Cytogenetic and Genome Research最新文献

Introduction: Radiotherapy outcome is governed by radiosensitivity and DNA repair capacity of tumour cells and their interaction with surrounding normal tissues and vice versa. As radiosensitivity varies with the origin and genetic makeup of the cell, this study compares direct and bystander responses in directly targeted to X-rays and non-targeted (bystander) tumour (MCF-7 and PC3) and normal (MCF10A and HPrEC) epithelial cells of breast and prostate origin.

Methods: Cells were exposed to X-rays (0, 2, and 4 Gy) by a clinical LINAC and co-cultured with corresponding un-irradiated cells. Micronucleus (MN) and clonogenic assays were adopted to quantify the DNA damage and survival fraction (SF), respectively, in all cells and Multicolour fluorescence in situ hybridization (m-FISH) in MCF-7 and PC3 cells to identify the chromosomes frequently involved in translocations.

Results: Directly targeted tumour and normal cells showed a significant increase in MN frequency and decrease in SF. MN frequency increased from 0.023 ± 0.004 (control) to 0.076 ± 0.008 (2 Gy), and 0.177 ± 0.013 (4 Gy) in MCF-7 cells. MCF10A showed MN frequency of 0.049 ± 0.007 (control), 0.128 ± 0.011 (2 Gy) and 0.219 ± 0.014 (4 Gy). SF was significantly higher in MCF-7 (0.39 ± 0.03 and 0.15 ± 0.02) cells than MCF10A (0.30 ± 0.02 and 0.12 ± 0.01). MN frequency in PC3 cells increased from 0.056 ± 0.007 (control) to 0.168 ± 0.012 (2 Gy) and 0.378 ± 0.019 (4 Gy). HPrEC exhibited MN frequency of 0.018 ± 0.004 (control), 0.058 ± 0.007 (2 Gy), and 0.147 ± 0.012 (4 Gy). SF was higher in HPrEC (0.72 ± 0.03 and 0.40 ± 0.02) cells than PC3 (0.22 ± 0.01 and 0.09 ± 0.004). Similarly, a significant increase in MN frequency was observed in the non-targeted cells when compared to that of control, confirming occurrence of radiation-induced bystander effect. Thus, the results indicate radiation sensitivity differs among the cell types. The m-FISH results reveal a non-random distribution of X-irradiation induced breaks and translocation. In directly targeted cells, chromosomes 7, 16, 17, 20, 21, 22 (MCF-7) and 3, 4, 6, 14, 17 (PC3) showed frequent involvement in translocations. Chromosomes 3, 4, 6, and 14 (MCF-7) and 10, 11, 17, and 18 (PC3) were frequently involved in non-targeted cells.

Conclusion: The present study results indicate that the tumour cells demonstrated higher radiosensitivity and a stronger bystander response than normal cells. Intrinsic molecular factors and genome organization affect both targeted and non-targeted responses, emphasizing their relevance for optimizing radiotherapy strategies.

Introduction: Cytogenetic findings are critical for determining prognosis, therapy and risk assessment in acute lymphoblastic leukaemia (ALL). Data on the epidemiology of cytogenetic findings in ALL from southern Asia is limited. This report documents the cytogenetic changes in ALL seen at a referral hospital in southern India and compares it with the literature.

Methods: Clinical profiling and conventional cytogenetic analysis (CCA) of all patients with reverse-transcription polymerase chain reaction (RT-PCR) for detection of cryptic t(12;21).

Results: Of 1968 ALL, 1,819 (92.4%) patients, age 0.3-84 years, (median 17) had successful CCA. There were 979 children (<18 years) and 840 adults. Abnormal karyotypes were found in 1368 (75.2%), B-ALL-78% and T-ALL-69%. Favorable-risk group included high hyperdiploidy (HeH, 17.4%), t(12;21) (9.8%), and t(1;19) (4.3%), with > 80% of HeH and t(12;21) in children. The unfavorable-risk group included t(9;22) (11.2%, 80% adults), hypodiploidy (8.0%), MYC (8q24) translocations (2.3%), and KMT2A/MLL(11q23) translocations (1.6%). In children, the frequency of HeH (26.8%) was lower than the West (30.7%) but higher than S.E. Asia (15.5%) while t(9;22) (4.2%) was higher than the West (2%) but lower than S.E. Asia (6.8%). In adults, frequencies again differed from S.E. Asia (HeH, 6.4% vs. 2.7% and t(9;22), 19.4% vs. 29.3%) but were comparable to the West.

