Frameshift Type Research Articles

Mutational spectrum of TP53 gene correlates with nivolumab treatment efficacy in advanced gastric cancer (TP53MUT study).

Although nivolumab has a high efficacy, reliable biomarkers are needed to predict the efficacy. We evaluated the nivolumab efficacy according to the TP53 mutation in advanced gastric cancer patients enrolled in the GI-SCREEN project. Sequence data of tumour specimens and clinicopathological information of 913 patients with advanced gastric cancer who were enrolled between April 2015 and March 2017 were obtained from the GI-SCREEN database. The follow-up information of 266 patients treated with nivolumab was also provided. Among 266 patients treated with nivolumab, the objective response rate (ORR) of TP53 wild type (wt) patients (24.6%) was higher than that of TP53 mutant patients (14.8%). Among TP53 mutant patients, the ORR of the frameshift type tended to be higher than the transition and transversion type (23.1%, 13.6%, and 13.0%, respectively). The median progression-free survival (PFS) was statistically longer in TP53 wt patients than in mutant patients (3.3 vs 2.1 months, HR 1.4, 95% CI 1.1-1.9). Among TP53 mutant patients, PFS was statistically longer in the frameshift type than in the transversion type. Nivolumab showed better efficacy in TP53 wt patients than in mutant patients. Among TP53 mutant patients, the frameshift type may have efficacy from nivolumab treatment.

ScanExitronLR: characterization and quantification of exitron splicing events in long-read RNA-seq data.

Exitron splicing is a type of alternative splicing where coding sequences are spliced out. Recently, exitron splicing has been shown to increase proteome plasticity and play a role in cancer. Long-read RNA-seq is well suited for quantification and discovery of alternative splicing events; however, there are currently no tools available for the detection and annotation of exitrons in long-read RNA-seq data. Here, we present ScanExitronLR, an application for the characterization and quantification of exitron splicing events in long-reads. From a BAM alignment file, reference genome and reference gene annotation, ScanExitronLR outputs exitron events at the individual transcript level. Outputs of ScanExitronLR can be used in downstream analyses of differential exitron splicing. In addition, ScanExitronLR optionally reports exitron annotations such as truncation or frameshift type, nonsense-mediated decay status and Pfam domain interruptions. We demonstrate that ScanExitronLR performs better on noisy long-reads than currently published exitron detection algorithms designed for short-read data. ScanExitronLR is freely available at https://github.com/ylab-hi/ScanExitronLR and distributed as a pip package on the Python Package Index. Supplementary data are available at Bioinformatics online.

The salience of a prior relationship between researcher and participants: Reflecting on acquaintance interviews

This article aims to contribute to the discussion on interviews in qualitative research. More specifically, we focus on acquaintance interviews (Garton & Copland, 2010), that is, interviews in which the interviewer and interviewees have already established a prior relationship. By using data from both authors’ doctoral studies in applied linguistics (Iikkanen, 2020; Roiha, 2019), we illustrate how this prior relationship becomes salient and is made use of in interviews. In this article, we focus on two themes, frame shifting and building rapport. The data excerpts presented in the article exemplify the types of frame shifts that took place in our acquaintance interviews. The findings also suggest that acquaintance interviews can offer researchers a fruitful arena for utilizing the already existing common ground between them and their research participants; a prior relationship serves as a resource to build rapport with interviewees. The ethical aspect involved in acquaintance interviews is also briefly discussed.

A Review on the Methods for Identification of Mutations in the Tumour Suppressor Gene Retinoblastoma RB1

Retinoblastoma is the most common intraocular cancer of childhood. RB1 is the gene responsible for causing retinoblastoma, spans more than 180 kilobases (kb) located on chromosome 13q14, which consist of 27 exons. Retinoblastoma in children may either be hereditary or non-hereditary. Mutations in RB1 gene are mostly point mutations of non-sense or missense type but could also be of frameshift type. These mutations can be identified from both blood and tumour samples by Sanger sequencing and other molecular identification techniques such as Multiplex Ligation-dependent Probe Amplification (MLPA). ‘Fragile’ codons are codons which gets point mutated to form stop codons so that the resulting protein will be incomplete or immature. In RB1, fragile codons get mutated predominantly and lead to the truncation of RB1 protein. The frequent mutations that predominantly occur in the arginine (CGA) codon, wherein changes in the single nucleotide results in the stop (UGA) codon, than any other fragile codon. The present paper reviews the role of RB1 mutations in retinoblastoma and the methods to identify it. We also make an attempt to identify the fragile codons in the RB genome based on the NCBI reference sequence NM_000321.2

