Mutant Allele Research Articles

Relationship of ACE1 and ACE2 genetic polymorphisms on SARS-CoV-2 infection and severity of symptoms in different regions of Iraq

This study was conducted in the laboratories of the Biology Department - College of Science - Tikrit University, the laboratories of the Food Science Department - College of Agriculture - University of Anbar, and the Public Health Laboratories - Anbar for the period from December 2021 AD until February 2022 AD, study involved taking samples from hospitalized COVID-19 patients of both sexes, after a confirmed positive PCR test result. As well as those lying in quarantine in three Iraqi governorates (the isolation unit in Karkh, Yarmouk and Kadhimiya hospitals, the Al-Shifa quarry hospital in Anbar, the public health laboratory in Anbar, and the quarantine hospital for thousands in Erbil), in addition to outpatient clinics. They were distributed by 30 patients and 20 healthy subjects from each governorate, with ages ranging from 18-80 years, randomly to men and women in order to determine the role of genetic polymorphisms in the ACE inhibitor gene in the study samples. The results of the genetic polymorphisms of ACE-1rs4646994, ACE-2rs2106809, and ACE-2rs4240157 showed that there were non-significant differences between the frequency of alleles and genotypes in the patient's group compared with the healthy group. The DD mutant genotype of ACE-1rs4646994 appeared in the patient's group in Baghdad and Anbar with a high percentage, while patients in Erbil showed the highest percentage of the heterozygous genotype ID compared to healthy subjects, with an OR= 0.922, OR= 2.750, and OR= 1.118, respectively, for the mutant allele D. Therefore, it is not considered a risk factor for the disease in Baghdad, in contrast to Anbar and Erbil. The polymorphism of ACE-2rs2106809, the homozygous genotype CC was dominant in patients in the aforementioned provinces and may not be considered a risk factor for the disease. The results of ACE-2rs4240157 gene polymorphism, the heterozygous CT genotype showed a high percentage in patients in Baghdad and, while in Anbar patients, the normal genotype TT appeared to be the highest percentage compared to healthy subjects. The C mutant allele in Baghdad, Anbar, and Erbil patients reached OR= 1.306, OR= 4.333, and OR= 9.00, respectively, so this allele is considered a risk factor for the disease. We can conclude from this study the role of each of the polymorphisms rs4646994 ACE-1 and rs4240157 ACE-2 in infection with COVID-19 and the severity of its symptoms according to the geographical region and race, in contrast to rs2106809 ACE-2, as it is possible to conduct clinical studies to demonstrate the role of genetic polymorphisms with Relationship to diseases depending on the region and race.

Development of a rapid detection assay for acetolactate synthase inhibitors resistance in three Amaranthus weed species through loop-mediated isothermal amplification.

The early detection of herbicide resistance in weeds is a key factor to avoid herbicide waste and improve agriculture sustainability. The present study aimed to develop and validate an allele-specific loop-mediated isothermal amplification (AS-LAMP) assay for the quick on-site detection of the resistance-endowing point mutation Trp-574-Leu in the acetolactate synthase (ALS) gene in three widely diffused Amaranthus weed species: Amaranthus retroflexus, Amaranthus hybridus and Amaranthus tuberculatus. The AS-LAMP protocol was developed on wild-type and ALS-mutant plants of the three species and revealed that the amplification approach with only the primer set specific for the mutant allele (574-Leu) was the most promising. The validation and estimation of the AS-LAMP performance evaluated by comparing the results with those of the molecular marker (cleaved amplified polymorphic sequences) indicated that, although the sensitivity and specificity were relatively high in all species (overall 100 and > 65%, respectively), precision was high for A. hybridus L. and A. retroflexus L. (75 and 79%, respectively), but quite low for A. tuberculatus (Moq.) J. D. Sauer (59%). The LAMP assay was also effective on crude genomic DNA extraction, allowing the quick detection of mutant plants in field situation (on site resistance detection). The proposed AS-LAMP method has proven to be a promising technique for rapid detection of resistance as a result of Trp-574-Leu on the two monoecious weedy Amaranthus species but resulted less effective in the genetically variable dioecious species A. tuberculatus. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The possible effects of the MTOR polymorphisms on preeclampsia susceptibility, severity, and onset: a case-control study and in silico analysis.

