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Keywords = DNA mismatch repair genes

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23 pages, 5771 KiB  
Article
Photobiomodulation of 450 nm Blue Light on Human Keratinocytes, Fibroblasts, and Endothelial Cells: An In Vitro and Transcriptomic Study on Cells Involved in Wound Healing and Angiogenesis
by Jingbo Shao, Sophie Clément, Christoph Reissfelder, Patrick Téoule, Norbert Gretz, Feng Guo, Sabina Hajizada, Stefanie Uhlig, Katharina Mößinger, Carolina de la Torre, Carsten Sticht, Vugar Yagublu and Michael Keese
Biomedicines 2025, 13(8), 1876; https://doi.org/10.3390/biomedicines13081876 - 1 Aug 2025
Viewed by 169
Abstract
Background: Blue light (BL) irradiation has been shown to induce photobiomodulation (PBM) in cells. Here, we investigate its influence on cell types involved in wound healing. Methods: Cellular responses of immortalized human keratinocytes (HaCaTs), normal human dermal fibroblasts (NHDFs), and human [...] Read more.
Background: Blue light (BL) irradiation has been shown to induce photobiomodulation (PBM) in cells. Here, we investigate its influence on cell types involved in wound healing. Methods: Cellular responses of immortalized human keratinocytes (HaCaTs), normal human dermal fibroblasts (NHDFs), and human umbilical vein endothelial cells (HUVECs) after light treatment at 450 nm were analyzed by kinetic assays on cell viability, proliferation, ATP quantification, migration assay, and apoptosis assay. Gene expression was evaluated by transcriptome analysis. Results: A biphasic effect was observed on HaCaTs, NHDFs, and HUVECs. Low-fluence (4.5 J/cm2) irradiation stimulated cell viability, proliferation, and migration. mRNA sequencing indicated involvement of transforming growth factor beta (TGF-β), ErbB, and vascular endothelial growth factor (VEGF) pathways. High-fluence (18 J/cm2) irradiation inhibited these cellular activities by downregulating DNA replication, the cell cycle, and mismatch repair pathways. Conclusions: HaCaTs, NHDFs, and HUVECs exhibited a dose-dependent pattern after BL irradiation. These findings broaden the view of PBM following BL irradiation of these three cell types, thereby promoting their potential application in wound healing and angiogenesis. Our data on low-fluence BL at 450 nm indicates clinical potential for a novel modality in wound therapy. Full article
(This article belongs to the Section Cell Biology and Pathology)
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14 pages, 3767 KiB  
Article
Unveiling Replication Timing-Dependent Mutational Biases: Mechanistic Insights from Gene Knockouts and Genotoxins Exposures
by Hadas Gross-Samuels, Amnon Koren and Itamar Simon
Int. J. Mol. Sci. 2025, 26(15), 7307; https://doi.org/10.3390/ijms26157307 - 29 Jul 2025
Viewed by 248
Abstract
Replication timing (RT), the temporal order of DNA replication during S phase, influences regional mutation rates, yet the mechanistic basis for RT-associated mutagenesis remains incompletely defined. To identify drivers of RT-dependent mutation biases, we analyzed whole-genome sequencing data from cells with disruptions in [...] Read more.
Replication timing (RT), the temporal order of DNA replication during S phase, influences regional mutation rates, yet the mechanistic basis for RT-associated mutagenesis remains incompletely defined. To identify drivers of RT-dependent mutation biases, we analyzed whole-genome sequencing data from cells with disruptions in DNA replication/repair genes or exposed to mutagenic compounds. Mutation distributions between early- and late-replicating regions were compared using bootstrapping and statistical modeling. We identified 14 genes that exhibit differential effects in early- or late-replicating regions, encompassing multiple DNA repair pathways, including mismatch repair (MLH1, MSH2, MSH6, PMS1, and PMS2), trans-lesion DNA synthesis (REV1) and double-strand break repair (DCLRE1A and PRKDC), DNA polymerases (POLB, POLE3, and POLE4), and other genes central to genomic instability (PARP1 and TP53). Similar analyses of mutagenic compounds revealed 19 compounds with differential effects on replication timing. These results establish replication timing as a critical modulator of mutagenesis, with distinct DNA repair pathways and exogenous agents exhibiting replication timing-specific effects on genomic instability. Our systematic bioinformatics approach identifies new DNA repair genes and mutagens that exhibit differential activity during the S phase. These findings pave the way for further investigation of factors that contribute to genome instability during cancer transformation. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
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12 pages, 910 KiB  
Article
Unusual Profile of Germline Genetic Variants in Unselected Colorectal Cancer Patients from a High-Prevalence Region in Panama
by Iván Landires, José Pinto, Raúl Cumbrera, Alexandra Nieto, Gumercindo Pimentel-Peralta, Yennifer Alfaro and Virginia Núñez-Samudio
Genes 2025, 16(8), 890; https://doi.org/10.3390/genes16080890 - 28 Jul 2025
Viewed by 479
Abstract
Background: The profile of germline genetic variants among colorectal cancer patients in Panama has not yet been explored. Methods: We recruited 95 patients with colorectal cancer in an Oncology Reference Hospital Unit in the Azuero region of central Panama, which exhibited the highest [...] Read more.
