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18 pages, 925 KB  
Article
Unveiling the Microbiota: A New Frontier in Breast Cancer Pathogenesis—A Single-Center Preliminary Study
by Rukie Ana Maria Ahmet, Andrei Gabriel Nascu, Georgiana Cristina Camen, Cosmin Vasile Obleaga, Dragos George Popa and Cecil Sorin Mirea
Diagnostics 2025, 15(17), 2147; https://doi.org/10.3390/diagnostics15172147 (registering DOI) - 25 Aug 2025
Abstract
Background: Breast cancer is the most common malignancy affecting women worldwide and continues to pose significant challenges despite progress in early detection and personalized therapies. While its pathogenesis has traditionally been associated with genetic, hormonal, and environmental factors, recent studies have highlighted the [...] Read more.
Background: Breast cancer is the most common malignancy affecting women worldwide and continues to pose significant challenges despite progress in early detection and personalized therapies. While its pathogenesis has traditionally been associated with genetic, hormonal, and environmental factors, recent studies have highlighted the potential role of dysbiosis—an imbalance in gut and systemic microbiota—in breast cancer development and progression. This article aims to examine the mechanisms through which systemic dysbiosis may contribute to breast cancer risk and explore its therapeutic implications. Methods: This study seeks to analyze and compare the fecal microbiota profiles of breast cancer patients and healthy individuals from a single center in Craiova, Romania, in order to identify microbial signatures linked to breast cancer and BRCA mutation status. Special attention is given to the gut–liver axis and its influence on estrogen circulation, a key factor in hormone-sensitive breast cancers. Results: Evidence suggests that dysbiosis can influence breast cancer progression by promoting chronic inflammation, impairing immune regulation, and altering estrogen metabolism through the gut–liver axis. These effects may contribute to tumor development, immune evasion, and therapeutic resistance. Interventions aimed at restoring microbial balance show promise in preclinical studies for mitigating these effects. Conclusions: Systemic dysbiosis represents a potentially modifiable risk factor in breast cancer. Microbiota profiling may serve as a useful biomarker for risk stratification and therapeutic response. Future research into microbiome-based interventions could offer novel approaches for prevention and treatment in breast cancer care. Full article
(This article belongs to the Special Issue Diagnosis, Treatment, and Prognosis of Breast Cancer)
10 pages, 474 KB  
Communication
Compound Heterozygous Complete Loss-of-Function SPINK1 Variants as a Novel Cause of Severe Infantile Isolated Exocrine Pancreatic Insufficiency
by Emmanuelle Masson, Marc Wangermez, David Tougeron, Vinciane Rebours, Claude Férec and Jian-Min Chen
Genes 2025, 16(9), 998; https://doi.org/10.3390/genes16090998 (registering DOI) - 25 Aug 2025
Abstract
Background/Objectives: While complete loss-of-function (LoF) SPINK1 variants in the simple heterozygous state cause chronic pancreatitis, biallelic complete LoF variants result in a rare pediatric disorder termed severe infantile isolated exocrine pancreatic insufficiency (SIIEPI). To date, only two individuals with a null SPINK1 genotype [...] Read more.
Background/Objectives: While complete loss-of-function (LoF) SPINK1 variants in the simple heterozygous state cause chronic pancreatitis, biallelic complete LoF variants result in a rare pediatric disorder termed severe infantile isolated exocrine pancreatic insufficiency (SIIEPI). To date, only two individuals with a null SPINK1 genotype have been reported—one homozygous for a whole-gene deletion and the other for an Alu insertion in the 3′ untranslated region. Here, we report the genetic basis of a third SIIEPI case, presenting in early infancy with severe exocrine pancreatic insufficiency and diffuse pancreatic lipomatosis. Methods: Targeted next-generation sequencing (NGS) was used to analyze the entire coding region and exon–intron boundaries of the SPINK1 gene. Copy number variant (CNV) analysis was performed with SeqNext, based on normalized amplicon coverage. Results: The proband harbored compound heterozygous complete LoF SPINK1 variants. One was the known NM_001379610.1:c.180_181del (p.(Cys61PhefsTer2)), inherited from the father. The second, initially detected as an exon 2 deletion and confirmed by quantitative fluorescent multiplex PCR (QFM-PCR), was further characterized by long-range PCR as a complex rearrangement comprising a 1185 bp deletion removing exon 2, a 118 bp templated insertion followed by a non-templated nucleotide, and an 8 bp deletion. The mutational signature is consistent with serial replication slippage or template switching involving translesion synthesis. This maternally inherited variant has not been previously reported. Conclusions: This study expands the mutational spectrum of SPINK1-related SIIEPI and suggests that this distinct pediatric disorder may be under recognized in clinical practice. Full article
(This article belongs to the Special Issue Genetics and Genomics of Heritable Pediatric Disorders)
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12 pages, 1408 KB  
Article
The Genetic Structure of Cape Verdean Population Revealed by Y-Chromosome STRs
by Rita Costa, Jennifer Fadoni, António Amorim and Laura Cainé
Genes 2025, 16(9), 999; https://doi.org/10.3390/genes16090999 (registering DOI) - 25 Aug 2025
Abstract
Background/Objectives: Y-chromosomal short tandem repeats (Y-STR) are genetic markers widely used in forensic and population genetics. However, despite their importance, many populations remain under-represented in published studies and genetic databases. One such population is the Cape Verdean, which, despite its unique history of [...] Read more.
