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Keywords = fluorescent in situ hybridization

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13 pages, 4253 KB  
Article
Satellite DNA in Populus and Molecular Karyotyping of Populus xiaohei and Its Derived Double Haploids
by Bo Liu, Xinyu Wang, Wenjie Shen, Meng Wang, Guanzheng Qu and Quanwen Dou
Plants 2025, 14(19), 3046; https://doi.org/10.3390/plants14193046 - 1 Oct 2025
Abstract
Karyotype analysis and the investigation of chromosomal variations in Populus are challenging due to its small and morphologically similar chromosomes. Despite its utility in chromosome identification and karyotype evolutionary research, satellite DNA (satDNA) remains underutilized in Populus. In the present study, 12 [...] Read more.
Karyotype analysis and the investigation of chromosomal variations in Populus are challenging due to its small and morphologically similar chromosomes. Despite its utility in chromosome identification and karyotype evolutionary research, satellite DNA (satDNA) remains underutilized in Populus. In the present study, 12 satDNAs were identified from P. trichocarpa, and the copy numbers and chromosomal distributions of each satDNA were analyzed bioinformatically in the reference genomes of P. trichocarpa, P. simonii, and P. nigra. Ten satDNA probes for fluorescence in situ hybridization (FISH) were successfully developed and validated on chromosomes of P. xiaohei (poplar hybrid P. simonii × P. nigra). By integrating bioinformatic genomic satDNA distribution patterns with experimental FISH signals, we constructed a molecular karyotype of P. xiaohei. Comparative analysis revealed errors in current poplar genome assemblies. Comparative karyotype analysis of P. xiaohei and its doubled haploid (DH) lines revealed chromosomal variations in the DH lines relative to the donor tree. The results demonstrate that the newly developed satDNA probes constitute robust cytogenetic tools for detecting structural variations in Populus, while molecular karyotyping provides new insights into the genetic mechanisms underlying chromosome variations in P. xiaohei and the DH plants derived. Full article
(This article belongs to the Section Plant Genetics, Genomics and Biotechnology)
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19 pages, 19265 KB  
Article
A Novel Microfluidic Platform for Circulating Tumor Cell Identification in Non-Small-Cell Lung Cancer
by Tingting Tian, Shanni Ma, Yan Wang, He Yin, Tiantian Dang, Guangqi Li, Jiaming Li, Weijie Feng, Mei Tian, Jinbo Ma and Zhijun Zhao
Micromachines 2025, 16(10), 1136; https://doi.org/10.3390/mi16101136 - 1 Oct 2025
Abstract
Circulating tumor cells (CTCs) are crucial biomarkers for lung cancer metastasis and recurrence, garnering significant clinical attention. Despite this, efficient and cost-effective detection methods remain scarce. Consequently, there is an urgent demand for the development of highly sensitive CTC detection technologies to enhance [...] Read more.
Circulating tumor cells (CTCs) are crucial biomarkers for lung cancer metastasis and recurrence, garnering significant clinical attention. Despite this, efficient and cost-effective detection methods remain scarce. Consequently, there is an urgent demand for the development of highly sensitive CTC detection technologies to enhance lung cancer diagnosis and treatment. This study utilized microspheres and A549 cells to model CTCs, assessing the impact of acoustic field forces on cell viability and proliferation and confirming capture efficiency. Subsequently, CTCs from the peripheral blood of patients with lung cancer were captured and identified using fluorescence in situ hybridization, and the results were compared to the immunomagnetic bead method to evaluate the differences between the techniques. Finally, epidermal growth factor receptor (EGFR) mutation analysis was conducted on CTC-positive samples. The findings showed that acoustic microfluidic technology effectively captures microspheres, A549 cells, and CTCs without compromising cell viability or proliferation. Moreover, EGFR mutation analysis successfully identified mutation types in four samples, establishing a basis for personalized targeted therapy. In conclusion, acoustic microfluidic technology preserves cell viability while efficiently capturing CTCs. When integrated with EGFR mutation analysis, it provides robust support for the precise diagnosis and treatment of lung cancer as well as personalized drug therapy. Full article
(This article belongs to the Special Issue Application of Microfluidic Technology in Bioengineering)
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16 pages, 1747 KB  
Article
Insights into the Prognostic Value of Telomere Length in Childhood Acute Lymphoblastic Leukemia
by Elena Vakonaki, Iordanis Pelagiadis, Stella Baliou, Manolis N. Tzatzarakis, Athanasios Alegakis, Ioanna Lygerou, Persefoni Fragkiadaki, Maria Stratigaki, Nikolaos Katzilakis, Aristidis Tsatsakis and Eftichia Stiakaki
Life 2025, 15(10), 1537; https://doi.org/10.3390/life15101537 - 1 Oct 2025
Abstract
Background: Although telomere length maintenance is a common characteristic of hematological malignancies, the role of telomere length as a prognostic factor to stratify acute lymphoblastic leukemia (ALL) patients depending on their risk of relapse remains elusive. Methods: This knowledge gap motivated us to [...] Read more.
