scholarly journals SEQUENCE SLIDER: integration of structural and genetic data to characterize isoforms from natural source

2021 ◽  
Author(s):  
Rafael Junqueira Borges ◽  
Guilherme Henrique Marchi Salvador ◽  
Daniel Pimenta ◽  
Lucilene Delazari dos Santos ◽  
Marcos Roberto de Mattos Fontes ◽  
...  
Keyword(s):  
De Novo ◽  
Point Mutations ◽  
Structural Data ◽  
Integrated Approach ◽  
Natural Source ◽  
Mass Spectrometry Data ◽  
Sequence Composition ◽  
Structural Descriptor ◽  
Peptide Database ◽  
Crotalus Durissus

Proteins isolated from natural source can be composed of a mixture of isoforms with similar physicochemical properties that coexists in final steps of purification, toxins being prominent examples. Sequence composition is enforced throughout structural studies even when unsubstantiated. Herein, we propose a novel perspective to address the usually neglected heterogeneity of natural products by integrating biophysical, genetic and structural data in our program SEQUENCE SLIDER. The aim is to assess the evidence supporting chemical composition in structure determination. Locally, we interrogate the experimental map to establish which side chains are supported by the structural data and the genetic information relating sequence conservation is integrated in this statistic. Hence, we build a constrained peptide database, containing most probable sequences to interpret mass spectrometry data (MS). In parallel, we perform MS de novo sequencing with genomic-based algorithms that foresee point mutations. We calibrated SLIDER with Gallus gallus lysozyme, for which sequence is unequivocally established and numerous natural isoforms are reported. We used SLIDER to characterise a metalloproteinase and a phospholipase A2-like protein from the venom of Bothrops moojeni and a crotoxin from Crotalus durissus collilineatus. This integrated approach offers a more realistic structural descriptor to characterize macromolecules isolated from natural source.

Targeting HER2 Alterations in Non–Small-Cell Lung Cancer: A Comprehensive Review

2020 ◽  
pp. 411-425 ◽  
Author(s):  
Jing Zhao ◽  
Yang Xia
Keyword(s):  
Lung Cancer ◽  
Small Cell Lung Cancer ◽  
Cell Lung Cancer ◽  
Kinase Inhibitors ◽  
Antitumor Agents ◽  
De Novo ◽  
Point Mutations ◽  
Small Cell ◽  
Small Cell Lung ◽  
Exon 20

PURPOSE HER2 is a critical gene that drives various solid tumors in addition to those of breast cancer. For example, HER2 plays a role in non–small-cell lung cancer (NSCLC). Overexpression, amplification, and point mutations in HER2 have been described in patients with NSCLC; however, the potential roles of these alterations remain unclear. METHODS We summarize the evidence regarding the distinct impacts of different HER2 aberrations on antitumor agents. Also, we update the therapeutic efficacy of HER2-targeted agents, including anti-HER2 antibodies, antibody-drug conjugates, and small-molecule tyrosine kinase inhibitors, tested in HER2-aberrant NSCLC. RESULTS Although these drugs are not yet standard treatments, certain patients may benefit from these therapies. In this review, we aim to provide an improved understanding of HER2 aberrations in NSCLC, including NSCLC biology and the impacts of each aberration on prognosis and standard treatment. We also highlight the potential of novel anti-HER2 therapies approved by regulatory bodies and those in clinical development. CONCLUSION Compared with HER2 amplification or overexpression, HER2 mutations, especially HER2 exon 20 mutations, are emerging as the most clear targetable driver for HER2-directed therapies in lung cancer. De novo and inducible HER2 pathway activation need to be differentially managed. Further investigations with new strategies are needed.

scholarly journals Genotyping structural variants in pangenome graphs using the vg toolkit