Background: The profile of germline genetic variants among colorectal cancer patients in Panama has not yet been explored. Methods: We recruited 95 patients with colorectal cancer in an Oncology Reference Hospital Unit in the Azuero region of central Panama, which exhibited the highest prevalence of colorectal cancer in Panama. DNA analysis was performed with a panel of 113 genes with germline mutations for cancer (TruSight® Cancer Sequencing Panel from Illumina, San Diego, CA, USA). Results: Among the 95 cases, 10 pathogenic/likely pathogenic variants (P/LP) were identified in the MUTYH, TP53, CHEK2, PALB2, ATM, and BARD1 genes, representing 10% of the total. The variant 1103G>A (p.Gly368Asp) in MUTYH was the most prevalent. The variant at c.1675_1676delCAinsTG (p.Gln559Ter) in PALB2 is new and is reported for the first time in this study. Variants were most frequently detected in the MUTYH and CHEK2 genes, affecting four and two patients, respectively. Notably, none of the 95 Panamanian patients in the initial colorectal cancer cohort had mutations in mismatch repair (MMR) genes. These genes are among the most frequently mutated in other cohorts around the world. Conclusions: The atypical profile of germline genetic variants in this population may be related to the unique characteristics of the Azuero population in Panama’s central region. This profile may partly explain the high prevalence of colorectal cancer among its inhabitants. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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19 pages, 6000 KiB  
Article
An Integrated Clinical, Germline, Somatic, and In Silico Approach to Assess a Novel PMS2 Gene Variant Identified in Two Unrelated Lynch Syndrome Families
by Candida Fasano, Antonia Lucia Buonadonna, Giovanna Forte, Martina Lepore Signorile, Valentina Grossi, Katia De Marco, Paola Sanese, Andrea Manghisi, Nicoletta Maria Tutino, Raffaele Armentano, Anna Maria Valentini, Vittoria Disciglio and Cristiano Simone
Cancers 2025, 17(14), 2308; https://doi.org/10.3390/cancers17142308 - 11 Jul 2025
Viewed by 351
Abstract
Background: Lynch syndrome (LS) is an autosomal dominant disease caused by germline pathogenic variants in one of the DNA mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) or the EPCAM gene. LS patients harboring genetic variants in [...] Read more.
