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Lee, S. R.

Publications and source records attributed to Lee, S. R..

13 recordsLinked to original sources

Physical restraint induces conditioned place aversion and region-specific c-Fos activation in mice

Linking environmental contexts with stressful experiences is critical for engaging adaptive responses necessary to avoid future threats. Yet, active context-dependent avoidance remains poorly understood. Here, we establish a restraint-induced conditioned place aversion (CPA) paradigm to examine how an acute physiological stressor acquires negative motivational value through contextual association. We found that mice repeatedly exposed to physical restraint in a contextually distinguishable chamber later avoid that location, demonstrating that restraint stress can drive learned aversion in the absence of continued exposure. To identify potential neuronal correlates underlying this learned association, we quantified c-Fos expression in several areas implicated in aversive motivation, emotional salience, and contextual encoding. We found that restraint within the context of the CPA paradigm was associated with increased c-Fos in the nucleus accumbens (NAc) and basolateral amygdala (BLA) while c-Fos expression increased in the ventral hippocampus in response to exposure to the contextual cues alone. These findings reveal region-specific activation in response to restraint stress and associated contextual cues. By connecting classical stress models and associative learning, this work provides a potential platform for further investigation of the neural mechanisms underlying stress-related negative affect and avoidance behaviors.

neuroscience↗

Multimodal Approach for Identification and Validation of Hepatocellular Carcinoma Targets for Radiotheranostics

Identifying tumor selective targets is critical for the development of precision diagnostic and therapeutic agents in oncology. Despite advances in precision oncology elsewhere, there are no FDA-approved hepatocellular carcinoma (HCC)-selective treatments. HCC is the most common type of liver cancer and accounts for significant morbidity and mortality worldwide. Here, we sought to integrate bulk (371 cases) and single cell RNA sequencing (scRNAseq, n=2 datasets, 34 cases, 102,956 cells) of patient samples to enrich for molecules that are overexpressed in HCC, which could serve as HCC-selective targets. To guide definitions of tumor and normal cell clusters with higher fidelity, we also imported a normal liver scRNAseq dataset. Using this integrated approach, we identified several HCC-selective plasma membrane molecules. To validate these targets, we performed immunohistochemical staining of HCC and normal tissue microarrays and confirmed HCC-selective staining of identified targets. Next, we verified the presence of these targets in several commercially available HCC cell lines by flow cytometry and western blot. Finally, we designed, engineered, and tested novel antibody-based positron emission tomography (immunoPET) agents to these targets in various murine models of liver cancer. Our findings confirm that we can leverage this multimodal approach to identify and validate of HCC-selective targets, which can be used to develop tumor-selective diagnostic and therapeutic radiopharmaceuticals, or radiotheranostics, and other precision oncology agents. One Sentence SummaryA multimodal pipeline defines and validates tumor-selective surface targets for radiotheranostic use in hepatocellular carcinoma.

cancer biology↗

Sex specific disruptions in Protein Kinase Cγ signaling in a mouse model of Spinocerebellar Ataxia Type 14

Spinocerebellar Ataxia Type 14 (SCA14) is an autosomal dominant neurodegenerative disease caused by mutations in the gene encoding protein kinase C gamma (PKC{gamma}), a Ca2+/diacylglycerol (DG)-dependent serine/threonine kinase dominantly expressed in cerebellar Purkinje cells. These mutations impair autoinhibitory constraints to increase the basal activity of the kinase, resulting in deficits in the cerebellum that are not observed upon simple deletion of the gene, and severe ataxia. To better understand the phenotypic impact of aberrant PKC{gamma} signaling in disease pathology, we developed a knock-in murine model of the SCA14 mutation {Delta}F48 in PKC{gamma}. This fully penetrant mutation is severe in humans and is mechanistically informative as it has high basal activity but is unresponsive to agonist stimulation. Genetic, behavioral, and molecular testing revealed that {Delta}F48 PKC{gamma} SCA14 mice have ataxia related phenotypes and an altered cerebellar phosphoproteome, effects that are more severe in male mice. Analysis of existing human data reveal that SCA14 has a significantly earlier age of onset for males compared with females. Our data from this clinically relevant mutation suggest that enhanced basal activity of PKC{gamma} is necessary and sufficient to cause ataxia and that treatment strategies to modulate aberrant PKC{gamma} may be particularly beneficial in males. SummaryNew mouse model of Spinocerebellar Ataxia Type 14 containing a clinically relevant mutation in PKC{gamma} identified underlying drivers of the disease and neuroprotection in females.

