Cytogenetic and Genome Research最新文献

Introduction MECOM rearrangements are frequently observed in myeloid neoplasms and associated with poor prognosis. Among the genomic alterations leading to MECOM rearrangements, t(2;3)(p13~p25;q26.2) accounts for approximately 13% of reported cases. However, the precise DNA breakpoints of this translocation have not been previously reported, nor has the mechanism by which it alters MECOM expression been fully elucidated. In this report, we describe two cases with myelodysplastic syndromes (MDS) and t(2;3)(p23;q26.2). Our genomic characterization of these two t(2;3) translocations provided insights into the molecular mechanism of MECOM activation. Case Presentation Case 1 is a 44-year-old female presented with new anemia and thrombocytopenia. She was treated with azacitidine. After two allogeneic stem cell transplants, her disease relapsed with rapid progression to acute myeloid leukemia (AML). Patient passed away one year after progression to AML and eight years after initial diagnosis. Case 2 is a 75-year-old female who was incidentally found to have macrocytic anemia with rare circulating blasts. She remained asymptomatic from anemia and did not require transfusions or treatment. Her disease progressed to MDS with excess blasts three years later. Patient was treated with azacitidine. Fifteen months later, her disease further progressed to AML. She passed away five months later and four and a half years after initial diagnosis. DNA sequencing analysis of these two cases revealed that the t(2;3)(p23;q26.2) breakpoints were within the regulatory regions of ZFP36L2 and THADA on chromosome 2 and the proximity of MECOM on chromosome 3, creating a novel regulatory configuration for MECOM. Notably, the translocation breakpoints differed by 270 kb on chromosome 2 and 93 kb on chromosome 3, resulting in distinct translocated regulatory elements with varying sizes and proximities to MECOM. These structural differences may influence the level of MECOM upregulation and contribute to variation in disease severity and progression. Conclusion Our findings highlighted that, despite cytogenetic similarity, different t(2;3) translocations may exert distinct regulatory effects depending on the precise breakpoint locations. Thus, molecular characterization of MECOM rearrangements is critical for understanding disease pathogenesis and prognosis in myeloid neoplasms and may lead to the development of novel treatment.

IIntroduction Radioiodine (131I) is commonly used for the treatment of hyperthyroidism and for differentiated thyroid cancer (DTC) as an ablative therapy. Radioiodine (131I) constitutes almost 90% of the therapies that are currently performed in the nuclear medicine field. In this study, retrospective cytogenetic follow up analysis was performed after 29 years (2023) and 30 years (2024) in a papillary thyroid cancer patient who received the second round of 131I treatment in 1994. Methods Metaphase chromosomes prepared from the in vitro culture of peripheral blood lymphocytes of the patient were utilized for the analysis of unstable (dicentrics and fragments) and stable chromosome aberrations (simple, complex and clonal). For dicentric chromosome detection, fluorescence in situ hybridization FISH) was performed using human centromere and telomere specific peptide nucleic acid probes. Chromosome translocations were detected by a cocktail of DNA probes for individual chromosomes (1, 2 and 4) and multicolor FISH probe for the entire human genome. Micronuclei were analyzed by cytokinesis block micronucleus assay. Absorbed radiation dose was estimated at 95% confidence intervals from the frequencies of chromosome aberrations (dicentric chromosomes and translocations) using correlation coefficients of the γ-rays dose response curve using the DoseEstimate_v5.1 algorithm. Results The percentage of cells with stable and unstable chromosome aberrations remained the same (~8%) in the patient during the entire retrospective study albeit variations in the frequencies of reciprocal and non-reciprocal translocations. The frequency of color junctions (chromosome exchange events) detected by the multicolor FISH technique showed a sharp increase in this study (0.33/cell) compared to our earlier study (0.19/cell). The persistence of clonal translocation involving chromosomes 14;15 was observed in 1-1.6% of the total cells analyzed. In the 29-year follow up study, one complex translocation involving chromosomes 1, 9 and 14 was detected by mFISH in a total of 200 cells. Discussion Our findings indicate that the past internal therapeutic exposure of radioiodine results in long-lasting chromosomal damage and the retrospective study of this nature will be useful for monitoring the progression of any oncogenic events driven by chromosomal instability in the hematopoietic system of 131I therapy patients.

Introduction: Robertsonian translocations (ROBs) or centric fusions of acrocentric chromosomes are the most common structural chromosomal rearrangements in mammals. ROBs are of medical and veterinary concern because of associated subfertility and congenital disorders but are also of interest as a mechanism of chromosome and karyotype evolution. While ROBs are well documented in humans, mice, and cattle/bovids, they are extremely rare in horses, despite the 18 acrocentric chromosomes in the horse karyotype.

Methods: We characterize the case using conventional and molecular cytogenetic approaches and DNA analysis.

Results: We report the first case of ROB between nonhomologous chromosomes in the horse, whereas the carrier was 50/50 mosaic for two different ROB cell lines - 63,XX,rob(17;27) and 63,XX,rob(17;29) and had no cells with normal karyotype. Both derivative ROB chromosomes had retained two structural centromeres which is also a typical feature of human and bovine ROBs. The clinical phenotype of the mare included small ovaries, irregular estrus, and two pregnancy losses - all consistent with ROB.

