Biology subjects

Miller, J. R.

Publications and source records attributed to Miller, J. R..

7 recordsLinked to original sources

bioRxiv2026

Hepatic stearoyl-CoA desaturase deficiency ameliorates hyperglycemia through bile acid signaling in an insulin-independent manner

Hyperglycemia in Type 1 Diabetes (T1D) is managed almost exclusively via exogenous insulin therapy, an approach restricted by significant glycemic fluctuations, long-term side effects such as weight gain, and high economic burden. Identifying physiological pathways capable of clearing blood glucose independent of insulin is therefore of paramount clinical importance. Here, we demonstrate that liver-specific stearoyl-CoA desaturase-1 (SCD1) deficiency protects against diabetic hyperglycemia and hepatic steatosis in an insulin-independent manner. SCD1 ablation decreases cellular oleate availability, altering lipid flux and redirecting excess cholesterol into alternative biosynthetic pathways. This redirection drives a 2-fold elevation in hepatic bile acids and a striking 10-fold increase in plasma bile acids, predominantly characterized by the accumulation of taurocholic acid. This shifted bile acid pool stimulates the expression of glucose transporter 1 (Glut1) in the liver via activation of the nuclear hormone receptor FXR, facilitating basal glucose clearance in the absence of insulin. Genetic deletion models show that while the hepatokine FGF21 serves as a partial mediator of this phenotype, the local bile acid-FXR axis remains a sufficient driver of systemic glucose clearance. Finally, we show that dietary oleate supplementation completely reverses this protective phenotype, turning down Glut1 expression and restoring overt diabetes. Together, our findings uncover a novel bile acid-FXR-Glut1 signaling axis triggered by SCD1 inhibition, offering a framework for insulin-independent glycemic control. Article HighlightsHere, we demonstrate that liver-specific stearoyl-CoA desaturase-1 (Scd1) deficiency protects against diabetic hyperglycemia and hepatic steatosis in an insulin-independent manner. Mechanistically, Scd1 ablation redirects excess cholesterol into bile synthesis, predominantly characterized by an increase in liver and plasma taurocholic acid. These shifted bile acids stimulate hepatic glucose transporter 1 (Glut1) expression via the farnesoid X receptor (FXR) activation to facilitate basal glucose clearance. While the hepatokine FGF21 acts as a partial systemic mediator, the local bile acid-Fxr axis remains a sufficient driver of clearance, a protective phenotype completely reversed by dietary oleate supplementation.

biochemistry↗

bioRxiv2023

Ribosomal DNA copy number is associated with body mass in humans and other mammals

Body mass results from a complex interplay between genetics and environment. The contribution of genetic variation to body mass has been extensively studied, but due to the technical limitations of platforms used for population scale studies, repetitive parts of the genome have not previously been considered. Here we applied genome-wide approaches to identify an association between adult body mass and the copy number (CN) of 45S-ribosomal DNA (rDNA). rDNA codes for the rRNA components of the ribosome and exists in hundreds of copies/cell in mammals. Inter-individual variation in rDNA CN has not previously been documented but has not been associated with a mammalian phenotype. Here, we show that germ-line inherited rDNA CN is associated with post-pubertal growth rate in rats and BMI in adult humans. rDNA CN variation is not associated with rRNA transcription rates in adult tissues, suggesting the mechanistic link occurs earlier in development. This is supported by our observation that it is growth rate and body mass, rather than obesity that are associated with copy number and that these phenotypes emerge prior to adulthood. We present hypotheses for future investigation into the mechanistic basis of this association.

genomics↗

bioRxiv2023

Structural evidence for MADS-box type I family expansion seen in new assemblies of A. arenosa and A. lyrata

Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago and are identified by genome-wide polymorphisms or morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based in the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS-box type I family of transcription factors are specifically expressed in the endosperm and has been proposed to play a role in endosperm-based hybridization barriers. The gene family is well known for a high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS-box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de-novo assembled and annotated chromosome-level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS-box type I gene family in Arabidopsis to predict orthologs, copy number and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS-box type I loci in endosperm-based hybridization barriers. We observed substantial differences in type-I expression between A. arenosa and A. lyrata ssp. petraea in the endosperm, suggesting a genetic cause for the endosperm-based hybridization barrier in A. arenosa and A. lyrata ssp. petraea hybrid seeds.

plant biology↗

bioRxiv2022

Multiomic profiling defines cell fate plasticity of in vitro-derived islets

Transplantation of insulin-secreting {beta}-cells differentiated from human pluripotent stem cells holds great potential as a cell therapy for treating insulin-dependent diabetes. While these stem cell-derived islets (SC-islets) are able to reverse diabetes in animal models, they are not fully equivalent to their in vivo counterparts. To better define the state of the cell types generated within these SC-islets and provide a resource for identifying deficiencies in lineage specification, we used single-cell multiomic sequencing to simultaneously measure the chromatin accessibility and transcriptional profiles of SC-islets at multiple time points as well as primary human islets. The integrated analysis of both the transcriptional and chromatin landscape for each cell provided greater resolution for defining cell identity, allowing us to derive novel gene lists for identifying each islet cell type. Furthermore, this multiomic analysis revealed that the difference between SC-{beta} cells and enterochromaffin-like cells, which are a major off-target from in vitro differentiation, is a gradient of progressive cell states rather than a stark difference in identity. The chromatin landscape of primary human islets was much more restricted, suggesting that stem cell-derived cells are not fully locked into their cell fate. While long term culture of SC-islets both in vitro and in vivo does close overall chromatin state, only in vivo transplantation directs cells toward their correct identities. Collectively, our multiomic analysis demonstrates that both the chromatin and transcriptional landscapes play significant roles in islet cell identity, and these data can be used as a resource to identify specific deficiencies in the chromatin and transcriptional state of SC-islet cell types.