Background: Lynch syndrome (LS) is an autosomal dominant disease caused by germline pathogenic variants in one of the DNA mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) or the EPCAM gene. LS patients harboring genetic variants in one of the MMR genes display a heterogeneous phenotype in terms of cancer penetrance (lifetime cancer risk) and expressivity (malignancies in gastrointestinal or other specific organs). Methods: DNA samples from the index cases of Family 1 and Family 2 were analyzed using a next-generation sequencing (NGS) multigene panel comprising 25 genes involved in major hereditary cancer predisposition syndromes. This NGS analysis revealed a variant of uncertain significance (VUS) in the PMS2 gene (NM_000535.7: c.184G>A; p.Gly62Arg) of both index cases, which was validated by Sanger sequencing. The structural and functional impact of this VUS was evaluated in silico using twelve different prediction tools and by immunohistochemical analysis of MMR proteins. Results: Based on the personal and family history of the two families, tumor pathology, and protein in silico analysis, the novel PMS2 gene variant described in this study may be associated with hereditary LS. Considering the low penetrance of PMS2 gene variants in LS-associated tumors and the intrafamilial variability of the associated clinical phenotypes, the multidisciplinary approach proposed in this study could significantly support the evaluation of suspected LS cases carrying PMS2 variants. Full article
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12 pages, 472 KiB  
Article
Impact of hMLH1 −93G>A (rs1800734) and hMSH2 1032G>A (rs4987188) Polymorphisms on Colorectal Cancer Susceptibility
by Bayram Bayramov, Nigar Karimova, Nigar Mehdiyeva, Hagigat Valiyeva, Rena Karimova, Royal Shirinov, Hazi Aslanov, Zumrud Safarzade, Orkhan Isayev and Nuru Bayramov
J. Mol. Pathol. 2025, 6(3), 15; https://doi.org/10.3390/jmp6030015 - 8 Jul 2025
Viewed by 318
Abstract
Background: This study is the first to investigate the association between colorectal cancer (CRC) risk and the hMLH1 −93G>A and hMSH2 1032G>A polymorphisms of mismatch repair (MMR) genes in the Azerbaijani population. Methods: Peripheral blood samples containing EDTA were collected from the study [...] Read more.
Background: This study is the first to investigate the association between colorectal cancer (CRC) risk and the hMLH1 −93G>A and hMSH2 1032G>A polymorphisms of mismatch repair (MMR) genes in the Azerbaijani population. Methods: Peripheral blood samples containing EDTA were collected from the study subjects (134 patients and 137 controls), and genomic DNA was extracted using the non-enzymatic salting-out method. Genotypes were determined by polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP), and the results were visualized through agarose gel electrophoresis. Results: Overall, no statistically significant correlation was observed between CRC risk and the hMLH1 −93G>A polymorphism in the heterozygous GA (OR = 0.760; 95% CI = 0.374–1.542; p = 0.446), the mutant AA (OR = 1.474; 95% CI = 0.738–2.945; p = 0.270), or the A allele (OR = 1.400; 95% CI = 0.984–1.995; p = 0.062). However, in contrast to the dominant model, a statistically significant association was found between the recessive model and an increased CRC risk, with an odds ratio of 1.788 (95% CI = 1.102–2.900; p = 0.018). The hMLH1 −93G>A polymorphism was identified at a significantly higher frequency across the TNM stages, with the distribution showing statistical significance (p < 0.05). Additionally, no statistically significant association was observed between the hMSH2 1032G>A polymorphism and CRC risk. Conclusions: Although no overall association was observed for hMLH1 −93G>A, our findings suggest a potential link with increased colorectal cancer risk under the recessive model in the Azerbaijani population. Further studies are warranted to confirm this model-specific association and investigate the underlying biological mechanisms. Full article
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19 pages, 24854 KiB  
Article
MiR5651, miR170-3p, and miR171a-3p Regulate Cadmium Tolerance by Targeting MSH2 in Arabidopsis thaliana
by Xianpeng Wang, Hetong Wang, Xiuru Sun, Zihan Tang, Zhouli Liu, Richard A. Ludlow, Min Zhang, Qijiang Cao, Wan Liu and Qiang Zhao
Plants 2025, 14(13), 2028; https://doi.org/10.3390/plants14132028 - 2 Jul 2025
Viewed by 323
Abstract
The DNA mismatch repair (MMR) system plays a crucial role in repairing DNA damage and regulating cell cycle arrest induced by cadmium (Cd) stress. To elucidate the mechanism by which miRNAs target AtMSH2 in regulating Arabidopsis’ response to Cd stress, the wild-type [...] Read more.
