Journal Description
Genes
Genes
is a peer-reviewed, open access journal of genetics and genomics published monthly online by MDPI. The Spanish Society for Nitrogen Fixation (SEFIN) is affiliated with Genes and its members receive discounts on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, MEDLINE, PMC, Embase, PubAg, and other databases.
- Journal Rank: JCR - Q2 (Genetics and Heredity) / CiteScore - Q2 (Genetics (clinical))
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 14.6 days after submission; acceptance to publication is undertaken in 3.4 days (median values for papers published in this journal in the second half of 2025).
- Recognition of Reviewers: Reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
2.8 (2024);
5-Year Impact Factor:
3.2 (2024)
Latest Articles
Transglutaminase 2 at the Interface of Gene Regulation and Antigen Processing in HLA-Restricted Immunity of Celiac Disease
Genes 2026, 17(5), 548; https://doi.org/10.3390/genes17050548 (registering DOI) - 3 May 2026
Abstract
Celiac disease (CD) is an immune-mediated enteropathy triggered by dietary gluten in genetically predisposed individuals. Although HLA-DQ2 and HLA-DQ8 are the primary genetic determinants of susceptibility, they are not sufficient to explain disease onset and progression. A key molecular event in CD pathogenesis
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Celiac disease (CD) is an immune-mediated enteropathy triggered by dietary gluten in genetically predisposed individuals. Although HLA-DQ2 and HLA-DQ8 are the primary genetic determinants of susceptibility, they are not sufficient to explain disease onset and progression. A key molecular event in CD pathogenesis is the post-translational modification of gluten peptides by transglutaminase 2 (TG2), which enhances their binding to HLA-DQ molecules and promotes CD4+ T cell activation. TG2 also acts as the principal autoantigen, driving the production of anti-TG2 autoantibodies through linked recognition mechanisms. Beyond its enzymatic activity, TG2 is tightly regulated by gene regulatory mechanisms, including cytokine-driven transcription, epigenetic modulation, and stress-responsive signaling pathways. These processes determine TG2 expression and activity in the intestinal mucosa, thereby influencing the efficiency of gluten peptide modification and antigen presentation. Here, we propose that TG2 operates at the interface between gene regulation and antigen processing, linking transcriptional control of TGM2 to HLA-restricted immune activation. In this framework, disease susceptibility arises from the coordinated interaction between HLA-dependent peptide presentation, TG2-mediated modification of gluten epitopes, and regulation of TG2 expression within the intestinal mucosa. This integrated model provides a mechanistic basis for disease heterogeneity and identifies TG2 as a central regulatory node and potential therapeutic target in CD.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessArticle
Integrated Evolutionary and Multi-Omic Analysis of STAT Family Activation Across Solid Tumors
by
Dunja Lukic, Pietro Hiram Guzzi and Federico Manuel Giorgi
Genes 2026, 17(5), 547; https://doi.org/10.3390/genes17050547 (registering DOI) - 3 May 2026
Abstract
Background/Objectives: The STAT (Signal Transducer and Activator of Transcription) family of seven transcription factors mediates cytokine and growth-factor signaling, regulating proliferation, differentiation, and immunity. While STAT3/STAT5 are established oncogenes and STAT1/STAT2 are classically viewed as tumor suppressors, emerging evidence indicates context-dependent roles
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Background/Objectives: The STAT (Signal Transducer and Activator of Transcription) family of seven transcription factors mediates cytokine and growth-factor signaling, regulating proliferation, differentiation, and immunity. While STAT3/STAT5 are established oncogenes and STAT1/STAT2 are classically viewed as tumor suppressors, emerging evidence indicates context-dependent roles in tumorigenesis. This study aimed to integrate evolutionary analysis with bulk transcriptomic, regulon, single-cell, and exploratory chromatin-binding analyses of the STAT family in human solid tumors. Methods: Orthologs and paralogs of human STAT genes (81 sequences total) were retrieved across vertebrates and invertebrates; a phylogenetic tree was constructed using MUSCLE alignment and Neighbor-Joining in MEGA12. Differential expression was assessed in TCGA solid tumors versus GTEx normal tissues. Master-regulator activity was inferred using the corto algorithm. Single-cell RNA-seq datasets were used to compare malignant and non-malignant cell populations. STAT1 chromatin binding was examined via ChIP-seq in interferon-stimulated HeLa and K562 cells. Results: Phylogeny resolved seven conserved vertebrate clades, with endocrine-responsive STAT3/STAT5 showing higher conservation and immune-associated STAT1/STAT2/STAT4/STAT6 exhibiting faster divergence. The majority of STAT genes were frequently upregulated across multiple solid tumors, with activated regulons confirming functional transcriptional engagement. Single-cell analysis demonstrated tumor-cell-autonomous upregulation of STAT1 and STAT2 in the HNSCC dataset. STAT1 ChIP-seq revealed asymmetric forward/reverse-strand read density around peak summits, supporting non-canonical DNA recognition. Conclusions: The STAT family operates as an evolutionarily conserved, broadly activated transcriptional module in human solid cancers, combining quantitative upregulation with qualitative shifts in DNA-binding dynamics. These findings refine our understanding of JAK/STAT signaling in oncology and highlight opportunities for network-targeted therapies.