cell biology↗

bioRxiv2022

Spatial and Temporal Regulation of Parent-of-Origin Allelic Expression in the Endosperm

Genomic imprinting promotes differential expression of parental alleles in the endosperm of flowering plants, and is regulated by epigenetic modification such as DNA methylation and histone tail modifications in chromatin. After fertilization, the endosperm develops through a syncytial stage before it cellularizes and becomes a nutrient source for the growing embryo. Both in early and late endosperm development regional compartmentalization has been shown, and different transcriptional domains suggest divergent spatial and temporal regional functions. The analysis of the role of parent-of-origin allelic expression in the endosperm as a whole and also investigation of domain specific functions has been hampered by the availability of the tissue for high-throughput transcriptome analyses and contamination from surrounding tissue. Here we have used Fluorescence-Activated Nuclear Sorting (FANS) of nuclear targeted eGFP fluorescent genetic markers to capture parental specific allelic expression from different developmental stages and specific endosperm domains. This RNASeq approach allows us to successfully identify differential genomic imprinting with temporal and spatial resolution. In a systematic approach we report temporal regulation of imprinted genes in the endosperm as well as region specific imprinting in endosperm domains. Our data identifies loci that are spatially differentially imprinted in one domain of the endosperm while biparentally expressed in other domains. This suggests that regulation of genomic imprinting is dynamic and challenges the canonical mechanisms for genomic imprinting.

genetics↗

bioRxiv2019

Regulation of Parent-of-Origin Allelic Expression in Arabidopsis thaliana endosperm

Genomic imprinting is an epigenetic phenomenon set in the gametes prior to fertilization that causes differential expression of parental alleles mainly in the endosperm of flowering plants. The overlap between previously identified panels of imprinted genes is limited. In order to achieve high resolution sequencing data we have used sequence capture technology to investigate imprinting. Here, we present a bioinformatics pipeline to assay parent-of-origin allele specific expression and report more than 300 loci with parental expression bias. We find that the level of expression from maternal and paternal alleles in most cases is not binary, instead favouring a differential dosage hypothesis for the evolution of imprinting in plants. To address imprinting regulation, we systematically employed mutations in regulative epigenetic pathways suggested to be major players in the process. We establish the mechanistic mode of imprinting for more than 50 loci regulated by DNA methylation and Polycomb-dependent histone methylation. However, the imprinting patterns of the majority of genes were not affected by these mechanisms. To this end we also demonstrate that the RNA-directed DNA methylation pathway alone does not influence imprinting patterns in a substantial manner, suggesting more complex epigenetic regulation pathways for the majority of identified imprinted genes.\n\nAuthor summaryExpression of gene copies only from the mother or the fathers genome, also termed imprinting, is a specialized epigenetic phenomenon that is found to be enriched at some genes expressed in the mammalian placenta and in the endosperm of the plant seed. Although several studies have reported on imprinted genes in plants, the identified loci are at large non-overlapping between reports. This motivated us to investigate in detail the expression pattern of imprinted genes in the endosperm and to determine how imprinting patterns are established at various imprinted loci. Although several underlying epigenetic regulation mechanisms have been demonstrated to establish imprinting patterns at certain genes, the majority of imprinted genes have not been linked to such mechanisms. In the present study we systematically investigated the mechanisms that are involved in establishing imprinting, by employing mutants of epigenetic regulators and high-throughput sequencing. In our high resolution study, we report more than 300 imprinted genes and demonstrate that the biological phenomenon imprinting involves gradual expression of parental gene copies rather than switching gene copies on or off. Notably, for the majority of imprinted genes, the mechanisms previously believed to be major to establish their imprinting patterns, are not responsible for mediating imprinting.

genetics↗

bioRxiv2017

Analysis of the Aedes albopictus C6/36 genome provides insight into cell line adaptations to in vitro viral propagation

BackgroundThe 50-year old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome.\n\nResultsThe C6/36 genome assembly has the largest contig N50 (3.3 Mbp) of any mosquito assembly, presents the sequences of both haplotypes for most of the diploid genome, reveals independent null mutations in both alleles of the Dicer locus, and indicates a male-specific genome. Gene annotation was computed with publicly available mosquito transcript sequences. Gene expression data from cell line RNA sequence identified enrichment of growth-related pathways and conspicuous deficiency in aquaporins and inward rectifier K+ channels. As a test of utility, RNA sequence data from Zika-infected cells was mapped to the C6/36 genome and transcriptome assemblies. Host subtraction reduced the data set by 89%, enabling faster characterization of non-host reads.\n\nConclusionsThe C6/36 genome sequence and annotation should enable additional uses of the cell line to study arbovirus vector interactions and interventions aimed at restricting the spread of human disease.

genomics↗