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Genes and Human Diseases: 3rd Edition
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Genes and Human Diseases: 3rd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 February 2026 | Viewed by 3658

Special Issue Editor

Prof. Dr. Mikhail I. Churnosov

E-Mail Website
Guest Editor
Department of Medical Biological Disciplines, Belgorod State University, 85 Pobedy Street, 308015 Belgorod, Russia
Interests: genes; human diseases; associations; biomarkers; bioinformatic analysis
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our previous Special Issue, “Genes and Human Diseases 2.0”. The study of the causes and mechanisms of human disease development, despite the numerous works carried out in this field, continues to be the focus of attention of various scientific research teams. The essential role of genetic factors in the formation of the vast majority of human diseases is beyond doubt. At the same time, despite the substantial accumulated factual material on this theme, there is no complete and definitive understanding of the pathogenetics of most human diseases at the moment. Often, the data obtained are not confirmed in subsequent studies, and in some cases, they are contradictory. It is necessary to continue further genetic-epidemiological studies in order to establish genetic factors that determine the susceptibility to various human diseases in different ethnic and territorial groups. Obtaining new data on the contribution of genetic factors to the formation of human diseases and the role of gene–gene and gene–environment interactions affecting the risk of developing diseases will significantly advance our understanding of the pathogenetics of diseases. Ultimately, this will create prerequisites for the use of candidate genes as effective biomarkers in practical medicine.This Special Issue will compile new data on the role of genetic factors in the formation of different human diseases to better-understand the genetic and molecular mechanisms of human disorder development.

Prof. Dr. Mikhail I. Churnosov
Guest Editor

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Keywords

  • genes
  • human diseases
  • genetic-epidemiological studies
  • genetic factors
  • susceptibility

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Published Papers (6 papers)

