Biology subjects

Miller, D. L.

Publications and source records attributed to Miller, D. L..

9 recordsLinked to original sources

bioRxiv2026

Meta-analysis of Genes and Pathways that Protect Against Hypoxia.

Oxygen is essential for all terrestrial animals, but there is dramatic variability in how well different animals and even different cell types can adapt to reduced oxygen availability. We used a meta-analysis of the literature, with a focus on mouse studies, to identify pathways that might act to protect animals in low oxygen environments. We identified 108 genes whose mRNA levels change under hypoxia, and 55 genes critical for mounting a response to hypoxia. With this data, we developed a list of conserved genes, and we tested three C.elegans genes previously uncharacterized in hypoxia, mxl-3, yap-1, and ador-1, and found that loss of function altered egg-laying during and after hypoxia. Our method provides a more targeted approach of how to screen for hypoxic phenotypes and study in more genetically tractable organisms to show mechanisms.

genetics↗

bioRxiv2025

Nested Connections: Local Phage and Broad Plasmid Sharing in the Honey Bee Mobilome

Honey bees rely on bacterial symbionts for their nutritional needs and for protection against invading pathogens. Genetic diversity among strains within the colony has the potential to impact symbiont function and subsequently the benefits that honey bees receive from them. Mobilized genes vectored by mobile genetic elements (MGEs) like phages, transposons, conjugative elements and plasmids, are known to rapidly alter bacterial phenotypes. We identified phages and plasmids in genomes of the symbiont Bombella apis between two colonies, with the goal of understanding which MGEs contribute to strain diversification as well as MGE distribution across colonies and between microbial species. Interestingly, we found some B. apis strains carry plasmids while all harbor a diversity of integrated phages, with only one phage clusters conserved across all. Identified B. apis phages are not found outside of the Bombella and Saccaribacter species, suggesting some host specificity for these MGEs. Of the five plasmids discovered, two appear to be phage-plasmids with high similarity to phages found in previously sequenced B. apis genomes. Interestingly, three plasmids in B. apis shared significant average nucleotide identity with known plasmids from acetic acid bacteria isolated from flowers, plants, and fermented foods. This result suggests that B. apis has acquired MGEs, either vertically or horizontally, from plant- and fermented-food associated AABs. Overall, our findings suggest that MGE content varies between colonies and has the potential to shape genetic and phenotypic variation between strains.

microbiology↗

bioRxiv2025

Extracellular Vesicle Gene Expression Enables Sensitive Detection of Colorectal Neoplasia

BACKGROUND & AIMSExtracellular vesicles (EVs), including exosomes, are emerging as promising carriers of disease-specific biomarkers due to their molecular cargo reflective of cellular origin. While cell-free DNA (cfDNA) methylation assays have recently been developed for colorectal cancer (CRC) screening and perform well for cancer detection, they show limited sensitivity for advanced adenomas (AA), a key precursor in the CRC pathway. To address this gap, we sought to determine whether other blood-based analytes, specifically EV-derived long and small RNA transcriptomes and EV proteomes, could improve detection of AA and early-stage CRC. In a prospective cohort, we performed a head-to-head comparison of EV transcriptomics, EV proteomics, and their combinations against cfDNA methylation, all measured from the same patient cohort, enabling a direct performance benchmark and identification of the most promising modality for larger-scale CRC screening studies. METHODSWe prospectively collected pre-colonoscopy plasma samples from 220 participants across three clinical sites. EVs were isolated and profiled using long RNA-seq, small RNA-seq, and Olink-based proteomics. cfDNA was analyzed for methylation patterns. Analyses were conducted according to a statistical analysis plan pre-specified before unblinding. Machine learning models were developed under nested cross-validation to evaluate sensitivity for detecting AA and CRC at a fixed specificity of 91%, consistent with clinical screening benchmarks. RESULTSEV-derived gene expression on long RNA demonstrated the highest sensitivity for detecting AA as well as CRC: 54.8% (95% CI, 26.4%-75.6%) for AA and 94.1% (95% CI, 79.2%-100%) for CRC. This outperformed cfDNA methylation (33.6% [95% CI, 9.7%-60.3%] for AA, 81.3% [95% CI, 64.6%- 93.9%] for CRC) and other EV-based modalities. In addition, for small RNA the sensitivities were 42.6% (95% CI, 35.9%-47.4%) for AA, and 78.9% (95% CI, 69.2%-83.0%) for CRC, while for proteomics the sensitivities were 30.0% (95% CI, 13.9%-40.0%) for AA, and 64.2% (95% CI, 43.6%-87.2%) for CRC. Transcriptomic profiles revealed progressive enrichment of hallmarks of cancer pathways, including apoptosis and epithelial-mesenchymal transition, across disease stages. Multiomic integration did not improve performance beyond EV transcriptomics alone. CONCLUSIONSBy directly comparing multiple EV-based and cfDNA analytes within the same patient cohort, we found that EV transcriptomics delivers the strongest diagnostic performance for both AA and CRC. This rigorous benchmarking approach allows clear prioritization of the most promising modality guiding the design of larger validation studies and accelerating development of next-generation, blood-based CRC screening tools.

