by Keyword: Genomics

Claussnitzer, Melina, Parikh, Victoria N, Wagner, Alex H, Arbesfeld, Jeremy A, Bult, Carol J, Firth, Helen V, Muffley, Lara A, Ba, Alex N Nguyen, Riehle, Kevin, Roth, Frederick P, Tabet, Daniel, Bolognesi, Benedetta, Glazer, Andrew M, Rubin, Alan F, (2024). Minimum information and guidelines for reporting a multiplexed assay of variant effect Genome Biology 25, 100

Multiplexed assays of variant effect (MAVEs) have emerged as a powerful approach for interrogating thousands of genetic variants in a single experiment. The flexibility and widespread adoption of these techniques across diverse disciplines have led to a heterogeneous mix of data formats and descriptions, which complicates the downstream use of the resulting datasets. To address these issues and promote reproducibility and reuse of MAVE data, we define a set of minimum information standards for MAVE data and metadata and outline a controlled vocabulary aligned with established biomedical ontologies for describing these experimental designs.

JTD Keywords: Genomics, standards, genetic variants, multiplexed assays of variant effect, mave, deep mutational scanning, dm

Fowler, DM, Adams, DJ, Gloyn, AL, Hahn, WC, Marks, DS, Muffley, LA, Neal, JT, Roth, FP, Rubin, AF, Starita, LM, Hurles, ME, Ahituv, N, Bahcal, OG, Baldridge, D, Berg, JS, Berger, AH, Bianchi, AH, Bolognesi, B, Boutros, M, Brenner, S, Brush, MH, Bryant, V, Bult, CJ, Bulyk, M, Call, M, Carter, H, Claussnitzer, M, Chen, F, Cline, MS, Cuperus, JT, Dawood, M, De Jong, HN, Dias, M, Dunn, M, Engreitz, J, Farh, K, Febbo, PG, Fields, S, Findlay, GM, Firth, H, Fraser, JS, Frazer, J, Frontini, M, Romero, IG, Glazer, AM, Guler, M, Hartmann-Petersen, R, Houlston, R, Huang, KL, Hutter, CM, Jagannathan, S, James, RG, Kampmann, M, Karchin, R, Kinney, JB, Komor, AC, Kosuri, S, Lehner, B, Lindorff-Larsen, K, Lombard, Z, MacArthur, DG, Martin, M, McDermott, U, McNulty, SM, Ba, ANN, O'Donnell-Luria, A, O'Roak, BJ, Parikh, VN, Parts, L, Pazin, MJ, Pesaran, T, Petrovski, S, Queitsch, C, Root, DE, Shendure, J, Spurdle, AB, Taylor, KL, Turnbull, C, Villen, J, Vissers, LELM, Wagner, AH, Wakefield, MJ, Weile, J, Xiao, J, (2023). An Atlas of Variant Effects to understand the genome at nucleotide resolution Genome Biology 24, 147

Sequencing has revealed hundreds of millions of human genetic variants, and continued efforts will only add to this variant avalanche. Insufficient information exists to interpret the effects of most variants, limiting opportunities for precision medicine and comprehension of genome function. A solution lies in experimental assessment of the functional effect of variants, which can reveal their biological and clinical impact. However, variant effect assays have generally been undertaken reactively for individual variants only after and, in most cases long after, their first observation. Now, multiplexed assays of variant effect can characterise massive numbers of variants simultaneously, yielding variant effect maps that reveal the function of every possible single nucleotide change in a gene or regulatory element. Generating maps for every protein encoding gene and regulatory element in the human genome would create an 'Atlas' of variant effect maps and transform our understanding of genetics and usher in a new era of nucleotide-resolution functional knowledge of the genome. An Atlas would reveal the fundamental biology of the human genome, inform human evolution, empower the development and use of therapeutics and maximize the utility of genomics for diagnosing and treating disease. The Atlas of Variant Effects Alliance is an international collaborative group comprising hundreds of researchers, technologists and clinicians dedicated to realising an Atlas of Variant Effects to help deliver on the promise of genomics.

