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16 pages, 1985 KB  
Article
Contrasting Satellitomes in New World and African Trogons (Aves, Trogoniformes)
by Luciano Cesar Pozzobon, Jhon Alex Dziechciarz Vidal, Felipe Lagreca Bitencour, Analía Del Valle Garnero, Ricardo José Gunski, Hélio Gomes da Silva Filho, Fabio Porto-Foresti, Ricardo Utsunomia, Marcelo de Bello Cioffi, Thales Renato Ochotorena de Freitas and Rafael Kretschmer
Genes 2025, 16(11), 1301; https://doi.org/10.3390/genes16111301 (registering DOI) - 1 Nov 2025
Abstract
Background/Objectives: Satellite DNAs (satDNAs) are tandemly repeated sequences that play essential roles in chromosome structure, genome organization, and evolution. Despite their importance, the satellitome (the complete collection of satDNAs) of most avian lineages remains unexplored. We sought to describe the repeatome of three [...] Read more.
Background/Objectives: Satellite DNAs (satDNAs) are tandemly repeated sequences that play essential roles in chromosome structure, genome organization, and evolution. Despite their importance, the satellitome (the complete collection of satDNAs) of most avian lineages remains unexplored. We sought to describe the repeatome of three trogonid species, Trogon surrucura, T. melanurus, and Apaloderma vittatum with a focus on the satellitome to evaluate the general features of this lineage. Methods: Herein, we provide the first comparative characterization of the repeatome, with a particular focus on the comparative characterization of satDNAs in three trogonid species: T. surrucura, T. melanurus, and A. vittatum. Using a combination of bioinformatic pipelines and cytogenetic approaches. Results: We identified 16 satDNA families in T. surrucura, 15 in T. melanurus, and only 3 in A. vittatum. Sequence comparisons revealed that five families are shared between the two Trogon species, consistent with the library hypothesis, whereas no satDNAs were shared with A. vittatum. While both Trogon species exhibited a predominance of GC-rich repeats, A. vittatum represents the first bird described with a satellitome dominated by AT-rich satDNAs. In situ mapping in T. surrucura revealed chromosome-specific satDNAs restricted to pairs 1 and 2 and a Z-specific repeat that was strongly accumulated on its long arms, an atypical feature among birds. Conversely, the W chromosome showed a surprisingly low number of satDNAs, limited to centromeric signals. Conclusions: Our results reveal highly divergent satellitome landscapes among trogonids, characterized by lineage-specific differences in repeat composition, abundance, and chromosomal distribution. These findings support the view that satDNAs are dynamic genomic elements, whose amplification, loss, and chromosomal redistribution can influence genome architecture and play a role in avian speciation. Full article
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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15 pages, 1014 KB  
Systematic Review
Efficacy and Safety of Isatuximab Combination Therapy in Multiple Myeloma: A Meta-Analysis of Randomized Controlled Trials
by Chi Wang, Zhengyang Xu, Meilin Jiang, Yuzhe Chen and Yu Lan
Cancers 2025, 17(21), 3494; https://doi.org/10.3390/cancers17213494 - 30 Oct 2025
Viewed by 152
Abstract
Background: This meta-analysis evaluates the efficacy and safety of isatuximab, an anti-CD38 monoclonal antibody, in combination regimens for newly diagnosed (NDMM) and relapsed/refractory multiple myeloma (RRMM). Methods: We systematically searched major databases for randomized controlled trials (RCTs) comparing isatuximab-based therapy with standard regimens [...] Read more.