The DNA mismatch repair (MMR) system plays a crucial role in repairing DNA damage and regulating cell cycle arrest induced by cadmium (Cd) stress. To elucidate the mechanism by which miRNAs target AtMSH2 in regulating Arabidopsis’ response to Cd stress, the wild-type Arabidopsis, Atmsh2 mutant, and three miRNA-overexpressing transgenic lines were grown hydroponically in half-strength MS solution containing cadmium (Cd) at concentrations of 0, 0.5, 1, 2, and 3 mg/L for 5 days. miRNA-seq analysis, bioinformatics prediction, dual-luciferase reporter assays, and qRT-PCR results demonstrated that miR5651, miR170-3p, and miR171a-3p specifically targeted AtMSH2 and their expression levels showed a significant negative correlation. Compared to wild-type (WT) Arabidopsis, Cd stress tolerance was significantly enhanced in miRNA-overexpressing transgenic lines. Moreover, exogenous application of these three miRNAs in half-strength MS liquid medium also markedly improved Cd stress tolerance in wild-type Arabidopsis. Furthermore, the expression of these three miRNAs expression was further upregulated by Cd stress in a dose-dependent manner. Additionally, DNA damage response in miRNA-overexpressing transgenic lines was promoted based on the expression of DNA repair, DNA damage signaling, and cell cycle genes, which differed from both wild-type and Atmsh2 plants. Taken together, miR5651, miR170-3p, and miR171a-3p participated in Cd stress response and improved plant Cd tolerance by mediating the expression of AtMSH2. Our study provides novel insights into the epigenetic mechanisms of Cd tolerance in plants, which sheds light on breeding for stress resilience in phytoremediation. Full article
(This article belongs to the Special Issue In Vivo and In Vitro Studies on Heavy Metal Tolerance in Plants)
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17 pages, 1988 KiB  
Article
Transcriptomic Profiling of Thermotolerant Sarcomyxa edulis PQ650759 Reveals the Key Genes and Pathways During Fruiting Body Formation
by Zitong Liu, Minglei Li, Hongyu Ma, Fei Wang, Lei Shi, Jinhe Wang, Chunge Sheng, Peng Zhang, Haiyang Yu, Jing Zhao and Yanfeng Wang
J. Fungi 2025, 11(7), 484; https://doi.org/10.3390/jof11070484 - 26 Jun 2025
Viewed by 377
Abstract
Sarcomyxa edulis is a characteristic low-temperature, edible mushroom in Northeast China. It has a delicious taste and rich nutritional and medicinal value. S. edulis can undergo explosive fruiting, neat fruiting, and unified harvesting, making it suitable for factory production. The molecular mechanisms underlying [...] Read more.
Sarcomyxa edulis is a characteristic low-temperature, edible mushroom in Northeast China. It has a delicious taste and rich nutritional and medicinal value. S. edulis can undergo explosive fruiting, neat fruiting, and unified harvesting, making it suitable for factory production. The molecular mechanisms underlying fruiting body development in S. edulis remain poorly understood. This study employed transcriptome analysis to compare the post-ripening mycelium (NPM) and primordial fruiting bodies (PRMs) of the thermostable S. edulis strain PQ650759, which uniquely forms primordia under constant temperature. A total of 4862 differentially expressed genes (DEGs) (|log2(fold change)| ≥ 1) were identified and found to be predominantly enriched in biological processes such as cell wall organization, DNA replication, and carbohydrate metabolism. KEGG pathway analysis revealed significant enrichment in 20 metabolic pathways, including mismatch repair, yeast cell cycle, and starch/sucrose metabolism. Ten candidate genes (e.g., SKP1, MRE11, GPI) linked to cell cycle regulation, DNA repair, and energy metabolism were randomly selected and prioritized for functional analysis. Quantitative PCR validation confirmed the reliability of transcriptome data, with expression trends consistent across both methods. Our findings provide critical insights into the molecular regulation of fruiting body development in S. edulis and establish a foundation for future mechanistic studies and strain optimization in industrial cultivation. Full article
(This article belongs to the Special Issue Fungal Metabolomics and Genomics)
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18 pages, 2729 KiB  
Article
Genetic Features of Tumours Arising in the Context of Suspected Hereditary Cancer Syndromes with RAD50, RAD51C/D, and BRIP1 Germline Mutations, Results of NGS-Reanalysis of BRCA/MMR-Negative Families
by Mónica Arranz-Ledo, Mar Infante, Enrique Lastra, Amaya Olaverri, Marta Orozco, Lucia C. Mateo, Noemí Martínez, Lara Hernández and Mercedes Durán
Genes 2025, 16(4), 458; https://doi.org/10.3390/genes16040458 - 16 Apr 2025
Cited by 1 | Viewed by 1336
Abstract
Background and Objectives: Despite the well-established role of the BRCA and mismatch repair (MMR) genes in DNA damage repair pathways, a substantial proportion of familial cancer cases still lack pathogenic variants in those genes. Next Generation Sequencing (NGS) panels have emerged as a [...] Read more.