Background: Although telomere length maintenance is a common characteristic of hematological malignancies, the role of telomere length as a prognostic factor to stratify acute lymphoblastic leukemia (ALL) patients depending on their risk of relapse remains elusive. Methods: This knowledge gap motivated us to examine telomere length values in children with ALL at the time of diagnosis and after treatment using quantitative polymerase chain reaction (qPCR) (n = 35). To achieve high-resolution precision and cell specificity, a quantitative fluorescence in situ hybridization (qFISH) technique was developed (n = 5). Results: The results demonstrated statistically significant evidence of telomere shortening in the lymphoblasts of children with ALL but not in the lymphocytes of children after remission following treatment. Our findings also suggested a significant association between telomere shortening and a high risk of relapse disease. Last but not least, our preliminary results showed a trend that telomere shortening was more pronounced in children with B-ALL compared to those with T-ALL in a non-significant manner. Conclusions: Consequently, the current study provides preliminary insights into the potentially substantial prognostic value of telomere length in the progression of pediatric ALL, with the possibility of predicting treatment response. To clarify the application of telomere length as a possible biomarker for disease progression and treatment response in children with ALL, the telomere length values of additional participants need to be examined in further studies. Full article
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16 pages, 871 KB  
Review
Uncovering the PML::RARA Fusion in Cytogenetically Cryptic and FISH-Negative Acute Promyelocytic Leukemia—A Case Report and Comprehensive Literature Review
by Busra N. Delikkaya, Jaime Eberle-Singh, Arianna B. Morton, Jerald Z. Gong and Jinglan Liu
Genes 2025, 16(10), 1159; https://doi.org/10.3390/genes16101159 - 29 Sep 2025
Abstract
The PML::RARA fusion resulting from t(15;17) is the genetic hallmark of acute promyelocytic leukemia (APL), typically detected by cytogenetics and/or fluorescence in situ hybridization (FISH) studies. Rarely, APL patients present with normal cytogenetics and FISH findings, complicating diagnosis and delaying life-saving therapy. We [...] Read more.
The PML::RARA fusion resulting from t(15;17) is the genetic hallmark of acute promyelocytic leukemia (APL), typically detected by cytogenetics and/or fluorescence in situ hybridization (FISH) studies. Rarely, APL patients present with normal cytogenetics and FISH findings, complicating diagnosis and delaying life-saving therapy. We report a 23-year-old male with clinical, morphologic and immunophenotypic features consistent with APL but negative for FISH studies. Despite prompt initiation of all-trans retinoic acid (ATRA) based on clinical suspicion, the patient succumbed to intracranial hemorrhage. Quantitative reverse transcriptase PCR (qRT-PCR) confirmed a long isoform PML::RARA fusion. A review of 34 published cytogenetics- and FISH-negative cases since 1995 demonstrates that RT-PCR-based methods reliably detect cryptic fusions. While advanced genomic approaches may identify these fusions at higher resolution, their accessibility, complexity, cost, and turnaround time often limit diagnostic utility in the urgent setting of APL. Given the extreme rarity of this subset, cytogenetics and FISH remain the standard frontline tests; however, these cases underscore the critical need to incorporate molecular testing into routine workflows. Early recognition and timely therapy are essential to reducing mortality in cryptic APL, and these cases also provide insight into mechanisms of atypical leukemia biology. Full article
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14 pages, 2426 KB  
Article
Molecular Profiling of SYT-SSX Fusion Transcripts for Enhanced Diagnosis of Synovial Sarcomas
by Sara Louati, Kaoutar Bentayebi, Ibtissam Saad, Yvonne Gloor, Nadia Senhaji, Abdelmajid Elmrini, Lahcen Belyamani, Rachid Eljaoudi, Marc Ansari, Sanae Bennis and Youssef Daali
J. Pers. Med. 2025, 15(10), 455; https://doi.org/10.3390/jpm15100455 - 29 Sep 2025
Abstract
Background/Objectives: Synovial sarcoma (SS) is an aggressive soft-tissue tumor characterized by the chromosomal translocation t(X;18) (p11.2;q11.2), most commonly involving the fusion of the SYT gene on chromosome 18 with the SSX1 or SSX2 genes on chromosome X. This study aims to explore [...] Read more.
