor, which aligns with the previous phylogenetic data. Our results demonstrate that cytogenomic studies might provide important data on Amaranthus species relationships elucidating taxonomy and evolution of these valuable crops. Full article

Multiple myeloma (MM) is one of the most common hematological malignancies and remains incurable. However, the survival of multiple myeloma patients has significantly increased due to the implementation of novel therapies along with autologous stem cell transplantation, changing the natural history of the disease. Consequently, there is an unmet need for more sensitive response assessment techniques capable of quantifying minimal tumor burden to identify patients at higher risk of early relapse. Multiparameter flow cytometry (MFC) is an essential tool for diagnosing and monitoring patients with various hematological conditions and has recently gained prominence in identifying, characterizing, and monitoring malignant plasma cells. The implementation of Next-Generation Flow (NGF) by EuroFlow aims to overcome the pitfalls of conventional MFC, including lack of standardization and lower sensitivity, by offering standardized and optimized protocols for evaluating response depth. Both MFC and NGF have wide-ranging applications in MM for diagnosis and measurable residual disease (MRD) monitoring. Plasma cell identification and clonality evaluation through MFC and NGF assist in diagnostic workup and are routinely used to assess therapeutic response through MRD analysis. Additionally, flow cytometry is applied for circulating tumor plasma cell (CTPC) enumeration, which has demonstrated significant prognostic value. Immune composition studies through MFC may provide better understanding of disease biology. Furthermore, MFC provides additional information about other bone marrow cell populations, assessing cellularity, immunophenotypic characteristics of plasma cells, and possible hemodilution. This review explores the applications of MFC and NGF in MM, highlighting their roles in diagnosis, response assessment, and prognosis. Beyond their established use in MRD monitoring, flow cytometry-derived immunophenotypic profiles show strong potential as cost-effective prognostic tools. We advocate for future studies to validate and integrate these markers into risk stratification models, complementing cytogenetic analyses and guiding individualized treatment strategies. Full article

Platinum-based chemotherapy resistance remains a critical barrier in colorectal cancer (CRC) treatment. In this study, cytogenetic karyotyping was combined with transcriptomic profiling (RNA-seq) to elucidate resistance mechanisms by comparing two CRC cell lines: oxaliplatin-sensitive HCT116 and its resistant derivative HCT116 oxpl-R. Karyotyping unveiled tetraploidization and extensive genomic rearrangements in resistant cells, accompanied by prominent transcriptomic changes: 1807 differentially expressed genes (1216 upregulated and 519 downregulated). Pathway enrichment highlighted altered redox homeostasis and metabolic adaptation. Specifically, HCT116 oxpl-R cells exhibited elevated reactive oxygen species (ROS) production and enhanced energy metabolism. These findings establish a direct association between structural genomic alterations, transcriptional rewiring, and functional phenotypes in platinum resistance, providing a framework for targeting metabolic vulnerabilities in refractory CRC. Full article

Psathyrostachys huashanica (2n = 2x = 14, NsNs) and Leymus mollis (2n = 4x = 28, NsNsXmXm) are important wild relatives of common wheat. The Ns chromosomes from two species have been successfully introgressed into wheat through distant hybridization. To compare the genetic effects and evolutionary relationship of Ns chromosomes from different genera in a wheat background, wheat-P. huashanica derivative WH15 and wheat-L. mollis derivative WM14-2 were selected. Sequential FISH-GISH showed that both WH15 and WM14-2 contained 40 wheat chromosomes (with 2D deletion) and two Ns chromosomes with different FISH karyotypes. Molecular markers and SNP array analysis revealed that the two lines both introduced 2Ns chromosomes. However, the P. huashanica 2Ns and L. mollis 2Ns had distinct sequence compositions, and the different SNPs between the two species 2Ns chromosomes were primarily clustered on the short arm. WH15 and WM14-2 exhibited significant differences in spike-related morphologies but shared leaf rust resistance and susceptibility to powdery mildew and Fusarium head blight. Cytogenetic analysis confirmed stable meiotic inheritance of the introduced 2Ns chromosomes. We further developed universal diagnostic markers for 2Ns chromosomes based on SLAF-seq. Therefore, substantial divergence likely exists between the Ns genomes of P. huashanica and L. mollis, and P. huashanica is probably not the direct Ns genome donor for Leymus. Our research-developed derivatives provide unique resources for comparative studies of the structural and functional evolution of homoeologous Ns chromosomes across genera, while offering valuable alleles for wheat improvement. Full article