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(This article belongs to the Special Issue Gene-Regulated Signaling Pathways in Cancer)
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Open AccessArticle
Genetic Association of HTR1B and HTR2A Gene Polymorphisms with ADHD in Korean Children and Adolescents: A Case Control Study
by
Yeongsuk Lee, Hyung Jun Kim, Han Jun Jin, Ho Jang Kwon, Se Hoon Shim and Myung Ho Lim
Genes 2026, 17(5), 546; https://doi.org/10.3390/genes17050546 (registering DOI) - 2 May 2026
Abstract
Objectives: Attention-deficit hyperactivity disorder (ADHD) is the most prevalent neurodevelopmental disorder diagnosed during childhood, primarily characterized by continuous symptoms of inattention, hyperactivity, and impulsivity. The present study aimed to investigate the genetic association between polymorphisms in the serotonergic system-related genes, HTR1B and HTR2A,
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Objectives: Attention-deficit hyperactivity disorder (ADHD) is the most prevalent neurodevelopmental disorder diagnosed during childhood, primarily characterized by continuous symptoms of inattention, hyperactivity, and impulsivity. The present study aimed to investigate the genetic association between polymorphisms in the serotonergic system-related genes, HTR1B and HTR2A, and the susceptibility to ADHD in a Korean sample. Methods: The study cohort consisted of 234 children diagnosed with ADHD and 1686 healthy controls. Clinical diagnosis was established based on the Diagnostic and Statistical Manual of Mental Disorders, 4th edition (DSM-IV) criteria. Genetic analysis focused on single nucleotide polymorphisms (SNPs) within the serotonergic pathway: rs6296 in HTR1B, and three SNPs (rs6311, rs6313, and rs9534495) in HTR2A. Genotype and allele frequencies were analyzed using Chi-square tests. Risk estimates were calculated as odds ratios (OR) with 95% confidence intervals (CI) across dominant, recessive, and additive inheritance models. Results: A statistically significant association was observed between the HTR2A rs9534495 polymorphism and ADHD. Specifically, significant associations were identified under the dominant (OR 0.67, 95% CI 0.48–0.93, p = 0.017), recessive (OR 0.67, 95% CI 0.48–0.93, p = 0.016), and additive (OR 0.80, 95% CI 0.65–1.00, p = 0.046) models. However, these significant findings did not persist after applying the Bonferroni correction for multiple comparisons. Conversely, no significant associations were detected for the HTR1B (rs6296) and the other HTR2A (rs6311, rs6313) polymorphisms. Conclusions: These findings suggest that genetic variations in the serotonergic system, particularly within the HTR2A gene, may contribute to the genetic susceptibility to ADHD. This study confirmed gene SNIPs associated with the serotonergic system in the pathophysiology of ADHD. Future research involving large-scale multi-ethnic cohorts, functional assays, and gene–environment interaction analyses is warranted to further elucidate the underlying mechanisms of serotonergic genes.
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(This article belongs to the Special Issue Feature Papers in "Neurogenetics and Neurogenomics": 2026)
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Open AccessArticle
Exploring the Mechanisms of Hydrangea macrophylla Adapting to Low Light-Induced Ornamental Whitening Through Physiological, Transcriptional, and Metabolomic Analyses
by
Wenji Li, Long Guo, Chuanshuai Li and Yao Li
Genes 2026, 17(5), 545; https://doi.org/10.3390/genes17050545 (registering DOI) - 2 May 2026
Abstract
Background/Objectives: To explore the mechanisms of Hydrangea macrophylla adapting to low light-induced ornamental whitening, this study established treatments involving normal light (CK, 200 μmol·m−2·s−1), moderate low light (L1, 100 μmol·m−2·s−1), and severe low light (L2,
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Background/Objectives: To explore the mechanisms of Hydrangea macrophylla adapting to low light-induced ornamental whitening, this study established treatments involving normal light (CK, 200 μmol·m−2·s−1), moderate low light (L1, 100 μmol·m−2·s−1), and severe low light (L2, 20 μmol·m−2·s−1). Methods: Meanwhile, physiological indicators, including growth, photosynthesis, and antioxidant activity, were assessed, alongside transcriptomic and metabolomic analyses. Results: Results indicate that L1 increased the proportion of leaf whitening area while maintaining plant growth (crown width, biomass), photosynthetic efficiency comparable to CK, and superior to L2. Concurrently, L1 activated a coordinated antioxidant defence system, namely by increasing the activity of key enzymes (e.g., SOD, GR) and the accumulation of protective metabolites (e.g., soluble proteins, total phenolics and total flavonoids), thereby minimising oxidative damage (low MDA). Multi-omics analyses revealed that L1 specifically activated these networks associated with carbon assimilation, energy metabolism, secondary metabolite synthesis, and hormone signalling, indicating a systemic molecular mechanism towards enhanced defence. Conclusions: In summary, moderate low light triggers a synergistic molecular network involving enhanced antioxidant defences and secondary metabolism, enabling H. macrophylla to maintain overall physiological homeostasis and healthy growth while exhibiting ornamental whitening phenotypes, thereby revealing a unique aesthetic adaptation mechanism to environmental stress.
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(This article belongs to the Section Plant Genetics and Genomics)
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Open AccessReview
The Evolution of the First Code
by
Lei Lei, Savio Torres de Farias and Zachary Frome Burton
Genes 2026, 17(5), 544; https://doi.org/10.3390/genes17050544 (registering DOI) - 2 May 2026
Abstract
Background/Objectives: tRNAs, tRNAomes, aminoacyl-tRNA synthetases (AARSs), the first proteins, ribosomes and the genetic code coevolved. We utilize sequence data to reconstruct key steps in establishing the first code on Earth. Methods: Networks were constructed to describe initial tRNAome and AARSome evolution. Results: tRNA-34
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Background/Objectives: tRNAs, tRNAomes, aminoacyl-tRNA synthetases (AARSs), the first proteins, ribosomes and the genetic code coevolved. We utilize sequence data to reconstruct key steps in establishing the first code on Earth. Methods: Networks were constructed to describe initial tRNAome and AARSome evolution. Results: tRNA-34 wobble and tRNA-37 modifications were necessary to evolve the code, as were additional tRNA modifications, so diverse tRNA modification enzymes (i.e., histidyl-tRNA -1 GTP synthase) are among the first proteins. tRNA-linked chemistry brought asparagine, glutamine, cysteine and possibly additional amino acids into the code. tRNA, tRNA modifications and tRNA-linked chemistry were core founding innovations for code evolution. Coevolution of AARSomes was also essential. Class II and class I AARSs have distinct folds but are nonetheless homologs by sequence. Early AARS enzymes folded around Zn motifs. Networks were generated for tRNAomes and AARSomes in ancient Archaea, because Archaea are the closest living organisms to the last universal common ancestor. Conclusions: The first code on Earth was surprisingly ordered, and the few apparent deviations from the regular order can yet be explained. Early in the evolution of the code, innovation was more strongly selected than accuracy. The code froze, however, because of evolving fidelity mechanisms. A historical record was documented in tRNA and in the genetic code structure and has been preserved in living organism sequences. AARSome structure describes the first code evolution more adequately than tRNAomes.