Preeclampsia (PE) is a gestational complication with developed hypertension and proteinuria. Evidence showed the role of mTOR in various cellular processes. Therefore, this study aimed to evaluate the effects of MTOR polymorphisms on susceptibility, severity, and onset of Preeclampsia (PE). A total of 250 PE pregnant women and 258 age-matched control subjects were recruited in this study. To genotype MTOR polymorphisms, the PCR-RFLP method was used. The SpliceAid 2 and PROMO tools were used for in silico analysis. The maternal MTOR rs17036508T/C polymorphism was associated with PE risk in various genetic models. There was no relationship between rs2536T/C and rs2295080T/G polymorphisms and PE. The TTC and TGC haplotypes of rs2536/ rs2295080/ rs17036508 polymorphisms were significantly higher in PE women. Subgroup analysis revealed the association between the MTOR rs2295080 variant and an increased risk of Early-onset PE (EOPE). However, the MTOR rs17036508 was associated with a higher risk of EOPE and Late- Onset PE. In addition, the MTOR rs2295080 could increase the risk of severe PE. The results of the in silico analysis showed that rs17036508 disrupted several binding motifs in the mutant sequence. The PROMO database revealed that the T to C substitution leads to the loss of the TFII-I binding site in the mutant allele. The MTOR rs17036508T/C polymorphism was associated with PE risk. There was an association between the MTOR rs2295080 variant and an increased risk of EOPE. The MTOR rs17036508T/C and rs2295080T/C variants could disrupt several binding motifs and TFII-I binding respectively.

A case report of carcinoma of the papilla of Vater associated with a hyperplasia-dysplasia-carcinoma sequence by pancreaticobiliary maljunction.

Pancreaticobiliary maljunction (PBM) is a known risk factor for biliary tract cancer. However, its association with carcinoma of the papilla of Vater (PVca) remains unknown. We report a case with PVca that was thought to be caused by the hyperplasia-dysplasia-carcinoma sequence, which is considered a mechanism underlying PBM-induced biliary tract cancer. A 70-year-old woman presented with white stool and had a history of cholecystectomy for the diagnosis of a non-dilated biliary tract with PBM. Esophagogastroduodenoscopy revealed a tumor in the papilla of Vater, and PVca was histologically proven by biopsy. We finally diagnosed her with PVca concurrent with non-biliary dilated PBM (cT1aN0M0, cStage IA, according to the Union for International Cancer Control, 8th edition), and subsequently performed subtotal stomach-preserving pancreaticoduodenectomy. Pathological findings of the resected specimen revealed no adenomas and dysplastic and hyperplastic mucosae in the common channel slightly upstream of the main tumor, suggesting a PBM related carcinogenic pathway with hyperplasia-dysplasia-carcinoma sequence. Immunostaining revealed positivity for CEA. CK7 positivity, CK20 negativity, and MUC2 negativity indicated that this PVca was of the pancreatobiliary type. Genetic mutations were exclusively detected in tumors and not in normal tissues, and bile ducts from formalin-fixed paraffin-embedded samples included mutated-ERBB2 (Mutant allele frequency, 81.95%). Moreover, of the cell-free deoxyribonucleic acid (cfDNA) extracted from liquid biopsy mutated-ERBB2 was considered the circulating-tumor deoxyribonucleic acid (ctDNA) of this tumor. Herein, we report the first case of PVca with PBM potentially caused by a "hyperplasia-dysplasia-carcinoma sequence" detected using immunostaining and next-generation sequencing. Careful follow-up is required if pancreaticobiliary reflux persists, considering the possible development of PVca.

Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice.

Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair, mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations - the frequencies of C>T, A>G, etc. - will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs (Sasani et al., 2022, Ashbrook et al., 2021). In this study we developed a new method to detect alleles associated with mutation spectrum variation and applied it to mutation data from the BXDs. We discovered an additional C>A mutator locus on chromosome 6 that overlaps Ogg1, a DNA glycosylase involved in the same base-excision repair network as Mutyh (David et al., 2007). Its effect depends on the presence of a mutator allele near Mutyh, and BXDs with mutator alleles at both loci have greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles and may be applicable to mutation data from humans and other model organisms.

Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice

Maintaining germline genome integrity is essential and enormously complex. Although many proteins are involved in DNA replication, proofreading, and repair, mutator alleles have largely eluded detection in mammals. DNA replication and repair proteins often recognize sequence motifs or excise lesions at specific nucleotides. Thus, we might expect that the spectrum of de novo mutations – the frequencies of C>T, A>G, etc. – will differ between genomes that harbor either a mutator or wild-type allele. Previously, we used quantitative trait locus mapping to discover candidate mutator alleles in the DNA repair gene Mutyh that increased the C>A germline mutation rate in a family of inbred mice known as the BXDs (Sasani et al., 2022, Ashbrook et al., 2021). In this study we developed a new method to detect alleles associated with mutation spectrum variation and applied it to mutation data from the BXDs. We discovered an additional C>A mutator locus on chromosome 6 that overlaps Ogg1, a DNA glycosylase involved in the same base-excision repair network as Mutyh (David et al., 2007). Its effect depends on the presence of a mutator allele near Mutyh, and BXDs with mutator alleles at both loci have greater numbers of C>A mutations than those with mutator alleles at either locus alone. Our new methods for analyzing mutation spectra reveal evidence of epistasis between germline mutator alleles and may be applicable to mutation data from humans and other model organisms.

Association of BRAF V600E Mutant Allele Proportion with the Dissemination Stage of Papillary Thyroid Cancer.

The early identification of aggressive forms of cancer is of high importance in treating papillary thyroid cancer (PTC). Disease dissemination is a major factor influencing patient survival. Mutation status of BRAF oncogene, BRAF V600E, is proposed to be an indicator of disease recurrence; however, its influence on PTC dissemination has not been deciphered. This study aimed to explore the association of the frequency of BRAF V600E alleles in PTC with disease dissemination. In this study, 173 PTC samples were analyzed, measuring the proportion of BRAF V600E alleles by qPCR, which was then normalized against the proportion of tumor cells. Semiquantitative analysis of BRAF V600E mutant protein was performed by immunohistochemistry. The BRAF V600E mutation was present in 60% of samples, while the normalized frequency of mutated BRAF alleles ranged from 1.55% to 92.06%. There was no significant association between the presence and/or proportion of the BRAF V600E mutation with the degree of PTC dissemination. However, the presence of the BRAF mutation was significantly linked with angioinvasion. This study's results suggest that there is a heterogeneous distribution of the BRAF mutation and the presence of oligoclonal forms of PTC. It is likely that the BRAF mutation alone does not significantly contribute to PTC aggressiveness.

The impact of MIR196A2 and MIR423 genes polymorphisms on the development of type 2 diabetes mellitus in a sample of the Iraqi population

PurposeMicro-RNAs, play a significant role in regulating essential physiological processes by controlling post-transcriptional gene expression. Several disorders have been linked to variations in the miRNA genes that generate sequences of mature micro-RNA. The current research aims to determine if the genetic variations rs6505162; C > A in the MIR423 gene and rs11614913; T > C in the MIR196A2 gene are associated with type 2 diabetes mellitus (T2DM). MethodThe tetra-primers amplification refractory mutation system-polymerase chain reaction technique was used to identify these two single nucleotide polymorphisms (SNPs). ResultsThe allele frequency of MIR423- rs6505162; C > A SNP was 0.47 for the wild allele (A) and 0.53 for the mutant allele (C) in the control group, while in the patients group the frequency was 0.54 and 0.46 for the A and C alleles respectively. No association was discovered between this SNP and T2DM (O.R = 0.75, P = 0.47 for AC genotype, and O.R = 0.53, P = 0.15 for CC genotype). The wild type of MIR196A2 rs11614913; C > T SNP showed a 100% prevalence in the study subjects, thus this SNP has no association with T2DM as well. ConclusionThe current investigation demonstrates that the incidence of T2DM is not associated with the MIR196A2-rs11614913; C > T, and MIR423-rs6505162; C > A SNPs.