Background: This meta-analysis evaluates the efficacy and safety of isatuximab, an anti-CD38 monoclonal antibody, in combination regimens for newly diagnosed (NDMM) and relapsed/refractory multiple myeloma (RRMM). Methods: We systematically searched major databases for randomized controlled trials (RCTs) comparing isatuximab-based therapy with standard regimens up to September 2025. Efficacy and safety analyses were performed separately for NDMM and RRMM populations using random-effects models. Efficacy outcomes included progression-free survival (PFS), overall survival (OS), overall response rate (ORR), very good partial response (VGPR) or better, and minimal residual disease (MRD) negativity rate. Safety was assessed by grade ≥ 3 adverse events. Results: In NDMM patients, isatuximab significantly improved PFS (HR = 0.66, 95% CI: 0.52–0.84, p = 0.001) and MRD negativity rates (RR = 1.28, 95% CI: 1.13–1.45, p < 0.001), but not OS (HR = 1.01, p = 0.937), ORR (RR = 1.02, p = 0.49), or VGPR or better (RR = 1.10, p = 0.13). In RRMM patients, isatuximab significantly improved PFS (HR = 0.61, 95% CI: 0.50–0.74, p < 0.001) and showed strong trends favoring OS (HR = 0.81, 95% CI: 0.65–1.00, p = 0.051) and ORR (RR = 1.30, 95% CI: 0.79–2.16, p = 0.303), while significantly increasing MRD negativity (RR = 4.37, 95% CI: 0.60–31.68, p = 0.144). A trend toward improved OS was observed in RRMM (HR = 0.81, p = 0.051). In NDMM, PFS benefit was significant for standard-risk but not high-risk cytogenetics. Safety analysis showed an increased risk of grade ≥ 3 adverse events RRMM (RR = 1.18, p < 0.001) but not in NDMM (RR = 1.08, p = 0.064), primarily driven by neutropenia (NDMM RR = 1.96, p = 0.003; RRMM RR = 1.77, p = 0.039) and pneumonia in NDMM (RR = 1.80, p = 0.001). Conclusion: Isatuximab-based regimens significantly improve PFS and depth of response with a manageable safety profile, supporting its use across MM settings, though efficacy in NDMM may vary by cytogenetic risk. Full article
(This article belongs to the Special Issue Multiple Myeloma: Diagnosis and Therapy)
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16 pages, 923 KB  
Article
Transcervical, Transabdominal and Transvaginal Chorionic Villus Sampling for Prenatal Diagnosis in Zagreb, Croatia: A Prospective Single-Operator Study on 5500 Cases
by Petra Podobnik, Tomislav Meštrović, Mario Podobnik, Ivan Bertović-Žunec, Igor Lončar, Kristian Kurdija, Dženis Jelčić, Zlata Srebreniković and Slava Podobnik-Šarkanji
Diagnostics 2025, 15(21), 2750; https://doi.org/10.3390/diagnostics15212750 - 30 Oct 2025
Viewed by 137
Abstract
Background/Objectives: Chorionic villus sampling (CVS) is a pivotal diagnostic tool for early prenatal detection of chromosomal and genetic abnormalities; however, the safety and diagnostic efficacy of different CVS approaches remain a subject of clinical interest. This monocentric study compares transcervical (TC-CVS), transabdominal [...] Read more.
Background/Objectives: Chorionic villus sampling (CVS) is a pivotal diagnostic tool for early prenatal detection of chromosomal and genetic abnormalities; however, the safety and diagnostic efficacy of different CVS approaches remain a subject of clinical interest. This monocentric study compares transcervical (TC-CVS), transabdominal (TA-CVS) and transvaginal (TV-CVS) techniques, focusing on procedure-related fetal loss and diagnostic yield. Methods: In this 15-year, single-operator prospective study, a total of 5500 women underwent CVS between 10 and 14 weeks of gestation at a single center. Sampling was performed via TA-CVS (n = 4500), TC-CVS (n = 850), or TV-CVS (n = 150). Outcomes assessed included fetal loss rates, sample adequacy, early complications and hemodynamic changes measured by Doppler ultrasound. A p-value < 0.05 (two-tailed) was considered statistically significant. Results: Spontaneous abortion rates were significantly lower following TA-CVS (0.18%; 8/4500) compared to TC-CVS (0.6%; 5/850) and TV-CVS (1.3%; 2/150) (χ2 = 24.56, p < 0.001). Post hoc pairwise analysis showed significantly lower fetal loss in TA-CVS compared to TC-CVS, but not between TA-CVS and TV-CVS. Cytogenetic abnormalities were detected in 220 cases (4.0%), and clinically significant copy number variants (CNVs) were confirmed in fetuses with major structural malformations. Five-year follow-up showed no diagnosed intellectual disability among assessed children. Optimal tissue weight (10–20 mg) was more frequent with TA-CVS (66.7%) than TC-CVS (35.3%) or TV-CVS (36.7%) (χ2 = 350.92, p < 0.001). In a Doppler subset (n = 400), uterine, spiral, and interplacental artery PI changes were non-significant; the umbilical (p = 0.032) and middle cerebral arteries (p < 0.001) showed transient PI reductions after sampling. Conclusions: Transabdominal CVS demonstrated the most favorable balance of safety and diagnostic quality, suggesting it should be the preferred first-line technique in early prenatal diagnosis. Standardized technique and operator training remain critical to optimize outcomes. Full article
(This article belongs to the Special Issue Diagnosis and Prognosis of Gynecological and Obstetric Diseases)
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12 pages, 263 KB  
Review
Navigating the New Era in Myelodysplastic Neoplasms: A Review of Prognostic Implications of the IPSS-M Score and 2022 WHO Classification
by Mihai-Emilian Lapadat, Oana Stanca, Nicoleta Mariana Berbec, Cristina Negotei and Andrei Colita
Hematol. Rep. 2025, 17(6), 58; https://doi.org/10.3390/hematolrep17060058 - 30 Oct 2025
Viewed by 110
Abstract
Myelodysplastic neoplasms represent a diverse group of clonal hematopoietic stem cell disorders characterized by ineffective hematopoiesis, peripheral cytopenias, and an inherent risk of progression to acute myeloid leukemia. Accurate risk assessment and patient stratification are critical to optimizing therapeutic approaches and clinical outcomes. [...] Read more.
