Different Types Of Mutations Research Articles

Novel variants of NEK9 associated with neonatal arthrogryposis: Two case reports and a literature review.

Objective: Pathogenic variants in NEK9 (MIM: 609798) have been identified in patients with lethal congenital contracture syndrome 10 (OMIM: 617022) and arthrogryposis, Perthes disease, and upward gaze palsy (APUG and OMIM: 614262). The shared core phenotype is multiple joint contractures or arthrogryposis. In the present study, three novel variants of NEK9 associated with neonatal arthrogryposis were reported. Methods: The clinical data of two premature infants and their parents were collected. The genomic DNA was extracted from their peripheral blood samples and subjected to trio-whole-exome sequencing (trio-WES) and copy number variation analysis. Results: Using trio-WES, a total of three novel pathogenic variants of NEK9 were detected in the two families. Patient 1 carried compound heterozygous variations of c.717C > A (p. C239*741) and c.2824delA (p.M942Cfs*21), which were inherited from his father and mother, respectively. Patient 2 also carried compound heterozygous variations of c.61G > T (p. E21*959) and c. 2824delA (p. M942Cfs*21), which were inherited from his father and mother, respectively. These variants have not been previously reported in the ClinVar, HGMD, or gnomAD databases. Conclusion: This is the first report about NEK9-related arthrogryposis in neonatal patients. The findings from this study suggest that different types of mutations in NEK9 lead to different phenotypes. Our study expanded the clinical phenotype spectrum and gene spectrum of NEK9-associated arthrogryposis.

Promene nivoa polnih hormona sa starenjem i njihov uticaj na glas

The aim of this study is to review modern literature to provide an insight into contemporary research into the etiology, pathophysiology and symptomatology of changes in hormone levels associated with aging and their pattern-consequential relationship with voice quality, with special reference to the analysis of different types of mutations (mutatio precox and mutatio perversa), menstrual and climacteric dysphonia. The criteria for inclusion of works obtained from the search were: works published during the last 15 years, published in English. Compared to the male voice, the female voice does not go through drastic changes during puberty. In males, the increased levels of testosterone and dihydrotestosterone during puberty are responsible for the enlargement of the laryngeal cartilage, which causes the basal tone to decrease by a third of an octave. If the child enters puberty prematurely, this hormone imbalance will lead to the appearance of voice pathology -mutation precox. Mutatio perversa occurs suddenly in females and is characterized by a deep male voice and other signs of virilization. The appearance of submucosal bleeding in the period before menstruation and the increased secretion of estrogen that leads to the appearance of edema will cause premenstrual dysphonia. Voice quality in this period is characterized by vocal fatigue, reduced voice range with loss of high tones, loss of vocal power and hoarseness of voice. Menopausal vocal syndrome is characterized by reduced flexibility and a reduced range of vibrational amplitude. It can be concluded that the vocal cords are a target organ, sensitive to fluctuations in the level of sex hormones due to the physiological aging process and the resulting endocrine disorders during life.

The metabolic sensitivity of hydrogen isotope fractionation differs between plant compounds

Hydrogen stable isotope analyses (δ2H) of plant derived organic compounds are a useful tool for ecological, environmental, and palaeoclimatological research. However, during organic compound synthesis, variable biosynthetic 2H-fractionation has been suggested to occur as a result of changes in plant carbon fluxes. So far, inference has been based on examining the δ2H patterns of plant compounds along environmental gradients, among plant species, and between plant organs. In an alternative approach, we used four plant species with four different types of mutations that cause impaired starch synthesis to assess whether variability in carbon metabolism affects the biosynthetic 2H-fractionation during cellulose, phytol, and acetogenic lipid synthesis. We found that mutants with impaired starch synthesis always had higher cellulose and phytol δ2H values compared to the wild type. By contrast, 2H-fractionation during acetogenic lipid biosynthesis generally did not show strong metabolic sensitivity. We rationalise these differences by considering the biosynthetic pathway of each compound and the likely source of the variable isotope fractionation. In different organic compounds, the sensitivity of variable biosynthetic 2H-fractionation to changes in C-metabolism depends on incorporation of specific H atoms from precursor molecules. As such, we determined that the similar increase in cellulose and phytol δ2H values as an effect of impaired starch synthesis most likely originates in triose-phosphates.