JTD Keywords: functional genomics, genome interpretation, global alliance, multiplexed assay of variant effect, saturation mutagenesis, Functional genomics, Genome interpretation, Global alliance, Multiplexed assay of variant effect, Saturation mutagenesis, Variant effect

Moussa, DG, Sharma, AK, Mansour, TA, Witthuhn, B, Perdigao, J, Rudney, JD, Aparicio, C, Gomez, A, (2022). Functional signatures of ex-vivo dental caries onset Journal Of Oral Microbiology 14, 2123624

The etiology of dental caries remains poorly understood. With the advent of next-generation sequencing, a number of studies have focused on the microbial ecology of the disease. However, taxonomic associations with caries have not been consistent. Researchers have also pursued function-centric studies of the caries microbial communities aiming to identify consistently conserved functional pathways. A major question is whether changes in microbiome are a cause or a consequence of the disease. Thus, there is a critical need to define conserved functional signatures at the onset of dental caries.Since it is unethical to induce carious lesions clinically, we developed an innovative longitudinal ex-vivo model integrated with the advanced non-invasive multiphoton second harmonic generation bioimaging to spot the very early signs of dental caries, combined with 16S rRNA short amplicon sequencing and liquid chromatography-mass spectrometry-based targeted metabolomics.For the first time, we induced longitudinally monitored caries lesions validated with the scanning electron microscope. Consequently, we spotted the caries onset and, associated with it, distinguished five differentiating metabolites - Lactate, Pyruvate, Dihydroxyacetone phosphate, Glyceraldehyde 3-phosphate (upregulated) and Fumarate (downregulated). Those metabolites co-occurred with certain bacterial taxa; Streptococcus, Veillonella, Actinomyces, Porphyromonas, Fusobacterium, and Granulicatella, regardless of the abundance of other taxa.These findings are crucial for understanding the etiology and dynamics of dental caries, and devising targeted interventions to prevent disease progression.© 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

JTD Keywords: bacteria, biofilms, children, dental caries, generation, genomics, longitudinal model, metabolism, metabolomics, microscopy, non-invasive bioimaging, oral microbiome, plaque, restorations, signatures, Dental caries, Field-emission sem, Signatures

Seuma, M, Faure, AJ, Badia, M, Lehner, B, Bolognesi, B, (2021). The genetic landscape for amyloid beta fibril nucleation accurately discriminates familial Alzheimer's disease mutations Elife 10, e63364

Plaques of the amyloid beta (A beta) peptide are a pathological hallmark of Alzheimer's disease (AD), the most common form of dementia. Mutations in A beta also cause familial forms of AD (fAD). Here, we use deep mutational scanning to quantify the effects of >14,000 mutations on the aggregation of A beta. The resulting genetic landscape reveals mechanistic insights into fibril nucleation, including the importance of charge and gatekeeper residues in the disordered region outside of the amyloid core in preventing nucleation. Strikingly, unlike computational predictors and previous measurements, the empirical nucleation scores accurately identify all known dominant fAD mutations in A beta, genetically validating that the mechanism of nucleation in a cell-based assay is likely to be very similar to the mechanism that causes the human disease. These results provide the first comprehensive atlas of how mutations alter the formation of any amyloid fibril and a resource for the interpretation of genetic variation in A beta.

JTD Keywords: aggregation, kinetics, oligomers, onset, rates, state, Aggregation, Alzheimer's, Amyloid, Computational biology, Deep mutagenesis, Genetics, Genomics, Kinetics, Nucleation, Oligomers, Onset, Precursor protein, Rates, S. cerevisiae, State, Systems biology

Sanchez-Herrero, J. F., Bernabeu, M., Prieto, A., Hüttener, M., Juárez, A., (2020). Gene duplications in the genomes of staphylococci and enterococci Frontiers in Molecular Biosciences 7, 160