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(This article belongs to the Special Issue The Origin and Evolution of Genetic Code)
Open AccessArticle
Molecular Spectrum of α-Thalassemia Mutations in Antalya, Türkiye and Their Relationship with Hematological Parameters
by
Özgür Erkal and Barış Paksoy
Genes 2026, 17(5), 543; https://doi.org/10.3390/genes17050543 (registering DOI) - 2 May 2026
Abstract
Background: Alpha-thalassemia is one of the most common hereditary hemoglobin disorders worldwide and is caused mainly by deletions in the α-globin gene cluster. Understanding the regional mutation spectrum is important for screening programs and genetic counseling. Methods: This retrospective study included 115 patients
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Background: Alpha-thalassemia is one of the most common hereditary hemoglobin disorders worldwide and is caused mainly by deletions in the α-globin gene cluster. Understanding the regional mutation spectrum is important for screening programs and genetic counseling. Methods: This retrospective study included 115 patients evaluated for suspected alpha-thalassemia in Antalya, Türkiye. Molecular analysis was performed using multiplex ligation-dependent probe amplification (MLPA) to detect deletions and duplications in the α-globin gene cluster. Hematological parameters and hemoglobin (Hb) fractions were analyzed and compared among mutation groups. Results: The most frequent mutation detected was the −α3.7 deletion followed by the (−α)20.5 deletion. Patients with compound heterozygous deletions demonstrated lower Hb, mean corpuscular volume (MCV), and mean corpuscular hemoglobin)_(MCH) values compared with other groups. Significant correlations were observed between Hb levels and red blood cell (RBC), MCV, and MCH, while red cell distribution width (RDW) showed an inverse relationship. Conclusions: The results demonstrate that −α3.7 and (−α)20.5 are the predominant α-globin gene variants in the Antalya region. These findings contribute to the characterization of the α-thalassemia mutation spectrum in a clinical cohort and may help improve carrier screening strategies, prenatal diagnosis programs, and genetic counseling services.
Full article
(This article belongs to the Section Human Genomics and Genetic Diseases)
Open AccessReview
Decoding Skin Aging Through Transcriptomic Clocks: Gene Expression Signatures, Associated Pathways, and Explainable AI
by
Vasiliki Kefala, Vasiliki-Sofia Grech, Niki Tertipi, Eleni Sfyri, Apostolos Beloukas and Efstathios Rallis
Genes 2026, 17(5), 542; https://doi.org/10.3390/genes17050542 - 1 May 2026
Abstract
Skin aging is a complex, multifactorial process driven by intrinsic biological mechanisms and environmental exposures, resulting in progressive functional and structural decline. Chronological age does not adequately capture this variability, highlighting the need for molecular biomarkers that reflect biological aging. In this context,
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Skin aging is a complex, multifactorial process driven by intrinsic biological mechanisms and environmental exposures, resulting in progressive functional and structural decline. Chronological age does not adequately capture this variability, highlighting the need for molecular biomarkers that reflect biological aging. In this context, transcriptomic aging clocks have emerged as a promising approach, as gene-expression profiles provide a dynamic representation of cellular and tissue states. This narrative review is based on a targeted literature search in PubMed and IEEE Xplore and focuses on transcriptomic aging clocks in human skin, with emphasis on gene-expression signatures, key biological pathways, and computational modeling strategies. These models consistently capture coordinated alterations in processes such as cellular senescence, DNA damage response, inflammation, and extracellular matrix remodeling. Representative transcriptomic frameworks, including models such as SkinAGE, illustrate the ability of gene-expression-based approaches to quantify biologically meaningful and dynamic aging states in the skin. Advances in machine-learning approaches, including deep learning and pathway-guided models, are critically evaluated, alongside the role of explainable artificial intelligence in enhancing model transparency and biological interpretability. Future developments are expected to integrate multi-omics data and digital twin frameworks, enabling the transition from static biomarkers toward dynamic, predictive, and personalized models of skin aging
Full article
(This article belongs to the Section RNA)
Open AccessArticle
Exploring Vascular Contributions to Migraine: Association Analysis of Small Vessel Disease Genetic Variants
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Zizi Molaee, Mohammed Al-Fayyadh, Robert A. Smith, Neven Maksemous and Lyn R. Griffiths
Genes 2026, 17(5), 541; https://doi.org/10.3390/genes17050541 - 1 May 2026
Abstract
Background: Migraine is a complex neurovascular disorder with a substantial genetic component, yet many contributing loci remain poorly characterised. Methods: This study investigated the association between 21 biologically prioritised single nucleotide variants (SNVs) and migraine susceptibility in a case-control cohort of
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Background: Migraine is a complex neurovascular disorder with a substantial genetic component, yet many contributing loci remain poorly characterised. Methods: This study investigated the association between 21 biologically prioritised single nucleotide variants (SNVs) and migraine susceptibility in a case-control cohort of 548 individuals of European ancestry, of whom 304 (164 cases, 140 controls) remained after quality control and principal component analysis (PCA). Genotyping was performed using a targeted Sequenom MassARRAY platform, and substantial missingness (mean 30.3% per SNV) was addressed using multiple imputation by chained equations (MICE). Association testing was conducted using three complementary logistic regression frameworks: unadjusted single-variant analysis, covariate-adjusted marginal models, and a multivariable joint model incorporating all SNVs with L2 regularisation. Results: Across analyses, two variants in ASTN2 (rs1052053 and rs6478241) showed the most robust associations with migraine, surviving Bonferroni correction in the joint model (p = 0.001 and p = 0.002, respectively) and false discovery rate (FDR) correction in marginal models (q = 0.003 for both). A third variant, rs7304841 (12p12), demonstrated a risk-increasing effect that reached FDR significance in marginal analysis (q = 0.035) and remained nominally significant in the joint model. In contrast, rs62624978 in CTC1 showed a strong signal in unadjusted analysis (OR = 0.217, p = 0.0014) and remained nominally significant after adjustment (p = 0.011), although it did not survive multiple-testing correction in imputed models. The joint model demonstrated good discriminatory performance (AUC = 0.822), though this is not intended as a predictive tool. Biologically, implicated loci suggest contributions from both neuronal circuit organisation (ASTN2) and telomere and vascular maintenance pathways (CTC1), supporting a broader neurovascular model of migraine susceptibility. Conclusions: These findings are consistent with shared genetic architecture between migraine and microvascular dysfunction, potentially involving endothelial integrity, neurovascular coupling, and cortical excitability mechanisms.