Clinical features of DDX41 mutation-related diseases: a systematic review with individual patient data.

Background:DDX41 serves as a DNA sensor in innate immunity and mutated DDX41 is pathogenic, mainly for myeloid neoplasms.Methods:In this study, “DDX41” was searched in PubMed and Web of Science between 1 January 2015 and 29 April 2021 with individual-patient data seeking. A meta-analysis was not valid here due to the absence of a large dataset. Thirty articles were finally included in the qualitative analysis and 277 patients from 20 studies without overlap were involved in the quantitative summary.Results:Pooled incidence was 3.3% (95% confidence interval 2.4–4.2%) of unselected myeloid neoplasms. Patients with hematologic disorders harboring mutated DDX41 were featured as 80% males, median 66 (20–88) years old at diagnosis, 75% acute myeloid leukemia (AML) or myelodysplastic syndromes (MDS), 64% with normal karyotype. Eighty-five percent of patients had germline variants which were nationally diverse and more of frameshift type, whereas 64% of patients had somatic DDX41 variants where p.R525H and missense dominated. ASXL1 and TP53 were the top frequent concomitant somatic mutations. Therapeutically, 70% overall response rate was obtained of hypomethylating agents in MDS, 96% complete remission of chemotherapy in AML, and 8% of relapse in hematopoietic stem cell transplant. Neither overall survival nor progression-free survival could be summed.Conclusions:Several significant clinical differences were observed in different diagnosis groups, familial and sporadic cases, and p.R525H compared with other somatic variants. In conclusion, myeloid neoplasms carrying DDX41 mutations were mainly older, male, MDS, and AML patients who had promising responses to treatment. Both germline and somatic DDX41 variants possessed unique characteristics and groups of interest presented certain differences worth further research. (CRD42021228886)

Protein phosphatase, Mg2+/Mn2+-dependent 1D (PPM1D) mutations in haematological cancer.

Until recently, the protein phosphatase, Mg2+/Mn2+-dependent 1D (PPM1D) gene had not been examined in haematological cancer, but several studies have now explored the functional role of this gene and its aberrations. It is often mutated in the context of clonal haemopoiesis (including in patients with lymphoma, myeloproliferative neoplasms and myelodysplastic syndrome) and mutations have been associated with exposure to cytotoxic and radiation therapy, development of therapy-related neoplasms and inferior survival. The vast majority of PPM1D mutations found in haematopoietic cells are of the nonsense or frameshift type and located within terminal exon 6. These genetic defects are rarely found in the blood of healthy individuals. PPM1D encodes the PPM1D phosphatase [also named wild-type p53-induced phosphatase 1 (WIP1)], which negatively regulates signalling molecules within the DNA damage response pathway, including tumour suppressor p53. Clonal expansion of PPM1D mutant haematopoietic cells can potentially be prevented with inhibitors; however, human trials are awaited. In the present review, we provide a review of the literature regarding PPM1D and its role in haematological cancer.

Rare Neurologic Disease-Associated Mutations of AIMP1 are Related with Inhibitory Neuronal Differentiation Which is Reversed by Ibuprofen.

