The Impact of Environmental Factors on Monogenic Mendelian Diseases

The impact of rare diseases on the quality of life in paediatric patients: current status

Rare diseases, also known as orphan diseases, are a group of disorders that affect a small percentage of the population. Despite individually affecting a small number of people, collectively, they impact millions worldwide. This is particularly significant in paediatric patients, highlighting the global scale of the issue. This review delves into the exact prevalence of rare diseases among children and adolescents and their diverse impact on the quality of life of patients and their families. The review sheds light on the complex interplay of genetic and environmental factors contributing to these conditions and the diagnostic challenges and delays often encountered in identifying and categorising these diseases. It is noted that although there have been significant strides in the field of genomic medicine and the development of orphan drugs, effective treatments remain limited. This necessitates a comprehensive, multidisciplinary approach to management involving various specialities working closely together to provide holistic care. Furthermore, the review addresses the psychosocial and economic burdens faced by families with paediatric patients suffering from rare diseases, highlighting the urgent need for enhanced support mechanisms. Recent technological and therapeutic advancements, including genomic sequencing and personalized medicine, offer promising avenues for improving patient outcomes. Additionally, the review underscores the role of policy and advocacy in advancing research, ensuring healthcare access, and supporting affected families. It emphasises the importance of increased awareness, education, and collaboration among healthcare providers, researchers, policymakers, and patient advocacy groups. It stresses the pivotal role each group plays in improving the diagnosis, treatment, and overall quality of life for paediatric patients with rare diseases.

Reduced Penetrance is Common Among Predicted Loss-of-Function Variants and is Likely Driven by Residual Allelic Activity

Loss-of-function genetic variants (LoFs) often result in severe phenotypes, including autosomal dominant diseases driven by haploinsufficiency. Due to low carrier frequencies, their penetrance is generally unknown but typically variable. Here, we investigate the penetrance of >6,000 predicted LoFs (pLoFs) linked to 91 haploinsufficient diseases using a cohort of ≈24,000 carriers with linked electronic health record data. We find evidence for widespread reduced penetrance, which persisted after accounting for variant annotation artifacts, missed diagnoses, and incomplete clinical data. We thus hypothesized that many pLoFs have incomplete penetrance, which may be driven by residual allelic activity. To test this, we trained machine learning models to predict pLoF penetrance using variant-specific genomic features that may correlate with incomplete loss-of-function. The models were predictive of pLoF penetrance across a range of diseases and variant types, including those with prior clinical evidence for pathogenicity. This suggests that many pLoFs have incomplete penetrance due to residual allelic activity, complicating disease prognostication in asymptomatic carriers.

Potential Impact of Physical Activity on Measures of Well-Being and Quality of Life in People with Rare Diseases: A Nationwide Cross-Sectional Study in Italy

BACKGROUND

Rare diseases constitute a heterogeneous group of approximately 7000-8000 conditions, distinguished by their low prevalence. Collectively, they present a significant global health challenge, affecting millions of people worldwide. It is estimated that rare diseases affect approximately 10% of the global population, which places a significant burden on individuals, families, and society. It is, therefore, important to consider strategies to improve the overall well-being and quality of life of individuals with rare diseases. One potential avenue for exploration is the incorporation of physical activity (PA). The scope of this study was to ascertain whether PA has a positive impact on measures of well-being and to determine its potential to enhance the quality of life of these individuals.

METHODS

The data were collected via an online survey. The one-way ANOVA test for multiple groups and multivariate Poisson models were employed to identify the significant predictors of the outcomes of interest.

RESULTS

The protective effects of PA become evident with a minimum of six hours of activity per week. Our data confirm that the weekly hours devoted to PA can serve as a significant protective factor for QoL. The study also provided some insights into the motivations behind patients' engagement in PA. These included improving QoL and physical well-being, as well as the desire to interact socially, with the goal of meeting friends or making new acquaintances. Finally, for adults and older adults, engaging in PA can also be a way to control weight.