Myelodysplastic neoplasms represent a diverse group of clonal hematopoietic stem cell disorders characterized by ineffective hematopoiesis, peripheral cytopenias, and an inherent risk of progression to acute myeloid leukemia. Accurate risk assessment and patient stratification are critical to optimizing therapeutic approaches and clinical outcomes. In 2022, significant advancements reshaped both the classification and prognostic stratification of MDSs. The revised WHO Classification introduced crucial genetically defined subtypes, particularly those involving biallelic TP53 inactivation and SF3B1 mutations, shifting the emphasis from traditional morphology-based criteria to molecular ones. Simultaneously, morphological subtypes such as hypoplastic and hyperfibrotic MDSs were established as distinct entities with unique prognostic implications. At the same time, the introduction of the International Molecular Prognostic Scoring System (IPSS-M) provided a more precise prognostic stratification by integrating comprehensive molecular data alongside traditional clinical and cytogenetic parameters. Several validation studies have confirmed IPSS-M’s superior discriminative power compared to previous models, notably IPSS-R, improving predictions regarding overall survival and leukemia transformation. Nevertheless, practical considerations regarding the widespread application of IPSS-M have emerged, including concerns over economic feasibility and accessibility of advanced molecular testing methods, such as extensive Next-Generation Sequencing panels. This review synthesizes the recent literature and critical studies validating these classification and prognostic updates, discussing their clinical impact, practical considerations, and implications for targeted therapeutic strategies. By focusing on molecular pathogenesis, the latest classification systems and prognostic models promise significant advances in patient-specific management, setting the stage for future innovations in treatment and improved patient outcomes. Full article
9 pages, 760 KB  
Case Report
CBFB::MYH11 Fusion Located on a Supernumerary Ring Chromosome 16 in Pediatric Acute Myeloid Leukemia: Diagnostic Challenges and Prognostic Implications
by Changqing Xia, Melissa Acquazzino, Pamela A. Althof, Marilu Nelson, Rachel A. Harris, Joanna R. Spaulding, Joseph D. Khoury and Zhenya Tang
Genes 2025, 16(11), 1283; https://doi.org/10.3390/genes16111283 - 29 Oct 2025
Viewed by 196
Abstract
We report a unique pediatric acute myeloid leukemia (AML) case characterized by a CBFB::MYH11 fusion located on a supernumerary ring chromosome 16. Following diagnosis through comprehensive blood and bone marrow assays, the patient was enrolled in the Children’s Oncology Group (COG) study AAML1831 [...] Read more.
We report a unique pediatric acute myeloid leukemia (AML) case characterized by a CBFB::MYH11 fusion located on a supernumerary ring chromosome 16. Following diagnosis through comprehensive blood and bone marrow assays, the patient was enrolled in the Children’s Oncology Group (COG) study AAML1831 and randomized to the experimental treatment arm (Arm B). She received induction chemotherapy with CPX-351 (liposomal daunorubicin and cytarabine), gemtuzumab and ozogamicin (GO), and the cardioprotectant dexrazoxane and achieved complete remission (CR). The patient completed the treatment with sustained CR for 18 months. This case represents a rare cytogenetic phenomenon that is not well-documented in the current literature. Through a review of relevant publications, we contextualize this case within the spectrum of core binding factor AML (CBF-AML), highlighting diagnostic approaches, treatment strategies, and prognostic implications, particularly in cases involving atypical CBFB::MYH11 fusions. The durable remission observed in this patient, despite the unusual cytogenetic presentation, provides valuable insights into therapeutic management. This report underscores the cytogenetic and molecular heterogeneity of CBFB::MYH11 AML and emphasizes the importance of comprehensive genetic profiling using advanced techniques such as chromosomal microarray and next-generation sequencing. Full article
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9 pages, 803 KB  
Case Report
Genomic Confluence: When Cerebrotendinous Xanthomatosis, Klinefelter Syndrome, and a BRCA2 Variant Intersect
by Harry Pachajoa, Sebastián Bonilla and Daniel Andrés Nieva-Posso
Int. J. Mol. Sci. 2025, 26(21), 10510; https://doi.org/10.3390/ijms262110510 - 29 Oct 2025
Viewed by 121
Abstract
Multilocus pathogenic variation—when multiple genetic disorders coexist in a single individual—remains rare but is increasingly recognized in the era of genomic medicine. Reporting such cases is essential for improving diagnostic accuracy, refining clinical management, and informing genetic counseling. We describe a pediatric case [...] Read more.