2019 ◽  
Author(s):  
Glenn Hickey ◽  
David Heller ◽  
Jean Monlong ◽  
Jonas A. Sibbesen ◽  
Jouni Sirén ◽  
...  
Keyword(s):  
De Novo ◽  
State Of The Art ◽  
Effective Means ◽  
Point Mutations ◽  
Structural Variants ◽  
Short Read ◽  
Yeast Strains ◽  
Sequencing Studies ◽  
Long Read

AbstractStructural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmarked vg against state-of-the-art SV genotypers using three sequence-resolved SV catalogs generated by recent long-read sequencing studies. In addition, we use assemblies from 12 yeast strains to show that graphs constructed directly from aligned de novo assemblies improve genotyping compared to graphs built from intermediate SV catalogs in the VCF format.

scholarly journals De Novo Mutational Signature Discovery in Tumor Genomes using SparseSignatures

2018 ◽  
Author(s):  
Avantika Lal ◽  
Keli Liu ◽  
Robert Tibshirani ◽  
Arend Sidow ◽  
Daniele Ramazzotti
Keyword(s):  
Cross Validation ◽  
De Novo ◽  
State Of The Art ◽  
Point Mutations ◽  
Simulated Data ◽  
Large Datasets ◽  
Genome Sequences ◽  
Mutational Signatures ◽  
Mutational Signature ◽  
Current State

AbstractCancer is the result of mutagenic processes that can be inferred from tumor genomes by analyzing rate spectra of point mutations, or “mutational signatures”. Here we present SparseSignatures, a novel framework to extract signatures from somatic point mutation data. Our approach incorporates DNA replication error as a background, employs regularization to reduce noise in non-background signatures, uses cross-validation to identify the number of signatures, and is scalable to large datasets. We show that SparseSignatures outperforms current state-of-the-art methods on simulated data using standard metrics. We then apply SparseSignatures to whole genome sequences of 147 tumors from pancreatic cancer, discovering 8 signatures in addition to the background.

scholarly journals An Efficient PET-MRI Medical Image Fusion based on IHS-NSCT-PCA Integrated Method

2019 ◽  
Vol 9 (2) ◽  
pp. 2073-2079
Keyword(s):  
Structural Data ◽  
Fusion Rule ◽  
Integrated Approach ◽  
Disease Diagnosis ◽  
Weighted Averaging ◽  
Fusion Algorithm ◽  
Integrated Method ◽  
Histogram Matching ◽  
Multiple Imaging ◽  
Fused Image

Merging of multiple imaging modalities leads to a single image that acquire high information content. These find useful applications in disease diagnosis and treatment planning. IHS-PCA method is a spatial domain approach for fusion that offersfinestvisibility but demands vast memory and it lacks steering information. We propose an integrated approach that incorporates NSCT combined with PCA utilizing IHS space and histogram matching. The fusion algorithm is applied on MRI with PET image and improved functional property was obtained. The IHS transform is a sharpening technique that converts multispectral image from RGB channels to Intensity Hue and Saturation independent values. Histogram matching is performed with intensity values of the two input images. Pathological details in images can be emphasized in multi-scale and multi-directions by using PCA withNSCT. Fusion rule applied is weighted averaging andprincipal components are used for dimensionality reduction. Inverse NSCT and Inverse IHS are performed so as to obtain the fused image in new RGB space. Visual and subjective investigation is compared with existing methods which demonstrate that our proposed technique gives high structural data content with high spatial and spectral resolution compared withearlier methods.

scholarly journals Extending the Coding Potential of Viral Genomes with Overlapping Antisense ORFs: A Case for the De Novo Creation of the Gene Encoding the Antisense Protein ASP of HIV-1

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 146
Author(s):  
Angelo Pavesi ◽  
Fabio Romerio
Keyword(s):  
De Novo ◽  
Point Mutations ◽  
Selective Advantage ◽  
Genomic Region ◽  
Fine Tuning ◽  
Sequence Evolution ◽  
Viral Genomes ◽  
Stop Codons ◽  
Hiv 1