CONCLUSIONS

It is becoming increasingly clear that individuals with rare diseases stand to benefit greatly from PA, so it is only sensible to educate them on the advantages of an active lifestyle.

Rare liver diseases in Egypt: Clinical and epidemiological characterization

Illnesses that afflict a tiny number of individuals are referred to as rare diseases (RDs), sometimes called orphan diseases. The local healthcare systems are constantly under financial, psychological, and medical strain due to low incidence rates, unusual presentations, flawed diagnostic standards, and a lack of treatment alternatives for these RDs. The effective management of the once widely spread viral hepatitis B and C has altered the spectrum of liver diseases in Egypt during the last several years. The detection of uncommon disorders such as autoimmune, cholestatic, and hereditary liver diseases has also been made easier by the increasing knowledge and greater accessibility of specific laboratory testing. Finally, despite Egypt's large population, there are more uncommon liver disorders than previously thought. This review article discusses the clinical and epidemiological characteristics of a few uncommon liver disorders and the information currently accessible concerning these illnesses in Egypt.

Genetically transitional disease: conceptual understanding and applicability to rheumatic disease

In genomic medicine, the concept of genetically transitional disease (GTD) refers to cases in which gene mutation is necessary but not sufficient to cause disease. In this Perspective, we apply this novel concept to rheumatic diseases, which have been linked to hundreds of genetic variants via association studies. These variants are in the 'grey zone' between monogenic variants with large effect sizes and common susceptibility alleles with small effect sizes. Among genes associated with rare autoinflammatory diseases, many low-frequency and/or low-penetrance variants are known to increase susceptibility to systemic inflammation. In autoimmune diseases, hundreds of HLA and non-HLA genetic variants have been revealed to be modest- to moderate-risk alleles. These diseases can be reclassified as GTDs. The same concept could apply to many other human diseases. GTD could improve the reporting of genetic testing results, diagnostic yields, genetic counselling and selection of therapy, as well as facilitating research using a novel approach to human genetic diseases.

A novel homozygote nonsense variant of MSH4 leads to primary ovarian insufficiency and non-obstructive azoospermia

BACKGROUND

Both non-obstructive azoospermia (NOA) and primary ovarian insufficiency (POI) are pathological conditions characterized by premature and frequently complete gametogenesis failure. Considering that the conserved meiosis I steps are the same between oogenesis and spermatogenesis, inherited defects in meiosis I may result in common causes for both POI and NOA. The present research is a retrospective investigation on an Iranian family with four siblings of both genders who were affected by primary gonadal failure.

METHODS

Proband, an individual with NOA, was subjected to clinical examination, hormonal assessment, and genetic consultation. After reviewing the medical history of other infertile members of the family, patients with NOA went through genetic investigations including karyotyping and assessment of Y chromosome microdeletions, followed by Whole exome sequencing (WES) on the proband. After analyzing WES data, the candidate variant was validated using Sanger sequencing and traced in the family.

RESULTS

WES analysis of the proband uncovered a novel homozygote nonsense variant, namely c.118C>T in MSH4. This variant resulted in the occurrence of a premature stop codon in residue 40 of MSH4. Notably, the variant was absent in all public exome databases and in the exome data of 400 fertile Iranian individuals. Additionally, the variant was found to co-segregate with infertility in the family. It was also observed that all affected members had homozygous mutations, while their parents were heterozygous and the fertile sister had no mutant allele, corresponding to autosomal recessive inheritance. In addition, we conducted a review of variants reported so far in MSH4, as well as available clinical features related to these variants. The results show that the testicular sperm retrieval and ovarian stimulation cycles have not been successful yet.

CONCLUSION

Overall, the results of this study indicate that the identification of pathogenic variants in this gene will be beneficial in selecting proper therapeutic strategies. Also, the findings of this study demonstrate that clinicians should obtain the history of other family members of the opposite sex when diagnosing for POI and/or NOA.