Background: Hypomyelinating leukodystrophy 3 (HLD3), previously characterized as a congenital diseases associated with oligodendrocyte myelination, is increasingly regarded as primarily affecting neuronal cells. Methods: We used N1E-115 cells as the neuronal cell model to investigate whether HLD3-associated mutant proteins of cytoplasmic aminoacyl-tRNA synthase complex-interacting multifunctional protein 1 (AIMP1) aggregate in organelles and affect neuronal differentiation. Results: 292CA frame-shift type mutant proteins harboring a two-base (CA) deletion at the 292th nucleotide are mainly localized in the lysosome where they form aggregates. Similar results are observed in mutant proteins harboring the Gln39-to-Ter (Q39X) mutation. Interestingly, the frame-shift mutant-specific peptide specifically interacts with actin to block actin fiber formation. The presence of actin with 292CA mutant proteins, but not with wild type or Q39X ones, in the lysosome is detectable by immunoprecipitation of the lysosome. Furthermore, expression of 292CA or Q39X mutants in cells inhibits neuronal differentiation. Treatment with ibuprofen reverses mutant-mediated inhibitory differentiation as well as the localization in the lysosome. Conclusions: These results not only explain the cell pathological mechanisms inhibiting phenotype differentiation in cells expressing HLD3-associated mutants but also identify the first chemical that restores such cells in vitro.

STUDY OF MUTAGENIC ACTIVITY NANO- AND MICROPARTICLES IN THE AMES TEST (SALMONELLA / MICROSOME)

Introduction. One of the important steps in assessing the nanoparticles (NP) safety is the analysis of mutagenic activity, including the evaluation of gene, chromosomal, and genomic mutations. Material and methods. The purpose of this investigation is to study the ability of different NP aqueus suspensions and the same compounds in microforms to unduce gene mutations in Salmonella/microsome test (Ames test). Anatase titanium dioxide NP coated with simethicone (33.16 ± 16.7 nm, 5-50000 μg/ml), magnetite NP coated with silicate (10 nm, 0.92-575 μg/ml), silver NP coated with аrabian gum (14 ± 0.2 nm, 5-50000 μg/ml), aluminum hydroxide nanofibres (50-70 nm, 24-3000 μg/ml) and multi-walled carbon nanotubes (Taunit MWСNTs, outer diameter 15-40 nm, inner diameter 3-8 nm, length 2 and more microns, 5-50000 μg/ml). In parallel, the mutagenic activity of equivalent microparticles was evaluated in experiments. Ames test (Salmonella/microsomes) registers gene mutations induced by a different mechanism of action, in the variant with preincubation. A set of Salmonella typhimurium indicator strains: TA 100 (base pair substitution mutations), TA 98 and TA 97 (mutations of the frameshift type of the genetic code) were used. Using addition the S9 microsomal activating mixture during the experiment makes it is possible to determine the effect not only of the substances themselves, but also of their metabolites. Conclusion. The investigated nanomaterials as well as their micro analogs in the studied dose range did not induce gene mutations in the Ames test both in presence and absence microsomal activating mixture.

Effects of mismatches distant from the target position on gene correction with a 5′-tailed duplex

The introduction of a 5'-tailed duplex (5'-TD) fragment into cells corrects a base-substitution mutation in a target DNA. We previously reported that the gene correction efficiency was improved when a frameshift type of second mismatch was present ∼330 bases distant from the target position, between the target DNA and the 5'-TD fragment. In this study, the effects of the second mismatches on the gene correction were further examined. Base-base mismatches 332 bases distant from the target position slightly enhanced gene correction, but less efficiently than the previously studied frameshift mismatches. The gene correction efficiency was also increased when the distance between the target position and the second frameshift mismatch was changed to ∼270 bases. These results suggested that the introduction of an appropriate second frameshift mismatch into the 5'-TD fragment improves the gene correction efficiency.

Biological Activity of Conventional and Organic Pomegranate Juices: Antioxidant and Antimutagenic Potential.