Genetic Evaluation of Interlukin-22 Single Nucleotide Polymorphism (rs1179251) with Plasmodium falciparum Clearance among Children Less Than 10 Years in the North Region of Cameroon

IL-22 is a pro and anti-inflammatory cytokine which induces the regeneration of hepatocytes cells during the immune response. Evidence has shown that genetic polymorphisms on IL-22 gene could affect the immune response and consequently the parasite clearance and the treatment outcome of malaria. This study aimed at determining the prevalence of the SNP rs1179251 of the Interleukin-22 gene and a possible association with P. falciparum clearance among children less than 10 years old in the North region of Cameroon. A case-control study was performed on 184 conveniently collected blood samples, spotted on Whartman No 3 filter paper from the SPAQ (Sulfadoxine-Pyrimethamine + Amodiaquine) clinical trial carried out in Garoua and Yagoua in 2015, from which DNA was extracted using Chelex-100 method. Genotyping of the IL-22 gene SNPs was performed using Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP). Parasite clearance was defined as the disappearance of pre-treatment parasites without subsequent recurrence, irrespective of whether recurrence is a reinfection or a recrudescing parasite. Treatment outcomes were classified according to the WHO guidelines; patients that experienced early treatment failure (ETF), and late parasitological failure (LPF) were classified as failures (56 cases), while patients that experienced adequate clinical parasitological response (ACPR) were classified as successes (128 controls). The chi square test was used to establish the association between the SNP rs1179251 and parasite clearance. A P-value less than 0.05 was considered as statistically significant. The findings revealed that the mutant allele C was the most predominant with a frequency of 74.46%, with the ancestral allele G having a frequency of 25.54%. These results showed that carriers of the mutant allele C could be 3.7 times more likely not to clear the parasites during treatment but this was not statistically significant (P=0.07, OR= 3.72). In conclusion, no association was found between the SNP rs1179251 of IL-22 gene and Plasmodium falciparum clearance. So, in spite of the importance of IL-22 gene in immune responses, the studied polymorphism does not serve a decisive role in Plasmodium falciparum clearance.

High incidence of sebaceous gland inflammation in aldose reductase-deficient mice

Aldose reductase is a member of the 1B1 subfamily of aldo-keto reductase gene superfamily. The action of aldose reductase (AR) has been implicated in the pathogenesis of a variety of disease states, most notably complications of diabetes mellitus including neuropathy, retinopathy, nephropathy, and cataracts. To explore for mechanistic roles for AR in disease pathogenesis, we established mutant strains produced using Crispr-Cas9 to inactivate the AKR1B3 gene in C57BL6 mice. Phenotyping AR-knock out (ARKO) strains confirmed previous reports of reduced accumulation of tissue sorbitol levels. Lens epithelial cells in ARKO mice showed markedly reduced epithelial-to-mesenchymal transition following lens extraction in a surgical model of cataract and posterior capsule opacification. A previously unreported phenotype of preputial sebaceous gland swelling was observed frequently in male ARKO mice homozygous for the mutant AKR1B3 allele. This condition, which was shown to be accompanied by infiltration of proinflammatory CD3+ lymphocytes, was not observed in WT mice or mice heterozygous for the mutant allele. Despite this condition, reproductive fitness of the ARKO strain was indistinguishable from WT mice housed under identical conditions. These studies establish the utility of a new strain of AKR1B3-null mice created to support mechanistic studies of cataract and diabetic eye disease.

An update on clinical presentation and responses to therapy of patients with hereditary hypophosphatemic rickets with hypercalciuria (HHRH)