Selenium and selenoproteins role in Parkinson's disease: Is there a link between selenoproteins and accumulated alpha-synuclein?

BACKGROUND

While Parkinson's disease (PD) etiology is not clear yet, accumulated alpha-synuclein is proposed to induce neurodegeneration. Selenium (Se) and its functional proteins play a key role in aggregation of misfolded proteins. However, their implications in neurodegenerative process are unclear.

AIM

Diagnosing Se and selenoprotein P (SelP), selenoprotein S (SelS) proportions in serum of PD patients to compare with healthy controls, whether the changes in their concentration could be a biomarker for PD.

METHODS

Se concentration was investigated in 30 PD patients and 30 controls using atomic absorption spectrometry. Also, alpha-Synuclein, SelP, and SelS levels were evaluated by ELISA. The parameters were compared in PD patients and controls. Also, the variations within the case group according to their age, disorder stage, and drug administration were evaluated.

RESULTS

PD subjects had higher Se concentration. The mean SelP in PD patients was lower from controls, whilst SelS levels were higher. Also, the concentration of alpha-synuclein was higher in PD patients. However, age, stage (except UPDRS III), and disorder duration had no influence on the Se and selenoproteins level, whilst there was a direct association between alpha-synuclein levels and disorder stage. Also, alpha-synuclein proportions in subjects using levodopa was significantly higher.

CONCLUSION

Our results suggest that serum levels of Se and SelP could be a biomarker or risk factor for PD. Although SelS interferes to reduce aggregated proteins, its pathway in PD is not clearly understood. Future studies could focus on how SelS can reduce on alpha-synuclein aggregation. Thus, other studies should be performed on this issue to induce the selenoproteins in PD.

SLC6A1 variant pathogenicity, molecular function and phenotype: a genetic and clinical analysis

Genetic variants in the SLC6A1 gene can cause a broad phenotypic disease spectrum by altering the protein function. Thus, systematically curated clinically relevant genotype-phenotype associations are needed to understand the disease mechanism and improve therapeutic decision-making. We aggregated genetic and clinical data from 172 individuals with likely pathogenic/pathogenic (lp/p) SLC6A1 variants and functional data for 184 variants (14.1% lp/p). Clinical and functional data were available for a subset of 126 individuals. We explored the potential associations of variant positions on the GAT1 3D structure with variant pathogenicity, altered molecular function and phenotype severity using bioinformatic approaches. The GAT1 transmembrane domains 1, 6 and extracellular loop 4 (EL4) were enriched for patient over population variants. Across functionally tested missense variants (n = 156), the spatial proximity from the ligand was associated with loss-of-function in the GAT1 transporter activity. For variants with complete loss of in vitro GABA uptake, we found a 4.6-fold enrichment in patients having severe disease versus non-severe disease (P = 2.9 × 10-3, 95% confidence interval: 1.5-15.3). In summary, we delineated associations between the 3D structure and variant pathogenicity, variant function and phenotype in SLC6A1-related disorders. This knowledge supports biology-informed variant interpretation and research on GAT1 function. All our data can be interactively explored in the SLC6A1 portal (https://slc6a1-portal.broadinstitute.org/).

Alopecia Areata: A Review of the Genetic Variants and Immunodeficiency Disorders Associated with Alopecia Areata

Alopecia areata (AA) is an autoimmune form of non-scarring hair loss that occurs on a spectrum from patchy loss of hair on the scalp, to complete hair loss. Histology features can vary, but increased abundance of telogen hair and miniaturized hair follicles are classic hallmarks [Clin Cosmet Investig Dermatol. 2015;8:397-403]. Additionally, lymphocytic infiltration of the hair bulb is a commonly observed histology feature of AA which underscores how the disease is an autoimmune-mediated one that results from immune-mediated attack of the hair follicle. In a healthy individual, the hair follicle is one of the body's immune-privileged sites, but the breakdown of this immune privilege is thought to be an important driver in AA disease development. Diagnosis of AA is usually based on phenotypic manifestations in conjunction with biopsies which can help conclude whether the hair loss is autoimmune based. However, varied manifestation of disease both clinically and histologically makes diagnosis criteria more ambiguous and early identification of disease harder to achieve. A better understanding of genes that are associated with increased AA risk may help elucidate potential gene targets for future therapeutics.