Background and Objectives: Despite the well-established role of the BRCA and mismatch repair (MMR) genes in DNA damage repair pathways, a substantial proportion of familial cancer cases still lack pathogenic variants in those genes. Next Generation Sequencing (NGS) panels have emerged as a powerful tool to identify hereditary cancer at-risk individuals and subsequently provide them with accurate management. Materials and Methods: Families harbouring PVs in RAD50, RAD51C, RAD51D, and BRIP1 were identified by analysing a cancer-predisposing genes panel using Ion S5 system technology. A retrospective cohort of 155 families tested only for the BRCAs of MMR genes were reanalysed, prompted by an increase in familial cases or new cancer diagnoses among index cases. Results: We identified 40 families through molecular reanalysis (33 with Hereditary Breast and Ovarian Cancer (HBOC) and 7 with Lynch Syndrome (LS)), with positive test results among 155 families lacking BRCA or MMR mutations. The most frequently mutated genes after ATM and CHEK2 were BRIP1, RAD51D, and RAD51C with 16, 13, and 9 positive families, respectively. The phenotype–genotype correlations not only revealed ovarian and HER-negative breast cancer predispositions but also other cancer types, particularly lung and gastric, and individuals with a second or third distinct cancer episode. Conclusions: Broader ranges of malignancies, including gastric, lung, and bladder, have been identified among BRIP1, RAD51D, and RAD51C positive families. The results generated using NGS provide a comprehensive genetic landscape in each patient that could explain the diversity of phenotypes shown in PV families that, combined with non-genetic factors, might enable accurate surveillance and personalized treatments. NGS reanalysis doubled our diagnostic yield and was a good strategy to identify hereditary cancer families that would otherwise be overlooked. Full article
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14 pages, 931 KiB  
Review
The Clinical Outcomes Among Patients Under 60 Years Old with Lynch Syndrome: Variations Based on Different Mutation Patterns
by Calin Muntean, Vasile Gaborean, Razvan Constantin Vonica, Alaviana Monique Faur, Vladut Iosif Rus, Ionut Flaviu Faur and Catalin Vladut Ionut Feier
Int. J. Mol. Sci. 2025, 26(7), 3383; https://doi.org/10.3390/ijms26073383 - 4 Apr 2025
Viewed by 806
Abstract
Lynch syndrome (LS)—also known as Hereditary Non-Polyposis Colorectal Cancer (HNPCC)—is caused by pathogenic germline mutations in DNA mismatch repair (MMR) genes such as MLH1, MSH2, MSH6, and PMS2. Although it accounts for only 1–5% of all colorectal cancers (CRCs), [...] Read more.
Lynch syndrome (LS)—also known as Hereditary Non-Polyposis Colorectal Cancer (HNPCC)—is caused by pathogenic germline mutations in DNA mismatch repair (MMR) genes such as MLH1, MSH2, MSH6, and PMS2. Although it accounts for only 1–5% of all colorectal cancers (CRCs), LS presents with a particularly high lifetime cancer risk and often occurs at younger ages. Identifying LS in patients under 60 years old is crucial for targeted surveillance and early interventions. Variations in clinical presentation and prognosis may exist based on the specific gene mutated, yet these patterns are not fully elucidated. This review aims to synthesize data on clinical outcomes among LS patients under 60, with an emphasis on how different MMR gene mutation patterns might influence prognosis, survival, and treatment decisions. Five population-based studies examining CRC patients younger than 60 years were included according to predefined eligibility criteria. Two independent reviewers screened and extracted data focusing on MMR deficiency detection methods (microsatellite instability [MSI] and/or immunohistochemistry [IHC]), rates of confirmed germline mutations, frequency of BRAF testing, and clinical endpoints such as stage distribution, survival outcomes, and