Background/Objectives: Y-chromosomal short tandem repeats (Y-STR) are genetic markers widely used in forensic and population genetics. However, despite their importance, many populations remain under-represented in published studies and genetic databases. One such population is the Cape Verdean, which, despite its unique history of admixture between European and sub-Saharan African populations, continues to be under-represented in global Y-STR reference databases. This study aims to characterize the Y-STR haplotype diversity and paternal lineage composition of the Cape Verdean population using a high-resolution STR panel. Methods: A total of 143 unrelated Cape Verdean men were analyzed using a set of 26 Y-STR loci, including rapidly mutating markers. Allele and haplotype frequencies were calculated, along with standard forensic parameters such as gene and haplotype diversity. Paternal lineages were inferred, and genetic relationships with other populations were evaluated using distance-based and graphical methods. Results: A total of 135 haplotypes were detected, with 88.8% being unique, yielding a haplotype diversity of 0.999. The most common haplogroups reflected both West African and European ancestry. Genetic distance analysis positioned the Cape Verdean population between African and European groups, supporting its intermediate and admixed genetic background. Conclusions: This study provides the first high-resolution Y-STR dataset for Cape Verdeans, contributing valuable reference data for forensic casework and population genetic studies. The results highlight the utility of extended Y-STR panels in admixed populations and underscore the need to enhance the representation of admixed populations in international forensic reference databases. Full article
(This article belongs to the Section Population and Evolutionary Genetics and Genomics)
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17 pages, 1420 KB  
Article
Genomic Evolution of SARS-CoV-2 Variants of Concern Under In Vitro Neutralising Selection Pressure Following Two Doses of the Pfizer-BioNTech BNT162b2 COVID-19 Vaccine
by Kerri Basile, Jessica E. Agius, Winkie Fong, Kenneth McPhie, Danny Ko, Linda Hueston, Connie Lam, David Pham, Sharon C.-A. Chen, Susan Maddocks, Matthew V. N. O’Sullivan, Dominic E. Dwyer, Vitali Sintchenko, Jen Kok and Rebecca J. Rockett
Viruses 2025, 17(9), 1161; https://doi.org/10.3390/v17091161 (registering DOI) - 25 Aug 2025
Abstract
We aimed to explore SARS-CoV-2 evolution during in vitro neutralisation using next generation sequencing, and to determine whether sera from individuals immunised with two doses of the Pfizer-BioNTech vaccine (BNT162b2) were as effective at neutralising the variant of concern (VOC) Delta (B.1.617.2) compared [...] Read more.
We aimed to explore SARS-CoV-2 evolution during in vitro neutralisation using next generation sequencing, and to determine whether sera from individuals immunised with two doses of the Pfizer-BioNTech vaccine (BNT162b2) were as effective at neutralising the variant of concern (VOC) Delta (B.1.617.2) compared to the earlier lineages Beta (B.1.351) and wild-type (A.2.2) virus. Using a live-virus SARS-CoV-2 neutralisation assay in Vero E6 cells, we determined neutralising antibody titres (nAbT) against three SARS-CoV-2 strains (wild type, Beta, and Delta) in 14 participants (vaccine-naïve (n = 2) and post-second dose of BNT162b2 vaccination (n = 12)), median age 45 years [IQR 29–65]; the median time after the second dose was 21 days [IQR 19–28]. The determination of nAbT was based on cytopathic effect (CPE) and in-house quantitative reverse transcriptase real-time quantitative polymerase chain reaction (RT-qPCR) to confirm SARS-CoV-2 replication. A total of 110 representative samples including inoculum, neutralisation breakpoints at 72 h, and negative and positive controls underwent genome sequencing. By integrating live-virus neutralisation assays with deep sequencing, we characterised both functional antibody responses and accompanying viral genetic changes. There was a reduction in nAbT observed against the Delta and Beta VOC compared with wild type, 4.4-fold (p ≤ 0.0006) and 2.3-fold (p = 0.0140), respectively. Neutralising antibodies were not detected in one vaccinated immunosuppressed participant and the vaccine-naïve participants (n = 2). The highest nAbT against the SARS-CoV-2 variants investigated was obtained from a participant who was vaccinated following SARS-CoV-2 infection 12 months prior. Limited consensus level mutations occurred in the various SARS-CoV-2 lineage genomes during in vitro neutralisation; however, consistent minority allele frequency variants (MFV) were detected in the SARS-CoV-2 polypeptide, spike (S), and membrane protein. Findings from countries with high COVID-19 incidence may not be applicable to low-incidence settings such as Australia; as seen in our cohort, nAbT may be significantly higher in vaccine recipients previously infected with SARS-CoV-2. Monitoring viral evolution is critical to evaluate the impact of novel SARS-CoV-2 variants on vaccine effectiveness, as mutational profiles in the sub-consensus genome could indicate increases in transmissibility and virulence or suggest the development of antiviral resistance. Full article
(This article belongs to the Special Issue Emerging Concepts in SARS-CoV-2 Biology and Pathology 2.0)
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23 pages, 2029 KB  
Review
Cystic Fibrosis and Male Infertility: From Genetics to Future Perspectives in Assisted Reproductive Technologies
by Aris Kaltsas
Genes 2025, 16(9), 994; https://doi.org/10.3390/genes16090994 (registering DOI) - 25 Aug 2025
Abstract
Background/Objectives: Male infertility is a prevalent and often underrecognized manifestation of cystic fibrosis (CF), primarily caused by congenital bilateral absence of the vas deferens (CBAVD) due to CFTR gene mutations. With improved life expectancy in CF patients, reproductive counseling and fertility management [...] Read more.