neuroscience↗

Post-transcriptional monoadenylation by TENT2 terminates human RNA polymerase III transcript 3' end processing and promotes 7SL RNA biogenesis

Small non-coding RNAs (sncRNAs) are subject to 3 end trimming and tailing activities that impact maturation versus degradation decisions during biogenesis. To investigate the dynamics of human sncRNA 3 end processing at a global level we performed genome-wide 3 end sequencing of nascently-transcribed and steady-state sncRNAs. This revealed widespread post-transcriptional adenylation of nascent sncRNAs, which came in two distinct varieties. One is characterized by oligoadenylation, which is transient, promoted by TENT4A/4B polymerases, and most commonly observed on unstable snoRNAs that are not fully processed at their 3 ends. The other is characterized by monoadenylation, which is broadly catalyzed by TENT2 and, in contrast to oligoadenylation, stably accumulates at the 3-end of sncRNAs, including Polymerase-III-transcribed (Pol-III) RNAs and a subset of small nuclear RNAs. Monoadenylation inhibits Pol-III RNA post-transcriptional 3 uridine trimming and extension and, in the case of 7SL RNAs, prevents their accumulation with nuclear La protein and promotes their biogenesis towards assembly into cytoplasmic signal recognition particles. Thus, the biogenesis of human sncRNAs involves widespread mono- or oligo-adenylation with divergent impacts on sncRNA fates.

molecular biology↗

Cold-inducible GOT1 activates the malate-aspartate shuttle in brown adipose tissue to support fuel preference for fatty acids

Brown adipose tissue (BAT) simultaneously metabolizes fatty acids (FA) and glucose under cold stress but favors FA as the primary fuel for heat production. It remains unclear how BAT steer fuel preference toward FA over glucose. Here we show that the malate-aspartate shuttle (MAS) is activated by cold in BAT and plays a crucial role in promoting mitochondrial FA utilization. Mechanistically, cold stress selectively induces glutamic-oxaloacetic transaminase (GOT1), a key MAS enzyme, via the {beta}-adrenergic receptor-PKA-PGC-1 axis. The increase in GOT1 activates MAS, transferring reducing equivalents from the cytosol to mitochondria. This process enhances FA oxidation in mitochondria while limiting glucose oxidation. In contrast, loss of MAS activity by GOT1 deficiency reduces FA oxidation, leading to increased glucose oxidation. Together, our work uncovers a unique regulatory mechanism and role for MAS in mitochondrial fuel selection and advances our understanding of how BAT maintains fuel preference for FA under cold conditions. HighlightsO_LIGot1 is markedly induced by cold in BAT via a {beta}-adrenergic receptor-PKA-PGC-1 axis C_LIO_LIThe increase in cytosolic GOT1 activates the malate-aspartate shuttle (MAS) C_LIO_LIMAS activation promotes fatty acid oxidation while reducing glucose oxidation C_LIO_LILoss of MAS activity in BAT by Got1 deletion shifts the fuel preference to glucose C_LI

cell biology↗

Fig4 confers tolerance to rapamycin in a Ste20-dependent manner independent of the Vac14 scaffold