Background/Objectives: Synovial sarcoma (SS) is an aggressive soft-tissue tumor characterized by the chromosomal translocation t(X;18) (p11.2;q11.2), most commonly involving the fusion of the SYT gene on chromosome 18 with the SSX1 or SSX2 genes on chromosome X. This study aims to explore the clinicopathological and molecular characteristics of synovial sarcoma in a cohort of Moroccan patients. Methods: We analyzed 48 cases of synovial sarcoma using formalin-fixed, paraffin-embedded (FFPE) tissue samples. Histological grading was performed according to the FNCLCC system. Immunohistochemical staining was employed to detect cytokeratin (CK) and epithelial membrane antigen (EMA). Molecular analysis included fluorescence in situ hybridization (FISH) to identify SS18 gene rearrangements and reverse transcription–polymerase chain reaction (RT-PCR) to detect SYT-SSX fusion transcripts. Results: Among the cohort, 56% of cases showed SS18 gene rearrangements via FISH, while RT-PCR confirmed the presence of SS18-SSX1 and SS18-SSX2 transcripts in 60% and 32% of cases, respectively. The remainder was classified as undifferentiated sarcoma. Notably, no significant associations were observed between SYT-SSX fusion type and clinicopathological features. Conclusions: These findings underscore the importance of integrating molecular techniques for precise diagnosis in synovial sarcoma. The results align with global patterns, emphasizing the necessity for molecular testing to enhance diagnostic accuracy and informing potential therapeutic advancements. Full article
(This article belongs to the Special Issue Cancer Biomarker and Molecular Oncology)
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14 pages, 826 KB  
Article
Cytogenetic Profile of Chromosomal Aberrations in Leukemia Using the Fluorescence In Situ Hybridization (FISH) Method at a Tertiary Institution in Gauteng Province
by Zamathombeni Duma, Karabo C. Matsepane, Koketso Nkoana, Sara M. Pheeha, Bathabile Mbele, Tandekile Simela-Tshabalala and Donald M. Tanyanyiwa
Diagnostics 2025, 15(19), 2429; https://doi.org/10.3390/diagnostics15192429 - 24 Sep 2025
Viewed by 168
Abstract
Background: Leukemia, a hematologic malignancy, is the major fluid tumor. However, there is a paucity in laboratory characterization in South Africa due to limited diagnostic infrastructure. Chromosomal aberrations play a crucial role in leukemia pathogenesis, influencing classification, prognosis, and treatment. Aim: This study [...] Read more.