recurrence. Risk of bias was assessed using standardized tools appropriate to each study design. The synthesis focused on comparing outcomes among individuals with MLH1, MSH2, MSH6, and PMS2 mutations, as well as delineating the proportion of patients with sporadic MSI under 60 years of age. Across the five studies, MSI positivity in CRC patients under 60 years ranged from 7.5% to 13%. The frequency of confirmed germline MMR mutations varied between 0.8% and 5.2% in specific cohorts, aligning with LS prevalence estimates of 1–5%. Different mutation patterns correlated with some variation in clinical presentation. Cases with MSH2 and MLH1 mutations more frequently exhibited synchronous or metachronous tumors, while MSH6 and PMS2 mutations displayed more heterogeneous IHC patterns. Where survival data were provided, LS patients under 60 years had better overall survival compared to MMR-proficient individuals, though some studies also noted a potential lack of benefit from standard 5-fluorouracil adjuvant therapy in MMR-deficient tumors. Screening by MSI or by IHC—supplemented with BRAF mutation testing to exclude sporadic MSI—facilitates early detection of LS in CRC patients under 60 and highlights notable differences between mutation types. Although overall outcomes for LS patients can be favorable, especially for stage II disease, the precise impact of each specific mutated gene on clinical course remains heterogeneous. Future large-scale prospective studies are needed to clarify optimal screening protocols and individualized treatment strategies for LS patients under 60. Full article
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15 pages, 2290 KiB  
Article
Tissue-Specific Effects of the DNA Helicase FANCJ/BRIP1/BACH1 on Repeat Expansion in a Mouse Model of the Fragile X-Related Disorders
by Diego Antonio Jimenez, Alexandra Walker, Karen Usdin and Xiaonan Zhao
Int. J. Mol. Sci. 2025, 26(6), 2655; https://doi.org/10.3390/ijms26062655 - 15 Mar 2025
Viewed by 874
Abstract
Fragile X-related disorders (FXDs) are caused by the expansion of a CGG repeat tract in the 5’-UTR of the FMR1 gene. The expansion mechanism is likely shared with the 45+ other human diseases resulting from repeat expansion, a process that has been shown [...] Read more.
Fragile X-related disorders (FXDs) are caused by the expansion of a CGG repeat tract in the 5’-UTR of the FMR1 gene. The expansion mechanism is likely shared with the 45+ other human diseases resulting from repeat expansion, a process that has been shown to require key mismatch repair (MMR) factors. FANCJ, a DNA helicase involved in unwinding unusual DNA secondary structures, has been implicated in a number of DNA repair processes including MMR. To test the role of FANCJ in repeat expansion, we crossed FancJ-null mice to an FXD mouse model. We found that loss of FANCJ resulted in a trend towards more extensive expansion that was significant for the small intestine and male germline. This finding has interesting implications for the expansion mechanism and raises the possibility that other DNA helicases may be important modifiers of expansion risk in certain cell types. Full article
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15 pages, 5075 KiB  
Article
Novel De Novo BRCA2 Variant in an Early-Onset Ovarian Cancer Reveals a Unique Tumor Evolution Pathway
by Gianmaria Miolo, Giovanni Canil, Maurizio Polano, Michele Dal Bo, Alessia Mondello, Antonio Palumbo, Fabio Puglisi and Giuseppe Corona
Int. J. Mol. Sci. 2025, 26(5), 2295; https://doi.org/10.3390/ijms26052295 - 5 Mar 2025
Viewed by 1171
Abstract
Ovarian cancer (OC) is a highly heterogeneous malignancy, often characterized by complex genomic alterations that drive tumor progression and therapy resistance. In this paper, we report a novel de novo BRCA2 germline variant NM_000059.3:c.(8693_8695delinsGT) associated with early-onset OC that featured two regions with [...] Read more.