Background/Objectives: Male infertility is a prevalent and often underrecognized manifestation of cystic fibrosis (CF), primarily caused by congenital bilateral absence of the vas deferens (CBAVD) due to CFTR gene mutations. With improved life expectancy in CF patients, reproductive counseling and fertility management have gained clinical relevance. Methods: This narrative review synthesizes current evidence on the genetic underpinnings, diagnostic evaluation, and reproductive management of male infertility in CF and CFTR-related disorders. It also highlights recent advances in assisted reproductive technologies (ART), the role of CFTR modulators, and emerging molecular research. Results: Most men with CF or CBAVD have intact spermatogenesis but present with obstructive azoospermia. Diagnosis relies on clinical examination, semen analysis, genetic testing, and imaging. Sperm retrieval combined with in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI) achieves high success rates. Genetic counseling is essential to assess reproductive risks and guide partner screening. New therapies—particularly CFTR modulators—have improved systemic health and fertility potential. Future directions include gene therapy, microfluidics-based sperm selection, and personalized molecular strategies. Conclusions: Male infertility in CF represents a treatable consequence of a systemic disease. Advances in reproductive medicine and precision genetics now offer affected men viable paths to biological parenthood while also emphasizing the broader health implications of male infertility. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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11 pages, 1285 KB  
Article
Parallel Neurological and Cardiac Progression in Hereditary Transthyretin Amyloidosis: An Integrated Clinical and Imaging Study
by Grazia Canciello, Stefano Tozza, Leopoldo Ordine, Brigida Napolitano, Giovanni Palumbo, Mariagiovanna Castiglia, Daniela Pacella, Raffaella Lombardi, Giovanni Esposito, Fiore Manganelli and Maria-Angela Losi
Diagnostics 2025, 15(17), 2143; https://doi.org/10.3390/diagnostics15172143 (registering DOI) - 25 Aug 2025
Abstract
Background: Hereditary transthyretin amyloidosis (ATTRv) is a rare, autosomal dominant multisystem disease caused by pathogenic variants in the transthyretin (TTR) gene. Although ATTRv is classically categorized into “cardiac” and “neurologic” phenotypes, recent evidence suggests a more complex and overlapping disease spectrum. Objectives: This [...] Read more.
Background: Hereditary transthyretin amyloidosis (ATTRv) is a rare, autosomal dominant multisystem disease caused by pathogenic variants in the transthyretin (TTR) gene. Although ATTRv is classically categorized into “cardiac” and “neurologic” phenotypes, recent evidence suggests a more complex and overlapping disease spectrum. Objectives: This study investigates the relationship between neurological staging and cardiac involvement through an integrated assessment of patients with confirmed TTR mutations. Methods and Results: Fifty-eight patients with genetically confirmed ATTRv (41% female, mean age 60 ± 15 years) were evaluated. Genotypes included Phe64Leu, Val30Met, Val122Ile, and others. Patients were stratified by neurological stage: G0 (asymptomatic carriers), G1 (symptomatic but ambulatory), and G2 (requiring walking support). Cardiac assessment included clinical evaluation, echocardiography with tissue Doppler, global longitudinal strain (GLS), and NT-proBNP levels. Cardiac markers worsened with neurological stage. NT-proBNP, left ventricular mass index, maximal wall thickness, and E/E′ ratio increased progressively, while GLS declined (G0: –19%, G1: –14%, G2: –13%; p < 0.001), indicating a progressive structural and functional myocardial disease. Ejection fraction remained preserved. Neurological stage independently predicted cardiac dysfunction after age adjustment. Conclusions: This is the first study to assess cardiac abnormalities across neurological stages in a well-characterized cohort of ATTRv patients. Cardiac involvement in ATTRv begins early, even in asymptomatic carriers, and progresses with neurological deterioration. GLS and diastolic parameters are sensitive indicators of early myocardial dysfunction, highlighting the need for integrated neurologic and cardiac monitoring in all patients with ATTRv, regardless of initial phenotype. Full article
(This article belongs to the Section Medical Imaging and Theranostics)
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17 pages, 5644 KB  
Article
Mutation Spectrum of GJB2 in Taiwanese Patients with Sensorineural Hearing Loss: Prevalence, Pathogenicity, and Clinical Implications
by Yi-Feng Lin, Che-Hong Chen, Chang-Yin Lee, Hung-Ching Lin and Yi-Chao Hsu
Int. J. Mol. Sci. 2025, 26(17), 8213; https://doi.org/10.3390/ijms26178213 - 24 Aug 2025
Abstract
Hearing loss is often caused by genetic and environmental factors, with inherited mutations responsible for 50–60% of cases. The GJB2 gene, encoding connexin 26, is a major contributor to nonsyndromic sensorineural hearing loss (NSHL) due to its role in cellular communication critical for [...] Read more.