Conclusion: CCA effectively provides diagnostic information in over 90% of ALL cases. While the spectrum of cytogenetic changes is similar to global data, there are significant regional variations in the frequencies of specific abnormalities.

Introduction: Homoeologous chromosomes within the grass tribe Triticeae have largely retained their cross-species colinearity. However, prior studies suggest that the karyotype of Aegilops uniaristata, a diploid wild relative of wheat (genome NN, 2n=2x=14), is noticeably different from most of the Triticeae species.

Methods: We used fluorescence in situ hybridization with a large collection of probes hybridizing to repetitive and coding regions of the Triticeae genomes to perform comparative cytogenetic analysis and establish the macrostructure of Ae. uniaristata chromosomes.

Results: Compared to wheat, all chromosomes of Ae. uniaristata, with the exception of 5N, were found significantly rearranged due to multiple inter- and intrachromosomal translocations and inversions. Discussion/ Conclusion: The N genome structure revealed in our study is useful for understanding karyotype evolution and facilitating introgression from Ae. uniaristata and the N genome of polyploid Aegilops species for wheat improvement.

Background: Genomic imprinting is a well-known phenomenon in which certain genes are expressed in a sex-of-the-parent-specific manner, resulting in mono-allelic expression.

Summary: Over the years, the diversity of mechanisms observed in imprinted gene clusters has provided a valuable model system for exploring the complexities of epigenetics, which can be extended to other cellular and disease models. This review examines these different mechanisms throughout early embryonic development and offers insights into the interactions among key players such as DNA methylation, histone modifications, and non-coding RNAs, as well as their regulatory impact on gene expression.

Key message: Genomic imprinting, although being a classical genetic concept, has emerged as a model system for understanding diverse epigenetic regulatory mechanisms. This review offers an overview of such regulatory mechanisms that have been learnt over the years through studies on imprinted clusters.

Background: The damselfishes, an extremely diverse group of herbivorous fish, stands out as an important and ubiquitous ecological component of coral reefs. In the Western South Atlantic, the genus Stegastes is the most representative, whose evolutionary paths and taxonomic status of insular endemic species have been better evaluated. To clarify the karyotypic evolution involved in the diversification of this group, cytogenetic analyses were performed in four nominal species (Stegastes variabilis and Stegastes fuscus, distributed in Brazilian coastal regions; Stegastes rocasensis and Stegastes sanctipauli, from Rocas Atoll and São Paulo and São Pedro Archipelago) and one subspecies (S. fuscus trindadensis, from Trindade and Martim Vaz Archipelago).

Results: Classical cytogenetic protocols and fluorescence in situ hybridization (FISH) with 18S and 5S rDNA probes were used for comparative analyses. All species had 2n = 48 chromosomes, with high FN values ranging from 88 to 92. Stegastes rocasensis and S. sanctipauli shared identical cytogenetic patterns, while S. f. trindadensis revealed a syntenic arrangement of 18S and 5S rDNA sites not found in S. fuscus from the Brazilian coast.

Conclusion: The karyotypic evolution of Stegastes was predominantly driven by multiple pericentric inversions (and/or centromere shifts), resulting in changes in the internal organization of chromosomes. S. rocasensis and S. sanctipauli have similar cytogenetical patterns, as well as S. fuscus and S. f. trindadensis indicating incipient evolutionary differentiation in insular species. Mapping other repetitive DNA sequences provided an exceptional opportunity to clarify chromosomal changes and their association with the evolutionary diversification of Stegastes species.