"CHildren with Inherited Platelet disorders Surveillance" (CHIPS) retrospective and prospective observational cohort study by Italian Association of Pediatric Hematology and Oncology (AIEOP).

Inherited thrombocytopenias (ITs) are rare congenital bleeding disorders characterized by different clinical expression and variable prognosis. ITs are poorly known by clinicians and often misdiagnosed with most common forms of thrombocytopenia. "CHildren with Inherited Platelet disorders Surveillance" study (CHIPS) is a retrospective - prospective observational cohort study conducted between January 2003 and January 2022 in 17 centers affiliated to the Italian Association of Pediatric Hematology and Oncology (AIEOP). The primary objective of this study was to collect clinical and laboratory data on Italian pediatric patients with inherited thrombocytopenias. Secondary objectives were to calculate prevalence of ITs in Italian pediatric population and to assess frequency and genotype-phenotype correlation of different types of mutations in our study cohort. A total of 139 children, with ITs (82 male - 57 female) were enrolled. ITs prevalence in Italy ranged from 0.7 per 100,000 children during 2010 to 2 per 100,000 children during 2022. The median time between the onset of thrombocytopenia and the diagnosis of ITs was 1 years (range 0 - 18 years). A family history of thrombocytopenia has been reported in 90 patients (65%). Among 139 children with ITs, in 73 (53%) children almost one defective gene has been identified. In 61 patients a pathogenic mutation has been identified. Among them, 2 patients also carry a variant of uncertain significance (VUS), and 4 others harbour 2 VUS variants. VUS variants were identified in further 8 patients (6%), 4 of which carry more than one variant VUS. Three patients (2%) had a likely pathogenic variant while in 1 patient (1%) a variant was identified that was initially given an uncertain significance but was later classified as benign. In addition, in 17 patients the genetic diagnosis is not available, but their family history and clinical/laboratory features strongly suggest the presence of a specific genetic cause. In 49 children (35%) no genetic defect were identified. In ninetyseven patients (70%), thrombocytopenia was not associated with other clinically apparent disorders. However, 42 children (30%) had one or more additional clinical alterations. Our study provides a descriptive collection of ITs in the pediatric Italian population.

Cystic fibrosis treatment; small molecule modulators vs genetic therapy

Cystic fibrosis, CF, is one of the most common life-shortening genetic diseases among Caucasian population. It is a recessive genetic disease that is mainly caused by different types of mutations affecting the gene encoding for the cystic fibrosis transmembrane conductance regulator, CFTR, protein. CFTR is a multifunctional protein found in multiple organs in the human body, acting mainly as a trans-epithelial channel which regulates the flow of chloride and bicarbonate ions across epithelial membranes leading to the formation of a thin slippery mucous layer. A malfunctioning CFTR protein would lead to the accumulation of a thick viscous mucous layer blocking pancreatic ducts, intestines and airways which is the primary reason of death. Treatment of cystic fibrosis was mainly addressing the symptoms to overcome the complications of the disease such as pneumonia, lung infections, pancreatitis, maldigestion and infertility. Since the early 2010’s, the development of an actual therapy has reached great milestones including small molecule modulators and genetic therapy. Small molecule therapy depends on the development of small pharmacological agents that can bind to the mutated CFTR protein restoring its function. Pharmacological agents can act through different mechanisms and be mainly classified to; correctors and potentiators. On the other hand, gene-editing techniques are evolving showing very promising results. Gene therapy entails the relocation of a proper copy of the CFTR gene in the aim of expressing a functional CFTR protein. In this review article, small molecule and genetic therapies will be discussed including their development, benefits and limitations.

P.28 Introduction of 12 novel pathogenic DMD variants, associated phenotypes and studies of dystrophin and MAST1 abundances