Ovarian cancer (OC) is a highly heterogeneous malignancy, often characterized by complex genomic alterations that drive tumor progression and therapy resistance. In this paper, we report a novel de novo BRCA2 germline variant NM_000059.3:c.(8693_8695delinsGT) associated with early-onset OC that featured two regions with differential MMR (Mismatch Repair) gene expression. To date, only six cases of de novo BRCA2 variants have been reported, none of which were associated with early-onset high-grade serous OC. The immunohistochemical analysis of MMR genes revealed two distinct tumor areas, separated by a clear topographic boundary, with the heterogeneous expression of MLH1 and PMS2 proteins. Seventy-five percent of the tumor tissue showed positivity, while the remaining 25% exhibited a complete absence of expression, underscoring the spatial variability in MMR gene expression within the tumor. Integrated comparative spatial genomic profiling identified several tumor features associated with the genetic variant as regions of loss of heterozygosity (LOH) that involved BRCA2 and MLH1 genes, along with a significantly higher mutational tumor burden in the tumor area that lacked MLH1 and PMS2 expression, indicating its further molecular evolution. The following variants were acquired: c.6572C>T in NOTCH2, c.1852C>T in BCL6, c.191A>T in INHBA, c.749C>T in CUX1, c.898C>A in FANCG, and c.1712G>C in KDM6A. Integrated comparative spatial proteomic profiles revealed defects in the DNA repair pathways, as well as significant alterations in the extracellular matrix (ECM). The differential expression of proteins involved in DNA repair, particularly those associated with MMR and Base Excision Repair (BER), highlights the critical role of defective repair mechanisms in driving genomic instability. Furthermore, ECM components, such as collagen isoforms, Fibrillin-1, EMILIN-1, Prolargin, and Lumican, were found to be highly expressed in the MLH1/PMS2-deficient tumor area, suggesting a connection between DNA repair deficiencies, ECM remodeling, and tumor progression. Thus, the identification of the BRCA2 variant sheds light on the poorly understood interplay between DNA repair deficiencies and ECM remodeling in OC, providing new insights into their dual role in shaping tumor evolution and suggesting potential targets for novel therapeutic strategies. Full article
(This article belongs to the Special Issue Molecular Diagnostics and Genomics of Tumors)
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22 pages, 27088 KiB  
Article
Integrated Analysis of Somatic DNA Variants and DNA Methylation of Tumor Suppressor Genes in Colorectal Cancer
by Hisashi Nishiki, Hiroki Ura, Sumihito Togi, Hisayo Hatanaka, Hideto Fujita, Hiroyuki Takamura and Yo Niida
Int. J. Mol. Sci. 2025, 26(4), 1642; https://doi.org/10.3390/ijms26041642 - 14 Feb 2025
Viewed by 1040
Abstract
DNA methylation of tumor suppressor genes in cancer is known to be a mechanism for silencing gene expression, but much remains unknown about its extent and relationship to somatic variants at the DNA sequence level. In this study, we comprehensively analyzed DNA methylation [...] Read more.
DNA methylation of tumor suppressor genes in cancer is known to be a mechanism for silencing gene expression, but much remains unknown about its extent and relationship to somatic variants at the DNA sequence level. In this study, we comprehensively analyzed DNA methylation and somatic variants of all gene regions across the genome of the major tumor suppressor genes, APC, TP53, SMAD4, and mismatch repair genes in colorectal cancer using a novel next-generation sequencing-based analysis method. The Targeted Methyl Landscape (TML) shows that DNA hypermethylation patterns of these tumor suppressor genes in colorectal cancer are more complex and widespread than previously thought. Extremely high levels of DNA methylation were observed in relatively long regions around exon 1A of APC and exon 1 and surrounding region of MLH1. DNA hypermethylation occurred whether or not somatic DNA variants were present in the tumor. Even in tumors where the loss of heterozygosity has been demonstrated by somatic variants alone, additional methylation of the same gene can occur. Our data demonstrate that somatic variants and hypermethylation of these tumor suppressor genes were considered independent, parallel events, not exclusive of each other or having one event affecting the other. Full article
(This article belongs to the Section Molecular Oncology)
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13 pages, 699 KiB  
Review
The Influence of Diet and Obesity in Lynch Syndrome: What Do We Know So Far
by Cláudio Rodrigues, Susana Couto Irving, Paula Alves, Mário Dinis-Ribeiro, Catarina Brandão and Marta Correia
Nutrients 2024, 16(24), 4352; https://doi.org/10.3390/nu16244352 - 17 Dec 2024
Cited by 2 | Viewed by 1515
Abstract
Of all new cases of colorectal cancer, Lynch syndrome (LS) accounts for approximately 3%. This syndrome is the most common hereditary cancer syndrome and is caused by pathogenic variants in the genes responsible for DNA mismatch repair. Although the relationship between colorectal cancer [...] Read more.