Background: Leukemia, a hematologic malignancy, is the major fluid tumor. However, there is a paucity in laboratory characterization in South Africa due to limited diagnostic infrastructure. Chromosomal aberrations play a crucial role in leukemia pathogenesis, influencing classification, prognosis, and treatment. Aim: This study aimed to characterize chromosomal aberrations in leukemia patients using the fluorescence in situ hybridization (FISH) method, with the goal of improving diagnostic precision and guiding tailored treatment in resource-limited settings. Methodology: This study was a retrospective analysis of 349 leukemia patient records from the NHLS Corporate Data Warehouse, covering cases diagnosed between January 2019 and January 2024. Chromosomal aberrations were assessed using FISH, including cases of CML, AML, CLL, and ALL. Results: CML was the most prevalent leukemia subtype (40%), followed by AML (31%). Age-specific distributions were significant across subtypes (p < 0.0001). FISH detected subtype-specific aberrations: t(1;19) and t(12;21) in 25% of ALL cases; t(8;21) and t(15;17) in 22–33% of AML cases; and t(9;22) in 100% of CML cases. In CLL, 13q deletions were most common (53% complex, 33% simple). Conclusions: This study reveals distinct chromosomal aberration patterns in leukemia patients in Gauteng, with CML as the most prevalent subtype. Distinct patterns were observed across ALL, AML, and CLL, with age and gender-specific trends. Findings highlight regional genetic influences, diagnostic gaps, and healthcare challenges, emphasizing the urgent need to expand cytogenetic and molecular testing to enable targeted diagnostics, risk stratification, and personalized therapies in sub-Saharan Africa. Full article
(This article belongs to the Section Pathology and Molecular Diagnostics)
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12 pages, 1247 KB  
Review
Imaging Flow Cytometry as a Molecular Biology Tool: From Cell Morphology to Molecular Mechanisms
by Yoshikazu Matsuoka
Int. J. Mol. Sci. 2025, 26(19), 9261; https://doi.org/10.3390/ijms26199261 - 23 Sep 2025
Viewed by 149
Abstract
Insights into the state of individual cells within a living organism are essential for identifying diseases and abnormalities. The internal state of a cell is reflected in its morphological features and changes in the localization of intracellular molecules. Using this information, it is [...] Read more.
Insights into the state of individual cells within a living organism are essential for identifying diseases and abnormalities. The internal state of a cell is reflected in its morphological features and changes in the localization of intracellular molecules. Using this information, it is possible to infer the state of the cells with high precision. In recent years, technological advancements and improvements in instrument specifications have made large-scale analyses, such as single-cell analysis, more widely accessible. Among these technologies, imaging flow cytometry (IFC) is a high-throughput imaging platform that can simultaneously acquire information from flow cytometry (FCM) and cellular images. While conventional FCM can only obtain fluorescence intensity information corresponding to each detector, IFC can acquire multidimensional information, including cellular morphology and the spatial arrangement of proteins, nucleic acids, and organelles for each imaging channel. This enables the discrimination of cell types and states based on the localization of proteins and organelles, which is difficult to assess accurately using conventional FCM. Because IFC can acquire a large number of single-cell morphological images in a short time, it is well suited for automated classification using machine learning. Furthermore, commercial instruments that combine integrated imaging and cell sorting capabilities have recently become available, enabling the sorting of cells based on their image information. In this review, we specifically highlight practical applications of IFC in four representative areas: cell cycle analysis, protein localization analysis, immunological synapse formation, and the detection of leukemic cells. In addition, particular emphasis is placed on applications that directly contribute to elucidating molecular mechanisms, thereby distinguishing this review from previous general overviews of IFC. IFC enables the estimation of cell cycle phases from large numbers of acquired cellular images using machine learning, thereby allowing more precise cell cycle analysis. Moreover, IFC has been applied to investigate intracellular survival and differentiation signals triggered by external stimuli, to monitor DNA damage responses such as γH2AX foci formation, and more recently, to detect immune synapse formation among interacting cells within large populations and to analyze these interactions at the molecular level. In hematological malignancies, IFC combined with fluorescence in situ hybridization (FISH) enables high-throughput detection of chromosomal abnormalities, such as BCR-ABL1 translocations. These advances demonstrate that IFC provides not only morphological and functional insights but also clinically relevant genomic information at the single-cell level. By summarizing these unique applications, this review aims to complement existing publications and provide researchers with practical insights into how IFC can be implemented in both basic and translational research. Full article
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21 pages, 6976 KB  
Article
Pc-AIF1 Is Expressed in Hemocyte-Rich and Neural Tissues and Links Immune Response and Regeneration in the Snail Model Pomacea canaliculata
by Anita Ferri, Sandro Sacchi, Nicola Franchi, Umberto Rosani and Davide Malagoli
Int. J. Mol. Sci. 2025, 26(18), 9022; https://doi.org/10.3390/ijms26189022 - 16 Sep 2025
Viewed by 269
Abstract
Allograft inflammatory factor-1 (AIF1) is a conserved calcium-binding protein involved in inflammatory and neuro-immune responses and expressed in Pomacea canaliculata (Pc-AIF1) during cephalic tentacle regeneration. Here, we investigated the expression and distribution of Pc-AIF1 in control conditions and during cephalic [...] Read more.