Pathogenic variants in solute carrier family 34, member 3 (SLC34A3), the gene encoding the sodium-dependent phosphate cotransporter 2c (NPT2c), cause hereditary hypophosphatemic rickets with hypercalciuria (HHRH). Here, we report a pooled analysis of clinical and laboratory records of 304 individuals from 145 kindreds, including 20 previously unreported HHRH kindreds, in which two novel SLC34A3 pathogenic variants were identified. Compound heterozygous/homozygous carriers show above 90% penetrance for kidney and bone phenotypes. The biochemical phenotype for heterozygous carriers is intermediate with decreased serum phosphate, tubular reabsorption of phosphate (TRP (%)), fibroblast growth factor 23, and intact parathyroid hormone, but increased serum 1,25-dihydroxy vitamin D, and urine calcium excretion causing idiopathic hypercalciuria in 38%, with bone phenotypes still observed in 23% of patients. Oral phosphate supplementation is the current standard of care, which typically normalizes serum phosphate. However, although in more than half of individuals this therapy achieves correction of hypophosphatemia it fails to resolve the other outcomes. The American College of Medical Genetics score correlated with functional analysis of frequent SLC34A3 pathogenic variants in vitro and baseline disease severity. The number of mutant alleles and baseline TRP (%) were identified as predictors for kidney and bone phenotypes, baseline TRP (%) furthermore predicted response to therapy. Certain SLC34A3/NPT2c pathogenic variants can be identified with partial responses to therapy, whereas with some overlap, others present only with kidney phenotypes and a third group present only with bone phenotypes. Thus, our report highlights important novel clinical aspects of HHRH and heterozygous carriers, raises awareness to this rare group of disorders and can be a foundation for future studies urgently needed to guide therapy of HHRH.

Association of inherited thrombophilia mutations and their combinations among palestinian women with unexplained recurrent miscarriage

BackgroundInherited thrombophilia (IT) has a complex pathophysiology and is associated with recurrent miscarriage (RM) by causing placental insufficiency and inhibiting fetal development. However, thrombophilia screening in unexplained RM cases is still questionable. This study aimed to investigate the association between the common eight IT mutations and their combinations among Palestinian women with unexplained RM.MethodsThis is an unmatched case-control study with 200 women (100 unexplained RM cases, 100 controls). Eight common IT mutations namely Factor V Leiden (FVL), prothrombin gene (FII) G202120A, Methylenetetrahydrofolate Reductase (MTHFR) gene (C677T and A1298C), B-fibrinogen gene − 455G > A, FV HR2 A4070G, Plasminogen activator inhibitor 1 (PAI1) 5G/4G and Factor XIIIA (FXIIIA) V34L; were analyzed. The first five mutations were analyzed by Restriction Fragment Length Polymorphism PCR and the other three mutations were analyzed using Amplification Refractory Mutation System PCR.ResultsThe prevalence of the eight IT mutations among the control group was in the order PAI1 5G/4G (69%), MTHFR C677T (53%) and A1298C (47%), BFG − 455G > A (35%), FVL and FV HR2 (each 18%), FXIIIA V34L (16%) and FII G20210A (3%). Patients had a higher percentage of MTHFR A1298C (heterozygotes and mutant homozygote) compared to controls (p = 0.016). Frequencies of mutant alleles MTHFR A1298C (p < 0.001) and FXIIIA V34L (p = 0.009) were higher among patients compared to controls. No significant differences were observed for all other mutations or mutant alleles. Most patients (75%) and controls (75%) have 2–4 mutant alleles out of 8 mutant alleles studied, while 1% of patients and 2% of controls have zero mutant alleles. None of the combinations of the most often studied mutations (FVL, FII G20210A, MTHFR C1677T, and MTHFR A1298C) showed a significant difference between patients and controls.ConclusionsThere was a significant association between unexplained RM and the mutant alleles of MTHFR A1298C and FXIIIA V34L. No significant association was observed between unexplained RM and the combination of both mutant alleles for the mutations studied. This study is the first Palestinian report that evaluates eight inherited thrombophilia mutations and their alleles’ combinations in unexplained RM cases.

Assessing sequence variation, haplotype analysis and molecular characterisation ofaspartate kinase2(ask2) gene regulating methionine biosynthesis in diverse maize inbreds.