Woodcreepers (Dendrocolaptinae) constitute a subfamily of Neotropical passerines currently recognized as a monophyletic group within Furnariidae. Although Furnariidae is one of the most diverse avian families in the Neotropics, cytogenetic data remain scarce. In this study, we present the first cytogenetic analysis of Lepidocolaptes falcinellus using conventional (Ag-NOR, C-banding) and molecular (hybridization in situ fluorescence—FISH with telomeric and 18S rDNA probes) approaches. The species exhibits a karyotype with 2n = 80 chromosomes, predominantly acrocentric macrochromosomes, and heterochromatin restricted to centromeric regions. Telomeric repeats were confined to terminal regions, and 18S rDNA sites (NORs) were detected on the short arm of chromosome pair 1. This pattern, also observed in other Dendrocolaptinae species, contrasts with the ancestral avian condition of NORs on microchromosomes, suggesting a derived, lineage-specific chromosomal signature. These results support the cytogenetic cohesion of Dendrocolaptinae and reinforce the potential of NOR localization as a phylogenetic marker within the group. Our findings contribute novel cytotaxonomic data that enhance the understanding of chromosomal evolution and systematics in Furnariidae. Full article

Molar pregnancy (MP) is a gestational disorder resulting from abnormal fertilization, leading to atypical trophoblastic proliferation and the formation of a complete or partial hydatidiform mole. This condition represents the most common form of gestational trophoblastic disease (GTD) and carries a significant risk of progression to gestational trophoblastic neoplasia (GTN). Although rare in high-income countries, MP remains up to ten times more prevalent in low-income and developing countries, contributing to preventable maternal morbidity and mortality. This narrative review provides an updated, practical overview of the clinical presentation, diagnosis, treatment, and follow-up of MP. A key focus is the challenge of early diagnosis, particularly given the increasing frequency of first-trimester detection, where classical histopathological criteria may be subtle, leading to diagnostic errors. The review innovates by integrating advanced diagnostic methods—combining histopathology, immunohistochemistry using p57Kip2, Ki-67, and p53 markers, along with cytogenetic analysis—to improve diagnostic accuracy in early gestation. The central role of referral centers is also emphasized, not only in facilitating timely treatment and access to chemotherapy, but also in implementing standardized post-molar follow-up protocols that reduce progression to GTN and maternal mortality. By focusing on both advanced diagnostic strategies and the organization of care through referral centers, this review offers a comprehensive, practice-oriented perspective to optimize patient outcomes in GTD and address persistent care gaps in high-burden regions. Full article

Nearly four decades have passed since fluorescence in situ hybridisation was first applied in plants to support molecular cytogenetic analyses across a wide range of species. Subsequent advances in DNA sequencing, bioinformatic analysis, and microscopy, together with the immunolocalisation of various nuclear components, have provided unprecedented insights into the cytomolecular organisation of the nuclear genome in both model and non-model plants, with crop species being perhaps the most significant. The ready availability of sequenced genomes is now facilitating the application of state-of-the-art cytomolecular techniques across diverse plant species. However, these same advances in genomics also pose a challenge to the future of plant molecular cytogenetics, as DNA sequence analysis is increasingly perceived as offering comparable insights into genome organisation. This perception persists despite the continued relevance of FISH-based approaches for the physical anchoring of genome assemblies to chromosomes. Furthermore, cytogenetic approaches cannot currently rival purely genomic methods in terms of throughput, standardisation, and automation. This review highlights the latest key topics in plant cytomolecular research, with particular emphasis on chromosome identification and karyotype evolution, chromatin and interphase nuclear organisation, chromosome structure, hybridisation and polyploidy, and cytogenetics-assisted crop improvement. In doing so, it underscores the distinctive contributions that cytogenetic techniques continue to offer in genomic research. Additionally, we critically assess future directions and emerging opportunities in the field, including those related to CRISPR/Cas-based live-cell imaging and chromosome engineering, as well as AI-assisted image analysis and karyotyping. Full article