Hearing loss is often caused by genetic and environmental factors, with inherited mutations responsible for 50–60% of cases. The GJB2 gene, encoding connexin 26, is a major contributor to nonsyndromic sensorineural hearing loss (NSHL) due to its role in cellular communication critical for auditory function. In Taiwan, common deafness-associated genes include GJB2, SLC26A4, OTOF, MYO15A, and MTRNR1, which were similar to those found in other populations. The most common pathogenic genes is GJB2 mutations and the hearing level in children with GJB2 p.V37I/p.V37I or p.V37I/c.235delC was estimated to deteriorate at approximately 1 decibel hearing level (dB HL)/year. We found another common mutation in Taiwan Biobank, GJB2 p.I203T, which were identified in our data and individuals carrying this mutation experienced more severe hearing loss, suggesting a synergistic effect of these mutations on auditory impairment. We suggest GJB2 whole genetic screening is recommended for clinical management and prevention strategies in Taiwan. This study used data from the Taiwan Biobank to analyze allele frequencies of GJB2 gene variants. Predictive software (PolyPhen-2 version 2.2, SIFT for missense variants 6.2.1, MutationTaster Ensembl 112 and Alphamissense CC BY-NC-SA 4.0) assessed the pathogenicity of specific mutations. Additionally, 82 unrelated NSHL patients were screened for mutations in these genes using PCR and DNA sequencing. The study explored the correlation between genetic mutations and the severity of hearing loss in patients. Several common GJB2 mutation sites were identified from the Taiwan Biobank, including GJB2 p.V37I (7.7%), GJB2 p.I203T (6%), GJB2 p.V27I (31%), and GJB2 p.E114G (22%). Bioinformatics analysis classified GJB2 p.I203T as pathogenic, while GJB2 p.V27I and GJB2 p.E114G were considered polymorphisms. Patients with GJB2 p.I203T mutation experienced more severe hearing loss, emphasizing the potential interaction between the gene in auditory impairment. The mutation patterns of GJB2 in the Taiwanese population are similar to other East Asian regions. Although GJB2 mutations represent the predominant genetic cause of hereditary hearing loss, the corresponding mutant proteins exhibit detectable aggregation, particularly at cell–cell junctions, suggesting at least partial trafficking to the plasma membrane. Genetic screening for these mutations—especially GJB2 p.I203T (6%), GJB2 p.V27I (31%), and GJB2 p.E114G (22%)—is essential for the effective diagnosis and management of non-syndromic hearing loss (NSHL) in Taiwan. We found GJB2 p.I203T which were identified in our data and individuals carrying this mutation experienced more severe hearing loss, suggesting a synergistic effect of these mutations on auditory impairment. We suggest whole GJB2 gene sequencing in genetic screening is recommended for clinical management and prevention strategies in Taiwan. These findings have significant clinical and public health implications for the development of preventive and therapeutic strategies. Full article
(This article belongs to the Special Issue Hearing Loss: Recent Progress in Molecular Genomics)
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17 pages, 1225 KB  
Review
The Role of Biomarkers in Surveillance of Ulcerative Colitis-Associated Colorectal Cancer: A Scoping Review
by Justin Kritzinger, Gynter Kotrri, Peter L. Lakatos, Talat Bessissow and Gary Wild
J. Clin. Med. 2025, 14(17), 5979; https://doi.org/10.3390/jcm14175979 - 24 Aug 2025
Abstract
Ulcerative colitis (UC) is associated with an elevated risk of colorectal cancer (CRC), driven by chronic inflammation and a distinct inflammation–dysplasia–carcinoma pathway. Conventional surveillance relies on colonoscopy and histologic assessment, but flat, multifocal dysplasia and sampling limitations challenge early detection. Tissue-based biomarkers offer [...] Read more.