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Research

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18 pages, 2524 KB  
Article
Transcriptional Consequences of MeCP2 Knockdown and Overexpression in Mouse Primary Cortical Neurons
by Mostafa Rezapour, Joshua Bowser, Christine Richardson and Metin Nafi Gurcan
Int. J. Mol. Sci. 2025, 26(18), 9032; https://doi.org/10.3390/ijms26189032 - 17 Sep 2025
Viewed by 245
Abstract
Rett syndrome (RTT) and MECP2 duplication syndrome, a subtype of autism spectrum disorder (ASD), are neurodevelopmental disorders caused by MeCP2 loss and gain of function, respectively. While MeCP2 is known to regulate transcription through its interaction with methylated DNA and chromatin-associated factors such [...] Read more.
Rett syndrome (RTT) and MECP2 duplication syndrome, a subtype of autism spectrum disorder (ASD), are neurodevelopmental disorders caused by MeCP2 loss and gain of function, respectively. While MeCP2 is known to regulate transcription through its interaction with methylated DNA and chromatin-associated factors such as topoisomerase IIβ (TOP2β), the downstream transcriptional consequences of MeCP2 dosage imbalance remain partially characterized. Here, we present a transcriptome-centered analysis of mouse primary cortical neurons subjected to MeCP2 knockdown (KD) or overexpression (OE), which model RTT and ASD-like conditions in parallel. Using a robust computational pipeline integrating generalized linear models with quasi-likelihood F-tests and Magnitude–Altitude Scoring (GLMQL-MAS), we identified differentially expressed genes (DEGs) in KD and OE relative to wild-type (WT) neurons. This study represents a computational analysis of secondary transcriptomic data aimed at nominating candidate genes for future experimental validation. Gene Ontology enrichment revealed both shared and condition-specific biological processes, with KD uniquely affecting neurodevelopmental and stress-response pathways, and OE perturbing extracellular matrix, calcium signaling, and neuroinflammatory processes. To prioritize robust and disease-relevant targets, we applied Cross-MAS and further filtered DEGs by correlation with MeCP2 expression and regulation directional consistency. This yielded 16 high-confidence dosage-sensitive genes that were capable of classifying WT, KD, and OE samples with 100% accuracy using PCA and logistic regression. Among these, RTT-associated candidates such as Plcb1, Gpr161, Mknk2, Rgcc, and Abhd6 were linked to disrupted synaptic signaling and neurogenesis, while ASD-associated genes, including Aim2, Mcm6, Pcdhb9, and Cbs, implicated neuroinflammation and metabolic stress. These findings establish a compact and mechanistically informative set of MeCP2-responsive genes, which enhance our understanding of transcriptional dysregulation in RTT and ASD and nominate molecular markers for future functional validation and therapeutic exploration. Full article
(This article belongs to the Special Issue Genes and Human Diseases: 3rd Edition)
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12 pages, 269 KB  
Article
Polymorphic Variants of Neurotrophic Factor Genes in Affective Disorders: Pilot Study
by Ekaterina V. Mikhalitskaya, Natalya M. Vyalova, Diana Z. Paderina, Olga V. Roschina, German G. Simutkin, Nikolay A. Bokhan and Svetlana A. Ivanova
Int. J. Mol. Sci. 2025, 26(16), 7982; https://doi.org/10.3390/ijms26167982 - 19 Aug 2025
Viewed by 398
Abstract
Neurotrophic factors are regulatory proteins of nervous tissue. They have a significant effect on all processes in neurons. Neurotrophic factors participate in the processes of neuronal differentiation, neurogenesis, synaptogenesis, and the regulation of neuronal plasticity. Numerous data in the literature indicate that disruption [...] Read more.
Neurotrophic factors are regulatory proteins of nervous tissue. They have a significant effect on all processes in neurons. Neurotrophic factors participate in the processes of neuronal differentiation, neurogenesis, synaptogenesis, and the regulation of neuronal plasticity. Numerous data in the literature indicate that disruption of the regulation of neurotrophic factors can play an important role in the etiology of affective disorders. We examined 235 patients with an affective disorder (F31, F32, F33, F34.1, ICD-10) and 187 healthy controls. The mental state of the patients was assessed by SIGH-SAD, HARS, and CGI scales. Genotyping of polymorphic variants of neurotrophic factor genes (BDNF, NGF, and NRG1) was performed using real-time PCR. Only one of the polymorphisms (rs7124442 in the BDNF gene) showed an association with the affective disorders. All polymorphisms (except rs11030104 in the BDNF gene) showed an association or associated trend with clinical characteristics of the disease, evaluated according to psychometric scales and response to therapy. Our results support the potential value of the studied neurotrophic genes as a neurobiological marker for depression pathogenesis, clinical characteristics, and response to treatment. Due to several limitations, further case–control studies with larger sample sizes and different ethnic groups are needed. Full article
(This article belongs to the Special Issue Genes and Human Diseases: 3rd Edition)
14 pages, 1119 KB  
Article
Genotype Structure Alterations in 5q SMA Patients as a Result of the Newborn Screening Program Implementation in the Russian Federation
by Maria A. Akhkiamova, Andrey V. Marakhonov, Victoria V. Zabnenkova, Kristina A. Mikhalchuk, Sergei V. Voronin, Sergey I. Kutsev, Victoria V. Musatova, Tatyana N. Kekeeva, Nina V. Ryadninskaya, Alena L. Chukhrova, Svetlana I. Braslavskaya, Polina A. Chausova, Tatyana S. Beskorovainaya, Aleksander V. Polyakov, Kirill V. Savostyanov, Ilya S. Zhanin, Fanil S. Bilalov, Alexander L. Koroteev, Dmitry Y. Trofimov, Tatyana A. Bairova, Gulnara N. Seitova, Sergei V. Mordanov, Svetlana A. Matulevich, Elena B. Nikolaeva and Olga A. Shchaginaadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2025, 26(16), 7891; https://doi.org/10.3390/ijms26167891 - 15 Aug 2025
Viewed by 499
Abstract
Since 2023, the Russian Federation (RF) has implemented an expanded newborn screening (NBS) program for 36 hereditary disorders, which now includes 5q spinal muscular atrophy (5q SMA). As a result of newborn screening for 5q SMA conducted in the RF during 2023–2024, 288 [...] Read more.
Since 2023, the Russian Federation (RF) has implemented an expanded newborn screening (NBS) program for 36 hereditary disorders, which now includes 5q spinal muscular atrophy (5q SMA). As a result of newborn screening for 5q SMA conducted in the RF during 2023–2024, 288 newborns with a homozygous deletion of exon 7 in the SMN1 gene were identified by molecular genetic methods. The overall observed incidence of 5q SMA was 1 in 8439 newborns, which does not significantly differ from the expected incidence of 1 in 7953 newborns, established by previous pilot screening projects (p > 0.05). A comparison of the genotypes of patients identified through selective and newborn screening showed statistically significant differences in the proportions of patients carrying two, three, and four or more copies of the SMN2 gene. These findings demonstrate that the NBS program is effective in detecting both individuals with more severe phenotypes, as expected, and those with milder forms of the disease. Full article
(This article belongs to the Special Issue Genes and Human Diseases: 3rd Edition)
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21 pages, 1997 KB  
Article
Genetic and Metabolic Factors of Familial Dysbetalipoproteinemia Phenotype: Insights from a Cross-Sectional Study
by Anastasia V. Blokhina, Alexandra I. Ershova, Anna V. Kiseleva, Evgeniia A. Sotnikova, Marija Zaicenoka, Anastasia A. Zharikova, Yuri V. Vyatkin, Vasily E. Ramensky, Elizaveta A. Novokhatskaya, Anna L. Borisova, Svetlana A. Shalnova, Alexey N. Meshkov and Oxana M. Drapkina
Int. J. Mol. Sci. 2025, 26(15), 7376; https://doi.org/10.3390/ijms26157376 - 30 Jul 2025
Viewed by 447
Abstract
Familial dysbetalipoproteinemia (FD) is a prevalent and highly atherogenic hyperlipoproteinemia associated with the ε2/ε2 APOE genotype or rare APOE variants. The contributions of additional genetic and clinical factors to the FD phenotype remain unclear. We investigated these factors in both autosomal recessive and [...] Read more.
Familial dysbetalipoproteinemia (FD) is a prevalent and highly atherogenic hyperlipoproteinemia associated with the ε2/ε2 APOE genotype or rare APOE variants. The contributions of additional genetic and clinical factors to the FD phenotype remain unclear. We investigated these factors in both autosomal recessive and autosomal dominant forms of FD. Targeted (n = 4666) and exome (n = 194) sequencing were used to identify the ε2/ε2 APOE genotype or rare FD-causative APOE variants. Twenty-four lipid-related genes and forty variants included in a polygenic risk score for hypertriglyceridemia (HTG) were analyzed. FD was defined by the presence of FD variants and triglycerides (TG) ≥ 1.5 mmol/L (main study group). The comparison group consisted of patients with FD variants but TG < 1.5 mmol/L. Univariable and multivariable regression analyses were performed. A total of 71 unrelated subjects were identified (45.1% male, median age 50 years). FD was diagnosed in 52 patients, while 19 had FD variants only. Age (p = 0.019), elevated polygenic risk for HTG (p = 0.001), and the presence of metabolic syndrome components (p = 0.014) were independently associated with the FD phenotype. TG levels were significantly associated with polygenic burden (0.05 mmol/L per percentile), the presence of additional rare lipid-related variants (7.0 mmol/L), and glucose metabolism disorders (3.62 mmol/L), together explaining 30% of TG variance in cross-validated model. These results highlight the interplay of genetic and metabolic factors in FD development and support the integration of HTG genetic risk scores and metabolic control into personalized FD management. Full article
(This article belongs to the Special Issue Genes and Human Diseases: 3rd Edition)
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Review