Multilocus pathogenic variation—when multiple genetic disorders coexist in a single individual—remains rare but is increasingly recognized in the era of genomic medicine. Reporting such cases is essential for improving diagnostic accuracy, refining clinical management, and informing genetic counseling. We describe a pediatric case with a complex phenotype resulting from the coexistence of two distinct genetic diagnoses—cerebrotendinous xanthomatosis (CTX), a rare autosomal recessive lipid storage disorder caused by biallelic mutations in the CYP27A1 gene and Klinefelter syndrome a common sex chromosome aneuploidy occurring in approximately 1 in 600 males, characterized by hypogonadism, gynecomastia, pubertal delay, infertility, micrognathia, and neurodevelopmental challenges—and an additional incidental finding with clinical relevance. The patient was born to consanguineous parents, presented with neurological symptoms, gastrointestinal dysfunction, endocrine abnormalities, and dysmorphic features. Trio-based exome sequencing identified a homozygous pathogenic variant in CYP27A1 consistent with CTX, while conventional G-banded karyotyping revealed a 47,XXY chromosomal pattern, confirming Klinefelter syndrome. Additionally, a heterozygous pathogenic variant in BRCA2 was incidentally detected, associated with hereditary cancer predisposition. The overlapping manifestations of CTX and Klinefelter syndrome produced a non-classical presentation that delayed diagnosis. Although the BRCA2 variant did not contribute to the current phenotype, it has important implications for future cancer surveillance and family risk assessment. This case underscores the importance of combining classical cytogenetic and modern genomic methods to elucidate complex phenotypes, particularly in consanguineous populations, and highlights the need for the multidisciplinary management of patients with multilocus or incidental findings. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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19 pages, 2740 KB  
Article
Genome-Wide SNP Analysis Reveals the Unique Genetic Diversity Represented by Fat-Tailed Coarse-Wooled Sheep Breeds of Kazakhstan
by Kairat Dossybayev, Makpal Amandykova, Daniya Ualiyeva, Tilek Kapassuly, Altynay Kozhakhmet, Elena Ciani, Bakytzhan Bekmanov and Rauan Amzeyev
Biology 2025, 14(11), 1478; https://doi.org/10.3390/biology14111478 - 23 Oct 2025
Viewed by 223
Abstract
Background: The fat-tailed coarse-wooled sheep breeds exhibit excellent reproductive performance, exceptional adaptability to pasture conditions, and high precocity, contributing to enhanced meat, fat, and wool productivity in sheep breeding. Despite the significant role of these sheep breeds in Kazakhstan’s livestock production, their genetics [...] Read more.
Background: The fat-tailed coarse-wooled sheep breeds exhibit excellent reproductive performance, exceptional adaptability to pasture conditions, and high precocity, contributing to enhanced meat, fat, and wool productivity in sheep breeding. Despite the significant role of these sheep breeds in Kazakhstan’s livestock production, their genetics remain poorly studied. This raises concerns about the potential loss of unique, breed-specific traits that could be important for the future development and resilience of Kazakh stan’s sheep farming sector. This study aimed to analyze genome-wide genotyping SNP data of local fat-tailed coarse-wooled sheep breeds (Kazakh fat-tailed coarse-wooled, Edilbay, and Gissar) to reveal their genetic diversity, breed characteristics, and phylogenetic relationships with worldwide domestic sheep breeds and wild sheep. Methods: The OvineSNP50 Genotyping BeadChip was used to obtain genome-wide SNP genotyping data from 160 fat-tailed coarse-wooled sheep from Kazakhstan. Population structure analysis, principal component analysis, phylogenetic and the maximum likelihood tree analysis were performed in comparison with foreign domestic sheep breeds and wild sheep populations. Results: Kazakh breeds exhibited high genetic diversity, with Edilbay showing the greatest allelic richness. PCA and Admixture revealed clear differentiation among the three breeds: Edilbay and Gissar formed homogeneous clusters, while Kazakh fat-tailed coarse-wooled sheep displayed admixture and substructure. Evidence of gene flow from Edilbay into other Kazakh populations supports its role as a genetic source for regional breeds. Phylogenetic analysis placed Kazakhstani sheep close to other Central Asian breeds, while clearly distinct from East Asian and European populations. Wild sheep (Argali and Urial) formed separate clades, with Kerman wild sheep clustering closer to Urial. Conclusions: Our results highlight the value of genotyping data for studying genetic diversity and population structure. Developing genetic resources for Kazakhstan’s native sheep breeds will help preserve their unique diversity and ensure it remains available for future use in breeding and adaptation efforts. Full article
(This article belongs to the Special Issue Genetic Variability within and between Populations)
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18 pages, 456 KB  
Review
Allogeneic Hematopoietic Stem Cell Transplantation for Infant Leukemia: A Single-Center Case Series and Narrative Review
by Irina Kostareva, Kirill Kirgizov, Irina Shubina, Nara Stepanyan, Nataliya Batmanova, Timur Valiev, Mihail Kiselevsky and Svetlana Varfolomeeva
Children 2025, 12(10), 1418; https://doi.org/10.3390/children12101418 - 20 Oct 2025
Viewed by 355
Abstract
Background/Objectives: Acute leukemias (AL) in children under 1-year-old are combined under the term “infant leukemia” and are a very rare malignancies, accounting for up to 5% of all childhood AL cases. The predominance of unfavorable clinical and laboratory characteristics leads to unsatisfactory treatment [...] Read more.