Summary StatementDisease-related Fig4 mutants displaying impaired association with the Fab1-Vac14-Fig4 complex confer tolerance to rapamycin in Saccharomyces cerevisiae independent of Vac14 in a Ste20-dependent manner. Fig4 can thus modulate homeostasis through association with pathways outside of the Fab1-Vac14-Fig4 complex in yeast. The lipid phosphatase Fig4 modulates the production and turnover of the signaling lipid PI3,5P2 through participation in a complex with its opposing kinase, Fab1, and the scaffold protein Vac14. Fig4 point mutations are associated with neurological diseases for which there are currently no specific therapies. Pathology involving Fig4 is generally attributed to disruption of the Fab1-Vac14-Fig4 complex. Through genetic manipulations in yeast we show that expression of Fig4 disease-related mutants confers tolerance to rapamycin, an inhibitor of the master growth activator TORC1. This phenotype is dominantly conferred at high temperatures by Fig4 mutants that bind poorly to Vac14 or by excess wild-type Fig4. Rapamycin tolerance does not require Fig4 catalytic activity or Vac14, suggesting that Fig4 mediates this altered stress response through context-inappropriate binding interactions with unknown proteins. The p21-activated kinase Ste20 is specifically required for this novel Vac14-independent Fig4 function. Our study shows that Fig4 can modulate homeostasis in Saccharomyces cerevisiae through interactions outside the Fab1-Vac14-Fig4 complex.

cell biology↗

Widely targeted metabolomic analysis reveals differences in volatile metabolites among four Angelica species

Angelica L. has attracted global interest for its traditional medicinal uses and commercial values. However, few studies have focused on the metabolomic differences among the Angelica species. In this study, employing the widely targeted metabolomics based on gas chromatography-tandem mass spectrometry, the metabolomes of four Angelica species were analyzed (Angelica sinensis (Oliv.) Diels (A. sinensis), Angelica biserrata (R.H.Shan & Yuan) C.Q.Yuan & R.H.Shan (A. biserrata), Angelica dahurica (Hoffm.) Benth. & Hook.f. ex Franch. & Sav. (A. dahurica), Angelica keiskei Koidz. (A. keiskei)). A total of 698 volatile metabolites were identified and classified into fifteen different categories. The metabolomic analysis indicated that 7-hydroxycoumarin and Z-ligustilide were accumulated at significantly higher levels in A. sinensis, whereas the opposite pattern was observed for bornyl acetate. In addition, a high correspondence between the dendrogram of metabolite contents and phylogenetic positions was detected in the four species. This study provides a biochemical map for the exploitation, application and development of the Angelica species as medicinal plants or health-related dietary supplements.

plant biology↗

Minor intron splicing efficiency increases with the development of lethal prostate cancer

Here we explored the role of minor spliceosome (MiS) function and minor intron-containing gene (MIG) expression in prostate cancer (PCa). We show MIGs are enriched as direct interactors of cancer-causing genes and their expression discriminates PCa progression. Increased expression of MiS U6atac snRNA, including others, and 6x more efficient minor intron splicing was observed in castration-resistant PCa (CRPC) versus primary PCa. Notably, androgen receptor signalling influenced MiS activity. Inhibition of MiS through siU6atac in PCa caused minor intron mis-splicing and aberrant expression of MIG transcripts and encoded proteins, which enriched for MAPK activity, DNA repair and cell cycle. Single cell-RNAseq confirmed cell cycle defects and lineage dependency on the MiS from primary to CRPC and neuroendocrine PCa. siU6atac was [~]50% more efficient in lowering tumor burden of CRPC cells and organoids versus current state-of-the-art combination therapy. In all, MiS is a strong therapeutic target for lethal PCa and potentially other cancers. Graphical AbstractU6atac expression, MiS activity, and minor intron splicing correlate with PCa therapy resistance and PCa progression to CRPC-adeno and transdifferentiation to CRPC-NE. One major MiS regulator during that process is the AR-axis, which is re-activated during CRPC-adeno and blocked in CRPC-NE. Molecularly, an increase in MiS dependent splicing promotes changes of transcriptome and proteome. This results in cell cycle activation, increased MAPK signalling and increased DNA repair. U6atac mediated MiS inhibition renders MiS splicing error-prone through increased intron retention and alternative splicing events, which results in cell cycle block and decreased MAPK signalling and DNA repair. MiS inhibition blocks all stages of PCa. Figure created with BioRender.com. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/471104v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@1c1c296org.highwire.dtl.DTLVardef@1ce1416org.highwire.dtl.DTLVardef@88d842org.highwire.dtl.DTLVardef@2ddf96_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