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38 pages, 1630 KB  
Review
Gene Therapy Approaches for Atherosclerosis Focusing on Targeting Lipid Metabolism and Inflammation
by Evgeny Bezsonov, Nikita Chernyi, Mane Saruhanyan, Dariia Shimchenko, Nikolai Bondar, Darina Gavrilova, Mirza S. Baig and Alexander Malogolovkin
Int. J. Mol. Sci. 2025, 26(14), 6950; https://doi.org/10.3390/ijms26146950 - 19 Jul 2025
Viewed by 1121
Abstract
Atherosclerosis is a complex disease characterized by pathological thickening of the arterial intima. The mechanisms underlying the induction and progression of atherosclerosis are convoluted and remain under active investigation, with key components such as lipid accumulation and local inflammation being identified. Several risk [...] Read more.
Atherosclerosis is a complex disease characterized by pathological thickening of the arterial intima. The mechanisms underlying the induction and progression of atherosclerosis are convoluted and remain under active investigation, with key components such as lipid accumulation and local inflammation being identified. Several risk factors (e.g., metabolic disorders, genetic background, diet, infections) have been shown to exacerbate disease progression, but their roles as clinically relevant markers remain to be established. Despite the growing body of evidence on the molecular pathogenesis of atherosclerosis, there is no effective preventive treatment against the development of this disease. In this review, we focus on gene targets for gene therapy as a novel potential approach to cure and prevent atherosclerosis. We critically review recent research demonstrating the therapeutic potential of viral vector-based (adeno-associated virus (AAV) and lentivirus) gene therapy for the treatment of atherosclerosis. We also summarize alternative gene targets and approaches (e.g., non-coding RNA (ncRNA), micro RNA (miRNA), small interfering RNA (siRNA), antisense oligonucleotide (ASO), CRISPR/Cas9) that aim to limit disease progression. We highlight the importance of local inflammation in the pathogenesis of atherosclerosis and propose gene targets with anti-inflammatory activity to inhibit the pathological inflammatory response. In addition, we provide perspectives on the future development of gene therapeutics and their potential applications. We anticipate that recent advances in gene therapy will help to identify new and effective targets to prevent atherosclerosis. Full article
(This article belongs to the Special Issue Genes and Human Diseases: 3rd Edition)
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Other

