Publications by authors named "Amy Sirr"

8 Publications

  • Page 1 of 1

Exploiting the Autozygome to Support Previously Published Mendelian Gene-Disease Associations: An Update.

Front Genet 2020 31;11:580484. Epub 2020 Dec 31.

Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.

There is a growing interest in standardizing gene-disease associations for the purpose of facilitating the proper classification of variants in the context of Mendelian diseases. One key line of evidence is the independent observation of pathogenic variants in unrelated individuals with similar phenotypes. Here, we expand on our previous effort to exploit the power of autozygosity to produce homozygous pathogenic variants that are otherwise very difficult to encounter in the homozygous state due to their rarity. The identification of such variants in genes with only tentative associations to Mendelian diseases can add to the existing evidence when observed in the context of compatible phenotypes. In this study, we report 20 homozygous variants in 18 genes (, and ) that satisfy the ACMG classification for pathogenic/likely pathogenic if the involved genes had confirmed rather than tentative links to diseases. These variants were selected because they were truncating, founder with compelling segregation or supported by robust functional assays as with the variant that we present its validation using yeast model. Our findings support the previously reported disease associations for these genes and represent a step toward their confirmation.
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http://dx.doi.org/10.3389/fgene.2020.580484DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7806527PMC
December 2020

A yeast-based complementation assay elucidates the functional impact of 200 missense variants in human PSAT1.

J Inherit Metab Dis 2020 07 27;43(4):758-769. Epub 2020 Feb 27.

Pacific Northwest Research Institute, Seattle, Washington.

Defects in serine biosynthesis resulting from loss of function mutations in PHGDH, PSAT1, and PSPH cause a set of rare, autosomal recessive diseases known as Neu-Laxova syndrome (NLS) or serine-deficiency disorders. The diseases present with a broad range of phenotypes including lethality, severe neurological manifestations, seizures, and intellectual disability. However, because L-serine supplementation, especially if started prenatally, can ameliorate and in some cases even prevent symptoms, knowledge of pathogenic variants is medically actionable. Here, we describe a functional assay that leverages the evolutionary conservation of an enzyme in the serine biosynthesis pathway, phosphoserine aminotransferase, and the ability of the human protein-coding sequence (PSAT1) to functionally replace its yeast ortholog (SER1). Results from our quantitative, yeast-based assay agree well with clinical annotations and expectations based on the disease literature. Using this assay, we have measured the functional impact of the 199 PSAT1 variants currently listed in ClinVar, gnomAD, and the literature. We anticipate that the assay could be used to comprehensively assess the functional impact of all SNP-accessible amino acid substitution mutations in PSAT1, a resource that could aid variant interpretation and identify potential NLS carriers.
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http://dx.doi.org/10.1002/jimd.12227DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7444316PMC
July 2020

Natural Variation in and Underlie Condition-Specific Growth Defects in .

G3 (Bethesda) 2018 01 4;8(1):239-251. Epub 2018 Jan 4.

Pacific Northwest Research Institute, Seattle, Washington 98122

Despite their ubiquitous use in laboratory strains, naturally occurring loss-of-function mutations in genes encoding core metabolic enzymes are relatively rare in wild isolates of Here, we identify a naturally occurring serine auxotrophy in a sake brewing strain from Japan. Through a cross with a honey wine (white tecc) brewing strain from Ethiopia, we map the minimal medium growth defect to , which encodes 3-phosphoserine aminotransferase and is orthologous to the human disease gene, To investigate the impact of this polymorphism under conditions of abundant external nutrients, we examine growth in rich medium alone or with additional stresses, including the drugs caffeine and rapamycin and relatively high concentrations of copper, salt, and ethanol. Consistent with studies that found widespread effects of different auxotrophies on RNA expression patterns in rich media, we find that the loss-of-function allele dominates the quantitative trait locus (QTL) landscape under many of these conditions, with a notable exacerbation of the effect in the presence of rapamycin and caffeine. We also identify a major-effect QTL associated with growth on salt that maps to the gene encoding the sodium exporter, We demonstrate that the salt phenotype is largely driven by variation in the promoter, which harbors a deletion that removes binding sites for the Mig1 and Nrg1 transcriptional repressors. Thus, our results identify natural variation associated with both coding and regulatory regions of the genome that underlie strong growth phenotypes.
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http://dx.doi.org/10.1534/g3.117.300392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5765352PMC
January 2018

Transcriptional Profiling of Biofilm Regulators Identified by an Overexpression Screen in .

