Replication stress causes delayed mitotic entry and chromosome 12 fragility at the ANKS1B large neuronal gene in human induced pluripotent stem cells

Substantial background level of replication stress is a feature of embryonic and induced pluripotent stem cells (iPSCs), which can predispose to numerical and structural chromosomal instability, including recurrent aberrations of chromosome 12. In differentiated cells, replication stress-sensitive genomic regions, including common fragile sites, are widely mapped through mitotic chromosome break induction by mild aphidicolin treatment, an inhibitor of replicative polymerases. IPSCs exhibit lower apoptotic threshold and higher repair capacity hindering fragile site mapping. Caffeine potentiates genotoxic effects and abrogates G2/M checkpoint delay induced by chemical and physical mutagens. Using 5-ethynyl-2'-deoxyuridine (EdU) for replication labeling, we characterized the mitotic entry dynamics of asynchronous iPSCs exposed to aphidicolin and/or caffeine. Under the adjusted timing of replication stress exposure accounting revealed cell cycle delay, higher metaphase chromosome breakage rate was observed in iPSCs compared to primary lymphocytes. Using differential chromosome staining and subsequent locus-specific fluorescent in situ hybridization, we mapped the FRA12L fragile site spanning the large neuronal ANKS1B gene at 12q23.1, which may contribute to recurrent chromosome 12 missegregation and rearrangements in iPSCs. Publicly available data on the ANKS1B genetic alterations and their possible functional impact are reviewed. Our study provides the first evidence of common fragile site induction in iPSCs and reveals potential somatic instability of a clinically relevant gene during early human development and in vitro cell expansion.

TNFRSF13B gene mutation in adult patient with common variable immunodeficiency. Case report

Common variable immunodeficiency (CVID) is one form of the primary immunodeficiencies (PIDs). CVID is characterized by variable clinical manifestations. Genetic alteration is a cause of the disease in many cases. In the current paper we described Patient N of 45 years old, who have been suffering from frequent various infections and therefore attended an immunologist and clinical geneticist. Immunoglobulins (Ig) A, M, and G deficiency was found in the patient. As a result of medical genetic counselling primary immunodeficiency has been suggested as a diagnosis. Further molecular genetic testing using clinical exome sequencing (Next Generation Sequencing method) revealed a likely-pathogenic variant c.204dupA (p.Leu69ThrfsX12, rs72553875) of TNFRSF13B gene in the patient. The gene variant was found in homozygous state. According to the international medical literature and genomic databases TNFRSF13B gene mutations lead to the CVID development and in some patients are characterized by isolated IgA deficiency and in the other group of patients can lead to decrease of IgA, IgM, and IgG. The patient had a family history of cancer and autoimmune inflammatory bowel disease (erosive-ulcerative enterocolitis). Moreover, one sibling of the patient died at the age of 3 weeks from complications of toxoplasmosis infection. The other sibling of 51 years old have been also suffering from recurrent infectious diseases. Thus, the genetic cause of the disease was identified in the proband. It has been shown that homozygosity for variant c.204dupA of TNFRSF13B gene is characterized by the deficiency of all three classes of Ig. Medical genetic counselling and modern molecular genetic methods application is an important step in management of people with signs of immunodeficiency. Such approach helps to make a diagnosis to the patient, to find an exact molecular reason of the condition, to use effective treatment, and to perform preventive measures in patient`s family.

Clinical features and functional analysis of novel SCN9A variants causing congenital insensitivity to pain

ABSTRACT

Pain perception is a fundamental protective mechanism that enables us to detect noxious stimuli. With a focus on finding treatments for pain, the molecular mechanisms and key players involved in pain perception are currently under intense study. Congenital insensitivity to pain is one of the rarest and most unusual pain disorders. One of the reasons of pure congenital absence of pain are pathogenic variants in the SCN9A gene, which encodes the α-subunit of the Nav1.7 voltage-gated sodium channel. To date, most of the described variants in SCN9A associated with congenital insensitivity to pain are biallelic frameshifting variants, and the extent to which splice-affecting variants contribute to this rare phenotype remains largely unknown. Here, we describe 4 novel variants in previously unreported patients with congenital insensitivity to pain, all carrying noncoding variants in a homozygous or compound-heterozygous state in the SCN9A gene. Functional analyses demonstrated that all variants affect mRNA splicing, leading to both out-of-frame and in-frame isoforms. In 1 case, a deep-intronic variant detected through whole-genome sequencing led to the inclusion of a pseudoexon in intron 9. Genotype-phenotype analysis did not reveal significant differences in phenotype severity among the patients, suggesting that in-frame shortening of the Nav1.7 protein completely disrupts its function. These findings broaden the understanding of SCN9A-related pain insensitivity and uncover the molecular mechanisms of novel noncoding variants in the SCN9A gene, which is crucial for the development of future tailored therapeutic approaches.