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14 pages, 1134 KB  
Case Report
13q Deletion Syndrome Presenting with Lymphopenia Detected Through Newborn Screening for Primary Immunodeficiencies
by Irina Efimova, Anna Mukhina, Zhanna Markova, Sergey Mordanov, Irina Soprunova, Dmitry Pershin, Natalya Balinova, Yunna Petrusenko, Dmitry Meleshko, Rena Zinchenko, Nadezhda Shilova, Sergey Voronin, Anna Shcherbina, Sergey Kutsev and Andrey Marakhonov
Int. J. Mol. Sci. 2025, 26(19), 9302; https://doi.org/10.3390/ijms26199302 - 23 Sep 2025
Viewed by 27
Abstract
The expanded newborn screening (NBS) program in the Russian Federation, launched in 2023, includes the detection of severe forms of T- and B-cell immunodeficiencies via TREC/KREC quantification. We report a rare case of a male infant having multiple congenital anomalies and lymphopenia identified [...] Read more.
The expanded newborn screening (NBS) program in the Russian Federation, launched in 2023, includes the detection of severe forms of T- and B-cell immunodeficiencies via TREC/KREC quantification. We report a rare case of a male infant having multiple congenital anomalies and lymphopenia identified through this program. Genetic testing revealed a 25.8 Mb terminal deletion spanning 13q31.2–qter, consistent with 13q deletion syndrome. Initial NBS revealed reduced TREC levels, prompting further evaluation. The patient exhibited a complex phenotype, including central nervous system malformation (alobar holoprosencephaly), severe congenital heart disease, renal hypoplasia, limb and genitourinary anomalies, and facial dysmorphism. Postnatal complications included pneumonia, pleuritis, and chylothorax. Flow cytometry demonstrated mild T- and B-cell lymphopenia. The genomic defect was characterized using long-read third-generation sequencing, enabling precise breakpoint identification and accurate mapping of deleted genes. The deletion was confirmed via subtelomeric FISH analysis. The patient died at 7 months of age due to the progression of underlying congenital anomalies and associated complications. Our findings broaden the clinical characterization of distal 13q deletion syndrome and demonstrate the value of long-read sequencing in structural chromosomal analysis. They further highlight the difficulties of caring for neonates having complex malformations and immune dysfunction. Given the potential for both primary and secondary immune disturbances, comprehensive immunological evaluation should be considered in patients having 13q deletion syndrome to improve diagnostic accuracy and inform appropriate clinical management. Full article
(This article belongs to the Special Issue Genes and Human Diseases: 3rd Edition)
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