Gene overprinting occurs when point mutations within a genomic region with an existing coding sequence create a new one in another reading frame. This process is quite frequent in viral genomes either to maximize the amount of information that they encode or in response to strong selective pressure. The most frequent scenario involves two different reading frames in the same DNA strand (sense overlap). Much less frequent are cases of overlapping genes that are encoded on opposite DNA strands (antisense overlap). One such example is the antisense ORF, asp in the minus strand of the HIV-1 genome overlapping the env gene. The asp gene is highly conserved in pandemic HIV-1 strains of group M, and it is absent in non-pandemic HIV-1 groups, HIV-2, and lentiviruses infecting non-human primates, suggesting that the ~190-amino acid protein that is expressed from this gene (ASP) may play a role in virus spread. While the function of ASP in the virus life cycle remains to be elucidated, mounting evidence from several research groups indicates that ASP is expressed in vivo. There are two alternative hypotheses that could be envisioned to explain the origin of the asp ORF. On one hand, asp may have originally been present in the ancestor of contemporary lentiviruses, and subsequently lost in all descendants except for most HIV-1 strains of group M due to selective advantage. Alternatively, the asp ORF may have originated very recently with the emergence of group M HIV-1 strains from SIVcpz. Here, we used a combination of computational and statistical approaches to study the genomic region of env in primate lentiviruses to shed light on the origin, structure, and sequence evolution of the asp ORF. The results emerging from our studies support the hypothesis of a recent de novo addition of the antisense ORF to the HIV-1 genome through a process that entailed progressive removal of existing internal stop codons from SIV strains to HIV-1 strains of group M, and fine tuning of the codon sequence in env that reduced the chances of new stop codons occurring in asp. Altogether, the study supports the notion that the HIV-1 asp gene encodes an accessory protein, providing a selective advantage to the virus.

scholarly journals De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families

2020 ◽  
Author(s):  
Jonathan R. Belyeu ◽  
Harrison Brand ◽  
Harold Wang ◽  
Xuefang Zhao ◽  
Brent S. Pedersen ◽  
...  
Keyword(s):  
De Novo ◽  
Genome Structure ◽  
Point Mutations ◽  
Large Family ◽  
Germline Mutations ◽  
Autism Spectrum ◽  
Parental Age ◽  
Single Nucleotide Variants ◽  
Multiple Testing Correction ◽  
Structural Mutations

AbstractEach human genome includes de novo mutations that arose during gametogenesis. While these germline mutations represent a fundamental source of new genetic diversity, they can also create deleterious alleles that impact fitness. The germline mutation rate for single nucleotide variants and factors that significantly influence this rate, such as parental age, are now well established. However, far less is known about the frequency, distribution, and features that impact de novo structural mutations. We report a large, family-based study of germline mutations, excluding aneuploidy, that affect genome structure among 572 genomes from 33 families in a multigenerational CEPH-Utah cohort and 2,363 cases of non-familial autism spectrum disorder (ASD), 1,938 unaffected siblings, and both parents (9,599 genomes in total). We find that de novo structural mutations detected by alignment-based, short-read WGS occurred at an overall rate of at least 0.160 events per genome in unaffected individuals and was significantly higher (0.206 per genome) in ASD cases. In both probands and unaffected samples, nearly 73% of de novo structural mutations arose in paternal gametes, and predict most de novo structural mutations to be caused by mutational mechanisms that do not require sequence homology. After multiple testing correction we did not observe a statistically significant correlation between parental age and the rate of de novo structural variation in offspring. These results highlight that a spectrum of mutational mechanisms contribute to germline structural mutations, and that these mechanisms likely have markedly different rates and selective pressures than those leading to point mutations.