In B-cell chronic lymphocytic leukemia (B-CLL), hypodiploidy is a rare but aggressive subtype of the disease with a very bad prognosis. Hypodiploidy, in contrast to normal B-CLL chromosomal aberrations, is marked by widespread genomic instability, which promotes treatment resistance and quick illness development. Its persistence after treatment implies that chromosomal loss gives cancerous clones a selection edge, which is made worse by telomere malfunction and epigenetic changes. Since thorough genetic profiling has a major impact on patient outcomes, advanced diagnostic methods are crucial for early detection. Treatment approaches must advance beyond accepted practices because of its resistance to traditional medicines. Hematopoietic stem cell transplantation (HSCT) and chimeric antigen receptor (CAR) T-cell therapy are two potential new therapeutic modalities. Relapse and treatment-related morbidity continue to be limiting concerns, despite the noteworthy improvements in outcomes in high-risk CLL patients receiving HSCT. Although more research is required, CAR T-cell treatment is effective in treating recurrent B-ALL and may also be used to treat B-CLL with hypodiploidy. Novel approaches are essential for enhancing patient outcomes and redefining therapeutic success when hypodiploidy challenges established treatment paradigms. Hypodiploidy is an uncommon yet aggressive form of B-CLL that has a very bad prognosis. Hypodiploidy represents significant chromosomal loss and structural imbalance, which contributes to a disordered genomic environment, in contrast to more prevalent cytogenetic changes. This instability promotes resistance to certain new drugs as well as chemoimmunotherapy and speeds up clonal evolution. Its persistence after treatment implies that hypodiploid clones have benefits in survival, which are probably strengthened by chromosomal segregation issues and damaged DNA repair pathways. Malignant progression and treatment failure are further exacerbated by telomere erosion and epigenetic dysregulation. The need for more sensitive molecular diagnostics is highlighted by the fact that standard karyotyping frequently overlooks hypodiploid clones, particularly those concealed by endoreduplication, despite the fact that these complications make early and correct diagnosis crucial. Hypodiploidy requires a move toward individualized treatment because of their link to high-risk genetic traits and resistance to conventional regimens. Although treatments like hematopoietic stem cell transplantation and CAR T-cells show promise, long-term management is still elusive. To improve long-term results and avoid early relapse, addressing this cytogenetic population necessitates combining high-resolution genomic technologies with changing therapy approaches. Full article

The wolf fish Hoplias malabaricus is a Neotropical species characterized by remarkable karyotypic diversity, including seven karyomorphs (KarA-G) with distinct sex chromosome systems. This study investigated the homologous XY (KarF) and XY₁Y₂ (KarG) sex chromosome systems present in this species by integrating cytogenetics and genomics to examine sex chromosomes’ composition through characterization of repeatome (satellite DNA and transposable elements) and sex-linked markers. Our analysis indicated that both karyomorphs are little differentiated in their sex chromosomes content revealed by satDNA mapping and putative sex-linked markers. Both repeatomes were mostly composed of transposable elements, but neither intra- (male versus female) nor interspecific (KarF x KarG) variations were found. In both systems, we demonstrated the occurrence of sex-specific sequences probably located on the non-recombining region of the Y chromosome supported by the accumulation of sex-specific haplotypes of HmfSat10-28/HmgSat31-28. This investigation offered valuable insights by highlighting the composition of homologous XY and XY₁Y₂ multiple sex chromosomes. Although homologous, the large Y chromosome in KarF corresponds to two separate linkage groups (Y₁ and Y₂) in KarG implying a specific meiotic arrangement involving the X chromosome in a meiotic trivalent chain. This scenario likely influenced recombination rates and, as a result, the genomic composition of these chromosomes. Full article