G3 (Bethesda) 2017 08 7;7(8):2845-2854. Epub 2017 Aug 7.

Pacific Northwest Research Institute, Seattle, Washington 98122

Biofilm formation by microorganisms is a major cause of recurring infections and removal of biofilms has proven to be extremely difficult given their inherent drug resistance . Understanding the biological processes that underlie biofilm formation is thus extremely important and could lead to the development of more effective drug therapies, resulting in better infection outcomes. Using the yeast as a biofilm model, overexpression screens identified , , , , , and as regulators of biofilm formation. Subsequent RNA-seq analysis of biofilm and nonbiofilm-forming strains revealed that all of the overexpression strains, other than and , were adopting a single differential expression profile, although induced to varying degrees. adopted a separate profile, while the expression profile of reflected the common pattern seen in most of the strains, plus substantial -specific expression changes. We interpret the existence of the common transcriptional pattern seen across multiple, unrelated overexpression strains as reflecting a transcriptional state, that the yeast cell can access through regulatory signaling mechanisms, allowing an adaptive morphological change between biofilm-forming and nonbiofilm states.
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http://dx.doi.org/10.1534/g3.117.042440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5555487PMC
August 2017

Independent Origins of Yeast Associated with Coffee and Cacao Fermentation.

Curr Biol 2016 Apr 24;26(7):965-71. Epub 2016 Mar 24.

Pacific Northwest Diabetes Research Institute, Seattle, WA 98122, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA. Electronic address:

Modern transportation networks have facilitated the migration and mingling of previously isolated populations of plants, animals, and insects. Human activities can also influence the global distribution of microorganisms. The best-understood example is yeasts associated with winemaking. Humans began making wine in the Middle East over 9,000 years ago [1, 2]. Selecting favorable fermentation products created specialized strains of Saccharomyces cerevisiae [3, 4] that were transported along with grapevines. Today, S. cerevisiae strains residing in vineyards around the world are genetically similar, and their population structure suggests a common origin that followed the path of human migration [3-7]. Like wine, coffee and cacao depend on microbial fermentation [8, 9] and have been globally dispersed by humans. Theobroma cacao originated in the Amazon and Orinoco basins of Colombia and Venezuela [10], was cultivated in Central America by Mesoamerican peoples, and was introduced to Europeans by Hernán Cortés in 1530 [11]. Coffea, native to Ethiopia, was disseminated by Arab traders throughout the Middle East and North Africa in the 6(th) century and was introduced to European consumers in the 17(th) century [12]. Here, we tested whether the yeasts associated with coffee and cacao are genetically similar, crop-specific populations or genetically diverse, geography-specific populations. Our results uncovered populations that, while defined by niche and geography, also bear signatures of admixture between major populations in events independent of the transport of the plants. Thus, human-associated fermentation and migration may have affected the distribution of yeast involved in the production of coffee and chocolate.
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http://dx.doi.org/10.1016/j.cub.2016.02.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4821677PMC
April 2016

Allelic variation, aneuploidy, and nongenetic mechanisms suppress a monogenic trait in yeast.

Genetics 2015 Jan 13;199(1):247-62. Epub 2014 Nov 13.

