Biology subjects

Liebman, S. W.

Publications and source records attributed to Liebman, S. W..

5 recordsLinked to original sources

bioRxiv2026

FIND: a software tool for identifying population-enriched pathogenic variants in gnomAD

Founder mutations are variants that arose in a single ancestor and became enriched in a descendant population through a bottleneck and endogamy. Identification of pathogenic founder mutations has facilitated efficient targeted screening. More broadly, even without confirmed founder status, identifying pathogenic variants that are enriched within specific populations reveals population-specific disease burden. However, many such variants remain hidden in plain sight within existing datasets. To address this gap, we developed FIND (Founder candidates hidden IN Data), a web tool that identifies variants in gnomAD with frequencies >0.00008 in one ancestry group and at least tenfold higher than in all others (after zeroing populations with fewer than five observed alleles). The search is restricted to looking at pathogenic, likely pathogenic, and predicted loss-of-function variants. Testing FIND on the genes FLNC, TMEM127, MYH7, BRCA1, and BRCA2 confirmed its utility and functionality by identifying twelve well-known founder or population-enriched mutations and, as candidate founders with unconfirmed founder status, five variants previously reported as recurrent in a population but never compared across populations and three not previously reported as population-enriched. Variants enriched in African American and admixed American populations were validated with the All of Us database, highlighting the utility of this approach for populations historically underrepresented in genetic studies. The source code is freely available at https://github.com/aacoder105/FIND under an MIT license, with a web interface at https://ethnic-variant-mutation-finder.onrender.com/.

genomics↗

bioRxiv2025

The types of prions and liquid-like aggregates formed by the yeast protein Rnq1 are controlled by interactions between its non-prion and prion domains

Prions are self-propagating protein conformations usually existing as amyloid aggregates. [PIN+], a prion form of the Rnq1 protein occasionally found in wild and laboratory yeast strains, facilitates both the de novo formation and destabilization of other yeast prions, and affects aggregation and toxicity of human misfolding disease proteins expressed in yeast. Rnq1 contains a short N-terminus with no confirmed function (the non-prion domain, NPD) and a C-terminus that carries four QN-rich regions and is sufficient for [PIN+] formation and maintenance (prion domain, PD). In the current study, a genetic screen identified the NPD T27P mutation that blocks transmission of the [PIN+] prion state from wild type Rnq1 (Rnq1WT) to mutant Rnq1T27P. The mutation doesnt prevent Rnq1T27P from switching to a prion state when overexpressed in vivo, or from forming amyloid fibers in vitro. Furthermore, like [PIN+WT], the newly formed [PIN+T27P]s promote the de novo appearance of the Sup35-based prion [PSI+]. We conclude that the NPD mutation creates a barrier for prion transmission from [PIN+WT] to Rnq1T27P. Because fluorescence microscopy shows that Rnq1T27P efficiently joins [PIN+WT] aggregates, the barrier is likely due to the inability of Rnq1T27P to propagate the specific [PIN+WT] conformational variant. Indeed, the analysis of [PIN+T27P]s resulting from rare transmission events from [PIN+WT] indicates that these [PIN+T27P]s must undergo conformational adaptation to yield more stable prion variants. Deletion analysis revealed that T27P constrains prion conformations through the first two QN-rich regions within the PD. The finding that Rnq1T27P-YFP readily forms non-amyloid liquid-like droplets, which Rnq1WT-YFP does not form, supports the idea that the NPD affects aggregation properties of the PD. We propose that these aggregation properties are essential for Rnq1s functions, such as controlling aggregation of other proteins. This provides new insight into the role of heterologous proteins and transmission barriers in the origins of protein misfolding diseases. Author SummaryProteins must fold into the right shapes to work properly. Sometimes they fold incorrectly and stick together, forming long fiber aggregates that damage cells. This kind of "protein misfolding" causes human diseases such as Alzheimers. Certain yeast proteins behave similarly, making them useful to study this process. We investigate a yeast protein called Rnq1, which has a region that helps it misfold into fibers. These fibers can also cause other, unrelated proteins to misfold. We found that a mutation in a different part of Rnq1-- outside the aggregation region -- reduces the ability of non-mutant Rnq1 fibers to convert mutant Rnq1 into growing fiber aggregates. We also identified which section of the aggregation region is affected by this mutation. Interestingly, although the rarely converted mutant aggregates grow poorly at first, they can eventually "adapt" into a shape that grows better. The same mutation also pushes Rnq1 to form liquid-like droplets instead of fibers. Our findings show that the non-aggregating part of Rnq1 controls how Rnq1 aggregates, and, consequently, the appearance and elimination of aggregates formed by other proteins. Our work also helps explain how barriers to misfolded protein growth can be overcome, which is relevant to understanding human protein misfolding diseases.

genetics↗

bioRxiv2024

A model of inborn metabolism errors associated with adenine amyloid-like fiber formation reduces TDP-43 aggregation and toxicity in yeast

TDP-43 is linked to human diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal degeneration (FTD). Expression of TDP-43 in yeast is known to be toxic, cause cells to elongate, form liquid-like aggregates, and inhibit autophagy and TOROID formation. Here, we used the apt1{Delta} aah1{Delta} yeast model of disorders of inborn errors of metabolism, previously shown to lead to intracellular adenine accumulation and adenine amyloid-like fiber formation, to explore interactions with TDP-43. Results show that the double deletion shifts the TDP-43 aggregates from a liquid-like, toward a more amyloid-like, state. At the same time the deletions reduce TDP-43s effects on toxicity, cell morphology, autophagy, and TOROID formation without affecting the level of TDP-43. This suggests that the liquid-like and not amyloid-like TDP-43 aggregates are responsible for the deleterious effects in yeast. How the apt1{Delta} aah1{Delta} deletions alter TDP-43 aggregate formation is not clear. Possibly, it results from adenine/TDP-43 fiber interactions as seen for other heterologous fibers. The work offers new insights into the potential interactions between metabolite-based amyloids and pathological protein aggregates, with broad implications for understanding protein misfolding diseases.

genetics↗

bioRxiv2018

TDP-43 is more toxic in respiring than in non-respiring cells, but respiration is not absolutely required for TDP-43 toxicity.