Background/Objectives: Acute leukemias (AL) in children under 1-year-old are combined under the term “infant leukemia” and are a very rare malignancies, accounting for up to 5% of all childhood AL cases. The predominance of unfavorable clinical and laboratory characteristics leads to unsatisfactory treatment results, even with the use of modern treatment protocols. Patients/Methods: A comprehensive search through MEDLINE, PubMed, Scopus, and ScienceDirect using infant leukemia-related keywords was performed and included a final set of 52 academic articles. Our own experience included 11 patients with infant leukemia underwent allo-HSCT (allogeneic hematopoietic stem cell transplantation) at the NN Blokhin National Medical Research Center of Oncology in 2021–2023. Types of leukemia included acute myeloid leukemia, lymphoblastic leukemia, and mixed-phenotype acute leukemia. The most frequent cytogenetic aberration was KMT2A. All patients were in clinical and hematological remission, but four had positive MRD status (minimal residual disease). Donors: haploidentical—5 (45.4%), matched unrelated donor—5 (45.4%), and matched related donor—1 (9.2%). Graft manipulations: post-transplant cyclophosphamide was given to three patients with haplo-HSCT, and TCRαβ/CD19 depletion was performed in two patients. The type of immunosuppressive therapy (IST) varied based on the donor. Conditioning regimens were myeloablative. Results: Median follow-up was 23.5 months. Acute GVHD grade I–II developed in two patients (18%) and grade III–IV in three patients (27%). The overall survival rate was 54.5% (n = 6). The relapse rate after allo-HSCT was 18% (n = 2). The most common cause of treatment failure was infectious complications in the early post-transplant period (70%). Conclusions: Our center’s experience demonstrated acceptable transplant-related mortality and satisfactory relapse rates after allo-HSCT in patients with infant leukemia. The treatment of acute leukemia in infants is challenging, and optimal protocols are being developed around the world specifically for these patients. Taking into account the characteristics of this age group, the choice of chemotherapy drug doses should be carefully considered, and the indications for allo-HSCT should be balanced. Full article
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24 pages, 2943 KB  
Article
Serum miR-34a as Indicator of Impaired Fibrinolytic Capacity in Pediatric Thrombosis Through Inadequate Regulation of the ACE/PAI-1 Axis
by Iphigenia Gintoni, Kleoniki Baldouni, Athina Dettoraki, Aikaterini Michalopoulou, Ioanna Papathanasiou, Aspasia Tsezou, Dimitrios Vlachakis, Helen Pergantou, George P. Chrousos and Christos Yapijakis
Int. J. Mol. Sci. 2025, 26(20), 10110; https://doi.org/10.3390/ijms262010110 - 17 Oct 2025
Viewed by 217
Abstract
Pediatric thrombosis (PT) represents a rare condition that can manifest from neonatal life to adolescence, encompassing life-threatening complications. Its pathogenesis is attributed to immature hemostasis in conjunction with environmental and genetic factors, predominantly including those resulting in increased levels of plasminogen activator inhibitor [...] Read more.
Pediatric thrombosis (PT) represents a rare condition that can manifest from neonatal life to adolescence, encompassing life-threatening complications. Its pathogenesis is attributed to immature hemostasis in conjunction with environmental and genetic factors, predominantly including those resulting in increased levels of plasminogen activator inhibitor 1 (PAI-1), the principal inhibitor of fibrinolysis, which is subject to upstream regulation by angiotensin-converting enzyme (ACE). Although the implication of microRNAs (miRNAs), epigenetic modulators of gene expression, has been demonstrated in adult thrombosis, evidence is lacking in the pediatric setting. Here, we investigated the involvement of two miRNA regulators of PAI-1 (SERPINE1 gene) in PT, in relation to clinical and genetic parameters that induce PAI-1 fluctuations. Following bioinformatic target-prediction, miRNA expression was assessed by quantitative real-time PCR in serum-samples of 19 pediatric patients with thrombosis (1–18 months post-incident), and 19 healthy controls. Patients were genotyped for the SERPINE1-4G/5G and ACE-I/D polymorphisms by PCR-based assays. Genotypic and thrombosis-related clinical data were analyzed in relation to miRNA-expression. Two miRNAs (miR-145-5p, miR-34a-5p) were identified to target SERPINE1 mRNA, with miR-34a additionally targeting the mRNA of ACE. The expression of miR-34a was significantly decreased in patients compared to controls (p = 0.029), while no difference was observed in miR-145 expression. Within patients, miR-34a expression demonstrated a peak 1–3 months post-thrombosis and was diminished upon treatment completion (p = 0.031), followed by a slight long-term increase. MiR-34a levels differed significantly by thrombosis site (p = 0.019), while a significant synergistic interaction between site and onset type (provoked/unprovoked) was detected (p = 0.016). Finally, an epistatic modification was observed in cerebral cases, since double homozygosity (4G/4G + D/D) led to a miR-34 decrease, with D/D carriership reversing the 4G/4G-induced upregulation of miR-34a (p = 0.006). Our findings suggest that in pediatric thrombosis, downregulation of miR-34a is indicative of impaired fibrinolytic capacity, attributed to deficient regulation of the inhibitory ACE/PAI-1 axis. Full article
(This article belongs to the Collection Feature Papers Collection in Biochemistry)
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20 pages, 1024 KB  
Review
Chromosomal Roadblocks in Male Fertility: Mechanisms, Risk Factors and Syndromes
by Achilleas G. Mitrakas, Christina-Angelika Alexiadi, Sofia Gargani, Triantafyllos Alexiadis, Sofia-Panagiota Alexopoulou, Olga Pagonopoulou and Maria Lambropoulou
Medicina 2025, 61(10), 1864; https://doi.org/10.3390/medicina61101864 - 16 Oct 2025
Viewed by 660
Abstract
Male infertility affects nearly 15% of couples worldwide, with chromosomal abnormalities representing a major underlying cause. This review explores how numerical and structural chromosomal anomalies, along with environmental exposures, lifestyle factors, and age-related genetic changes, disrupt spermatogenesis and contribute to infertility. It synthesizes [...] Read more.