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(This article belongs to the Special Issue Feature Papers in "Neurogenetics and Neurogenomics": 2026)
Open AccessArticle
Uncovering Latent Structure in Gliomas Using Multi-Omics Factor Analysis
by
Catarina Gameiro Carvalho, Alexandra M. Carvalho and Susana Vinga
Genes 2026, 17(5), 540; https://doi.org/10.3390/genes17050540 - 1 May 2026
Abstract
Background: Gliomas are the most common malignant brain tumors in adults, characterized by a poor prognosis. Although the current World Health Organization (WHO) classification provides clear guidelines for classifying oligodendroglioma, astrocytoma, and glioblastoma patients, significant heterogeneity persists within each class, limiting the effectiveness
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Background: Gliomas are the most common malignant brain tumors in adults, characterized by a poor prognosis. Although the current World Health Organization (WHO) classification provides clear guidelines for classifying oligodendroglioma, astrocytoma, and glioblastoma patients, significant heterogeneity persists within each class, limiting the effectiveness of current treatment strategies. With the increasing availability of large-scale multi-omics datasets resulting from advancements in sequencing technologies and online repositories that provide them, such as The Cancer Genome Atlas (TCGA), it is now possible to investigate these tumors at multiple molecular levels. Methods: In this work, we apply integrative multi-omics analysis to explore the interplay between genomic (mutations), epigenomic (DNA methylation), and transcriptomic (mRNA and miRNA) layers. Our approach relies on Multi-Omics Factor Analysis (MOFA), a Bayesian latent factor analysis model designed to capture sources of variation across different omics types. Results: Our results highlight distinct molecular profiles across the three glioma types and identify potential relationships between methylation and genetic expression. In particular, we uncover novel candidate biomarkers associated with survival as well as a transcriptional profile associated with neural system development. Conclusions: These findings may contribute to more personalized therapeutic strategies, potentially improving treatment effectiveness and survival outcomes in this disease.
Full article
(This article belongs to the Section Bioinformatics)
Open AccessArticle
Expanding the Genetic Landscape of Congenital Stationary Night Blindness Through the Analysis of Consanguineous Pakistani Families
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Razia Parveen, Muhammad Iqbal, Shahbaz Khan, Abdur Rashid, Helen Nabiryo Frederiksen, Sergey Oreshkov, Ghulam Mustafa, Muhammad Asif Naeem, Hafiz Muhammad Azhar Baig and Muhammad Ansar
Genes 2026, 17(5), 539; https://doi.org/10.3390/genes17050539 - 1 May 2026
Abstract
Background/Objectives: The current study was designed to identify the underlying genetic causes of congenital stationary night blindness (CSNB) in the indigenous consanguineous families from the Southern Punjab region of Pakistan, a population where the inherited retinal disorders are relatively common. Methods:
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Background/Objectives: The current study was designed to identify the underlying genetic causes of congenital stationary night blindness (CSNB) in the indigenous consanguineous families from the Southern Punjab region of Pakistan, a population where the inherited retinal disorders are relatively common. Methods: A detailed questionnaire and medical examination were done to check the presence of CSNB in the affected individuals of the enrolled families. Whole-exome sequencing (WES) was performed to identify the pathogenic variants, followed by segregation analyses to confirm the segregation of the identified variants with the disease phenotype in the available affected individuals of the families. Results: We identified two novel and three known pathogenic variants in SAG, GRK1, TRPM1, SLC24A1, and GPR179, having established roles in CSNB. Two novel variants, NM_001252020.1 (p.Gly1020Arg) and NM_001004334.3 (p.Trp508Ter), were identified, and their segregation was confirmed in two families, PKIURP102 and PKIURP564, respectively. NM_002929.3 (p.Arg19Ter) and NM_001301032.1 (p.Phe538CysfsTer23) were the reported variants identified in PKIURP17 and PKIURP528 families, respectively. NM_000541.5 (p.Glu306Ter) was identified in two independent families, PKIURP552 and PKIURP565. Conclusions: Identification of five pathogenic variants in five different genes shows the genetic heterogeneity of CSNB in Pakistani patients. Our findings also expand the mutational spectrum of CSNB in the Pakistani population and may help in the identification of mutational hotspots and may help in the genetic diagnosis of CSNB in consanguineous populations.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
DHT-Induced lncRNA AC092718.4 Promotes Prostate Cancer Cell Proliferation via ceRNA Mechanism
by
Lian Jin, Shan Feng, Wei-Jie Sun, Jun Ouyang, Feng Liu, Bai-Cheng Lu, Ya-Ping Zhang and Hui Zhao
Genes 2026, 17(5), 538; https://doi.org/10.3390/genes17050538 - 1 May 2026
Abstract
Background/Objectives: The androgen receptor (AR)-driven transcriptional program plays a pivotal role in the development and progression of prostate cancer. The binding of androgen dihydrotestosterone (DHT) to AR initiates transcriptional activation, thereby altering the transcriptional landscape. DHT-induced long non-coding RNAs (lncRNAs) have been