Ulcerative colitis (UC) is associated with an elevated risk of colorectal cancer (CRC), driven by chronic inflammation and a distinct inflammation–dysplasia–carcinoma pathway. Conventional surveillance relies on colonoscopy and histologic assessment, but flat, multifocal dysplasia and sampling limitations challenge early detection. Tissue-based biomarkers offer promise in improving risk stratification and identifying patients at high risk for UC-associated CRC (UC-CRC). This review explores key categories of tissue biomarkers with potential clinical utility, including genetic mutations, epigenetic alterations, microRNA expression profiles, and markers of genomic instability such as telomere shortening, copy number variants, and aneuploidy. Many of these molecular alterations precede histologic dysplasia and reflect a “field effect,” suggesting their potential role in early cancer detection. Despite compelling associations between these biomarkers and neoplastic progression, most lack prospective validation and are not yet ready for routine clinical use. Future research should prioritize the development of integrated biomarker panels and validate their predictive accuracy in longitudinal UC cohorts. Molecular profiling may ultimately enable personalized, risk-adapted surveillance strategies that improve early detection while minimizing unnecessary interventions. Full article
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24 pages, 520 KB  
Systematic Review
Application of Artificial Intelligence in Inborn Errors of Immunity Identification and Management: Past, Present, and Future: A Systematic Review
by Ivan Taietti, Martina Votto, Marta Colaneri, Matteo Passerini, Jessica Leoni, Gian Luigi Marseglia, Amelia Licari and Riccardo Castagnoli
J. Clin. Med. 2025, 14(17), 5958; https://doi.org/10.3390/jcm14175958 (registering DOI) - 23 Aug 2025
Viewed by 51
Abstract
Background: Inborn errors of immunity (IEI) are mainly genetically driven disorders that affect immune function and present with highly heterogeneous clinical manifestations, ranging from severe combined immunodeficiency (SCID) to adult-onset immune dysregulatory diseases. This clinical heterogeneity, coupled with limited awareness and the [...] Read more.
Background: Inborn errors of immunity (IEI) are mainly genetically driven disorders that affect immune function and present with highly heterogeneous clinical manifestations, ranging from severe combined immunodeficiency (SCID) to adult-onset immune dysregulatory diseases. This clinical heterogeneity, coupled with limited awareness and the absence of a universal diagnostic test, makes early and accurate diagnosis challenging. Although genetic testing methods such as whole-exome and genome sequencing have improved detection, they are often expensive, complex, and require functional validation. Recently, artificial intelligence (AI) tools have emerged as promising for enhancing diagnostic accuracy and clinical decision-making for IEI. Methods: We conducted a systematic review of four major databases (PubMed, Scopus, Web of Science, and Embase) to identify peer-reviewed English-published studies focusing on the application of AI techniques in the diagnosis and treatment of IEI across pediatric and adult populations. Twenty-three retrospective/prospective studies and clinical trials were included. Results: AI methodologies demonstrated high diagnostic accuracy, improved detection of pathogenic mutations, and enhanced prediction of clinical outcomes. AI tools effectively integrated and analyzed electronic health records (EHRs), clinical, immunological, and genetic data, thereby accelerating the diagnostic process and supporting personalized treatment strategies. Conclusions: AI technologies show significant promise in the early detection and management of IEI by reducing diagnostic delays and healthcare costs. While offering substantial benefits, limitations such as data bias and methodological inconsistencies among studies must be addressed to ensure broader clinical applicability. Full article
(This article belongs to the Special Issue Inborn Errors of Immunity: Advances in Diagnosis and Treatment)
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11 pages, 2175 KB  
Case Report
First Case in Lithuania of an Autosomal Recessive Mutation in the DNAJC30 Gene as a Cause of Leber’s Hereditary Optic Neuropathy
by Liveta Sereikaite, Alvita Vilkeviciute, Brigita Glebauskiene, Rasa Traberg, Arvydas Gelzinis, Raimonda Piskiniene, Reda Zemaitiene, Rasa Ugenskiene and Rasa Liutkeviciene
Genes 2025, 16(9), 993; https://doi.org/10.3390/genes16090993 (registering DOI) - 23 Aug 2025
Viewed by 39
Abstract
Background: Leber’s hereditary optic neuropathy (LHON) is the most common mitochondrial disorder and an inherited optic neuropathy. Recently, two different LHON inheritance types have been discovered: mitochondrially inherited LHON (mtLHON) and autosomal recessive LHON (arLHON). Our case report is the first diagnosed case [...] Read more.