Plant tissue culture has been recognized as an essential technology in plant science research. This process is widely used to regenerate and conserve phenotypically and genetically identical plant resources. The advancements in tissue culture methods have become a feasible option for the micropropagation of plants at the commercial level. The success of commercial micropropagation necessitates genetic stability among regenerated plants. Sometimes, in vitro-grown plants show genetic and epigenetic alterations due to stressful artificial culture conditions, media compositions, and explant types. As a result, it is essential to ensure genetic stability among tissue culture-derived plantlets at a very early stage. Somaclonal variations can be detected by phenotypic assessment, cytogenetic, DNA-based molecular markers, bisulfite sequencing, and RNA sequencing. This review aims to describe the causes behind somaclonal variation, the selection of somaclonal variants, and their uses in crop and plant improvement at the commercial level. This study discusses the optimization processes of undesirable genetic and epigenetic variation among micropropagated plants and their application in global horticulture, agriculture, and forestry. Full article

Expanding genetic variability of cultivated cotton (Gossypium hirsutum) is essential for improving fiber quality and pest resistance. This study synthesized allotetraploids through interspecific hybridization between G. herbaceum (A₁) and G. nelsonii (G₃). Upon chromosome doubling using 0.2% colchicine, fertile F₁C allotetraploids (A₁A₁G₃G₃) were developed. Cytogenetic analysis confirmed chromosome stability of synthetic allotetraploids, and 74 polymorphic SSR markers verified hybridity and parental contributions. The F₁C hybrids exhibited enhanced resistance to cotton aphids (Aphis gossypii) and whiteflies (Aleyrodidae), with respective infestation rates of 5.2–5.6% and 5.4–5.8%, lower than those of G. hirsutum cv. Ravnak-1 (22.1% and 23.9%). Superior fiber length (25.0–26.0 mm) was observed in complex hybrids and backcross progeny, confirming the potential for trait introgression into elite cultivars. Phylogenetic analysis based on SSR data clearly differentiated G. herbaceum from Australian wild species, demonstrating successful bridging of divergent genomes. The F₁C hybrids consistently expressed dominant G. nelsonii-derived traits regardless of the hybridization direction and clustered phylogenetically closer to the wild parent. These synthetic allotetraploids could broaden the genetic base of G. hirsutum, addressing cultivation constraints through improved biotic stress resilience and fiber quality traits. The study establishes a robust framework for utilizing wild Gossypium species to overcome genetic bottlenecks in conventional cotton breeding programs. Full article

Diffuse large B-cell lymphoma (DLBCL), recognized as the most prevalent variant of adult non-Hodgkin lymphoma, presents considerable challenges in diagnosis owing to its diverse morphological features and frequent extranodal involvement, which may frequently mimic nonhematopoietic neoplasms. The 2022 WHO Classification of Lymphoid and Hematopoietic Tissues provides essential updates, highlighting the necessity of combining morphology, immunohistochemistry, cytogenetics, and molecular testing for precise subclassification. This review presents a practical method for differentiating DLBCL from other aggressive B-cell neoplasms, such as Burkitt lymphoma, B-lymphoblastic lymphoma, and mantle cell lymphoma. It highlights vital diagnostic tools, including CD45, B/T-cell markers, germinal center markers, and the Hans algorithm, as well as the role of FISH in identifying rearrangements of key genes MYC, BCL2, and BCL6, which are significant for recognizing double-hit and triple-hit lymphomas. Special focus is given to EBV-associated DLBCL and uncommon subtypes featuring plasmablastic or ALK-positive traits. This review aims to enhance diagnostic accuracy and ensure appropriate treatment strategies for patients with large B-cell lymphomas by emphasizing thorough morphological evaluation, specific adjunct testing, and adherence to the most recent classification standards. Full article