Pacific Northwest Diabetes Research Institute, Seattle, Washington 98122

Clinically relevant features of monogenic diseases, including severity of symptoms and age of onset, can vary widely in response to environmental differences as well as to the presence of genetic modifiers affecting the trait's penetrance and expressivity. While a better understanding of modifier loci could lead to treatments for Mendelian diseases, the rarity of individuals harboring both a disease-causing allele and a modifying genotype hinders their study in human populations. We examined the genetic architecture of monogenic trait modifiers using a well-characterized yeast model of the human Mendelian disease classic galactosemia. Yeast strains with loss-of-function mutations in the yeast ortholog (GAL7) of the human disease gene (GALT) fail to grow in the presence of even small amounts of galactose due to accumulation of the same toxic intermediates that poison human cells. To isolate and individually genotype large numbers of the very rare (∼0.1%) galactose-tolerant recombinant progeny from a cross between two gal7Δ parents, we developed a new method, called "FACS-QTL." FACS-QTL improves upon the currently used approaches of bulk segregant analysis and extreme QTL mapping by requiring less genome engineering and strain manipulation as well as maintaining individual genotype information. Our results identified multiple distinct solutions by which the monogenic trait could be suppressed, including genetic and nongenetic mechanisms as well as frequent aneuploidy. Taken together, our results imply that the modifiers of monogenic traits are likely to be genetically complex and heterogeneous.
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http://dx.doi.org/10.1534/genetics.114.170563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286688PMC
January 2015

Aneuploidy underlies a multicellular phenotypic switch.

Proc Natl Acad Sci U S A 2013 Jul 28;110(30):12367-72. Epub 2013 Jun 28.

Institute for Systems Biology, Seattle, WA 98109, USA.

Although microorganisms are traditionally used to investigate unicellular processes, the yeast Saccharomyces cerevisiae has the ability to form colonies with highly complex, multicellular structures. Colonies with the "fluffy" morphology have properties reminiscent of bacterial biofilms and are easily distinguished from the "smooth" colonies typically formed by laboratory strains. We have identified strains that are able to reversibly toggle between the fluffy and smooth colony-forming states. Using a combination of flow cytometry and high-throughput restriction-site associated DNA tag sequencing, we show that this switch is correlated with a change in chromosomal copy number. Furthermore, the gain of a single chromosome is sufficient to switch a strain from the fluffy to the smooth state, and its subsequent loss to revert the strain back to the fluffy state. Because copy number imbalance of six of the 16 S. cerevisiae chromosomes and even a single gene can modulate the switch, our results support the hypothesis that the state switch is produced by dosage-sensitive genes, rather than a general response to altered DNA content. These findings add a complex, multicellular phenotype to the list of molecular and cellular traits known to be altered by aneuploidy and suggest that chromosome missegregation can provide a quick, heritable, and reversible mechanism by which organisms can toggle between phenotypes.
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http://dx.doi.org/10.1073/pnas.1301047110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3725063PMC
July 2013

High-throughput tetrad analysis.

Nat Methods 2013 Jul 12;10(7):671-5. Epub 2013 May 12.

Institute for Systems Biology, Seattle, Washington, USA.

Tetrad analysis has been a gold-standard genetic technique for several decades. Unfortunately, the need to manually isolate, disrupt and space tetrads has relegated its application to small-scale studies and limited its integration with high-throughput DNA sequencing technologies. We have developed a rapid, high-throughput method, called barcode-enabled sequencing of tetrads (BEST), that uses (i) a meiosis-specific GFP fusion protein to isolate tetrads by FACS and (ii) molecular barcodes that are read during genotyping to identify spores derived from the same tetrad. Maintaining tetrad information allows accurate inference of missing genetic markers and full genotypes of missing (and presumably nonviable) individuals. An individual researcher was able to isolate over 3,000 yeast tetrads in 3 h, an output equivalent to that of almost 1 month of manual dissection. BEST is transferable to other microorganisms for which meiotic mapping is significantly more laborious.
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http://dx.doi.org/10.1038/nmeth.2479DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3696418PMC
July 2013