Background: Leber’s hereditary optic neuropathy (LHON) is the most common mitochondrial disorder and an inherited optic neuropathy. Recently, two different LHON inheritance types have been discovered: mitochondrially inherited LHON (mtLHON) and autosomal recessive LHON (arLHON). Our case report is the first diagnosed case of arLHON in a patient of Lithuanian descent and confirms the DnaJ Heat Shock Protein Family (Hsp40) Member C30 (DNAJC30) c.152A>G p.(Tyr51Cys) founder variant. Case Presentation: A 34-year-old Lithuanian man complained of headache and sudden, painless loss of central vision in his right eye. On examination, the visual acuity of the right and left eyes was 0.1 and 1.0, respectively. Visual-field examination revealed a central scotoma in the right eye, and visual evoked potentials (VEPs) showed prolonged latency in both eyes. Optical coherence tomography showed thickening of the retinal nerve fiber layer in the upper quadrant of the optic disk in the left eye. Magnetic resonance imaging of the head showed evidence of optic nerve inflammation in the right eye. Blood tests were within normal range and showed no signs of inflammation. Retrobulbar neuritis of the right eye was suspected, and the patient was treated with steroids, which did not improve visual acuity. He later developed visual loss in the left eye as well. A genetic origin of the optic neuropathy was suspected, and a complete mitochondrial DNA analysis was performed, but it did not reveal any pathologic mutations. Over time, the visual acuity of both eyes slowly deteriorated, and the retinal nerve fiber layer (RNFL) thinning of the optic disks progressed. A multidisciplinary team of specialists concluded that vasculitis or infectious disease was unlikely to be the cause of the vision loss, and a genetic cause for the disease was still suspected, although a first-stage genetic test did not yield the diagnosis. Thirty-three months after disease onset, whole-exome sequencing revealed a pathogenic variant in the DNAJC30 gene, leading to the diagnosis of arLHON. Treatment with Idebenone was started 35 months after the onset of the disease, resulting in no significant worsening of the patient’s condition. Conclusion: This case highlights the importance of considering arLHON as a possible diagnosis for patients with optic neuropathy, because the phenotype of arLHON appears to be identical to that of mtLHON and cannot be distinguished by clinicians. Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
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23 pages, 5200 KB  
Article
Genomic Insights into Tumorigenesis in Newly Diagnosed Multiple Myeloma
by Marina Kyriakou and Costas Papaloukas
Diagnostics 2025, 15(17), 2130; https://doi.org/10.3390/diagnostics15172130 - 23 Aug 2025
Viewed by 143
Abstract
Background: Multiple Myeloma (MM) is a malignant plasma cell dyscrasia that progresses through the consecutive asymptomatic, often undiagnosed, precancerous stages of Monoclonal Gammopathy of Undetermined Significance (MGUS) and Asymptomatic Multiple Myeloma (SMM). MM is characterized by low survival rates, severe complications and [...] Read more.
Background: Multiple Myeloma (MM) is a malignant plasma cell dyscrasia that progresses through the consecutive asymptomatic, often undiagnosed, precancerous stages of Monoclonal Gammopathy of Undetermined Significance (MGUS) and Asymptomatic Multiple Myeloma (SMM). MM is characterized by low survival rates, severe complications and drug resistance; therefore, understanding the molecular mechanisms of progression is crucial. This study aims to detect genetic mutations, both germline and somatic, that contribute to disease progression and drive tumorigenesis at the final stage of MM, using samples from patients presenting MGUS or SMM, and newly diagnosed MM patients. Methods: Mutations were identified through a fully computational pipeline, implemented in a Linux and RStudio environment, applied to each patient sequence, obtained through single-cell RNA-sequencing (scRNA-seq), separately. Structural and functional mutation types were identified by stage, along with the affected genes. The analysis included quality control, removal of the Unique Molecular Identifiers (UMIs), trimming, genome mapping and result visualization. Results: The findings revealed frequent germline and somatic mutations, with distinct structural and functional patterns across disease stages. Mutations in key genes were identified, pointing to molecules that may play a central role in carcinogenesis and disease progression. Notable examples include the HLA-A, HLA-B and HLA-C genes, as well as the KIF, EP400 and KDM gene families, with the first four already confirmed. Comparative analysis between the stages highlighted molecular transition events from one stage to another. Emphasis was given to novel genes discovered in newly diagnosed MM patients, that might contribute to the tumorigenesis that takes place. Conclusions: This study contributes to the understanding of the genetic basis of plasma cell dyscrasias and the transition events between the stages, offering insights that could aid in early detection and diagnosis, guide the development of personalized therapeutic strategies, and improve the understanding of mechanisms responsible for resistance to existing therapies. Full article
(This article belongs to the Section Pathology and Molecular Diagnostics)
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19 pages, 724 KB  
Article
Analyzing the Gaps in Breast Cancer Diagnostics in Poland—A Retrospective Observational Study in the Data Donation Model
by Wojciech Sierocki, Ligia Kornowska, Oliver Slapal, Agata Koska, Gabriela Sierocka, Alicja Dudek, Claudia Dompe, Michał Suchodolski, Przemysław Keczmer and Magdalena Roszak
Diagnostics 2025, 15(17), 2127; https://doi.org/10.3390/diagnostics15172127 - 22 Aug 2025
Viewed by 145
Abstract
Background: Breast cancer is a major health concern in Poland, with significant incidence and mortality rates despite national screening programs. This retrospective study aimed to evaluate critical aspects of breast cancer management, focusing on waiting times, treatment coordination, cancer characteristics, diagnostic testing, and [...] Read more.