Incomplete Penetrance and Variable Expressivity: From Clinical Studies to Population Cohorts

The same genetic variant found in different individuals can cause a range of diverse phenotypes, from no discernible clinical phenotype to severe disease, even among related individuals. Such variants can be said to display incomplete penetrance, a binary phenomenon where the genotype either causes the expected clinical phenotype or it does not, or they can be said to display variable expressivity, in which the same genotype can cause a wide range of clinical symptoms across a spectrum. Both incomplete penetrance and variable expressivity are thought to be caused by a range of factors, including common variants, variants in regulatory regions, epigenetics, environmental factors, and lifestyle. Many thousands of genetic variants have been identified as the cause of monogenic disorders, mostly determined through small clinical studies, and thus, the penetrance and expressivity of these variants may be overestimated when compared to their effect on the general population. With the wealth of population cohort data currently available, the penetrance and expressivity of such genetic variants can be investigated across a much wider contingent, potentially helping to reclassify variants that were previously thought to be completely penetrant. Research into the penetrance and expressivity of such genetic variants is important for clinical classification, both for determining causative mechanisms of disease in the affected population and for providing accurate risk information through genetic counseling. A genotype-based definition of the causes of rare diseases incorporating information from population cohorts and clinical studies is critical for our understanding of incomplete penetrance and variable expressivity. This review examines our current knowledge of the penetrance and expressivity of genetic variants in rare disease and across populations, as well as looking into the potential causes of the variation seen, including genetic modifiers, mosaicism, and polygenic factors, among others. We also considered the challenges that come with investigating penetrance and expressivity.

Compound Heterozygous COX20 Variants Impair the Function of Mitochondrial Complex IV to Cause a Syndrome Involving Ophthalmoplegia and Visual Failure

The cytochrome c oxidase 20 (COX20) gene encodes a protein with a crucial role in the assembly of mitochondrial complex IV (CIV). Mutations in this gene can result in ataxia and muscle hypotonia. However, ophthalmoplegia and visual failure associated with COX20 mutation have not been examined previously. Moreover, the mechanism causing the phenotype of patients with COX20 variants to differ from that of patients with mutations in other genes impairing CIV assembly is unclear. In this investigation, the aim was to assess the relation between COX20 variants and CIV assembly. We performed detailed clinical, physical, and biochemical investigations of affected individuals. Western blotting, reverse transcription-polymerase chain reaction, and blue native-polyacrylamide gel electrophoresis were used to analyze the expression level of COX20 and oxidative phosphorylation. A Seahorse XF Cell Mito Stress Test and enzymatic activity analysis were performed to evaluate mitochondrial function. Whole-exome sequencing revealed the same compound heterozygous mutations (c.41A > G and c.222G > T, NM_198076) in COX20 in two siblings. This is the first description of ophthalmoplegia and visual failure associated with COX20 variants. In vitro analysis confirmed that the COX20 protein level was significantly decreased, impairing the assembly and activity of CIV in patients' fibroblast. Overexpression of COX20 using a transduced adenovirus partially restored the function of the patients' fibroblasts. Early-onset complex movement disorders may be closely related to COX20 variants. Our results broaden the clinical phenotypes of patients with COX20 variants showing ophthalmoplegia and visual failure. Additionally, dysfunction of COX20 protein can impair the assembly and activity of CIV.