Acute myeloid leukemia (AML) with RUNX1::RUNX1T1 fusion is well known to often demonstrate aberrant upregulation of CD19 expression. We studied the clinicopathologic and genetic features of 16 cases of AML with various RUNX1 lesions, including mutations, copy number gains, and translocations other than fusions with RUNX1T1. Most of these cases were classified as AML-myelodysplasia-related or AML-post-cytotoxic therapy based on the cytogenetic and molecular work-up. These neoplasms showed partial expression of one or more B-cell antigens by flow cytometry and/or immunohistochemistry, fulfilling the criteria for mixed-phenotype acute leukemia (MPAL)-B/myeloid (i.e., ≥20% blasts expressing B and myeloid lineage antigens) in most cases. These findings suggest that AML cases with RUNX1 lesions including mutations, copy number gains, and translocations other than RUNX1T1 fusion, also commonly express B-cell markers, imparting a “mixed-lineage-like” immunophenotype in cases of AML that otherwise fulfill the criteria for other defined subtypes. We present these cases as to caution regarding this potential diagnostic pitfall and favor a diagnosis of AML with RUNX1 lesion(s) in the setting of a case of AML with myeloid/B-cell antigen expression, a history of myelodysplasia or cytotoxic therapy, the demonstration of pDC differentiation by flow cytometry (generally associated with the presence of a RUNX1 mutation), and the presence of a RUNX1 lesion (mutation, copy number gain, and/or translocation exclusive of a rearrangement with RUNX1T1). Full article

Background: Treatment of multiple myeloma has advanced tremendously with the approval of anti-CD38 antibodies. Their efficacy is impressive but still controversial in the 1q amplification subgroup (amp1q). This retrospective study aims to provide real-world data. Methods: This trial is analyzing 74 patients with relapsed/refractory multiple myeloma treated with CD38Abs at the Medical University of Innsbruck (2016–2023). High-risk (HR) cytogenetics according to R-ISS (t(4;14), t(14;16), t(14;20), del(17p)), the presence of amp(1q21), the frequency of two HR markers (double hit), and the high-risk criteria agreed at IMS 2024 (HR-IMS24) were considered. Results: The median age of the 74 patients (62.1% male) was 62 years, with a median follow-up of six years. Most patients received third-line therapy (37.8%). R-ISS HR was documented in 39.2% of patients, double hit in 13.5% of patients, and HR-IMS24 in 32.4% of patients, while amp1q was detected in 35.1% of patients. The median OS was 66 months (35–89), and the median PFS was 17 months (6.5–26.9). While neither R-ISS HR nor isolated amp1q had an impact on progression-free survival (e.g., amp1q 7.03: 1.95–22.44; p = 0.347), the occurrence of a double-hit pattern significantly impaired PFS and OS (6.2: 1.4–16.4 months; p = 0.044; OS, 42.8: 25.9–74.6 months; p = 0.035). Patients fulfilling the HR-IMS24 criteria (32.4%, 24 patients) also exhibited an impaired PFS and OS (7: 2.7–18.1 months, p = 0.023; 40.12: 21.1–74.5 months, p = 0.01). Conclusions: This retrospective study highlights the durable effect of daratumumab on cytogenetic abnormalities, particularly amp1q. However, patients who meet the criteria for double-hit myeloma or the high-risk IMS2024 criteria remain a difficult-to-treat patient population who require early access to new treatment approaches. Full article

In this study, we sampled malaria mosquito larvae in natural and artificial breeding places to study the geographical distribution, ecological preferences, and chromosomal variability of different species of the genus Anopheles in the territory of the Crimean Peninsula and the Black Sea coast of the Caucasus. Species were diagnosed using a combination of morphological, cytogenetic, and molecular markers. The ecological conditions of the larval habitats, such as dissolved oxygen content in the water, acidity, salinity, and temperature, were measured. Seven species of malaria mosquitoes were identified in the pool of 2229 individual mosquitoes collected at 56 breeding sites, including An. atroparvus, An. claviger, An. daciae (formerly identified as An. messeae s. l.), An. hyrcanus, An. maculipennis s. s., An. plumbeus, and An. melanoon. The previously recorded species of An. algeriensis, An. messeae s. s., An. sacharovi, and An. superpictus were not found in this study. Anopheles maculipennis was dominant in typical anophylogenic water bodies. Anopheles plumbeus, which used to breed mainly in tree holes in coastal forests, has spread to urban settlements along the Black Sea coast and breeds in artificial containers. Chromosomal polymorphism was studied and found in An. atroparvus and An. daciae populations. Differences in the chromosomal composition of An. daciae populations in Crimea and on the Black Sea coast of the Caucasus were revealed. The Crimean population had a low level of polymorphism in autosomal inversions. The data obtained in this study can be used to inform a better control of potential malaria vectors in the Black Sea coastal region. Full article