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Background/Objectives: The androgen receptor (AR)-driven transcriptional program plays a pivotal role in the development and progression of prostate cancer. The binding of androgen dihydrotestosterone (DHT) to AR initiates transcriptional activation, thereby altering the transcriptional landscape. DHT-induced long non-coding RNAs (lncRNAs) have been recognized as crucial players in prostate cancer pathogenesis. This study aims to identify and explore the important role of such lncRNAs in prostate cancer. Methods: This study first analyzed transcriptome data from an androgen-dependent cell line, LNCaP, treated with different DHT concentrations and found a batch of lncRNAs exhibiting DHT concentration dependence. TCGA data suggested a correlation between the DHT-induced lncRNA and prostate cancer. Finally, a series of in vivo and in vitro experiments confirmed the effect and mechanism of lncRNA in prostate cancer. Results: AC092718.4 was highly expressed in AR-positive prostate cancer cell lines and tissues, and its expression in patients with Gleason scores 6–9 was significantly higher than in a normal control group. Notably, the expression level of AC092718.4 was upregulated in a concentration-dependent manner with DHT. In vitro experiments revealed that overexpression of AC092718.4 promoted cell proliferation and inhibited cell apoptosis. Conversely, knockdown of AC092718.4 suppressed tumorigenesis in vivo. Furthermore, our investigation into the pathogenetic mechanism demonstrated that AC092718.4 could act as an miRNA sponge for miR-138-5p, attenuating its inhibitory effect on downstream oncogenes, such as FERMT2, RHOC, and HIF1A. These AC092718.4/miR-138-5p/mRNA axes, in turn, facilitated the progression of prostate cancer. Conclusions: For the first time, we demonstrate that AC092718.4 may function as an oncogenic factor in prostate cancer. The AC0927.8.4/miR-138-5p/mRNA axes potentially offer promising diagnostic and therapeutic targets for prostate cancer.
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(This article belongs to the Section RNA)
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Open AccessCase Report
A Novel Variant in an Israeli Bedouin Family: The First Reported Cases of Carbonic Anhydrase VA (CA5A) Deficiency in Israel
by
Nitzan Abelson, Eyal Kristal, Eli Hershkovitz, Ohad Wormser, Vadim Dolgin, Shirly Amar and Orna Staretz-Chacham
Genes 2026, 17(5), 537; https://doi.org/10.3390/genes17050537 - 1 May 2026
Abstract
Carbonic anhydrase VA (CA5A) deficiency (OMIM 615751) is an ultra-rare inborn error of metabolism, presenting in newborns, infants, and young children with a pentad of encephalopathy, hyperammonemia, lactic acidosis, ketonuria, and hypoglycemia. We present two cases: a case of a healthy Bedouin infant
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Carbonic anhydrase VA (CA5A) deficiency (OMIM 615751) is an ultra-rare inborn error of metabolism, presenting in newborns, infants, and young children with a pentad of encephalopathy, hyperammonemia, lactic acidosis, ketonuria, and hypoglycemia. We present two cases: a case of a healthy Bedouin infant admitted with hyperammonemic encephalopathy that required urgent hemodialysis, and her younger sibling, who presented with a milder episode. Molecular analysis confirmed the diagnosis of CA5A deficiency due to a homozygous missense variant in the CA5A gene. Both patients had a favorable outcome with continued normal development. These were the first identified cases of CA5A deficiency in the Bedouin population, emphasizing the importance of a high index of suspicion, early genetic consultation and diagnosis, and prompt treatment at the earliest possible stage of a hyperammonemic crisis.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
Somatic Mutation Trajectories Define Prognostically Distinct Subtypes and Shape the Tumor Microenvironment in Gastric Cancer
by
Yikang Shen, Huaxin Pang, Haiyu Liu, Pengzhen Ma, Mingrui Liu, Yaning Li, Qihao Wang, Xiaoxia Xie, Xiaoping Zhang and Yufeng Zhao
Genes 2026, 17(5), 536; https://doi.org/10.3390/genes17050536 - 30 Apr 2026
Abstract
Objective: Gastric cancer (GC) is characterized by molecular heterogeneity, yet current classifications are largely based on cross-sectional molecular profiles and do not account for the temporal order of mutation accumulation. This study aimed to reconstruct somatic mutation trajectories to identify prognostically distinct subtypes
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Objective: Gastric cancer (GC) is characterized by molecular heterogeneity, yet current classifications are largely based on cross-sectional molecular profiles and do not account for the temporal order of mutation accumulation. This study aimed to reconstruct somatic mutation trajectories to identify prognostically distinct subtypes and to examine transcriptomic and microenvironmental features associated with these inferred trajectories. Methods: We applied the Subtype and Stage Inference (SuStaIn) algorithm to TCGA-STAD somatic mutation data to infer the temporal sequence of mutation accumulation. Stage-correlated gene expression analysis was performed to identify genes whose expression levels changed with evolutionary stage. The tumor microenvironment (TME) was characterized using EcoTyper and single-cell RNA sequencing deconvolution, while drug sensitivity was estimated through transcriptome-based IC50 prediction. The clinical relevance of the inferred trajectories was further evaluated in three independent external transcriptomic cohorts. Results: We identified two distinct evolutionary trajectories: the Accelerated Path (AP, 65%) and the Gradual Path (GP, 35%). In the AP, TP53 mutations were positioned at an earlier evolutionary stage (Stage 3) compared to the GP (Stage 8). AP patients had significantly worse overall survival (Hazard Ratio = 1.437, p = 0.044, adjusted for clinical stage and molecular subtypes). The AP was associated with stage-correlated downregulation of the sodium channel gene SCN4A (ρ = −0.36, p < 0.001) and an increase in a squamous-associated gene expression score, while the GP showed stage-correlated expression changes in the mitochondrial gene SDHD (ρ = −0.35, p < 0.001). The AP was further characterized by higher inferred abundance of extracellular matrix CAFs (eCAFs) and lower inferred immune cell scores, whereas the GP was associated with higher inferred signatures of activated B cells and effector memory T cells. Computational drug sensitivity modeling predicted a negative correlation between AP stage and IC50 values for 5-Fluorouracil and Docetaxel. Conclusions: Two distinct mutational ordering patterns identified by SuStaIn are associated with divergent transcriptomic features, TME compositions, and clinical outcomes in gastric cancer. The AP subtype is characterized by early TP53 mutations, SCN4A downregulation, and a stromal-enriched microenvironment, while the GP subtype is associated with later TP53 mutations, SDHD-correlated expression, and higher inferred immune cell scores. The reproducibility of these associations was confirmed in independent cohorts. The computational drug sensitivity predictions and the proposed mechanistic links between gene expression patterns and clinical outcomes should be viewed as hypothesis-generating findings that require prospective and functional validation.