The trans-activating response DNA-binding protein 43 (TDP-43) is a transcriptional repressor and splicing factor. TDP-43 is normally mostly in the nucleus, although it shuttles to the cytoplasm. Mutations in TDP-43 are one cause of familial amyotrophic lateral sclerosis (ALS). In neurons of these patients, TDP-43 forms cytoplasmic aggregates. In addition, wild-type TDP-43 is also frequently found in neuronal cytoplasmic aggregates in patients with neurodegenerative diseases not caused by TDP-43 mutations. TDP-43 expressed in yeast causes toxicity and forms cytoplasmic aggregates. This disease model has been validated because genetic modifiers of TDP-43 toxicity in yeast have led to the discovery that conserved genes in humans are ALS genetic risk factors. While it is still unknown how TDP-43 is associated with toxicity, several studies find that TDP-43 alters mitochondrial function. We now report that TDP-43 is much more toxic when yeast is grown in non-fermentable media requiring respiration than when grown on fermentable carbon sources. However, we also establish that TDP-43 remains toxic in the absence of respiration. Thus, there is a TDP-43 toxicity target in yeast distinct from respiration and respiration is not required for this toxicity. Since we find that H2O2 increases the toxicity of TDP-43, the free oxygen radicals associated with respiration could likewise enhance the toxicity of TDP-43. In this case, the TDP-43 toxicity targets in the presence or absence of respiration could be identical, with the free radical oxygen species produced by respiration activating TDP-43 to become more toxic or making TDP-43 targets more vulnerable.\n\nHighlightsO_LITDP-43 toxicity and aggregation is enhanced when yeast are grown in media that requires respiration.\nC_LIO_LIRespiration is not the sole target of TDP-43 toxicity because TDP-43 still aggregates and is toxic in cells that are not respiring.\nC_LIO_LIHydrogen peroxide enhances TDP-43 toxicity in the absence of respiration suggesting that reactive oxygen species (ROS) produced by respiration may likewise enhance TDP-43 toxicity.\nC_LIO_LIROS could activate TDP-43 to become more toxic or make TDP-43 targets more vulnerable.\nC_LI\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC=\"FIGDIR/small/415893_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@85d24aorg.highwire.dtl.DTLVardef@1b103d3org.highwire.dtl.DTLVardef@72280dorg.highwire.dtl.DTLVardef@a3a82e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2018

A yeast model of calcium-responsive transactivator protein (CREST) proteinopathy shows that PBP1/ATXN2 modifies CREST aggregation and toxicity.

Proteins associated with familial neurodegenerative disease often aggregate in patients neurons. Several such proteins, e.g. TDP-43, aggregate and are toxic when expressed in yeast. Deletion of the ATXN2 ortholog, PBP1, reduces yeast TDP-43 toxicity, which led to identification of ATXN2 as an amyotrophic lateral sclerosis (ALS) risk factor and therapeutic target. Likewise, new yeast neurodegenerative disease models could facilitate identification of other risk factors and targets. Mutations in SS18L1, encoding the calcium-responsive transactivator (CREST) chromatin-remodeling protein, are associated with ALS. We show that CREST is toxic in yeast and forms nuclear and occasionally cytoplasmic foci that stain with Thioflavin-T, a dye indicative of amyloid-like protein. Like the yeast chromatin-remodeling factor SWI1, CREST inhibits silencing of FLO genes. Toxicity of CREST is enhanced by the [PIN+] prion and reduced by deletion of the HSP104 chaperone required for the propagation of many yeast prions. Likewise, deletion of PBP1 reduced CREST toxicity and aggregation. In accord with the yeast data, we show that the Drosophila ortholog of human ATXN2, dAtx2, is a potent enhancer of CREST toxicity. Downregulation of dAtx2 in flies overexpressing CREST in retinal ganglion cells was sufficient to largely rescue the severe degenerative phenotype induced by human CREST. Overexpression caused considerable co-localization of CREST and PBP1/ATXN2 in cytoplasmic foci in both yeast and mammalian cells. Thus, co-aggregation of CREST and PBP1/ATXN2 may serve as one of the mechanisms of PBP1/ATXN2-mediated toxicity. These results extend the spectrum of ALS associated proteins whose toxicity is regulated by PBP1/ATXN2, suggesting that therapies targeting ATXN2 may be effective for a wide range of neurodegenerative diseases.\n\nAuthor summaryMutations in the calcium-responsive transactivator (CREST) protein have been shown to cause amyotrophic lateral sclerosis (ALS). Here we show that the human CREST protein expressed in yeast forms largely nuclear aggregates and is toxic. We also show that the HSP104 chaperone required for propagation of yeast prions is likewise required for CREST toxicity. Furthermore deletion of HSP104 affects CREST aggregation. ATXN2, previously shown to modify ALS toxicity caused by mutations in the TDP-43 encoding gene, also modifies toxicity of CREST expressed in either yeast or flies. In addition, deletion of the yeast ATXN2 ortholog reduces CREST aggregation. These results extend the spectrum of ALS associated proteins whose toxicity is regulated by ATXN2, suggesting that therapies targeting ATXN2 may be effective for a wide range of neurodegenerative diseases.

molecular biology↗