Allograft inflammatory factor-1 (AIF1) is a conserved calcium-binding protein involved in inflammatory and neuro-immune responses and expressed in Pomacea canaliculata (Pc-AIF1) during cephalic tentacle regeneration. Here, we investigated the expression and distribution of Pc-AIF1 in control conditions and during cephalic tentacle regeneration. A transcriptomic analysis of 315 RNA-seq datasets revealed maximal Pc-AIF1 expression in circulating hemocytes and hemocyte-rich tissues. Pc-AIF1 was also highly expressed in neural ganglia. Fluorescence in situ hybridization (FISH) evidenced Pc-AIF1 in circulating hemocytes and in the phagocytic hemocyte aggregates in the posterior kidney. qPCR showed the constitutive expression of Pc-AIF1 in cerebral ganglia. FISH experiments showed Pc-AIF1-positive cells within the cephalic tentacle blastema at 24 h post-amputation (hpa). Even if the amputation left them untouched, both the ipsilateral and contralateral cerebral ganglia increased Pc-AIF1 expression until 48 hpa. Immunocytochemical experiments evidenced positive cells to RCA120 (a microglial marker in mammals) among circulating hemocytes, in the connective tissue surrounding the cerebral ganglia, and within the regenerating tentacles. These findings suggest that Pc-AIF1 is a neuro-immune marker constitutively expressed in hemocyte populations and neural tissues; it is associated with the immediate hemocyte response to wounding and the neuro-immune interplay during the regeneration of sensory organs. Full article
(This article belongs to the Section Molecular Biology)
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16 pages, 8433 KB  
Article
Hi-C Technology Reveals Actionable Gene Fusions and Rearrangements in Diffuse Large B-Cell Lymphoma Unidentified by Conventional FISH
by Sichen Liang, Candice Ament, Melanie Klausner, Victoria Stinnett, Laura Morsberger, Jen Ghabrial, William Middlezong, Anthony D. Schmitt, Alex R. Hastie and Ying S. Zou
Genes 2025, 16(9), 1093; https://doi.org/10.3390/genes16091093 - 16 Sep 2025
Viewed by 339
Abstract
Background/Objectives: Fluorescence in situ hybridization (FISH) is a standard diagnostic tool for detecting gene fusions and rearrangements in lymphomas but is limited by incomplete genomic coverage, dependence on predefined probes, and difficulty identifying atypical or noncanonical fusion partners. These constraints often result in [...] Read more.
Background/Objectives: Fluorescence in situ hybridization (FISH) is a standard diagnostic tool for detecting gene fusions and rearrangements in lymphomas but is limited by incomplete genomic coverage, dependence on predefined probes, and difficulty identifying atypical or noncanonical fusion partners. These constraints often result in inconclusive diagnoses in complex lymphoma cases. This study evaluates a novel Hi-C-based sequencing assay from formalin-fixed paraffin-embedded (FFPE) samples to detect clinically significant gene fusions and rearrangements in cases where conventional FISH was inconclusive or expected biomarkers were not detected. Methods: Five diffuse large B-cell lymphoma cases with previously atypical gene fusions or rearrangements by FISH were analyzed using both standard FISH and a Hi-C-based lymphoma assay. Standard FISH was performed using break-apart probes targeting MYC, BCL2, and BCL6, and dual-fusion probes targeting IGH::MYC and IGH::BCL2. The Hi-C assay utilized high-resolution sequencing of FFPE tissue to map chromatin interactions and identify structural variations across the genome and assessment of their clinical relevance. Results: In this series of five lymphoma cases, Hi-C detected additional structural variants beyond those identified by FISH. It identified typical and atypical translocation partners of key oncogenes (MYC, BCL2, BCL6), cryptic breakpoints, and novel genomic events, including TP53 loss, KMT2A amplification, and complex rearrangements, which were undetectable by FISH. The Hi-C assay’s whole-genome coverage enabled comprehensive profiling. Conclusions: The Hi-C-based lymphoma assay offers a transformative diagnostic tool, overcoming FISH limitations by providing unbiased, high-resolution detection of structural variations. This approach enhances diagnostic accuracy and supports personalized therapeutic strategies in lymphoma management, warranting further validation for clinical adoption. Full article
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12 pages, 269 KB  
Article
The Effect of HER2 Status on Gastric Cancer Survival and the Clinical Implications of the HER2-Low Definition: A Retrospective Study
by Mehmet Uzun, Savas Gokcek, Melis Kilinc, Ferhat Ekinci, Tugay Avci, Atike Pinar Erdogan, Elif Atag and Ilkay Tugba Unek
Medicina 2025, 61(9), 1675; https://doi.org/10.3390/medicina61091675 - 15 Sep 2025
Viewed by 387
Abstract
Background and Objectives: HER-2 expression plays a critical role in the biological behavior and treatment of gastric cancer. With the emergence of HER-2-targeted therapies, classification into negative, low, and positive groups has gained clinical importance. The present study focused on assessing the [...] Read more.