Duchenne muscular dystrophy (DMD) affects one in 3,500-5,600 of male newborns, making it the most common inherited muscular dystrophy. Becker muscular dystrophy (BMD), its milder form, is much rarer, affecting only one in about 18,000 male newborns. Both are caused by different types of mutations in the <i>DMD</i> gene. The encoded protein dystrophin stabilises the plasma membrane of the muscle cell as part of the dystrophin-glycoprotein-complex. Current research into DMD and BMD can explain about 92% of the phenotypes based on their genotypes through the frame-shift hypothesis. However, the remaining 8% are not adequately explained by this hypothesis, so that there is a need for further research to explain - not only - intermediate courses. We screened the cohort of DMD and BMD patients treated at the department of pediatric neurology of the University Hospital Essen for novel pathogenic <i>DMD</i> variants and corresponding phenotypes. We analysed the protein signatures (including post-translational modifications), measured dystrophin levels and studied the interactions of dystrophin and MAST1 in different biomaterials. Here, we report on 12 novel pathogenic variants, which have not yet been described in literature and link though to several several atypical phenotypes. Clinical findings were correlated with abundances of dystrophin and MAST1 toward an attempt of patient stratification. Knowing about novel genotypes and its corresponding (evolving) phenotype is very important in terms of counselling of affected families. Analysing the protein signatures and dystrophin levels as well as interaction partners is crucial to better understand the pathophysiology of dystrophin expression, especially in view of the development of new therapeutic approaches.

Characteristics of genetic changes in the &lt;i&gt;SMN1&lt;/i&gt; gene in spinal muscular atrophy 5q

Background. Proximal spinal muscular atrophy 5q (5q‑SMA) is one of the most common neuromuscular diseases, which is caused by mutations of the SMN1 gene. Despite the fact that most studies consider SMN1 “deletion” as the most common cause of 5q‑SMA, gene loss is in fact associated with both classical deletions and conversions of SMN1 and SMN2, as well as with formation of chimeric structures. Up to now, far too little attention has been paid to the prevalence of types of SMN1 loss. However, different types of mutations can have different influence on the clinical findings and the effectiveness of therapy. A deeper study of the structure of these genes will allow us to determine the predictors of response to treatment and bring us closer to understanding the reasons for the instability of the SMN region.Aim. To study genetic changes in the SMN1 gene, as well as the number of copies of the SMN1 and SMN2 genes in 5q‑SMA.Materials and methods. The study involved 703 patients, for whom the analysis of the number of copies of SMN1 and SMN2 was performed in the center of molecular medicine of I.P. Pavlov First Saint Petersburg State Medical University for 2018–2021. Gene copy number analysis was performed by multiplex ligation‑dependent probe amplification (MLPA) using the SALSA MLPA P021 SMA kit (MRC Holland).Results. Among 703 participants, a homozygous SMN1 deletion was found in 167 (24 %), 76 (11 %) were carriers of the deletion and no aberrations were found in the remaining 460 (65 %). Among patients with a homozygous deletion, 41 (24 %) cases of a true deletion were identified. Also, 11 (7 %) cases of partial deletion with a homozygous loss of the 7th exon and heterozygous of the 8th exon of SMN1 were identified. The most common type of aberration was the conversion of SMN1 to SMN2 – 94 (56 %) cases, which is characterized by a homozygous loss of SMN1 and a reciprocal increase in SMN2 copies. In addition, 21 (13 %) cases of the formation of hybrid genes were found.Conclusion. Types of genetic aberrations in 5q‑SMA have not been studied enough yet. A search of the literature revealed very few studies which results are comparable with ours. However, further research of genetic changes in SMN1 and SMN2 might bring more clarity on the causes and mechanisms of this disease, and get us closer to finding the most effective method of treatment.

Selection in a growing colony biases results of mutation accumulation experiments

Mutations provide the raw material for natural selection to act. Therefore, understanding the variety and relative frequency of different type of mutations is critical to understanding the nature of genetic diversity in a population. Mutation accumulation (MA) experiments have been used in this context to estimate parameters defining mutation rates, distribution of fitness effects (DFE), and spectrum of mutations. MA experiments can be performed with different effective population sizes. In MA experiments with bacteria, a single founder is grown to a size of a colony (~ 108). It is assumed that natural selection plays a minimal role in dictating the dynamics of colony growth. In this work, we simulate colony growth via a mathematical model, and use our model to mimic an MA experiment. We demonstrate that selection ensures that, in an MA experiment, fraction of all mutations that are beneficial is over-represented by a factor of almost two, and that the distribution of fitness effects of beneficial and deleterious mutations are inaccurately captured in an MA experiment. Given this, the estimate of mutation rates from MA experiments is non-trivial. We then perform an MA experiment with 160 lines of E. coli, and show that due to the effect of selection in a growing colony, the size and sector of a colony from which the experiment is propagated impacts the results. Overall, we demonstrate that the results of MA experiments need to be revisited taking into account the action of selection in a growing colony.