Traditional maize grain is deficient in methionine, an essential amino acid required for proper growth and development in humans and poultry birds. Thus, development of high methionine maize (HMM) assumes great significance in alleviating malnutrition through sustainable and cost-effective approach. Of various genetic loci, aspartate kinase2 (ask2) gene plays a pivotal role in regulating methionine accumulation in maize. Here, we sequenced the entire ask2 gene of 5394bp with 13 exons in five wild and five mutant maize inbreds to understand variation at nucleotide level. Sequence analysis revealed that an SNP in exon-13 caused thymine to adenine transversion giving rise to a favourable mutant allele associated with leucine to glutamine substitution in mutant ASK2 protein. Gene-based diversity analysis with 11 InDel markers grouped 48 diverse inbreds into three major clusters with an average genetic dissimilarity of 0.570 (range, 0.0-0.9). The average major allele frequency, gene diversity and PIC are 0.693, 0.408 and 0.341, respectively. A total of 45 haplotypes of the ask2 gene were identified among the maize inbreds. Evolutionary relationship analysis performed among 22 orthologues grouped them into five major clusters. The number of exons varied from 7 to 17, with lengthvarying from 12 to 495bp among orthologues. ASK2 protein with 565 amino acids was predicted to be in homo-dimeric state with lysine and tartaric acid as binding ligands. Amino acid kinase and ACT domains were found to be conserved in maize and orthologues. The study depicted the presence of enough genetic diversity in ask2 gene in maize, and development of HMM can be accelerated through introgression of favourable allele of ask2 into the parental lines of elite hybrids using molecular breeding.

Erken Başlangıçlı Parkinson Hastalığı ve Genetik Sonuçları

Genetic and environmental factors play an important role in the development and progression of Parkinson’s Disease(PD). In this study, it was aimed to evaluate the genetic test results and clinical findings of early-onset Parkinson's Disease (EOPD) followed up in the movement disorders outpatient clinic of our hospital by comparing them with the literature. Patients who were followed up with the diagnosis of EOPD in the Movement Disorders Outpatient Clinic of Neurology Department, Marmara University Faculty of Medicine and whose genetic tests were performed; demographic characteristics, clinical findings and genetic test results were analyzed retrospectively. Forty-three EOPD patients (13 females, 30 males) who were genetically tested were enrolled in the study. The mean age was 52.3 (range; 31-64 years), and the mean age of disease onset was 42.8 (range; 25-49 years). Seven different mutations for PARK-2 and PINK-1 were detected in 93% of the patients for whom genetic testing was requested. Genetic mutation was not detected in 7% of the patients. While 57.5% of the patients with a positive genetic test had prodromal symptoms such as hyposmia, constipation and Rapid Eye Movement(REM) Sleep Behaviour Disorder (RBD), none of the patients with a negative genetic test had prodromal symptoms. It has been shown that some of the benign allelic mutations detected in EOPD patients may be genetic risk factors for EOPD. In our study, we wanted to draw attention to the need for multicenter studies with larger numbers of patients and healthy controls to determine the relationship between benign allelic mutations and EOPD.

Haplotype analysis, regulatory elements and docking simulation of structural models of different AT3 copies in the genus Capsicum

Capsaicinoids are responsible for the pungency in Capsicum species. These are synthesized by the Capsaicin synthase (CS) encoded by the AT3 gene, which catalyzes the transference of an acyl moiety from a branched-chain fatty acid-CoA ester to the vanillylamine to produce capsaicinoids. Some AT3 gene copies have been identified on the Capsicum genome. The absence of capsaicinoid in some nonpungent accessions is related to mutant AT3 alleles. The differences between CS protein copies can affect the tridimensional structure of the protein and the affinity for its substrates, and this could affect fruit pungency. This study characterized 32 AT3 sequences covering Capsicum pungent and non-pungent accessions. These were clustered in AT3-D1 and AT3-D2 groups and representative sequences were analyzed. Genomic upstream analysis shows different regulatory elements, mainly responsive to light and abiotic stress. AT3-D1 and AT3-D2 gene expression was confirmed in fruit tissues of C. annuum. Amino acid substitutions close to the predictable HXXXD and DFGWG motifs were also identified. AT3 sequences were modeled showing a BAHD acyltransferase structure with two connected domains. A pocket with different shape, size and composition between AT3 models was found inside the protein, with the conserved motif HXXXD exposed to it, and a channel for their accessibility. CS substrates exhibit high interaction energies with the His and Asp conserved residues. AT3 models have different interaction affinities with the (E)-8-methylnon-6-enoyl-CoA, 8-methylnonanoyl-CoA and vanillylamine substrates. These results suggested that AT3-D1 and AT3-D2 sequences encode CS enzymes with different regulatory factors and substratum affinities. Communicated by Ramaswamy H. Sarma

Impact of RB1 gene screening from blood collected on a single day from 411 family members of 113 Retinoblastoma survivors in India.