Full article
(This article belongs to the Special Issue Computational Genomics and Bioinformatics of Cancer)
Open AccessArticle
Leveraging Whole-Exome Sequencing to Decipher the Genetic Landscape of Three Genodermatoses’ Cases in Middle Eastern Pediatric Patients
by
Ayat Kadhi, Pierre Abi Akl, Ossama Abbas, Elias El-Tayar, Georges Nemer and Mazen Kurban
Genes 2026, 17(5), 535; https://doi.org/10.3390/genes17050535 - 30 Apr 2026
Abstract
Introduction: Recent advancements in genomic technologies have significantly improved the resolution of genetic variants driving rare genodermatoses, a heterogeneous group of inherited skin disorders caused by pathogenic variants affecting skin structure and function. However, many genodermatoses remain molecularly uncharacterized, particularly in Middle Eastern
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Introduction: Recent advancements in genomic technologies have significantly improved the resolution of genetic variants driving rare genodermatoses, a heterogeneous group of inherited skin disorders caused by pathogenic variants affecting skin structure and function. However, many genodermatoses remain molecularly uncharacterized, particularly in Middle Eastern populations. Objectives: This study aimed to evaluate the diagnostic accuracy and inherent challenges of utilizing (WES) for genodermatoses within a Middle Eastern context. Methods: We performed WES on three unrelated Middle Eastern pediatric patients presenting with genodermatoses. Genetic variants were prioritized and adjudicated according to ClinVar and the American College of Medical Genetics and Genomics (ACMG) guidelines. Results: WES identified pathogenic variants in three pediatric cases presenting with genodermatoses. Findings included a GJB2 missense variant (c.148G>T; p.Asp50Asn) associated with keratitis–ichthyosis–deafness (KID) syndrome. This represents one of the first documented cases in a Middle Eastern population. Two additional patients presenting with epidermolysis bullosa harbored truncating variants in COL7A1 (c.497dup; p.Val168Glyfs12) and EXPH5 (c.5786del; p.Pro1929Leufs8), respectively; the latter also carried a KRT5 missense variant (c.1607G>A; p.Ser536Asn). Conclusions: WES is a robust diagnostic adjunct for resolving ambiguity in rare genodermatoses, though its efficacy remains contingent on the availability of regional genomic references. Within pediatric dermatology, systematic exome sequencing serves as a powerful facilitator for transitioning from clinical suspicion to definitive molecular characterization. Collectively, these findings highlight the essential role of regionally representative genomic datasets in the accurate interpretation of novel variants and the advancement of precision dermatology.
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(This article belongs to the Section Human Genomics and Genetic Diseases)
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Open AccessArticle
QTL Mapping of SPAD Values Associated with Leaf Color in Bunching Onion
by
Tetsuya Nakajima, Kouei Fujii, Kenji Watanabe, Yoichi Mizukami, Masaru Bamba, Shusei Sato and Masayoshi Shigyo
Genes 2026, 17(5), 534; https://doi.org/10.3390/genes17050534 - 30 Apr 2026
Abstract
Background/Objectives: The dark green leaf color trait in bunching onion (Allium fistulosum L.) is an important agronomic trait closely associated with market value; however, its genetic basis remains poorly understood. This study aimed to identify quantitative trait loci (QTLs) associated with
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Background/Objectives: The dark green leaf color trait in bunching onion (Allium fistulosum L.) is an important agronomic trait closely associated with market value; however, its genetic basis remains poorly understood. This study aimed to identify quantitative trait loci (QTLs) associated with leaf color using SPAD values as a phenotypic indicator. Methods: An population derived from a cross between the dark green line YSG1go and the light green line Asagikei-KUJYO was used. A linkage map was constructed based on RNA-seq-derived SNP markers, and SPAD values were measured for QTL analysis. Results: The linkage map consisted of eight linkage groups with a total length of 2103.0 cM and 765 mapped markers. SPAD values showed significant differences between the parental lines, with high broad-sense heritability ( = 0.76), indicating a strong genetic contribution to this trait. Multiple significant QTLs were detected on chromosomes 4 and 5, each explaining 27.4–38.1% of the phenotypic variance. The direction of allelic effects differed among QTLs, suggesting that favorable alleles are distributed between the parental lines. In addition, genes related to chloroplast protein translation were identified within the QTL regions. Conclusions: SPAD values are a suitable indicator for genetic analysis of leaf color in bunching onion, and the QTLs identified in this study provide valuable information for molecular breeding aimed at improving dark green leaf color.