Background and Objectives: HER-2 expression plays a critical role in the biological behavior and treatment of gastric cancer. With the emergence of HER-2-targeted therapies, classification into negative, low, and positive groups has gained clinical importance. The present study focused on assessing the link between HER-2 status and clinical–pathological variables, metastatic involvement, and overall survival (OS) among advanced gastric cancer patients. Materials and Methods: A total of 300 patients with advanced gastric adenocarcinoma were retrospectively analyzed. The mean age of the 300 patients included in the study was 61.8 years, and 70% of them were male. Based on immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH), patients were classified as HER-2-negative (IHC 0), HER-2-low (IHC 1+ or 2+/FISH-negative), or HER-2-positive (IHC 3+ or 2+/FISH-positive). Clinicopathological variables, metastatic sites, and OS were compared among groups using Pearson’s Chi-square, Fisher’s exact test, ANOVA, and Kaplan–Meier survival analysis. Results: Significant differences were observed among HER-2 subgroups in pathological subtype (p = 0.006), liver metastasis (p = 0.009), lung metastasis (p = 0.006), and other metastatic sites (p = 0.001). HER-2-positive patients demonstrated higher rates of adenocarcinoma histology and increased liver and lung metastases. In female patients, HER-2 status was significantly associated with lung (p = 0.001) and other metastases (p < 0.001). Median OS for the entire cohort was 9.83 months (95% CI: 8.29–11.36). HER-2-positive patients had a significantly longer OS (15.06 months) compared with HER-2-negative patients (8.73 months; p = 0.039). Conclusions: HER-2 status is an important predictor of metastatic behavior and survival in advanced gastric cancer. HER-2-positive patients display distinct metastatic patterns and improved outcomes, supporting the value of HER-2-targeted therapies. The HER-2-low group may represent a biologically and clinically relevant intermediate subtype requiring further investigation. Full article
(This article belongs to the Special Issue Prophylaxis, Diagnosis, and Treatment Strategies of Gastric Cancer)
16 pages, 3399 KB  
Article
Uncovering Rare Structural Chromosomal Rearrangements: Insights from Molecular Cytogenetics
by Márta Czakó, András Szabó, Ágnes Till, Anna Zsigmond and Kinga Hadzsiev
Int. J. Mol. Sci. 2025, 26(18), 8886; https://doi.org/10.3390/ijms26188886 - 12 Sep 2025
Viewed by 250
Abstract
Complex chromosomal rearrangements (CCRs) are rare structural abnormalities involving at least three chromosomal breakpoints and often two or more chromosomes. Owing to their inherent genomic complexity, CCRs are frequently associated with abnormal phenotypes, including developmental delay, congenital anomalies, and infertility. In this study, [...] Read more.
Complex chromosomal rearrangements (CCRs) are rare structural abnormalities involving at least three chromosomal breakpoints and often two or more chromosomes. Owing to their inherent genomic complexity, CCRs are frequently associated with abnormal phenotypes, including developmental delay, congenital anomalies, and infertility. In this study, we report four male patients, three of them with de novo rare structural chromosomal rearrangement detected through a combination of Giemsa-Trypsin (GTG) banding, fluorescence in situ hybridization (FISH), and high-resolution microarray techniques (SNP array and array CGH). Each of the four cases turned out to be of a different type: in addition to two exceptional CCRs, an inv dup del 18q and a cluster rearrangement involving the long arm of chromosome 4 were identified. Despite the limitations of the testing methods, we performed a detailed analysis of the relationship between the most detailed genotype data and the associated phenotype. Our study provides further valuable evidence that the use of molecular cytogenetic methods is of paramount importance even in cases with abnormal karyotypes detected by light microscopy, as high-resolution data may reveal unsuspected genomic complexity, which is essential for genetic counseling in these patients. Full article
(This article belongs to the Special Issue Exploring Rare Diseases: Genetic, Genomic and Metabolomic Advances)
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20 pages, 12921 KB  
Article
Ole-e-1 Interacts with FWL Genes to Modulate Cell Division and Determine Fruit Size in Pears
by Jingyi Sai, Yue Wen, Yan Zhang, Xiaoqiu Pu, Chen Chen, Lei Wang, Mengli Zhu and Jia Tian
Int. J. Mol. Sci. 2025, 26(18), 8804; https://doi.org/10.3390/ijms26188804 - 10 Sep 2025
Viewed by 196
Abstract
The fw2.2 (fruit weight 2.2) gene negatively regulates cell division and significantly influences fruit size, but its regulatory mechanisms in pears remain unclear. Here, we investigated how pear FWL (fw2.2-like) genes control cell division using Duli pear, Korla fragrant [...] Read more.