Uncovering incontinentia pigmenti: From DNA sequence to pathophysiology.

Incontinentia pigmenti (IP) is an X-linked dominant genodermatosis. The disease is known to be caused by recurrent deletion of exons 4–10 of the Inhibitor Of Nuclear Factor Kappa B Kinase Regulatory Subunit Gamma (IKBKG) gene located at the Xq28 chromosomal region, which encodes for NEMO/IKKgamma, a regulatory protein involved in the nuclear factor kappa B (NF-κB) signaling pathway. NF-κB plays a prominent role in the modulation of cellular proliferation, apoptosis, and inflammation. IKBKG mutation that results in a loss-of-function or dysregulated NF-κB pathway contributes to the pathophysiology of IP. Aside from typical skin characteristics such as blistering rash and wart-like skin growth presented in IP patients, other clinical manifestations like central nervous system (CNS) and ocular anomalies have also been detected. To date, the clinical genotype-phenotype correlation remains unclear due to its highly variable phenotypic expressivity. Thus, genetic findings remain an essential tool in diagnosing IP, and understanding its genetic profile allows a greater possibility for personalized treatment. IP is slowly and gradually gaining attention in research, but there is much that remains to be understood. This review highlights the progress that has been made in IP including the different types of mutations detected in various populations, current diagnostic strategies, IKBKG pathophysiology, genotype-phenotype correlation, and treatment strategies, which provide insights into understanding this rare mendelian disorder.

Patterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon.

Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable "occupancy" in the pan-genome - genes which are either present in all studied genotypes or missing in some genotypes - show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B.distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.

In Silico Pleiotropy Analysis in KEGG Signaling Networks Using a Boolean Network Model.

Pleiotropy, which refers to the ability of different mutations on the same gene to cause different pathological effects in human genetic diseases, is important in understanding system-level biological diseases. Although some biological experiments have been proposed, still little is known about pleiotropy on gene–gene dynamics, since most previous studies have been based on correlation analysis. Therefore, a new perspective is needed to investigate pleiotropy in terms of gene–gene dynamical characteristics. To quantify pleiotropy in terms of network dynamics, we propose a measure called in silico Pleiotropic Scores (), which represents how much a gene is affected against a pair of different types of mutations on a Boolean network model. We found that our model can identify more candidate pleiotropic genes that are not known to be pleiotropic than the experimental database. In addition, we found that many types of functionally important genes tend to have higher values than other genes; in other words, they are more pleiotropic. We investigated the relations of with the structural properties in the signaling network and found that there are highly positive relations to degree, feedback loops, and centrality measures. This implies that the structural characteristics are principles to identify new pleiotropic genes. Finally, we found some biological evidence showing that analysis is relevant to the real pleiotropic data and can be considered a novel candidate for pleiotropic gene research. Taken together, our results can be used to understand the dynamics pleiotropic characteristics in complex biological systems in terms of gene–phenotype relations.

Molecular Aspects of Distal Kidney Tubular Acidosis in Children, Its Long-Term Outcome, and Relationship with Hyperammonemia.

Objective:We aimed to present the characteristics, genetic analysis results, long-term prognosis of our patients with distal kidney tubular acidosis, and the relationship between hyperammonemia and distal kidney tubular acidosis.Materials and Methods:Biochemical, clinical, and imaging findings were collected at presentation and the last clinic visit, and results of the genetic analysis were recorded.Results:Our study included 9 patients (3 female, 33%). The median age at diagnosis was 3 months, and the median follow-up period was 111 months. Height standard deviation scores were less than −2 in 4 (44%) patients at presentation and in 3 (33%) at the last clinic visit. The median estimated glomerular filtration rate was 98 mL/min/1.73 m2 at presentation and 126 mL/min/1.73 m2 at the last clinic visit. We have found 8 different types of mutations of 2 genes, including 6 in the ATP6V0A4 gene, 2 in the SLCA4A1 gene, and 2 of them were novel. At the time of presentation, nephrocalcinosis and hypercalciuria were present in all our patients, but at the last visit, only 1 patient had hypercalciuria. Sensorineural hearing loss was found in 4 of our patients with a mutation in the ATP6V0A4 gene. Serum ammonia levels were found to be high in 3 patients with mutations in the ATP6V0A4 gene.Conclusion:Adequate metabolic control is essential for optimal growth and preserved kidney function in distal kidney tubular acidosis patients. Distal kidney tubular acidosis may be associated with hyperammonemia. We recommend keeping potassium levels at high-normal levels to reduce ammonia levels, especially in the absence of acidosis.