The impact of mutational processes on structural genomic plasticity in cancer cells

Structural genome alterations are determinants of cancer ontogeny and therapeutic response. While bulk genome sequencing has enabled delineation of structural variation (SV) mutational processes which generate patterns of DNA damage, we have little understanding of how these processes lead to cell-to-cell variations which underlie selection and rates of accrual of different genomic lesions. We analysed 309 high grade serous ovarian and triple negative breast cancer genomes to determine their mutational processes, selecting 22 from which we sequenced >22,000 single cell whole genomes across a spectrum of mutational processes. We show that distinct patterns of cell-to-cell variation in aneuploidy, copy number alteration (CNA) and segment length occur in homologous recombination deficiency (HRD) and fold-back inversion (FBI) phenotypes. Widespread aneuploidy through induction of HRD through BRCA1 and BRCA2 inactivation was mirrored by continuous whole genome duplication in HRD tumours, contrasted with early ploidy fixation in FBI. FBI tumours exhibited copy number distributions skewed towards gains, widespread clone-specific variation in amplitude of high-level amplifications, often impacting oncogenes, and break-point variability consistent with progressive genomic diversification, which we termed serriform structural variation (SSV). SSVs were consistent with a CNA-based molecular clock reflecting a continual and distributed process across clones within tumours. These observations reveal previously obscured genome plasticity and evolutionary properties with implications for cancer evolution, therapeutic targeting and response.

cancer biology↗

Single cell fitness landscapes induced by genetic and pharmacologic perturbations in cancer

Tumour fitness landscapes underpin selection in cancer, impacting etiology, evolution and response to treatment. Progress in defining fitness landscapes has been impeded by a lack of timeseries perturbation experiments over realistic intervals at single cell resolution. We studied the nature of clonal dynamics induced by genetic and pharmacologic perturbation with a quantitative fitness model developed to ascribe quantitative selective coefficients to individual cancer clones, enable prediction of clone-specific growth potential, and forecast competitive clonal dynamics over time. We applied the model to serial single cell genome (>60,000 cells) and transcriptome (>58,000 cells) experiments ranging from 10 months to 2.5 years in duration. We found that genetic perturbation of TP53 in epithelial cell lines induces multiple forms of copy number alteration that confer increased fitness to clonal populations with measurable consequences on gene expression. In patient derived xenografts, predicted selective coefficients accurately forecasted clonal competition dynamics, that were validated with timeseries sampling of experimentally engineered mixtures of low and high fitness clones. In cisplatin-treated patient derived xenografts, the fitness landscape was inverted in a time-dependent manner, whereby a drug resistant clone emerged from a phylogenetic lineage of low fitness clones, and high fitness clones were eradicated. Moreover, clonal selection mediated reversible drug response early in the selection process, whereas late dynamics in genomically fixed clones were associated with transcriptional plasticity on a fixed clonal genotype. Together, our findings outline causal mechanisms with implication for interpreting how mutations and multi-faceted drug resistance mechanisms shape the etiology and cellular fitness of human cancers.