Discussion: We discuss the role of centromeric satellite sequences in the formation of ROBs but also differences in the prevalence of ROBs in different species, regardless of the number of acrocentric chromosomes. In this context, further molecular studies of the presented case may provide additional clues about the features of centromeric satellite repeats that facilitate or prevent ROBs in general.

Introduction: In birds, males have the homogametic sex chromosomes ZZ, whereas females have the heterogametic ZW. Similar to mammalians, avian Z and W chromosomes are believed to have originated from a pair of autosomes. Over evolutionary time, the W chromosome degenerated, losing many genes. The remaining W-linked genes retain homologs on the Z chromosome. One such gene is UBAP2, which participates in cellular metabolism and signaling through the ubiquitin-proteasome pathway in mammals. However, the functions of its avian homologs, UBAP2Z (Z-linked) and UBAP2W (W-linked), remain poorly understood. To investigate the functional divergence between them in birds, we analyzed their mRNA and protein expression in embryonic gonads of Japanese quail.

Methods: Using RNA-seq data of embryonic gonads of Japanese quail, contigs were generated by de novo assembly. The nucleotide sequences were predicted from the contigs by blastn analysis. Expression levels were calculated by bowtie2 and RSEM. Immunohistochemistry and Western blotting employing monoclonal antibodies specific to UBAP2Z and UBAP2W were generated to investigate protein expression and localization. Additionally, far-Western blotting was performed to examine protein-protein interactions.

Results: UBAP2Z and UBAP2W nucleotide and amino acid sequences showed high similarity and shared a conserved N-terminal UBA domain. However, UBAP2W expression was consistently lower than that of UBAP2Z and showed a distinct localization pattern from UBAP2Z in embryonic gonads. In males, UBAP2Z was expressed in seminiferous tubules, while in females, it localized to the medulla. By contrast, UBAP2W was exclusively observed in the cortex of female gonads, particularly at developmental stage HH38. Furthermore, UBAP2Z and UBAP2W interacted with different binding partners, indicating divergence in their molecular function.

Conclusion: These findings indicate that UBAP2W has a distinct female-specific functional role in avian gonadal differentiation. We propose that UBAP2W contributes to ovarian development and oogenesis through the ubiquitin-proteasome pathway, while UBAP2Z is involved in general cellular regulation across sexes. This study highlights functional divergence between Z- and W-linked paralogs in birds and provides new insights into sex chromosome evolution and gonadal development.

Background: Chromosomal microarray analysis (CMA) is a first-tier diagnostic test for children with unexplained developmental and/or congenital anomalies. This study aimed to evaluate the diagnostic contribution of CMA in a large, phenotypically diverse Turkish pediatric cohort.

Methods: CMA was performed in 1,022 children presenting with developmental delay, intellectual disability, autism spectrum disorder, epilepsy, and/or congenital anomalies. Copy number variants (CNVs) were classified as pathogenic, likely pathogenic, or variants of uncertain significance based on American College of Medical Genetics guidelines.

Results: CNVs were identified in 279 patients (27.3%), totaling 315 CNVs. Of these, 151 patients (14.8%) carried at least one pathogenic or likely pathogenic CNV, representing the diagnostic yield of the study. CNVs were more frequently classified as pathogenic when presenting as deletions. The diagnostic rate was higher among patients with syndromic features (20.2%) compared to those with isolated developmental delay/intellectual disability (11.8%). Among patients with CNVs, 139 (49.8%) exhibited phenotypes consistent with well-characterized genomic syndromes. In addition, rare but clinically significant CNVs were also identified, involving well-established dosage-sensitive genes. Notably, chromosomes X, 15, and 16 were among the most frequently affected, reflecting known genomic hotspots associated with neurodevelopmental and structural phenotypes.

Conclusion: CMA is a powerful diagnostic tool in the evaluation of pediatric patients with neurodevelopmental and structural disorders. This study emphasizes the added value of high-resolution CNV detection and careful clinical phenotyping to optimize diagnostic yield and guide precision care in clinically heterogeneous pediatric populations.

Introduction: Reproductive failure has been associated with various chromosomal abnormalities, including small supernumerary marker chromosomes (sSMCs). In rare cases, uniparental disomy (UPD) may also contribute to reproductive problems, particularly when involving imprinted regions or in cases of isodisomy where autosomal recessive disorders may manifest. UPD involving chromosome 1 (UPD1) is rare and has not been linked to a consistent phenotype.

Case presentation: We present a 27-year-old woman with a 5-year history of reproductive difficulty, including one biochemical pregnancy loss and one clinically recognized miscarriage at 8 weeks of gestation. Cytogenetic analysis revealed mosaicism for a small sSMC derived from chromosome 1. SNP microarray identified complete UPD1 without copy number changes. Fluorescence in situ hybridization (FISH) confirmed centromeric material of chromosome 1 in the marker chromosome.