To analyse the profile and implication of genetic testing in a cohort of retinoblastoma (RB) patients and their families conducted on a single day during World Retinoblastoma Awareness Week 2017. Retrospective analysis of blood samples were collected from 411 subjects, including 113 probands at a camp organised for RB awareness and were analysed for RB1 mutations by Sanger sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA). If germline mutations were detected, the parents and siblings of the proband were tested for the same mutation. Germline RB1 mutations were identified in 61/113(54%) probands with a mutation detection rate of 96% (47/49) and 22% (14/64) for bilateral and unilateral RB, respectively. Ten novel pathogenic mutations were identified. Splice mutation was most common (31%) followed by nonsense mutation (26%). The mean age at RB diagnosis was significantly lower in patients having germline RB1 mutation (mean 10.7 months ±2.5) compared to those without (mean 27.2 months ±6.5) (p = <0.0001). Parental transmission of the mutant allele was detected in 15/61(25%) cases of which 11(18%) parents were unaffected indicating incomplete penetrance. The origin of the variant allele was both paternal (n = 7) and maternal (n = 4) wherein 5 were bilateral and 6 unilateral. The detection of a germline mutation impacts the proband and family members due to its implications on change in prognosis, frequency of subsequent evaluations, screening for ocular and non-ocular cancers, and surveillance of family and future progeny.

First report of ATP2A2 somatic mosaicism occurring during embryogenesis in transient acantholytic dermatosis

AbstractTransient acantholytic dermatosis (TAD) is a relatively common skin disease that typically affects older individuals, which shows clinical and histologic similarities to autosomal dominant Darier disease. TAD was recently shown to be caused by somatic ATP2A2 damaging variants. In this study, we performed Sanger sequencing and droplet digital PCR (ddPCR) in a Japanese elderly male with TAD to identify ATP2A2 somatic mosaicism occurring during embryogenesis for the first time and mutant allelic fraction (MAF). Sanger sequencing revealed a known heterozygous substitution c.1645C&gt;T, p.Arg549* in ATP2A2 from blood and the affected skin containing the epidermis and dermis, whereas the signals of the mutated allele were weaker, suggesting that discrepancy of signal intensities demonstrates the presence of somatic mosaicism. By ddPCR, the normal and mutant allele were identified in genomic DNAs and the MAFs were 20.1% (affected skin) and 14.7% (blood), respectively. In the present case, somatic mosaicisms observed in ectodermal (epidermis) and mesodermal (dermis and blood) origin DNA can be explained by a mutational event during the early‐stage differentiation of embryonic epiblast in embryogenesis, and mutant embryonic cells somewhat preferentially differentiate to form the epidermis, rather than the dermis and blood. Disrupted intracellular Ca2+ homoeostasis through clinical deterioration together with ATP2A2 somatic mosaicism in this patient might result in transient skin eruptions.

Detection of (pre)cancerous colorectal lesions in Lynch syndrome patients by microsatellite instability liquid biopsy

Lynch syndrome (LS) is an inherited condition characterized by an increased risk of developing cancer, in particular colorectal cancer (CRC). Microsatellite instability (MSI) is the main feature of (pre)cancerous lesions occurring in LS patients. Close endoscopic surveillance is the only option available to reduce CRC morbidity and mortality. However, it may fail to intercept interval cancers and patients’ compliance to such an invasive procedure may decrease over the years. The development of a minimally invasive test able to detect (pre)cancerous colorectal lesions, could thus help tailor surveillance programs in LS patients. Taking advantage of an endoscopic surveillance program, we retrospectively assessed the instability of five microsatellites (BAT26, BAT25, NR24, NR21, and Mono27) in liquid biopsies collected at baseline and possibly at two further endoscopic rounds. For this purpose, we tested a new multiplex drop-off digital polymerase chain reaction (dPCR) assay, reaching mutant allele frequencies (MAFs) as low as 0.01%. Overall, 78 plasma samples at the three time-points from 18 patients with baseline (pre)cancerous lesions and 18 controls were available for molecular analysis. At baseline, the MAFs of BAT26, BAT25 and NR24 were significantly higher in samples of patients with lesions but did not differ with respect to the grade of dysplasia or any other clinico-pathological characteristics. When all markers were combined to determine MSI in blood, this test was able to discriminate lesion-bearing patients with an AUC of 0.80 (95%CI: 0.66; 0.94).