None of the health claims about pomegranate juices has been approved yet by European Food Safety Authority (EFSA). There is a general perception among consumers that organic foods are healthier, tastier, and more nutritive than the conventional products. The aim of this research was to study the differences in the biological activity between ready-for-consumption juices obtained from pomegranates fruits grown under conventional and organic agricultural practices. Antioxidant activity has been evaluated by three methods (DPPH•, ABTS+, and FRAP), together with the total contents of phenolics and punicalagin (HPLC-DAD); besides, the Ames test was used to evaluate the antimutagenic potential of the juices. Pomegranate juice, either from conventionally or organically grown fruits, was antimutagenic (mean of 51 and 90% for Salmonella typhimurium TA100 and TA98, respectively) and it was capable of protecting DNA from both, base-pair or frame-shift type of mutations. In fact, the antimutagenicity of conventional pomegranate juice was higher than that achieved by the organic sample; this finding was linked to a higher punicalagin content (201 and 104mgL-1 for conventional and organic juices, respectively).

Late-onset Charcot–Marie–Tooth disease 4F caused by periaxin gene mutation

We identified the main features of Charcot-Marie-Tooth (CMT) disease, type 4F, caused by a periaxin gene (PRX) mutation in Japanese patients. Periaxin is known as one of the key myelination molecules, forming tight junction between myelin loop and axon. We collected 427 DNA samples from individuals with CMT or CMT-related neuropathy, negative for PMP22 duplication. We investigated PRX mutations using a purpose-built resequencing array screen during the period 2006-2012. We detected two types of PRX mutations in three patients; one patient showed a novel homozygous p.D651N mutation and the other two showed homozygous p.R1070X mutation. All PRX mutations reported so far have been of nonsense or frameshift type. In this study, we found homozygous missense mutation p.D651N. Aspartate 651 is located in a repeat domain; its position might indicate an important function. PRX mutations usually lead to early-onset, autosomal-recessive demyelinating CMT neuropathy 4F (CMT4F) or Dejerine-Sottas disease; their clinical phenotypes are severe. In our three patients, the onset of the disease was at the age of 27years or later, and their clinical phenotypes were milder compared with those reported in previous studies. We showed a variation of clinical phenotypes for CMT4F caused by a novel, nonsense PRX mutation.

Circular Code Signal in Frameshift Genes

A trinucleotide circular code is a set of trinucleotides allowing the reading frame in genes to be retrieved locally, i.e. anywhere in genes and in particular without start codon, and automatically with a window of a few nucleotides. In 1996, a common circular code X has been identified simultaneously in two large populations of eukaryotic and prokaryotic genes. The method proposed here identifies periodic signals of this code X in the two frameshift types (+1 and -1) of both eukaryotic and prokaryotic frameshift genes. As expected by the code theory, the circular code modulo 3 signals move in the same direction of translational frameshifting. Finally, in 68% of frameshift genes in the RECODE 2 database, the frameshift type (+1 and -1) is automatically identified using only this circular code periodic signal. This circular code information constitutes a new structural property of frameshift genes. It may be used directly or in association with existing methods to identify frameshift genes in genomes and their encoded proteins.

Evaluation of mutagenic activity in the Nakdong river and advanced drinking water treatment processes

The previously proved method of Ames test was followed to measure the mutagenic activity. We used Salmonella typhimurium which has special gene mutation site with a single compound characteristic and histidine operon, and measured at the four (Gumi, Gangjung, Gachang, Hyunpung) branch points of Nakdong river for one year. We used Standard Methods for general water analysis with the items as water temperature, pH, DO, BOD, COD, KMnO4, T-N, T-P, NH3-N, TOC, and AOX. Hyunpung branch, where the Nakdong and the Gumho river seems to be mixed enough, showed higher mutagenic activity than the other 3 branches. Every point of Nakdong river showed the TA98 mutagenic activity higher than 2, while TA100 was lower than 2. Most of the mutagenic activity was detected from methanol extracts. These results indicate that Nakdong river water quality is getting deteriorated, and that Nakdong river is influencing the mutagenic activity by Frame-shift type mutation and its polar substances. Correlations (R) between mutagenic activity and concentrations of water analysis items as TOC, AOX, BOD, COD, T-N, and T-P, resulted as 0.768, 0.787, 0.743, 0.688, 0.757, 0.628, respectively, and mutagenic activities of TA98 and TA100, after the treatment of ozone and activated carbon, decreased by chlorine pre-treatment. Finally, if the injected concentration of ozone was higher than 1.0 mL, TA98 and TA100 showed lower mutagenic activities than 2.