Structural and biophysical studies of new L-asparaginase variants: lessons from random mutagenesis of the prototypic Escherichia coli Ntn-amidohydrolase.

This work reports the results of random mutagenesis of the Escherichia coli class 2 L-asparaginase EcAIII belonging to the Ntn-hydrolase family. New variants of EcAIII were studied using structural, biophysical and bioinformatic methods. Activity tests revealed that the L-asparaginase activity is abolished in all analyzed mutants with the absence of Arg207, but some of them retained the ability to undergo the autoproteolytic maturation process. The results of spectroscopic studies and the determined crystal structures showed that the EcAIII fold is flexible enough to accept different types of mutations; however, these mutations may have a diverse impact on the thermal stability of the protein. The conclusions from the experiments are grouped into six lessons focused on (i) the adaptation of the EcAIII fold to new substitutions, (ii) the role of Arg207 in EcAIII activity, (iii) a network of residues necessary for autoprocessing, (iv) the complexity of the autoprocessing reaction, (v) the conformational changes observed in enzymatically inactive variants and (vi) the cooperativity of the EcAIII dimer subunits. Additionally, the structural requirements (pre-maturation checkpoints) that are necessary for the initiation of the autocleavage of Ntn-hydrolases have been classified. The findings reported in this work provide useful hints that should be considered before planning enzyme-engineering experiments aimed at the design of proteins for therapeutic applications. This is especially important for L-asparaginases that can be utilized in leukemia therapy, as alternative therapeutics are urgently needed to circumvent the severe side effects associated with the currently used enzymes.

Coagulation Factor VII: Genetic, Molecular, and Clinical Characteristics

: Coagulation factor VII (FVII) is a vitamin K-dependent serine protease that plays a pivotal role in normal hemostasis. Mature FVII is a glycoprotein comprised γ-carboxyglutamic acid-rich (Gla) domain, two epidermal growth factor (EGF)-like domains, an activation domain, and a serine protease domain. FVII requires proteolytic activation followed by tissue factor (TF) binding for maximal activity. The F7 gene (14.8 kb) is located on 13q34, composed of nine exons and eight introns. The congenital FVII deficiency is a rare coagulopathy with an autosomal recessive pattern of inheritance that occurs due to mutation in the F7 gene. A considerable number of mutations of different types have been identified throughout this gene affecting the expression, structure, and post-translational alterations of the protein. FVII deficiency is the most frequently recessively inherited bleeding disorder. Subjects with FVII deficiency show a wide range of symptoms, including cutaneous hemorrhage, mucosal hemorrhage, gastrointestinal bleeding, joint bleeding, and central nervous system (CNS) hemorrhage. Unlike other coagulation factor deficiencies, serum levels of FVII do not demonstrate the severity of the disease, and there is no direct correlation between serum levels and clinical complications. Replacement therapy is the treatment of choice for FVII deficiency. Various therapeutic products such as prothrombin complex concentrate, plasma-derived FVII concentrate, fresh frozen plasma, and activated recombinant FVII are available to treat FVII deficient individuals. This review aims to provide information on molecular, biochemical, and clinical aspects of coagulation FVII, its role in hemostasis, and the consequences of its deficiency.

Generation of Human Patient iPSC-derived Retinal Organoids to Model Retinitis Pigmentosa.

Retinitis pigmentosa (RP) is a rare and inherited retinal degenerative disease with a prevalence of approximately 1/4,000 people worldwide. The majority of RP patients have progressive photoreceptor degeneration leading to peripheral vision loss, night blindness, and finally, total blindness. To date, thousands of mutations in more than 90 genes have been reported to be associated with RP. Currently, there are few animal models available for all the affected genes and different types of mutations, which largely hampers the deciphering of the mechanisms underlying the gene/mutation pathology and limits treatment and drug development. Patient induced pluripotent stem cell (iPSC)-derived 3D retinal organoids (ROs) have provided a better system to model the human early-onset disease than cells and animals. In order to study RP, those patient-derived 3D retinal organoids were utilized to recapitulate the clinical phenotypes of RP. In the RP patient-derived ROs, Rhodopsin mislocalization was clearly displayed. Compared with other animal models, patient iPSC-derived retinal organoid models more closely recapitulated RP features and represent an ideal approach for investigating the disease pathogenesis and for drug development.