Introduction: Sex chromosomes often evolve through suppressed recombination and accumulation of transposable elements (TEs) on the sex-limited chromosome, leading to divergence and eventual degeneration. The clam shrimp Eulimnadia texana possesses proto-sex chromosomes (Z and W) at an early evolutionary stage, providing a unique opportunity to examine the initial genomic changes underlying sex chromosome differentiation. Additionally, both sex chromosomes are expressed in homogametic ZZ and WW shrimp, allowing a regular expression of both sex chromosomes in homozygotes.

Methods: We analyzed newly assembled ZZ (male) and previously published WW (hermaphrodite) genomes of E. texana. Sex-linked markers were mapped to identify the Z chromosome. TEs were annotated using a species-specific repeat library and RepeatMasker. The Z and W chromosomes were divided into bins and randomization tests compared TE accumulation between the sex chromosomes as well as between corresponding regions within these two chromosomes; the latter was focused on the putative sex-determining regions of both the Z and W. Kimura distance-based analyses were used to estimate TE age divergence.

Results: The Z chromosome showed no significant TE enrichment relative to autosomes but was enriched for DNA transposons. The W chromosome exhibited significantly higher retrotransposon (LTR and LINE) accumulation. Only the sex-determining region of the W showed significantly elevated retrotransposon content compared to the Z. TE age landscapes indicated recent bursts of retrotransposon activity on the W.

Conclusion: These findings support theoretical predictions that retrotransposons accumulate in non-recombining regions, while DNA transposons are associated with recombining chromosomes. The W chromosome of E. texana shows early signs of differentiation, with localized retrotransposon buildup, while the Z remains autosome-like. This study highlights E. texana as a valuable model for understanding the genomic mechanisms of early sex chromosome evolution.

Introduction: DMRT1 on the Z chromosome is a conserved male sex-determining gene in birds. In chickens, a representative model species of Neognathae, the function of DMRT1 has been well characterized. In contrast, Palaeognathae species such as the emu possess less differentiated sex chromosomes and thus provide a valuable system for investigating avian sex determination, yet molecular studies remain limited. We investigated the timing of sex determination and the expression of key genes involved in gonadal differentiation in emu and further characterized DMRT1 variants.

Methods: Sex determination stage was identified by anatomical comparison of male and female embryonic gonads. Expression of seven genes (DMRT1, AMH, SOX9, NR5A1, FOXL2, CYP19A1, and RSPO1) was examined by mRNA-seq and RT-PCR. DMRT1 splicing variants were predicted by in silico analysis and 3' RACE was used to identify alternative polyadenylation (APA) variants.

Results: The gonadal differentiation occurred at HH25-28 based on gonadal morphology. Gene expression analysis revealed emu-specific patterns not observed in chickens. Notably, RSPO1 was highly expressed in females at HH24-25, preceding DMRT1 expression in males at HH28-29, suggesting ovarian differentiation begins earlier. We identified three splicing variants and four APA variants of DMRT1, with variant 1 predominant during gonadal development.

Conclusion: These findings suggest that while molecular sex differentiation mechanisms are largely conserved between Palaeognathae and Neognathae, they differ in parts. In particular, early RSPO1 expression may initiate ovarian differentiation prior to testis determination by DMRT1. The presence of emu-specific DMRT1 variants further indicates possible species-specific mechanisms in testis development.

Introduction: The domestic guinea pig (Cavia porcellus, Caviidae) is an important laboratory species, model for human medical research, worldwide spread pet and a source of food in specific parts of South America. Data on chromosomal abnormalities in guinea pigs are really limited, probably due to the complexity of their karyotype (2n = 64).

Methods: G- and C-banding and fluorescence in situ hybridization (FISH) using human chromosome-specific painting probes were used to analyze the karyotype and identify chromosomes involved in a newly discovered Robertsonian translocation.

Results: Karyotype 63,XY,rob(13;19) was revealed in a phenotypically normal, fertile domestic guinea pig male. The chromosomes involved in the fusion were verified using FISH with human whole chromosome probes and known guinea pig - human chromosome synteny.

Conclusion: This finding adds to the limited cytogenetic data available on the guinea pig, and provides a basis for further investigation of their chromosomal variation and its biological significance. Our results indicate the need for chromosome studies in this cytogenetically mostly neglected species, especially in breeding populations used for biomedical research.

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.