The fw2.2 (fruit weight 2.2) gene negatively regulates cell division and significantly influences fruit size, but its regulatory mechanisms in pears remain unclear. Here, we investigated how pear FWL (fw2.2-like) genes control cell division using Duli pear, Korla fragrant pear, and Yali pear. During the cell division phase, fluorescence in situ hybridization (FISH) revealed stronger expression of FWL1 and FWL5 in smaller fruits compared to larger ones, with both genes localized in the core and flesh tissues. Gene silencing experiments demonstrated that silencing of FWL5 leads to a significant increase in the number of cells, with a concomitant enlargement of the fruit. Yeast two-hybrid screening identified 147 proteins interacting with FWL5, showing substantial overlap with FWL1 interactors. Key candidates included metallothionein-like protein (MT) and Ole-e-1, with the latter displaying a positive correlation with fruit size during cell division. Bimolecular fluorescence complementation (BiFC) confirmed direct interactions between Ole-e-1 and both FWL1/FWL5. Functional analysis indicated the Ole-e-1 gene family has diverse roles in pear development. We propose that Ole-e-1 interacts with FWL genes to modulate cell division, thereby determining final fruit size. This study uncovers a novel regulatory axis linking cell cycle control and fruit size in pears. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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12 pages, 393 KB  
Review
Research Progress on 35S rDNA and 5S rDNA in Sugarcane: Challenges and Prospects
by Xueting Li, Yirong Guo, Zhejun Guo, Nannan Zhang, Yawen Lei, Enping Cai, Zuhu Deng and Jiayun Wu
Int. J. Mol. Sci. 2025, 26(18), 8773; https://doi.org/10.3390/ijms26188773 - 9 Sep 2025
Viewed by 460
Abstract
rDNA is abundant in various organisms, typically expressed as conserved tandem repeats. It plays a crucial role in ribosome synthesis, gene transcription, and expression, and it affects the occurrence of diseases in both animals and plants, aging, protein synthesis, genomic stability, and genome [...] Read more.
rDNA is abundant in various organisms, typically expressed as conserved tandem repeats. It plays a crucial role in ribosome synthesis, gene transcription, and expression, and it affects the occurrence of diseases in both animals and plants, aging, protein synthesis, genomic stability, and genome evolution across a wide range of organisms. Among the different types of rDNA, 35S rDNA (also referred to as 45S rDNA) and 5S rDNA are particularly important in plant research. The use of 35S rDNA and 5S rDNA as probes has enabled the study of chromosomal composition, revealing species characteristics that are valuable for crop breeding, evolutionary biology, systematics, and other fields. This review focuses on the application of 35S rDNA and 5S rDNA and discusses research findings on sugarcane and its related germplasm that have been obtained through fluorescence in situ hybridization. This information has provided a foundation for understanding the genetic relationships, genetics, breeding, and evolutionary classification of sugarcane. Full article
(This article belongs to the Section Molecular Plant Sciences)
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15 pages, 3450 KB  
Article
High-Intensity In Situ Fluorescence Imaging of MicroRNA in Cells Based on Y-Shaped Cascade Assembly
by Yan Liu, Xueqing Fan, Xinying Zhou, Zhiqi Zhang, Qi Yang, Rongjie Yang, Yingxue Li, Anran Zheng, Lianqun Zhou, Wei Zhang and Jinze Li
Chemosensors 2025, 13(9), 343; https://doi.org/10.3390/chemosensors13090343 - 6 Sep 2025
Viewed by 1341
Abstract
MicroRNAs are closely associated with various physiological and pathological processes, making their in situ fluorescence imaging crucial for functional studies and disease diagnosis. Current methods for the in situ fluorescence imaging of microRNA predominantly rely on linear signal amplification, resulting in relatively weak [...] Read more.