genomics↗

bioRxiv2025

Deep Profiling of EV Long RNAs Reveals Biofluid-Specific Transcriptomes and Splicing Landscapes

RNA profiling of extracellular vesicles (EVs) from human biofluids has historically been limited to small RNA species, with long RNAs--such as mRNA exons and long non-coding RNAs--remaining largely underexplored. Moreover, the dominance of hematopoietic-derived EVs in complex fluids like plasma has posed significant challenges for detecting low-abundance, tissue-specific transcripts. Here, we establish foundational transcriptomic maps of long RNAs in EVs from plasma, urine, and cerebrospinal fluid (CSF) using ultra-deep whole transcriptome sequencing (WTS), revealing both fluid-specific and shared expression and splicing signatures. We then introduce a targeted RNA capture method that enriches for all protein-coding and long non-coding transcripts, dramatically enhancing sensitivity for gene and splice variant detection. Applying this approach to brain-specific transcripts, we achieve >85-fold enrichment of target gene expression and, on average, 3.1-fold increase in detected splice junctions per gene compared to untargeted WTS. As a proof of concept, we apply this brain-targeted RNA panel to EVs from plasma in a Parkinsons disease cohort of 40 plasma samples and compare its performance to exome sequencing as well as untargeted WTS. This work advances EV transcriptomics into the long RNA domain and establishes a framework for high-sensitivity, noninvasive biomarker profiling across tissues and diseases.

genomics↗

bioRxiv2021

Nuclear Hormone Receptor NHR-49 controls a HIF-1-independent hypoxia adaptation pathway in Caenorhabditis elegans

The response to insufficient oxygen (hypoxia) is orchestrated by the conserved Hypoxia-Inducible Factor (HIF). However, HIF-independent hypoxia response pathways exist that act in parallel to HIF to mediate the physiological hypoxia response. Here, we describe a HIF-independent hypoxia response pathway controlled by Caenorhabditis elegans Nuclear Hormone Receptor NHR-49, an orthologue of mammalian Peroxisome Proliferator-Activated Receptor alpha (PPAR). We show that nhr-49 is required for worm survival in hypoxia and is synthetic lethal with hif-1 in this context, demonstrating that these factors act independently. RNA-seq analysis shows that in hypoxia nhr-49 regulates a set of genes that are hif-1-independent, including autophagy genes that promote hypoxia survival. We further show that Nuclear Hormone Receptor nhr-67 is a negative regulator and Homeodomain-interacting Protein Kinase hpk-1 is a positive regulator of the NHR-49 pathway. Together, our experiments define a new, essential hypoxia response pathway that acts in parallel to the well-known HIF-mediated hypoxia response.

genetics↗

bioRxiv2019

C. elegans RHY-1 and CYSL-1 act independently of HIF-1 to promote survival in hydrogen sulfide.

Hydrogen sulfide (H2S) is an endogenously produced signaling molecule that can be cytoprotective, especially in conditions of ischemia/reperfusion injury. However, exposure to exogenous H2S can be toxic, perhaps due to unregulated activation of endogenous H2S signaling pathways. We use the nematode C. elegans to define mechanisms that mediate the physiological effects of H2S in animals. We have previously shown that in C. elegans the hypoxia inducible factor (hif-1) coordinates the initial transcriptional response to H2S and is essential to survive exposure to low concentrations of H2S. In this study, we performed a forward genetic screen to identify mutations that suppress the lethality of hif-1 mutant animals in H2S. The mutations we recovered do not suppress embryonic lethality or reproductive arrest of hif-1 mutant animals in hypoxia, nor can they improve viability of hif-1 mutant animals exposed to hydrogen cyanide, indicating that these are specific for H2S. We found that the hif-1 suppressor mutations activate the skn-1/Nrf2 transcription factor. Activation of SKN-1 by hif-1 suppressor mutations increased the expression of a subset of H2S-responsive genes, consistent with our previous finding that skn-1 plays a role in the transcriptional response to H2S. Using transgenic rescue, we show a single gene, rhy-1, alone is sufficient to protect hif-1 mutant animals in H2S. Our data indicate that RHY-1 acts in concert with CYSL-1, an orthologue of human cystathionine {beta}-synthase, to promote survival in H2S. The rhy-1 gene encodes a predicated O-acyltransferase enzyme that has previously been shown to negatively regulate HIF-1 activity. Our studies reveal a novel function of RHY-1, which is independent of hif-1, that protects against toxic effects of H2S.