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(This article belongs to the Special Issue Genetic and Breeding Improvement of Horticultural Crops)
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Current and Emerging Therapeutic Strategies for the Treatment of Duchenne Muscular Dystrophy
by
Miguel A. Lopez Perez and Noah L. Weisleder
Genes 2026, 17(5), 533; https://doi.org/10.3390/genes17050533 - 30 Apr 2026
Abstract
Background/Objectives: Duchenne muscular dystrophy (DMD) is a fatal, progressive neuromuscular disorder caused by mutations in the dystrophin gene, leading to the absence of functional dystrophin protein. As the largest gene in the human genome, the DMD locus is highly susceptible to mutations,
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Background/Objectives: Duchenne muscular dystrophy (DMD) is a fatal, progressive neuromuscular disorder caused by mutations in the dystrophin gene, leading to the absence of functional dystrophin protein. As the largest gene in the human genome, the DMD locus is highly susceptible to mutations, contributing to a prevalence of approximately 1 in 3800–6300 live male births worldwide. This review aims to provide a comprehensive and critical synthesis of current and emerging therapeutic strategies for DMD. Methods: We conducted a narrative review of the literature, integrating findings from clinical trials, regulatory approvals, and preclinical studies. We categorized therapeutic approaches into mutation-agnostic and mutation-specific strategies, with emphasis on the mechanism of action, clinical progress, and translational limitations. Results: Current standards of care, including corticosteroids and supportive interventions, remain foundational in disease management. Mutation-specific approaches such as exon skipping and adeno-associated virus (AAV)-mediated gene replacement can restore dystrophin expression, although clinical benefit remains variable and is influenced by factors such as mutation type, delivery efficiency, and durability. Emerging genome editing strategies offer the potential for permanent correction but face significant challenges related to delivery, safety, and scalability. Emerging mutation-agnostic therapies targeting inflammation, fibrosis, and membrane instability provide broader applicability but do not directly address the underlying genetic defect. Across modalities, key limitations include modest functional outcomes, safety concerns, and variability in clinical trial endpoints. Conclusions: The DMD therapeutic landscape is rapidly evolving, and future progress will likely depend on optimizing delivery platforms, improving durability, and integrating combination strategies to address the multifaceted nature of disease progression.
Full article
(This article belongs to the Special Issue Genetic Diagnosis and Treatment of Duchenne Muscular Dystrophy)
Open AccessArticle
Possible Founder Effect of the CDKN2A c.146T>C Variant in the Mexican Population: Phenotypic Characterization
by
María Lourdes Garza-Rodríguez, Eren Adrián Alejandro Vargas-Márquez, Dione Aguilar, Samantha Trujillo-Bornios, Hugo Leonid Gallardo-Blanco, Oscar Vidal-Gutiérrez, Diana Cristina Pérez-Ibave and Carlos Horacio Burciaga-Flores
Genes 2026, 17(5), 532; https://doi.org/10.3390/genes17050532 - 30 Apr 2026
Abstract
Background: Germline CDKN2A variants are associated with Familial Atypical Mole-Malignant Melanoma (FAMMM) syndrome. This syndrome involves an increased risk of melanoma, pancreatic cancer, and, in specific populations, duodenal cancer, breast cancer, and astrocytoma. The CDKN2A (c.146T>C) variant has been found in hereditary cancer
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Background: Germline CDKN2A variants are associated with Familial Atypical Mole-Malignant Melanoma (FAMMM) syndrome. This syndrome involves an increased risk of melanoma, pancreatic cancer, and, in specific populations, duodenal cancer, breast cancer, and astrocytoma. The CDKN2A (c.146T>C) variant has been found in hereditary cancer patients within the Mexican population. Furthermore, the phenotype linked to this variant in Mexico differs from that observed in other groups. This study aims to evaluate the founder effect of the CDKN2A (c.146T>C) variant through epidemiological analysis and to describe the phenotype within our population. Patients and Methods: We examined 72 Mexican patients (14 probands from distinct families, 48 relatives, and 10 nonrelated probands) carrying the CDKN2A (c.146T>C) form three hereditary cancer centers between September 2023 and September 2025. Results: Of the 72 individuals analyzed, 52 (72.22%) tested positive. A cancer diagnosis was established in 27 (37.50%) of the individuals analyzed. Breast cancer was the most common neoplasia, accounting for 19 cases (70.37%), followed by melanoma with 4 cases (14.81%) and ovarian cancer with 2 cases (7.40%). Three patients (11.11%) had two distinct primary neoplasms. Conclusions: Based on our findings and the fact that this variant has been reported nearly exclusively in the Mexican population, we conclude that it has a founder effect in this population. Additionally, the phenotype associated with this variant can vary among populations, with breast cancer being the most common carcinoma rather than melanoma among Mexican carriers, highlighting the importance of updating screening guidelines.
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(This article belongs to the Section Molecular Genetics and Genomics)
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Open AccessArticle
Type 1 Diabetes and Multiple Sclerosis Share General Autoimmunity Genetic Variation
by
Maristella Steri, Alessandro Testori, Valeria Orrù and Magdalena Zoledziewska
Genes 2026, 17(5), 531; https://doi.org/10.3390/genes17050531 - 30 Apr 2026
Abstract
Background/Objectives: Type 1 diabetes (T1D) and multiple sclerosis (MS) are autoimmune, multifactorial, organ-specific disorders mediated by immune cells. Their co-occurrence has been partially attributed to shared genetics and environmental factors. We aimed to dissect the shared genetic architecture between T1D and MS
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Background/Objectives: Type 1 diabetes (T1D) and multiple sclerosis (MS) are autoimmune, multifactorial, organ-specific disorders mediated by immune cells. Their co-occurrence has been partially attributed to shared genetics and environmental factors. We aimed to dissect the shared genetic architecture between T1D and MS using large-scale genome-wide association studies (GWASs) and colocalization analyses. Methods: We applied a Bayesian colocalization framework to two large-scale GWAS data sets: a T1D study comprising 18,942 cases and 501,638 controls, and an MS GWAS including 14,802 cases and 26,703 controls. Results: We identified 26 shared colocalizing association signals between T1D and MS. Among them, seven loci (EOMES, RGS14, DLL1, ZNF438/ZEB1, SESN3, WARS1/SLC25A47, and IRF8) were novel for T1D and two (UBAC2 and LAT) for MS. Several signals showed supportive evidence in additional datasets and demonstrated functional annotation characteristics consistent with disease involvement. Conclusions: Colocalization can be a powerful discovery tool for disorders with co-divided genetic architecture, as prioritizing shared rather than individual causal variants may enhance the detection of novel loci. Our findings indicate that T1D and MS predominantly share general autoimmune susceptibility signals (17/26), rather than disease-specific (private), often with opposite direction of effect (9/26), underscoring their immunological heterogeneity.