MicroRNAs are closely associated with various physiological and pathological processes, making their in situ fluorescence imaging crucial for functional studies and disease diagnosis. Current methods for the in situ fluorescence imaging of microRNA predominantly rely on linear signal amplification, resulting in relatively weak imaging signals. This study introduces a Y-shaped cascade assembly (YCA) method for high-brightness microRNA imaging in cells. Triggered by target microRNA, catalytic hairpin assembly forms double-stranded DNA (H). Through annealing and hybridization, a Y-shaped structure (P) is created. These components assemble into DNA nanofluorescent particles with multiple FAM fluorophores, significantly amplifying fluorescence signals. Optimization experiments revealed that a 1:1 ratio of P to H and an assembly time of 60 min yielded the best results. Under these optimal conditions, the resulting fluorescent nanoparticles exhibited diameters of 664.133 nm, as observed by DLS. In Huh7 liver cancer cells, YCA generated DNA nanoparticles with a fluorescence intensity increase of 117.77%, triggered by target microRNA-21, producing high-intensity fluorescence images and enabling qualitative detection of microRNA-21. The YCA in situ imaging method offers excellent imaging quality and high efficiency, providing a robust and reliable analytical tool for the diagnosis and monitoring of microRNA-related diseases. Full article
(This article belongs to the Special Issue Advancements of Chemosensors and Biosensors in China—2nd Edition)
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12 pages, 876 KB  
Article
Development of a Cytogenetic Double-Hit Model for Survival Prediction in Multiple Myeloma
by Chenxing Du, Jian Cui, Jingyu Xu, Wenqiang Yan, Lingna Li, Weiwei Sui, Shuhui Deng, Shuhua Yi, Yan Xu, Chengwen Li, Jiawei Zhao, Dehui Zou, Lugui Qiu and Gang An
Cancers 2025, 17(16), 2703; https://doi.org/10.3390/cancers17162703 - 20 Aug 2025
Viewed by 721
Abstract
Background: High-risk chromosomal abnormalities (HRCAs) detected by fluorescence in situ hybridization (FISH) have a well-established adverse prognostic impact in multiple myeloma (MM). It is increasingly recognized that the coexistence of two or more HRCAs identifies a particularly poor-risk subgroup, often referred to as [...] Read more.
Background: High-risk chromosomal abnormalities (HRCAs) detected by fluorescence in situ hybridization (FISH) have a well-established adverse prognostic impact in multiple myeloma (MM). It is increasingly recognized that the coexistence of two or more HRCAs identifies a particularly poor-risk subgroup, often referred to as double- or multiple-hit MM. However, there is currently no consensus on its definition. Methods: We retrospectively analyzed a multicenter cohort of 1122 newly diagnosed MM patients from 2008 to 2019. Double-hit MM was defined as the coexistence of at least two of the following four HRCAs: t(14;16), gain(1q), del(17p), and del(1p). Based on this definition, we constructed a novel prognostic model, the HBDH (Institute of Hematology & Blood Diseases Hospital) double-hit model, and assessed its prognostic value for progression-free survival (PFS) and overall survival (OS). Results: According to the HBDH model, double-hit patients showed significantly inferior outcomes compared to non-double-hit patients, with median PFS of 20.6 vs. 53.3 months (p < 0.001) and median OS of 40.2 vs. 84.2 months (p < 0.001). The addition of del(13q), t(4;14), or t(11;14) did not improve the prognostic performance of the model. Importantly, the HBDH model was independent of the International Staging System (ISS), elevated LDH, and advanced age. Conclusions: The HBDH double-hit model identifies a subset of ultra-high-risk MM patients carrying at least two major HRCAs, providing a simple and robust framework for prognostic stratification and a potential reference for future biologically driven treatment approaches. Full article
(This article belongs to the Special Issue Myeloma: Pathogenesis and Targeted Therapies)
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