Male infertility affects nearly 15% of couples worldwide, with chromosomal abnormalities representing a major underlying cause. This review explores how numerical and structural chromosomal anomalies, along with environmental exposures, lifestyle factors, and age-related genetic changes, disrupt spermatogenesis and contribute to infertility. It synthesizes findings from cytogenetic, molecular, and clinical studies, with particular focus on mechanisms such as meiotic nondisjunction, spindle assembly checkpoint dysfunction, and alterations in cohesin and synaptonemal complex proteins. Chromosomal abnormalities, both numerical and structural, emerge as key contributors to male infertility by impairing chromosomal segregation and recombination, often leading to azoospermia or oligospermia. Meiotic checkpoint failures and recombination errors further exacerbate the production of aneuploid sperm. Environmental toxins, oxidative stress, and poor nutrition disrupt hormonal balance and chromatin integrity, while advancing paternal age is associated with increased sperm aneuploidy and impaired meiotic control, with implications for assisted reproduction. Specific syndromes, including AZF deletions, Kallmann syndrome, and 46,XX testicular DSD, exemplify the direct genetic impact on male fertility. Overall, chromosomal abnormalities are central to the pathophysiology of male infertility, arising from intrinsic meiotic errors as well as extrinsic environmental and lifestyle factors. Integrating cytogenetic diagnostics, genetic counseling, and lifestyle interventions is essential for comprehensive fertility assessment and management. Further research into molecular biomarkers and targeted therapies could enhance diagnosis, improve treatment strategies, and lead to better reproductive outcomes. Full article
(This article belongs to the Special Issue From Conception to Birth: Embryonic Development and Disease)
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13 pages, 1418 KB  
Article
Investigating the “Dark” Genome: First Report of Partington Syndrome in Cyprus
by Constantia Aristidou, Athina Theodosiou, Pavlos Antoniou, Angelos Alexandrou, Ioannis Papaevripidou, Ludmila Kousoulidou, Pantelitsa Koutsou, Anthi Georghiou, Türem Delikurt, Elena Spanou, Nicole Salameh, Paola Evangelidou, Kyproula Christodoulou, Alain Verloes, Violetta Christophidou-Anastasiadou, George A. Tanteles and Carolina Sismani
Genes 2025, 16(10), 1224; https://doi.org/10.3390/genes16101224 - 15 Oct 2025
Viewed by 392
Abstract
Background/Objectives: X-linked intellectual disability (XLID) is a highly heterogeneous disorder accounting for ~10% of all males with ID. Next-generation sequencing (NGS) has revolutionized the discovery of causal XLID genes and variants; however, many cases remain unresolved. We present a four-generation syndromic XLID [...] Read more.