Background: Breast cancer is a major health concern in Poland, with significant incidence and mortality rates despite national screening programs. This retrospective study aimed to evaluate critical aspects of breast cancer management, focusing on waiting times, treatment coordination, cancer characteristics, diagnostic testing, and staging. Methods: We retrospectively analyzed 587 medical records of breast cancer patients (585 female, 2 male) collected between March 2023 and June 2024 through a data donation model. Data included tumor characteristics (histological type, grade, stage, biological subtype, receptor status, Ki-67), diagnostic and genetic tests, and timelines of key events in the diagnostic and therapeutic pathways. Results: Although referral to first oncology consult (18 days) and MDT referral/admission to treatment (10 days) met NFZ guidelines, diagnosis to surgery (94 days) and diagnosis to drug treatment (109 days) were significantly delayed. No records showed oncology coordinator assignment or educational material provision. Clinically, invasive carcinoma NST (77%) and early-stage (IA/IIA, 61%) were prevalent, with Luminal B (HER2-negative) being the most common biological subtype. BRCA1/2 testing was common, but Oncotype DX was not. For 314 HR+ HER2- patients, stage IA (44%) was most common, with no BRCA1/2 mutations found. Conclusion: Breast cancer care in the Łódź voivodeship falls short of national guidelines due to long waiting times and poor care coordination, a problem worsened by incomplete data. Improving record-keeping and speeding up diagnostic and treatment pathways are crucial for better breast cancer management in Poland. While patient data donation can help analyze real clinical pathways, data completeness, and consistency remain challenges. Full article
(This article belongs to the Special Issue Diagnosis, Treatment, and Prognosis of Breast Cancer)
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19 pages, 974 KB  
Systematic Review
Paroxysmal Dyskinesias in Paediatric Age: A Systematic Review
by Giulia Pisanò, Martina Gnazzo, Giulia Sigona, Carlo Alberto Cesaroni, Agnese Pantani, Anna Cavalli, Susanna Rizzi, Daniele Frattini and Carlo Fusco
J. Clin. Med. 2025, 14(17), 5925; https://doi.org/10.3390/jcm14175925 - 22 Aug 2025
Viewed by 99
Abstract
Background: Paroxysmal dyskinesias (PDs) are rare, episodic movement disorders characterized by sudden and involuntary hyperkinetic motor events. In paediatric populations, their diagnosis is often complicated by clinical overlap with epilepsy and other neurological conditions. Genetic underpinnings have increasingly been recognized as key to [...] Read more.
Background: Paroxysmal dyskinesias (PDs) are rare, episodic movement disorders characterized by sudden and involuntary hyperkinetic motor events. In paediatric populations, their diagnosis is often complicated by clinical overlap with epilepsy and other neurological conditions. Genetic underpinnings have increasingly been recognized as key to understanding phenotypic heterogeneity and guiding treatment. Objectives: This systematic review aims to provide a comprehensive overview of paediatric PD, with a focus on genetic aetiologies, clinical features, subtype classification, and therapeutic approaches, including genotype–treatment correlations. Methods: We systematically reviewed the literature from 2014 to 2025 using PubMed. Inclusion criteria targeted paediatric patients (aged 0–18 years) with documented paroxysmal hyperkinetic movements and genetically confirmed or clinically suggestive PD. Data were extracted regarding demographics, dyskinesia subtypes, age at onset, genetic findings, and treatment efficacy. Gene categories were classified as PD-specific or pleiotropic based on functional and clinical features. Results: We included 112 studies encompassing 605 paediatric patients. The most common subtype was Paroxistic Kinesigenic Dyskinesia (PKD). Male sex was more frequently reported. The mean onset age was 5.99 years. A genetic diagnosis was confirmed in 505 patients (83.5%), involving 38 different genes. Among these, PRRT2 was the most frequently implicated gene, followed by SLC2A1 and ADCY5. Chromosomal abnormalities affecting the 16p11.2 region were identified in ten patients, including deletions and duplications. Among the 504 patients with confirmed monogenic variants, 390 (77.4%) had mutations in PD-specific genes, while 122 (24.2%) carried pleiotropic variants. Antiseizure drugs—particularly sodium channel blockers such as carbamazepine and oxcarbazepine—were the most frequently reported treatment, with complete efficacy documented in 59.7% of the studies describing their use. Conclusions: Paediatric PDs exhibit significant clinical and genetic heterogeneity. While PRRT2 remains the most common genetic aetiology, emerging pleiotropic genes highlight the need for comprehensive diagnostic strategies. Sodium channel blockers are effective in a subset of genetically defined PD, particularly PRRT2-positive cases. Patients with pathogenic variants in other genes, such as ADCY5 and SLC2A1, may benefit from specific therapies that can potentially change their clinical course and prognosis. These findings support genotype-driven management approaches and underscore the importance of genetic testing in paediatric movement disorders. Full article
(This article belongs to the Section Clinical Pediatrics)
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15 pages, 1126 KB  
Review
Maturity-Onset Diabetes of the Young 10 (MODY10): A Comprehensive Review of Genetics, Clinical Features, and Therapeutic Advances
by Ali Mazloum, Sofya G. Feoktistova, Anna Gubaeva, Almaqdad Alsalloum, Olga N. Mityaeva, Alexander Kim, Natalia A. Bodunova, Mary V. Woroncow and Pavel Yu Volchkov
Int. J. Mol. Sci. 2025, 26(16), 8110; https://doi.org/10.3390/ijms26168110 - 21 Aug 2025
Viewed by 217
Abstract
Maturity-onset diabetes of the young type 10 (MODY10) is a monogenic diabetes subtype caused by heterozygous mutations in the insulin gene (INS), leading to defective proinsulin processing, endoplasmic reticulum (ER) stress, and β-cell dysfunction. Current management relies on sulfonylureas or insulin [...] Read more.