G.P.13.09 Muscle biopsy mRNA-based analysis of point mutations in DMD gene in Spanish patients

Duchenne and Becker muscular dystrophies (DMD/BMD) are the most common X-linked disorders, causing progressive weakness. Both muscular disorders are produced by mutations in the dystrophin gene. The most common mutations are large intragenic deletions and duplications that account for 75% of all cases. In DMD patients the majority of cases the DMD deletions or duplications are frameshift type, and in BMD patients the deletions or duplications are in-frame type. The remaining cases are due to small mutations consisting in nonsense mutations, missense mutations, splicing mutations, frameshift small deletions or insertions and midintronic insertions.

Three novel mutations of the PAX6 gene in Japanese aniridia patients

Mutations in the PAX6 gene of Japanese aniridia patients were analyzed. Four types of mutations including one known (474delC) and three novel (786_787ins10, 678_688del11 and 572_575delAATCins14) were found in six patients from four families. A patient with the mutation 572_575delAATCins14 also manifested VATER association. This is the first case of aniridia accompanied by VATER association. All of mutations found in this study are frameshift type, resulting in premature termination of translation. The database for PAX6 gene mutation has been made using a graphical data display system MutationView ( http://mutview.dmb.med.keio.ac.jp/ ).

Mutator specificity of Escherichia coli alkB117 allele.

The Escherichia coli AlkB protein encoded by alkB gene was recently found to repair cytotoxic DNA lesions 1-methyladenine (1-meA) and 3-methylcytosine (3-meC) by using a novel iron-catalysed oxidative demethylation mechanism that protects the cell from the toxic effects of methylating agents. Mutation in alkB results in increased sensitivity to MMS and elevated level of MMS-induced mutations. The aim of this study was to analyse the mutational specificity of alkB117 in a system developed by J.H. Miller involving two sets of E. coli lacZ mutants, CC101-106 allowing the identification of base pair substitutions, and CC107-CC111 indicating frameshift mutations. Of the six possible base substitutions, the presence of alkB117 allele led to an increased level of GC-->AT transitions and GC-->TA and AT-->TA transversions. After MMS treatment the level of GC-->AT transitions increased the most, 22-fold. Among frameshift mutations, the most numerous were -2CG, -1G, and -1A deletions and +1G insertion. MMS treatment appreciably increased all of the above types of frameshifts, with additional appearance of the +1A insertion.

Novel and natural knockout lung cancer cell lines for the LKB1/STK11 tumor suppressor gene.

Germline mutations of the LKB1 gene are responsible for Peutz-Jeghers syndrome (PJS), an autosomal dominant inherited disorder bestowing an increased risk of cancer. We have recently demonstrated that LKB1 inactivating mutations are not confined to PJS, but also appear in lung adenocarcinomas of sporadic origin, including primary tumors and lung cancer cell lines. To accurately determine the frequency of inactivating LKB1 gene mutations in lung tumors we have sequenced the complete coding region of LKB1 in 21 additional lung cancer cell lines. Here we describe the mutational status of LKB1 gene in 30 lung cancer cell lines from different histopathological types, including 11 lung adenocarcinomas (LADs) and 11 small cell lung cancers (SCLCs). LKB1 gene alterations were present in six (54%) of the LAD cell lines tested but in none of the other histological types. Similar to our previous observations in primary tumors, all point mutations were of the nonsense or frameshift type, leading to an abnormal, truncated protein. Moreover, 2 cell lines (A427 and H2126) harbored large gene deletions that spanned several exons. Hence, we have identified additional lung cancer cell lines carrying inactivating mutations of the LKB1 tumor suppressor gene, further attesting to the significance of this gene in the development of LADs and providing new natural LKB1 knockouts for studies of the biological function of the LKB1 protein.