Conclusion: To the best of our knowledge, this is the first reported case combining mosaic sSMC(1) and complete UPD1 in a phenotypically healthy woman with reproductive failure. The coexistence of these abnormalities likely reflects a postzygotic chromosomal rescue mechanism. These findings underscore the diagnostic value of integrated cytogenomic analyses in unexplained reproductive failure and subfertility.

Background: Structural variants (SVs) are defined as genomic variants affecting more than 50 base pairs. They include deletions, insertions, inversions, translocations, tandem repeats, and copy number variations. These SVs contribute significantly to genetic complexity and are involved in human evolution, genetic disorders, and cancer. Over 50% of the SVs cannot be detected due to limitations in methods and technologies. The short-read sequencing technologies (SRSs) are limited in detecting single-nucleotide variants and have limited usage for analysis of complex genomic loci, repeat regions, and phasing.

Summary: The advent of long-read sequencing (LRS) technologies, such as Oxford Nanopore and PacBio, has revolutionized SV detection. These platforms enable the accurate characterization of diverse variant types, ranging from simple deletions to complex chromothripsis events, and support de novo assembly, haplotype phasing, and the resolution of repetitive or structurally complex genomic regions. One major outcome is the completion of the telomere-to-telomere human reference genome. This review summarizes recent advances in LRS for SV detection, including sequencing platforms, bioinformatic tools, data analysis, and validation strategies. The clinical applications, particularly in the diagnosis of rare diseases, are illustrated with two cases that were successfully resolved using both LRS approaches.

Key message: LRS can overcome the limitations of SRS in SV detection, providing more accurate insights into genome disorders. It enables the detection of repeat and difficult-to-resolve regions of the genome and facilitates clinical diagnoses to base-level breakpoint detection. Despite challenges such as high cost, data interpretation, and clinical linking, continued advancements are elevating LRS as an invaluable tool in precision genomic medicine.

Introduction: Induced pluripotent stem (iPS) cells share key features with embryonic stem (ES) cells, including similar limitations such as the accumulation of (epi)genetic and genomic alterations. However, sex chromosome instability in mouse iPS cells remains poorly understood. This retrospective study aimed to investigate this phenomenon by analyzing mouse iPS cell clones. Specifically, we examined whether factors such as passage number, cell sex, founder cell type, or reprogramming method influence the presence or absence of sex chromosome abnormalities.

Methods: Sex chromosome stability was evaluated in 26 independent male and female mouse iPS cell clones using standard karyotyping techniques. Additionally, we analyzed an artificially generated XXY iPS cell model, in which an extra X chromosome was introduced into a normal XY cell line. Statistical analyses were conducted on the karyotyping results and correlated with both continuous variables (e.g., passage number) and categorical variables (e.g., cell sex, founder cell type, and reprogramming method).

Results: Female iPS cell clones displayed significantly higher levels of sex chromosome instability compared to their male counterparts, regardless of the founder cell type or reprogramming strategy. A similar pattern of X chromosome instability was also observed in the XXY iPS cell model.

Conclusion: Our findings demonstrate that sex chromosome instability occurs in mouse iPS cells, as previously reported in mouse ES cells, suggesting a conserved phenomenon across pluripotent stem cell types. Importantly, the presence of multiple X chromosomes in the pluripotent state appears to contribute to this instability. Further studies are required to elucidate the underlying molecular mechanisms.

Introduction: The influence of X/Y-autosomal translocations on reproductive competence is determined by both the cytogenetic positioning of translocation breakpoints and the potential disruption of critical genomic regions essential for reproductive physiology, particularly gene-dense Y-chromosomal segments or X-chromosome loci associated with ovarian folliculogenesis. This investigation examined 4 cases of cytogenetically balanced X/Y-autosomal translocations through the single-nucleotide polymorphism (SNP) and preimplantation genetic testing for structural rearrangements (SNP-based PGT-SR), enabling concurrent assessment of embryonic chromosomal integrity and precise differentiation between euploid embryos and balanced translocation carriers.

Cases presentation: Cases 1-2 exhibited Y-autosomal translocations with breakpoints localized to the azoospermia factor critical region, while cases 3-4 demonstrated X-autosomal translocations where breakpoints mapped outside ovarian functional domains (Xq13-q28). Embryo selection utilizing SNP-based PGT-SR achieved clinical transfer of euploid embryos lacking the parental translocation in cases 2 and 4. Case 3, following multidisciplinary counseling, opted for transfer of a balanced translocation carrier euploid embryo with conserved genomic architecture. Prenatal diagnostic evaluations demonstrated complete concordance with PGT-SR outcomes.

Conclusion: The impact of chromosomal translocation on reproduction is contingent upon whether the breakpoint location influences critical functional regions. SNP-based PGT-SR can accurately determine the genetic status of embryos exhibiting balanced X/Y-autosomal translocations by systematically evaluating the integrity of the embryo's genetic material. This approach enhances detection accuracy and mitigates the risk of transmitting the translocation to subsequent generations.