Background/Objectives: X-linked intellectual disability (XLID) is a highly heterogeneous disorder accounting for ~10% of all males with ID. Next-generation sequencing (NGS) has revolutionized the discovery of causal XLID genes and variants; however, many cases remain unresolved. We present a four-generation syndromic XLID family with multiple males exhibiting variable degree of ID, focal dystonia and epilepsy. Methods: Extensive cytogenetic and targeted genetic testing was initially performed, followed by whole-exome sequencing (WES) and short-read whole-genome sequencing (WGS). Apart from the routine NGS analysis pipelines, sequencing data was revisited by focusing on poorly covered/mapped regions on chromosome X (chrX), to potentially reveal unidentified clinically relevant variants. Candidate variant validation and family segregation analysis were performed with Sanger sequencing. Results: All initial diagnostic testing was negative. Subsequently, 300 previously reported “dark” chrX coding DNA sequences, overlapping 97 genes, were cross-checked against 29 chrX genes highly associated (p < 0.05) with ID and focal dystonia, according to Phenomizer. Manual inspection of the existing NGS data in two low-coverage regions, chrX:25013469-25013696 and chrX:111744737-111744820 (hg38), revealed a recurrent pathogenic ARX variant NM_139058.3:c.441_464dup p.(Ala148_Ala155dup) (ARXdup24) associated with non-syndromic or syndromic XLID, including Partington syndrome. Sanger sequencing confirmed ARXdup24 in all affected males, with carrier status in their unaffected mothers, and absence in other unaffected relatives. Conclusions: After several years of diagnostic odyssey, the pathogenic ARXdup24 variant was unmasked, supporting a genotype–phenotype correlation in the first Partington syndrome family in Cyprus. This study highlights that re-examining underrepresented genomic regions and using phenotype-driven tools can provide critical diagnostic insights in unresolved XLID cases. Full article
(This article belongs to the Special Issue Molecular Basis and Genetics of Intellectual Disability)
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8 pages, 241 KB  
Article
The First Report of a Non-Canonical Telomeric Motif in Neuroptera: (TTGGG)n in Chromosomes of Nineta flava (Scopoli, 1763), Chrysopidae
by Desislava Stoianova and Snejana Grozeva
Genes 2025, 16(10), 1201; https://doi.org/10.3390/genes16101201 - 14 Oct 2025
Viewed by 290
Abstract
Background: Telomeres are nucleoprotein complexes that maintain chromosome integrity in eukaryotes. In insects, the canonical telomeric repeat (TTAGG)n is considered ancestral, though alternative motifs exist across various orders. Neuroptera, comprising about 5800 species, remains understudied regarding telomeric sequences, with data available for [...] Read more.
Background: Telomeres are nucleoprotein complexes that maintain chromosome integrity in eukaryotes. In insects, the canonical telomeric repeat (TTAGG)n is considered ancestral, though alternative motifs exist across various orders. Neuroptera, comprising about 5800 species, remains understudied regarding telomeric sequences, with data available for only seven species across three families. Previous studies reported the absence of (TTAGG)n in Chrysopidae species, contrasting with its presence in other Neuroptera families. This study aimed to identify and characterize telomeric motifs in Chrysopidae using chromosome-level genome assemblies and search for retrotransposon insertions. Methods: We analyzed chromosome-level genome assemblies from four Chrysopidae species: three Chrysopinae—Chrysoperla carnea (Stephens, 1836), Chrysopa pallens (Rambur, 1838), and Nineta flava (Scopoli, 1763); and one Nothochrysinae—Nothochrysa capitata (Fabricius, 1793). Terminal sequences of chromosome pseudomolecules were examined using Geneious Prime®, applying five specific criteria for optimal telomeric sequence identification. We searched for SART and TRAS retrotransposons using the graphical sequence panel in GenBank. Results: We identified (TTGGG)n as the telomeric motif in N. flava, representing the first report of this pentanucleotide repeat in telomeres of Neuroptera. Arrays ranged from 228 to 8005 bp across seven terminal locations in five chromosome pseudomolecules. In N. capitata, we detected (TTAGG)n arrays (2316–3808 bp) at four terminal locations. No telomeric motifs meeting all criteria were found in C. carnea and C. pallens. No SART/TRAS retrotransposons were detected in any species. Conclusions: This study reveals previously unknown telomeric diversity within Chrysopidae, with both canonical (TTAGG)n and novel (TTGGG)n motifs present. The discovery of (TTGGG)n in Neuroptera expands known telomeric sequence diversity in this order. Full article
(This article belongs to the Section Animal Genetics and Genomics)
17 pages, 2431 KB  
Article
Genetic Diversity and Population Structure of Fat-Tailed Coarse-Wooled Sheep Breeds Ovis aries from Kazakhstan
by Kairat Dossybayev, Daniya Ualiyeva, Tilek Kapassuly, Makpal Amandykova, Altynay Kozhahmet, Bakytzhan Bekmanov, Rauan Amzeyev and Saitou Naruya
Vet. Sci. 2025, 12(10), 988; https://doi.org/10.3390/vetsci12100988 - 13 Oct 2025
Viewed by 423
Abstract
Sheep play a central role in Kazakhstan’s pastoral economy, yet the maternal genetic composition of its traditional breeds remains poorly characterized. We analyzed partial mitochondrial D-loop sequences (848 bp) from 115 individuals of three fat-tailed coarse-wooled breeds (Edilbay, Kazakh fat-tailed coarse-wooled, and Gissar) [...] Read more.