CHARACTERISTICS AND RESULTS OF A SURGICAL TREATMENT OF PATIENTS WITH A HYPERTROPHIC CARDIOMYOPATHY

Hypertrophic cardiomyopathy (HCM) is diagnosed in a presence of severe hypertrophy of the walls of the left ventricle (LV) with a predominant remodeling of n the interventricular septum and the posterior LV wall, when the LV outflow tract (LVOT) begins to obstruct outflow hemodynamics. Because of an extreme genetic etiology diversity of the pathology, the genes that cause it e remain unknown in about 40% of patients with HCM. With the development of NGS technologies, the work of identifying of new mutations has become slightly easier. In addition to rare pathogenic variants of the sarcomeric protein gene, relatively common genetic variants associated with HCM are increasingly being recognized. We performed an examination of 43 patients at the RIOC and ID JSC from January 2017 to August 2021 were examined, 21 of whom had severe HCM with LVOT obstruction that required surgical treatment. Pathology in female population occurred in 67% of cases, in men it was 2 times less - 33 22 patients (51%) had an obstructive form of HCM. The other 21 patients have initial signs of HCM (are under observation) and 35% were asymptomatic patients. IT was established that 56% of the cohort had different types of mutations, in which it was found that 75% of patients had monomutations, and 25% had 2 mutations. In most cases, mutations were found in the myosin heavy chain (MYH7 - 42%) and myosin-binding protein C (MYBPC3 - 17%). In the group ofpatients that underwent a surgical treatment, 12 patients (57%) of patients had various mutations. Also, in 4 patients, we tracked the family history. Morrow myectomy was performed in 21 patients, 95% of them additionally underwent mitral valve repair with removal of secondary chords. In all operated patients, the pressure gradient on the LVOT decreased from 2 to 7+ 1.7 mm Hg. There were no lethal outcomes.

Analysis of virological response to therapy and resistance profile in treatment-experienced and naive HIV-1 infected Romanian patients receiving regimens containing darunavir boosted with ritonavir or cobicistat.

77% of Romanians infected with HIV receive antiretroviral therapy, with the challenge of maintaining long-term therapeutic success (the viral load becoming/remaining undetectable). The main purpose of this study was to provide comparative analysis of the long-term virological response to therapeutic regimens containing pharmacokinetically enhanced darunavir (DRV) with ritonavir (RTV) or cobicistat (COBI). The second aim was to evaluate the viral resistance profile to therapy, by number/type/frequency of viral mutations. This retrospective study was conducted on 462 patients infected with subtype F HIV-1, registered at the "Matei Bals" National Institute of Infectious Diseases, between 2018 and 2021: 384 patients received (among other ARV) DRV 600mg, enhanced with RTV 100mg (twice daily) and 78 patients received DRV 800mg boosted with COBI 150mg (once daily). The virological response was measured by determining the viral load (HIV-1 RNA copies/mL), while the incidence of viral resistance to therapy was assessed by genotyping tests. Comparing the patients with undetectable viremia, from the 1st visit to the 3rd one, the outcomes showed that at the last visit, 84.6% subjects in the DRV/c group achieved virological efficiency over those from DRV/r group (76.8%). The differences observed between this time points are statistically significant p<0.05. DRV/c administered in combination with other ARV, in subtype F HIV-1 infected patients, proved to be more virologically effective, maintaining a favorable long-time result. When comparing the outcomes of the two groups, a statistically significant difference of p<0.05 was obtained. 32 patients (27 from DRV/r group and 5 from DRV/c group) were evaluated with persistent HIV-1 ARN plasma load >1000 copies/mL, during all 3 clinical visits. They formed a research sub-group evaluated in terms of resistance to therapy and were reported as virological failures. 28.12% of the sub-group with persistent HIV-1 RNA >1000 copies/mL were from the DRV/r group and only 3.12% from the DRV/c group. Drug mutations (DRM) involved in antiretroviral resistance/sensitivity occurred both in the protease gene, and in the reverse transcriptase gene, with the involved ARV classes being protease inhibitors, nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors. 16 different types of mutations were evaluated in the PR gene and 20 mutations were evaluated in RT gene.