cancer biology↗

Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires

Essential features of cancer tissue cellular heterogeneity such as negatively selected genome topologies, sub-clonal mutation patterns and genome replication states can only effectively be studied by sequencing single-cell genomes at scale and high fidelity. Using an amplification-free single-cell genome sequencing approach implemented on commodity hardware (DLP+) coupled with a cloud-based computational platform, we define a resource of 40,000 single-cell genomes characterized by their genome states, across a wide range of tissue types and conditions. We show that shallow sequencing across thousands of genomes permits reconstruction of clonal genomes to single nucleotide resolution through aggregation analysis of cells sharing higher order genome structure. From large-scale population analysis over thousands of cells, we identify rare cells exhibiting mitotic mis-segregation of whole chromosomes. We observe that tissue derived scWGS libraries exhibit lower rates of whole chromosome anueploidy than cell lines, and loss of p53 results in a shift in event type, but not overall prevalence in breast epithelium. Finally, we demonstrate that the replication states of genomes can be identified, allowing the number and proportion of replicating cells, as well as the chromosomal pattern of replication to be unambiguously identified in single-cell genome sequencing experiments. The combined annotated resource and approach provide a re-implementable large scale platform for studying lineages and tissue heterogeneity.

genomics↗

Genetic Diversity Patterns and Domestication Origin of Soybean

Understanding diversity and evolution of a crop is an essential step to implement a strategy to expand its germplasm base for crop improvement research. Samples intensively collected from Korea, which is a small but central region in the distribution geography of soybean, were genotyped to provide sufficient data to underpin genome-wide population genetic questions. After removing natural hybrids and duplicated or redundant accessions, we obtained a non-redundant set comprising 1,957 domesticated and 1,079 wild accessions to perform population structure analyses. Our analysis demonstrates that while wild soybean germplasm will require additional sampling from diverse indigenous areas to expand the germplasm base, the current domesticated soybean germplasm is saturated in terms of genetic diversity. We then showed that our genome-wide polymorphism map enabled us to detect genetic loci underling flower color, seed-coat color, and domestication syndrome. A representative soybean set consisting of 194 accessions were divided into one domesticated subpopulation and four wild subpopulations that could be traced back to their geographic collection areas. Population genomics analyses suggested that the monophyletic group of domesticated soybeans was originated in eastern Japan. The results were further substantiated by a phylogenetic tree constructed from domestication-associated single nucleotide polymorphisms identified in this study.

plant biology↗

Natural Genetic Variation Modifies Gene Expression Dynamics at the Protein Level During Pheromone Response in Saccharomyces cerevisiae

Heritable variation in gene expression patterns plays a fundamental role in trait variation and evolution, making understanding the mechanisms by which genetic variation acts on gene expression patterns a major goal for biology. Both theoretical and empirical work have largely focused on variation in steady-state mRNA levels and mRNA synthesis rates, particularly of protein-coding genes. Yet in order for this variation to affect higher order traits it must lead to differences at the protein level. Variation in protein-specific processes including protein synthesis rates and protein decay rates could amplify, mask, or even reverse effects transmitted from the transcript level, but the extent to which this happens is unclear. Moreover, mechanisms that underlie protein expression variation under dynamic conditions have not been examined. To address this challenge, we analyzed how mRNA and protein expression dynamics covary between two strains of Saccharomyces cerevisiae during mating pheromone response. Although divergent steady-state mRNA expression levels explained divergent steady-state protein levels for four out of five genes in our study, the same was true for only one out of five genes for expression dynamics. By integrating decay rate and allele-specific protein expression analyses, we resolved that expression divergence for Fig1p was caused by genetic variation acting in trans on protein synthesis rate, expression divergence for Ina1p was caused by cis-by-trans epistatic effects on transcript level and protein synthesis rate, and expression divergence for Fus3p and Tos6p were caused by divergence in protein synthesis rates. Our study demonstrates that steady-state analysis of gene expression is insufficient to understand the impact of genetic variation on gene expression variation. An integrated and dynamic approach to gene expression analysis - comparing mRNA levels, protein levels, protein decay rates, and allele-specific protein expression - allows for a detailed analysis of the genetic mechanisms underlying protein expression divergences.

genetics↗