Gene duplications are a feature of bacterial genomes. In the present work we analyze the extent of gene duplications in the genomes of three microorganisms that belong to the Firmicutes phylum and that are etiologic agents of several nosocomial infections: Staphylococcus aureus, Enterococcus faecium, and Enterococcus faecalis. In all three groups, there is an irregular distribution of duplications in the genomes of the strains analyzed. Whereas in some of the strains duplications are scarce, hundreds of duplications are present in others. In all three species, mobile DNA accounts for a large percentage of the duplicated genes: phage DNA in S. aureus, and plasmid DNA in the enterococci. Duplicates also include core genes. In all three species, a reduced group of genes is duplicated in all strains analyzed. Duplication of the deoC and rpmG genes is a hallmark of S. aureus genomes. Duplication of the gene encoding the PTS IIB subunit is detected in all enterococci genomes. In E. faecalis it is remarkable that the genomes of some strains encode duplicates of the prgB and prgU genes. They belong to the prgABCU cluster, which responds to the presence of the peptide pheromone cCF10 by expressing the surface adhesins PrgA, PrgB, and PrgC.

JTD Keywords: Bacterial genomics, Enterococcus faecalis, Enterococcus faecium, Gene duplication, Staphylococcus aureus

Said Al-Tawaha, A.R.M., Singh, S., Singh, V., Kafeel, U., Naikoo, M.I., Kumari, A., Amanullah, I., Al-Tawaha, A.R., Qaisi, A.M., Khanum, S., Thangadurai, D, Sangeetha, J., Islam, S., Etesami, H., Kerkoub, N., Amrani, A., Labidi, Z., Maaref, H., Nasri, H., Sanmukh, S.G., Torrents, E. , (2020). Improving water use efficiency and nitrogen use efficiency in rice through breeding and genomics approaches Rice Research for Quality Improvement: Genomics and Genetic Engineering (ed. Roychoudhury, A.), Springer (Singapore, Singapore) Volume 2: Nutrient Biofortification and Herbicide and Biotic Stress Resistance in Rice, 307-337

Rice is a staple food of more than half of the world’s population; more than 3.5 billion inhabitants depend on rice for obtaining 20% of their daily calorie intake. Nitrogen is the most important for crop growth and yield potential. Indeed, nitrogen is essential to stimulate tillering, leaf growth, photosynthesis, and protein synthesis. Significant achievements have recently been observed at the molecular level in nitrogen use efficiency and water use efficiency in plants. In this chapter we will discuss the following issue: (i) definition of both nitrogen use efficiency and water use efficiency, (ii) genes responsible for nitrogen use efficiency and water use efficiency, (iii) best ways for improving water and nutrient use efficiency in rice, and (iv) optimizing nitrogen options for improving water and nitrogen use efficiency of rice under different water regimes.

JTD Keywords: Rice, Water use efficiency, Nitrogen use efficiency, Breeding, Genomics approaches

Bolognesi, Benedetta, Faure, Andre J., Seuma, Mireia, Schmiedel, Jörrn M., Tartaglia, Gian Gaetano, Lehner, Ben, (2019). The mutational landscape of a prion-like domain Nature Communications 10, (1), 4162

Insoluble protein aggregates are the hallmarks of many neurodegenerative diseases. For example, aggregates of TDP-43 occur in nearly all cases of amyotrophic lateral sclerosis (ALS). However, whether aggregates cause cellular toxicity is still not clear, even in simpler cellular systems. We reasoned that deep mutagenesis might be a powerful approach to disentangle the relationship between aggregation and toxicity. We generated >50,000 mutations in the prion-like domain (PRD) of TDP-43 and quantified their toxicity in yeast cells. Surprisingly, mutations that increase hydrophobicity and aggregation strongly decrease toxicity. In contrast, toxic variants promote the formation of dynamic liquid-like condensates. Mutations have their strongest effects in a hotspot that genetic interactions reveal to be structured in vivo, illustrating how mutagenesis can probe the in vivo structures of unstructured proteins. Our results show that aggregation of TDP-43 is not harmful but protects cells, most likely by titrating the protein away from a toxic liquid-like phase.

JTD Keywords: Computational biology and bioinformatics, Genomics, Mechanisms of disease, Neurodegeneration, Systems biology