biochemistry↗

bioRxiv2019

Epigenetic bookmarking of H2S exposure in Caenorhabditis elegans

Physiological memories of environmental stress can serve to predict future environmental changes, allowing the organism to initiate protective mechanisms and survive. Although physiological memories, or bookmarks, of environmental stress have been described in a wide range of organisms, from bacteria to plants to humans, the mechanism by which these memories persist in the absence of stress is still largely unknown. We have discovered that C. elegans transiently exposed to low doses of hydrogen sulfide (H2S) survive subsequent exposure to otherwise lethal H2S concentrations and induce H2S-responsive transcripts more robustly than naive controls. H2S bookmarking can occur at any developmental stage and persists through cell divisions and development but is erased by fasting. We show that maintenance of the H2S bookmark requires the SET-2 histone methyltransferase and the CoREST-like demethylase complex. We propose a model in which exposure to low doses of H2S generates a long-lasting, epigenetic memory by modulating H3K4me2 modifications at specific promoters. Understanding the fundamental aspects of H2S bookmarking in this tractable system can provide mechanistic insight into how environmental exposures are translated into the epigenetic landscape in animals.

genetics↗

bioRxiv2018

Fasting protects hypoxia-induced defects in proteostasis in C. elegans

Low oxygen conditions (hypoxia) can impair essential physiological processes and cause cellular damage and death. We have shown that specific hypoxic conditions disrupt protein homeostasis in C. elegans, leading to protein aggregation and proteotoxicity. Here, we show that nutritional cues regulate this effect of hypoxia on proteostasis. Animals fasted prior to hypoxic exposure develop dramatically fewer protein aggregates compared to their fed counterparts, indicating that the effect of hypoxia is abrogated. Fasting is effective at protecting against hypoxia-induced proteostasis defects in multiple developmental stages, tissues, and in different models of misfolded or aggregation prone proteins. Our data also demonstrate that the effect of fasting is induced and reversed quite rapidly, suggesting that the nutritional environment experienced at the onset of hypoxia dictates at least some aspects of the physiological response to hypoxia. We further demonstrate that the insulin/IGF-like signaling pathway plays a role in mediating the protective effects of fasting in hypoxia. Animals with mutations in daf-2, the C. elegans insulin-like receptor, display wild-type levels of hypoxia-induced protein aggregation upon exposure to hypoxia when fed, but are not protected by fasting. However, we found that DAF-2 acts independently of the FOXO transcription factor, DAF-16, to mediate the protective effects of fasting. These results suggest a non-canonical role for the insulin/IGF-like signaling pathway in coordinating the effects of hypoxia and nutritional state on proteostasis.\n\nAuthor SummaryWhen blood flow to various parts of the body becomes restricted, those tissues suffer from a lack of oxygen, a condition called hypoxia. Hypoxia can cause cellular damage and death, such as is observed as a result of stroke and cardiovascular disease. We have found that in the model organism C. elegans (a roundworm) specific concentrations of hypoxia cause aggregation of polyglutamine proteins - the same kind of proteins that are found in an aggregated state in the neurodegenerative disorder Huntingtons disease. Here, we show that that worms can be protected from hypoxia-induced protein aggregation if they are fasted (removed from their food source) prior to experiencing hypoxia. Furthermore, we show that the insulin receptor is required for this protection. The insulin receptor is responsible for detecting insulin, a hormone that is released after feeding. Worms with a nonfunctional version of the insulin receptor displayed hypoxia-induced protein aggregation despite being fasted before the hypoxic exposure. Our results highlight a new role for the insulin signaling pathway in coordinating the effects of both hypoxia and nutritional state on protein aggregation.

physiology↗

bioRxiv2017

C. elegans HIF-1 is broadly required for survival in hydrogen sulfide

Hydrogen sulfide is common in the environment, and is also endogenously produced by animal cells. Although hydrogen sulfide is often toxic, exposure to low levels of hydrogen sulfide improves outcome in a variety of mammalian models of ischemia-reperfusion injury. In Caenorhabditis elegans, the initial transcriptional response to hydrogen sulfide depends on the hif-1 transcription factor, and hif-1 mutant animals die when exposed to hydrogen sulfide. In this study, we use rescue experiments to identify tissues in which hif-1 is required to survive exposure to hydrogen sulfide. We find that expression of hif-1 from the unc-14 promoter is sufficient to survive hydrogen sulfide. Although unc-14 is generally considered to be a pan-neuronal promoter, we show that it is active in many non-neuronal cells as well. Using other promoters, we show that pan-neuronal expression of hif-1 is not sufficient to survive exposure to hydrogen sulfide. Our data suggest that hif-1 is required in many different tissues to direct the essential response to hydrogen sulfide.

cell biology↗