Sheep play a central role in Kazakhstan’s pastoral economy, yet the maternal genetic composition of its traditional breeds remains poorly characterized. We analyzed partial mitochondrial D-loop sequences (848 bp) from 115 individuals of three fat-tailed coarse-wooled breeds (Edilbay, Kazakh fat-tailed coarse-wooled, and Gissar) to assess genetic diversity, population structure, and phylogenetic relationships. Ninety-eight haplotypes were identified, indicating high haplotype diversity (Hd = 0.996 ± 0.002) and moderate nucleotide diversity (π = 0.02624 ± 0.00048). Haplotypes clustered into haplogroups A (57.4%) and B (42.6%), with Edilbay dominating the star-like cluster of haplogroup A, consistent with recent expansion. AMOVA revealed that most variation (92.03%) occurred within populations, with no significant differentiation among breeds. Phylogenetic analyses placed Edilbay close to the most recent common ancestor of fat-tailed domestic sheep and the wild Ovis species, suggesting retention of an ancestral lineage. These findings highlight Kazakhstan as a genetic crossroads in sheep history and underscore the conservation value of its maternal diversity. Full article
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15 pages, 2026 KB  
Article
Genomic Characterization of a Novel Yezo Virus Revealed in Ixodes pavlovskyi Tick Virome in Western Siberia
by Maxim Apanasevich, Nikita Dubovitskiy, Anastasiya Derko, Anna Khozyainova, Alexander Tarasov, Alina Kokhanenko, Gleb Artemov, Evgeny Denisov, Alexander Shestopalov and Kirill Sharshov
Viruses 2025, 17(10), 1362; https://doi.org/10.3390/v17101362 - 11 Oct 2025
Viewed by 490
Abstract
Ixodid ticks are blood-sucking ectoparasites of vertebrates. They constitute an integral part of natural foci and are responsible for the worldwide transmission of infections to humans, which can result in severe symptoms. For instance, the Tomsk region, where three abundant tick species ( [...] Read more.
Ixodid ticks are blood-sucking ectoparasites of vertebrates. They constitute an integral part of natural foci and are responsible for the worldwide transmission of infections to humans, which can result in severe symptoms. For instance, the Tomsk region, where three abundant tick species (Dermacentor reticulatus, Ixodes pavlovskyi, I. persulcatus) occur, is an endemic area for tick-borne encephalitis virus (TBEV). An increasing number of novel infectious agents carried by ticks have been identified using metagenomic sequencing. A notable example is the Yezo virus (Orthonairovirus yezoense, YEZV), which was discovered in patients with fever after tick bites in Japan and China between 2014 and 2025. For the first time, we have performed metagenomic sequencing of the virome of ticks collected in the Tomsk region. In a sample obtained from a pool of I. pavlovskyi ticks, all three segments of the YEZV genome were detected. The phylogenetic analysis showed that the newly identified isolate formed a sister group to previously described virus isolates, indicating the presence of a new genetic variant. This study presents the first report of YEZV detection in I. pavlovskyi ticks in the Tomsk region, thereby expanding the geographical range and number of vector species for YEZV and highlighting the importance of monitoring viral agents circulating among ticks in Western Siberia. Full article
(This article belongs to the Special Issue Tick-Borne Viruses: Transmission and Surveillance, 2nd Edition)
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12 pages, 1845 KB  
Article
Unraveling Wing Shape Variation in Malaria Mosquitoes from the Arctic Edge: A Geometric Morphometric Study in Western Siberia
by Ximena Calderon, Gleb Artemov, Vladimir A. Burlak, Svetlana Alexeeva, Raquel Hernández-P, Manuel J. Suazo, Laura M. Pérez, Hugo A. Benítez and Margarita Correa
Animals 2025, 15(20), 2949; https://doi.org/10.3390/ani15202949 - 11 Oct 2025
Viewed by 253
Abstract
In Russia, Western Siberia, Anopheles from maculipennis subgroup comprises three vector species: An. messeae, An. daciae, An. beklemishevi, and the hybrid between An. messeae and An. daciae (Anopheles m-d), which exhibit complex cryptic morphological traits. Traditional morphological methods, such [...] Read more.
In Russia, Western Siberia, Anopheles from maculipennis subgroup comprises three vector species: An. messeae, An. daciae, An. beklemishevi, and the hybrid between An. messeae and An. daciae (Anopheles m-d), which exhibit complex cryptic morphological traits. Traditional morphological methods, such as egg morphology and exochorion coloration, have proven insufficient for reliably distinguishing these closely related species due to overlapping characteristics and high intra-species variability. To overcome these limitations, geometric morphometrics (GM) has emerged as a powerful tool for analyzing cryptic morphology. This article focuses on wing venation patterns, where GM provides precise, quantitative data based on defined anatomical landmarks, enabling detailed assessment of size and shape variation among species. Procrustes ANOVA, principal component analysis (PCA), and canonical variate analysis (CVA) were employed to assess shape variation and species differentiation. Centroid size and its relationship to shape variation were examined using multivariate regression. Despite significant morphological differences, the overlap observed in hybrids (An. m-d) reflects their intermediate position between the parental species. Our analyses revealed significant differences in wing shape and size among An. messeae, An. daciae, An. beklemishevi, and their hybrids, with hybrids showing intermediate morphologies. Landmarks on radial and medial veins were the most consistent contributors to species separation. No evidence of static allometry was detected, and wing shape differences were not explained by size. These findings demonstrate that wing morphometrics, combined with molecular identification, provides a reliable framework for species delimitation and surveillance of malaria vectors in temperate regions. Full article
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