Of all new cases of colorectal cancer, Lynch syndrome (LS) accounts for approximately 3%. This syndrome is the most common hereditary cancer syndrome and is caused by pathogenic variants in the genes responsible for DNA mismatch repair. Although the relationship between colorectal cancer risk and diet is well established, little is known regarding the influence of diet and nutritional characteristics on LS’s clinical evolution. There is some evidence suggesting that individuals living with LS should follow general guidelines for diet and alcohol restriction/moderation, so as to achieve and maintain a favorable weight status and overall health and quality of life. However, more research is needed, preferentially from clinical studies of a prospective nature with robust designs, to better inform diet and behavioral patterns targeting cancer prevention in LS. Full article
(This article belongs to the Section Nutrition and Obesity)
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10 pages, 2493 KiB  
Case Report
A Rare Case of a Malignant Proliferating Trichilemmal Tumor: A Molecular Study Harboring Potential Therapeutic Significance and a Review of Literature
by Mokhtar H. Abdelhammed, Hanna Siatecka, A. Hafeez Diwan, Christie J. Finch, Angela D. Haskins, David J. Hernandez and Ya Xu
Dermatopathology 2024, 11(4), 354-363; https://doi.org/10.3390/dermatopathology11040038 - 10 Dec 2024
Cited by 1 | Viewed by 1935
Abstract
Malignant proliferating trichilemmal tumors (MPTTs), arising from the external root sheath of hair follicles, are exceptionally rare, with limited documentation of their genetic alterations. We present a case of a 64-year-old African American woman who initially presented with a gradually enlarging nodule on [...] Read more.
Malignant proliferating trichilemmal tumors (MPTTs), arising from the external root sheath of hair follicles, are exceptionally rare, with limited documentation of their genetic alterations. We present a case of a 64-year-old African American woman who initially presented with a gradually enlarging nodule on her posterior scalp. An initial biopsy at an outside hospital suggested metastatic adenocarcinoma or squamous cell carcinoma (SCC) of an uncertain origin. A subsequent wide local excision revealed a 2.0 cm tumor demonstrating characteristic trichilemmal keratinization, characterized by an abrupt transition from the nucleated epithelium to a laminated keratinized layer, confirming MPTT. Immunohistochemistry demonstrated diffuse p53 expression, patchy CD 34 expression, focal HER2 membranous expression, and patchy p16 staining (negative HPV ISH). A molecular analysis identified TP53 mutation and amplifications in the ERBB2 (HER2), BRD4, and TYMS. Additional gene mutations of uncertain significance included HSPH1, ATM, PDCD1 (PD-1), BARD1, MSH3, LRP1B, KMT2C (MLL3), GNA11, and RUNX1. Assessments for the homologous recombination deficiency, PD-L1 expression, gene rearrangement, altered splicing, and DNA mismatch repair gene expression were negative. The confirmation of ERBB2 (HER2) amplification in the MPTT through a molecular analysis suggests potential therapeutic avenues involving anti-HER2 monoclonal antibodies. The presence of the TP53 mutation, without the concurrent gene mutations typically observed in SCC, significantly aided in this differential diagnosis. Full article
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14 pages, 343 KiB  
Review
Gynecological Insights into Lynch Syndrome—A Comprehensive Review of Cancer Screening and Prevention
by Elena Chitoran, Roxana-Elena Bohiltea, Vlad Rotaru, Cristiana-Elena Durdu, Madalina-Nicoleta Mitroiu and Laurentiu Simion
Medicina 2024, 60(12), 2013; https://doi.org/10.3390/medicina60122013 - 6 Dec 2024
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Abstract
Lynch syndrome, one of the most common genetic syndromes predisposing to cancer, is associated with a series of malignant conditions, among which the most frequent is colorectal cancer, but gynecologic cancers (especially endometrial) are also quite common. Despite the significant progress made in [...] Read more.
Lynch syndrome, one of the most common genetic syndromes predisposing to cancer, is associated with a series of malignant conditions, among which the most frequent is colorectal cancer, but gynecologic cancers (especially endometrial) are also quite common. Despite the significant progress made in understanding this condition over time, there are still aspects in managing this condition that have not demonstrated clear benefits. This article aims to summarize the recommendations of international societies and present the latest developments in managing Lynch syndrome, focusing on gynecologic cancer screening and possible prevention strategies. Advances in genetic testing procedures and discoveries related to the association between oncological pathology frequency and the affected pathogenic variant type will probably lead to personalized medicine focused on the individual patient in the coming years. Although various screening methods for gynecological cancers in patients with Lynch syndrome have been used over time, they have not shown significant survival benefits. This highlights the need for studying and implementing new screening and diagnostic methods, which have been under investigation in recent years and are mentioned in this article. Full article
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