Maturity-onset diabetes of the young type 10 (MODY10) is a monogenic diabetes subtype caused by heterozygous mutations in the insulin gene (INS), leading to defective proinsulin processing, endoplasmic reticulum (ER) stress, and β-cell dysfunction. Current management relies on sulfonylureas or insulin therapy, but these fail to address the underlying genetic defect. Recent research has elucidated the molecular mechanisms of MODY10, including ER stress induced by proinsulin misfolding, activation of the unfolded protein response (UPR), and β-cell apoptosis. Emerging therapies such as Adeno-Associated Virus (AAV)-mediated gene delivery to induce the glucose-responsive hepatic insulin expression, plasmid-based single-chain insulin analogs, and cell-based therapies show promise in preclinical studies. However, critical challenges remain, including immune responses to AAV vectors, incomplete correction of dominant-negative mutant effects, and the need for long-term safety data. This review summarizes current knowledge on MODY10 genetics, pathophysiology, and therapeutic innovations, while identifying key gaps for future research to enable precision medicine approaches. Full article
(This article belongs to the Special Issue Type 1 Diabetes: Molecular Mechanisms and Therapeutic Approach)
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33 pages, 3689 KB  
Article
Research on a Multi-Agent Job Shop Scheduling Method Based on Improved Game Evolution
by Wei Xie, Bin Du, Jiachen Ma, Jun Chen and Xiangle Zheng
Symmetry 2025, 17(8), 1368; https://doi.org/10.3390/sym17081368 - 21 Aug 2025
Viewed by 113
Abstract
As the global manufacturing industry’s transformation accelerates toward being intelligent, “unmanned”, and low-carbon, manufacturing workshops face conflicts between production schedules and transportation tasks, leading to low efficiency and resource waste. This paper presents a multi-agent collaborative scheduling optimization method based on a hybrid [...] Read more.
As the global manufacturing industry’s transformation accelerates toward being intelligent, “unmanned”, and low-carbon, manufacturing workshops face conflicts between production schedules and transportation tasks, leading to low efficiency and resource waste. This paper presents a multi-agent collaborative scheduling optimization method based on a hybrid game–genetic framework to address issues like high AGV (Automated Guided Vehicle) idle rates, excessive energy consumption, and uncoordinated equipment scheduling. The method establishes a trinity system integrating distributed decision-making, dynamic coordination, and environment awareness. In this system, the multi-agent decision-making and collaboration process exhibits significant symmetry characteristics. All agents (machine agents, mobile agents, etc.) follow unified optimization criteria and interaction rules, forming a dynamically balanced symmetric scheduling framework in resource competition and collaboration, which ensures fairness and consistency among different agents in task allocation, path planning, and other links. An improved best-response dynamic algorithm is employed in the decision-making layer to solve the multi-agent Nash equilibrium, while the genetic optimization layer enhances the global search capability by encoding scheduling schemes and adjusting crossover/mutation probabilities using dynamic competition factors. The coordination pivot layer updates constraints in real time based on environmental sensing, forming a closed-loop optimization mechanism. Experimental results show that, compared with the traditional genetic algorithm (TGA) and particle swarm optimization (PSO), the proposed method reduces the maximum completion time by 54.5% and 44.4% in simple scenarios and 57.1% in complex scenarios, the AGV idling rate by 68.3% in simple scenarios and 67.5%/77.6% in complex scenarios, and total energy consumption by 15.7%/10.9% in simple scenarios and 25%/18.2% in complex scenarios. This validates the method’s effectiveness in improving resource utilization and energy efficiency, providing a new technical path for intelligent scheduling in manufacturing workshops. Meanwhile, its symmetric multi-agent collaborative framework also offers a reference for the application of symmetry in complex manufacturing system optimization. Full article
(This article belongs to the Section Computer)
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