Mutational effects of chronic gamma radiation throughout the life cycle of Arabidopsis thaliana: Insight into radiosensitivity in the reproductive stage

Organisms living on Earth have always been exposed to natural sources of ionizing radiation, but following recent nuclear disasters, these background levels have often increased regionally due to the addition of man-made sources of radiation. To assess the mutational effects of ubiquitously present radiation on plants, we performed a whole-genome resequencing analysis of mutations induced by chronic irradiation throughout the life cycle of Arabidopsis thaliana grown under controlled conditions. We obtained resequencing data from 36 second generation post-mutagenesis (M2) progeny derived from 12 first generation (M1) lines grown under gamma-irradiation conditions, ranging from 0.0 to 2.0 Gray per day (Gy/day), to identify de novo mutations, including single base substitutions (SBSs) and small insertions/deletions (INDELs). The relationship between de novo mutation frequency and radiation dose rate from 0.0 to 2.0 Gy/day was assessed by statistical modeling. The increase in de novo mutations in response to irradiation dose fit the negative binomial model, which accounted for the high variability of mutation frequency observed. Among the different types of mutations, SBSs were more prevalent than INDELs, and deletions were more frequent than insertions. Furthermore, we observed that the mutational effects of chronic radiation were greater during the reproductive stage. These results will provide valuable insights into practical strategies for analyzing mutational effects in wild plants growing in environments with various mutagens.

Abstract A038: Does mutation rate of cancer cells change as the stage of the disease advances?

Abstract Tumorigenesis begins with cells that have normal mutation rates. As the cells become immortal and accumulate different numbers of mutations along the way, current literature splits in two describing if and how mutation rates increase as the cancer progresses. Some argue that as the mutation rates are small (mutation rate in healthy cells is per nucleotide site per cell division) and malignant cells are loaded with thousands of different types of mutations, they must have acquired a mutator phenotype early in their development. Others argue that immortality of malignant cells, and their rate of proliferation is responsible for their genetic instability and number of mutations observed in their genome. We conduct a review of the literature with the key words “mutation rate” and “cancer” in their title. We review 123 papers and found that description of mutation rates varied in the published work. This leads to estimates of mutation rates in cancer from per nucleotide site per cell division. Some of this variation in mutational rates arises across different organs of the body, for instance liver cells have a higher mutation rate than heart and brain. Cancer treatments such as chemotherapy influence mutation rate, and mutation rate of drug and multidrug resistance cancer cell is higher than newly diagnosed cancer cells. Further, mutation rate is defined differently in different literature, some papers measure the mutation rate in a population or a gene, some calculate it per base pair, genome, or mitosis. Here we provide a comprehensive picture of published mutation rates across different cancer types in order to inform cancer models and treatment plans for individual patients. We propose a unified framework for discussing and reporting mutation rate of cancer cells and formulations on how to switch between definitions. Citation Format: Fargam Neinavaie, Andrew Kramer. Does mutation rate of cancer cells change as the stage of the disease advances? [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A038.

Recent Advances in Syndactyly: Basis, Current Status and Future Perspectives.

A comprehensive summary of recent knowledge in syndactyly (SD) is important for understanding the genetic etiology of SD and disease management. Thus, this review article provides background information on SD, as well as insights into phenotypic and genetic heterogeneity, newly identified gene mutations in various SD types, the role of HOXD13 in limb deformities, and recently introduced modern surgical techniques for SD. This article also proposes a procedure for genetic analysis to obtain a clearer genotype–phenotype correlation for SD in the future. We briefly describe the classification of non-syndromic SD based on variable phenotypes to explain different phenotypic features and mutations in the various genes responsible for the pathogenesis of different types of SD. We describe how different types of mutation in HOXD13 cause various types of SD, and how a mutation in HOXD13 could affect its interaction with other genes, which may be one of the reasons behind the differential phenotypes and incomplete penetrance. Furthermore, we also discuss some recently introduced modern surgical techniques, such as free skin grafting, improved flap techniques, and dermal fat grafting in combination with the Z-method incision, which have been successfully practiced clinically with no post-operative complications.