Structure and Function of the Ribosomal Frameshifting Pseudoknot RNA from Beet Western Yellow Virus

AbstractMany viruses reprogram ribosomes to produce two different proteins from two different reading frames. So‐called −1 frameshifting often involves pairwise alignment of two adjacent tRNAs at a ‘slippery' sequence in the ribosomal A and P sites such that an overlapping codon is shifted upstream by one base relative to the zero frame. In the majority of cases, an RNA pseudoknot located downstream stimulates this type of frameshift. Crystal structures of the frameshifting RNA pseudoknot from Beet Western Yellow Virus (BWYV) have provided a detailed picture of the tertiary interactions stabilizing this folding motif, including a minor‐groove triplex and quadruple‐base interactions. The structure determined at atomic resolution revealed the locations of several magnesium ions and provided insights into the role of structured water stabilizing the RNA. Systematic in vitro and in vivo mutational analyses based on the structural results revealed specific tertiary interactions and regions in the pseudoknot that drastically change frameshifting efficiency. Here, we summarize recent advances in our understanding of pseudoknot‐mediated ribosomal frameshifting on the basis of the insights gained from structural and functional studies of the RNA pseudoknot from BWYV.

Spontaneous Hotspot Mutations Resistant to Mismatch Correction in Escherichia coli: Transcription-dependent Mutagenesis Involving Template-switching Mechanisms

The generation and stabilization of spontaneous mutations are affected by many factors, including the accuracy of DNA replication, the generation of spontaneous DNA lesions, and the capacity of mutation-avoidance systems. However, little is known about the causes of spontaneous mutations in cells with fully active mutation-avoidance systems. Using the rpsL forward mutation assay, we previously found that the directionality of replication fork movement significantly affects spontaneous mutagenesis in Escherichia coli. In particular, sequence substitutions and a hotspot type of single-base frameshift, both of which are caused by quasipalindrome-directed mutagenesis, appeared to depend on the directionality of the replication fork. These mutations are also resistant to post-replicative mismatch correction. Here, we show that the level of transcription of the rpsL gene strongly affects spontaneous mutagenesis at two mutational hotspot sites in the target sequence, one for a T→G base substitution and the other for a+1 single-base frameshift. Mutation frequencies at the hotspot sites were below a detectable level when the transcription of the target sequence was tightly suppressed, but were dramatically increased when the target sequence was highly transcribed. Both of the hotspot mutations were also dependent on the directionality of the replication fork and were caused by quasipalindrome-directed mutagenesis. The frequencies of the hotspot mutations were unchanged in a mismatch-repair deficient strain, indicating that the hotspot mutations are resistant to the mismatch correction. Based on these findings, we propose a novel mutagenic process for these hotspot mutations that depends on transcription and involves template-switching mechanisms induced by spontaneous DNA lesions.

Assessment of occupational health hazards in scrap-tire shredding facilities

Occupational hygiene conditions in scrap-tire shredding facilities were assessed to identify potential health risk factors for workers and provide a basis for developing future control measures. Specifically, noise, volatile organics and particulate levels were measured at two plants. Particulate/dust levels were measured via filter collection, and were analyzed gravimetrically. Sound pressure levels were measured and their spectral properties analyzed. Moreover, the major chemical species in the samples were identified using GC/MS. Finally, the mutagenic activity associated with the airborne particulates was assessed using a typical Ames test applied to Salmonella strains TA98 and TA100, with or without bio-activation. The noise levels were steady and high throughout the facilities, ranging from 85 to ∼100 dBA. The octave band spectrum analysis reveals pattern similarity among the different areas. Levels of volatile organics were not significant, but a few mutagens/carcinogens, such as styrene, benzothiazole, phthalate ester and naphthalene were identified. Total particulate levels ranged from 0.43 to 6.54 mg/m 3, while respirable particulates were in the range 0.23–1.25 mg/m 3. Ames testing revealed indirect mutagenicity on strain TA98, indicating possible effects of frame-shift type mutagens. Chemical analysis of airborne particulates confirmed the presence of amines, aniline, quinoline, amides and benzothiazole, which are potentially convertible to frame-shift type mutagenic nitrosoamines. Noise appears to be an occupational hazard for workers at scrap-tire shredding facilities, but the risk associated with the mutagenic/carcinogenic property of particulates requires further confirmation.