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(This article belongs to the Special Issue Genetic Aspects of Autoimmune Diseases)
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Identifying Genetic Factors Contributing to Non-Syndromic Early-Onset Childhood Obesity Utilizing Whole-Exome Sequencing in Consanguineous Families
by
Hazal Banu Olgun Celebioglu, Ayse Pinar Ozturk, Sukran Poyrazoglu and Feyza Nur Tuncer
Genes 2026, 17(5), 530; https://doi.org/10.3390/genes17050530 - 29 Apr 2026
Abstract
Purpose: Obesity, characterized by abnormal fat accumulation with comorbidities, continues to increase dramatically, particularly in the pediatric population. Identifying the environmental and genetic causes underlying the development of obesity during early childhood is crucial for establishing preventive and protective treatments for this complex
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Purpose: Obesity, characterized by abnormal fat accumulation with comorbidities, continues to increase dramatically, particularly in the pediatric population. Identifying the environmental and genetic causes underlying the development of obesity during early childhood is crucial for establishing preventive and protective treatments for this complex disease. We aimed to investigate genetic variants related to non-syndromic early-onset childhood obesity. Methods: Whole-exome sequencing was performed in three independent consanguineous families with obesity, including three index cases and two additional affected siblings. Non-synonymous variants with minor allele frequency < 0.01 in all normal populations were filtered using the Genomize-SEQ Platform. Variant confirmations and familial segregations were analyzed by Sanger sequencing. Results: WES revealed a shared ATXN3 gene variant and two known variants of the SH2B1 and ADIPOQ genes, which were reported to be associated with obesity. Additionally, five heterozygous novel gene variants of the ANKK1, NEGR1, OGDH, ABCB1, and GSK3B genes were identified, which are predicted to cause excessive fat accumulation and disruption of energy balance in individuals. Conclusions: We suggest that the cumulative effects of all obesity-associated detected variants lead to the early-onset obesity phenotype observed in individuals. Hence, periodic follow-up and treatment opportunities are recommended for index cases, alongside the adoption of a more active lifestyle and healthy nutrition practices.
Full article
(This article belongs to the Special Issue Genes and Pediatrics)
Open AccessArticle
Expanding the Mutation Spectrum of Non-Syndromic Retinitis Pigmentosa in Consanguineous Pakistani Families: Unraveling Novel Pathogenic Variants in RP1, PDE6B, and PRCD Genes for Precision Diagnosis
by
Tayyaba Shan, Nimra Mukhtar, Sayyed Hammad Ullah, Asad Ullah, Asfandyar Ahmad Khan, Yumei Li, Meng Wang, Raeesa Tehreem, Amtul Aziz, Kiran Afshan, Rui Chen and Sabika Firasat
Genes 2026, 17(5), 529; https://doi.org/10.3390/genes17050529 - 29 Apr 2026
Abstract
Background: Non-syndromic retinitis pigmentosa (RP) is characterized by rod–cone degeneration, resulting in night blindness, visual field constriction, and eventual blindness. Recessively inherited RP is predominantly exacerbated in consanguineous populations, such as Pakistan. This study aimed to perform the genetic analysis of sixteen
[...] Read more.
Background: Non-syndromic retinitis pigmentosa (RP) is characterized by rod–cone degeneration, resulting in night blindness, visual field constriction, and eventual blindness. Recessively inherited RP is predominantly exacerbated in consanguineous populations, such as Pakistan. This study aimed to perform the genetic analysis of sixteen non-syndromic RP segregating Pakistani families, and to summarize the mutation spectrum of non-syndromic RP in our population by reviewing related literature. Methods: We screened 16 non-syndromic RP families using targeted capture panel sequencing of 344 genes related to inherited retinal dystrophies. Variants were prioritized based on rarity (minor allele frequency (MAF) < 0.001 in the gnomAD South Asian subset), pathogenicity assessments using ACMG/AMP criteria, and REVEL scores (>0.5). Candidate variants were validated for familial segregation through Sanger sequencing. Results: We identified 15 distinct variants across 14 genes associated with non-syndromic retinitis pigmentosa, comprising 6 missense, 7 nonsense, 1 frameshift, and 2 splice-site variants, including 4 novel variants, i.e., p.(Val220Met) and p.(Pro1282SerfsTer2) in RP1, 1 each in PDE6B (c.2021+5G>A), and PRCD p.(Ser38Ter). Homozygosity predominated, underscoring the impact of consanguinity on the burden of autosomal recessive disease in the present cohort, while the CERKL disease-causing mutation, i.e., p.(Arg257Ter), recurred in two families. Conclusions: This study expands Pakistan’s non-syndromic RP mutational spectrum by identifying novel variants in RP1, PDE6B, and PRCD, alongside recurrent CERKL and RHO mutations of the local population. The literature review suggests that RP1, TULP1, and PDE6B are among the most mutated genes in our population, supporting the value of population-specific genetic panels to enhance diagnostics and carrier screening.
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(This article belongs to the Special Issue The Genetic Lens: A New Era in Ophthalmology)
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