Two different thymidylate kinase gene homologues, including one that has catalytic activity, are encoded in the onion yellows phytoplasma genome

Microbiology ◽  
2003 ◽  
Vol 149 (8) ◽  
pp. 2243-2250 ◽  
Author(s):  
Shin-ichi Miyata ◽  
Kenro Oshima ◽  
Shigeyuki Kakizawa ◽  
Hisashi Nishigawa ◽  
Hee-Young Jung ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Genomic Library ◽  
De Novo ◽  
Bacterial Species ◽  
Point Mutations ◽  
Kinase Gene ◽  
Thymidylate Kinase ◽  
Pcr Products ◽  
Multiple Copies ◽  
Salvage Pathways

Thymidylate kinase (TMK) catalyses the phosphorylation of dTMP to form dTDP in both the de novo and salvage pathways of dTTP synthesis in both prokaryotes and eukaryotes. Two homologues of bacterial thymidylate kinase genes were identified in a genomic library of the onion yellows (OY) phytoplasma, a plant pathogen that inhabits both plant phloem and the organs of insects. Southern blotting analysis suggested that the OY genome contained one copy of the tmk-b gene and multiple copies of the tmk-a gene. Sequencing of PCR products generated by amplification of tmk-a enabled identification of three other copies of tmk-a, although the ORF in each of these was interrupted by point mutations. The proteins, TMK-a and TMK-b, encoded by the two intact genes contained conserved motifs for catalytic activity. Both proteins were overexpressed as fusion proteins with a polyhistidine tag in Escherichia coli and purified, and TMK-b was shown to have thymidylate kinase activity. This is believed to be the first report of the catalytic activity of a phytoplasmal protein, and the OY phytoplasma is the first bacterial species to be found to have two intact homologues of tmk in its genome.

Molecular genetic analysis of Saccharomyces cerevisiae C1-tetrahydrofolate synthase mutants reveals a noncatalytic function of the ADE3 gene product and an additional folate-dependent enzyme

1990 ◽  
Vol 10 (11) ◽  
pp. 5679-5687
Author(s):  
C K Barlowe ◽  
D R Appling
Keyword(s):  
Saccharomyces Cerevisiae ◽  
De Novo ◽  
Point Mutations ◽  
Gene Replacement ◽  
Molecular Genetic Analysis ◽  
Yeast Cells ◽  
Yeast Saccharomyces Cerevisiae ◽  
Purine Synthesis

In eucaryotes, 10-formyltetrahydrofolate (formyl-THF) synthetase, 5,10-methenyl-THF cyclohydrolase, and NADP(+)-dependent 5,10-methylene-THF dehydrogenase activities are present on a single polypeptide termed C1-THF synthase. This trifunctional enzyme, encoded by the ADE3 gene in the yeast Saccharomyces cerevisiae, is thought to be responsible for the synthesis of the one-carbon donor 10-formyl-THF for de novo purine synthesis. Deletion of the ADE3 gene causes adenine auxotrophy, presumably as a result of the lack of cytoplasmic 10-formyl-THF. In this report, defined point mutations that affected one or more of the catalytic activities of yeast C1-THF synthase were generated in vitro and transferred to the chromosomal ADE3 locus by gene replacement. In contrast to ADE3 deletions, point mutations that inactivated all three activities of C1-THF synthase did not result in an adenine requirement. Heterologous expression of the Clostridium acidiurici gene encoding a monofunctional 10-formyl-THF synthetase in an ade3 deletion strain did not restore growth in the absence of adenine, even though the monofunctional synthetase was catalytically competent in vivo. These results indicate that adequate cytoplasmic 10-formyl-THF can be produced by an enzyme(s) other than C1-THF synthase, but efficient utilization of that 10-formyl-THF for purine synthesis requires a nonenzymatic function of C1-THF synthase. A monofunctional 5,10-methylene-THF dehydrogenase, dependent on NAD+ for catalysis, has been identified and purified from yeast cells (C. K. Barlowe and D. R. Appling, Biochemistry 29:7089-7094, 1990). We propose that the characteristics of strains expressing full-length but catalytically inactive C1-THF synthase could result from the formation of a purine-synthesizing multienzyme complex involving the structurally unchanged C1-THF synthase and that production of the necessary one-carbon units in these strains is accomplished by an NAD+ -dependent 5,10-methylene-THF dehydrogenase.

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