Phenolic-rich extract of avocado Persea americana (var. Colinred) peel blunts paraquat/maneb-induced apoptosis through blocking phosphorylation of LRRK2 kinase in human nerve-like cells

It is increasingly evident that LRRK2 kinase activity is involved in oxidative stress (OS)-induced apoptosis-a type of regulated cell death and neurodegeneration, suggesting LRRK2 inhibition as a potential therapeutic target. We report that a phenolic-rich extract of avocado Persea americana var. Colinred peel (CRE, 0.01 mg/ml) restricts environmental neurotoxins paraquat (1 mM)/maneb (0.05 mM)-induced apoptosis process through blocking reactive oxygen species (ROS) signaling and concomitant inhibition of phosphorylation of LRRK2 in nerve-like cells (NLCs). Indeed, PQ + MB at 6 h exposure significantly increased ROS (57 ± 5%), oxidation of protein DJ-1cys106SOH into DJ-1Cys106SO3 ([~3.7 f(old)-(i)ncrease]), augmented p-(S935)-LRRK2 kinase (~20-f(old) (i)ncrease), induced nuclei condensation/fragmentation (28 ± 6%), increased the expression of PUMA (~6.2-fi), and activated CASPASE-3 (CASP-3, ~4-fi) proteins; but significantly decreased mitochondrial membrane potential (ΔΨm, ~48 ± 4%), all markers indicative of apoptosis compared to untreated cells. Remarkably, CRE significantly diminished both OS-signals (i.e., DCF+ cells, DJ-1Cys106SO3) as well as apoptosis markers (e.g., PUMA, CASP-3, loss of ΔΨm, p-LRRK2 kinase) in NLCs exposed to PQ + MB. Furthermore, CRE dramatically reestablishes the transient intracellular Ca2+ flow (~300%) triggered by dopamine (DA) in neuronal cells exposed to PQ + MB. We conclude that PQ + MB-induced apoptosis in NLCs through OS-mechanism, involving DJ-1, PUMA, CASP-3, LRRK2 kinase, mitochondria damage, DNA fragmentation, and alteration of DA-receptors. Our findings imply that CRE protects NLCs directly via antioxidant mechanism and indirectly by blocking LRRK2 kinase against PQ + MB stress stimuli. These data suggest that CRE might be a potential natural antioxidant.

Integrating network pharmacology and in vitro model to investigate hippocampal neurotoxicity induced by atrazine

Atrazine (ATR), a commonly applied herbicide in agriculture, has been found to cause hippocampal injury in rodents. However, the underlying toxicological targets and mechanisms are unclear. In this study, network pharmacology analysis and in vitro model were integrated to investigate the effect and mechanism of ATR-induced hippocampal neurotoxicity. In total, 71 targets of hippocampal neurotoxicity induced by ATR were predicted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes enrichment (KEGG) enrichment analysis suggested that these targets were related to multiple GO terms and signaling pathways. To further investigate the underlying mechanisms, the top 10 hub targets were screened and included tumor protein p53 (Tp53), caspase 3 (Casp3), prostaglandin-endoperoxide synthase 2 (Ptgs2), cAMP-responsive element-binding protein 1 (Creb1), estrogen receptor 1 (Esr1), Jun proto-oncogene (Jun), brain-derived neurotrophic factor (Bdnf), catalase (Cat), sirtuin 1 (Sirt1) and Fos proto-oncogene (Fos). Moreover, the cell counting kit-8 (CCK8) and lactate dehydrogenase (LDH) assay showed that ATR had time and dose-dependent cytotoxicity on H19-7 cells. TUNEL staining revealed that ATR increased the apoptotic ratio. In addition, Real-time quantitative polymerase chain reaction (RT-qPCR) results indicated that the mRNA expression levels of all hub targets showed significant changes, except Esr1 and Jun. Our study demonstrated that ATR mainly acted on multiple targets and signaling pathways to exert its hippocampal neurotoxicity. These results provided initial evidence for the further exploration of the toxicological mechanism of ATR.