Generation and characterisation of an Arabidopsis thaliana f3h/fls1/ans triple mutant that accumulates eriodictyol derivatives

BackgroundFlavonoids are plant specialised metabolites, which derive from phenylalanine and acetate metabolism. They possess a variety of beneficial characteristics for plants and humans. Several modification steps in the synthesis of tricyclic flavonoids cause for the amazing diversity of flavonoids in plants. The 2-oxoglutarate-dependent dioxygenases (2-ODDs) flavanone 3-hydroxylase (F3H, synonym FHT), flavonol synthase (FLS) and anthocyanidin synthase (ANS, synonym leucoanthocyanidin dioxygenase (LDOX)), catalyse oxidative modifications to the central C ring. They are highly similar and have been shown to catalyse, at least in part, each other’s reactions. FLS and ANS have been identified as bifunctional enzymes in many species, including Arabidopsis thaliana, stressing the capability of plants to bypass missing or mutated reaction steps on the way to flavonoid production. However, little is known about such bypass reactions and the flavonoid composition of plants lacking all three central flavonoid 2-ODDs.ResultsTo address this issue, we generated a f3h/fls1/ans mutant, as well as the corresponding double mutants and investigated the flavonoid composition of this mutant collection. The f3h/fls1/ans mutant was further characterised at the genomic level by analysis of a nanopore DNA sequencing generated genome sequence assembly and at the transcriptomic level by RNA-Seq analysis. The mutant collection established, including the novel double mutants f3h/fls1 and f3h/ans, was used to validate and analyse the multifunctionalities of F3H, FLS1, and ANS in planta. Metabolite analyses revealed the accumulation of eriodictyol and additional glycosylated derivatives in mutants carrying the f3h mutant allele, resulting from the conversion of naringenin to eriodictyol by flavonoid 3’-hydroxylase (F3’H) activity.ConclusionsWe describe the in planta multifunctionality of the three central flavonoid 2-ODDs from A. thaliana and identify a bypass in the f3h/fls1/ans triple mutant that leads to the formation of eriodictyol derivatives. As (homo-)eriodictyols are known as bitter taste maskers, the annotated eriodictyol (derivatives) and in particular the observations made on their in planta production, could provide valuable insights for the creation of novel food supplements.

Impact of KRAS mutations and co-mutations on clinical outcomes in pancreatic ductal adenocarcinoma

The relevance of KRAS mutation alleles to clinical outcome remains inconclusive in pancreatic adenocarcinoma (PDAC). We conducted a retrospective study of 803 patients with PDAC (42% with metastatic disease) at MD Anderson Cancer Center. Overall survival (OS) analysis demonstrated that KRAS mutation status and subtypes were prognostic (p < 0.001). Relative to patients with KRAS wildtype tumors (median OS 38 months), patients with KRASG12R had a similar OS (median 34 months), while patients with KRASQ61 and KRASG12D mutated tumors had shorter OS (median 20 months [HR: 1.9, 95% CI 1.2–3.0, p = 0.006] and 22 months [HR: 1.7, 95% CI 1.3–2.3, p < 0.001], respectively). There was enrichment of KRASG12D mutation in metastatic tumors (34% vs 24%, OR: 1.7, 95% CI 1.2–2.4, p = 0.001) and enrichment of KRASG12R in well and moderately differentiated tumors (14% vs 9%, OR: 1.7, 95% CI 1.05–2.99, p = 0.04). Similar findings were observed in the external validation cohort (PanCAN’s Know Your Tumor® dataset, n = 408).